diff --git a/content/0.index.md b/content/0.index.md
index f48c4a6b0a3e18bfcccaa3730aa941dfaefcc4ca..d8abcc9c4ad242ca909a74cee6a818519c10047b 100644
--- a/content/0.index.md
+++ b/content/0.index.md
@@ -25,7 +25,7 @@ Bacteria and their phages have co-existed for billions of years. The pressure of
The first discovered anti-phage system, a Restriction-Modification (RM) system, was described in the early 1950s :ref{doi=10.1128/jb.64.4.557-569.1952,10.1128/jb.65.2.113-121.1953}. In the following decades, a handful of other systems were discovered :ref{doi=10.1016/j.mib.2005.06.006}. In 2007, CRISPR-Cas systems were discovered to be anti-phage systems :ref{doi=10.1126/science.1138140}. As CRISPR-Cas systems and RM systems are extremely prevalent in bacteria, it was thought for some years that the antiviral immune system of bacteria had been mostly elucidated.
-Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, it was revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11}. This led to a guilt-by-association hypothesis: if a gene or a set of genes is frequently found in bacterial genomes in close proximity to known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This hypothesis was tested systematically in a landarmark study in 2018 :ref{doi=10.1126/science.aar4120} leading to the discovery of 10 novel anti-phage systems. This started the uncovering of an impressive diversity of defense systems in a very short amount of time :ref{doi=10.1038/s41579-023-00934-x}.
+Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, it was revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11}. This led to a guilt-by-association hypothesis: if a gene or a set of genes is frequently found in bacterial genomes near known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This hypothesis was tested systematically in a landmark study in 2018 :ref{doi=10.1126/science.aar4120} leading to the discovery of 10 novel anti-phage systems. This started the uncovering of an impressive diversity of defense systems in a very short amount of time :ref{doi=10.1038/s41579-023-00934-x}.
To date over 150 types of defense systems have been described, unveiling an unsuspected diversity of molecular mechanisms. The antiviral immune systems of bacteria therefore appear much more complex than previously envisioned, and new discoveries do not seem to be slowing down.
@@ -35,6 +35,6 @@ The fast pace of discoveries in the field can be intimidating to newcomers and c
1. A “general concepts†section, introducing key notions and ideas to understand anti-phage defense
2. A section introducing succinctly each of the defense systems currently known.
-This wiki is only a first version, and is intended to evolve based on the ideas and needs of the people using it. Whether it is to suggest new pages or to edit existing ones, all contributions are more than welcomed: please do not hesitate to contact us to participate!
+This wiki is only a first version and is intended to evolve based on the ideas and needs of the people using it. Whether it is to suggest new pages or to edit existing ones, all contributions are more than welcome: please do not hesitate to contact us to participate!
diff --git a/content/1.help/1.DefenseFinder.md b/content/1.help/1.DefenseFinder.md
index f5fbf3361baba4f9d982ffa5cd6a86668199078d..df1a8c49d89f911e8eeb8c4fb8b3b8405934f3e8 100644
--- a/content/1.help/1.DefenseFinder.md
+++ b/content/1.help/1.DefenseFinder.md
@@ -17,14 +17,14 @@ Analyses are kept for 6 months, or with a maximum of 10 jobs.
{max-width=750px}
-In the Analyses panel, each past job is kept for 6 months. Next to the name of the input file (1) there is a rolling circle until the job finishes to run, which become a number. One can edit the job name (by default it's the file's name) by clicking on the small pen (2), or can delete a job (3). To visualize the results, one can click on Results (4) or on the job's name.
+In the Analyses panel, each past job is kept for 6 months. Next to the name of the input file (1) there is a rolling circle until the job finishes running, which becomes a number. One can edit the job name (by default it's the file's name) by clicking on the small pen (2), or can delete a job (3). To visualize the results, one can click on Results (4) or on the job's name.
{max-width=750px}
-The result consists in 3 tables :
+The result consists of 3 tables :
-- Systems table : Shown by default. One system per line. On the column type, there is the name of the system, and one can click on it to be redirected to the corresponding wiki page (1).
-- Genes table (2): One gene per line. Those are genes from the aforementioned system, with some addition information on the quality of the hit. The key between both table is `sys_id`
+- Systems table: Shown by default. One system per line. On the column type, there is the name of the system, and one can click on it to be redirected to the corresponding wiki page (1).
+- Genes table (2): One gene per line. Those are genes from the aforementioned system, with some addition information on the quality of the hit. The key between both tables is `sys_id``
- HMMER table (3): One gene per line. Here it's all the genes hit by a hmm profile, even when the gene is not part of a defense system.
diff --git a/content/1.help/2.Contributing-Wiki.md b/content/1.help/2.Contributing-Wiki.md
index d30d0bfda6f77f9dd195341e6ff09c3696f7e760..2363589eccec3ecfabacf82b8db01c7b847c4262 100644
--- a/content/1.help/2.Contributing-Wiki.md
+++ b/content/1.help/2.Contributing-Wiki.md
@@ -7,10 +7,10 @@ layout: article
## 1/ Create an account
-The wiki is based on gitlab pages, and we are using the gitlab's instance of the Pasteur Institute. To contribute, users need to be part of the project.
+The wiki is based on GitLab pages, and we are using the GitLab's instance of the Pasteur Institute. To contribute, users need to be part of the project.
-On every page, there is a button at the bottom proposing to "Edit on Gitlab". It will allow anyone registered to edit a given page seamlessly.
-But on the first try, the following dialog will be prompted. If you have a Pasteur account, chose 1, otherwise chose 2. In External account, you can connect with a third-party account such as Github, bitbucket or google.
+On every page, there is a button at the bottom proposing to "Edit on GitLab". It will allow anyone registered to edit a given page seamlessly.
+But on the first try, the following dialog will be prompted. If you have a Pasteur account, choose 1, otherwise choose 2. In an External account, you can connect with a third-party account such as Github, bitbucket or Google.
If you have neither, register on Github first (it's always useful).
{max-width=750px}
@@ -19,25 +19,25 @@ Once your account is created, you need to request access to the project, on the
{max-width=600px}
-Click, and wait for an admin approval.
+Click, and wait for admin approval.
## 2/ Edit a page
-Once you have access to the project (the previous step is done once), you can edit easily each page of the wiki, and post [issues](https://gitlab.pasteur.fr/mdm-lab/wiki/-/issues) (if you have question about something or remarks with anything from content to design).
+Once you have access to the project (the previous step is done once), you can edit easily each page of the wiki, and post [issues](https://gitlab.pasteur.fr/mdm-lab/wiki/-/issues) (if you have questions about something or remarks with anything from content to design).
-To edit a page, just click on the Edit on Gitlab button at the bottom of every page of the wiki, and it will lead you to the corresponding page of the wiki.
+To edit a page, just click on the Edit on GitLab button at the bottom of every page of the wiki, and it will lead you to the corresponding page of the wiki.
From this page, you can :
1. Edit the text you'd like
-2. Preview the change you've done (final modification might a bit different, especially if you use plugins to view citations or pdb structures)
-3. Once you've finished you edits, you can specify what you did (e.g. "Re-wrote history of defense systems")
-4. This field is for the branch name, you can let it with the default value, or specify a more meaningful name (note that it's good to have your user name in the branch name so we can)
+2. Preview the change you've done (the final modification might be a bit different, especially if you use plugins to view citations or PDB structures)
+3. Once you've finished your edits, you can specify what you did (e.g. "Re-wrote history of defense systems")
+4. This field is for the branch name, you can leave it with the default value, or specify a more meaningful name (note that it's good to have your user name in the branch name so we can)
{max-width=750px}
Then it asks you to create a merge request.
-In other words, the modifications you made will not be reflected on the website until a few automatic checks passed (which should be ok since you modified only some text) and that another person reviewed the change, and accept the merge request.
+In other words, the modifications you made will not be reflected on the website until a few automatic checks passed (which should be ok since you modified only some text) and another person reviewed the change, and accepted the merge request.
To do so, just fill in the description (1) of what you did, or anything that you would like the person who will accept the merge request to know, and just hit (2) "Create a merge request".
@@ -45,10 +45,10 @@ To do so, just fill in the description (1) of what you did, or anything that you
## 3/ Tips to write Markdown
-As a general advice, check an already written file to see how other pages are written.<br><br>
+As general advice, check an already written file to see how other pages are written.<br><br>
-The files you edit are in markdown, which is pretty basic language but that can let you do many things, such as tables, links and such with a particular syntax.
-You can check more about this syntax here : <https://docs.gitlab.com/ee/user/markdown.html><br><br>
+The files you edit are in markdown, which is a pretty basic language that can let you do many things, such as tables, links and such with a particular syntax.
+You can check more about this syntax here: <https://docs.gitlab.com/ee/user/markdown.html><br><br>
To add images, you need to upload the image in the `/content/public` folder (and possibly in the corresponding folder of the defense system)
and you can specify its path in the markdown file as follows :<br>
@@ -61,7 +61,7 @@ where `/path/within/public` is the relative path to the `public` folder (the abs
In addition to this, there are some specificities to this wiki :<br><br>
-**1. Each system's page has *frontmatter*, which is a piece of code that will be used to populate the table of the list of system. It has the following syntax :**
+**1. Each system's page has *frontmatter*, which is a piece of code that will be used to populate the table of the list of systems. It has the following syntax :**
```yaml
---
@@ -106,7 +106,7 @@ This part is a bit tricky to edit. Your first option is to create an issue or se
The second option is that you can try within this live editor : https://mermaid.live/
You can copy paste everything that is within `<mermaid></mermaid>` tags in the editor field of the [live editor](https://mermaid.live/), it should reproduce what you site on the website. From there you can try to modify it until you get what you want.
-Here is the documentation about mermaid (the software behind this syntax) : https://mermaid.js.org/intro/
+Here is the documentation about Mermaid (the software behind this syntax): https://mermaid.js.org/intro/
**Custom containers:**
@@ -186,9 +186,9 @@ This is an info box
### 4/ Review a Merge Request
-You can review other person's merge request by going the [merge request's pages](https://gitlab.pasteur.fr/mdm-lab/wiki/-/merge_requests).
+You can review other people's merge requests by going to the [merge request](https://gitlab.pasteur.fr/mdm-lab/wiki/-/merge_requests)'s pages](https://gitlab.pasteur.fr/mdm-lab/wiki/-/merge_requests).
-On a given page, you can see what modifications where made for this merge request (1), then you can comment if you have anything to say (2 and 3).
+On a given page, you can see what modifications were made for this merge request (1), and then you can comment if you have anything to say (2 and 3).
And finally, you can approve (4) the MR if you find it worth publishing on the website.
{max-width=750px}
@@ -197,8 +197,8 @@ If you want to modify further the file or other file within the same merge reque
{max-width=750px}
-The Web IDE editor allows you to edit multiple file at once for a given commit. This editor is also accessible from the merge request's page under the "Code" button in the upper right corner of the page.
+The Web IDE editor allows you to edit multiple files at once for a given commit. This editor is also accessible from the merge request's page under the "Code" button in the upper right corner of the page.
## Contribute to the code
-Contribution to the code and design are open. Please read the [README](https://gitlab.pasteur.fr/mdm-lab/wiki) on how to deploy the website locally (and see the modification you're doing live).
+Contribution to the code and design is open. Please read the [README](https://gitlab.pasteur.fr/mdm-lab/wiki) on how to deploy the website locally (and see the modification you're doing live).
diff --git a/content/2.general-concepts/1.abortive-infection.md b/content/2.general-concepts/1.abortive-infection.md
index 51ce4c4cf75ef6cafe8de0cca8b0715041b01a62..47117692496b76be8230b4efd6e358af40212dc1 100644
--- a/content/2.general-concepts/1.abortive-infection.md
+++ b/content/2.general-concepts/1.abortive-infection.md
@@ -31,7 +31,7 @@ Controlled cell death upon detection of the phage infection stops the propagatio
:ref{doi=10.1016/S0960-9822(00)00124-X,10.1016/j.mib.2005.06.006}.
Abortive infection can thus be thought of as a form of bacterial altruism.
-With the recent developments in phage-defense systems and microbial immunity (see :ref{doi=10.1038/s41579-023-00934-x} for a review), many newly identifed anti-phage defense systems are thought to function through abortive infection. Abortive defense systems often detect the phage infection at the later stage through protein sensing or the monitoring of host integrity but can also be based on nucleic acid sensing. Upon sensing, a diverse set of effectors can be used to reduce metabolism or induce cell-death (e.g., NAD+ depletion, translation interruption or membrane depolarisation). The diversity of and mechanisms of abortive infection were recently reviewd here :ref{doi=10.1146/annurev-virology-011620-040628}, while the evolutionary success of this paradoxical altruistic form of immunity has recently been discussed here :ref{doi=10.1016/j.mib.2023.102312}.
+With the recent developments in phage-defense systems and microbial immunity (see :ref{doi=10.1038/s41579-023-00934-x} for a review), many newly identified anti-phage defense systems are thought to function through abortive infection. Abortive defense systems often detect the phage infection at a later stage through protein sensing or the monitoring of host integrity but can also be based on nucleic acid sensing. Upon sensing, a diverse set of effectors can be used to reduce metabolism or induce cell-death (e.g., NAD+ depletion, translation interruption or membrane depolarisation). The diversity of and mechanisms of abortive infection were recently reviewed here :ref{doi=10.1146/annurev-virology-011620-040628}, while the evolutionary success of this paradoxical altruistic form of immunity has recently been discussed here :ref{doi=10.1016/j.mib.2023.102312}.
Although abortive infection is currently often understood as leading to cell-death, it should be noted that its original definition appeared to be broader and that some mechanisms currently included as abortive infection may only lead to metabolic stalling or dormancy.
diff --git a/content/2.general-concepts/2.defense-systems_trigger.md b/content/2.general-concepts/2.defense-systems_trigger.md
index 5e088ed2afcb2696c73054366f994eb1014ca875..978cd68ba71ee20f6a723646ca63e22e30a97e73 100644
--- a/content/2.general-concepts/2.defense-systems_trigger.md
+++ b/content/2.general-concepts/2.defense-systems_trigger.md
@@ -12,13 +12,13 @@ Upon phage infection, the bacterial immune system senses a specific phage compon
## Diversity
-Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas, recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation :ref{doi=10.1101/2023.03.07.531596}. In other cases, defense systems are activated by protein coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein :ref{doi=10.1126/science.abm4096}. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2023.02.029}. For a comprehensive coverage of all recent phage detection mechanisms the recent review by Huiting and Bondy-Denomy :ref{doi=10.1016/j.mib.2023.102325} is highly recommended.
+Various determinants of the phage can elicit bacterial immunity either in a direct or indirect manner. The most common and well-known prokaryotic anti-phage systems, restriction enzymes and CRISPR-Cas recognize and cleave phage DNA or RNA. More recently, a CBASS system has been found to directly bind to a structured phage RNA that triggers immune activation :ref{doi=10.1101/2023.03.07.531596}. In other cases, defense systems are activated by protein-coding phage genes. In some cases, the phage protein is directly sensed by the defense systems, as has been beautifully demonstrated for the Avs systems that directly bind either the phage terminase or portal protein :ref{doi=10.1126/science.abm4096}. In other cases, the phage protein can be sensed indirectly by the defense system, for example by detecting its activity in the cell. Such an indirect mechanism has been found for example in the case of some retron defense systems that are triggered by phage tampering with the RecBCD protein complex :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2023.02.029}. For comprehensive coverage of all recent phage detection mechanisms, the recent review by Huiting and Bondy-Denomy :ref{doi=10.1016/j.mib.2023.102325} is highly recommended.
## Method of discovery:
-The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system :ref{doi=10.1016/j.cell.2023.02.029,10.1016/j.mib.2023.102325}. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases expression of this phage component without any other phage genes is sufficient to elicit the activity of bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase, Dazbog activation by expression of a phage DNA methylase, retron activation by either phage SSB proteins :ref{doi=10.1016/j.cell.2023.02.029} or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein :ref{doi=10.1038/s41586-022-05444-z} and many more :ref{doi=10.1016/j.mib.2023.102325}. Additional biochemical pulldown assays can be used to assess binding of the defense system to the suspected phage trigger.
-One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest, and then assayed for immune activation. This approach was successfully applied for identification phage components that trigger diverse Avs systems :ref{doi=10.1126/science.abm4096}.
+The main method used to pinpoint phage components that trigger a specific defense system of interest has been through a simple classic genetics approach, whereby mutant phages that overcome the defense system are examined. Such mutants often occur spontaneously and can thus be selected for by simply picking phage plaques that are able to form on a lawn of bacteria expressing the defense system :ref{doi=10.1016/j.cell.2023.02.029,10.1016/j.mib.2023.102325}. The hypothesis is that the phage mutant escapes bacterial immunity due to a mutation in the component sensed by the system. Thus, sequencing these phage mutants and identification of the mutated locus is the first required step. To validate that the mutated phage component is indeed the actual trigger of the defense system, follow up experiments are required. For example, in some cases, expression of this phage component without any other phage genes is sufficient to elicit the activity of the bacterial immune system. This approach was used to identify Borvo activation by expression of the phage DNA polymerase, Dazbog activation by expression of a phage DNA methylase, retron activation by either phage SSB proteins :ref{doi=10.1016/j.cell.2023.02.029} or by proteins that inhibit the host RecBCD3, CapRel triggering by the phage Capsid protein :ref{doi=10.1038/s41586-022-05444-z} and many more :ref{doi=10.1016/j.mib.2023.102325}. Additional biochemical pulldown assays can be used to assess the binding of the defense system to the suspected phage trigger.
+One major caveat in the above approach is that in some cases mutant phages that escape the immune system cannot be isolated. This can occur for example if the defense system senses a general fold of a highly conserved and essential phage protein. In this case, a simple mutation in the protein will not suffice for the phage to escape detection. In such cases, an alternative approach can be used that does not rely on isolation of escape mutants. An overexpression library of all phage genes can be co-expressed with the defense system of interest and then assayed for immune activation. This approach was successfully applied for the identification of phage components that trigger diverse Avs systems :ref{doi=10.1126/science.abm4096}.
## General concepts
-Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4. These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.chom.2022.02.018,10.1006/jmbi.1995.0343}. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages.
+Although much is still unknown regarding how bacterial immune systems sense phage infection, by combining the data observed so far, several general concepts in immune sensing are beginning to come to light. First, mechanistically diverse immune systems appear to have converged to sense common conserved phage components4. These include the phage core replication machinery, host takeover machinery and structural components. Second, several studies have found cases in which defense occurs in a multi-layered fashion, whereby a second system is activated when the first one fails :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.chom.2022.02.018,10.1006/jmbi.1995.0343}. Research in upcoming years is expected to reveal additional guiding principles in the ways bacteria detect phages.
diff --git a/content/2.general-concepts/3.defense-systems-effectors.md b/content/2.general-concepts/3.defense-systems-effectors.md
index 675f952135b53a54c3459ca38e5f25b2cab8fe56..461d46fecee0aef8ecd5ff66ac4f81fc6932d795 100644
--- a/content/2.general-concepts/3.defense-systems-effectors.md
+++ b/content/2.general-concepts/3.defense-systems-effectors.md
@@ -18,9 +18,8 @@ The effector components of anti-phage systems are very diverse, and can be arbit
## Nucleic-acid-degrading effectors.
-Many defense systems target (either through cleavage or modification) nucleic acids to mediate the immune response.
-These nucleic acids targeting systems are divided between systems that specifically target phage nucleic acids to stop
-phage replication, and systems that untargetedly affect bacterial and viral nucleic acids to halt the growth of both the
+Many defense systems target (either through cleavage or modification) nucleic acids to mediate the immune response.
+These nucleic acid-targeting systems are divided between systems that specifically target phage nucleic acids to stop phage replication, and systems that untargetedly affect bacterial and viral nucleic acids to halt the growth of both the
infected host and the phage.
Nucleic-acid-degrading systems include [RM](/defense-systems/rm), [CRISPR-Cas](/defense-systems/cas), [Ssp](/defense-systems/sspbcde) and [Ddn](/defense-systems/dnd), certain types of [CBASS](/defense-systems/cbass), [Avs](/defense-systems/avs) and [Lamassu](/defense-systems/lamassu-fam), [PrrC](/defense-systems/prrc), [RloC](/defense-systems/rloc)...
@@ -38,4 +37,4 @@ They include for instance bacterial Gasdermins, RexAB, Pif, AbiZ, certain types
## Other types of effectors.
-Finally, some types of less prevalent effectors were not included into these broad categories. This includes protein modifying effectors, and some chemical defense systems.
+Finally, some types of less prevalent effectors were not included in these broad categories. This includes protein-modifying effectors and some chemical defense systems.
diff --git a/content/2.general-concepts/4.defense-systems-discovery.md b/content/2.general-concepts/4.defense-systems-discovery.md
index 1347fd5217f1878db49bc9f0a30c854d149fae0c..52a561f29cc28e28d1e8c702aaf8fdf43826feab 100644
--- a/content/2.general-concepts/4.defense-systems-discovery.md
+++ b/content/2.general-concepts/4.defense-systems-discovery.md
@@ -10,7 +10,7 @@ contributors:
Anti-phage defense systems have been discovered through various research methodologies and scientific investigations.
