From 92f434329f3663fe622c54b71b458b1a57faf700 Mon Sep 17 00:00:00 2001
From: ftesson <florian.tesson@pasteur.fr>
Date: Fri, 17 Nov 2023 14:59:01 +0100
Subject: [PATCH] Put relevant abstract in frontmatter
---
content/3.defense-systems/abic.md | 13 ++---------
content/3.defense-systems/abid.md | 13 ++---------
content/3.defense-systems/abie.md | 14 ++---------
content/3.defense-systems/abig.md | 13 ++---------
content/3.defense-systems/abih.md | 14 ++---------
content/3.defense-systems/abii.md | 12 ++--------
content/3.defense-systems/abij.md | 13 ++---------
content/3.defense-systems/abik.md | 14 ++---------
content/3.defense-systems/abil.md | 13 ++---------
content/3.defense-systems/abin.md | 12 ++--------
content/3.defense-systems/abio.md | 13 ++---------
content/3.defense-systems/abip2.md | 14 ++---------
content/3.defense-systems/abiq.md | 14 ++---------
content/3.defense-systems/abir.md | 13 ++---------
content/3.defense-systems/abit.md | 13 ++---------
content/3.defense-systems/abiu.md | 13 ++---------
content/3.defense-systems/abiv.md | 13 ++---------
content/3.defense-systems/abiz.md | 12 ++--------
content/3.defense-systems/aditi.md | 12 ++--------
content/3.defense-systems/azaca.md | 12 ++--------
content/3.defense-systems/borvo.md | 12 ++--------
content/3.defense-systems/bsta.md | 16 ++-----------
content/3.defense-systems/bunzi.md | 11 ++-------
.../3.defense-systems/butters_gp30_gp31.md | 10 ++------
content/3.defense-systems/butters_gp57r.md | 10 ++------
content/3.defense-systems/caprel.md | 16 ++-----------
content/3.defense-systems/card_nlr.md | 11 ++-------
content/3.defense-systems/cbass.md | 16 ++-----------
content/3.defense-systems/charlie_gp32.md | 10 ++------
content/3.defense-systems/dartg.md | 12 ++--------
content/3.defense-systems/dazbog.md | 11 ++-------
content/3.defense-systems/dctpdeaminase.md | 11 ++-------
content/3.defense-systems/dgtpase.md | 12 ++--------
content/3.defense-systems/disarm.md | 13 ++---------
content/3.defense-systems/dmdde.md | 11 ++-------
content/3.defense-systems/dnd.md | 13 ++---------
content/3.defense-systems/dodola.md | 12 ++--------
content/3.defense-systems/dpd.md | 12 ++--------
content/3.defense-systems/drt.md | 13 ++---------
content/3.defense-systems/druantia.md | 12 ++--------
content/3.defense-systems/dsr.md | 13 ++---------
content/3.defense-systems/eleos.md | 12 ++--------
content/3.defense-systems/fs_giy_yig.md | 10 ++------
content/3.defense-systems/fs_hepn_tm.md | 10 ++------
content/3.defense-systems/fs_hp.md | 10 ++------
content/3.defense-systems/fs_hp_sdh_sah.md | 11 ++-------
content/3.defense-systems/fs_hsdr_like.md | 10 ++------
content/3.defense-systems/fs_sma.md | 11 ++-------
content/3.defense-systems/gabija.md | 13 ++---------
content/3.defense-systems/gao_ape.md | 11 ++-------
content/3.defense-systems/gao_her.md | 12 ++--------
content/3.defense-systems/gao_hhe.md | 12 ++--------
content/3.defense-systems/gao_iet.md | 12 ++--------
content/3.defense-systems/gao_mza.md | 12 ++--------
content/3.defense-systems/gao_ppl.md | 11 ++-------
content/3.defense-systems/gao_qat.md | 12 ++--------
content/3.defense-systems/gao_rl.md | 12 ++--------
content/3.defense-systems/gao_tery.md | 11 ++-------
content/3.defense-systems/gao_tmn.md | 11 ++-------
content/3.defense-systems/gao_upx.md | 11 ++-------
content/3.defense-systems/gaps1.md | 10 ++------
content/3.defense-systems/gaps2.md | 11 ++-------
content/3.defense-systems/gaps4.md | 10 ++------
content/3.defense-systems/gaps6.md | 10 ++------
content/3.defense-systems/gasdermin.md | 11 ++-------
content/3.defense-systems/hachiman.md | 19 ++-------------
content/3.defense-systems/hna.md | 11 ++-------
content/3.defense-systems/isg15-like.md | 11 ++-------
content/3.defense-systems/jukab.md | 11 ++-------
content/3.defense-systems/kiwa.md | 12 ++--------
content/3.defense-systems/lamassu-fam.md | 23 ++-----------------
content/3.defense-systems/lit.md | 14 ++---------
content/3.defense-systems/mads.md | 11 ++-------
content/3.defense-systems/mazef.md | 11 ++-------
content/3.defense-systems/menshen.md | 12 ++--------
