From 61a8c21b3056ed1894cc38a9201651328ace09f4 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 7 Sep 2023 13:08:00 +0200
Subject: [PATCH] Update content
---
components/content/ProseImg.vue | 38 ++
components/content/ReferencesList.vue | 10 +-
content/2.defense-systems/abi2.md | 27 ++
content/2.defense-systems/abia.md | 43 +++
content/2.defense-systems/abie.md | 121 +++----
content/2.defense-systems/avast.md | 98 +++++-
package-lock.json | 17 +-
public/AVAST_I.svg | 229 ++++++++++++
public/AVAST_II.svg | 273 +++++++++++++++
public/AVAST_III.svg | 288 +++++++++++++++
public/AVAST_IV.svg | 303 ++++++++++++++++
public/AVAST_V.svg | 322 +++++++++++++++++
public/Abi2.svg | 304 ++++++++++++++++
public/AbiA_large.svg | 327 +++++++++++++++++
public/AbiA_small.svg | 335 ++++++++++++++++++
public/AbiE.svg | 410 ++++++++++++++++++++++
public/Distribution_AVAST.svg | 481 ++++++++++++++++++++++++++
public/Distribution_Abi2.svg | 386 +++++++++++++++++++++
public/Distribution_AbiA.svg | 465 +++++++++++++++++++++++++
public/Distribution_AbiE.svg | 416 ++++++++++++++++++++++
20 files changed, 4801 insertions(+), 92 deletions(-)
create mode 100644 components/content/ProseImg.vue
create mode 100644 content/2.defense-systems/abi2.md
create mode 100644 content/2.defense-systems/abia.md
create mode 100644 public/AVAST_I.svg
create mode 100644 public/AVAST_II.svg
create mode 100644 public/AVAST_III.svg
create mode 100644 public/AVAST_IV.svg
create mode 100644 public/AVAST_V.svg
create mode 100644 public/Abi2.svg
create mode 100644 public/AbiA_large.svg
create mode 100644 public/AbiA_small.svg
create mode 100644 public/AbiE.svg
create mode 100644 public/Distribution_AVAST.svg
create mode 100644 public/Distribution_Abi2.svg
create mode 100644 public/Distribution_AbiA.svg
create mode 100644 public/Distribution_AbiE.svg
diff --git a/components/content/ProseImg.vue b/components/content/ProseImg.vue
new file mode 100644
index 00000000..55d8d853
--- /dev/null
+++ b/components/content/ProseImg.vue
@@ -0,0 +1,38 @@
+<template>
+ <v-img :src="refinedSrc" :alt="alt" :width="width" :height="height"></v-img>
+</template>
+
+<script setup lang="ts">
+import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
+import { useRuntimeConfig, computed } from '#imports'
+
+const props = defineProps({
+ src: {
+ type: String,
+ default: ''
+ },
+ alt: {
+ type: String,
+ default: ''
+ },
+ width: {
+ type: [String, Number],
+ default: undefined
+ },
+ height: {
+ type: [String, Number],
+ default: undefined
+ }
+})
+
+const refinedSrc = computed(() => {
+ if (props.src?.startsWith('/') && !props.src.startsWith('//')) {
+ const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+ if (_base !== '/' && !props.src.startsWith(_base)) {
+ return joinURL(_base, props.src)
+ }
+ }
+ return props.src
+})
+</script>
+
\ No newline at end of file
diff --git a/components/content/ReferencesList.vue b/components/content/ReferencesList.vue
index 825e7853..af798cdc 100644
--- a/components/content/ReferencesList.vue
+++ b/components/content/ReferencesList.vue
@@ -1,11 +1,6 @@
<template>
<ClientOnly fallback-tag="span" fallback="Loading references...">
- <v-list
- v-if="computedItems.length > 0"
- :items="computedItems"
- item-props
- lines="three"
- >
+ <v-list v-if="computedItems.length > 0" :items="computedItems" item-props lines="three">
<template #subtitle="{ item }">
<div>{{ item.subtitle }}</div>
<div>{{ item.containerTitle }} ({{ item.year }})</div>
@@ -22,6 +17,9 @@
<script setup lang="ts">
import { computed, ref } from "vue";
import { useFetch as useFetchVueUse } from "@vueuse/core";
+
+// import { select, selectAll } from 'unist-util-select';
+
const props = defineProps<{
items: string[];
}>();
diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
new file mode 100644
index 00000000..351668ba
--- /dev/null
+++ b/content/2.defense-systems/abi2.md
@@ -0,0 +1,27 @@
+---
+title: Abi2
+---
+
+## Example of genomic structure
+
+The Abi2 system is composed of one protein: Abi_2.
