From 35e756ef8a4cc9cfe6d3159f48bb692a3e4dfb5d Mon Sep 17 00:00:00 2001
From: ftesson <florian.tesson@pasteur.fr>
Date: Thu, 28 Sep 2023 16:18:07 +0200
Subject: [PATCH] Change names for different systems + Add new systems + Remove
double titles
---
content/2.defense-systems/abi2.md | 1 -
content/2.defense-systems/abia.md | 1 -
content/2.defense-systems/abib.md | 1 -
content/2.defense-systems/abic.md | 1 -
content/2.defense-systems/abid.md | 1 -
content/2.defense-systems/abie.md | 1 -
content/2.defense-systems/abig.md | 1 -
content/2.defense-systems/abih.md | 1 -
content/2.defense-systems/abii.md | 1 -
content/2.defense-systems/abij.md | 1 -
content/2.defense-systems/abik.md | 1 -
content/2.defense-systems/abil.md | 1 -
content/2.defense-systems/abin.md | 1 -
content/2.defense-systems/abio.md | 1 -
content/2.defense-systems/abip2.md | 1 -
content/2.defense-systems/abiq.md | 1 -
content/2.defense-systems/abir.md | 1 -
content/2.defense-systems/abit.md | 1 -
content/2.defense-systems/abiu.md | 1 -
content/2.defense-systems/abiv.md | 1 -
content/2.defense-systems/abiz.md | 1 -
content/2.defense-systems/aditi.md | 1 -
content/2.defense-systems/avs.md | 2 +-
content/2.defense-systems/azaca.md | 1 -
content/2.defense-systems/borvo.md | 1 -
content/2.defense-systems/brex.md | 1 -
content/2.defense-systems/bsta.md | 1 -
content/2.defense-systems/bunzi.md | 1 -
.../2.defense-systems/butters_gp30_gp31.md | 21 +++++++++++++++++++
content/2.defense-systems/butters_gp57r.md | 21 +++++++++++++++++++
content/2.defense-systems/caprel.md | 1 -
content/2.defense-systems/card_nlr.md | 21 +++++++++++++++++++
content/2.defense-systems/cbass.md | 1 -
content/2.defense-systems/charlie_gp32.md | 21 +++++++++++++++++++
content/2.defense-systems/dartg.md | 1 -
content/2.defense-systems/dazbog.md | 1 -
content/2.defense-systems/dctpdeaminase.md | 1 -
content/2.defense-systems/detocs.md | 21 +++++++++++++++++++
content/2.defense-systems/dgtpase.md | 3 ---
content/2.defense-systems/disarm.md | 1 -
content/2.defense-systems/dmdde.md | 3 +--
content/2.defense-systems/dnd.md | 1 -
content/2.defense-systems/dodola.md | 1 -
content/2.defense-systems/dpd.md | 3 +--
content/2.defense-systems/drt.md | 1 -
content/2.defense-systems/druantia.md | 1 -
content/2.defense-systems/dsr.md | 1 -
content/2.defense-systems/eleos.md | 1 -
content/2.defense-systems/fs_giy_yig.md | 21 +++++++++++++++++++
content/2.defense-systems/fs_hepn_tm.md | 21 +++++++++++++++++++
content/2.defense-systems/fs_hp.md | 21 +++++++++++++++++++
content/2.defense-systems/fs_hp_sdh_sah.md | 21 +++++++++++++++++++
content/2.defense-systems/fs_hsdr_like.md | 21 +++++++++++++++++++
content/2.defense-systems/fs_sma.md | 21 +++++++++++++++++++
content/2.defense-systems/gabija.md | 1 -
content/2.defense-systems/gao_ape.md | 1 -
content/2.defense-systems/gao_her.md | 1 -
content/2.defense-systems/gao_hhe.md | 1 -
content/2.defense-systems/gao_iet.md | 1 -
content/2.defense-systems/gao_mza.md | 1 -
content/2.defense-systems/gao_ppl.md | 1 -
content/2.defense-systems/gao_qat.md | 1 -
content/2.defense-systems/gao_rl.md | 1 -
content/2.defense-systems/gao_tery.md | 1 -
content/2.defense-systems/gao_tmn.md | 1 -
content/2.defense-systems/gao_upx.md | 1 -
content/2.defense-systems/gaps1.md | 21 +++++++++++++++++++
content/2.defense-systems/gaps2.md | 21 +++++++++++++++++++
content/2.defense-systems/gaps4.md | 21 +++++++++++++++++++
content/2.defense-systems/gaps6.md | 21 +++++++++++++++++++
content/2.defense-systems/gasdermin.md | 1 -
content/2.defense-systems/hachiman.md | 1 -
content/2.defense-systems/hna.md | 21 +++++++++++++++++++
content/2.defense-systems/isg15-like.md | 1 -
content/2.defense-systems/jukab.md | 21 +++++++++++++++++++
content/2.defense-systems/kiwa.md | 1 -
content/2.defense-systems/lamassu-fam.md | 1 -
content/2.defense-systems/lit.md | 1 -
content/2.defense-systems/mads.md | 21 +++++++++++++++++++
content/2.defense-systems/mazef.md | 21 +++++++++++++++++++
content/2.defense-systems/menshen.md | 1 -
content/2.defense-systems/mmb_gp29_gp30.md | 21 +++++++++++++++++++
content/2.defense-systems/mok_hok_sok.md | 1 -
content/2.defense-systems/mokosh.md | 1 -
content/2.defense-systems/mqsrac.md | 1 -
content/2.defense-systems/nhi.md | 1 -
content/2.defense-systems/nixi.md | 1 -
content/2.defense-systems/nlr.md | 1 -
content/2.defense-systems/old_exonuclease.md | 1 -
content/2.defense-systems/olokun.md | 1 -
content/2.defense-systems/pago.md | 1 -
content/2.defense-systems/panchino_gp28.md | 21 +++++++++++++++++++
content/2.defense-systems/paris.md | 2 +-
content/2.defense-systems/pd-lambda-1.md | 1 -
content/2.defense-systems/pd-lambda-2.md | 1 -
content/2.defense-systems/pd-lambda-3.md | 1 -
content/2.defense-systems/pd-lambda-4.md | 1 -
content/2.defense-systems/pd-lambda-5.md | 1 -
content/2.defense-systems/pd-lambda-6.md | 1 -
content/2.defense-systems/pd-t4-1.md | 1 -
content/2.defense-systems/pd-t4-10.md | 1 -
content/2.defense-systems/pd-t4-2.md | 1 -
content/2.defense-systems/pd-t4-3.md | 1 -
content/2.defense-systems/pd-t4-4.md | 1 -
content/2.defense-systems/pd-t4-5.md | 1 -
content/2.defense-systems/pd-t4-6.md | 1 -
content/2.defense-systems/pd-t4-7.md | 1 -
content/2.defense-systems/pd-t4-8.md | 1 -
content/2.defense-systems/pd-t4-9.md | 1 -
content/2.defense-systems/pd-t7-1.md | 1 -
content/2.defense-systems/pd-t7-2.md | 1 -
content/2.defense-systems/pd-t7-3.md | 1 -
content/2.defense-systems/pd-t7-4.md | 1 -
content/2.defense-systems/pd-t7-5.md | 1 -
content/2.defense-systems/pfiat.md | 1 -
content/2.defense-systems/phrann_gp29_gp30.md | 8 +++----
content/2.defense-systems/pif.md | 1 -
content/2.defense-systems/prrc.md | 1 -
content/2.defense-systems/psyrta.md | 1 -
content/2.defense-systems/pycsar.md | 1 -
content/2.defense-systems/radar.md | 1 -
content/2.defense-systems/retron.md | 1 -
content/2.defense-systems/rexab.md | 1 -
content/2.defense-systems/rloc.md | 1 -
content/2.defense-systems/rm.md | 1 -
content/2.defense-systems/rnlab.md | 3 +--
content/2.defense-systems/rosmerta.md | 1 -
content/2.defense-systems/rst_2tm_1tm_tir.md | 1 -
content/2.defense-systems/rst_3hp.md | 1 -
content/2.defense-systems/rst_duf4238.md | 1 -
content/2.defense-systems/rst_gop_beta_cll.md | 1 -
.../2.defense-systems/rst_helicaseduf2290.md | 1 -
.../2.defense-systems/rst_hydrolase-3tm.md | 1 -
.../2.defense-systems/rst_rt-nitrilase-tm.md | 1 -
content/2.defense-systems/rst_tir-nlr.md | 1 -
content/2.defense-systems/sanata.md | 1 -
content/2.defense-systems/sefir.md | 1 -
content/2.defense-systems/septu.md | 1 -
content/2.defense-systems/shango.md | 3 +--
content/2.defense-systems/shedu.md | 1 -
content/2.defense-systems/shosta.md | 1 -
content/2.defense-systems/sofic.md | 1 -
content/2.defense-systems/spbk.md | 1 -
content/2.defense-systems/sspbcde.md | 1 -
content/2.defense-systems/stk2.md | 1 -
content/2.defense-systems/thoeris.md | 1 -
content/2.defense-systems/tiamat.md | 1 -
content/2.defense-systems/uzume.md | 1 -
content/2.defense-systems/viperin.md | 1 -
content/2.defense-systems/wadjet.md | 1 -