content/3.defense-systems/mmb_gp29_gp30.md | 10 ++------
content/3.defense-systems/mok_hok_sok.md | 12 ++--------
content/3.defense-systems/mokosh.md | 12 ++--------
content/3.defense-systems/mqsrac.md | 3 +--
content/3.defense-systems/nhi.md | 12 ++--------
content/3.defense-systems/nixi.md | 11 ++-------
content/3.defense-systems/nlr.md | 12 ++--------
content/3.defense-systems/old_exonuclease.md | 7 +-----
content/3.defense-systems/olokun.md | 11 ++-------
content/3.defense-systems/pago.md | 17 ++------------
content/3.defense-systems/panchino_gp28.md | 11 ++-------
content/3.defense-systems/paris.md | 12 ++--------
content/3.defense-systems/pd-lambda-1.md | 12 ++--------
content/3.defense-systems/pd-lambda-2.md | 12 ++--------
content/3.defense-systems/pd-lambda-3.md | 12 ++--------
content/3.defense-systems/pd-lambda-4.md | 11 ++-------
content/3.defense-systems/pd-lambda-5.md | 12 ++--------
content/3.defense-systems/pd-lambda-6.md | 11 ++-------
content/3.defense-systems/pd-t4-1.md | 12 ++--------
content/3.defense-systems/pd-t4-10.md | 11 ++-------
content/3.defense-systems/pd-t4-2.md | 12 ++--------
content/3.defense-systems/pd-t4-3.md | 11 ++-------
content/3.defense-systems/pd-t4-4.md | 12 ++--------
content/3.defense-systems/pd-t4-5.md | 12 ++--------
content/3.defense-systems/pd-t4-6.md | 12 ++--------
content/3.defense-systems/pd-t4-7.md | 11 ++-------
content/3.defense-systems/pd-t4-8.md | 12 ++--------
content/3.defense-systems/pd-t4-9.md | 12 ++--------
content/3.defense-systems/pd-t7-1.md | 11 ++-------
content/3.defense-systems/pd-t7-2.md | 12 ++--------
content/3.defense-systems/pd-t7-3.md | 11 ++-------
content/3.defense-systems/pd-t7-4.md | 12 ++--------
content/3.defense-systems/pd-t7-5.md | 11 ++-------
content/3.defense-systems/pfiat.md | 12 ++--------
content/3.defense-systems/phrann_gp29_gp30.md | 12 ++--------
content/3.defense-systems/pif.md | 14 ++---------
content/3.defense-systems/prrc.md | 13 ++---------
content/3.defense-systems/psyrta.md | 13 ++---------
content/3.defense-systems/pycsar.md | 12 ++--------
content/3.defense-systems/radar.md | 16 ++-----------
content/3.defense-systems/retron.md | 13 ++---------
content/3.defense-systems/rexab.md | 12 ++--------
content/3.defense-systems/rloc.md | 13 ++---------
content/3.defense-systems/rm.md | 12 ++--------
content/3.defense-systems/rnlab.md | 12 ++--------
content/3.defense-systems/rosmerta.md | 12 ++--------
content/3.defense-systems/rst_2tm_1tm_tir.md | 12 ++--------
content/3.defense-systems/rst_3hp.md | 11 ++-------
content/3.defense-systems/rst_duf4238.md | 12 ++--------
content/3.defense-systems/rst_gop_beta_cll.md | 12 ++--------
.../3.defense-systems/rst_helicaseduf2290.md | 12 ++--------
.../3.defense-systems/rst_hydrolase-3tm.md | 12 ++--------
.../3.defense-systems/rst_rt-nitrilase-tm.md | 12 ++--------
content/3.defense-systems/rst_tir-nlr.md | 12 ++--------
content/3.defense-systems/sanata.md | 12 ++--------
content/3.defense-systems/sefir.md | 17 ++------------
content/3.defense-systems/septu.md | 14 ++---------
content/3.defense-systems/shango.md | 22 ++----------------
content/3.defense-systems/shedu.md | 12 ++--------
content/3.defense-systems/shosta.md | 14 ++---------
content/3.defense-systems/sofic.md | 12 ++--------
content/3.defense-systems/spbk.md | 12 ++--------
content/3.defense-systems/sspbcde.md | 13 ++---------
content/3.defense-systems/stk2.md | 12 ++--------
content/3.defense-systems/thoeris.md | 13 ++---------
content/3.defense-systems/tiamat.md | 12 ++--------
content/3.defense-systems/uzume.md | 11 ++-------
content/3.defense-systems/viperin.md | 12 ++--------
content/3.defense-systems/wadjet.md | 12 ++--------
content/3.defense-systems/zorya.md | 13 ++---------
145 files changed, 288 insertions(+), 1478 deletions(-)
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index 3e70eaa0..d0d0f008 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF16872
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiC
@@ -54,14 +56,3 @@ A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Klebsiella
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index e2a37864..6e389247 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiD
@@ -48,14 +50,3 @@ AbiD systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index f2b7575e..eb657d76 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiE
@@ -67,15 +69,3 @@ AbiE systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkt1419
-
----
-::
-
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index f3958bf6..046dc968 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10899, PF16873
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiG
@@ -55,14 +57,3 @@ AbiG systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abih.md b/content/3.defense-systems/abih.md
index a5957d00..8b51c5cf 100644
--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14253
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiH
@@ -50,15 +52,3 @@ AbiH systems were experimentally validated using:
A system from *lactococci* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1111/j.1574-6968.1996.tb08446.x
-
----
-::
-
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index 1e1d819a..fea7a1be 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiI
@@ -49,13 +51,3 @@ AbiI systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 1e5f58de..19a1441f 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14355
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiJ
@@ -50,14 +52,3 @@ AbiJ systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 9bb989a3..9806f66d 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiK
@@ -50,15 +52,3 @@ AbiK systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
-
----
-::
-
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index 2453dab6..0c21f903 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304, PF13707
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiL
@@ -57,14 +59,3 @@ AbiL systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index f356f965..e9c798a2 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiN
@@ -49,13 +51,3 @@ AbiN systems were experimentally validated using:
A system from *lactococcal prophage* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 5547f58a..9164a091 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01443, PF09848
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiO
@@ -50,14 +52,3 @@ AbiO systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index c0f80220..98dad857 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiP2
@@ -52,15 +54,3 @@ Subsystem RT-Abi-P2 with a system from *Escherichia coli* in *Escherichia coli*
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
-
----
-::
-
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index dab1ef15..a821c24b 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13958
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiQ
@@ -50,15 +52,3 @@ AbiQ systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1128/AEM.64.12.4748-4756.1998
-
----
-::
-
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index b856d890..c3dcb75d 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiR
@@ -64,14 +66,3 @@ AbiR systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against c2 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 296cfe9b..6615b17c 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18864
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiT
@@ -57,14 +59,3 @@ AbiT systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index f01863b3..f78fa37a 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10592
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiU
@@ -50,14 +52,3 @@ AbiU systems were experimentally validated using:
A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
-
----
-::
-
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index 36136ea3..b5927dfc 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18728
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiV
@@ -50,14 +52,3 @@ AbiV systems were experimentally validated using:
A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against sk1, p2, jj50, P008, bIL170, c2, bIL67, ml3, eb1 (Haaber et al., 2008)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1128/AEM.00780-08