+
+Here is an example found in the RefSeq database:
+
+
+
+Abi2 system in the genome of *Clostridium butyricum* (GCF_014131795.1) is composed of 1 protein: Abi_2 (WP_035763709.1).
+
+## Distribution of the system among prokaryotes
+
+The Abi2 system is present in a total of 176 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes (5.3 %).
+
+
+
+
+*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+
+## Relevant abstracts
+
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
new file mode 100644
index 00000000..aa9ddc5b
--- /dev/null
+++ b/content/2.defense-systems/abia.md
@@ -0,0 +1,43 @@
+# AbiA
+
+## Example of genomic structure
+
+The AbiA system have been describe in a total of 2 subsystems.
+
+Here is some example found in the RefSeq database:
+
+
+
+AbiA_large subsystem in the genome of *Lactobacillus amylovorus* (GCF_002706375.1) is composed of 1 protein: AbiA_large (WP_056940268.1).
+
+
+
+AbiA_small subsystem in the genome of *Mesobacillus foraminis* (GCF\_003667765.1) is composed of 2 proteins: AbiA\_small (WP\_121614402.1)and, AbiA\_SLATT (WP\_121614403.1).
+
+## Distribution of the system among prokaryotes
+
+The AbiA system is present in a total of 35 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (0.2 %).
+
+
+
+*Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+
+## Experimental validation
+
+AbiA systems were experimentally validated using:
+
+A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
+
+## Relevant abstracts
+
+**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
+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.
+
+**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
+The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
+
+**Mestre, M. R. et al. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Research 50, 6084-6101 (2022).**
+Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
+
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index 94a93783..7d9fb371 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -1,67 +1,54 @@
----
-title: AbiE
----
-
-# AbiE system
-
-AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.
-
-It is classified as an Abortive infection system.
-
-## Mechanism
-
-AbiE systems are encoded by two mandatory genes, abiEi and abiEii (1,2).  The latter encodes for AbiEii, a GTP-binding nucleotidyltransferase (NTase) which expression induce a reversible growth arrest.  On the other hand, abiEi encodes for a AbiEi a transcriptional autorepressor that  binds to the promoter of the abiE operon.
-
-Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin system, where the antitoxin and toxin are both proteins that do not directly interact with each other.
-
-## Relevant Abstracts
-
-Garvey P, Fitzgerald GF, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995 Dec;61(12):4321-8. doi: 10.1128/aem.61.12.4321-4328.1995. PMID: 8534099; PMCID: PMC167743.
