diff --git a/content/0.index.md b/content/0.index.md index be3dcf617b3da4071cf24f9efac765b684d9105b..a1c92a986b2d08701d532d667fe6cd444aa2be78 100644 --- a/content/0.index.md +++ b/content/0.index.md @@ -4,36 +4,36 @@ layout: article navigation: icon: 'md:home' relevantAbstracts: - - doi: 10.1126/science.1138140 - - doi: 10.1038/nmicrobiol.2017.92 - - doi: 10.1128/jb.65.2.113-121.1953 - - doi: 10.1126/science.aar4120 - - doi: 10.1126/science.aba0372 - - doi: 10.1038/s41586-019-1894-8 - doi: 10.1128/jb.64.4.557-569.1952 + - doi: 10.1128/jb.65.2.113-121.19 - doi: 10.1128/JB.05535-11 + - doi: 10.1126/science.aar4120 + - doi: 10.1038/s41579-023-00934-x + - doi: 10.1126/science.1138140 + - doi: 10.1126/science.aba0372 - doi: 10.1016/j.cell.2021.12.029 - - + - doi: 10.1038/nmicrobiol.2017.92 + - doi: 10.1038/s41586-019-1894-8 --- ## Introduction -Bacteriophages, or phages for short, are viruses that infect bacteria and hijack bacterial cellular machinery to reproduce themselves. Phages are extremely abundant entities, and could be responsible for up to 20-40% of bacterial mortality daily :ref{doi=10.1038/s41586-019-1894-8}. Therefore, phage infection constitutes a very strong evolutionary pressure for bacteria. +Bacteria and their phages have co-existed for billions of years. The pressure of phage infection is thought to be a major driver of bacterial evolution and has favored the development of a diversity of anti-phage weapons. These weapons, namely anti-phage defense systems can be defined as single genes or groups of genes that partially or fully inhibit phage infection. For reviews on anti-phage systems, see : :ref{doi=10.1038/s41586-019-1894-8, 10.1146/annurev-micro-020722-013730, 10.1016/j.mib.2005.06.006, 10.1038/s41579-023-00934-x}. -In response to this evolutionary pressure, bacteria have developed an arsenal of anti-phage defense systems. The term "defense system" here designates either a single gene or a set of genes, which expression provides the bacteria with some level of resistance against phage infection. +## A brief history of anti-phage systems -## History +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. -The first anti-phage defense system was discovered in the early 1950s by two separate teams of researchers :ref{doi=10.1128/jb.64.4.557-569.1952}, :ref{doi=10.1128/jb.65.2.113-121.1953}. Luria and Human reported a mysterious phenomenon, where one phage was only capable of infecting a specific bacterial strain once. The progeny phages produced by this first round of infection had lost their ability to infect the same strain again, yet remained able to infect other bacterial strains. For them, this could only mean that "the genotype of the host in which a virus reproduces affects the phenotype of the new virus" :ref{doi=10.1128/jb.64.4.557-569.1952}. A similar phenomenon was shortly after described by Bertani and Wiegle. +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{10.1038/s41579-023-00934-x}. -Their work was in fact the first report of what would later be named Restriction-Modification ([RM](/defense-systems/rm)) system, which is considered to be the first anti-phage defense system discovered. +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. -The sighting of a second defense system occured more than 40 years later, in the late 1980s, when several teams around the world observed arrays containing short, palindromic DNA repeats clustered together on the bacterial genome :ref{doi=10.1038/nmicrobiol.2017.92}. Yet, the biological function of these repeats was only elucidated in 2007, when a team of researchers demonstrated that these repeats were part of a new anti-phage defense systems :ref{doi=10.1126/science.1138140}, known as [CRISPR-Cas system](https://en.wikipedia.org/wiki/CRISPR). +## Introducing the defense finder wiki -Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, Makarova and colleagues 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 concept had a large role in the discovery of an impressive diversity of defense systems in a very short amount of time. +The fast pace of discoveries in the field can be intimidating to newcomers and can make it difficult for all to keep track of new discoveries. For this reason, we decided to implement a collaborative knowledge base for the community. This wiki is divided in two sections: +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. -## List of known defense systems +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! -To date, more than 150 anti-phage defense systems have