-
----
-::
-
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index 4497aa72..1e5e23f2 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Membrane disrupting
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
---
# AbiZ
@@ -49,13 +51,3 @@ AbiZ systems were experimentally validated using:
A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against Phi31.2, ul36, phi31, phi48, phi31.1, Q30, Q36, Q33, phi50, phi48 (Durmaz et al., 2007)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1128/JB.00904-06
-
----
-::
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index f7a1e705..360dfef7 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18928
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Aditi
@@ -57,13 +59,3 @@ Aditi systems were experimentally validated using:
A system from *Saccharibacillus kuerlensis* in *Bacillus subtilis* has an anti-phage effect against phi105, Rho14, SPP1 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 51d8cf1f..2f1da606 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00271
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Azaca
@@ -66,13 +68,3 @@ A system from *Bacillus massilioanorexius* in *Escherichia coli* has an anti-pha
A system from *Bacillus massilioanorexius* in *Bacillus subtilis* has an anti-phage effect against SBSphiC (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 2b6c3368..05dc49b4 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF12770
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Borvo
@@ -50,13 +52,3 @@ Borvo systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 9d021f99..a037bd48 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2021.09.002
---
# BstA
@@ -81,17 +83,3 @@ A system from *Escherichia coli* in *Salmonella Typhimurium* has an anti-phage e
A system from *Salmonella Typhimurium's BTP1* in *Escherichia coli* has an anti-phage effect against Lambda, Phi80, P1vir, T7 (Owen et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2021.09.002
-
----
-::
-
-
-## References
-
-1. Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. PMID: 34597593; PMCID: PMC8585504.
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index 9fc80b18..18b2b78e 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Bunzi
@@ -56,12 +58,3 @@ Bunzi systems were experimentally validated using:
A system from *Ligilactobacillus animalis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1 (Jumbo) (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/butters_gp30_gp31.md b/content/3.defense-systems/butters_gp30_gp31.md
index 48881175..1fc19bc4 100644
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1128/mSystems.00534-20
---
# Butters_gp30_gp31
@@ -30,11 +32,3 @@ dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31-plddts_84.75463.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1128/mSystems.00534-20
-
----
-::
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index ad95f49b..45b8d07b 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1101/2023.01.03.522681
---
# Butters_gp57r
@@ -23,11 +25,3 @@ dataUrl: /butters_gp57r/Butters_gp57r__gp57r-plddts_90.7432.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.01.03.522681
-
----
-::
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 7ed9c7fa..dec211bd 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
PFAM: PF04607
+relevantAbstracts:
+ - doi: 10.1038/s41586-022-05444-z
---
# CapRel
@@ -66,17 +68,3 @@ A system from *Enterobacter chengduensis* in *Escherichia coli* has an anti-phag
A system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against SECphi18 (Zhang et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-022-05444-z
-
----
-::
-
-
-## References
-Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature. 2022 Dec;612(7938):132-140. doi: 10.1038/s41586-022-05444-z. Epub 2022 Nov 16. PMID: 36385533.
-
diff --git a/content/3.defense-systems/card_nlr.md b/content/3.defense-systems/card_nlr.md
index 6e30f08a..88b8b390 100644
--- a/content/3.defense-systems/card_nlr.md
+++ b/content/3.defense-systems/card_nlr.md
@@ -7,18 +7,11 @@ tableColumns:
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.