content/2.defense-systems/zorya.md | 1 -
151 files changed, 451 insertions(+), 139 deletions(-)
create mode 100644 content/2.defense-systems/butters_gp30_gp31.md
create mode 100644 content/2.defense-systems/butters_gp57r.md
create mode 100644 content/2.defense-systems/card_nlr.md
create mode 100644 content/2.defense-systems/charlie_gp32.md
create mode 100644 content/2.defense-systems/detocs.md
create mode 100644 content/2.defense-systems/fs_giy_yig.md
create mode 100644 content/2.defense-systems/fs_hepn_tm.md
create mode 100644 content/2.defense-systems/fs_hp.md
create mode 100644 content/2.defense-systems/fs_hp_sdh_sah.md
create mode 100644 content/2.defense-systems/fs_hsdr_like.md
create mode 100644 content/2.defense-systems/fs_sma.md
create mode 100644 content/2.defense-systems/gaps1.md
create mode 100644 content/2.defense-systems/gaps2.md
create mode 100644 content/2.defense-systems/gaps4.md
create mode 100644 content/2.defense-systems/gaps6.md
create mode 100644 content/2.defense-systems/hna.md
create mode 100644 content/2.defense-systems/jukab.md
create mode 100644 content/2.defense-systems/mads.md
create mode 100644 content/2.defense-systems/mazef.md
create mode 100644 content/2.defense-systems/mmb_gp29_gp30.md
create mode 100644 content/2.defense-systems/panchino_gp28.md
diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index 7403ca3a..d3c02731 100644
--- a/content/2.defense-systems/abi2.md
+++ b/content/2.defense-systems/abi2.md
@@ -7,7 +7,6 @@ tableColumns:
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.
---
-# Abi2
# Abi2
The Abi2 system is composed of one protein: Abi_2.
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
index 9061dfd6..a7055ea9 100644
--- a/content/2.defense-systems/abia.md
+++ b/content/2.defense-systems/abia.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiA
# AbiA
The AbiA system have been describe in a total of 2 subsystems.
diff --git a/content/2.defense-systems/abib.md b/content/2.defense-systems/abib.md
index 62da9295..1951d72e 100644
--- a/content/2.defense-systems/abib.md
+++ b/content/2.defense-systems/abib.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiB
# AbiB
The AbiB system is composed of one protein: AbiB.
diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md
index efd2c8e3..cc1dd91b 100644
--- a/content/2.defense-systems/abic.md
+++ b/content/2.defense-systems/abic.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiC
# AbiC
The AbiC system is composed of one protein: AbiC.
diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md
index 26d443aa..0ae3b82f 100644
--- a/content/2.defense-systems/abid.md
+++ b/content/2.defense-systems/abid.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiD
# AbiD
The AbiD system is composed of one protein: AbiD.
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index aa61f1dd..23d85dda 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiE
# AbiE
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
diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md
index 8593fa97..7a013fbd 100644
--- a/content/2.defense-systems/abig.md
+++ b/content/2.defense-systems/abig.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiG
# AbiG
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md
index 5fdab8fa..333517d5 100644
--- a/content/2.defense-systems/abih.md
+++ b/content/2.defense-systems/abih.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiH
# AbiH
## Example of genomic structure
diff --git a/content/2.defense-systems/abii.md b/content/2.defense-systems/abii.md
index c30ab04c..92b213f9 100644
--- a/content/2.defense-systems/abii.md
+++ b/content/2.defense-systems/abii.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiI
# AbiI
## Example of genomic structure
diff --git a/content/2.defense-systems/abij.md b/content/2.defense-systems/abij.md
index 56e1d908..83dfbe0e 100644
--- a/content/2.defense-systems/abij.md
+++ b/content/2.defense-systems/abij.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiJ
# AbiJ
## Example of genomic structure
diff --git a/content/2.defense-systems/abik.md b/content/2.defense-systems/abik.md
index 3f5c36c3..6923486b 100644
--- a/content/2.defense-systems/abik.md
+++ b/content/2.defense-systems/abik.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiK
# AbiK
## Example of genomic structure
diff --git a/content/2.defense-systems/abil.md b/content/2.defense-systems/abil.md
index 1841dd43..3dee3534 100644
--- a/content/2.defense-systems/abil.md
+++ b/content/2.defense-systems/abil.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiL
# AbiL
## Example of genomic structure
diff --git a/content/2.defense-systems/abin.md b/content/2.defense-systems/abin.md
index cc2692a5..466e2528 100644
--- a/content/2.defense-systems/abin.md
+++ b/content/2.defense-systems/abin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiN
# AbiN
## Example of genomic structure
diff --git a/content/2.defense-systems/abio.md b/content/2.defense-systems/abio.md
index ab5f15f6..d89e1c5c 100644
--- a/content/2.defense-systems/abio.md
+++ b/content/2.defense-systems/abio.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiO
# AbiO
## Example of genomic structure
diff --git a/content/2.defense-systems/abip2.md b/content/2.defense-systems/abip2.md
index f9ea0ddd..1156872d 100644
--- a/content/2.defense-systems/abip2.md
+++ b/content/2.defense-systems/abip2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiP2
# AbiP2
## Example of genomic structure
diff --git a/content/2.defense-systems/abiq.md b/content/2.defense-systems/abiq.md
index 0b4e4c79..f9438c7c 100644
--- a/content/2.defense-systems/abiq.md
+++ b/content/2.defense-systems/abiq.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiQ
# AbiQ
## Example of genomic structure
diff --git a/content/2.defense-systems/abir.md b/content/2.defense-systems/abir.md
index 7004d5a1..996b6ac5 100644
--- a/content/2.defense-systems/abir.md
+++ b/content/2.defense-systems/abir.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiR
# AbiR
## Example of genomic structure
diff --git a/content/2.defense-systems/abit.md b/content/2.defense-systems/abit.md
index 5d32c877..b1865fe5 100644
--- a/content/2.defense-systems/abit.md
+++ b/content/2.defense-systems/abit.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiT
# AbiT
## Example of genomic structure
diff --git a/content/2.defense-systems/abiu.md b/content/2.defense-systems/abiu.md
index c1b8e9b3..96aba147 100644
--- a/content/2.defense-systems/abiu.md
+++ b/content/2.defense-systems/abiu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiU
# AbiU
## Example of genomic structure
diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md
index 4b369c63..eefbabd3 100644
--- a/content/2.defense-systems/abiv.md
+++ b/content/2.defense-systems/abiv.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiV
# AbiV
## Example of genomic structure
diff --git a/content/2.defense-systems/abiz.md b/content/2.defense-systems/abiz.md
index 267a963e..b58ed7f1 100644
--- a/content/2.defense-systems/abiz.md