-The first defense systems that were discovered and characterized were restriction modifications (RM) and CRISPR-cas systems, in the 1960s and early 2000s respectively. These systems are the most abundantly encoded in prokaryotic genomes and were discovered by researchers that observed heritable bacterial resistance of certain strains to bacteriophages. A combination of functional studies, bacterial genetics, and biochemical assays enabled to elucidate their mechanisms of action, leading to the development of tools that revolutionized molecular biology and genetic engineering.
+The first defense systems that were discovered and characterized were restriction modifications (RM) and CRISPR-cas systems, in the 1960s and early 2000s respectively. These systems are the most abundantly encoded in prokaryotic genomes and were discovered by researchers who observed heritable bacterial resistance of certain strains to bacteriophages. A combination of functional studies, bacterial genetics, and biochemical assays enabled to elucidate of their mechanisms of action, leading to the development of tools that revolutionized molecular biology and genetic engineering.
-In recent years, the discovery and characterization of dozens of novel anti-phage defense systems involve a combination of bioinformatics, genomics analysis and experimental approaches. The computational pipeline that has allowed to identify and validate numerous systems in the past years is based on the observation that anti-phage defense systems tend to co-localize on prokaryotic chromosomes in regions denoted as defense islands. Using this principle, recent studies have discovered more than 150 novel systems, by identifying and testing single or multi protein uncharacterized systems that are enriched within such defense islands. Candidate systems are typically cloned into heterologous expression hosts, to validate their anti-phage function. The mechanisms of many these newly discovered systems remain unknown.
+In recent years, the discovery and characterization of dozens of novel anti-phage defense systems involve a combination of bioinformatics, genomics analysis and experimental approaches. The computational pipeline that has allowed to identify and validate numerous systems in the past years is based on the observation that anti-phage defense systems tend to co-localize on prokaryotic chromosomes in regions denoted as defense islands. Using this principle, recent studies have discovered more than 150 novel systems, by identifying and testing single or multi-protein uncharacterized systems that are enriched within such defense islands. Candidate systems are typically cloned into heterologous expression hosts, to validate their anti-phage function. The mechanisms of many of these newly discovered systems remain unknown.
diff --git a/content/2.general-concepts/5.defense-islands.md b/content/2.general-concepts/5.defense-islands.md
index d012e33a0fb7ed1007afdb6ec25e91d6f7969761..75216b8b6eda4513235c44bfb056fe7cdb3ede2a 100644
--- a/content/2.general-concepts/5.defense-islands.md
+++ b/content/2.general-concepts/5.defense-islands.md
@@ -11,8 +11,8 @@ contributors:
# Defense Islands
-**Defense islands** are regions of prokaryotic genomes enriched in defense systems. Their existence first described in Makarova *et al.* :ref{doi=10.1128/JB.05535-11}, who observed that genes encoding defense systems (mainly Restriction Modification enzymes, Toxin-Antitoxin systems, but notably not CRISPR) tended to cluster preferentially on specific portions of bacterial genomes. They postulated that unknown genes commonly found associated to these regions would likely have a defensive role themselves, and confirmed bioinformatically that many of them were indeed diverged versions of classical defense systems. Other systems of genes commonly found in defense islands were later isolated and heterologously expressed to experimentally confirm to have a defensive role (BREX, DISARM). Doron *et al.* :ref{doi=10.1126/science.aar4120}, later followed by Millmann *et al.* :ref{doi=10.1016/j.chom.2022.09.017}, used the colocalization of genes in defense islands to generate many candidate systems and test them experimentally in high throughput screens, leading to the discovery of a large number of new defense systems.
+**Defense islands** are regions of prokaryotic genomes enriched in defense systems. Their existence was first described in Makarova *et al.* :ref{doi=10.1128/JB.05535-11}, who observed that genes encoding defense systems (mainly Restriction Modification enzymes, Toxin-Antitoxin systems, but notably not CRISPR) tended to cluster preferentially on specific portions of bacterial genomes. They postulated that unknown genes commonly found associated with these regions would likely have a defensive role themselves, and confirmed bioinformatically that many of them were indeed diverged versions of classical defense systems. Other systems of genes commonly found in defense islands were later isolated and heterologously expressed to experimentally confirm to have a defensive role (BREX, DISARM). Doron *et al.* :ref{doi=10.1126/science.aar4120}, later followed by Millmann *et al.* :ref{doi=10.1016/j.chom.2022.09.017}, used the colocalization of genes in defense islands to generate many candidate systems and test them experimentally in high throughput screens, leading to the discovery of a large number of new defense systems.
-The reasons leading to the formation and maintenance of defense islands are still unclear. Makarova *et al.* :ref{doi=10.1128/JB.05535-11} observed a that defense islands often associated with mobile genetic elements, suggesting that defense systems travel through horizontal gene transfer, taking advantage of the MGEs' mobility. This observation in itself could explain the non-random localization of defense systems in the preferred "landing pads" (=*sinks*) of mobile genetic elements. Whether the colocalization of defense systems into these islands is purely due to there horizontal transmission, or whether they reflect a deeper functional implication such as coregulation and coordination, remains debated.
+The reasons leading to the formation and maintenance of defense islands are still unclear. Makarova *et al.* :ref{doi=10.1128/JB.05535-11} observed that defense islands are often associated with mobile genetic elements, suggesting that defense systems travel through horizontal gene transfer, taking advantage of the MGEs' mobility. This observation in itself could explain the non-random localization of defense systems in the preferred "landing pads" (=*sinks*) of mobile genetic elements. Whether the colocalization of defense systems into these islands is purely due to their horizontal transmission, or whether they reflect a deeper functional implication such as coregulation and coordination, remains debated.
diff --git a/content/2.general-concepts/6.defensive-domains.md b/content/2.general-concepts/6.defensive-domains.md
index 28fc16d4d3d051f6066638a9e7d996444438de7b..90652fa2390b393d61cf119450de747c3b9e911e 100644
--- a/content/2.general-concepts/6.defensive-domains.md
+++ b/content/2.general-concepts/6.defensive-domains.md
@@ -9,15 +9,15 @@ contributors:
## What are protein domains ?
-Proteins can typically be decomposed into a set of structural or functional units called "domains" where each individual domain has a specific biological function (e.g. catalyzing a chemical reaction or binding to another protein). The combination of one or several protein domains within a protein determines its biological function.
+Proteins can typically be decomposed into a set of structural or functional units called "domains" where each domain has a specific biological function (e.g. catalyzing a chemical reaction or binding to another protein). The combination of one or several protein domains within a protein determines its biological function.
{max-width=500px}
-To examplify this idea, the figure is a depiction of the ThsA protein involved in the [Thoeris](/defense-systems/thoeris) defense system in *Bacillus cereus*. The protein is composed of two domains : a SIR2-like domain (blue) and a SLOG domain (green). The SLOG domain of ThsA is able to bind to cyclic Adenosine Diphosphate Ribose (cADPR), a signalling molecule produced by ThsB upon phage infection. Binding of cADPR activates the Nicotinamide Adenine Dinucleotide (NAD) depletion activity of the SIR2-like domain which causes abortive infection. This shows how the presence of two domains in this protein allows it to be activated by the sensor component of the system (ThsB) and to trigger the immune response mechanism :ref{doi=10.1038/s41586-021-04098-7}.
+To examplify this idea, the figure is a depiction of the ThsA protein involved in the [Thoeris](/defense-systems/thoeris) defense system in *Bacillus cereus*. The protein is composed of two domains: a SIR2-like domain (blue) and a SLOG domain (green). The SLOG domain of ThsA can bind to cyclic Adenosine Diphosphate Ribose (cADPR), a signalling molecule produced by ThsB upon phage infection. The binding of cADPR activates the Nicotinamide Adenine Dinucleotide (NAD) depletion activity of the SIR2-like domain which causes abortive infection. This shows how the presence of two domains in this protein allows it to be activated by the sensor component of the system (ThsB) and to trigger the immune response mechanism :ref{doi=10.1038/s41586-021-04098-7}.
## Domain characterization helps to understand the biological function of a protein
-Although a considerable diversity of molecular mechanisms have been described for defense systems, it is striking to observe that some functional domains are recurrently involved in antiphage defense :ref{doi=10.1038/s41586-021-04098-7}. When studying the presence of a new defense system, the *in silico* characterization of the domains present in the system can provide valuable information regarding the molecular mechanism of the system. If one protein of the system contains for example a TerB domain, this might indicate that the system is involved in membrane integrity surveillance as this domain was previously shown to be associated with the periplasmic membrane :ref{doi=10.1016/j.chom.2022.09.017}. If a protein of the system contains a TIR domain this might indicate that the system possess a NAD degradation activity or that the protein could multimerize as both functions have been shown for this domain in the past :ref{doi=10.3389/fimmu.2021.784484}.
+Although a considerable diversity of molecular mechanisms have been described for defense systems, it is striking to observe that some functional domains are recurrently involved in antiphage defense :ref{doi=10.1038/s41586-021-04098-7}. When studying the presence of a new defense system, the *in silico* characterization of the domains present in the system can provide valuable information regarding the molecular mechanism of the system. If one protein of the system contains for example a TerB domain, this might indicate that the system is involved in membrane integrity surveillance as this domain was previously shown to be associated with the periplasmic membrane :ref{doi=10.1016/j.chom.2022.09.017}. If a protein of the system contains a TIR domain this might indicate that the system possesses a NAD degradation activity or that the protein could multimerize as both functions have been shown for this domain in the past :ref{doi=10.3389/fimmu.2021.784484}.
## Domains can be conserved throughout evolution
diff --git a/content/2.general-concepts/8.anti-defense-systems.md b/content/2.general-concepts/8.anti-defense-systems.md
index d743a668c59cc7cce51d7c54143ddff7029a1486..8401a15736ba5cf626750344a69fc76b3381b8a4 100644
--- a/content/2.general-concepts/8.anti-defense-systems.md
+++ b/content/2.general-concepts/8.anti-defense-systems.md
@@ -8,15 +8,15 @@ contributors:
# Anti-defense systems:
-This article is non-exhaustive but introduces the topic of an-defense systems. Several reviews mentioned here did a great in-depth characterization of the known anti-defense phage mechanism :ref{doi=10.3389/fmicb.2023.1211793,10.1016/j.jmb.2023.167974,10.1038/nrmicro3096}.
-Several strategies allow phages to avoid bacterial defenses to successfully complete an infectious cycle. In particular, anti-defense proteins are bacteriophage proteins that specifically act against a bacterial defense system, and thus allow bacteriophages to bypass the bacterial immune system. The most well-described category of anti-defense proteins are the anti-CRISPR proteins (Acr), that have been thoroughly reviewed previously :ref{doi=10.1038/nrmicro.2017.120,10.1016/j.jmb.2023.167974}. However, concomitant with the renewed interest of the field to identify new bacterial defense systems, many anti-defense proteins targeting diverse defense systems have recently been described. Using a non-exhaustive list of anti-defense proteins as examples, I will outline several general categories of anti-defense mechanism. However, I will not focus on another common phage anti-defense strategy that relies on modifying their components, such as mutating the proteins that trigger the defense to escape, or changing their DNA to avoid targeting by restriction-modification or CRISPR systems.
+This article is non-exhaustive but introduces the topic of anti-defense systems. Several reviews mentioned here did a great in-depth characterization of the known anti-defense phage mechanism :ref{doi=10.3389/fmicb.2023.1211793,10.1016/j.jmb.2023.167974,10.1038/nrmicro3096}.
+Several strategies allow phages to avoid bacterial defenses to successfully complete an infectious cycle. In particular, anti-defense proteins are bacteriophage proteins that specifically act against a bacterial defense system and thus allow bacteriophages to bypass the bacterial immune system. The most well-described category of anti-defense proteins is the anti-CRISPR proteins (Acr), which have been thoroughly reviewed previously :ref{doi=10.1038/nrmicro.2017.120,10.1016/j.jmb.2023.167974}. However, concomitant with the renewed interest of the field to identify new bacterial defense systems, many anti-defense proteins targeting diverse defense systems have recently been described. Using a non-exhaustive list of anti-defense proteins as examples, I will outline several general categories of anti-defense mechanisms. However, I will not focus on another common phage anti-defense strategy that relies on modifying their components, such as mutating the proteins that trigger the defense to escape or changing their DNA to avoid targeting by restriction-modification or CRISPR systems.
-Anti-defense proteins are crucial to understand the evolutionary arms race between bacteria and their phages, as they likely drive the diversification of bacterial defense systems. Some defense system even evolved to recognize anti-defense proteins as activators, providing multiple lines of defense during phage infection :ref{doi=10.1016/j.cell.2023.02.029}. Moreover, these proteins are also important to mediate phage/phage interactions. Indeed, anti CRISPR proteins were suggested to be involved in phage/phage collaboration, in which a primo-infection by a phage carrying an anti-CRISPR protein is unsuccessful but leaves the bacteria immunosuppressed and therefore sensitive to a second phage infection :ref{doi=10.1016/j.jmb.2023.167974}. Considering the importance of overcoming bacterial defenses for phages, it is likely that a significant part of the phage proteins of unknown function currently found in phage sequenced genomes act as anti-defense. Some anti-defense proteins were shown to colocalize in phage genomes, suggesting comparative genomics could be used to identify now anti-defense proteins, similar to what has been done very successfully for bacteria :ref{doi=10.1038/s41467-020-19415-3}. In general, recent studies have used a range of screening methods to identify new anti-defense proteins, and it is expected that many new anti-defense proteins will be described in the coming years.
+Anti-defense proteins are crucial to understand the evolutionary arms race between bacteria and their phages, as they likely drive the diversification of bacterial defense systems. Some defense systems even evolved to recognize anti-defense proteins as activators, providing multiple lines of defense during phage infection :ref{doi=10.1016/j.cell.2023.02.029}. Moreover, these proteins are also important in mediating phage/phage interactions. Indeed, anti-CRISPR proteins were suggested to be involved in phage/phage collaboration, in which a primo-infection by a phage carrying an anti-CRISPR protein is unsuccessful but leaves the bacteria immunosuppressed and therefore sensitive to a second phage infection :ref{doi=10.1016/j.jmb.2023.167974}. Considering the importance of overcoming bacterial defenses for phages, it is likely that a significant part of the phage proteins of unknown function currently found in phage-sequenced genomes act as anti-defense. Some anti-defense proteins were shown to colocalize in phage genomes, suggesting comparative genomics could be used to identify new anti-defense proteins, similar to what has been done very successfully for bacteria :ref{doi=10.1038/s41467-020-19415-3}. In general, recent studies have used a range of screening methods to identify new anti-defense proteins, and it is expected that many new anti-defense proteins will be described in the coming years.
## Anti-defense proteins target all stages of bacterial defenses
Most anti-defense proteins described to date directly bind a bacterial defense protein to block its activity. However, several other strategies have been described such as post-translational modification of a target, spatial segregation or signaling molecule degradation :ref{doi=10.3389/fmicb.2023.1211793}. They have been described to target all stages of bacterial defense.
-Bacterial defenses can be separated in two broad categories: external and internal defenses.
+Bacterial defenses can be separated into two broad categories: external and internal defenses.
### External defenses
@@ -27,13 +27,13 @@ Bacteria can hide receptors behind surface structures such as extracellular poly
Bacteria encode a variety of defense systems that prevent phage infection from progressing in various ways. Despite all this variability, all bacterial defense systems are schematically composed of three parts: a sensor recognizing the infection, an effector that achieves protection and a way to transmit the information between the sensor and the effector, either through signaling molecules or protein-protein interactions. Phage anti-defense proteins can target all three of these components.
- Sensor targeting:
- Competitive binding to the sensor: an anti-DSR2 protein from phages phi3T and SPbeta can bind the bacterial DSR2 protein and prevent the physical interaction between DSR2 and its phage activator, the tail tube protein :ref{doi=10.1038/s41564-022-01207-8}. Moreover, Ocr protein from T7 can mimic a B-form DNA oligo and acts as a competitive inhibitor of bacterial type I restriction modification systems :ref{doi=10.1016/s1097-2765(02)00435-5}.
- - Masking the activator: some jumbo phages are able to produce a nucleus-like proteinaceous structure that hides phage DNA and replication machinery away from DNA-targeted systems such as type I CRISPR system :ref{doi=10.1038/s41564-019-0612-5}.
+ - Masking the activator: some jumbo phages can produce a nucleus-like proteinaceous structure that hides phage DNA and replication machinery away from DNA-targeted systems such as type I CRISPR system :ref{doi=10.1038/s41564-019-0612-5}.
- Transmission targeting:
- - Degradation of signaling molecules: many systems rely on the production of a nucleotidic signaling molecule after phage sensing to activate the effector such as Pycsar, CBASS, and Thoeris systems. Phages possess proteins that can degrade these molecules to prevent effector activation, such as the anti CBASS Acb1 from phage T4 and the anti Pycsar Apyc1 from phage SBSphiJ :ref{doi=10.1038/s41586-022-04716-y}.
+ - Degradation of signaling molecules: many systems rely on the production of a nucleotidic signaling molecule after phage sensing to activate the effector such as Pycsar, CBASS, and Thoeris systems. Phages possess proteins that can degrade these molecules to prevent effector activation, such as the anti-CBASS Acb1 from phage T4 and the anti-Pycsar Apyc1 from phage SBSphiJ :ref{doi=10.1038/s41586-022-04716-y}.
- Sequestration of signaling molecules: an alternative strategy is to bind the signaling molecule very tightly without degrading it, which still prevents effector activation but is presumably easier to evolve than a catalysis-dependent degradation. These phage proteins are called sponges, and two were identified as anti-Thoeris: Tad1 from phage SBSphiJ7 and Tad2 from phage SPO1 and SPO1L3 :ref{doi=10.1038/s41586-022-05375-9,10.1038/s41586-023-06869-w}.
- Effector targeting:
- - Direct binding to block activity: Multiple anti-CRISPR protein have been described that can directly bind all the different components of the Cas complex to prevent DNA degradation :ref{doi=10.3389/fmicb.2023.1211793,10.1146/annurev-genet-120417-031321}. So far, this is the most abundant category of anti-defense protein described, and it is not restricted to only anti-CRISPR proteins.
- - Antitoxin mimicking: toxin-antitoxin defense systems rely on a toxin effector and an antitoxin that will toxin-mediated toxicity in absence of phage infection. Phages can highjack this process by mimicking the antitoxin to prevent toxin activity even during infection. For instance, phage Ï•TE can produce a short repetitive RNA that mimics the ToxI RNA antitoxin of type III toxin-antitoxin system ToxIN and evade defense mediated by this system :ref{doi=10.1371/journal.pgen.1003023}.
+ - Direct binding to block activity: Multiple anti-CRISPR proteins have been described that can directly bind all the different components of the Cas complex to prevent DNA degradation :ref{doi=10.3389/fmicb.2023.1211793,10.1146/annurev-genet-120417-031321}. So far, this is the most abundant category of anti-defense protein described, and it is not restricted to only anti-CRISPR proteins.
+ - Antitoxin mimicking: toxin-antitoxin defense systems rely on a toxin effector and an antitoxin that will toxin-mediated toxicity in the absence of phage infection. Phages can hijack this process by mimicking the antitoxin to prevent toxin activity even during infection. For instance, phage Ï•TE can produce a short repetitive RNA that mimics the ToxI RNA antitoxin of type III toxin-antitoxin system ToxIN and evades defense mediated by this system :ref{doi=10.1371/journal.pgen.1003023}.
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 02eafd5e677d71b3b5519e39953b361c70774de5..f4104dea4fb4188975a1f7e533c4fdfea41233aa 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -25,7 +25,7 @@ AbiA is one of the so-called "Abi" systems for "Abortive infection" discovered i
Since it was discovered a similarity in amino acids was found with [AbiK](/defense-systems/abik).
-However, with the discovery of dozens of new systems, it was categorized as one of the UG/Abi defense systems :ref{doi=10.1093/nar/gkac467} along with [DRT](/defense-systems/drt) different subsystems, [Abik](/defense-systems/abik), [AbiP2](/defense-systems/abip2) and [Rst_RT_Nitralase_TM](/defense-systems/rst_rt-nitrilase-tm).
+However, with the discovery of dozens of new systems, it was categorized as one of the UG/Abi defense systems :ref{doi=10.1093/nar/gkac467} along with [DRT](/defense-systems/drt) different subsystems, [AbiK](/defense-systems/abik), [AbiP2](/defense-systems/abip2) and [Rst_RT_Nitralase_TM](/defense-systems/rst_rt-nitrilase-tm).
Those systems are characterized by the presence of a reverse transcriptase domain of the "Unknown Group RT".
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index ee28e8af9f8fe212b7b534b105fdd267a102de7c..8cace816741bb18f92c97fb4d14fe83002522bc9 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -24,7 +24,7 @@ relevantAbstracts:
AbiB is a single-protein abortive infection defense system from *Lactococcus* that degrades mRNA.