-
-The lactococcal plasmid pNP40, from Lactococcus lactis subsp. lactis biovar diacetylactis DRC3, confers complete resistance to the prolate-headed phage phi c2 and the small isometric-headed phage phi 712 in L. lactis subsp. lactis MG1614. A 6.0-kb NcoI fragment of pNP40 cloned in the lactococcal Escherichia coli shuttle vector pAM401 was found to confer partial resistance to phi 712. Subcloning and deletion analysis of the recombinant plasmid pPG01 defined a 2.5-kb ScaIHpaI fragment as conferring phage insensitivity. Sequence analysis of this region confirmed the presence of two overlapping open reading frames (ORFs). Further subcloning of pNP40 to characterize the resistance determinant active against phi c2 identified a 5.6-kb EcoRV fragment of pNP40 which, when cloned in pAM401, conferred partial resistance to both phi c2 and phi 712. Subcloning and deletion analysis of the recombinant plasmid pCG1 defined a 3.7-kb EcoRV-XbaI fragment as encoding phage insensitivity. DNA sequence analysis of this region revealed the presence of a single complete ORF. The introduction of a frameshift mutation at the unique BglII site within this ORF disrupted the phage resistance phenotype, confirming that this ORF is responsible for the observed phage insensitivity. The mechanisms encoded by pPG01 and pCG1 in L. lactis subsp. lactis MG1614 conformed to the criteria defining abortive infection and were designated AbiE and AbiF, respectively. Analysis of the phage DNA content of phi 712-infected hosts containing AbiF demonstrated that it inhibited the rate of phage DNA replication, while AbiE had little effect on phage DNA replication, suggesting a later target of inhibition. The predicted protein product of abiF shows significant homology to the products of two other lactococcal abortive infection genes, abiD and abiD1
-
-<br/>
-
-Tangney M, Fitzgerald GF. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. FEMS Microbiol Lett. 2002 Apr 23;210(1):67-72. doi: 10.1111/j.1574-6968.2002.tb11161.x. PMID: 12023079.
-
-Four lactococcal abortive infection mechanisms were introduced into strains which were sensitive hosts for P335 type phages and plaque assay experiments performed to assess their effect on five lactococcal bacteriophages from this family. Results indicate that AbiA inhibits all five P335 phages tested, while AbiG affects φP335 itself and φQ30 but not the other P335 species phages. AbiA was shown to retard phage Q30 DNA replication as previously reported for other phages. It was also demonstrated that AbiG, previously shown to act at a point after DNA replication in the cases of c2 type and 936 type phages, acts at the level of, or prior to phage Q30 DNA replication. AbiE and AbiF had no effect on the P335 type phages examined.
-
-<br/>
-
-Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42(7):4590-4605. doi:10.1093/nar/gkt1419
-
-Bacterial abortive infection (Abi) systems are ‘altruistic’ cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin–antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins
-
-<br/>
-
-Li Z, Song Q, Wang Y, Xiao X, Xu J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles. 2018 May;22(3):347-357. doi: 10.1007/s00792-018-1002-2. Epub 2018 Jan 15. PMID: 29335804.
-
-Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized. In Escherichia coli, overexpression of the toxin gene pygT inhibited its growth while the toxic effect can be suppressed by introducing the antitoxin gene pygA in the same cell. PygAT also enhances the stability of shuttle plasmids with archaeal plasmid replication protein Rep75 in E. coli. In P. yayanosii, disruption of antitoxin gene pygA cause a significantly growth delayed under high hydrostatic pressure (HHP). The antitoxin protein PygA can specifically bind to the PygAT promoter region and regulate the transcription of pygT gene in vivo. These results show that PygAT is a functional TA system in P. yayanosii, and also may play a role in the adaptation to HHP environment.
-
-<br/>
-
-Hampton HG, Jackson SA, Fagerlund RD, Vogel AIM, Dy RL, Blower TR, Fineran PC. AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. J Mol Biol. 2018 Apr 13;430(8):1141-1156. doi: 10.1016/j.jmb.2018.02.022. Epub 2018 Mar 6. PMID: 29518409.
-
-Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation
-
-<br/>
-
-Beck IN, Usher B, Hampton HG, Fineran PC, Blower TR. Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochem J. 2020 Jun 26;477(12):2401-2419. doi: 10.1042/BCJ20200368. PMID: 32519742; PMCID: PMC7319586.