PFAM: PF00082, PF00089, PF00614, PF01223, PF13091, PF13191, PF13365
+relevantAbstracts:
+ - doi: 10.1101/2023.05.28.542683
---
# CARD_NLR
## To do
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.05.28.542683
-
----
-::
-
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 12f93515..1837c383 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Signaling molecules
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
PFAM: PF00004, PF00027, PF00899, PF01048, PF01734, PF06508, PF10137, PF14461, PF14464, PF18134, PF18138, PF18144, PF18145, PF18153, PF18159, PF18167, PF18173, PF18178, PF18179, PF18186, PF18303, PF18967
+relevantAbstracts:
+ - doi: 10.1016/j.molcel.2019.12.009
---
# CBASS
@@ -179,17 +181,3 @@ A system from *Enterobacter cloacae* in *Escherichia coli* has an anti-phage eff
A system from *Pseudomonas aeruginosa* in *Pseudomonas aeruginosa* has an anti-phage effect against PaMx41, PaMx33, PaMx35, PaMx43 (Huiting et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.molcel.2019.12.009
- - doi: 10.1016/j.molcel.2021.10.020
- - doi: 10.1038/s41564-020-0777-y
- - doi: 10.1038/s41586-019-1605-5
- - doi: 10.1038/s41586-020-2719-5
-
----
-::
-
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 45d8ee98..b710df9d 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# Charlie_gp32
@@ -23,11 +25,3 @@ dataUrl: /charlie_gp32/Charlie_gp32__gp32-plddts_82.99758.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
-
----
-::
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 79546aa6..5ef91153 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading (ADP-ribosylation)
PFAM: PF01661, PF14487
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01153-5
---
# DarTG
@@ -57,13 +59,3 @@ DarTG systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against RB69, T5, SECphi18, Lust (Leroux et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01153-5
-
----
-::
-
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index c771b8e9..39dbb54f 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Dazbog
@@ -74,12 +76,3 @@ A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect a
A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against Fado, SPR (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index d8a12c5a..74ea41fb 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF00383, PF14437
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01162-4
---
# dCTPdeaminase
@@ -68,12 +70,3 @@ Subsystem AvcID with a system from *Vibrio parahaemolyticus* in *Escherichia col
Subsystem AvcID with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against T2, T3 (Hsueh et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01162-4
----
-::
-
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index b3413fc8..b1f9cc31 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direc
Effector: Nucleotide modifying
PFAM: PF01966, PF13286
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01162-4
---
# dGTPase
@@ -56,13 +58,3 @@ A system from *Pseudoalteromonas luteoviolacea* in *Escherichia coli* has an ant
A system from *Shewanella putrefaciens* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2, T6, T7, SECphi17 (Tal et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01162-4
-
----
-::
-
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index 295c7d93..ffb59f3f 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
+relevantAbstracts:
+ - doi: 10.1038/s41467-022-30673-1
---
# DISARM
@@ -63,14 +65,3 @@ A system from *Bacillus paralicheniformis* in *Bacillus subtilis* has an anti-ph
A system from *Serratia sp. SCBI* in *Escherichia coli* has an anti-phage effect against T1, Nami, T7, M13 (Aparicio-Maldonado et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41467-022-30673-1
- - doi: 10.1038/s41564-017-0051-0
-
----
-::
-
diff --git a/content/3.defense-systems/dmdde.md b/content/3.defense-systems/dmdde.md
index a52da2f6..3d919a8b 100644
--- a/content/3.defense-systems/dmdde.md
+++ b/content/3.defense-systems/dmdde.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1038/s41586-022-04546-y
---
# DmdDE
@@ -47,12 +49,3 @@ dataUrl: /dmdde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-022-04546-y
-
----
-::
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index a6e2ffb0..d9a89471 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
+relevantAbstracts:
+ - doi: 10.1038/nchembio.2007.39
---
# Dnd
@@ -140,14 +142,3 @@ Dnd systems were experimentally validated using:
Subsystem DndCDEA-PbeABCD with a system from *Halalkalicoccus jeotgali* in *Natrinema sp. CJ7-F* has an anti-phage effect against SNJ1 (Xiong et al., 2019)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nchembio.2007.39
- - doi: 10.1038/s41467-019-09390-9
-
----
-::
-
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 83277bd8..68cee01d 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00004, PF07724, PF07728
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Dodola
@@ -57,13 +59,3 @@ Dodola systems were experimentally validated using:
A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SPP1 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index 62211f4e..0c3d7491 100644
--- a/content/3.defense-systems/dpd.md