## Molecular mechanism
-AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs :ref{doi=10.1046/j.1365-2958.1996.371896.x} that is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
+AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs :ref{doi=10.1046/j.1365-2958.1996.371896.x} which is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
## Example of genomic structure
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index 2844485cd00c8238f6925ef53a6348c1e1aa6e34..fecb2697b08c4d922cd9813c0b68e44e9567efbd 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -23,7 +23,7 @@ relevantAbstracts:
## Description
-AbiD is a single gene system system discovered in May 1995 in the plasmid pBF61 of *Lactococcus lactis* :ref{doi=10.1128/aem.61.5.2023-2026.1995}. An homolog of AbiD, named AbiD1 was discovered in July 1995 :ref{doi=10.1128/jb.177.13.3818-3823.1995}.
+AbiD is a single gene system discovered in May 1995 in the plasmid pBF61 of *Lactococcus lactis* :ref{doi=10.1128/aem.61.5.2023-2026.1995}. An homolog of AbiD, named AbiD1 was discovered in July 1995 :ref{doi=10.1128/jb.177.13.3818-3823.1995}.
AbiD is one of the so-called "Abi" systems for "Abortive infection" discovered in the 90's in research related to the dairy industry :ref{doi=10.1016/j.mib.2005.06.006}. AbiR is classified as a possible abortive infection in :ref{doi=10.1016/j.mib.2023.102312}.
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index eae76d7abb9cb80d4fccb147bf757f8451d90d89..ba985159e2198ba52e9b5a975650d42d5a84c912 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -26,7 +26,7 @@ AbiL was discovered in Lactococcus lactis. A plasmid containing the defense syst
## Molecular mechanism
-Abortive infection. the PF13707 domain includes the RloB protein that is found within a bacterial restriction modification operon. This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins.
+Abortive infection. the PF13707 domain includes the RloB protein that is found within a bacterial restriction-modification operon. This family includes the AbiLii protein that is found as part of a plasmid-encoded phage abortive infection mechanism. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins.
## Example of genomic structure
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index d0c32de0605305c87b06f8a685f52cad7c466c87..e03736bfe45674394cc26b04b3eef1d9a28825e6 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -27,7 +27,7 @@ AbiR is one of the so-called "Abi" systems for "Abortive infection" discovered i
AbiR is composed of 3 genes: AbiRa, AbiRb, AbiRc.
AbiRa encodes a sigma70 RNA polymerase subunit. AbiRb as homology with ParB nuclease domain according to HHpred.
-AbiRc has two different domains: a N_terminal PLD domain (PF13091) and at the C term an SNF2 DNA dependant ATPase.
+AbiRc has two different domains: an N_terminal PLD domain (PF13091) and at the C term an SNF2 DNA-dependent ATPase.
## Molecular mechanism
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index b82a40a23cccb53dbcb5725d6c5e4b5b14f229f2..a391cf2470e4741c0c46b64e19a0c95b6f48665c 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -24,7 +24,7 @@ relevantAbstracts:
AbiU is a single-protein abortive infection defense system described in *Lactococcus*.
## Molecular mechanism
-The molecular mechanism of AbiU is not well understood. It was shown that cells expressing AbiU showed delayed transcription of phage DNA, although how it is achieved, or how does it protect the bacterial culture is not understood. AbiU was shown to be encoded near another gene that seems to be an inhibitor of defense :ref{doi=10.1128/AEM.67.11.5225-5232.2001}.
+The molecular mechanism of AbiU is not well understood. It was shown that cells expressing AbiU showed delayed transcription of phage DNA, although how it is achieved, or how it protects the bacterial culture is not understood. AbiU was shown to be encoded near another gene that seems to be an inhibitor of defense :ref{doi=10.1128/AEM.67.11.5225-5232.2001}.
## Example of genomic structure
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index 7a5d02b95e09a9a951a4e512d8a38812027e5417..df5b0e8035195c883a017c0dc7885b942c049194 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -20,7 +20,7 @@ relevantAbstracts:
## Description
Aditi was discovered among other systems in 2022 :ref{doi=10.1016/j.chom.2022.09.017}.
-Aditi is composed of two genes: DitA, DitB. Both are of unknown function, and have no homology to any known domain.
+Aditi is composed of two genes: DitA, DitB. Both are of unknown function and have no homology to any known domain.
Aditi is named after the Hindu guardian goddess of all life.
## Molecular mechanisms
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index a83a158b05f95815146766eecd13e365ab42248b..6ee263662bbce9de4b52c6b075045a433116ef49 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -39,9 +39,9 @@ Avs systems sometimes include additional essential small genes on top of the can
## Example of genomic structure
-The Avs system have been describe in a total of 5 subsystems (in the old classification).
+The Avs system has been described in a total of 5 subsystems (in the old classification).
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 9a733dd640be311d0b5fcd4e8082c824977e234f..0b0ae0f2733b516ec3421590c5ba4cc35d34cdce 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -22,10 +22,10 @@ relevantAbstracts:
# Borvo
## Description
-Borvo is a single-gene anti-phage system that was identify through bioinformatic prediction and experimental validation :ref{doi=10.1016/j.chom.2022.09.017}.
+Borvo is a single-gene anti-phage system that was identified through bioinformatic prediction and experimental validation :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
-Mutations in the phage DNA polymerase can allow phages to escape Borvo defense, indicating that it could be the trigger of the system :ref{doi=10.1016/j.cell.2023.02.029}. Borvo is a suspected abortive infection :ref{doi=10.1016/j.cell.2023.02.029}. However as far as we are aware, the precise molecular mechanism of Borvo is unknown.
+Mutations in the phage DNA polymerase can allow phages to escape Borvo defense, indicating that it could be the trigger of the system :ref{doi=10.1016/j.cell.2023.02.029}. Borvo is a suspected abortive infection :ref{doi=10.1016/j.cell.2023.02.029}. However, as far as we are aware, the precise molecular mechanism of Borvo is unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 2ac1e7a1c9852a0c5aabf71dca25c39c0994cb38..966c9c7d803444dbde3200d308fe81b5f20139ad 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -23,11 +23,11 @@ BstA is a family of defense systems. BtsA systems from *Salmonella enterica subs
The majority of BstA systems appear to be prophage-encoded, as 79% of BstA homologs found in a set of Gram-negative bacterial genomes were associted with phage genes :ref{doi=10.1016/j.chom.2021.09.002}.
-Interestingly, part of the BstA locus appears to encode an anti-BstA genetic element (*aba*), which prevents auto-immunity for prophages encoding the BstA locus. The aba element appears to be specific to a given BstA locus, as replacing the aba element from a BstA locus with the aba element from an other BstA system does not prevent auto-immunity :ref{doi=10.1016/j.chom.2021.09.002}.Â
+Interestingly, part of the BstA locus appears to encode an anti-BstA genetic element (*aba*), which prevents auto-immunity for prophages encoding the BstA locus. The aba element appears to be specific to a given BstA locus, as replacing the aba element from a BstA locus with the aba element from another BstA system does not prevent auto-immunity :ref{doi=10.1016/j.chom.2021.09.002}.Â
## Molecular mechanism
-The defense mechanism encoded by BstA remains to be elucidated. Experimental observation suggest that BtsA could act through an abortive infection mechanism. Fluorescence microscopy experiments suggest that the BstA protein colocalizes with phage DNA. The BstA protein appears to inhibit phage DNA replication during lytic phage infection cycles :ref{doi=10.1016/j.chom.2021.09.002}.
+The defense mechanism encoded by BstA remains to be elucidated. Experimental observation suggests that BtsA could act through an abortive infection mechanism. Fluorescence microscopy experiments suggest that the BstA protein colocalizes with phage DNA. The BstA protein appears to inhibit phage DNA replication during lytic phage infection cycles :ref{doi=10.1016/j.chom.2021.09.002}.
## Example of genomic structure
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index bb4e378c11c2f3c58f7ddc507385a7705d97c6a2..af5609943f197909f11aac3ada629f883465178c 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -18,7 +18,7 @@ relevantAbstracts:
# Bunzi
## Description
-The Bunzi system is composed of 2 proteins: BnzB and, BnzA. Bunzi is a serpent water spirit and goddess of rain in traditional Kongo religion.
+The Bunzi system is composed of 2 proteins: BnzB and, BnzA. Bunzi is a serpent water spirit and goddess of rain in the traditional Kongo religion.
There was some homology noted with PFAMS Pfam08000, Pfam05099, Pfam07889 and a TerB domain :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular Mechanism
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 894056d3a0536a8b19deb5bbac852e889c8310a5..2706fafef3d9f0f73c47136ed2a180ef9a053997 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -20,14 +20,14 @@ relevantAbstracts:
# CapRel
## Description
-CapRel is a fused toxin-antitoxin system that is active against diverse phages when expressed in *Escherichia coli* :ref{doi=10.1038/s41586-022-05444-z}. CapRel belongs to the family of toxSAS toxin-antitoxin systems. CapRel is an Abortive infection system which is found in Cyanobacteria, Actinobacteria, and Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages.
+CapRel is a fused toxin-antitoxin system that is active against diverse phages when expressed in *Escherichia coli* :ref{doi=10.1038/s41586-022-05444-z}. CapRel belongs to the family of toxSAS toxin-antitoxin systems. CapRel is an Abortive infection system that is found in Cyanobacteria, Actinobacteria, Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages.
## Molecular mechanism
-The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition :ref{doi=10.1038/s41586-022-05444-z}. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
+The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However, during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition :ref{doi=10.1038/s41586-022-05444-z}. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
-Different CapRel homologues confer defense against different phages, suggesting variable phage specificity of CapRel system which seems to be mediated by the C-terminal region of CapRel.
+Different CapRel homologs confer defense against different phages, suggesting variable phage specificity of CapRel system which seems to be mediated by the C-terminal region of CapRel.
## Example of genomic structure
diff --git a/content/3.defense-systems/card_nlr.md b/content/3.defense-systems/card_nlr.md
index ea80ff9028681e5a459b91290d4d70ac045fbb74..013d88f4b050df564a04bb5120a771988f0f2c19 100644
--- a/content/3.defense-systems/card_nlr.md
+++ b/content/3.defense-systems/card_nlr.md
@@ -18,7 +18,7 @@ relevantAbstract:
# CARD_NLR
## Description
-Pore-forming proteins called gasdermins control cell-death response to infection in animals. Gasdermins are also present in bacteria where they have been shown to act as an abortive infection system that permeabilizes the cell membrane before phage release :ref{doi=10.1126/science.abj8432,10.1101/2023.05.28.542683}. In *Lysobacter*, the gasdermin operon includes two genes encoding trypsin-like protease domains, and a gene encoding an ATPase domain :ref{doi=10.1101/2023.05.28.542683}. Intact active sites for the second protease and the ATPase, but not the first protease, are required for succesful phage defense :ref{doi=10.1126/science.abj8432}. The domain architecture of the ATPase suggests it belongs to a protein family that is considered the ancestor of the eukaryotic nucleotide oligomerization domain (NOD)-like receptor (NLR) protein family :ref{doi=10.1101/2023.05.28.542683}. In animals, NLR initiates the formation of the inflammasome complex :ref{doi=10.1126/science.abe3069}. The second protease contains a region with similar structure to human CARD domain :ref{doi=10.1101/2023.05.28.542683}. The CARD domain takes part on the assembly of immune protein complexes :ref{doi=10.1038/sj.cdd.4401890}. The CARD-like domain in the *Lysobacter* system is required for succesful phage defense :ref{doi=10.1101/2023.05.28.542683}. Homology searches recovered multiple bacterial operons that include two proteases, one of them containing a CARD-like domain, and a NLR-like protein. In most cases, the effector gasdermin gene was replaced by another gene:ref{doi=10.1101/2023.05.28.542683}. The operon found in *Pedobacter rhizosphaerae* exhibits phage defense capabilities and contains a protein with phospholipase and endonuclease domains replacing the gasdermin gene. This system confers protection against the same phages as the *Lysobacter* gasdermin containing system, suggesting that the proteases and ATPase participate in phage specificity and recognition.
+Pore-forming proteins called gasdermins control cell-death response to infection in animals. Gasdermins are also present in bacteria where they have been shown to act as an abortive infection system that permeabilizes the cell membrane before phage release :ref{doi=10.1126/science.abj8432,10.1101/2023.05.28.542683}. In *Lysobacter*, the gasdermin operon includes two genes encoding trypsin-like protease domains, and a gene encoding an ATPase domain :ref{doi=10.1101/2023.05.28.542683}. Intact active sites for the second protease and the ATPase, but not the first protease, are required for successful phage defense :ref{doi=10.1126/science.abj8432}. The domain architecture of the ATPase suggests it belongs to a protein family that is considered the ancestor of the eukaryotic nucleotide oligomerization domain (NOD)-like receptor (NLR) protein family :ref{doi=10.1101/2023.05.28.542683}. In animals, NLR initiates the formation of the inflammasome complex :ref{doi=10.1126/science.abe3069}. The second protease contains a region with a similar structure to the human CARD domain :ref{doi=10.1101/2023.05.28.542683}. The CARD domain takes part in the assembly of immune protein complexes :ref{doi=10.1038/sj.cdd.4401890}. The CARD-like domain in the *Lysobacter* system is required for successful phage defense :ref{doi=10.1101/2023.05.28.542683}. Homology searches recovered multiple bacterial operons that include two proteases, one of them containing a CARD-like domain, and an NLR-like protein. In most cases, the effector gasdermin gene was replaced by another gene:ref{doi=10.1101/2023.05.28.542683}. The operon found in *Pedobacter rhizosphaerae* exhibits phage defense capabilities and contains a protein with phospholipase and endonuclease domains replacing the gasdermin gene. This system confers protection against the same phages as the _Lysobacter_ gasdermin-containing system, suggesting that the proteases and ATPase participate in phage specificity and recognition.
## Molecular mechanisms
For the *Lysobacter* system, the effector has been described as a pore-formin protein that disrupts the cell membrane :ref{doi=10.1101/2023.05.28.542683}. To our knowledge, other parts of the molecular mechanisms have yet to be elucidated.
diff --git a/content/3.defense-systems/cas.md b/content/3.defense-systems/cas.md
index 70fed3eeabb2f9ad32d9a4d1174829be6e1f46b0..8952c38074aa1cd16339be9344ab87d286f96584 100644
--- a/content/3.defense-systems/cas.md
+++ b/content/3.defense-systems/cas.md
@@ -14,10 +14,10 @@ For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https:/
## Example of genomic structure
-CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
+CRISPR-Cas systems have been classified into 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
-Here is example of each of the 6 family found in the RefSeq database:
+Here is an example of each of the 6 families found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 781d10e9d0b0efb16d67532d8a8d7ad21f3f2a90..52de807bdf84f28f89f7ef34b685c318adcac8e3 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -24,7 +24,7 @@ relevantAbstracts:
A total of 4 subsystems have been described for the CBASS system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 188564c34a2016a84bc4fcf1d6b62ab3e79170b7..a6a766755a1422a829712e7ac1a8dd6222ab2ec8 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -27,7 +27,7 @@ The DarTG defense system is a toxin-antitoxin (TA) system that provides defense
## Molecular mechanism
-DarT uses NAD+ to ADP-ribosylates tymidines on ssDNA, while DarG catalyses the reverse reaction. ADP-ribosylation of ssDNA prevents DNA replication and triggers the cell's SOS response. While initially proposed to work on bacterial ssDNA as a TA system :ref{doi=10.1016/j.molcel.2016.11.014}, Leroux et al. :ref{doi=10.1038/s41564-022-01153-5} show that it mostly modifies viral DNA and therefore block viral replication and perturb the transcription of phage genes. They conclude that "DarTG does not ultimately kill the host cell as in a conventional Abi mechanism, but instead acts to thwart phage replication directly."
+DarT uses NAD+ to ADP-ribosylates thymidine on ssDNA, while DarG catalyzes the reverse reaction. ADP-ribosylation of ssDNA prevents DNA replication and triggers the cell's SOS response. While initially proposed to work on bacterial ssDNA as a TA system :ref{doi=10.1016/j.molcel.2016.11.014}, Leroux et al. :ref{doi=10.1038/s41564-022-01153-5} show that it mostly modifies viral DNA and therefore blocks viral replication and perturb the transcription of phage genes. They conclude that "DarTG does not ultimately kill the host cell as in a conventional Abi mechanism, but instead acts to thwart phage replication directly."
## Example of genomic structure
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index 2f47c1a0b22981acff38147bd851ef4d27a6624d..ce5bcf5a7fd8e6c2e59f3340f77251bcc854c8df 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -19,7 +19,7 @@ contributors :
## Description
-The Dazbog system is composed of 2 proteins: DzbB and, DzbA. Dazbog was name after a slavic god, likely a solar deity.DzbA has homology to Pfam14072 :ref{doi=10.1016/j.chom.2022.09.017}
+The Dazbog system is composed of 2 proteins: DzbB and, DzbA. Dazbog was named after a Slavic god, likely a solar deity.DzbA has homology to Pfam14072 :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index 9deca9d9da826edf5b061fd5c83b2642c739037b..a3a3cf777c8426481b453e587672b8bfa292267d 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -25,9 +25,9 @@ This system is mostly found in Proteobacteria but a few examples also exist in A
Those systems can be found in plasmids (around 8%).
## Mechanism
-When activated by a phage infection, dCTPdeaminase, will convert deoxycytidine (dCTP/dCDP/dCMP) into deoxyuridine.
+When activated by a phage infection, dCTPdeaminase will convert deoxycytidine (dCTP/dCDP/dCMP) into deoxyuridine.
This action will deplete the pool of CTP nucleotide necessary for the phage replication and will stop the infection.
-The trigger for dCTPdeaminase may be linked to the shutoff of RNAP ($\sigma$ S-dependent host RNA polymerase) that occur during phage infections.
+The trigger for dCTPdeaminase may be linked to the shutoff of RNAP ($\sigma$ S-dependent host RNA polymerase) that occurs during phage infections.
## Example of genomic structure
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index 37075254b4b3afa36927d1a0b2977ad98ed0b616..333cff0f5ca9a7719f773e60637843e0c7fc8b60 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -13,7 +13,7 @@ relevantAbstracts:
# DdmDE
## Example of genomic structure
-The DmdDE is composed of 2 proteins: DdmE and DdmD.
+The DdmDE is composed of 2 proteins: DdmE and DdmD.
Here is an example found in the RefSeq database:
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 2cf2123045056c20160c5eb2f4ff5be2c1ed0079..e3b063f060ea0ac93fd768830bd83148fbee44f0 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -22,21 +22,21 @@ relevantAbstracts:
# Detocs
## Description
-Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems. Upon phage recognition, Detocs degrades ATP, which can lead to premature phage lysis or abortive infection depending on the infecting phage, in a way that is currently not fully understood. Detocs shares homology with the bacterial two-component system, a well known bacterial gene regulation system composed of an environment sensor and a cytosolic response regulator mediating gene expression.
+Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems. Upon phage recognition, Detocs degrades ATP, which can lead to premature phage lysis or abortive infection depending on the infecting phage, in a way that is currently not fully understood. Detocs shares homology with the bacterial two-component system, a well-known bacterial gene regulation system composed of an environment sensor and a cytosolic response regulator mediating gene expression.
## Molecular mechanism
-Detocs is a family of 3-gene systems that resembles bacterial two component systems. Two component systems are common prokaryotic gene regulation modules made of two component, a sensor kinase and response regulator. The sensor typically senses an environmental signal through its N-terminal domain, leading to the autophosphorylation of a conserved histidine in its kinase C-terminal domain. This phosphate group is then transfered to the N-terminal receiver domain of the response regulator, which activates the response regulator's C-terminal domain, usually a DNA binding domain involved in gene regulation. This allows bacteria to modify gene expression based on environemental cues.
+Detocs is a family of 3-gene systems that resembles bacterial two-component systems. Two-component systems are common prokaryotic gene regulation modules made of two components, a sensor kinase and a response regulator. The sensor typically senses an environmental signal through its N-terminal domain, leading to the autophosphorylation of a conserved histidine in its kinase C-terminal domain. This phosphate group is then transferred to the N-terminal receiver domain of the response regulator, which activates the response regulator's C-terminal domain, usually a DNA binding domain involved in gene regulation. This allows bacteria to modify gene expression based on environmental cues.
-Detocs DtcA ressembles an intracellular sensor kinase. Its N-terminal end comprises tetratricopeptide repeats that are usually involved in protein/protein interactions and are believed to be responsible for sensing phage infection, while its C-terminal end possesses a kinase domain. Detocs DtcC, resembles a response regulator. It has an N-terminal receiver domain, and its C-terminal is variable depending on systems and it always contains a predicted effector domain (PNP, nuclease, transmembrane, hydrolase...). Unlike two-component system, Detocs encodes an additional third protein, DtcB, with a standalone receiver domain that is not linked to any effector domain. A point mutation in the receiving aspartate of DtcB is toxic, while overexpression of DtcB impairs the defense capacity of Detocs. Therefore, DtcB likely serves as a “buffer†protein that absorbs phosphate signals that result from inadvertent leaky activation of DtcA in the absence of phage infection, thus preventing autoimmunity.