-
-Toxin-antitoxin systems play key roles in bacterial adaptation, including protection from antibiotic assault and infection by bacteriophages. The type IV toxin-antitoxin system AbiE encodes a DUF1814 nucleotidyltransferase-like toxin, and a two-domain antitoxin. In Streptococcus agalactiae, the antitoxin AbiEi negatively autoregulates abiE expression through positively co-operative binding to inverted repeats within the promoter. The human pathogen Mycobacterium tuberculosis encodes four DUF1814 putative toxins, two of which have antitoxins homologous to AbiEi. One such M. tuberculosis antitoxin, named Rv2827c, is required for growth and whilst the structure has previously been solved, the mode of regulation is unknown. To complete the gaps in our understanding, we first solved the structure of S. agalactiae AbiEi to 1.83 Å resolution for comparison with M. tuberculosis Rv2827c. AbiEi contains an N-terminal DNA binding domain and C-terminal antitoxicity domain, with bilateral faces of opposing charge. The overall AbiEi fold is similar to Rv2827c, though smaller, and with a 65° difference in C-terminal domain orientation. We further demonstrate that, like AbiEi, Rv2827c can autoregulate toxin-antitoxin operon expression. In contrast with AbiEi, the Prv2827c promoter contains two sets of inverted repeats, which bind Rv2827c with differing affinities depending on the sequence consensus. Surprisingly, Rv2827c bound with negative co-operativity to the full Prv2827c promoter, demonstrating an unexpectedly complex form of transcriptional regulation.
-
-<br/>
-
-Hampton HG, Smith LM, Ferguson S, Meaden S, Jackson SA, Fineran PC. Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microb Genom. 2020 Nov;6(11):mgen000458. doi: 10.1099/mgen.0.000458. PMID: 33074086; PMCID: PMC7725324.\*\*
-
-Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin-antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to 'shut down', limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in Serratia and shown the consequences of AbiE induction.
-
-## Sources
-
-::references-list
----
-items:
- - 10.1093/nar/gkt1419
- - 10.1128/aem.61.12.4321-4328.1995
----
-::
+---
+title: AbiE
+---
+
+## Description
+
+AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.Â
+
+It is classified as an Abortive infection system.
+
+## Molecular mechanism
+
+AbiE systems are encoded by two mandatory genes, abiEi and abiEii (1,2).  The latter encodes for AbiEii, a GTP-binding nucleotidyltransferase (NTase) which expression induce a reversible growth arrest.  On the other hand, abiEi encodes for a AbiEi a transcriptional autorepressor that  binds to the promoter of the abiE operon.
+
+Based on this mechanisms, AbiE systems are classified as Type IV Toxin-Antitoxin system, where the antitoxin and toxin are both proteins that do not directly interact with each other.
+
+## Example of genomic structure
+
+The AbiE system is composed of 2 proteins: AbiEi_1 and, AbiEii.
+
+Here is an example found in the RefSeq database:
+
+
+
+
+AbiE system in the genome of *Desulfuromonas versatilis* (GCF\_019704135.1) is composed of 2 proteins: AbiEi\_1 (WP\_221251730.1)and, AbiEii (WP\_221251731.1).
+
+## Distribution of the system among prokaryotes
+
+The AbiE system is present in a total of 962 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes (16.4 %).
+
+
+
+*Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+
+## Experimental validation
+
+AbiE systems were experimentally validated using:
+
+A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
+
+## Relevant abstracts
+
+**Chopin, M.-C., Chopin, A. & Bidnenko, E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 8, 473-479 (2005).**
+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.
+
+**Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. & Fineran, P. C. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 42, 4590-4605 (2014).**
+Bacterial abortive infection (Abi) systems are 'altruistic' cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin-antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase ? family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.
+
+**Forde, A. & Fitzgerald, G. F. Bacteriophage defence systems in lactic acid bacteria. Antonie Van Leeuwenhoek 76, 89-113 (1999).**
+The study of the interactions between lactic acid bacteria and their bacteriophages has been a vibrant and rewarding research activity for a considerable number of years. In the more recent past, the application of molecular genetics for the analysis of phage-host relationships has contributed enormously to the unravelling of specific events which dictate insensitivity to bacteriophage infection and has revealed that while they are complex and intricate in nature, they are also extremely effective. In addition, the strategy has laid solid foundations for the construction of phage resistant strains for use in commercial applications and has provided a sound basis for continued investigations into existing, naturally-derived and novel, genetically-engineered defence systems. Of course, it has also become clear that phage particles are highly dynamic in their response to those defence systems which they do encounter and that they can readily adapt to them as a consequence of their genetic flexibility and plasticity. This paper reviews the exciting developments that have been described in the literature regarding the study of phage-host interactions in lactic acid bacteria and the innovative approaches that can be taken to exploit this basic information for curtailing phage infection.
