diff --git a/composables/useRefinedUrl.ts b/composables/useRefinedUrl.ts
index 5dae55fbef92e88cd88426e274abb779d4e5b65d..057021a2878100de53d06aff2be9ef73b663b7d5 100644
--- a/composables/useRefinedUrl.ts
+++ b/composables/useRefinedUrl.ts
@@ -10,7 +10,6 @@ export function useRefinedUrl(url: string | Ref<string>) {
const _base = withLeadingSlash(
withTrailingSlash(useRuntimeConfig().app.baseURL)
);
- console.log(_base)
if (_base !== "/" && !sanitzedUrl.startsWith(_base)) {
return joinURL(_base, sanitzedUrl);
}
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 731d84b636203f0e47e4d323491ff65ca2399d71..685ddb6dbcdf3bceac2001da71af2bc1eae16cc5 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -10,9 +10,23 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF12770
+
+contributors:
+ - Héloïse Georjon
+
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
+ - doi: 10.1016/j.cell.2023.02.029
---
# 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}.
+
+## 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.
+
## Example of genomic structure
The Borvo system is composed of one protein: BovA.
@@ -71,13 +85,4 @@ 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: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index 9c346e976eb33457504d3a41bf1ee3081f793562..208c3406b33ff30c1f0081a2efa1476e06da0e0a 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -3,23 +3,34 @@ title: dGTPase
layout: article
tableColumns:
article:
- doi: 10.1016/j.cell.2021.09.031
+ doi: 10.1038/s41564-022-01158-0
abstract: |
- The cyclic pyrimidines 3',5'-cyclic cytidine monophosphate (cCMP) and 3',5'-cyclic uridine monophosphate (cUMP) have been reported in multiple organisms and cell types. As opposed to the cyclic nucleotides 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP), which are second messenger molecules with well-established regulatory roles across all domains of life, the biological role of cyclic pyrimidines has remained unclear. Here we report that cCMP and cUMP are second messengers functioning in bacterial immunity against viruses. We discovered a family of bacterial pyrimidine cyclase enzymes that specifically synthesize cCMP and cUMP following phage infection and demonstrate that these molecules activate immune effectors that execute an antiviral response. A crystal structure of a uridylate cyclase enzyme from this family explains the molecular mechanism of selectivity for pyrimidines as cyclization substrates. Defense systems encoding pyrimidine cyclases, denoted here Pycsar (pyrimidine cyclase system for antiphage resistance), are widespread in prokaryotes. Our results assign clear biological function to cCMP and cUMP as immunity signaling molecules in bacteria.
+ DNA viruses and retroviruses consume large quantities of deoxynucleotides (dNTPs) when replicating. The human antiviral factor SAMHD1 takes advantage of this vulnerability in the viral lifecycle, and inhibits viral replication by degrading dNTPs into their constituent deoxynucleosides and inorganic phosphate. Here, we report that bacteria use a similar strategy to defend against bacteriophage infection. We identify a family of defensive bacterial deoxycytidine triphosphate (dCTP) deaminase proteins that convert dCTP into deoxyuracil nucleotides in response to phage infection. We also identify a family of phage resistance genes that encode deoxyguanosine triphosphatase (dGTPase) enzymes, which degrade dGTP into phosphate-free deoxyguanosine and are distant homologues of human SAMHD1. Our results suggest that bacterial defensive proteins deplete specific deoxynucleotides (either dCTP or dGTP) from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication. Our study shows that manipulation of the dNTP pool is a potent antiviral strategy shared by both prokaryotes and eukaryotes.
Sensor: Monitoring of the host cell machinery integrity
- Activator: Direc
+ Activator: Direct
Effector: Nucleotide modifying
PFAM: PF01966, PF13286
+contributors:
+ - Aude Bernheim
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01158-0
---
# 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.
+
+## 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"*.
+
## Example of genomic structure
The dGTPase system is composed of one protein: Sp_dGTPase.
Here is an example found in the RefSeq database:
-{max-width=750px}
+{max-width=750px}
dGTPase system in the genome of *Acinetobacter pittii* (GCF_002012285.1) is composed of 1 protein: Sp_dGTPase (WP_213033921.1).
@@ -29,7 +40,7 @@ The dGTPase system is present in a total of 353 different species.
Among the 22k complete genomes of RefSeq, this system is present in 1532 genomes (6.7 %).
-{max-width=750px}
+{max-width=750px}
*Proportion of genome encoding the dGTPase system for the 14 phyla with more than 50 genomes in the RefSeq database.*
@@ -111,13 +122,3 @@ 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/s41564-022-01162-4
-
----
-::
-
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 69795322ddf03f89d374b26942d155f4976b9c61..c58f0115867db5952b5c41660cf52607e438ba87 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -10,9 +10,22 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00004, PF07724, PF07728
+contributors:
+ - Ernest Mordret
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Dodola
+
+## 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. It is composed of two proteins, DolA and DolB
+
+## Molecular mechanisms
+
+The molecular mechanism is unknown. DolA contains a DUF6414 domain, and DolB contains a ClpB-like domain.