+Detocs DtcA resembles an intracellular sensor kinase. Its N-terminal end comprises tetratricopeptide repeats that are usually involved in protein/protein interactions and are believed to be responsible for sensing phage infection, while its C-terminal end possesses a kinase domain. Detocs DtcC resembles a response regulator. It has an N-terminal receiver domain, and its C-terminal is variable depending on the systems and it always contains a predicted effector domain (PNP, nuclease, transmembrane, hydrolase...). Unlike a two-component system, Detocs encodes an additional third protein, DtcB, with a standalone receiver domain that is not linked to any effector domain. A point mutation in the receiving aspartate of DtcB is toxic, while overexpression of DtcB impairs the defense capacity of Detocs. Therefore, DtcB likely serves as a “buffer†protein that absorbs phosphate signals that result from inadvertent leaky activation of DtcA in the absence of phage infection, thus preventing autoimmunity.
-The best described Detocs system uses a PNP effector, which was shown to specifically cleave ATP molecules into adenine and ribose-5’-triphosphate, both in vitro and during phage infection. Detocs activity leads to a drastic reduction in ATP and dATP levels during infection and to an accumulation of adenine. In parallel, ADP, AMP, dADP and dAMP levels are also reduced, likely in an indirect manner. Detocs induces growth arrest of T5-infected cells, but not of SECphi27-infected cells, suggesting that the outcome of infection following ATP degradation is phage-specific. The exact way in which this leads to defense against phages is not yet clear, but is believed to be a form of abortive infection. While PNP effectors represent 80% of Detocs operons, other cell-killing effectors can be found in a minority of Detocs systems. A Detocs operon with a transmembrane α/β hydrolase effector from *Enterobacter cloacae* JD6301 was able to efficiently protect *E. coli* against diverse phages :ref{doi=10.1016/j.cell.2023.07.020}.
+The best-described Detocs system uses a PNP effector, which was shown to specifically cleave ATP molecules into adenine and ribose-5’-triphosphate, both in vitro and during phage infection. Detocs activity leads to a drastic reduction in ATP and dATP levels during infection and to an accumulation of adenine. In parallel, ADP, AMP, dADP and dAMP levels are also reduced, likely in an indirect manner. Detocs induces growth arrest of T5-infected cells, but not of SECphi27-infected cells, suggesting that the outcome of infection following ATP degradation is phage-specific. The exact way in which this leads to defense against phages is not yet clear, but is believed to be a form of abortive infection. While PNP effectors represent 80% of Detocs operons, other cell-killing effectors can be found in a minority of Detocs systems. A Detocs operon with a transmembrane α/β hydrolase effector from *Enterobacter cloacae* JD6301 was able to efficiently protect *E. coli* against diverse phages :ref{doi=10.1016/j.cell.2023.07.020}.
## Example of genomic structure
A total of 4 subsystems have been described for the Detocs system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index d88cd781a312225c93fe65455211c5391b1aa971..693604aa0f5762973f3105dfdda1a43639fd329d 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -19,10 +19,10 @@ relevantAbstracts:
# dGTPase
## Description
-dGTPase are a family of proteins discovered in :ref{doi=10.1038/s41564-022-01158-0}. It degrades dGTP into phosphate-free deoxyguanosine. It was suggested that these *"bacterial defensive proteins deplete deoxynucleotides from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication"*. The mechanism is remindful of the mechanism of SAMHD1 in humans.
+dGTPase is a family of proteins discovered in :ref{doi=10.1038/s41564-022-01158-0}. It degrades dGTP into phosphate-free deoxyguanosine. It was suggested that these *"bacterial _defensive proteins deplete_ _deoxynucleotides__ from the_ nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication"*. The mechanism is remindful of the mechanism of SAMHD1 in humans.
## Molecular mechanism
-dGTPase degrades dGTP into phosphate-free deoxyguanosine. Phage mutants which overcome this defense carry mutations in phage-RNAP-modifying proteins suggesting, that *"phage-mediated inhibition of host transcription may be involved in triggering the activation of bacterial dNTP-depletion"*.
+dGTPase degrades dGTP into phosphate-free deoxyguanosine. Phage mutants that overcome this defense carry mutations in phage-RNAP-modifying proteins suggesting, that *"phage-mediated inhibition of host transcription may be involved in triggering the activation of bacterial dNTP-depletion"*.
## Example of genomic structure
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index f29c2ab66e9c75c07179e22103f8b343a319127d..d65b4f566fb0c6ed09a5fc78d75298ed0a6b0e5c 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -28,9 +28,9 @@ DISARM (Defense Island System Associated with Restriction-Modification) is a def
DISARM allows phage adsorption but prevents phage replication. DISARM is thought to cause intracellular phage DNA decay :ref{doi=10.1038/s41564-017-0051-0}, but the molecular of this potential DNA degradation remains unknown.
-The *drmMII* gene of DISARM system from *Bacillus paralicheniformis* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of *drmMII,* this DISARM system appears toxic to the cells :ref{doi=10.1038/s41564-017-0051-0}. These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity.Â
+The *drmMII* gene of the DISARM system from *Bacillus paralicheniformis* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of *drmMII,* this DISARM system appears toxic to the cells :ref{doi=10.1038/s41564-017-0051-0}. These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity.Â
-Yet this system was also shown to protect against phages whose genomes are exempt of CCWGG motifs :ref{doi=10.1038/s41564-017-0051-0}. Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a *Serratia sp.* does not result in autoimmunity :ref{doi=10.1101/2021.12.28.474362}. Both these results suggest additional phage DNA recognition mechanisms.Â
+Yet this system was also shown to protect against phages whose genomes are exempt from CCWGG motifs :ref{doi=10.1038/s41564-017-0051-0}. Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a *Serratia sp.* does not result in autoimmunity :ref{doi=10.1101/2021.12.28.474362}. Both these results suggest additional phage DNA recognition mechanisms.Â
Hints of these additional mechanisms can be found in recent structural studies, which show that DrmA and DrmB form a complex that can bind single-stranded DNA :ref{doi=10.1038/s41467-022-30673-1}. Moreover, the DrmAB complex seems to exhibit strong ATPase activity in the presence of unmethylated DNA, and reduced ATPase activity in the presence of a methylated DNA substrate :ref{doi=10.1038/s41467-022-30673-1}. Finally, binding of unmethylated single-stranded DNA appears to mediate major conformational change of the complex, which was hypothesized to be responsible for downstream DISARM activation :ref{doi=10.1038/s41467-022-30673-1}.
@@ -43,7 +43,7 @@ These three core genes are accompanied by a methyltransferase, which can be eith
A total of 2 subsystems have been described for the DISARM system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 3beff1a2a50c4bc92313dcd3fbb263880349159e..804eb72f0c183ea9f36f274d99a888861e5e3498 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -20,7 +20,7 @@ relevantAbstracts:
## Description
-Dodola is named after a figure from Slavic mythology, often associated with rain and fertility. The Dodola defense system was first discovered through its common association with known defense systems, and characterized in B. subtilis, demonstrating its efficacy against the SPP1 phage :ref{doi=10.1016/j.chom.2022.09.017}.
+Dodola is named after a figure from Slavic mythology, often associated with rain and fertility. The Dodola defense system was first discovered through its common association with known defense systems, and characterized in *B. subtilis*, demonstrating its efficacy against the SPP1 phage :ref{doi=10.1016/j.chom.2022.09.017}.
Dodola is composed of two proteins, DolA and DolB. DolA contains a DUF6414 domain, and DolB contains a ClpB-like domain.
## Molecular mechanisms
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index 8255fad55504ead7ac6fbb56fde09a185f324bac..da164ec7de526e35cbaed462aaff449929a85516 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -39,13 +39,13 @@ So far, DRTs have been classified in 9 different types. Essential components of
## Molecular mechanism
To our knowledge, the molecular mechanism is unknown.
-Similarly, for the other systems of this family, the molecular mechanism remain unknown.
+Similarly, for the other systems of this family, the molecular mechanism remains unknown.
## Example of genomic structure
A total of 9 subsystems have been described for the DRT system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
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diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 7707a5fb889bfc76daabe7f61ee7e7f50cf95e42..9c3a28eac055f94d0024ea78da1fea9d56032cd6 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -20,7 +20,7 @@ relevantAbstracts:
A total of 2 subsystems have been described for the Dsr system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
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diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index 26cc80ba635c61df534d12fe484536a6d4819783..2cca1a44917bcf08d54a09d09ce72429a76bc2dc 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -21,7 +21,7 @@ relevantAbstracts:
## Description
-\The Eleos (for the greek goddess of mercy) system was previously described as the Dynamins-like system in :ref{doi=10.1016/j.chom.2022.09.017}. It is formed by the LeoA and LeoBC proteins. LeoBC has been found to be analogous to GIMAPs (GTPases immunity-associated proteins), that are interferon inducible :ref{doi=10.1101/2022.12.12.520048}. LeoA in *E. coli* ETEC H10407 localises to the periplasm and has been suggested to potientiate bacterial virulence. Its crystal structure has been solved :ref{doi=10.1371/journal.pone.0107211}. Eleos from *Bacillus vietnamensis* NBRC 101237 has been found to protect against jumbo-phages in *Bacillus subtilis* :ref{doi=10.1016/j.chom.2022.09.017}.
+\The Eleos (for the Greek goddess of mercy) system was previously described as the Dynamins-like system in :ref{doi=10.1016/j.chom.2022.09.017}. It is formed by the LeoA and LeoBC proteins. LeoBC has been found to be analogous to GIMAPs (GTPases immunity-associated proteins), that are interferon-inducible :ref{doi=10.1101/2022.12.12.520048}. LeoA in *E. coli* ETEC H10407 localizes to the periplasm and has been suggested to potentiate bacterial virulence. Its crystal structure has been solved :ref{doi=10.1371/journal.pone.0107211}. Eleos from *Bacillus vietnamensis* NBRC 101237 has been found to protect against jumbo-phages in *Bacillus subtilis* :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanism
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index 29ae01a78a19503af7b13716792c93300421b433..a1f7163c79496999fef179958d72bd162bce7796 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -18,8 +18,11 @@ relevantAbstracts:
# FS_HP
## Description
-PICIs (Phage-inducible chromosomal islands) are highly mobile genetic elements that reside in the bacterial chromosome in the absence of a helper phage. Following infection by the helper phage, PICIs excise and replicate by hijacking the helper phage machinery. The FS_HP system was discovered in E. fergusonii through manual search for immune systems in flanking regions of gram-negative PICIs :ref{doi=10.1016/j.cell.2022.07.014}. It is composed by a single protein with a hypothetical domain, from which it derives the HP part of its name. The system showcases a broad defense spectrum. It was tested against 15 lytic phages in 3 gram negative bacteria, and protected the bacterial host against 3 unrelated phages in 2 different bacteria species. FS_HP also blocked the formation of phage particles upon induction of the P22 S. enterica prophage. Therefore, the system can block phage in both lytic and lysogenic life cycles. It was also shown to reduce the production of transducing particles.
+
+PICIs (Phage-inducible chromosomal islands) are highly mobile genetic elements that reside in the bacterial chromosome in the absence of a helper phage. Following infection by the helper phage, PICIs excise and replicate by hijacking the helper phage machinery. The FS_HP system was discovered in *E. _fergusonii_ through the manual search for immune systems in flanking regions of gram-negative PICIs :ref{doi=10.1016/j.cell.2022.07.014}. It is composed of a single protein with a hypothetical domain, from which it derives the HP part of its name. The system showcases a broad defense spectrum. It was tested against 15 lytic phages in 3 gram-negative bacteria and protected the bacterial host against 3 unrelated phages in 2 different bacteria species. FS_HP also blocked the formation of phage particles upon induction of the P22 *S. enterica* prophage. Therefore, the system can block phage in both lytic and lysogenic life cycles. It was also shown to reduce the production of transducing particles.
+
## Molecular mechanisms
+
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 73607bfee0336315f1d7986e47ba0b19c1738263..a349f90673bac07815c6b5fd4b3217d7c1fabf3b 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -19,7 +19,7 @@ relevantAbstracts:
SMA (single-protein MazF-like antiphage system) was identified in a phage-inducible chromosomal island (PICI) found in *Staphylococcus aureus* :ref{doi=10.1016/j.cell.2022.07.014}. SMA was shown to inhibit phage infection and to inhibit the formation of new virions after prophage induction.
## Molecular mechanisms
-The SMA protein comprises a domain analogous to MazF. MazF a protein that is normally part of the MazEF toxin-antitoxin systems, in which MazF is a toxic endoribonuclease that targets mRNA :ref{doi=10.1016/s1097-2765(03)00402-7}.
+The SMA protein comprises a domain analogous to MazF. MazF is a protein that is normally part of the MazEF toxin-antitoxin systems, in which MazF is a toxic endoribonuclease that targets mRNA :ref{doi=10.1016/s1097-2765(03)00402-7}.
As far as we are aware, the precise molecular mechanism of SMA is unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index 337a6209a0865e89d1c03539c923acb4f55c4b19..de1d9d908661263771b344a123e41ac8e373d555 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -24,14 +24,14 @@ relevantAbstracts:
## Description
-Gabija is named after the Lithuanian spirit of fire, protector of home and family. It is a two gene defense system found in 8.5% of the 4360 bacterial and archeal genomes that were initially analyzed in :ref{doi=10.1126/science.aar4120}. Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers :ref{doi=10.1038/s41586-023-06855-2,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1038/s41586-023-06855-2,10.1038/s41586-023-06869-w}.
+Gabija is named after the Lithuanian spirit of fire, protector of home and family. It is a two-gene defense system found in 8.5% of the 4360 bacterial and archeal genomes that were initially analyzed in :ref{doi=10.1126/science.aar4120}. Both proteins are necessary for defense and are forming a heteromeric octamer complex: GajA forms a central tetramer surrounded by two GajB dimers :ref{doi=10.1038/s41586-023-06855-2,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti-defense 1 (Gad1) :ref{doi=10.1038/s41586-023-06855-2,10.1038/s41586-023-06869-w}.
## Molecular mechanism
The precise mechanism of the Gabija system remains to be fully described, yet studies suggest that it could act through a dual phage inhibition mechanism.
-GajA was shown to be a sequence-specific DNA nicking endonuclease, whose activity is inhibited by nucleotide concentration. This nucleotide sensing is mediated by GajA ATPase-like domain. Accordingly, GajA would be fully inhibited at cellular nucleotides concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated :ref{doi=10.1093/nar/gkab277}.Â
-Moreover, a later study suggests that the *gajB* gene encode an NTPase, which would form a complex with GajA to achieve anti-phage defense. GajB is activated by DNA termini produced by GajA activity and then hydrolyzes (d)A/(d)GTP, depleting essential nucleotides and increasing GajA activity :ref{doi=10.1016/j.chom.2023.06.014}.
-Therefore, both proteins would be cooperating to achieve both nucleotide depletion and DNA cleavage, causing abortive infection.
+GajA was shown to be a sequence-specific DNA-nicking endonuclease, whose activity is inhibited by nucleotide concentration. This nucleotide sensing is mediated by GajA ATPase-like domain. Accordingly, GajA would be fully inhibited at cellular nucleotide concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated :ref{doi=10.1093/nar/gkab277}.Â
+Moreover, a later study suggests that the _gajB_ gene encodes an NTPase, which would form a complex with GajA to achieve anti-phage defense. GajB is activated by DNA termini produced by GajA activity and then hydrolyzes (d)A/(d)GTP, depleting essential nucleotides and increasing GajA activity :ref{doi=10.1016/j.chom.2023.06.014}.
+Therefore, both proteins would cooperate to achieve both nucleotide depletion and DNA cleavage, causing abortive infection.
## Example of genomic structure
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index 1cc620743bfc3faefdfd50536a51256737df1bef..b48136d42b5cfa9db41b98b0cae2f5452c53b377 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# ApeA
## Description
-ApeA is defense system composed of one protein, initially described as a member of the HEPN superfamily which groups proteins with nucleotide binding activity ([CL0291](https://www.ebi.ac.uk/interpro/set/pfam/CL0291/)).
+ApeA is a defense system composed of one protein, initially described as a member of the HEPN superfamily which groups proteins with nucleotide binding activity ([CL0291](https://www.ebi.ac.uk/interpro/set/pfam/CL0291/)).
ApeA is predicted to act *via* an abortive infection mechanism.
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index 84dd739cb85bb3131b4fcd9bd8ae795dd2ce18dd..22bf41e8afddddb596c4a848977124b7ba3312ee 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -23,7 +23,7 @@ relevantAbstracts:
A total of 2 subsystems have been described for the Gao_Her system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 5b20fd748da07ee5cd39ff86b80c930c460c863b..d4984059424eba4fc169f874e1dffa880e6c2448 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# Gao_Hhe
## Description
-The Gao_hhe system is composed by a single protein. It was predicted through a guilty by association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1093/nar/gkad317}. It contains a predicted helicase and a Vsr (very short patch repair) endonuclease domain :ref{doi=10.1093/nar/gkad317,10.1128/jvi.00599-23}.
+The Gao_hhe system is composed of a single protein. It was predicted through a guilty-by-association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1093/nar/gkad317}. It contains a predicted helicase and a Vsr (very short patch repair) endonuclease domain :ref{doi=10.1093/nar/gkad317,10.1128/jvi.00599-23}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index 3ea6b9d54a7f32c4300991acab791fae14bd75e2..bdd2ac84ba6728cdc4c6d1e5731e9fed09008508 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -17,9 +17,13 @@ relevantAbstracts:
# Gao_upx
## Description
-The Gao_upx system is composed by a single protein. It was predicted through a guilty by association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1126/science.aba0372}. It's been identified as part of a highly conserved core defense hotspot in *Pseudomonas aeruginosa* strains :ref{doi=10.1093/nar/gkad317}.
+
+The Gao_upx system is composed of a single protein. It was predicted through a guilty-by-association approach independent of domain annotations and validated in a heterologous system :ref{doi=10.1126/science.aba0372}. It's been identified as part of a highly conserved core defense hotspot in *Pseudomonas aeruginosa* strains :ref{doi=10.1093/nar/gkad317}.
+
## Molecular mechanisms
+
As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The Gao_Upx is composed of 1 protein: UpxA.
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index 476d7eeee51f90ec13994732d90c7f9062f240ec..e694ec4cbc68feea3ffb5ea0deedb68ce5a0668f 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -18,7 +18,8 @@ relevantAbstracts:
# GAPS1
## Description
-The GAPS1 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in *Vibrio*, and cloned into *E. coli* K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. GAPS1 contains a predicted nuclease domain whose mutation prevents defense activity, however DNA degradation was not detected in targeted phage :ref{doi=10.1101/2023.03.28.534373}. Mutations in the folded capsid protein (Gp10) of phage T7 result in a escape phenotype, with GAPS1 shown to be activated upon Gp10 expression, suggesting activation of the system at late stages of the infection cycle :ref{doi=10.1101/2023.03.28.534373}.
+
+The GAPS1 system is composed of a single protein. It was found in Gamma-Mobile-Trio (GMT) protein containing genomic island in *Vibrio*, and cloned into *E. coli* K-12 :ref{doi=10.1101/2023.03.28.534373}. The name GAPS derives from the "GMT-encoded Anti-Phage System" acronym. GAPS1 contains a predicted nuclease domain whose mutation prevents defense activity, however DNA degradation was not detected in targeted phage :ref{doi=10.1101/2023.03.28.534373}. Mutations in the folded capsid protein (Gp10) of phage T7 result in an escape phenotype, with GAPS1 shown to be activated upon Gp10 expression, suggesting activation of the system at late stages of the infection cycle :ref{doi=10.1101/2023.03.28.534373}.
## Molecular mechanisms
The molecular mechanism remains to be fully elucidated.
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index 5a40c1ebc45bcb25949750ec537f0269fc3fa249..32d72ca9f1a0719534f1c53af0978260b83dc1d1 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -15,13 +15,13 @@ relevantAbstracts:
# GAPS4
## Description
+
GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.
-GAPS4 is present in both Gram positive and Gram negative
-GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
+GAPS4 is present in both Gram-positive and Gram-negative GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
## Molecular mechanism
-GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system works causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
+GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
## Example of genomic structure
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 0baccd2b1fe9eb04660b78e893a2f2be9880600c..bd7db813bca0b47bfa496464fb6e3c661dce20eb 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -26,17 +26,7 @@ GAPS6 is composed of two proteins, [GAPS6a](https://www.ncbi.nlm.nih.gov/protein
GAPS6b is essential for the defense phenotype, however it is not known whether GAPS6b could be sufficient.
GAPS6b is composed of TPR repeats at the N-terminus, possibly allowing ligand binding and a predicted RNAse domain (PINc, PF08745.14) at the C-terminus. PINc domains have been implicated as toxins in bacterial toxin-antitoxin modules :ref{doi=10.1093/protein/gzq081}. The PINc domain is required for the anti-phage defense activity of GAPS6.
-## Example of genomic structure
-
-TODO
-
-## Distribution
-
-TODO
-
-## Predicted structure
-=======
## Example of genomic structure
The GAPS6 is composed of 2 proteins: GAPS6a and GAPS6b.
@@ -60,8 +50,9 @@ Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 5
## Structure
->>>>>>> content/3.defense-systems/gaps6.md
+
### GAPS6
+
##### Example 1
::molstar-pdbe-plugin
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 194afdb147d52f4da782616c50b2dc6b651c3e03..beb8bda0407c8636b5f14c187bd16c60fdc2e678 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -21,11 +21,11 @@ relevantAbstracts:
## Description
-Gasdermin proteins were initially discovered in humans. Recently there were shown to be present in multiple bacteria, where they are almost always encoded in an operon together with a protease. The experimental validation of the antiphage activity of bacterial gasdermins was demonstrated through the heterologous experession of a 4-genes operon from Lysobacter in E. coli :ref{doi=10.1126/science.abj8432} :ref{doi=10.1101/2023.05.28.542683}.