+++ b/content/2.defense-systems/abiz.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# AbiZ
# AbiZ
## Example of genomic structure
diff --git a/content/2.defense-systems/aditi.md b/content/2.defense-systems/aditi.md
index b3c28638..f458596b 100644
--- a/content/2.defense-systems/aditi.md
+++ b/content/2.defense-systems/aditi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Aditi
# Aditi
## Example of genomic structure
diff --git a/content/2.defense-systems/avs.md b/content/2.defense-systems/avs.md
index bc7e2b04..5b66512b 100644
--- a/content/2.defense-systems/avs.md
+++ b/content/2.defense-systems/avs.md
@@ -12,7 +12,7 @@ tableColumns:
---
# Avs
-# Avs
+
## Description
Avs (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
diff --git a/content/2.defense-systems/azaca.md b/content/2.defense-systems/azaca.md
index 3b38e0a9..c106da47 100644
--- a/content/2.defense-systems/azaca.md
+++ b/content/2.defense-systems/azaca.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Azaca
# Azaca
## Example of genomic structure
diff --git a/content/2.defense-systems/borvo.md b/content/2.defense-systems/borvo.md
index c17923bc..4f2b3b35 100644
--- a/content/2.defense-systems/borvo.md
+++ b/content/2.defense-systems/borvo.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Borvo
# Borvo
## Example of genomic structure
diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md
index 71046b35..e9cb8dd0 100644
--- a/content/2.defense-systems/brex.md
+++ b/content/2.defense-systems/brex.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# BREX
# BREX
## Description
diff --git a/content/2.defense-systems/bsta.md b/content/2.defense-systems/bsta.md
index 1fa1c169..3b06e7f6 100644
--- a/content/2.defense-systems/bsta.md
+++ b/content/2.defense-systems/bsta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# BstA
# BstA
## Description
diff --git a/content/2.defense-systems/bunzi.md b/content/2.defense-systems/bunzi.md
index e747f3f4..8b1612a2 100644
--- a/content/2.defense-systems/bunzi.md
+++ b/content/2.defense-systems/bunzi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Bunzi
# Bunzi
## Example of genomic structure
diff --git a/content/2.defense-systems/butters_gp30_gp31.md b/content/2.defense-systems/butters_gp30_gp31.md
new file mode 100644
index 00000000..6f03ec35
--- /dev/null
+++ b/content/2.defense-systems/butters_gp30_gp31.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp30_gp31
+tableColumns:
+ article:
+ doi: 10.1128/mSystems.00534-20
+ abstract: |
+ Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance., A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems., IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
+---
+
+# Butters_gp30_gp31
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1128/mSystems.00534-20
+
+---
+::
diff --git a/content/2.defense-systems/butters_gp57r.md b/content/2.defense-systems/butters_gp57r.md
new file mode 100644
index 00000000..520d08dd
--- /dev/null
+++ b/content/2.defense-systems/butters_gp57r.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp57r
+tableColumns:
+ article:
+ doi: 10.1101/2023.01.03.522681
+ abstract: |
+ During lysogeny temperate phages establish a truce with the bacterial host. In this state, the phage genome (prophage) is maintained within the host environment. Consequently, many prophages have evolved systems to protect the host from heterotypic viral attack. This phenomenon of prophages mediating defense of their host against competitor phages is widespread among temperate mycobacteriophages. We previously showed that the Mycobacterium phage Butters prophage encodes a two-component system (gp30/31) that inhibits infection from a subset of mycobacteriophages that include PurpleHaze, but not Island3. Here we show that Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages. Gp57r acts post-DNA injection and its antagonism results in the impairment of Island3 DNA amplification. Gp57r inhibition of Island3 is absolute with no defense escape mutants. However, mutations mapping to minor tail proteins allow PurpleHaze to overcome gp57r defense. Gp57r has a HEPN domain which is present in many proteins involved in inter-genomic conflicts, suggesting that gp57r may inhibit heterotypic phage infections via its HEPN domain. We also show that Butters gp57r has orthologues in clinical isolates of Mycobacterium abscessus sp. including the phage therapy candidate strain GD91 which was found to be resistant to the panel of phages tested. It is conceivable that this GD91 orthologue of gp57r may mediate resistance to the subset of phages tested. Challenges of this nature underscore the importance of elucidating mechanisms of antiphage systems and mutations that allow for escape from inhibition. IMPORTANCE The evolutionary arms race between phages and their bacteria host is ancient. During lysogeny, temperate phages establish a ceasefire with the host where they do not kill the host but derive shelter from it. Within the phenomenon of prophage-mediated defense, some temperate phages contribute genes that make their host more fit and resistant to infections by other phages. This arrangement has significance for both phage and bacterial evolutionary dynamics. Further, the prevalence of such antiphage systems poses a challenge to phage therapy. Thus, studies aimed at elucidating antiphage systems will further our understanding of phage-bacteria evolution as well as help with efforts to engineer therapeutic phages that circumvent antiphage systems.
+---
+
+# Butters_gp57r
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.01.03.522681
+
+---
+::
diff --git a/content/2.defense-systems/caprel.md b/content/2.defense-systems/caprel.md
index ee88be4f..1ad55442 100644
--- a/content/2.defense-systems/caprel.md
+++ b/content/2.defense-systems/caprel.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
---
-# CapRel
# CapRel
## Description
diff --git a/content/2.defense-systems/card_nlr.md b/content/2.defense-systems/card_nlr.md
new file mode 100644
index 00000000..8cc15bd7
--- /dev/null
+++ b/content/2.defense-systems/card_nlr.md
@@ -0,0 +1,21 @@
+---
+title: CARD_NLR
+tableColumns:
+ article:
+ doi: 10.1101/2023.05.28.542683
+ abstract: |
+ Caspase recruitment domains (CARDs) and pyrin domains are important facilitators of inflammasome activity and pyroptosis. Upon pathogen recognition by NLR proteins, CARDs recruit and activate caspases, which, in turn, activate gasdermin pore forming proteins to and induce pyroptotic cell death. Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized. We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors. We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another. We also detect a phage protein with a predicted CARD-like structure that can inhibit the CARD-containing bacterial gasdermin system. Our results suggest that CARD domains represent an ancient component of innate immune systems conserved from bacteria to humans, and that CARD-dependent activation of gasdermins is conserved in organisms across the tree of life.