+
## Example of genomic structure
The Dodola system is composed of 2 proteins: DolA and, DolB.
@@ -75,13 +88,5 @@ 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/gabija.md b/content/3.defense-systems/gabija.md
index df8a8f7254dc6f9679db7fbfe0c48774ef58a380..b8f9aee15bd99f816f32a9354fbfc2e373d5e6ee 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -10,18 +10,28 @@ tableColumns:
Activator: Direct
Effector: Degrading nucleic acids
PFAM: PF00580, PF11398, PF13175, PF13245, PF13304, PF13361, PF13476
+contributors:
+ - Nathalie Bechon
+relevantAbstracts:
+ - doi: 10.1093/nar/gkab277
+ - doi: 10.1126/science.aar4120
+ - doi: 10.1016/j.chom.2023.06.014
+ - doi: 10.1101/2023.05.01.538945
+ - doi: 10.1101/2023.05.01.538930
---
# Gabija
-## Description
-According to recent studies, GajA is a sequence-specific DNA nicking endonuclease, whose activity is inhibited by nucleotide concentration. Accordingly, GajA would be fully inhibited at cellular nucleotides concentrations. It was hypothesized that upon nucleotide depletion during phage infection, GajA would become activated (2).Â
+## Description
-Another study suggests that the *gajB* gene could encode for an NTPase, which would form a complex with GajA to achieve anti-phage defense (3).
+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 :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=10.1101/2023.05.01.538945,10.1093/nar/gkad951}. A phage protein inhibiting Gabija function was described, Gabidja anti defense 1 (Gad1) :ref{doi=10.1101/2023.05.01.538945,10.1101/2023.05.01.538930}.
## Molecular mechanism
-The precise mechanism of the Gabija system remains to be fully described, yet studies suggest that it could act either as a nucleic acid degrading system or as an abortive infection system.
+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.
## Example of genomic structure
@@ -105,14 +115,3 @@ 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: 10.1093/nar/gkab277
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 9b9f35cd60a16f2d7830ae5933b0e72e4b13a9f8..ee1822f24a3bf851788d42ddd5e35db07faf0f51 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -10,9 +10,20 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF04480, PF13086, PF13087, PF13195, PF18741
+contributors:
+ - Marian Dominguez-Mirazo
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# 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}.
+
+## Molecular mechanisms
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The Gao_Hhe system is composed of one protein: HheA.
@@ -71,13 +82,5 @@ 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: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index f3b8512e590487d8c0a5dd50894a13eaffd00227..16ae4736c5dddccddbe1e33e635f572d7af1c4c5 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -9,9 +9,22 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+contributors:
+ - Lucas Paoli
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Tmn
+
+## Description
+
+The Gao_Tmn system is named after the first author of the first paper describing it :ref{doi=10.1126/science.aba0372} and contains the description of the gene identified: a transmembrane NTPase.
+
+## Molecular mechanisms
+
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The Gao_Tmn system is composed of one protein: TmnA.
@@ -70,12 +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: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index c27a42ee2588c9ef4a8e0ce04208938828a9d8fa..1d94d0369e1986e7b805d99c5cd8071dc182f3aa 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -10,9 +10,22 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF16162
+contributors:
+ - Lucas Paoli
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
+ - doi: 10.1101/2023.02.26.530102
---
# Kiwa
+
+## Description
+
+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}.
+
## Example of genomic structure
The Kiwa system is composed of 2 proteins: KwaA and, KwaB.
@@ -76,13 +89,4 @@ 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: 10.1126/science.aar4120
-
----
-::
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index bc38138ccec76b6fa41cd20f4be2f3a706835a16..8865a980f48922504d598a0f3e0476dd1f1c4413 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -10,9 +10,22 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF03235, PF05973, PF12476, PF13175, PF13304, PF13476
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Menshen
+
+## 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}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The Menshen system is composed of 3 proteins: NsnA, NsnB and, NsnC_2623244837.
@@ -93,13 +106,3 @@ 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: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index a3d556b07d3e8b3f646e87f3cb605fc3fc30b24d..685b244930892f01c866f7870eb57a02e440e3a0 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -6,13 +6,27 @@ tableColumns:
doi: 10.1016/j.chom.2022.03.001
abstract: |
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve antiphage defense. However, the prevalence and effectiveness of minimal, single-component systems that cleave DNA remain unknown. Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity). This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates. Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in antiphage defense.
- Sensor: Unknown
- Activator: Unknown
- Effector: Nucleic acid degrading (?)