+Gasdermin proteins were initially discovered in humans. Recently they were shown to be present in multiple bacteria, where they are almost always encoded in an operon together with a protease. The experimental validation of the antiphage activity of bacterial gasdermins was demonstrated through the heterologous expression of a 4-genes operon from Lysobacter in *E. coli* :ref{doi=10.1126/science.abj8432,10.1101/2023.05.28.542683}.
## Molecular Mechanism
-Akin to their human counterparts, bacterial gasdermins encode a C-terminal inhibotry domain. Following phage infection, proteases associated to bacterial gasdermin cleave this domain triggering oligomerization of gasdermins into large, membrane-breaching pores :ref{doi=10.1126/science.abj8432} leading to cell death:ref{doi=10.1101/2023.05.28.542683}. As such gasdermins containing systems are abortive infection systems. rIIB, a protein allowing T6 to overcome RexAB system was shown to activate gasdermin. It was further shown that CARD domain are also essential in bacterial gasdermins defense :ref{doi=10.1101/2023.05.28.542683}.
+Akin to their human counterparts, bacterial gasdermins encode a C-terminal inhibitory domain. Following phage infection, proteases associated with bacterial gasdermin cleave this domain triggering oligomerization of gasdermins into large, membrane-breaching pores :ref{doi=10.1126/science.abj8432} leading to cell death:ref{doi=10.1101/2023.05.28.542683}. As such gasdermins containing systems are abortive infection systems. rIIB, a protein allowing T6 to overcome the RexAB system was shown to activate gasdermin. It was further shown that CARD domains are also essential in bacterial gasdermins defense :ref{doi=10.1101/2023.05.28.542683}.
## Example of genomic structure
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index 1da9281874b6590558800b1613a92539dd4e106a..345a632fbc5e329f8f4e029e670221df7bfc476d 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -17,9 +17,14 @@ relevantAbstracts:
# Hachiman
## Description
-Hachiman Type 1 systems were the first discovered and can be found in 3.4% of microbial genomes (1). Hachiman Type 1 systems are encoded by two genes, *hamA* (annotated as a Domain of Unknown Function, DUF) and *hamB* (annotated as a helicase) (1).Â
+Hachiman Type 1 systems were the first discovered and can be found in 3.4% of microbial genomes :ref{doi=10.1126/science.aar4120}. Hachiman Type 1 systems are encoded by two genes, *hamA* (annotated as a Domain of Unknown Function, DUF) and *hamB* (annotated as a helicase) :ref{doi=10.1126/science.aar4120}.Â
-More recently, Hachiman Type 2 systems were discovered and appeared to include a third gene, encoded for a DUF protein (HamC) (2).
+More recently, Hachiman Type 2 systems were discovered and appeared to include a third gene, encoded for a DUF protein (HamC) :ref{doi=10.1093/nar/gkac400}.
+
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 83b8203aa8da8de9d4fb15f0f376ed0702bd4724..0d63bcc8ad85025c72f71dd2d2fa286621a4b887 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -21,11 +21,11 @@ relevantAbstracts:
## Description
-ISG15-like (Interferon-stimulated gene 15 - like) systems (also known as Bil systems for Bacterial ISG15-like systems) are a 4 gene defense system comprising a homolog of ubiquitin-like ISG15 (BilA), ubiquitin-conjugating enzymes E1 (BilD) and E2 (BilB), and a deubiquitinase (BilC) :ref{doi=10.1101/2023.09.04.556158,10.1016/j.chom.2022.09.017}. It has been shown to defend against muliple coliphages :ref{doi=10.1016/j.chom.2022.09.017}. The Bil system is analogous to the ISG15 system in humans, that protects against virus.
+ISG15-like (Interferon-stimulated gene 15 - like) systems (also known as Bil systems for Bacterial ISG15-like systems) are a 4-gene defense system comprising a homolog of ubiquitin-like ISG15 (BilA), ubiquitin-conjugating enzymes E1 (BilD) and E2 (BilB), and a deubiquitinase (BilC) :ref{doi=10.1101/2023.09.04.556158,10.1016/j.chom.2022.09.017}. It has been shown to defend against multiple coliphages :ref{doi=10.1016/j.chom.2022.09.017}. The Bil system is analogous to the ISG15 system in humans, which protects against viruses.
## Molecular mechanism
-Hör et al., have shown that the ISG15-like system defends bacteria against phages by impairing infectivity of newly synthezised phages. It does so by preventing tail assembly that leads to non-infective tailless phages or by producing modified tails with an obstructed tail tip that are not capable of infecting. More specifically, BilA is conjugated to the central tail fiber (CTF) protein of the phage :ref{doi=10.1101/2023.09.04.556158}.
+Hör et al., have shown that the ISG15-like system defends bacteria against phages by impairing the infectivity of newly synthesized phages. It does so by preventing tail assembly that leads to non-infective tailless phages or by producing modified tails with an obstructed tail tip that are not capable of infecting. More specifically, BilA is conjugated to the central tail fiber (CTF) protein of the phage :ref{doi=10.1101/2023.09.04.556158}.
## Example of genomic structure
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 0c5ddce45dca0c1dc94ec0f856dffdc695e45444..3549ac94bdd364fef4522cd14f8cf1422f219cf2 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -24,7 +24,7 @@ relevantAbstracts:
The Kiwa antiviral defense system was first described in :ref{doi=10.1126/science.aar4120} and further described in :ref{doi=10.1101/2023.02.26.530102}. It is named after one of the divine guardians of the ocean in the MÄori traditions. Kiwa is composed of two proteins: KwaA and KwaB.
## Molecular mechanisms
-KwaA detects phage infection by detecting the inhibition of the host RNA polymerase by phages. This triggers the reponse by KwaB, which decreases phage DNA replication through a RecBCD-depdendent pathway :ref{doi=10.1101/2023.02.26.530102}.
+KwaA detects phage infection by detecting the inhibition of the host RNA polymerase by phages. This triggers the response by KwaB, which decreases phage DNA replication through a RecBCD-dependent pathway :ref{doi=10.1101/2023.02.26.530102}.
## Example of genomic structure
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index a084162df8910f3ef96fad93b70f478853b023bb..5d328bccb22eee4609c772c6a630fa8d2003a30f 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -28,13 +28,13 @@ The original types of Lamassu systems are Lamassu Type 1 :ref{doi=10.1126/scienc
Lamassu has been suggested to be a large family of defense systems, that can be classified into multiple subtypes :ref{doi=10.1016/j.chom.2022.09.017}.Â
-These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC*. In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein :ref{doi=10.1101/2022.05.11.491447}. This effector  can be proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains :ref{doi=10.1016/j.chom.2022.09.017}. Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes :ref{doi=10.1016/j.chom.2022.09.017}.
+These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC*. In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein :ref{doi=10.1101/2022.05.11.491447}. This effector  can be proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains :ref{doi=10.1016/j.chom.2022.09.017}. Systems of the extended Lamassu family can be found in 10% of prokaryotic genomes :ref{doi=10.1016/j.chom.2022.09.017}.
-Lamassu were also described as DdmABC in *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y,10.1101/2022.11.18.517080}. They were found to be antiplasmids and thus to eliminate plasmids from seventh pandemic *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y}. The DdmABC system corresponds to a Lamassu-Fam Cap4 nuclease system.
+Lamassu were also described as DdmABC in *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y,10.1101/2022.11.18.517080}. They were found to be anti plasmids and thus to eliminate plasmids from the seventh pandemic _Vibrio_ cholerae* :ref{doi=10.1038/s41586-022-04546-y}. The DdmABC system corresponds to a Lamassu-Fam Cap4 nuclease system.
## Molecular mechanism
-Lamassu systems function through abortive infection (Abi), but the molecular mechanism remains to be described. It was shown that, in Vibrio cholerae palindromic DNA sequences that are predicted to form stem-loop hairpin trigger the system :ref{doi=10.1101/2022.11.18.517080}.
+Lamassu systems function through abortive infection (Abi), but the molecular mechanism remains to be described. It was shown that, in *Vibrio cholerae* palindromic DNA sequences that are predicted to form stem-loop hairpin trigger the system :ref{doi=10.1101/2022.11.18.517080}.
## Example of genomic structure
@@ -43,7 +43,7 @@ LmuA is the effector and encode for different domains depending on the subsystem
A total of 11 subsystems have been described for the Lamassu-Fam system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index cf1d9bdbd0319afd775db591ecd685084523a933..23a2334dee6e38da26d15b776220eebabcf131ca 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -24,11 +24,11 @@ relevantAbstracts:
## Description
-Lit was first identified in 1989 :ref{doi=10.1128/jb.169.3.1232-1238.1987}, stands for late inhibitors of T4, and was found to inhibit phage T4 in Escherichia coli (K12). The Lit gene is found in the e14 cryptic prophage :ref{doi=10.1128/jb.170.5.2056-2062.1988}. Lit is also partially active against other T-even phages :ref{doi=10.1073/pnas.91.2.802}.
+Lit was first identified in 1989 :ref{doi=10.1128/jb.169.3.1232-1238.1987}, stands for late inhibitors of T4 and was found to inhibit phage T4 in Escherichia coli (K12). The Lit gene is found in the e14 cryptic prophage :ref{doi=10.1128/jb.170.5.2056-2062.1988}. Lit is also partially active against other T-even phages :ref{doi=10.1073/pnas.91.2.802}.
## Molecular mechanisms
-The Lit system detects cleaves EF-Tu translation factor :ref{doi=10.1073/pnas.91.2.802} at a late stage of phage maturation, when the major capsid protein binds to EF-Tu and triggers its cleavage by Lit :ref{doi=10.1074/jbc.M002546200}. As a result, the translation is inhbited, which ultimately leads to cell death. Lit is part of the abortive infection category of defense systems.
+The Lit system detects cleaves EF-Tu translation factor :ref{doi=10.1073/pnas.91.2.802} at a late stage of phage maturation, when the major capsid protein binds to EF-Tu and triggers its cleavage by Lit :ref{doi=10.1074/jbc.M002546200}. As a result, the translation is inhibited, which ultimately leads to cell death. Lit is part of the abortive infection category of defense systems.
## Example of genomic structure
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index aae29f8c159cd027ad90bbf973f968c054fceab7..e94ce77d88a389813f4eedfe3f76c6b517b488ce 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -20,7 +20,7 @@ relevantAbstracts:
## Description
-The Menshen system has been identified by Millman et al. as a three protein system NsnA, NsnB and NsnC. Menshen from *Solibacillus silvestris* StLB046 confers resistance in *E. coli* and *B. subtilis* against some phages :ref{doi=10.1016/j.chom.2022.09.017}.
+The Menshen system has been identified by Millman et al. as a three-protein system NsnA, NsnB and NsnC. Menshen from *Solibacillus silvestris* StLB046 confers resistance in *E. coli* and *B. subtilis* against some phages :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanism
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index 7b214492437f2c73905fdd4d33207e478e358fba..8b543a8f6b2cccf6dbe9147da46bd7e3f80d8295 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -15,10 +15,10 @@ relevantAbstract:
# MMB gp29-gp30
## Description
-MMB gp29-gp30 is a defense system which was in the MichelleMyBell (MMB) temperate mycobacteriophage. It is an example of prophage-mediated defense :ref{doi=10.1038/nmicrobiol.2016.251}.
+MMB gp29-gp30 is a defense system that was found in the MichelleMyBell (MMB) temperate mycobacteriophage. It is an example of prophage-mediated defense :ref{doi=10.1038/nmicrobiol.2016.251}.
## Molecular mechanisms
-To the extent of our knowledge, the precise mechanism of action of MMB gp29-gp30 is not known. The system was shown to protect against lytic infection by temperate phage (e.g. phage Tweety) and does not act through abotive infection. Cells that survive infection tend to become lysogens for the infecting phage. It was also shown that the expression of gp29 alone was toxic in *M. smegmatis* :ref{doi=10.1038/nmicrobiol.2016.251}.
+To the extent of our knowledge, the precise mechanism of action of MMB gp29-gp30 is not known. The system was shown to protect against lytic infection by temperate phage (e.g. phage Tweety) and does not act through abortive infection. Cells that survive infection tend to become lysogens for the infecting phage. It was also shown that the expression of gp29 alone was toxic in *M. smegmatis* :ref{doi=10.1038/nmicrobiol.2016.251}.
## Example of genomic structure
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index 48ce106a899436c9e28b5967e779a5608b7aa945..2e7db476b05ea07b9f1dc5e0f3f0a333d56c6451 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -27,7 +27,7 @@ This system defends against T4 phages only, as far as we currently know.
## Molecular mechanism
-Upon infection of phage T4, the transcription is halted by the phage, which leads to a decreasing level of the antitoxin Sok within a few minutes. The Hok proteins manage to be process in their active form and trigger cell death by depolarization of the membrane :ref{doi=10.1006/jmbi.1995.0186} before the later stage of the phage infection (assembly, packaging and lysis).
+Upon infection of phage T4, the transcription is halted by the phage, which leads to a decreasing level of the antitoxin Sok within a few minutes. The Hok proteins manage to be processed in their active form and trigger cell death by depolarization of the membrane :ref{doi=10.1006/jmbi.1995.0186} before the later stage of the phage infection (assembly, packaging and lysis).
## Example of genomic structure
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index d52939e12af30acd7b311545f659fc503a466125..5f6f2d867996b3b518705720329cada5c53278c9 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -20,7 +20,7 @@ relevantAbstract:
# Mokosh
## Description
-The Mokosh system was discovered in *E. coli* by examining clusters of genes enrinched in defense islands :ref{doi=10.1016/j.chom.2022.09.017}. It contains genes with an RNA helicase domain and a predicted phospholipase D domain (PLD) nuclease domain. Mutations in the ATP-binding domain of the helicase, and in the active site of the PLD nuclease disrupt phage defense. The system is divided in two types. Mokosh type I has two genes, one gene containing the RNA helicase domain and an additional serine-threonine kinase domain (STK), and one gene containing the PLD nuclease. Type II Mokosh is formed of a single gene containing both the helicase and nuclease domains. Recent efforts have shown homology between the Mokosh system and human proteins involved in the piRNA pathway, a defense mechanism of animal germlines that prevents expression of transposable elements :ref{doi=10.1101/2022.12.12.520048}. The system gets its name from the goddess protector of women's destiny in Slavic mythology :ref{doi=10.1016/j.chom.2022.09.017}.
+The Mokosh system was discovered in *E. coli* by examining clusters of genes enriched in defense islands :ref{doi=10.1016/j.chom.2022.09.017}. It contains genes with an RNA helicase domain and a predicted phospholipase D domain (PLD) nuclease domain. Mutations in the ATP-binding domain of the helicase, and the active site of the PLD nuclease disrupt phage defense. The system is divided into two types. Mokosh type I has two genes, one gene containing the RNA helicase domain and an additional serine-threonine kinase domain (STK), and one gene containing the PLD nuclease. Type II Mokosh is formed of a single gene containing both the helicase and nuclease domains. Recent efforts have shown homology between the Mokosh system and human proteins involved in the piRNA pathway, a defense mechanism of animal germlines that prevents expression of transposable elements :ref{doi=10.1101/2022.12.12.520048}. The system gets its name from the goddess protector of women's destiny in Slavic mythology :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 1341d9b0ef98b3223835d7e7763599619b810929..e2db62b38858dfa353bb5a2ee4b1cfb7f145e0d0 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -17,10 +17,10 @@ relevantAbstracts:
# NixI
## Description
-Phage-inducible chromosomal island-like elements (PLEs) are chromosomally-integrated phage parasites described in *Vibrio cholerae* :ref{doi=10.7554/eLife.53200}. PLEs excise in response to infection by phage ICP1 and halt its progeny production. PLE halts ICP1 infection by means of redirecting virion packaging and interfiring with ICP1 genome replication :ref{doi=10.1093/nar/gkz1005}. NixI is a PLE-encoded nuclease that nicks the ICP1 genome at specific sites preventing transition to the rolling circle replication (RCR) :ref{doi=10.1093/nar/gkac002}.
+Phage-inducible chromosomal island-like elements (PLEs) are chromosomally-integrated phage parasites described in *Vibrio cholerae* :ref{doi=10.7554/eLife.53200}. PLEs excise in response to infection by phage ICP1 and halt its progeny production. PLE halts ICP1 infection by redirecting virion packaging and interfering with ICP1 genome replication :ref{doi=10.1093/nar/gkz1005}. NixI is a PLE-encoded nuclease that nicks the ICP1 genome at specific sites preventing transition to the rolling circle replication (RCR) :ref{doi=10.1093/nar/gkac002}.
## Molecular mechanisms
-The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double stranded breaks :ref{doi=10.1093/nar/gkac002}.
+The NixI endonuclease cleaves the ICP1 genome at the GNAANCTT motif :ref{doi=10.1093/nar/gkac002}. It creates nicks and does not cause double-stranded breaks :ref{doi=10.1093/nar/gkac002}.
## Example of genomic structure
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index f1f4d4b7db85e320ff359d4979b01769bb4d9f72..72e3535bbb489731e7330fcc74dbba3ca71fb287 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -20,10 +20,10 @@ relevantAbstracts:
# Old_exonuclease
## Description
-The OLD proteins are a family of nucleases present in bacteria, archaea, and viruses :ref{doi=10.1093/nar/gkz703}. The OLD protein found in the P2 *E.coli* prophage is the best characterized one. The protein is an exonuclease that digests dsDNA in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. It also has nuclease activity against single stranded DNA and RNA :ref{doi=10.1128/jb.177.3.497-501.1995}. It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accesory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}. The protein also contains an ATPase domain that affects nuclease activity :ref{doi=10.1128/jb.177.3.497-501.1995}. Inhibition of the RecBCD complex activates the OLD nuclease :ref{doi=10.1016/j.mib.2023.102325}. OLD proteins are divided into two classes based on amino acid sequence conservation and gene neighborhood :ref{doi=10.1093/nar/gkz703}. The P2 associated protein belongs to class 2 :ref{doi=10.1093/nar/gkz703}.
+The OLD proteins are a family of nucleases present in bacteria, archaea, and viruses :ref{doi=10.1093/nar/gkz703}. The OLD protein found in the P2 *E.coli* prophage is the best characterized one. The protein is an exonuclease that digests dsDNA in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. It also has nuclease activity against single-stranded DNA and RNA :ref{doi=10.1128/jb.177.3.497-501.1995}. It's been shown to protect against phage lambda :ref{doi=10.1128/jb.177.3.497-501.1995}, and when cloned with the P2 Tin accessory gene, it was shown to protect against other *E. coli* phages :ref{doi=10.1016/j.chom.2022.02.018}. The protein also contains an ATPase domain that affects nuclease activity :ref{doi=10.1128/jb.177.3.497-501.1995}. Inhibition of the RecBCD complex activates the OLD nuclease :ref{doi=10.1016/j.mib.2023.102325}. OLD proteins are divided into two classes based on amino acid sequence conservation and gene neighborhood :ref{doi=10.1093/nar/gkz703}. The P2-associated protein belongs to class 2 :ref{doi=10.1093/nar/gkz703}.
## Molecular Mechanisms
-The old_exonuclease is dsDNA exonuclease that digest in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
+The old_exonuclease is dsDNA exonuclease that digests in the 5' to 3' direction :ref{doi=10.1128/jb.177.3.497-501.1995}. To our knowledge, other aspects of the molecular mechanisms remain unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 9c1b1d68aee751c0ab6c016f22820dae4f6aee31..1a7f78e6ef5eec96aa2b80398ee0edf8f0a4dbb8 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -23,13 +23,13 @@ relevantAbstracts:
## Description
-The system Olokun is composed of 2 genes OloA (Adaptin_N domain) and OloB (nuclease domain) of unknown function.
+The system Olokun is composed of 2 genes OloA (Adaptin_N domain) and OloB (nuclease domain) of unknown function.
This system was experimentally validated in _Escherichia coli_ and protects against LambdaVir and SECphi27 infection.
-The system is named after a revered deity of the Yoruba religion, associated with the deep sea and depicted as an enormously powerful figure. They are believed to posses immense wealth, are associated with health, fertility and prosperity, and revered for their ability for inducing profound transformation and renewal. They are frequently depicted as a mermaid or merman, with both masculine and feminine aspects, reflecting the diversity and depth of the ocean.
+The system is named after a revered deity of the Yoruba religion, associated with the deep sea and depicted as an enormously powerful figure. They are believed to possess immense wealth, are associated with health, fertility and prosperity, and are revered for their ability to induce profound transformation and renewal. They are frequently depicted as a mermaid or mermen, with both masculine and feminine aspects, reflecting the diversity and depth of the ocean.
## Molecular mechanisms
-To our knowledde, the molecular mechanism is unknown. Please update.
+To our knowledge, the molecular mechanism is unknown. Please update.