been described. An exhaustive list of the systems with experimentally validated anti-phage activity can be found [here](/defense-systems). diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md index a9e9832212d624a6e356197b63d8a4fbd205e173..b137056a383e5ca479570ff2952c86d2ff338cdc 100644 --- a/content/3.defense-systems/abib.md +++ b/content/3.defense-systems/abib.md @@ -9,12 +9,24 @@ tableColumns: Sensor: Unknown Activator: Unknown Effector: Unknown +contributors: + - Nathalie Bechon relevantAbstracts: - doi: 10.1023/A:1002027321171 - doi: 10.1016/j.mib.2005.06.006 + - doi: 10.1128/aem.57.12.3547-3551.1991 + - doi: 10.1046/j.1365-2958.1996.371896.x --- # AbiB + +## Description +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. + +## Example of genomic structure The AbiB system is composed of one protein: AbiB. Here is an example found in the RefSeq database: diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md index 97814afc25df4611378b86a9146fb5de52679782..497cb4cef52c3084492255313ebbddf85fd23e50 100644 --- a/content/3.defense-systems/abiu.md +++ b/content/3.defense-systems/abiu.md @@ -3,16 +3,29 @@ title: AbiU layout: article tableColumns: article: - doi: 10.1016/j.mib.2005.06.006 + doi: 10.1128/AEM.67.11.5225-5232.2001 abstract: | - Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance. + This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis. AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10−1, 1.0 × 10−2, and 1.0 × 10−1, respectively. abiU involves two open reading frames,abiU1 (1,772 bp) and abiU2 (1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2. Sensor: Unknown Activator: Unknown Effector: Unknown PFAM: PF10592 +contributor: + - Nathalie Bechon +relevant-abstracts + - doi: 10.1023/A:1002027321171 + - doi: 10.1016/j.mib.2005.06.006 + - doi: 10.1128/AEM.67.11.5225-5232.2001 --- # AbiU + +## Description +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}. + ## Example of genomic structure The AbiU system is composed of one protein: AbiU. @@ -70,14 +83,3 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -::relevant-abstracts ---- -items: - - doi: 10.1023/A:1002027321171 - - doi: 10.1016/j.mib.2005.06.006 - ---- -:: - diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md index 03ba456f9a740655cbecf61af13b22f43e3dfdef..255e8c7fe03295c8ba71002f67dfa972ef288aaa 100644 --- a/content/3.defense-systems/brex.md +++ b/content/3.defense-systems/brex.md @@ -10,6 +10,8 @@ tableColumns: Activator: Unknown Effector: Unknown PFAM: PF00069, PF00176, PF00270, PF00271, PF01507, PF01555, PF02384, PF04851, PF07669, PF07714, PF08378, PF08665, PF08747, PF08849, PF10923, PF13337, PF16565 +contributors: + - Marian Dominguez-Mirazo relevantAbstracts: - doi: 10.1093/nar/gkaa290 - doi: 10.1093/nar/gky1125 @@ -20,30 +22,30 @@ relevantAbstracts: ## Description -BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems (1,2). BREX systems are found in around 10% of sequenced microbial genomes (1). +BREX (for Bacteriophage Exclusion) is a family of anti-phage defense systems. BREX systems are active against both lytic and lysogenic phages. They allow phage adsorption but block phage DNA replication, and are considered to be [RM](/defense-systems/rm)-like systems :ref{doi=10.15252/embj.201489455,10.1093/nar/gkaa290}. BREX systems are found in around 10% of sequenced microbial genomes :ref{doi=10.15252/embj.201489455}. -BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific (1). +BREX systems can be divided into six subtypes, and are encoded by 4 to 8 genes, some of these genes being mandatory while others are subtype-specific :ref{doi=10.15252/embj.201489455}. ## Molecular mechanism -*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome (1). The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems. +*B. cereus* BREX Type 1 system was reported to methylate target motifs in the bacterial genome :ref{doi=10.15252/embj.201489455}. The methylation activity of this system has been hypothesized to allow for self from non-self discrimination, as it is the case for Restriction-Modification ([RM)](/defense-systems/rm) systems. -However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids (1). +However, the mechanism through which BREX Type 1 systems defend against phages is distinct from RM systems, and does not seem to degrade phage nucleic acids :ref{doi=10.15252/embj.201489455}. To date, BREX molecular mechanism remains to be described. ## Example of genomic structure -The BREX system have been describe in a total of 6 subsystems. +There are 6 subsystems described for the BREX system. -BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes (1). +BREX systems necessarily include the pglZ gene (encoding for a putative alkaline phosphatase), which is accompanied by either brxC or pglY. These two genes share only a distant homology but have been hypothesized to fulfill the same function among the different BREX subtypes :ref{doi=10.15252/embj.201489455}. -Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC).  