+---
+
+# CARD_NLR
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.05.28.542683
+
+---
+::
diff --git a/content/2.defense-systems/cbass.md b/content/2.defense-systems/cbass.md
index 12d4998c..8a16ae01 100644
--- a/content/2.defense-systems/cbass.md
+++ b/content/2.defense-systems/cbass.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
---
-# CBASS
# CBASS
## Example of genomic structure
diff --git a/content/2.defense-systems/charlie_gp32.md b/content/2.defense-systems/charlie_gp32.md
new file mode 100644
index 00000000..39c1703a
--- /dev/null
+++ b/content/2.defense-systems/charlie_gp32.md
@@ -0,0 +1,21 @@
+---
+title: Charlie_gp32
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# Charlie_gp32
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/dartg.md b/content/2.defense-systems/dartg.md
index ce8d8989..ebe19f6d 100644
--- a/content/2.defense-systems/dartg.md
+++ b/content/2.defense-systems/dartg.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (ADP-ribosylation)
---
-# DarTG
# DarTG
## Example of genomic structure
diff --git a/content/2.defense-systems/dazbog.md b/content/2.defense-systems/dazbog.md
index 349869bc..8bd4c17f 100644
--- a/content/2.defense-systems/dazbog.md
+++ b/content/2.defense-systems/dazbog.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Dazbog
# Dazbog
## Example of genomic structure
diff --git a/content/2.defense-systems/dctpdeaminase.md b/content/2.defense-systems/dctpdeaminase.md
index f4747904..563e14d0 100644
--- a/content/2.defense-systems/dctpdeaminase.md
+++ b/content/2.defense-systems/dctpdeaminase.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# dCTPdeaminase
# dCTPdeaminase
## Description
dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when express heterologously in another Escherichia coli.
diff --git a/content/2.defense-systems/detocs.md b/content/2.defense-systems/detocs.md
new file mode 100644
index 00000000..4fa1a737
--- /dev/null
+++ b/content/2.defense-systems/detocs.md
@@ -0,0 +1,21 @@
+---
+title: Detocs
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2023.07.020
+ abstract: |
+ During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
+---
+
+# Detocs
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2023.07.020
+
+---
+::
diff --git a/content/2.defense-systems/dgtpase.md b/content/2.defense-systems/dgtpase.md
index 9c2c4b66..8226a1a3 100644
--- a/content/2.defense-systems/dgtpase.md
+++ b/content/2.defense-systems/dgtpase.md
@@ -10,9 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# dGTPase
-# dGTPase
-# dGTPase
# dGTPase
## Example of genomic structure
diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md
index 6f040479..0ad07b78 100644
--- a/content/2.defense-systems/disarm.md
+++ b/content/2.defense-systems/disarm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# DISARM
# DISARM
## Description
diff --git a/content/2.defense-systems/dmdde.md b/content/2.defense-systems/dmdde.md
index b77c8a64..1aa12aa1 100644
--- a/content/2.defense-systems/dmdde.md
+++ b/content/2.defense-systems/dmdde.md
@@ -4,10 +4,9 @@ tableColumns:
article:
doi: 10.1038/s41586-022-04546-y
abstract: |
- Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2–4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
+ Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
---
-# DmdDE
# DmdDE
## Example of genomic structure
diff --git a/content/2.defense-systems/dnd.md b/content/2.defense-systems/dnd.md
index 1c5201d9..79d1ed31 100644
--- a/content/2.defense-systems/dnd.md
+++ b/content/2.defense-systems/dnd.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# Dnd
# Dnd
## Example of genomic structure
diff --git a/content/2.defense-systems/dodola.md b/content/2.defense-systems/dodola.md
index 8e4cddbb..367f760d 100644
--- a/content/2.defense-systems/dodola.md
+++ b/content/2.defense-systems/dodola.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Dodola
# Dodola
## Example of genomic structure
diff --git a/content/2.defense-systems/dpd.md b/content/2.defense-systems/dpd.md
index 76d72202..ff62362f 100644
--- a/content/2.defense-systems/dpd.md
+++ b/content/2.defense-systems/dpd.md
@@ -4,10 +4,9 @@ tableColumns:
article:
doi: 10.1073/pnas.1518570113
abstract: |
- The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction–modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
+ The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
---
-# Dpd
# Dpd
## Example of genomic structure
diff --git a/content/2.defense-systems/drt.md b/content/2.defense-systems/drt.md
index 1b7ae810..8430ad29 100644
--- a/content/2.defense-systems/drt.md
+++ b/content/2.defense-systems/drt.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# DRT
# DRT
## Example of genomic structure
diff --git a/content/2.defense-systems/druantia.md b/content/2.defense-systems/druantia.md
index 80e690cd..88068ad1 100644
--- a/content/2.defense-systems/druantia.md
+++ b/content/2.defense-systems/druantia.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Druantia
# Druantia
## Example of genomic structure
diff --git a/content/2.defense-systems/dsr.md b/content/2.defense-systems/dsr.md
index 908c36bc..b4b959f9 100644
--- a/content/2.defense-systems/dsr.md
+++ b/content/2.defense-systems/dsr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Dsr
# Dsr
## Example of genomic structure
diff --git a/content/2.defense-systems/eleos.md b/content/2.defense-systems/eleos.md
index b9710709..9c114b95 100644
--- a/content/2.defense-systems/eleos.md
+++ b/content/2.defense-systems/eleos.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Eleos
# Eleos
The Eleos system was previously described as the Dynamins-like system in (Millman et al, 2022).
diff --git a/content/2.defense-systems/fs_giy_yig.md b/content/2.defense-systems/fs_giy_yig.md
new file mode 100644
index 00000000..5d946fe1
--- /dev/null
+++ b/content/2.defense-systems/fs_giy_yig.md
@@ -0,0 +1,21 @@
+---
+title: FS_GIY_YIG
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_GIY_YIG
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hepn_tm.md b/content/2.defense-systems/fs_hepn_tm.md
new file mode 100644
index 00000000..239eb07f
--- /dev/null
+++ b/content/2.defense-systems/fs_hepn_tm.md
@@ -0,0 +1,21 @@
+---
+title: FS_HEPN_TM
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HEPN_TM
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp.md b/content/2.defense-systems/fs_hp.md
new file mode 100644
index 00000000..7e66e331
--- /dev/null
+++ b/content/2.defense-systems/fs_hp.md
@@ -0,0 +1,21 @@
+---
+title: FS_HP
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HP
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp_sdh_sah.md b/content/2.defense-systems/fs_hp_sdh_sah.md
new file mode 100644
index 00000000..8e64de23
--- /dev/null
+++ b/content/2.defense-systems/fs_hp_sdh_sah.md
@@ -0,0 +1,21 @@
+---
+title: FS_HP_SDH_sah
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HP_SDH_sah
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hsdr_like.md b/content/2.defense-systems/fs_hsdr_like.md
new file mode 100644
index 00000000..3f668c21
--- /dev/null
+++ b/content/2.defense-systems/fs_hsdr_like.md
@@ -0,0 +1,21 @@
+---
+title: FS_HsdR_like
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HsdR_like
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_sma.md b/content/2.defense-systems/fs_sma.md
new file mode 100644
index 00000000..de46a350
--- /dev/null
+++ b/content/2.defense-systems/fs_sma.md
@@ -0,0 +1,21 @@
+---
+title: FS_Sma
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_Sma
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/gabija.md b/content/2.defense-systems/gabija.md
index 2f0dbf0d..97410e3c 100644
--- a/content/2.defense-systems/gabija.md
+++ b/content/2.defense-systems/gabija.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Degrading nucleic acids
---
-# Gabija
# Gabija
## Description
diff --git a/content/2.defense-systems/gao_ape.md b/content/2.defense-systems/gao_ape.md
index db2e7fc3..c104f609 100644
--- a/content/2.defense-systems/gao_ape.md
+++ b/content/2.defense-systems/gao_ape.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ape
# Gao_Ape
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_her.md b/content/2.defense-systems/gao_her.md
index 62c7d6db..1d848a7e 100644
--- a/content/2.defense-systems/gao_her.md
+++ b/content/2.defense-systems/gao_her.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Her
# Gao_Her
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_hhe.md b/content/2.defense-systems/gao_hhe.md
index 078ea6d6..9df0702d 100644
--- a/content/2.defense-systems/gao_hhe.md