## Example of genomic structure
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 4a2e37c667638aae0e0cd91039213f6856791776..ca0df7147e0e80fe44e7098c6c3593963f9654b7 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -32,37 +32,36 @@ relevantAbstracts:
# pAgo
## Description
-Argonaute proteins comprise a diverse protein family and can be found in both prokaryotes and eukaryotes :ref{doi=10.1016/j.mib.2023.102313}. Despite low sequence conservation, eAgos and long pAgos generally have a conserved domain architecture and share a common mechanism of action; they use a 5'-phosphorylated single stranded nucleic acid guide (generally 15-22 nt in length) to target complementary nucleic acid sequences :ref{doi=10.1038/nsmb.2879} eAgos strictly mediate RNA-guided RNA silencing, while pAgos show higher mechanistic diversification, and can make use of guide RNAs and/or single-stranded guide DNAs to target RNA and/or DNA targets :ref{doi=10.1016/j.mib.2023.102313}. Depending on the presence of catalytic residues and the degree of complementarity between the guide and target sequences, eAgo and pAgos either cleave the target, or recruit and/or activate accessory proteins. This can result in degradation of the target nucleic acid, but might also trigger alternative downstream effects, ranging from poly(A) tail shortening and RNA decapping :ref{doi=10.1016/J.CELL.2018.03.006} or chromatin formation in eukaryotes :ref{doi=10.1038/s41580-022-00528-0}, to abortive infection in prokaryotes :ref{doi=10.1016/j.tcb.2022.10.005}.
+Argonaute proteins comprise a diverse protein family and can be found in both prokaryotes and eukaryotes :ref{doi=10.1016/j.mib.2023.102313}. Despite low sequence conservation, eAgos and long pAgos generally have a conserved domain architecture and share a common mechanism of action; they use a 5'-phosphorylated single-stranded nucleic acid guide (generally 15-22 nt in length) to target complementary nucleic acid sequences :ref{doi=10.1038/nsmb.2879} eAgos strictly mediate RNA-guided RNA silencing, while pAgos show higher mechanistic diversification, and can make use of guide RNAs and/or single-stranded guide DNAs to target RNA and/or DNA targets :ref{doi=10.1016/j.mib.2023.102313}. Depending on the presence of catalytic residues and the degree of complementarity between the guide and target sequences, eAgo and pAgos either cleave the target or recruit and/or activate accessory proteins. This can result in degradation of the target nucleic acid, but might also trigger alternative downstream effects, ranging from poly(A) tail shortening and RNA decapping :ref{doi=10.1016/J.CELL.2018.03.006} or chromatin formation in eukaryotes :ref{doi=10.1038/s41580-022-00528-0}, to abortive infection in prokaryotes :ref{doi=10.1016/j.tcb.2022.10.005}.
## Molecular mechanism
-Based on their phylogeny, Agos have been subdivided in various (sub)clades. eAgos are generally subdivided in the AGO and PIWI clades, but these will not be discussed further here. pAgos can be further subdivided in long-A pAgos, long-B pAgos, short pAgos, SiAgo-like pAgos, and PIWI-RE proteins :ref{doi=10.1128/mBio.01935-18,10.1016/j.mib.2023.102313,10.1016/j.tcb.2022.10.005,10.1186/1745-6150-8-13,10.1186/1745-6150-4-29}. Below, we briefly outline the general mechanism of pAgos that have a demonstrated role in host defense.
+Based on their phylogeny, Agos have been subdivided into various (sub)clades. eAgos are generally subdivided into the AGO and PIWI clades, but these will not be discussed further here. pAgos can be further subdivided into long-A pAgos, long-B pAgos, short pAgos, SiAgo-like pAgos, and PIWI-RE proteins :ref{doi=10.1128/mBio.01935-18,10.1016/j.mib.2023.102313,10.1016/j.tcb.2022.10.005,10.1186/1745-6150-8-13,10.1186/1745-6150-4-29}. Below, we briefly outline the general mechanism of pAgos that have a demonstrated role in host defense.
### Long-A pAgos
-Akin to eAgos, most long A-pAgos characterized to date have a N-L1-PAZ-L2-MID-PIWI domain architecture :ref{doi=10.1038/nsmb.2879}. In contrast to eAgos, however, certain long-A pAgos use a single stranded guide DNA to bind and cleave complementary target DNA sequences :ref{doi=10.1093/nar/gkz306,10.1093/nar/gkz379,10.1038/s41586-020-2605-1,10.1093/nar/gkv415,10.1038/nature12971,10.1038/nmicrobiol.2017.35}. Long-A pAgos are preferentially programmed with guide DNAs targeting invading DNA through a poorly understood mechanism, which might involve DNA repair proteins :ref{doi=10.1038/s41586-020-2605-1} or the pAgo itself :ref{doi=10.1016/j.molcel.2017.01.033,10.1038/nmicrobiol.2017.34}. Most long-A pAgos have an intact catalytic site in the PIWI domain which allows to cleave their targets :ref{doi=10.1073/pnas.1321032111}. As such, they act as an innate immune system that clear plasmid and phage DNA from the cell :ref{doi=10.1093/nar/gkz379,10.1038/s41586-020-2605-1,10.1093/nar/gkv415,10.1038/nature12971,10.1093/nar/gkad290}.
+Akin to eAgos, most long A-pAgos characterized to date have a N-L1-PAZ-L2-MID-PIWI domain architecture :ref{doi=10.1038/nsmb.2879}. In contrast to eAgos, however, certain long-A pAgos use a single-stranded guide DNA to bind and cleave complementary target DNA sequences :ref{doi=10.1093/nar/gkz306,10.1093/nar/gkz379,10.1038/s41586-020-2605-1,10.1093/nar/gkv415,10.1038/nature12971,10.1038/nmicrobiol.2017.35}. Long-A pAgos are preferentially programmed with guide DNAs targeting invading DNA through a poorly understood mechanism, which might involve DNA repair proteins :ref{doi=10.1038/s41586-020-2605-1} or the pAgo itself :ref{doi=10.1016/j.molcel.2017.01.033,10.1038/nmicrobiol.2017.34}. Most long-A pAgos have an intact catalytic site in the PIWI domain which allows to cleave their targets :ref{doi=10.1073/pnas.1321032111}. As such, they act as an innate immune system that clears plasmid and phage DNA from the cell :ref{doi=10.1093/nar/gkz379,10.1038/s41586-020-2605-1,10.1093/nar/gkv415,10.1038/nature12971,10.1093/nar/gkad290}.
-Within the long-A pAgo clade various subclades of other pAgos exist that rely on distinct function mechanisms. For example, various long-A pAgo can (additionally) use guide RNAs and/or cleave RNA targets. Furthermore, CRISPR-associated pAgos use 5'-OH guide RNAs to target DNA :ref{doi=10.1073/pnas.1524385113}, and PliAgo-like pAgos use small DNA guides to target RNA :ref{doi=10.1038/s41467-022-32079-5}. Certain long-A pAgos genetically co-localize with other putative enzymes including (but not limited to) putative nucleases, helicases, DNA-binding proteins, or PLD-like proteins :ref{doi=10.1038/nsmb.2879,10.1128/mBio.01935-18}. The relevance of these associations is currently unknown.
+Within the long-A pAgo clade, various subclades of other pAgos exist that rely on distinct function mechanisms. For example, various long-A pAgo can (additionally) use guide RNAs and/or cleave RNA targets. Furthermore, CRISPR-associated pAgos use 5'-OH guide RNAs to target DNA :ref{doi=10.1073/pnas.1524385113}, and PliAgo-like pAgos use small DNA guides to target RNA :ref{doi=10.1038/s41467-022-32079-5}. Certain long-A pAgos genetically co-localize with other putative enzymes including (but not limited to) putative nucleases, helicases, DNA-binding proteins, or PLD-like proteins :ref{doi=10.1038/nsmb.2879,10.1128/mBio.01935-18}. The relevance of these associations is currently unknown.
### Long-B pAgos
-Akin to long-A pAgogs, long B-pAgos have a N-L1-PAZ-L2-MID-PIWI domain composition, but most have a shorter PAZ* domain, and in contrast to long-A pAgos all long-B pAgos are catalytically inactive :ref{doi=10.1128/mBio.01935-18}. Long-B pAgos characterized to date use guide RNAs to bind invading DNA :ref{doi=10.1038/s41598-023-32600-w,10.1016/j.molcel.2013.08.014,10.1038/s41467-023-42793-3}. In absence of co-encoded proteins, long-B pAgos repress invader activity :ref{doi=10.1016/j.molcel.2013.08.014}. In addition, most long-B pAgos are co-encoded with effector proteins including (but not limited to) SIR2, nucleases, membrane proteins, and restriction endonucleases :ref{doi=10.1038/nsmb.2879,10.1128/mBio.01935-18,10.1186/1745-6150-4-29,10.1038/s41467-023-42793-3}. These effector proteins are activated upon pAgo-mediated invader detection, and generally catalyze reactions that result in cell death :ref{doi=10.1038/s41467-023-42793-3}. As such, long-B pAgo together with their associated proteins mediate abortive infection.
+Akin to long-A pAgogs, long B-pAgos have a N-L1-PAZ-L2-MID-PIWI domain composition, but most have a shorter PAZ* domain, and in contrast to long-A pAgos all long-B pAgos are catalytically inactive :ref{doi=10.1128/mBio.01935-18}. Long-B pAgos characterized to date use guide RNAs to bind invading DNA :ref{doi=10.1038/s41598-023-32600-w,10.1016/j.molcel.2013.08.014,10.1038/s41467-023-42793-3}. In the absence of co-encoded proteins, long-B pAgos repress invader activity :ref{doi=10.1016/j.molcel.2013.08.014}. In addition, most long-B pAgos are co-encoded with effector proteins including (but not limited to) SIR2, nucleases, membrane proteins, and restriction endonucleases :ref{doi=10.1038/nsmb.2879,10.1128/mBio.01935-18,10.1186/1745-6150-4-29,10.1038/s41467-023-42793-3}. These effector proteins are activated upon pAgo-mediated invader detection, and generally catalyze reactions that result in cell death :ref{doi=10.1038/s41467-023-42793-3}. As such, long-B pAgo together with their associated proteins mediate abortive infection.
### Short pAgos
-Short pAgos are truncated: they only contain the MID and PIWI domains essential for guide-mediate target binding :ref{doi=10.1016/j.tcb.2022.10.005}. They are catalytically inactive and are co-encoded with an APAZ domain that is fused to one of various effector domains. In short pAgo systems characterized to date, the short pAgo and the APAZ domain-containing protein form a heterodimeric complex :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. Within this complex, the short pAgo uses a guide RNA to bind complementary target DNAs. This triggers catalytic activation of the effector domain fused to the APAZ domain, generally resulting in cell death :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. As such, short pAgo systems mediate abortive infection.
+Short pAgos are truncated: they only contain the MID and PIWI domains essential for guide-mediate target binding :ref{doi=10.1016/j.tcb.2022.10.005}. They are catalytically inactive and are co-encoded with an APAZ domain that is fused to one of the various effector domains. In short pAgo systems characterized to date, the short pAgo and the APAZ domain-containing protein form a heterodimeric complex :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. Within this complex, the short pAgo uses a guide RNA to bind complementary target DNAs. This triggers catalytic activation of the effector domain fused to the APAZ domain, generally resulting in cell death :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. As such, short pAgo systems mediate abortive infection.
-Based on their phylogeny, short pAgos are subdivided in S1A, S1B, S2A, and S2B clades :ref{doi=10.1128/mBio.01935-18,10.1016/j.tcb.2022.10.005}. In clade S1A and S1B (SPARSA) systems, APAZ is fused to an SIR2 domain. In clade S2A (SPARTA) systems, APAZ is fused to a TIR domain. Both SPARSA and SPARTA systems trigger cell death by depletion of NAD(P)+ :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. In S2B clade systems, APAZ is fused to one or more effector domains, including Mrr-like, DUF4365, RecG/DHS-like and other domains. In all clade S1A SPARSA systems, but also for certain other systems within other clades, the effector-APAZ is fused to the short pAgo.
+Based on their phylogeny, short pAgos are subdivided in S1A, S1B, S2A, and S2B clades :ref{doi=10.1128/mBio.01935-18,10.1016/j.tcb.2022.10.005}. In clade S1A and S1B (SPARSA) systems, APAZ is fused to a SIR2 domain. In clade S2A (SPARTA) systems, APAZ is fused to a TIR domain. Both SPARSA and SPARTA systems trigger cell death by depletion of NAD(P)+ :ref{doi=10.1016/j.cell.2022.03.012,10.1038/s41564-022-01239-0}. In S2B clade systems, APAZ is fused to one or more effector domains, including Mrr-like, DUF4365, RecG/DHS-like and other domains. In all clade S1A SPARSA systems, but also for certain other systems within other clades, the effector-APAZ is fused to the short pAgo.
### Pseudo-short pAgos
-Akin to short pAgos, pseudo-short pAgos are comprised of the MID and PIWI domains only :ref{doi=10.1016/j.tcb.2022.10.005}. However, they do not phylogenetically cluster with canonical short pAgos and do not colocalize with effector-APAZ proteins. Instead, certain pseudo-short are found across the long-A and long-B pAgo clades (e.g. Archaeoglobus fulgidus pAgo, a truncated long-B pAgo :ref{doi=10.1038/s41598-023-32600-w,10.1038/s41598-021-83889-4}), while others form a distinct branch in the phylogenetic pAgo tree (see SiAgo-like pAgos below).
+Akin to short pAgos, pseudo-short pAgos are comprised of the MID and PIWI domains only :ref{doi=10.1016/j.tcb.2022.10.005}. However, they do not phylogenetically cluster with canonical short pAgos and do not colocalize with effector-APAZ proteins. Instead, certain pseudo-short are found across the long-A and long-B pAgo clades (e.g. *Archaeoglobus fulgidus* pAgo, a truncated long-B pAgo :ref{doi=10.1038/s41598-023-32600-w,10.1038/s41598-021-83889-4}), while others form a distinct branch in the phylogenetic pAgo tree (see SiAgo-like pAgos below).
### SiAgo-like pAgos
-SiAgo-like pAgos are pseudo-short pAgos that form an separate branch in the phylogenetic tree of pAgos. They are named after the type system from Sulfolobus islandicus :ref{doi=10.1016/j.chom.2022.04.015}. SiAgo is comprised of MID and PIWI domains, and is co-encoded with Ago associated proteins Aga1 and Aga2. SiAgo and Aga1 form a cytoplasmic heterodimeric complex. While it is currently unknown what guide/target types activate the SiAgo/Aga1 complex, it is directed toward membrane-localized Aga2 upon viral infection. This triggers Aga2-mediated membrane depolarization and causes cell death :ref{doi=10.1016/j.chom.2022.04.015}.
+SiAgo-like pAgos are pseudo-short pAgos that form a separate branch in the phylogenetic tree of pAgos. They are named after the type system from *Sulfolobus islandicus* :ref{doi=10.1016/j.chom.2022.04.015}. SiAgo is comprised of MID and PIWI domains and is co-encoded with Ago-associated proteins Aga1 and Aga2. SiAgo and Aga1 form a cytoplasmic heterodimeric complex. While it is currently unknown what guide/target types activate the SiAgo/Aga1 complex, it is directed toward membrane-localized Aga2 upon viral infection. This triggers Aga2-mediated membrane depolarization and causes cell death :ref{doi=10.1016/j.chom.2022.04.015}.
## Example of genomic structure
A total of 6 subsystems have been described for the pAgo system.
-
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
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diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index d8c6b3960d6f11b3e5c20b94a8f7256be9345688..dd807547ab74e9e298b26637ced87a42e9fb6a02 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -17,11 +17,11 @@ relevantAbstracts:
## Description
-The Panchino gp28 defense system was described in :ref{doi=10.1038/nmicrobiol.2016.251} and is named after the Panchino prophage (on which it is located) and the corresponding gene. It is a single gene system.
+The Panchino gp28 defense system was described in :ref{doi=10.1038/nmicrobiol.2016.251} and is named after the Panchino prophage (on which it is located) and the corresponding gene. It is a single-gene system.
## Molecular mechanisms
-Panchino gp28 is act as a single gene type I restriction system :ref{doi=10.1038/nmicrobiol.2016.251,10.1016/j.mib.2023.102321}.
+Panchino gp28 acts as a single gene type I restriction system :ref{doi=10.1038/nmicrobiol.2016.251,10.1016/j.mib.2023.102321}.
## Example of genomic structure
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index c76b61dfbb73aa631d4df0375412fbe50b82b815..978b86f0ee45402b49c5bbc3a74f45b2abbd22d2 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -17,11 +17,11 @@ relevantAbstracts:
---
# PD-Lambda-5
-##Description
+## Description
PD-lambda-5 is a two-gene system identified in a P2-like prophage. It encodes a protein with a nuclease and a HEPN domain, and a predicted methyltransferase. It confers broad anti-phage defense and does not seem to mediate abortive infection.
##Molecular mechanism
-PD-lambda-5 molecular mechanism has not been described to date. It confers protection against a broad range of phages, and does not seem to be an abortive infection system.
+PD-lambda-5 molecular mechanism has not been described to date. It confers protection against a broad range of phages and does not seem to be an abortive infection system.
## Example of genomic structure
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 98dce35ff8270fe2061c1a632f8d57f16b6e315f..4156c477aab7ba0219d87d8957a04eb527a51596 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# PD-T4-10
## Description
-The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. This ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting to a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
+The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A. These ORFs are overlapping and PD-T4-10_B is toxic while PD-T4-10_A neutralizes its toxicity, hinting at a toxin-antitoxin (TA) mechanism. It confers resitance to T2, T4, T6 and SECphi27 through an Abi defense mechanism :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index debef120710c9486600bd8432321784be27baafc..49ce922eb8b82c751f35b612031dad87cafe0fe2 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -19,7 +19,7 @@ relevant abstracts:
## Description
-PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse E.coli, and cloned back in a derivative of K12. Fragments containing the PD-T4-3 gene were shown to provide resistance to phage T4. The protein is characterized by a GIY-YIG nuclease domain, and mutations inactivating this domain abolished the resistance phenotype. It was originally found on a µ-like prophage
+PD-T4-3 is a single gene system isolated during an experimental screen of fosmids derived from 71 strains of diverse *E.coli*, and cloned back in a derivative of K12. Fragments containing the PD-T4-3 gene were shown to provide resistance to phage T4. The protein is characterized by a GIY-YIG nuclease domain, and mutations inactivating this domain abolished the resistance phenotype. It was originally found on a µ-like prophage
## Molecular mechanism
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 16599207f0091122f835466f0c07785e80cad9ad..e11dfb58da0fe501cb6597873bb9a5c5255ebe0a 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# PD-T4-6
## Description
-The PD-T4-6 system is composed of a single protein. It was discovered via a selection screening of 71 *E. coli* strains challenged with diverse phage. The name stands from Phage Defense (PD) and the phage with which the strain was challenge (T4) :ref{doi=10.1038/s41564-022-01219-4}. The system has been identified as an Abortive Infection (Abi) system :ref{doi=10.1038/s41564-022-01219-4,10.1016/j.mib.2023.102312}. The protein was found within a P2-like prophage and contains a predicted Der/Thr kinase domain. Site-specific mutation in the domain reduces phage protection :ref{doi=10.1038/s41564-022-01219-4}.
+The PD-T4-6 system is composed of a single protein. It was discovered via a selection screening of 71 *E. coli* strains challenged with diverse phage. The name stands from Phage Defense (PD) and the phage with which the strain was challenged (T4) :ref{doi=10.1038/s41564-022-01219-4}. The system has been identified as an Abortive Infection (Abi) system :ref{doi=10.1038/s41564-022-01219-4,10.1016/j.mib.2023.102312}. The protein was found within a P2-like prophage and contains a predicted Der/Thr kinase domain. Site-specific mutation in the domain reduces phage protection :ref{doi=10.1038/s41564-022-01219-4}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index 8f82d3c2b2491c51bbfa88b8df0175952f8d4da6..959807384c6b4e98534cda54b8b336f44e977576 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -24,7 +24,7 @@ protect against T2,T4,T6
## Molecular mechanism
-Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism
+Vassalo et al. :ref{doi=10.1038/s41564-022-01219-4} state that PD-T4-7 functions through an abortive infection mechanism.
## Example of genomic structure
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index 9180716197242b6c01cef156b0d2e336a5626d5e..1676453ec2c2aa4ceff560a753ec8e8a73c45707 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -19,7 +19,7 @@ relevantAbstracts:
# PD-T4-8
## Description
-PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defence system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
+PD-T4-8 is composed of a single protein that contains a DUF4263 domain found in the [Shedu](/defense-systems/shedu) defense system :ref{doi=10.1038/s41564-022-01219-4}. PD-T4-8 from *Escherichia coli* RCP52534.1 confers resistance against T2, T4, T6, SECphi18 and SECphi27.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index 865b7ed64684c4c1b8cf2f65590771b838b39e8b..fc58c6972f91d0f14eefc8b76e1800780dc0924b 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -18,7 +18,7 @@ relevantAbstracts:
# PD-T7-1
## Description
-PD-T7-1 is a single gene defense systems which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
+PD-T7-1 is a single gene defense system that was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
@@ -34,12 +34,8 @@ Here is an example found in the RefSeq database:
The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is composed of 1 protein: PD-T7-1 (WP_004150873.1)
## Distribution of the system among prokaryotes
-<<<<<<< content/3.defense-systems/pd-t7-1.md
-The PD-T7-1 system is present in a total of 136 different species.