Four other genes  are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase),  *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) (1,2). +Goldfarb and colleagues reported a 6-gene cassette from *Bacillus cereus* as being the model for BREX Type 1. BREX Type 1 are the most widespread BREX systems, and present two core genes (pglZ and brxC).  Four other genes  are associated with BREX Type 1 : *pglX (*encoding for a putative methyltransferase),  *brxA (*encoding an RNA-binding anti-termination protein)*, brxB (*unknown functio*n), brxC (*encoding for a protein with ATP-binding domain) and *brxL* (encoding for a putative protease) :ref{doi=10.15252/embj.201489455,10.1093/nar/gkaa290}. -Type 2 BREX systems include the system formerly known as Pgl , which is comprised of four genes  (pglW, X, Y, and Z) (3), to which Goldfarb and colleagues found often associated two additional genes (brxD, and brxHI). +Type 2 BREX systems include the system formerly known as Pgl, which is comprised of four genes (pglW, X, Y, and Z) :ref{doi=10.1093/nar/gky1125}, to which :ref{doi=10.15252/embj.201489455} found often associated two additional genes (brxD, and brxHI). -Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in Goldfarb *et al*., 2015. +Although 4 additional BREX subtypes have been proposed, BREX Type 1 and Type 2 remain the only ones to be experimentally validated. A detailed description of the other subtypes can be found in :ref{doi=10.15252/embj.201489455}. Here is some example found in the RefSeq database: diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md index 5373c9a07deedb702db438182fc136e5cfdf5445..5509c215d320be6c19aac18323da8dfa1888fce7 100644 --- a/content/3.defense-systems/mokosh.md +++ b/content/3.defense-systems/mokosh.md @@ -10,9 +10,21 @@ tableColumns: Activator: Unknown Effector: Unknown PFAM: PF00069, PF07714, PF08378, PF13086, PF13087, PF13091, PF13245, PF13604 +contributors: + - Marian Dominguez-Mirazo +relevantAbstract: + - doi: 10.1016/j.chom.2022.09.017 + - doi: 10.1101/2022.12.12.520048 --- # 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}. + +## Molecular mechanisms +As far as we are aware, the molecular mechanism is unknown. + ## Example of genomic structure The Mokosh system have been describe in a total of 2 subsystems. @@ -126,13 +138,5 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts -::relevant-abstracts ---- -items: - - doi: 10.1016/j.chom.2022.09.017 - ---- -:: diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md index d87f647bf994e64711bc05ca07733ae66668314e..be35419789befee2618fed2688db18f9b93bd93e 100644 --- a/content/3.defense-systems/old_exonuclease.md +++ b/content/3.defense-systems/old_exonuclease.md @@ -8,11 +8,23 @@ tableColumns: The Old protein of bacteriophage P2 is responsible for interference with the growth of phage lambda and for killing of recBC mutant Escherichia coli. We have purified Old fused to the maltose-binding protein to 95% purity and characterized its enzymatic properties. The Old protein fused to maltose-binding protein has exonuclease activity on double-stranded DNA as well as nuclease activity on single-stranded DNA and RNA. The direction of digestion of double-stranded DNA is from 5' to 3', and digestion initiates at either the 5'-phosphoryl or 5'-hydroxyl terminus. The nuclease is active on nicked circular DNA, degrades DNA in a processive manner, and releases 5'-phosphoryl mononucleotides. Sensor: Unknown Activator: Unknown - Effector: Unknown + Effector: Nucleic acid degrading PFAM: PF13175, PF13304 +contributors: + - Marian Dominguez-Mirazo +relevantAbstracts: + - doi: 10.1128/jb.177.3.497-501.1995 + - doi: 10.1128/jb.177.3.497-501.1995 --- # 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}. + +## 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. + ## Example of genomic structure The Old_exonuclease system is composed of one protein: Old_exonuclease. @@ -71,9 +83,3 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).