+++ b/content/2.defense-systems/gao_hhe.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Hhe
# Gao_Hhe
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_iet.md b/content/2.defense-systems/gao_iet.md
index bf817a95..8b7957a0 100644
--- a/content/2.defense-systems/gao_iet.md
+++ b/content/2.defense-systems/gao_iet.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Iet
# Gao_Iet
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_mza.md b/content/2.defense-systems/gao_mza.md
index 668ce15d..87a59887 100644
--- a/content/2.defense-systems/gao_mza.md
+++ b/content/2.defense-systems/gao_mza.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Mza
# Gao_Mza
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_ppl.md b/content/2.defense-systems/gao_ppl.md
index 107aaf34..06870207 100644
--- a/content/2.defense-systems/gao_ppl.md
+++ b/content/2.defense-systems/gao_ppl.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ppl
# Gao_Ppl
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_qat.md b/content/2.defense-systems/gao_qat.md
index 131275c5..aa56459f 100644
--- a/content/2.defense-systems/gao_qat.md
+++ b/content/2.defense-systems/gao_qat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Qat
# Gao_Qat
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_rl.md b/content/2.defense-systems/gao_rl.md
index c639d824..7f4ec5d5 100644
--- a/content/2.defense-systems/gao_rl.md
+++ b/content/2.defense-systems/gao_rl.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_RL
# Gao_RL
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_tery.md b/content/2.defense-systems/gao_tery.md
index 1c2611ad..c00fc534 100644
--- a/content/2.defense-systems/gao_tery.md
+++ b/content/2.defense-systems/gao_tery.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_TerY
# Gao_TerY
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_tmn.md b/content/2.defense-systems/gao_tmn.md
index bc179c08..948e8490 100644
--- a/content/2.defense-systems/gao_tmn.md
+++ b/content/2.defense-systems/gao_tmn.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Tmn
# Gao_Tmn
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_upx.md b/content/2.defense-systems/gao_upx.md
index 4469dd3f..6380af64 100644
--- a/content/2.defense-systems/gao_upx.md
+++ b/content/2.defense-systems/gao_upx.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Upx
# Gao_Upx
## Example of genomic structure
diff --git a/content/2.defense-systems/gaps1.md b/content/2.defense-systems/gaps1.md
new file mode 100644
index 00000000..317126a9
--- /dev/null
+++ b/content/2.defense-systems/gaps1.md
@@ -0,0 +1,21 @@
+---
+title: GAPS1
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS1
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps2.md b/content/2.defense-systems/gaps2.md
new file mode 100644
index 00000000..4b63ea07
--- /dev/null
+++ b/content/2.defense-systems/gaps2.md
@@ -0,0 +1,21 @@
+---
+title: GAPS2
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS2
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps4.md b/content/2.defense-systems/gaps4.md
new file mode 100644
index 00000000..982c9a60
--- /dev/null
+++ b/content/2.defense-systems/gaps4.md
@@ -0,0 +1,21 @@
+---
+title: GAPS4
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS4
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps6.md b/content/2.defense-systems/gaps6.md
new file mode 100644
index 00000000..36906584
--- /dev/null
+++ b/content/2.defense-systems/gaps6.md
@@ -0,0 +1,21 @@
+---
+title: GAPS6
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of defense islands may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS6
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gasdermin.md b/content/2.defense-systems/gasdermin.md
index 24e06d78..0f0fa0d5 100644
--- a/content/2.defense-systems/gasdermin.md
+++ b/content/2.defense-systems/gasdermin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# GasderMIN
# GasderMIN
## Example of genomic structure
diff --git a/content/2.defense-systems/hachiman.md b/content/2.defense-systems/hachiman.md
index f893d777..71b90a84 100644
--- a/content/2.defense-systems/hachiman.md
+++ b/content/2.defense-systems/hachiman.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Hachiman
# Hachiman
## Description
diff --git a/content/2.defense-systems/hna.md b/content/2.defense-systems/hna.md
new file mode 100644
index 00000000..1717a49b
--- /dev/null
+++ b/content/2.defense-systems/hna.md
@@ -0,0 +1,21 @@
+---
+title: Hna
+tableColumns:
+ article:
+ doi: 10.1016/j.chom.2023.01.010
+ abstract: |
+ There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
+---
+
+# Hna
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.chom.2023.01.010
+
+---
+::
diff --git a/content/2.defense-systems/isg15-like.md b/content/2.defense-systems/isg15-like.md
index aac319fd..d5894b86 100644
--- a/content/2.defense-systems/isg15-like.md
+++ b/content/2.defense-systems/isg15-like.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# ISG15-like
# ISG15-like
## Example of genomic structure
diff --git a/content/2.defense-systems/jukab.md b/content/2.defense-systems/jukab.md
new file mode 100644
index 00000000..e4c71ee1
--- /dev/null
+++ b/content/2.defense-systems/jukab.md
@@ -0,0 +1,21 @@
+---
+title: JukAB
+tableColumns:
+ article:
+ doi: 10.1101/2022.09.17.508391
+ abstract: |
+ Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
+---
+
+# JukAB
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2022.09.17.508391
+
+---
+::
diff --git a/content/2.defense-systems/kiwa.md b/content/2.defense-systems/kiwa.md
index e5826c28..044f267b 100644
--- a/content/2.defense-systems/kiwa.md
+++ b/content/2.defense-systems/kiwa.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Kiwa
# Kiwa
## Example of genomic structure
diff --git a/content/2.defense-systems/lamassu-fam.md b/content/2.defense-systems/lamassu-fam.md
index edf177a6..628f2f7b 100644
--- a/content/2.defense-systems/lamassu-fam.md
+++ b/content/2.defense-systems/lamassu-fam.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
---
-# Lamassu-Fam
# Lamassu-Fam
## Description
diff --git a/content/2.defense-systems/lit.md b/content/2.defense-systems/lit.md
index f3b1f404..63950ee2 100644
--- a/content/2.defense-systems/lit.md
+++ b/content/2.defense-systems/lit.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Other (Cleaves an elongation factor, inhibiting cellular translation
---
-# Lit
# Lit
## Example of genomic structure
diff --git a/content/2.defense-systems/mads.md b/content/2.defense-systems/mads.md
new file mode 100644
index 00000000..77782681
--- /dev/null
+++ b/content/2.defense-systems/mads.md
@@ -0,0 +1,21 @@
+---
+title: MADS
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.30.534895
+ abstract: |
+ The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
+---
+
+# MADS
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.30.534895
+
+---
+::
diff --git a/content/2.defense-systems/mazef.md b/content/2.defense-systems/mazef.md
new file mode 100644
index 00000000..1ee0682e
--- /dev/null
+++ b/content/2.defense-systems/mazef.md
@@ -0,0 +1,21 @@
+---
+title: MazEF
+tableColumns:
+ article:
+ doi: 10.1007/s00438-004-1048-y
+ abstract: |
+ The Escherichia coli gene pair mazEF is a regulatable chromosomal toxin-antitoxin module: mazF encodes a stable toxin and mazE encodes for a labile antitoxin that overcomes the lethal effect of MazF. Because MazE is labile, inhibition of mazE expression results in cell death. We studied the effect of mazEF on the development of bacteriophage P1 upon thermoinduction of the prophage P1CM c1ts and upon infection with virulent phage particles (P1vir). In several E. coli strains, we showed that the ?mazEF derivative strains produced significantly more phages than did the parent strain. In addition, upon induction of K38(P1CM c1ts), nearly all of the ?mazEF mutant cells lysed; in contrast, very few of the parental mazEF + K38 cells underwent lysis. However, most of these cells did not remain viable. Thus, while the ?mazEF cells die as a result of the lytic action of the phage, most of the mazEF + cells are killed by a different mechanism, apparently through the action of the chromosomal mazEF system itself. Furthermore, the introduction of lysogens into a growing non-lysogenic culture is lethal to ?mazEF but not for mazEF + cultures. Thus, although mazEF action causes individual cells to die, upon phage growth this is generally beneficial to the bacterial culture because it causes P1 phage exclusion from the bacterial population. These results provide additional support for the view that bacterial cultures may share some of the characteristics of multicellular organisms.