+++ b/content/3.defense-systems/dpd.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF00176, PF00270, PF00271, PF01227, PF01242, PF04055, PF04851, PF06508, PF13091, PF13353, PF13394, PF14072
+relevantAbstracts:
+ - doi: 10.1073/pnas.1518570113
---
# Dpd
@@ -120,13 +122,3 @@ dataUrl: /dpd/Dpd,Dpd__DpdK,0,DF-plddts_93.96529.pdb
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1073/pnas.1518570113
-
----
-::
-
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index c2247f60..2ec5d5d6 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1093/nar/gkac467
---
# DRT
@@ -178,14 +180,3 @@ Subsystem RT(UG7) (Type 8) with a system from *Escherichia coli* in *Escherichia
Subsystem RT (UG28) (Type 9) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1093/nar/gkac467
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 7306c6b0..c9de12be 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Druantia
@@ -132,13 +134,3 @@ Druantia systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, P1, Lambda, T3, T7, PhiV-1, Lambdavir, SECphi18, SECphi27 (Gao et al., 2020; Doron et al., 2018)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 22ee59e3..3b49a999 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF13289
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01207-8
---
# Dsr
@@ -69,14 +71,3 @@ Subsystem DSR2 with a system from *Bacillus subtilis* in *Bacillus subtilis * ha
Subsystem DSR1 with a system from *Bacillus subtilis* in *Bacillus subtilis * has an anti-phage effect against phi29 (Garb et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01207-8
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index d60586e6..c6cbbadc 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00350, PF01926, PF18709
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Eleos
@@ -59,13 +61,3 @@ Eleos systems were experimentally validated using:
A system from *Bacillus vietnamensis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1(Jumbo) (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 5cde4e31..9342d98a 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_GIY_YIG
@@ -23,11 +25,3 @@ dataUrl: /fs_giy_yig/FS_GIY_YIG__GIY_YIG-plddts_93.05664.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index e147130b..165e6d84 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HEPN_TM
@@ -30,11 +32,3 @@ dataUrl: /fs_hepn_tm/FS_HEPN_TM__TM-plddts_90.28126.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index ee17cc9a..cfe0ccfa 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HP
@@ -23,11 +25,3 @@ dataUrl: /fs_hp/FS_HP__HP-plddts_94.44828.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 49fb231d..82ced52d 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF01972
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HP_SDH_sah
@@ -31,12 +33,3 @@ dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah-plddts_95.32024.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
-
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index ad60e69e..b2f4f5ff 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_HsdR_like
@@ -30,11 +32,3 @@ dataUrl: /fs_hsdr_like/FS_HsdR_like__HdrR-plddts_88.7069.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 55512c53..fe279a9d 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF02452
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.07.014
---
# FS_Sma
@@ -24,12 +26,3 @@ dataUrl: /fs_sma/FS_Sma__Sma-plddts_94.14969.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.07.014
-
----
-::
-
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index d961bb83..c8a48a03 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Degrading nucleic acids
PFAM: PF00580, PF11398, PF13175, PF13245, PF13304, PF13361, PF13476
+relevantAbstracts:
+ - doi: 10.1093/nar/gkab277
---
# Gabija
@@ -71,14 +73,3 @@ A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect
A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1093/nar/gkab277
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index 22b3714d..f0be2f71 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Ape
@@ -49,12 +51,3 @@ Gao_Ape systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T3, T7, PhiV-1 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index 87bee93f..40e30c02 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01935, PF10412, PF13289
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Her
@@ -79,13 +81,3 @@ Subsystem SIR2 + HerA with a system from *Escherichia coli* in *Escherichia coli
Subsystem DUF4297 + HerA with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1, Lambda, T3, T7 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 2ad765ff..864731c5 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF04480, PF13086, PF13087, PF13195, PF18741
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Hhe
@@ -50,13 +52,3 @@ Gao_Hhe systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 29aab706..2528e419 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00004, PF00082
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Iet
@@ -57,13 +59,3 @@ Gao_Iet systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_mza.md b/content/3.defense-systems/gao_mza.md