+ Sensor: Phage protein sensing
+ Activator: Direct binding
+ Effector: Nucleic acid degrading
PFAM: PF01443, PF09848, PF13604
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.03.001
+ - doi: 10.1016/j.chom.2022.09.017
---
# Nhi
+
+## Description
+
+The Nhi (nuclease-helicase immunity) system targets and degrades specific phage DNA replication intermediates :ref{doi=10.1016/j.chom.2022.03.001}. Nayeemul Bari et al. showed that Nhi from *Staphylococcus epidermidis* protects against a diverse panel of staphylococcal phages and Millman et al. showed that a protein Nhi-like (that shares the domain organization with Nhi but not the sequence) from *Bacillus cereus* protects against some Bacillus phages :ref{doi=10.1016/j.chom.2022.03.001,10.1016/j.chom.2022.09.017}.
+
+## Molecular mechanisms
+
+Nhi contains two domains, a nuclease and a helicase domain that are both needed for the anti-phage activity. The nuclease domain has 3′–5′ exonuclease and plasmid nicking activities while the helicase unwinds dsDNA biderctionally. Nhi specifically recognizes phage single-stranded DNA binding proteins (SSB) that cover the phage genome to target this DNA for degradation thanks to its helicase and nuclease domains :ref{doi=10.1016/j.chom.2022.03.001}.
+
## Example of genomic structure
The Nhi system is composed of one protein: Nhi.
@@ -108,13 +122,3 @@ 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: 10.1016/j.chom.2022.03.001
-
----
-::
-
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index 4d1dd64a46710df95c293b9b3d668bd700618ddc..cf9aa0a4969da1bbb0b8bdd40dae4376ea232b2f 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -10,9 +10,23 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10544, PF13250, PF13455
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
+
---
# PD-Lambda-1
+
+## Description
+
+The PD-Lambda-1 system is composed of one protein, PD-Lambda-1, and confers resistance to LambdaVir :ref{doi=10.1038/s41564-022-01219-4}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The PD-Lambda-1 system is composed of one protein: PD-Lambda-1.
@@ -68,13 +82,5 @@ 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: 10.1038/s41564-022-01219-4
----
-::
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index f25888260eeb703899d5703e76fcebfe948983fc..aaa7a1cab979592db7726be13b4dc1b544b3d31d 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -10,9 +10,20 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF09509
+contributors:
+ - Héloïse Georjon
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-3
+
+## Description
+PD-Lambda-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E.coli* :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-Lambda-3 system is composed of 2 proteins: PD-Lambda-3_B and, PD-Lambda-3_A.
@@ -83,13 +94,4 @@ 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-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 64b7f079c49a83e3a817d7290ceaedf1b758d013..ac6ae462b194a8f84446b58b011227e7c679cec5 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -9,9 +9,21 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: Unknown
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# 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}.
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The PD-T4-10 system is composed of 2 proteins: PD-T4-10_B and, PD-T4-10_A.
@@ -78,12 +90,3 @@ 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: 10.1371/journal.pgen.1010065
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index 3d988e96435b804a27b338da755dc604299df9b1..cbfc5762fbc50de6e93a766d73086d315fb88968 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -10,9 +10,20 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14082
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# 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.
+
+## Molecular mechanisms
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The PD-T4-8 system is composed of one protein: PD-T4-8.
@@ -72,13 +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: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index ea981d3ee1e2afbc332250b415679a39607328b8..2672d4863fb216850c5a11fcae3487791cb25ed0 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -9,9 +9,21 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+
+contributors:
+ - Héloïse Georjon
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-3
+## Description
+
+PD-T7-3 systems were discovered to be anti-phage systems during an experimental screen performed on *E. coli* strains :ref{doi=10.1038/s41564-022-01219-4}
+
+## Molecular mechanisms
+As far as we are aware, the molecular mechanism of PD-T7-3 is unknown.
+
## Example of genomic structure
The PD-T7-3 system is composed of one protein: PD-T7-3.
@@ -73,12 +85,4 @@ 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/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index 7bd485dd5a75f48df425dbdcbd29a1e0bd0f79a0..bd08dc329afc9a28d99c22fe6ee4fb36ba80effe 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -9,9 +9,23 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+ PFAM: Unknown
+contributors:
+ - Alba Herrero del Valle
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_3HP
+
+## Description
+
+The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
## Example of genomic structure
The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3.
@@ -82,12 +96,4 @@ 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: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index 1a7f6d2ff8582a5168c40f9242234e6d8b7c1a3b..5fc9a496e876a4981119ea0836cf04c513a8026c 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -10,9 +10,23 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08843
+contributors:
+ - Alba Herrero del Valle
+
+relevantAbstracts:
+ - doi: 10.1016/j.molcel.2013.02.002
---
# SanaTA
+
+## 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}.