** -Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements. - - diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md index 0d0eef96fb06e33a218fdf3217d16338c1c249bb..e9be02d76a7e3723153640ffba8bc5976ba05e1a 100644 --- a/content/3.defense-systems/pd-lambda-5.md +++ b/content/3.defense-systems/pd-lambda-5.md @@ -10,9 +10,19 @@ tableColumns: Activator: Unknown Effector: Unknown PFAM: PF02086 +contributors: + - Nathalie Bechon +relevantAbstracts: + - doi: 10.1038/s41564-022-01219-4 --- # PD-Lambda-5 +##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. + ## Example of genomic structure The PD-Lambda-5 system is composed of 2 proteins: PD-Lambda-5_A and, PD-Lambda-5_B. @@ -83,13 +93,3 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -::relevant-abstracts ---- -items: - - doi: 10.1038/s41564-022-01219-4 - ---- -:: - diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md index 21c35ecf5417359d2b0cddf0dd4287459635c7c5..8eb17137f0068cf1d5e42dc98a7c90e1d9d98387 100644 --- a/content/3.defense-systems/pd-t4-4.md +++ b/content/3.defense-systems/pd-t4-4.md @@ -10,9 +10,19 @@ tableColumns: Activator: Unknown Effector: Unknown PFAM: PF13175, PF13304 +contributors: + - Nathalie Bechon +relevantAbstracts + - doi: 10.1038/s41564-022-01219-4 --- # PD-T4-4 +## Description +PD-T4-4 is a defense system composed of two proteins, a P-loop NTPase and a nuclease, that is most likely protecting the bacterial population through abortive infection. It was identified from an ICE in an *E. coli* genome. + +## Molecular mechanisms +PD-T4-4 molecular mechanism is currently unknown, although it is most likely an abortive infection system. + ## Example of genomic structure The PD-T4-4 system is composed of 2 proteins: PD-T4-4_A and, PD-T4-4_B. @@ -21,7 +31,7 @@ Here is an example found in the RefSeq database: {max-width=750px} -PD-T4-4 system in the genome of *Escherichia coli* (GCF_013376895.1) is composed of 2 proteins: PD-T4-4_B (WP_176670803.1)and, PD-T4-4_A (WP_027920142.1). +PD-T4-4 system in the genome of *Escherichia coli* (GCF_013376895.1) is composed of 2 proteins: PD-T4-4_B (WP_176670803.1) and, PD-T4-4_A (WP_027920142.1). ## Distribution of the system among prokaryotes @@ -78,13 +88,4 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -::relevant-abstracts ---- -items: - - doi: 10.1038/s41564-022-01219-4 - ---- -:: diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md index f0e618cdddf5bccd45846e27307c20b8b726f503..5eb31a5ee2aaf8287eb9fa9e0a7df04ea76ce495 100644 --- a/content/3.defense-systems/pd-t4-6.md +++ b/content/3.defense-systems/pd-t4-6.md @@ -5,14 +5,25 @@ tableColumns: article: doi: 10.1038/s41564-022-01219-4 abstract: | - The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species. + The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse *E. coli* strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in *E. coli*, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in *E. coli* and provide an approach for mapping defence systems in other species. Sensor: Unknown Activator: Unknown Effector: Unknown PFAM: PF00069, PF03793, PF07714 +contributors: + - Marian Dominguez-Mirazo +relevantAbstracts: + - doi: 10.1038/s41564-022-01219-4 + --- # 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}. + +## Molecular mechanisms +As far as we are aware, the molecular mechanism is unknown. + ## Example of genomic structure The PD-T4-6 system is composed of one protein: PD-T4-6. @@ -70,13 +81,3 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -::relevant-abstracts ---- -items: - - doi: 10.1038/s41564-022-01219-4 - ---- -:: - diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md index 105acc2765957ae00466b71f76b31164aafd99ef..7b51d8f5042796081d530d4ca7328c4f1551ab5c 100644 --- a/content/3.defense-systems/prrc.md +++ b/content/3.defense-systems/prrc.md @@ -10,9 +10,25 @@ tableColumns: Activator: Direct Effector: Nucleic acid degrading PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF13166, PF18766 +contributors: + - Ernest Mordret +relevant abstracts: + - doi: 10.1186/1743-422X-7-360 + - doi: 10.1006/jmbi.1995.0343 --- # PrrC + +## 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. + +## 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. + + ## Example of genomic structure The PrrC system is composed of 4 proteins: EcoprrI, Type_I_S, PrrC and, Type_I_REases. @@ -78,14 +94,3 @@ end style Title3 fill:none,stroke:none,stroke-width:none style Title4 fill:none,stroke:none,stroke-width:none </mermaid> -## Relevant abstracts - -::relevant-abstracts ---- -items: - - doi: 10.1006/jmbi.1995.0343 - - doi: 10.1186/1743-422X-7-360 - ---- -:: -