-=======
Among the 22,803 complete genomes of RefSeq, the PD-T7-1 is detected in 748 genomes (3.28 %).
->>>>>>> content/3.defense-systems/pd-t7-1.md
The system was detected in 146 different species.
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index 040189252632e7468ff78ffe1e090d66b9829b2e..f021b1133b134379ea366c18ee7139d526f2efb0 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -21,17 +21,17 @@ relevant abstracts:
## Description
-The PrrC system protects bacteria against phages via an abortive infection. It is composed of a single effector protein, but relies on the presence of a full type Ic restriction-modification system in the vicinity. PrrC proteins are therefore typically found embedded in a larger RM system.
+The PrrC system protects bacteria against phages via an abortive infection. It is composed of a single effector protein but relies on the presence of a full type Ic restriction-modification system in the vicinity. PrrC proteins are therefore typically found embedded in a larger RM system.
## Molecular mechanism
The effector protein prrC complements a RM system by cutting tRNALys in the anticodon loop, upstream of the wobble nucleotide and causes the arrest of phage protein synthesis and phage growth.
-prrC serves as a guardian of the acrivity of EcoprrI, which can be inactivated by the Stp peptide of phage T4 at the beginning of infection. Inactivation of EcoprrI by Stp induces a conformation change that in turn activates PrrC, releasing its nuclease activity and stalling host and phage growth :ref{doi=10.1006/jmbi.1995.0343}.
-Because it sabotages the host's translation machinery, prrC is considered to be an abortive infection system.
+PrrC serves as a guardian of the activity of EcoprrI, which can be inactivated by the Stp peptide of phage T4 at the beginning of infection. Inactivation of EcoprrI by Stp induces a conformation change that in turn activates PrrC, releasing its nuclease activity and stalling host and phage growth :ref{doi=10.1006/jmbi.1995.0343}.
+Because it sabotages the host's translation machinery, PrrC is considered to be an abortive infection system.
## Example of genomic structure
-The PrrC is composed of the PrrC protein and a type I restriction modification system.
+The PrrC is composed of the PrrC protein and a type I restriction-modification system.
Here is an example found in the RefSeq database:
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index d6752dd09de33c1382fdb025619971e7422749a4..a2e9e5f7107ea18380b9df7856d4c1c4c09c261f 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -22,7 +22,7 @@ relevantAbstracts:
## Description
-Originally found in a high throughput shotgun cloning of bacterial fragments in E. coli looking for Toxin-Antitoxin pairs. PsyrTA is composed of two proteins, PsyrT, the toxin, is a RecQ family DNA helicase, and PsyrA, the antitoxin, was shown to be a Nucleotide-binding protein. Note that that system is sometimes called RqlHI :ref{doi=10.1371/journal.ppat.1005317}, where RqlH refers to PsyrT and RqlI to PsyrA
+Originally found in a high throughput shotgun cloning of bacterial fragments in E. coli looking for Toxin-Antitoxin pairs. PsyrTA is composed of two proteins, PsyrT, the toxin, is a RecQ family DNA helicase, and PsyrA, the antitoxin, was shown to be a Nucleotide-binding protein. Note that that system is sometimes called RqlHI :ref{doi=10.1371/journal.ppat.1005317}, where RqlH refers to PsyrT and RqlI to PsyrA.
## Molecular mechanisms
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index 77c07d531f1d905a2b23506aed2d8a23c9d5d77e..4224cb4a6551c026436b12e111bf2bd1273286e9 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -17,7 +17,7 @@ relevantAbstracts:
# Pycsar
## Example of genomic structure
-The Pycsar is composed of at least 2 proteins: a Cyclase and Effector.
+The Pycsar is composed of at least 2 proteins: a Cyclase and an Effector.
Like the CBASS system, it can encode for a variety of different effectors.
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index fe2b0087ef3f2daafc62d428048f48fcf184273d..5c5e11c2db31cabb253d2cc8eb6ae16cc39592e2 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -21,11 +21,11 @@ relevantAbstracts:
# RADAR
## Description
-RADAR (Restriction by an Adenosine Deaminase Acting on RNA) is comprised of two genes, encoding respectively for an adenosine triphosphatase (RdrA) and  a divergent adenosine deaminase (RdrB), which are in some cases associated with a small membrane protein (RdrC or D). They were first uncovered in a study exploring content of defense islands :ref{doi=10.1126/science.aba0372}.Â
+RADAR (Restriction by an Adenosine Deaminase Acting on RNA) is comprised of two genes, encoding respectively for an adenosine triphosphatase (RdrA) and a divergent adenosine deaminase (RdrB), which are in some cases associated with a small membrane protein (RdrC or D). They were first uncovered in a study exploring the content of defense islands :ref{doi=10.1126/science.aba0372}.Â
## Molecular mechanism
In the initial study describing RADAR, RADAR was found to perform RNA editing of adenosine to inosine during phage infection :ref{doi=10.1126/science.aba0372}. Editing sites were broadly distributed on the host transcriptome, which could prove deleterious leading to observed growth arrest of RADAR upon phage infection. Â
-Further structural studies revealed potential different mechanism of actions :ref{doi=10.1016/j.cell.2023.01.026,10.1016/j.cell.2023.01.012}. RdrA and RdrB assemble to form a giant 10 MDa complex. The RADAR defense system limits phage replication by catalyzing ATP deamination. Within this system, RdrB functions as an adenosine deaminase, leading to the buildup of ITP (Inosine Tri-Phosphate) and dITP. RdrA induces RdrB activity and potentially regulates the detection of phage infections.
+Further structural studies revealed potentially different mechanisms of actions :ref{doi=10.1016/j.cell.2023.01.026,10.1016/j.cell.2023.01.012}. RdrA and RdrB assemble to form a giant 10 MDa complex. The RADAR defense system limits phage replication by catalyzing ATP deamination. Within this system, RdrB functions as an adenosine deaminase, leading to the buildup of ITP (Inosine Tri-Phosphate) and dITP. RdrA induces RdrB activity and potentially regulates the detection of phage infections.
## Example of genomic structure
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index c70ac99b9a78de7481b501f16e46f99c2f203eb3..4eec0086d3a9c4c42c5997bedecae361bfddfcc6 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -38,20 +38,20 @@ Retrons are distinct genetic elements found in bacterial genomes that code for a
### Discovery
Discovery
-Retrons were originally discovered in 1984 in Myxococcus xanthus, when Yee et al. :ref{doi=10.1016/0092-8674(84)90541-5} identified a high copy, short, single-stranded linear ex-chromosomal DNA fragment in the gram-negative bacterium, Myxococcus xanthus. These multi-copy single-stranded DNA fragments were termed msDNA. Further studies showed that this single-stranded DNA (ssDNA) is covalently linked to an RNA molecule :ref{doi=10.1016/0092-8674(87)90596-4}. Although at the time reverse transcriptases were only known from Eukaryotes and viruses, Inouye and colleagues hypothesized that msDNA must be a product of a reverse transcription reaction :ref{doi=10.1016/j.gene.2016.10.031}. Five years later an RT was shown to be associated with the biosynthesis of msDNA :ref{doi=10.1016/0092-8674(89)90593-X,10.1016/0092-8674(89)90592-8}, this was the first discovery of an RT in bacteria.
+Retrons were originally discovered in 1984 in *Myxococcus xanthus*, when Yee et al. :ref{doi=10.1016/0092-8674(84)90541-5} identified a high copy, short, single-stranded linear ex-chromosomal DNA fragment in the gram-negative bacterium, Myxococcus xanthus. These multi-copy single-stranded DNA fragments were termed msDNA. Further studies showed that this single-stranded DNA (ssDNA) is covalently linked to an RNA molecule :ref{doi=10.1016/0092-8674(87)90596-4}. Although at the time reverse transcriptases were only known from Eukaryotes and viruses, Inouye and colleagues hypothesized that msDNA must be a product of a reverse transcription reaction :ref{doi=10.1016/j.gene.2016.10.031}. Five years later an RT was shown to be associated with the biosynthesis of msDNA :ref{doi=10.1016/0092-8674(89)90593-X,10.1016/0092-8674(89)90592-8}, this was the first discovery of an RT in bacteria.
-Although retrons were biochemically well studied and characterized, it was only 36 years after msDNA discovery, when their biological function was discovered :ref{doi=10.1126/science.abf6127}. In a systematic screen for the discovery of novel anti-phage defense systems in bacterial genomes :ref{doi=10.1016/j.chom.2022.09.017}, Millman et al. discovered a new defense system that contained a retron element (Retron-Eco8), further analysis showed that retrons are enriched in bacterial defense islands and together with their accessory proteins many were shown to confer defense against phage infection :ref{doi=10.1016/j.cell.2020.09.065}. An independent screen for defense systems, later that same year, also reported similar conclusions showing retrons function in antiphage defense :ref{doi=10.1126/science.aba0372}.
+Although retrons were biochemically well studied and characterized, it was only 36 years after msDNA discovery, that their biological function was discovered :ref{doi=10.1126/science.abf6127}. In a systematic screen for the discovery of novel anti-phage defense systems in bacterial genomes :ref{doi=10.1016/j.chom.2022.09.017}, Millman et al. discovered a new defense system that contained a retron element (Retron-Eco8), further analysis showed that retrons are enriched in bacterial defense islands and together with their accessory proteins many were shown to confer defense against phage infection :ref{doi=10.1016/j.cell.2020.09.065}. An independent screen for defense systems, later that same year, also reported similar conclusions showing retrons function in antiphage defense :ref{doi=10.1126/science.aba0372}.
-Due to their ability to produce high copy of DNA within the cell, since their discovery retrons have served as a fertile ground for biotechnological applications :ref{doi=10.1073/pnas.2018181118,10.1038/s41589-021-00927-y,10.1038/s41596-023-00819-6}
+Due to their ability to produce a high copy of DNA within the cell, since their discovery retrons have served as a fertile ground for biotechnological applications :ref{doi=10.1073/pnas.2018181118,10.1038/s41589-021-00927-y,10.1038/s41596-023-00819-6}
## Molecular mechanisms
### General
-When the retron ncRNA (msr-msd) is transcribed it folds into a typical structure that is recognized by the RT :ref{doi=10.1016/S0021-9258(18)83336-1}. The RT then reverse transcribes a portion of the ncRNA (msd), starting from the 2′-end of a conserved guanosine residue found immediately after a double-stranded RNA structure within the ncRNA :ref{doi=10.1016/0092-8674(89)90592-8}. During reverse transcription, cellular RNase H degrades the segment of the ncRNA that serves as template, but not other parts of the ncRNA (msr), yielding the mature RNA-DNA hybrid (msDNA) :ref{doi=10.1016/0092-8674(89)90592-8}. In some cases cellular nucleases have been shown to further process the msDNA :ref{doi=10.1111/j.1365-2958.1992.tb01788.x,10.1006/plas.1997.1298,10.1007/s12275-015-5304-0}.
+When the retron ncRNA (msr-msd) is transcribed it folds into a typical structure that is recognized by the RT :ref{doi=10.1016/S0021-9258(18)83336-1}. The RT then reverse transcribes a portion of the ncRNA (msd), starting from the 2′-end of a conserved guanosine residue found immediately after a double-stranded RNA structure within the ncRNA :ref{doi=10.1016/0092-8674(89)90592-8}. During reverse transcription, cellular RNase H degrades the segment of the ncRNA that serves as a template, but not other parts of the ncRNA (msr), yielding the mature RNA-DNA hybrid (msDNA) :ref{doi=10.1016/0092-8674(89)90592-8}. In some cases cellular nucleases have been shown to further process the msDNA :ref{doi=10.1111/j.1365-2958.1992.tb01788.x,10.1006/plas.1997.1298,10.1007/s12275-015-5304-0}.
### Retron-Eco6 (Ec48)
-The Retron-Eco6 system encodes in addition to the retron an effector protein containing 2 transmembrane domains (2TM). Retron-Eco6 was shown to protect bacteria against phage through abortive infection (Abi) by guarding the integrity of the RecBCD complex in the cell. Many phages inhibit RecBCD in order to successfully infect the cell. Upon inhibition of RecBCD, the effector protein turns the membrane permeable and the cells lyse within 45 minutes post infection :ref{doi=10.1016/j.cell.2020.09.065}.
+The Retron-Eco6 system encodes in addition to the retron an effector protein containing 2 transmembrane domains (2TM). Retron-Eco6 was shown to protect bacteria against phage through abortive infection (Abi) by guarding the integrity of the RecBCD complex in the cell. Many phages inhibit RecBCD to successfully infect the cell. Upon inhibition of RecBCD, the effector protein turns the membrane permeable and the cells lyse within 45 minutes post infection :ref{doi=10.1016/j.cell.2020.09.065}.
### Retron-Sen2 (St85), Retron-Eco9
The Retron-Sen2 system was shown to function as a three-partite toxin-antitoxin (TA) system. The accessory gene RcaT acts as a bona fide toxin and ectopically inhibits growth. The Retron-RT-msDNA complex acts as an antitoxin alleviating RcaT toxicity.
@@ -62,7 +62,7 @@ Several triggers were identified for the Sen2-TA system, including Dam that was
A total of 16 subsystems have been described for the Retron system.
-Here is some examples found in the RefSeq database:
+Here are some examples found in the RefSeq database:
{max-width=750px}
diff --git a/content/3.defense-systems/rm.md b/content/3.defense-systems/rm.md
index 2b888439e9b89a4279a3a8a17fa043dcd8990169..86a783839caf73cf90cf283c7738f40c549d5cb7 100644
--- a/content/3.defense-systems/rm.md
+++ b/content/3.defense-systems/rm.md
@@ -24,7 +24,7 @@ relevantAbstracts:
Restriction modification systems are the most abundant antiphage systems. They already have their own [Wikipedia page](https://en.wikipedia.org/wiki/Restriction_modification_system)
## Molecular Mechanisms
-Several reviews detail the molecular mechanisms of restriction modification systems. For example in :ref{doi=10.1016/j.mib.2005.06.003}:
+Several reviews detail the molecular mechanisms of restriction-modification systems. For example in :ref{doi=10.1016/j.mib.2005.06.003}:
"Bacterial restriction-modification (R-M) systems function as prokaryotic immune systems that attack foreign DNA entering the cell :ref{doi=10.1128/jb.65.2.113-121.1953}. Typically, R-M systems have enzymes responsible for two opposing activities: a restriction endonuclease (REase) that recognizes a specific DNA sequence for cleavage and a cognate methyltransferase (MTase) that confers protection from cleavage by methylation of adenine or cytosine bases within the same recognition sequence. REases recognize ‘non-self’ DNA (Figure 1), such as that of phage and plasmids, by its lack of characteristic modification within specific recognition sites :ref{doi=10.1093/nar/29.18.3705}. Foreign DNA is then inactivated by endonucleolytic cleavage. Generally, methylation of a specific cytosine or adenine within the recognition sequence confers protection from restriction. Host DNA is normally methylated by the MTase following replication, whereas invading non-self DNA is not."
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 2dd952ecdbd57f5bc1147752dd60b55c5663af45..d1f935bd8f8721e5dfd0177f68d87a6ee183175a 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -24,7 +24,7 @@ RnlAB is a type II toxin-antitoxin system, in which RnlA is the toxin and RnlB t
## Molecular mechanisms
-The RnlA toxin has a RNase activity. RnlB (formerly yfjO) is the antitoxin and suppresses the RNase LS activity :ref{doi=10.1534/genetics.110.121798}.
+The RnlA toxin has an RNase activity. RnlB (formerly yfjO) is the antitoxin and suppresses the RNase LS activity :ref{doi=10.1534/genetics.110.121798}.
## Example of genomic structure
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index b8aef238a85befddd493be551a50c932111aab59..7158b02ef7aeadcfcdc5dc01fa832a740aa4c8bf 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -12,6 +12,7 @@ tableColumns:
PFAM: PF01381, PF06114, PF12844, PF13443, PF13560
contributors:
- Lucas Paoli
+ - Gemma Atkinson
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
---
@@ -20,7 +21,7 @@ relevantAbstracts:
## Description
-The RosmerTA system was found to have antiviral activity and named after Gallo-Roman goddess of fertility by Millman et al. 2022 :ref{doi=10.1016/j.chom.2022.09.017}.
+The RosmerTA system was found to have antiviral activity and was named after the Gallo-Roman goddess of fertility by Millman et al. 2022 :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanisms
diff --git a/content/3.defense-systems/rst_2tm_1tm_tir.md b/content/3.defense-systems/rst_2tm_1tm_tir.md
index 0d680fdb6cd56c27e8309843d0690d262cdabe16..7346d9f485ab545dee74b6a08f234133858299a3 100644
--- a/content/3.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/3.defense-systems/rst_2tm_1tm_tir.md
@@ -15,14 +15,13 @@ contributors:
relevantAbstracts:
- doi: 10.1016/j.chom.2022.02.018
-
---
# Rst_2TM_1TM_TIR
## Description
-The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, that contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, that contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}. Rousset et al. suggested that the TIR containing protein could generate a nucleotide messenger that in turn could activate the associated transmembrane proteins.
+The Rst_2TM_1TM_TIR system is carried by the P2-like phage AC1 and protects *Escherichia coli* C against lambda, LF82_P8 and P2 phages. This system is composed of three proteins, Rst_TIR_tm, which contains a TIR (Toll/interleukin-1 receptor) domain, Rst_1TM_TIR, which contains a transmembrane helix (TM) and Rst_2TM_TIR, that contains two TMs :ref{doi=10.1016/j.chom.2022.02.018}. Rousset et al. suggested that the TIR-containing protein could generate a nucleotide messenger that in turn could activate the associated transmembrane proteins.
## Molecular mechanisms
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index c3273fb0fd1c3be31734279029d4d16af092b8e7..6ccaa522a092efce626700794c2c523a0c76c7d2 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -20,7 +20,7 @@ relevant abstracts:
## Description
-Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide E.coli with a strong resistance against phage T7.
+Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide *E.coli* with a strong resistance against phage T7.
## Molecular mechanism
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index 448f56264a1d3e8e4426b8d37e7c1a651bb7dc5e..abf7b36f5fbedbf2e6dbbf20c43cb837346d1d7f 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -22,11 +22,11 @@ relevantAbstracts:
## Description
-The Rst_HelicaseDUF2290 system was discovered during a screen for defense systems targeted at hotspots of antiphage activity in phages and phage-satellites. It is composed of 2 proteins, an helicase and a protein with the domain DUF2290.
+The Rst_HelicaseDUF2290 system was discovered during a screen for defense systems targeted at hotspots of antiphage activity in phages and phage-satellites. It is composed of 2 proteins, a helicase and a protein with the domain DUF2290.
## Molecular mechanism
-The molecular mechanism of the Rst_HelicaseDUF2290 is unkown.
+As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index e0506ada301529ec22e756312cf8ac07d226f5d9..a552fe94237d06c5937a062f0838e711932ffd30 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -22,9 +22,9 @@ relevantAbstracts:
## Description
RT-nitrilase-Tm (also named UG5-large) is a two-gene defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.018} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae).
-The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase) ; the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.
+The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase); the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.
-The presence of an RT protein allows to draw a parallel between this system and the [DRT defense system](/defense-systems/drt).
+The presence of an RT protein allows to draw a parallel between this system and [DRT](/defense-systems/drt), [AbiA](/defense-systems/abia), [AbiK](/defense-systems/abik) and [AbiP2](/defense-systems/abip2).
## Molecular mechanism
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index 7f2a5457cff0bc89ebd197ac7c4c0d2f061267a1..207067b453e755b5456e7ce55f7ef20a7c79f37d 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -20,7 +20,7 @@ relevantAbstracts:
## Description
-The Rst_TIR-NLR system is named after the first author of the paper describing it (Rousset et al. 2022) and the domains of the only protein it contains (TIR, toll-interleukin-1 receptor, and NLR, nucleotide-binding leucine rich repeat receptor) :ref{doi=10.1016/j.chom.2022.02.018}.
+The Rst_TIR-NLR system is named after the first author of the paper describing it (Rousset et al. 2022) and the domains of the only protein it contains (TIR, toll-interleukin-1 receptor, and NLR, nucleotide-binding leucine-rich repeat receptor) :ref{doi=10.1016/j.chom.2022.02.018}.
This system is very similar to other bacterial defense systems: bNACHT (https://defense-finder.pasteur.cloud/wiki/defense-systems/nlr), CARD_NLR (https://defense-finder.pasteur.cloud/wiki/defense-systems/card_nlr), Avs (AVAST) (https://defense-finder.pasteur.cloud/wiki/defense-systems/avs).
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index db49c97c83a2d027e6b635db4b41e6790f76427c..187e94ca5e308d20dcb9439e59f09cecf8564e5a 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -21,7 +21,7 @@ relevantAbstracts:
## Description
-The SanaTA system is composed of 2 proteins: SanaT and, SanaA, where SanaT encodes a toxin and SanaA encodes an antitoxin to form a toxin-antitoxin (TA) system. The toxin protein, SanaT, contains a Nucleotidyl transferase domain (PF08843). This system provides resistance against mutated T7 phages that lack the nonessential 4.5 gene in *Shewanella sp.* ANA-3. Sberro et al. showed that the defensiveness of sanaTA depends on the cleavage of SanaA by the Lon system, a protease that degrades the antitoxin to allow the activity of the toxin :ref{doi=10.1016/j.molcel.2013.02.002}.