+
+## Molecular mechanism
+
+It has been shown to function as a toxin-antitoxin (TA) system.
+
## Example of genomic structure
The SanaTA system is composed of 2 proteins: SanaT and, SanaA.
@@ -75,13 +89,5 @@ 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.molcel.2013.02.002
----
-::
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index a6a15c5f295b7e005a611af25bcbdf33d64daf00..b26a2440b82a1ff77bff1ca211842bae1dfc5a7f 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -10,9 +10,28 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14082
+contributors:
+ - Aude Bernheim
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
+ - doi: 10.1101/2023.08.10.552762
+ - doi: 10.1101/2023.08.10.552793
---
# Shedu
+
+## Description
+The Shedu antiphage system consists of a single protein, SduA, which acts as a nuclease with a conserved DUF4263 domain belonging to the PD-(D/E)XK nuclease superfamily. The system was named after an Assyrian Mythical Deity. The N-terminal domain is very diverse including diverse nucleic acid binding, enzymatic, and other domains.
+
+
+## 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 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}
+*"The N-terminal domains of SduA form a clamp that recognizes free DNA ends. End binding positions the DNA over the PD/ExK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5’ end. The end-directed DNA nicking activity of Shedu prevents propagation of linear DNA in vivo"*. In E. coli, T6 phages can escape Shedu immunity by suppressing their recombination-dependent DNA replication pathway.
+
+
## Example of genomic structure
The Shedu system is composed of one protein: SduA.
@@ -71,13 +90,4 @@ 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: 10.1126/science.aar4120
-
----
-::
diff --git a/pages/predicted-structure.vue b/pages/predicted-structure.vue
index cce6065289af8de97dc49ab3c3071b404247ec9d..b783a347255709e715bf9bb0fa23d63bef50c25b 100644
--- a/pages/predicted-structure.vue
+++ b/pages/predicted-structure.vue
@@ -72,7 +72,7 @@ watch(facetDistribution, (facetDistri) => {
<v-toolbar-title>Predicted Structures summary ({{ itemsLength }})
</v-toolbar-title>
<JsonCSV :data="items" name="predicted-structures-summary-defense-system.csv">
- <v-btn icon>
+ <v-btn disabled icon>
<v-icon icon="md:download"></v-icon>
<v-tooltip activator="parent" location="bottom">Download {{ itemsLength }} entries</v-tooltip>
</v-btn>
diff --git a/pages/refseq.vue b/pages/refseq.vue
index dc16513d8e46e3387fe7139c6e14083149213c61..ffb9fc6ae599faba5d097043c75de2b8c590c741 100644
--- a/pages/refseq.vue
+++ b/pages/refseq.vue
@@ -194,7 +194,7 @@ const computedDistriTaxoOptions = computed(() => {
});
// const datatable = ref(null)
const hasToGenerateDownload = ref(false)
-let itemsToDownload = ref()
+let itemsToDownload = ref([])
watch(hasToGenerateDownload, (val) => {
console.log(val)
@@ -211,8 +211,8 @@ watch(hasToGenerateDownload, (val) => {
<v-app-bar-nav-icon></v-app-bar-nav-icon>
<v-toolbar-title>RefSeq Entries ({{ itemsLength }})
</v-toolbar-title>
- <JsonCSV :data="itemsToDownload" name="refseq-defenes-system.csv">
- <v-btn icon @click="hasToGenerateDownload = true">
+ <JsonCSV :data="itemsToDownload" name="refseq-defenes-system.csv">
+ <v-btn disabled icon @click="hasToGenerateDownload = true">
<v-icon icon="md:download"></v-icon>
<v-tooltip activator="parent" location="bottom">Download {{ itemsLength }} entries</v-tooltip>
</v-btn>
diff --git a/stores/pfam.ts b/stores/pfam.ts
index b6eb282c030a952f4fb58b35ad997c8995f98d81..60de2d5f30482e73e316649f161c5d45ebc9d1cb 100644
--- a/stores/pfam.ts
+++ b/stores/pfam.ts
@@ -3,6 +3,9 @@ import { ref } from 'vue'
import * as d3 from "d3";
import { unref } from 'vue'
+
+// const { refinedUrl: refinedPfamUrl } = useRefinedUrl('/pfam-a-hmm.csv')
+
export interface PfamContent {
body: PfamHmm[]
}
@@ -24,7 +27,8 @@ export const usePfamStore = defineStore('pfam', () => {
async function initPfam() {
if (pfam.value.size < 1) {
- const data = await d3.csv("/pfam-a-hmm.csv");
+ // const data = await d3.csv(refinedPfamUrl.value);
+ const data = await d3.csv('/pfam-a-hmm.csv');
if (data.length > 1) {
pfam.value = new Map(data.map(pfam => {
return [pfam.AC.split(".")[0], { ...unref(pfam) }];