+
diff --git a/content/2.defense-systems/avast.md b/content/2.defense-systems/avast.md
index a0b7e355..c4e3d3a6 100644
--- a/content/2.defense-systems/avast.md
+++ b/content/2.defense-systems/avast.md
@@ -2,25 +2,101 @@
title: AVAST
---
-# AVAST System
-
+## Description
AVAST (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
AVAST systems are composed of NTPases of the STAND (signal transduction ATPases with numerous associated domains) superfamily (1). Â STAND-NTPases typically contain a C-terminal helical sensor domain that activates the N-terminal effector domain upon target recognition (1).
In eukaryotes, STAND-NTPases are associated with programmed cell death, therefore Gao and colleagues hypothesized that AVAST might function through an Abortive infection mechanism.
+## Example of genomic structure
+
+The AVAST system have been describe in a total of 5 subsystems.
+
+Here is some example found in the RefSeq database:
+
+
+
+
+AVAST_I subsystem in the genome of *Vibrio sp.* (GCF\_905175355.1) is composed of 3 proteins: Avs1A (WP\_208445041.1), Avs1B (WP\_208445042.1)and, Avs1C (WP_108173272.1).
+
+
+
+
+AVAST_II subsystem in the genome of *Escherichia coli* (GCF_018884505.1) is composed of 1 protein: Avs2A (WP_032199984.1).
+
+
+
+
+AVAST_III subsystem in the genome of *Enterobacter cancerogenus* (GCF_002850575.1) is composed of 2 proteins: Avs3B (WP_199559884.1)and, Avs3A (WP_101737373.1).
+
+
+
+
+AVAST_IV subsystem in the genome of *Escherichia coli* (GCF_016903595.1) is composed of 1 protein: Avs4A (WP_000240574.1).
+
+
+
+
+AVAST_V subsystem in the genome of *Leclercia adecarboxylata* (GCF_006171285.1) is composed of 1 protein: Avs5A (WP_139565349.1).
+
+## Distribution of the system among prokaryotes
+
+The AVAST system is present in a total of 363 different species.
+
+Among the 22k complete genomes of RefSeq, this system is present in 1046 genomes (4.6 %).
+
+
+
+*Proportion of genome encoding the AVAST system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+
+## Experimental validation
+
+AVAST systems were experimentally validated using:
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Salmonella enterica * has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022)
+
+Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Klebsiella pneumoniae * has an anti-phage effect against Pokey (Fillol-Salom et al., 2022)
+
+Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2020)
+
+Subsystem STAND (Type 2) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1 (Gao et al., 2020)
+
+Subsystem DUF4297-STAND (Type 3) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020)
+
+Subsystem Mrr-STAND (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
+
+Subsystem SIR2-STAND (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020)
+
+Subsystem SeAvs1 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
+
+Subsystem EcAcs1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
+
+Subsystem EpAvs1 with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022)
+
+Subsystem SeAvs3 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem KvAvs3 with a system from *Klebsiella variicola* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
+
+Subsystem EcAvs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022)
+
+Subsystem Ec2Avs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2022)
+
+Subsystem EcAvs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem Ec2Avs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
+
+Subsystem KpAvs4 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
+
+Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia coli* has an anti-phage effect against T7 (Gao et al., 2022)
+
## Relevant abstracts
-**Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes.** ***Science*****. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372**
+**Gao, L. A. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 377, eabm4096 (2022).**
+Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
+**Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077-1084 (2020).**
Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. By systematic defense gene prediction and heterologous reconstitution, here we discover 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.
-## References
-
-::references-list
----
-items:
- - 10.1126/science.aba0372
----
-::
\ No newline at end of file
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--
GitLab