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components/content/RefseqDb.vue
View file @ 608b3ba8
......@@ -172,7 +172,8 @@ function namesToAccessionChips(names: string[]) {
return { ...it, href: new URL(it.title, "http://toto.pasteur.cloud").toString() }
})
}
const taxoPanel: Ref<number> = ref(0)
const systemPanel: Ref<number> = ref(0)
</script>
......@@ -192,7 +193,7 @@ function namesToAccessionChips(names: string[]) {
<v-col :cols="fullWidth ? 12 : 6">
<v-card color="transparent" flat>
<v-expansion-panels>
<v-expansion-panels v-model="systemPanel">
<v-expansion-panel elevation="3">
<v-expansion-panel-title color="grey-lighten-4">Systems</v-expansion-panel-title>
<v-expansion-panel-text>
......@@ -204,14 +205,17 @@ function namesToAccessionChips(names: string[]) {
</v-col>
<v-col :cols="fullWidth ? 12 : 6">
<v-card flat color="transparent">
<v-expansion-panels>
<v-expansion-panel elevation="3">
<v-expansion-panels v-model="taxoPanel">
<v-expansion-panel elevation="3" :value="true">
<v-expansion-panel-title color="grey-lighten-4">
Taxonomic
</v-expansion-panel-title>
<v-expansion-panel-text>
<v-select v-model="selectedTaxoRank" :items="availableTaxo" density="compact"
label="Select taxonomic rank"></v-select>
<PlotFigure defer :options="unref(computedDistriTaxoOptions)"></PlotFigure>
......
components/content/StructureDb.vue
View file @ 608b3ba8
......@@ -3,18 +3,17 @@ import type { SortItem } from "@/components/ServerDbTable.vue"
import { ServerDbTable } from "#components"
const sortBy: Ref<SortItem[]> = ref([{ key: 'system', order: "asc" }])
const itemValue = ref("id");
const facets: Ref<string[]> = ref(["system", "completed",
"plddts",])
const facets: Ref<string[]> = ref(["system", "completed"])
const headers: Ref<Object[]> = ref([
{ title: "System", key: "system" },
{ title: "pdb file", key: "pdb" },
{ title: "fasta", key: "fasta_file" },
// { title: "pdb file", key: "pdb" },
// { title: "fasta", key: "fasta_file" },
{ title: "Proteins in structure", key: 'proteins_in_the_prediction', sortable: false },
{ title: "System genes", key: "system_genes", sortable: false },
{ title: "Sys id", key: "nb_sys" },
{ title: "Completed", key: "completed" },
{ title: "Predition type", key: "prediction_type" },
{ title: "Prediction type", key: "prediction_type" },
{ title: "Num of genes", key: "system_number_of_genes" },
{ title: "pLDDT", key: "plddts" },
{ title: "iptm+ptm", key: "iptm+ptm" },
......@@ -34,8 +33,12 @@ const dataTableServerProps = computed(() => {
}
})
function namesToCollapsibleChips(names: string[]) {
return names.filter((it) => it !== "").map(it => ({ title: it.split("__").pop() }))
function namesToCollapsibleChips(names: string[], file: string | null = null) {
if (file === null) {
return names.filter((it) => it !== "").map(it => ({ title: it.split("__").pop() }))
} else {
return names.filter((it) => it !== "").map(it => ({ title: it.split("__").pop(), href: `/wiki/${toSystemName(file)}/${file}` }))
}
}
function pdbNameToCif(pdbPath: string) {
......@@ -53,7 +56,8 @@ function toSystemName(rawName: string) {
<ServerDbTable title="Predicted Structures" db="structure" :sortBy="sortBy" :facets="facets"
:data-table-server-props="dataTableServerProps">
<template #[`item.proteins_in_the_prediction`]="{ item }">
<CollapsibleChips :items="namesToCollapsibleChips(item.proteins_in_the_prediction)"></CollapsibleChips>
<CollapsibleChips :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.fasta_file)">
</CollapsibleChips>
</template>
<template #[`item.system_genes`]="{ item }">
<CollapsibleChips :items="namesToCollapsibleChips(item.system_genes)"></CollapsibleChips>
......
content/0.index.md
View file @ 608b3ba8
......@@ -4,17 +4,16 @@ 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
......@@ -31,7 +30,7 @@ Their work was in fact the first report of what would later be named Restriction
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).
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.
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 }.
## List of known defense systems
......
content/3.defense-systems/abib.md
View file @ 608b3ba8
......@@ -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:
......
content/3.defense-systems/abiu.md
View file @ 608b3ba8
......@@ -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
---
::
content/3.defense-systems/brex.md
View file @ 608b3ba8
......@@ -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:
......
content/3.defense-systems/mokosh.md
View file @ 608b3ba8
......@@ -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
---
::
content/3.defense-systems/old_exonuclease.md
View file @ 608b3ba8
......@@ -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.
content/3.defense-systems/pd-t4-4.md
View file @ 608b3ba8
......@@ -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:
![pd-t4-4](/pd-t4-4/PD-T4-4.svg){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
---
::
content/3.defense-systems/pd-t4-6.md
View file @ 608b3ba8
......@@ -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
---
::