+---
+
+# MazEF
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1007/s00438-004-1048-y
+
+---
+::
diff --git a/content/2.defense-systems/menshen.md b/content/2.defense-systems/menshen.md
index b219cfe8..ec508e9f 100644
--- a/content/2.defense-systems/menshen.md
+++ b/content/2.defense-systems/menshen.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Menshen
# Menshen
## Example of genomic structure
diff --git a/content/2.defense-systems/mmb_gp29_gp30.md b/content/2.defense-systems/mmb_gp29_gp30.md
new file mode 100644
index 00000000..4003dd63
--- /dev/null
+++ b/content/2.defense-systems/mmb_gp29_gp30.md
@@ -0,0 +1,21 @@
+---
+title: MMB_gp29_gp30
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# MMB_gp29_gp30
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/mok_hok_sok.md b/content/2.defense-systems/mok_hok_sok.md
index 414f643a..33a83651 100644
--- a/content/2.defense-systems/mok_hok_sok.md
+++ b/content/2.defense-systems/mok_hok_sok.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Mok_Hok_Sok
# Mok_Hok_Sok
## Example of genomic structure
diff --git a/content/2.defense-systems/mokosh.md b/content/2.defense-systems/mokosh.md
index e46e8009..d455ce34 100644
--- a/content/2.defense-systems/mokosh.md
+++ b/content/2.defense-systems/mokosh.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Mokosh
# Mokosh
## Example of genomic structure
diff --git a/content/2.defense-systems/mqsrac.md b/content/2.defense-systems/mqsrac.md
index 934810f7..a4c93c5c 100644
--- a/content/2.defense-systems/mqsrac.md
+++ b/content/2.defense-systems/mqsrac.md
@@ -7,7 +7,6 @@ tableColumns:
Myriad bacterial anti-phage systems have been described and often the mechanism of programmed cell death is invoked for phage inhibition. However, there is little evidence of ‘suicide’ under physiological conditions for these systems. Instead of death to stop phage propagation, we show here that persister cells, i.e., transiently-tolerant, dormant, antibiotic-insensitive cells, are formed and survive using the Escherichia coli C496_10 tripartite toxin/antitoxin system MqsR/MqsA/MqsC to inhibit T2 phage. Specifically, MqsR/MqsA/MqsC inhibited T2 phage by one million-fold and reduced T2 titers by 500-fold. During T2 phage attack, in the presence of MqsR/MqsA/MqsC, evidence of persistence include the single-cell physiological change of reduced metabolism (via flow cytometry), increased spherical morphology (via transmission electron microscopy), and heterogeneous resuscitation. Critically, we found restriction-modification systems (primarily EcoK McrBC) work in concert with the toxin/antitoxin system to inactivate phage, likely while the cells are in the persister state. Phage attack also induces persistence in Klebsiella and Pseudomonas spp. Hence, phage attack invokes a stress response similar to antibiotics, starvation, and oxidation, which leads to persistence, and this dormant state likely allows restriction/modification systems to clear phage DNA.
---
-# MqsRAC
# MqsRAC
## Example of genomic structure
diff --git a/content/2.defense-systems/nhi.md b/content/2.defense-systems/nhi.md
index d3ed4b73..0f2ce747 100644
--- a/content/2.defense-systems/nhi.md
+++ b/content/2.defense-systems/nhi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (?)
---
-# Nhi
# Nhi
## Example of genomic structure
diff --git a/content/2.defense-systems/nixi.md b/content/2.defense-systems/nixi.md
index 0befa10a..5b44630e 100644
--- a/content/2.defense-systems/nixi.md
+++ b/content/2.defense-systems/nixi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# NixI
# NixI
## Example of genomic structure
diff --git a/content/2.defense-systems/nlr.md b/content/2.defense-systems/nlr.md
index 8b997d62..d8a572cf 100644
--- a/content/2.defense-systems/nlr.md
+++ b/content/2.defense-systems/nlr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# NLR
# NLR
## Example of genomic structure
diff --git a/content/2.defense-systems/old_exonuclease.md b/content/2.defense-systems/old_exonuclease.md
index 01c94eb8..069b112f 100644
--- a/content/2.defense-systems/old_exonuclease.md
+++ b/content/2.defense-systems/old_exonuclease.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Old_exonuclease
# Old_exonuclease
## Example of genomic structure
diff --git a/content/2.defense-systems/olokun.md b/content/2.defense-systems/olokun.md
index e3c07e3a..5b4693f4 100644
--- a/content/2.defense-systems/olokun.md
+++ b/content/2.defense-systems/olokun.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Olokun
# Olokun
## Example of genomic structure
diff --git a/content/2.defense-systems/pago.md b/content/2.defense-systems/pago.md
index eae65575..bf67ee06 100644
--- a/content/2.defense-systems/pago.md
+++ b/content/2.defense-systems/pago.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse (Nucleotide modifyingn, Membrane disrupting)
---
-# pAgo
# pAgo
## Example of genomic structure
diff --git a/content/2.defense-systems/panchino_gp28.md b/content/2.defense-systems/panchino_gp28.md
new file mode 100644
index 00000000..b1d1891b
--- /dev/null
+++ b/content/2.defense-systems/panchino_gp28.md
@@ -0,0 +1,21 @@
+---
+title: Panchino_gp28
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# Panchino_gp28
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/paris.md b/content/2.defense-systems/paris.md
index 8a1a858e..6a881f78 100644
--- a/content/2.defense-systems/paris.md
+++ b/content/2.defense-systems/paris.md
@@ -11,7 +11,7 @@ tableColumns:
---
# Paris
-# Paris
+
## Description
PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
diff --git a/content/2.defense-systems/pd-lambda-1.md b/content/2.defense-systems/pd-lambda-1.md
index e0894156..7eda7e6d 100644
--- a/content/2.defense-systems/pd-lambda-1.md
+++ b/content/2.defense-systems/pd-lambda-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-1
# PD-Lambda-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-2.md b/content/2.defense-systems/pd-lambda-2.md
index 063ee69f..44c4f60e 100644
--- a/content/2.defense-systems/pd-lambda-2.md
+++ b/content/2.defense-systems/pd-lambda-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-2
# PD-Lambda-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-3.md b/content/2.defense-systems/pd-lambda-3.md
index a79919bd..70004319 100644
--- a/content/2.defense-systems/pd-lambda-3.md
+++ b/content/2.defense-systems/pd-lambda-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-3
# PD-Lambda-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-4.md b/content/2.defense-systems/pd-lambda-4.md
index cbc0f346..416d9938 100644
--- a/content/2.defense-systems/pd-lambda-4.md
+++ b/content/2.defense-systems/pd-lambda-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-4
# PD-Lambda-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-5.md b/content/2.defense-systems/pd-lambda-5.md
index a13d1c07..eef05860 100644
--- a/content/2.defense-systems/pd-lambda-5.md
+++ b/content/2.defense-systems/pd-lambda-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-5
# PD-Lambda-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-6.md b/content/2.defense-systems/pd-lambda-6.md
index 190e8c01..6fe30c0b 100644
--- a/content/2.defense-systems/pd-lambda-6.md
+++ b/content/2.defense-systems/pd-lambda-6.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-6
# PD-Lambda-6
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-1.md b/content/2.defense-systems/pd-t4-1.md
index bf193777..7d9cdb30 100644
--- a/content/2.defense-systems/pd-t4-1.md
+++ b/content/2.defense-systems/pd-t4-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-1
# PD-T4-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-10.md b/content/2.defense-systems/pd-t4-10.md
index 30e09353..703a26ad 100644