+The SanaTA system is composed of 2 proteins: SanaT and, SanaA, where SanaT encodes a toxin and SanaA encodes an antitoxin to form a toxin-antitoxin (TA) system. The toxin protein, SanaT, contains a nucleotidyltransferase domain (PF08843). This system provides resistance against mutated T7 phages that lack the nonessential 4.5 gene in *Shewanella sp.* ANA-3. Sberro et al. showed that the defensiveness of sanaTA depends on the cleavage of SanaA by the Lon system, a protease that degrades the antitoxin to allow the activity of the toxin :ref{doi=10.1016/j.molcel.2013.02.002}.
## Molecular mechanism
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index d83d29ee6dd6368364f6c0b02df137546107b920..5d38f899f22044809401e52083532bbf50968956 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -21,15 +21,15 @@ relevantAbstracts:
# SEFIR
## Description
-The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage Phi29 :ref{doi=10.1016/j.chom.2022.09.017}.
+The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes and were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage Phi29 :ref{doi=10.1016/j.chom.2022.09.017}.
-Bacterial SEFIR domains were named after their eukaryotic homologs which were already known to be part of several eukayrotic immune proteins (e.g. SEFs and Interleukin-17 Receptors):ref{doi=10.1016/S0968-0004(03)00067-7}.
+Bacterial SEFIR domains were named after their eukaryotic homologs which were already known to be part of several eukaryotic immune proteins (e.g. SEFs and Interleukin-17 Receptors):ref{doi=10.1016/S0968-0004(03)00067-7}.
-Homologs of SEFIR domain proteins were also found in archaeal species : _Methanosarcina barkeri_ and _Methanosarcina mazei_ :ref{doi=10.1016/j.chom.2022.09.017}.
+Homologs of SEFIR domain proteins were also found in archaeal species: _Methanosarcina barkeri_ and _Methanosarcina mazei_ :ref{doi=10.1016/j.chom.2022.09.017}.
## Molecular mechanism
-SEFIR was shown to protect against phage infection through an abortive infection mechanism *via* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain which shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR super family) :ref{doi=10.1016/j.chom.2022.09.017}.
+SEFIR was shown to protect against phage infection through an abortive infection mechanism *via* NAD+ depletion. This is similar to what can be observed in other defense systems containing a TIR domain that shares homology with the SEFIR domain (in eukaryotes, both domains are part of the STIR superfamily) :ref{doi=10.1016/j.chom.2022.09.017}.
## Example of genomic structure
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index 7da5e0811bb0f3feb45147722e6339ed2be43ecc..539915c4e3618f4a9a831da589d5b4e1d66afe78 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -25,7 +25,7 @@ The Septu defense system was discovered in 2018 in *Bacillus* :ref{doi=10.1126/s
The Septu defense system is composed of two proteins PtuA and PtuB: PtuA encoding for an ATPase (AAA15/AAA21) and PtuB with an HNH endonuclease domain.
-After the discovery of Septu, two studies discovered separately another form of Septu :ref{doi=10.1093/nar/gkab883,10.1016/j.cell.2020.09.065}. This new subtype encodes a third protein with a reverse transcriptase domain. This system is either referred as Septu Type II :ref{doi=10.1093/nar/gkab883} or as [Retron](/defense-systems/retron) subtype RT-I-A :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2020.09.065}.
+After the discovery of Septu, two studies discovered separately another form of Septu :ref{doi=10.1093/nar/gkab883,10.1016/j.cell.2020.09.065}. This new subtype encodes a third protein with a reverse transcriptase domain. This system is either referred to as Septu Type II :ref{doi=10.1093/nar/gkab883} or as [Retron](/defense-systems/retron) subtype RT-I-A :ref{doi=10.1016/j.cell.2020.09.065,10.1016/j.cell.2020.09.065}.
The Septu defense system is part of a large category of systems that encodes the AAA15/21 ABC ATPase :ref{doi=10.1111/mmi.15074}.
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index a878f553b457e9781f50df1b5cabe3b8130bca32..8b4cf8c3d87a7bc7d46eeedc29f66b70c9f04af6 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -19,13 +19,13 @@ relevantAbstracts:
# Shango
## Description
-Shango is a three genes defense system which was discovered in parallel in two works in both *E.coli* and *P.aeruginosa* and was shown to have antiphage activity against the Lambda-phage in *E.coli* :ref{doi=10.1016/j.chom.2022.09.017} and against diverse podo- and siphoviridae in *P.aeruginosa* :ref{doi=10.1093/nar/gkad317}.
+Shango is a three genes defense system that was discovered in parallel in two works in both *E.coli* and *P.aeruginosa* and was shown to have antiphage activity against the Lambda-phage in *E.coli* :ref{doi=10.1016/j.chom.2022.09.017} and against diverse podo- and siphoviridae in *P.aeruginosa* :ref{doi=10.1093/nar/gkad317}.
-Shango is composed of (i) a TerB-like domain, (ii) an Helicase and (iii) an ATPase. The TerB domain was previously shown to be associated to the perisplasmic membrane of bacteria :ref{doi=10.4149/gpb_2011_03_286}.
+Shango is composed of (i) a TerB-like domain, (ii) a Helicase and (iii) an ATPase. The TerB domain was previously shown to be associated with the periplasmic membrane of bacteria :ref{doi=10.4149/gpb_2011_03_286}.
## Molecular mechanism
-The exact mechanism of action of the Shango defense has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated to the periplasmic membrane could indicate that Shango might be involved in membrane surveillance :ref{doi=10.1016/j.chom.2022.09.017}.
+The exact mechanism of action of the Shango defense has not yet been characterized, but it was shown that the TerB domain and the catalytic activity of the ATPase and the Helicase are required to provide antiviral defense. The fact that TerB domains are known to be associated with the periplasmic membrane could indicate that Shango might be involved in membrane surveillance :ref{doi=10.1016/j.chom.2022.09.017}.
## Example of genomic structure
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index fdc8c3d908c5a619bf0926403fb8df287b09df0b..70e98e5c13c0ea04a5a524f552c2d86508fc4865 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -25,7 +25,7 @@ The Shedu antiphage system consists of a single protein, SduA, which acts as a n
## Molecular Mechanism
-The Shedu protein is proposed to act as a nuclease, and its N-terminal domain inhibit its activation until triggered by phage infection.
+The Shedu protein is proposed to act as a nuclease, and its N-terminal domain inhibits its activation until triggered by phage infection.
The activation of the protein was described in :ref{doi=10.1101/2023.08.10.552793}.
In B. cereus Shedu, *"a key catalytic residue in Shedu’s nuclease domain is sequestered away from the catalytic site. Activation involves a conformational change that completes the active site and promotes assembly of a homo-octamer for coordinated double-strand DNA cleavage. Removal of Shedu’s N-terminal domain ectopically activates the enzyme, suggesting that this domain allosterically inhibits Shedu in the absence of infection."*
The nuclease activity and specific sensing of an E. coli Shedu was described in :ref{doi=10.1101/2023.08.10.552762}
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 6d1e9a31a011d9e552f9520d5cbca81ebbb02e13..bfdceb771407db73daaa78ccd9b2f5900f44c20a 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02481
+contributors:
+ - Florian Tesson
relevantAbstracts:
- doi: 10.1016/j.chom.2022.09.017
- doi: 10.1016/j.chom.2022.02.018
@@ -20,12 +22,12 @@ relevantAbstracts:
## Description
-ShosTA system was first described as a Toxin/Antitoxin system in 2012 :ref{doi=10.1101/gr.133850.111} without demonstration of antiphage activity. In 2022, a paper described the same system as "DprA + PRTase" inside P2 like prophages and prooves its antiphage activity. Finally, the antiphage activity was also prooved in another study with the original name ShosTA :ref{doi=10.1016/j.chom.2022.09.017}.
+ShosTA system was first described as a Toxin/Antitoxin system in 2012 :ref{doi=10.1101/gr.133850.111} without demonstration of antiphase activity. In 2022, a paper described the same system as "DprA + PRTase" inside P2-like prophages and proved its antiphage activity. Finally, the antiphage activity was also proved in another study with the original name ShosTA :ref{doi=10.1016/j.chom.2022.09.017}.
-This system is composed of two protein: ShosT and ShosA encoding for Hydrolase/PRTase and DprA (nucleotid binding) respectively.
+This system is composed of two proteins: ShosT and ShosA encoding for Hydrolase/PRTase and DprA (nucleotide binding) respectively.
## Molecular mechanism
-The ShosTA system is a toxin (ShosT) antitoxin (ShosA) system. The domains of ShosT (Hydrolase and PRTase) allows us to hypothesize a toxicity linked to host protein degradation.
+The ShosTA system is a toxin (ShosT) antitoxin (ShosA) system. The domains of ShosT (Hydrolase and PRTase) allow us to hypothesize toxicity linked to host protein degradation.
## Example of genomic structure
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index 73583cc29ac3b6078d13e5a3d785f93b03e69a21..c53f4c7d7e9a1dc6d210c0e042920341ea521270 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Direct
Effector: Other (protein modifying)
PFAM: PF00069, PF07714
+contributors:
+ - Héloïse Georjon
+ - Hugo Vaysset
+ - Florian Tesson
relevantAbstracts:
- doi: 10.1016/j.chom.2016.08.010
---
@@ -17,11 +21,11 @@ relevantAbstracts:
# Stk2
## Description
-Eukaryotic-like serine/threonine kinases have a variety of functions in prokaryotes. Recently, a single-gene system (Stk2) encoding for a Serine/threonine kinase from Staphylococcus epidermidis has been found to have anti-phage activity both in its native host and in a heterologous S.aureus host (Depardieu et al., 2016).
+Eukaryotic-like serine/threonine kinases have a variety of functions in prokaryotes. Recently, a single-gene system (Stk2) encoding for a Serine/threonine kinase from *Staphylococcus epidermidis* has been found to have anti-phage activity both in its native host and in a heterologous S.aureus host :ref{doi=10.1016/j.chom.2016.08.010}.
## Molecular mechanism
-Stk2 is an Abortive infection system, which triggers cell death upon phage infection, probably through phosphorylation of diverse essential cellular pathways (Depardieu et al., 2016). Stk2 was shown to detect a phage protein named Pack, which was proposed to be involved in phage genome packaging (Depardieu et al., 2016)
+Stk2 is an Abortive infection system, which triggers cell death upon phage infection, probably through phosphorylation of diverse essential cellular pathways :ref{doi=10.1016/j.chom.2016.08.010}. Stk2 was shown to detect a phage protein named Pack, which was proposed to be involved in phage genome packaging :ref{doi=10.1016/j.chom.2016.08.010}.
## Example of genomic structure
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index f5060a0c394da92cce98d048d6e656928c3e7f11..0998e44f8c2defb866d7a8c236f51c4f8a537e7a 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -23,9 +23,9 @@ relevantAbstracts:
# Thoeris
## Description
-Thoeris is a two-gene defense system identified in more than 2000 bacterial genomes. It consists of the genes ThsA and thsB. Its anti-phage function was experimentally validated in *Bacillus subtilis* :ref{doi=10.1126/science.aar4120}. In response to phage infection, it produces an isomer of cyclic ADP-ribose, which leads to depletion of NAD+ and results in abortive infection.
+Thoeris is a two-gene defense system identified in more than 2000 bacterial genomes. It consists of the genes ThsA and thsB. Its anti-phage function was experimentally validated in *Bacillus subtilis* :ref{doi=10.1126/science.aar4120}. In response to phage infection, it produces an isomer of cyclic ADP-ribose, which leads to the depletion of NAD+ and results in abortive infection.
-ThsA contains the sirtuin-like domain which binds to nicotinamide adenine dinucleotide (NAD) metabolites. The N112A point mutation neutralizes the Thoeris defense system and abolishes the NAD+ hydrolase activity of thsA :ref{doi=10.1126/science.aar4120}. It lacks a N-terminal transmembrane domain, and is predicted to be cytoplasmic.
+ThsA contains the sirtuin-like domain which binds to nicotinamide adenine dinucleotide (NAD) metabolites. The N112A point mutation neutralizes the Thoeris defense system and abolishes the NAD+ hydrolase activity of thsA :ref{doi=10.1126/science.aar4120}. It lacks a N-terminal transmembrane domain and is predicted to be cytoplasmic.
ThsB contains a TIR domain :ref{doi=10.1126/science.aar4120} is proposed to participate in the recognition of phage infection, as various thsB proteins sense different phage components.ThsB is found in more than 50% of Thoeris systems in multiple diverse copies :ref{doi=10.1126/science.aar4120}.
@@ -33,7 +33,7 @@ ThsB contains a TIR domain :ref{doi=10.1126/science.aar4120} is proposed to part
The Thoeris system functions by degrading NAD+ (a cofactor of central metabolism) to stop the growth of phage-infected cells and prevent the transmission of the phage to neighboring bacteria :ref{doi=10.1038/s41467-020-16703-w}.
-The protein ThsB, featuring the TIR domain, plays a cruial role in identifying phage invasion. Upon detecting the infection, the TIR domain becomes enzymatically active, initiating the synthesis of a cADPR isomer molecule :ref{doi=10.1038/s41586-021-04098-7}. This molecule acts as a signal, binding to the ThsA effector, likely through its C-terminal SLOG domain, thereby activating its NADase activity :ref{doi=10.1038/s41586-021-04098-7}. Consequently, the NADase effector reduces NAD+ cellular levels, creating an environment unsuitable for phage replication :ref{doi=10.1038/s41586-021-04098-7,10.1038/s41467-020-16703-w}.
+The protein ThsB, featuring the TIR domain, plays a crucial role in identifying phage invasion. Upon detecting the infection, the TIR domain becomes enzymatically active, initiating the synthesis of a cADPR isomer molecule :ref{doi=10.1038/s41586-021-04098-7}. This molecule acts as a signal, binding to the ThsA effector, likely through its C-terminal SLOG domain, thereby activating its NADase activity :ref{doi=10.1038/s41586-021-04098-7}. Consequently, the NADase effector reduces NAD+ cellular levels, creating an environment unsuitable for phage replication :ref{doi=10.1038/s41586-021-04098-7,10.1038/s41467-020-16703-w}.
## Example of genomic structure
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index 4dd0e869939515c9e4f2b8096fab14f9c46c2bbe..b122fec251b7b609b610cdd5f4c197755475eaf9 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -21,8 +21,8 @@ relevantAbstracts:
# Tiamat
## Description
-This defense system is composed of one gene refered to as TmtA.
-This systems is widespread across diverse prokaryotic phyla, and was experimentally validated in _Escherichia coli_ (confers protection against phages T6 and T5).
+This defense system is composed of one gene referred to as TmtA.
+This system is widespread across diverse prokaryotic phyla and was experimentally validated in _Escherichia coli_ (confers protection against phages T6 and T5).
## Molecular mechanism
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index d02242bd985bb45d68bc1447d533b36cbd628726..925ec0abaac9554037ad46550441dae412dcfef2 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -12,6 +12,7 @@ tableColumns:
PFAM: PF04055, PF13353
contributors:
- Marian Dominguez-Mirazo
+ - Heloïse Georjon
relevantAbstracts:
- doi: 10.1038/s41586-020-2762-2
---
@@ -19,18 +20,18 @@ relevantAbstracts:
# Viperin
## Description
-Viperins, for "Virus Inhibitory Protein, Endoplasmic Reticulum-associated, INterferon-inducible", are antiviral enzymes whose expression is stimulated by interferons in eukaryotic cells. They are important components of eukaryotic innate immunity, and present antiviral activity against a wide diversity of viruses, including double-stranded DNA viruses, single-strand RNA viruses and retroviruses :ref{doi=10.1146/annurev-virology-011720-095930}. Â
+Viperins, for "Virus Inhibitory Protein, Endoplasmic Reticulum-associated, INterferon-inducible", are antiviral enzymes whose expression is stimulated by interferons in eukaryotic cells. They are important components of eukaryotic innate immunity and present antiviral activity against a wide diversity of viruses, including double-stranded DNA viruses, single-strand RNA viruses and retroviruses :ref{doi=10.1146/annurev-virology-011720-095930}. Â
-Recently, Â Viperin-like enzymes were found in prokaryotes (pVips). Â Strikingly, like their eukaryotic counter-part with eukaryotic viruses, pVips provide clear protection against phage infection to their host, and therefore constitute a new defense system :ref{doi=10.1038/s41586-020-2762-2}. Like eukaryotic Viperins, pVips produce modified nucleotides that block phage transcription, acting as chain terminators. They constitute a form of chemical defense. A recent study reported that pVips can be found in around 0.5% of prokaryotic genomes :ref{doi=10.1038/s41467-022-30269-9}.
+Recently, Â Viperin-like enzymes were found in prokaryotes (pVips). Â Strikingly, like their eukaryotic counter-part with eukaryotic viruses, pVips provide clear protection against phage infection to their host and therefore constitute a new defense system :ref{doi=10.1038/s41586-020-2762-2}. Like eukaryotic Viperins, pVips produce modified nucleotides that block phage transcription, acting as chain terminators. They constitute a form of chemical defense. A recent study reported that pVips can be found in around 0.5% of prokaryotic genomes :ref{doi=10.1038/s41467-022-30269-9}.
## Molecular mechanism
{max-width=750px}
Fig.1: Catalytic activity of human Viperin generates ddhCTP :ref{doi=10.1002/1873-3468.13778}
-Viperins are members of the radical S-adenosylmethionine (rSAM) superfamily. This group of enzymes use a [4Fe-4S] cluster to cleave S-adenosylmethionine (SAM) reductively, generating a radical which is generally transferred to a substrate. It was demonstrated that through their [4Fe-4S] cluster catalytic activity, eukaryotic viperins convert a ribonucleotide, the cytidine triphosphate (CTP) into a modified ribonucleotide, the 3'-deoxy-3',4'-didehydro-CTP (ddhCTP) :ref{doi=10.1038/s41586-018-0238-4}.Â
+Viperins are members of the radical S-adenosylmethionine (rSAM) superfamily. This group of enzymes uses a 4Fe-4S] cluster to cleave S-adenosylmethionine (SAM) reductively, generating a radical that is generally transferred to a substrate. It was demonstrated that through their [4Fe-4S] cluster catalytic activity, eukaryotic viperins convert a ribonucleotide, the cytidine triphosphate (CTP) into a modified ribonucleotide, the 3'-deoxy-3',4'-didehydro-CTP (ddhCTP) :ref{doi=10.1038/s41586-018-0238-4}.Â
-Prokaryotic Viperins also convert ribonucleotides triphosphate into modified ribonucleotides, but contrary to their eukaryotic counterparts can use a diversity of substrates to produce  ddhCTP, or ddh-guanosine triphosphate (ddhGTP), or ddh-uridine triphosphate (ddhUTP), or several of these nucleotides for certain pVips :ref{doi=10.1038/s41586-020-2762-2}.
+Prokaryotic Viperins also convert ribonucleotides triphosphate into modified ribonucleotides, but contrary to their eukaryotic counterparts can use a diversity of substrates to produce ddhCTP, or ddh-guanosine triphosphate (ddhGTP), or ddh-uridine triphosphate (ddhUTP), or several of these nucleotides for certain pVips :ref{doi=10.1038/s41586-020-2762-2}.
Compared to the initial ribonucleotide triphosphate, the modified ddh-nucleotide product of Viperins lacks a hydroxyl group at the 3′ carbon of the ribose (Fig.1). The ddh-nucleotides produced by Viperins can be used as substrates by some viral RNA polymerases. Because of their lost hydroxyl group at the 3’carbon of the ribose, once incorporated into the newly forming viral RNA chain, these ddh-nucleotides act as chain terminators. By preventing further polymerization of the viral RNA chain, ddh-nucleotides can inhibit viral replication :ref{doi=10.1038/s41586-020-2762-2,10.1038/s41586-018-0238-4}.
diff --git a/content/5.structure.md b/content/5.structure.md
index cda38cfc3688703db6edcb95143f554439e3013b..e6838a1f4756254d27dab6bdf8ede57a95573449 100644
--- a/content/5.structure.md
+++ b/content/5.structure.md
@@ -8,7 +8,7 @@ navigation:
# Structure's prediction DB
In the following tables are various structures that were generated by Alphafold for all monomers, hetero- and homo-dimers for a given system.
-In the page for each system is the structure for the monomers and real structure when it exists.
+On the page for each system is the structure for the monomers and the real structure when it exists.
Scores are reported for each structure. Average pLDDTs for monomer and IPTM+PTM and pDock scores for multimers.
@@ -20,8 +20,8 @@ Some structures could not be determined for technical reasons and are in the pro
<br><br>
::tip
-One can search any text in the ***Search*** field or select a subset of the dataset based on a combination of condition in the ***Filter results*** field.
-Columns with score can be filtered with the sliders to filter scores within a given range.
+One can search any text in the ***Search*** field or select a subset of the dataset based on a combination of condition in the ***Filter results*** field.
+Columns with scores can be filtered with the sliders to filter scores within a given range.
::