--- a/content/2.defense-systems/pd-t4-10.md
+++ b/content/2.defense-systems/pd-t4-10.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-10
# PD-T4-10
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-2.md b/content/2.defense-systems/pd-t4-2.md
index 4c058c11..2dd4523e 100644
--- a/content/2.defense-systems/pd-t4-2.md
+++ b/content/2.defense-systems/pd-t4-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-2
# PD-T4-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-3.md b/content/2.defense-systems/pd-t4-3.md
index c61bcf03..49c94b69 100644
--- a/content/2.defense-systems/pd-t4-3.md
+++ b/content/2.defense-systems/pd-t4-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-3
# PD-T4-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-4.md b/content/2.defense-systems/pd-t4-4.md
index 7fafa2ee..d0b68a43 100644
--- a/content/2.defense-systems/pd-t4-4.md
+++ b/content/2.defense-systems/pd-t4-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-4
# PD-T4-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-5.md b/content/2.defense-systems/pd-t4-5.md
index c7e600d2..856b8818 100644
--- a/content/2.defense-systems/pd-t4-5.md
+++ b/content/2.defense-systems/pd-t4-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-5
# PD-T4-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-6.md b/content/2.defense-systems/pd-t4-6.md
index 0a63138b..b47fb45a 100644
--- a/content/2.defense-systems/pd-t4-6.md
+++ b/content/2.defense-systems/pd-t4-6.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-6
# PD-T4-6
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-7.md b/content/2.defense-systems/pd-t4-7.md
index 7279ce0a..8042bc4c 100644
--- a/content/2.defense-systems/pd-t4-7.md
+++ b/content/2.defense-systems/pd-t4-7.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-7
# PD-T4-7
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-8.md b/content/2.defense-systems/pd-t4-8.md
index 99dde5a1..34c7eccf 100644
--- a/content/2.defense-systems/pd-t4-8.md
+++ b/content/2.defense-systems/pd-t4-8.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-8
# PD-T4-8
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-9.md b/content/2.defense-systems/pd-t4-9.md
index c7425ba9..23424c29 100644
--- a/content/2.defense-systems/pd-t4-9.md
+++ b/content/2.defense-systems/pd-t4-9.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-9
# PD-T4-9
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-1.md b/content/2.defense-systems/pd-t7-1.md
index aea267ed..7374c6a0 100644
--- a/content/2.defense-systems/pd-t7-1.md
+++ b/content/2.defense-systems/pd-t7-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-1
# PD-T7-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-2.md b/content/2.defense-systems/pd-t7-2.md
index 936f9bd2..e2890ee3 100644
--- a/content/2.defense-systems/pd-t7-2.md
+++ b/content/2.defense-systems/pd-t7-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-2
# PD-T7-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-3.md b/content/2.defense-systems/pd-t7-3.md
index 68a80228..f7451c72 100644
--- a/content/2.defense-systems/pd-t7-3.md
+++ b/content/2.defense-systems/pd-t7-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-3
# PD-T7-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-4.md b/content/2.defense-systems/pd-t7-4.md
index f819d8a2..c7693137 100644
--- a/content/2.defense-systems/pd-t7-4.md
+++ b/content/2.defense-systems/pd-t7-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-4
# PD-T7-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-5.md b/content/2.defense-systems/pd-t7-5.md
index 859515e9..908910e3 100644
--- a/content/2.defense-systems/pd-t7-5.md
+++ b/content/2.defense-systems/pd-t7-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-5
# PD-T7-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pfiat.md b/content/2.defense-systems/pfiat.md
index 29b87685..7638ef7d 100644
--- a/content/2.defense-systems/pfiat.md
+++ b/content/2.defense-systems/pfiat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PfiAT
# PfiAT
## Example of genomic structure
diff --git a/content/2.defense-systems/phrann_gp29_gp30.md b/content/2.defense-systems/phrann_gp29_gp30.md
index 26f84206..3149e458 100644
--- a/content/2.defense-systems/phrann_gp29_gp30.md
+++ b/content/2.defense-systems/phrann_gp29_gp30.md
@@ -1,14 +1,14 @@
---
-title: phrann_gp29_gp30
+title: Phrann_gp29_gp30
tableColumns:
article:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
- Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
---
-# phrann_gp29_gp30
-# phrann_gp29_gp30
+# Phrann_gp29_gp30
+
## Example of genomic structure
The phrann_gp29_gp30 system is composed of 2 proteins: gp30 and, gp29.
diff --git a/content/2.defense-systems/pif.md b/content/2.defense-systems/pif.md
index 4c3fbfac..58444a2c 100644
--- a/content/2.defense-systems/pif.md
+++ b/content/2.defense-systems/pif.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting (?)
---
-# Pif
# Pif
## Example of genomic structure
diff --git a/content/2.defense-systems/prrc.md b/content/2.defense-systems/prrc.md
index 39e3b19c..317ff23b 100644
--- a/content/2.defense-systems/prrc.md
+++ b/content/2.defense-systems/prrc.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# PrrC
# PrrC
## Example of genomic structure
diff --git a/content/2.defense-systems/psyrta.md b/content/2.defense-systems/psyrta.md
index 2bba747f..616000fa 100644
--- a/content/2.defense-systems/psyrta.md
+++ b/content/2.defense-systems/psyrta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PsyrTA
# PsyrTA
## Example of genomic structure
diff --git a/content/2.defense-systems/pycsar.md b/content/2.defense-systems/pycsar.md
index 1bbf925f..7888ee67 100644
--- a/content/2.defense-systems/pycsar.md
+++ b/content/2.defense-systems/pycsar.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting, Nucleotides modifying
---
-# Pycsar
# Pycsar
## Example of genomic structure
diff --git a/content/2.defense-systems/radar.md b/content/2.defense-systems/radar.md
index 191d0d51..4305d715 100644
--- a/content/2.defense-systems/radar.md
+++ b/content/2.defense-systems/radar.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RADAR
# RADAR
## Description
diff --git a/content/2.defense-systems/retron.md b/content/2.defense-systems/retron.md
index 9fd21f64..ab9d432b 100644
--- a/content/2.defense-systems/retron.md
+++ b/content/2.defense-systems/retron.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse
---
-# Retron
# Retron
## Description
diff --git a/content/2.defense-systems/rexab.md b/content/2.defense-systems/rexab.md
index fbc34b38..46cff76a 100644
--- a/content/2.defense-systems/rexab.md
+++ b/content/2.defense-systems/rexab.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# RexAB
# RexAB
## Example of genomic structure
diff --git a/content/2.defense-systems/rloc.md b/content/2.defense-systems/rloc.md
index 68d1fc32..a413fe3a 100644
--- a/content/2.defense-systems/rloc.md
+++ b/content/2.defense-systems/rloc.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RloC
# RloC
## Example of genomic structure
diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md
index 70abce91..60dd9da7 100644
--- a/content/2.defense-systems/rm.md
+++ b/content/2.defense-systems/rm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RM
# RM
## Example of genomic structure
diff --git a/content/2.defense-systems/rnlab.md b/content/2.defense-systems/rnlab.md
index c011da5f..0f9acc42 100644
--- a/content/2.defense-systems/rnlab.md
+++ b/content/2.defense-systems/rnlab.md
@@ -4,13 +4,12 @@ tableColumns:
article:
doi: 10.1534/genetics.110.121798
abstract: |
- RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA–rnlB define a new toxin–antitoxin (TA) system.
+ RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
---
-# RnlAB
# RnlAB
## Example of genomic structure
diff --git a/content/2.defense-systems/rosmerta.md b/content/2.defense-systems/rosmerta.md
index 89ad12cb..d9ffb12f 100644
--- a/content/2.defense-systems/rosmerta.md
+++ b/content/2.defense-systems/rosmerta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# RosmerTA
# RosmerTA
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_2tm_1tm_tir.md b/content/2.defense-systems/rst_2tm_1tm_tir.md
index bcdaa389..761b4a4f 100644
--- a/content/2.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/2.defense-systems/rst_2tm_1tm_tir.md
@@ -7,7 +7,6 @@ tableColumns:
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.
---
-# Rst_2TM_1TM_TIR
# Rst_2TM_1TM_TIR
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_3hp.md b/content/2.defense-systems/rst_3hp.md
index c1098654..b31ab1f8 100644
--- a/content/2.defense-systems/rst_3hp.md
+++ b/content/2.defense-systems/rst_3hp.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_3HP
# Rst_3HP
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_duf4238.md b/content/2.defense-systems/rst_duf4238.md
index bb167151..262546f1 100644
--- a/content/2.defense-systems/rst_duf4238.md
+++ b/content/2.defense-systems/rst_duf4238.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_DUF4238
# Rst_DUF4238
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_gop_beta_cll.md b/content/2.defense-systems/rst_gop_beta_cll.md
index c6049f36..22080679 100644
--- a/content/2.defense-systems/rst_gop_beta_cll.md
+++ b/content/2.defense-systems/rst_gop_beta_cll.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_gop_beta_cll
# Rst_gop_beta_cll
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_helicaseduf2290.md b/content/2.defense-systems/rst_helicaseduf2290.md
index 51a229be..d935ef2d 100644
--- a/content/2.defense-systems/rst_helicaseduf2290.md
+++ b/content/2.defense-systems/rst_helicaseduf2290.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_HelicaseDUF2290
# Rst_HelicaseDUF2290
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_hydrolase-3tm.md b/content/2.defense-systems/rst_hydrolase-3tm.md
index be86ec80..00edbe61 100644
--- a/content/2.defense-systems/rst_hydrolase-3tm.md
+++ b/content/2.defense-systems/rst_hydrolase-3tm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_Hydrolase-3Tm
# Rst_Hydrolase-3Tm
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_rt-nitrilase-tm.md b/content/2.defense-systems/rst_rt-nitrilase-tm.md
index 5522003e..a4453e14 100644
--- a/content/2.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/2.defense-systems/rst_rt-nitrilase-tm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_RT-nitrilase-Tm
# Rst_RT-nitrilase-Tm
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_tir-nlr.md b/content/2.defense-systems/rst_tir-nlr.md
index 59f5c281..c7e52d93 100644
--- a/content/2.defense-systems/rst_tir-nlr.md
+++ b/content/2.defense-systems/rst_tir-nlr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_TIR-NLR
# Rst_TIR-NLR
## Example of genomic structure
diff --git a/content/2.defense-systems/sanata.md b/content/2.defense-systems/sanata.md
index 54a92cf6..d3867a55 100644
--- a/content/2.defense-systems/sanata.md
+++ b/content/2.defense-systems/sanata.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SanaTA
# SanaTA
## Example of genomic structure
diff --git a/content/2.defense-systems/sefir.md b/content/2.defense-systems/sefir.md
index e299110e..b6b84790 100644
--- a/content/2.defense-systems/sefir.md
+++ b/content/2.defense-systems/sefir.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SEFIR
# SEFIR
## Description
The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage phi29 [1].
diff --git a/content/2.defense-systems/septu.md b/content/2.defense-systems/septu.md
index 487f76c7..17e4a741 100644
--- a/content/2.defense-systems/septu.md
+++ b/content/2.defense-systems/septu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Septu
# Septu
## Example of genomic structure
diff --git a/content/2.defense-systems/shango.md b/content/2.defense-systems/shango.md
index 399734e0..0ce65b43 100644
--- a/content/2.defense-systems/shango.md
+++ b/content/2.defense-systems/shango.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Shango
# Shango
## Description
@@ -67,4 +66,4 @@ Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J
[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690)
-[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
\ No newline at end of file
+[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
diff --git a/content/2.defense-systems/shedu.md b/content/2.defense-systems/shedu.md
index d775b451..6b939d87 100644
--- a/content/2.defense-systems/shedu.md
+++ b/content/2.defense-systems/shedu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Shedu
# Shedu
## Example of genomic structure
diff --git a/content/2.defense-systems/shosta.md b/content/2.defense-systems/shosta.md
index 9c1c779c..f4b0e62d 100644
--- a/content/2.defense-systems/shosta.md
+++ b/content/2.defense-systems/shosta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# ShosTA
# ShosTA
## Example of genomic structure
diff --git a/content/2.defense-systems/sofic.md b/content/2.defense-systems/sofic.md
index 3d1ca7e5..b8d6f66d 100644
--- a/content/2.defense-systems/sofic.md
+++ b/content/2.defense-systems/sofic.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SoFIC
# SoFIC
## Example of genomic structure
diff --git a/content/2.defense-systems/spbk.md b/content/2.defense-systems/spbk.md
index d7b93c17..221db9e4 100644
--- a/content/2.defense-systems/spbk.md
+++ b/content/2.defense-systems/spbk.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SpbK
# SpbK
## Example of genomic structure
diff --git a/content/2.defense-systems/sspbcde.md b/content/2.defense-systems/sspbcde.md
index fc7e5865..38618b53 100644
--- a/content/2.defense-systems/sspbcde.md
+++ b/content/2.defense-systems/sspbcde.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# SspBCDE
# SspBCDE
## Example of genomic structure
diff --git a/content/2.defense-systems/stk2.md b/content/2.defense-systems/stk2.md
index 3a1fa18f..0cd7d51e 100644
--- a/content/2.defense-systems/stk2.md
+++ b/content/2.defense-systems/stk2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Other (protein modifying)
---
-# Stk2
# Stk2
## Description
diff --git a/content/2.defense-systems/thoeris.md b/content/2.defense-systems/thoeris.md
index 51772f36..8ccf5b66 100644
--- a/content/2.defense-systems/thoeris.md
+++ b/content/2.defense-systems/thoeris.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Thoeris
# Thoeris
## Example of genomic structure
diff --git a/content/2.defense-systems/tiamat.md b/content/2.defense-systems/tiamat.md
index 169abf12..0959ef39 100644
--- a/content/2.defense-systems/tiamat.md
+++ b/content/2.defense-systems/tiamat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Tiamat
# Tiamat
## Example of genomic structure
diff --git a/content/2.defense-systems/uzume.md b/content/2.defense-systems/uzume.md
index 167eb495..11e72a49 100644
--- a/content/2.defense-systems/uzume.md
+++ b/content/2.defense-systems/uzume.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Uzume
# Uzume
## Example of genomic structure
diff --git a/content/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md
index 8bf85a84..46a2fdf9 100644
--- a/content/2.defense-systems/viperin.md
+++ b/content/2.defense-systems/viperin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Viperin
# Viperin
## Description
diff --git a/content/2.defense-systems/wadjet.md b/content/2.defense-systems/wadjet.md
index 1b77a8a7..8fa050f0 100644
--- a/content/2.defense-systems/wadjet.md
+++ b/content/2.defense-systems/wadjet.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# Wadjet
# Wadjet
## Example of genomic structure
diff --git a/content/2.defense-systems/zorya.md b/content/2.defense-systems/zorya.md
index f5acde75..6cb8efbe 100644
--- a/content/2.defense-systems/zorya.md
+++ b/content/2.defense-systems/zorya.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Zorya
# Zorya
## Example of genomic structure
--
GitLab