index e8eab809..2b33a1c5 100644
--- a/content/3.defense-systems/gao_mza.md
+++ b/content/3.defense-systems/gao_mza.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00023, PF04542, PF04545, PF10592, PF10593, PF13589, PF13606, PF14390
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Mza
@@ -78,13 +80,3 @@ Gao_Mza systems were experimentally validated using:
A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, Lambda, M13 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index 818c4a67..21d85d3d 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Ppl
@@ -49,12 +51,3 @@ Gao_Ppl systems were experimentally validated using:
A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index 3199a3e1..2feb9bd0 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01026, PF07693
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Qat
@@ -71,13 +73,3 @@ Gao_Qat systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_rl.md b/content/3.defense-systems/gao_rl.md
index a4c90e5b..47acada5 100644
--- a/content/3.defense-systems/gao_rl.md
+++ b/content/3.defense-systems/gao_rl.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF04465, PF04851, PF06634, PF12635, PF13091, PF13287, PF13290
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_RL
@@ -71,13 +73,3 @@ Gao_RL systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda, M13 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 7d4f8c1c..3979ae25 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_TerY
@@ -63,12 +65,3 @@ Gao_TerY systems were experimentally validated using:
A system from *Citrobacter gillenii* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index 339529f5..c4c4dc31 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Tmn
@@ -49,12 +51,3 @@ Gao_Tmn systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, P1, PhiV-1, PhiX (Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index 61497b90..f9fea3f5 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# Gao_Upx
@@ -49,12 +51,3 @@ Gao_Upx systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, PhiV-1(Gao et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index ead7f405..95395e20 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS1
@@ -23,11 +25,3 @@ dataUrl: /gaps1/GAPS1__GAPS1-plddts_91.57482.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
-
----
-::
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 361f3889..6febf6df 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF00533, PF01653, PF03119, PF03120, PF12826, PF14520
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS2
@@ -24,12 +26,3 @@ dataUrl: /gaps2/GAPS2__GAPS2-plddts_87.94657.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
-
----
-::
-
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index c8474543..9e7dce5c 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS4
@@ -30,11 +32,3 @@ dataUrl: /gaps4/GAPS4__GAPS4b-plddts_86.45931.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
-
----
-::
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 558f7076..84180620 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1101/2023.03.28.534373
---
# GAPS6
@@ -30,11 +32,3 @@ dataUrl: /gaps6/GAPS6__GAPS6b-plddts_90.04892.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.28.534373
-
----
-::
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 9e92e61c..373b3047 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Membrane disrupting
+relevantAbstracts:
+ - doi: 10.1126/science.abj8432
---
# GasderMIN
@@ -84,12 +86,3 @@ GasderMIN systems were experimentally validated using:
A system from *Lysobacter enzymogenes* in *Escherichia coli* has an anti-phage effect against T5, T4, T6 (Johnson et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.abj8432
-
----
-::
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index fec562a1..4e460a11 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00270, PF00271, PF04851, PF08878, PF14130
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Hachiman
@@ -67,20 +69,3 @@ A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect
Subsystem Hachiman Type II with a system from *Sphingopyxis witflariensis* in *Escherichia coli* has an anti-phage effect against T3, PVP-SE1 (Payne et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
-
-## References
-
-1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
-
-2. Payne LJ, Todeschini TC, Wu Y, Perry BJ, Ronson CW, Fineran PC, Nobrega FL, Jackson SA. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021 Nov 8;49(19):10868-10878. doi: 10.1093/nar/gkab883. PMID: 34606606; PMCID: PMC8565338.
-
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index a2a47871..d1a54d91 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF00270, PF04851, PF13307
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2023.01.010
---
# Hna
@@ -24,12 +26,3 @@ dataUrl: /hna/Hna__Hna-plddts_91.2064.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2023.01.010
-
----
-::
-
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 6bfea784..a7eb0029 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# ISG15-like
@@ -195,12 +197,3 @@ A system from *Paraburkholderia caffeinilytica* in *Escherichia coli* has an ant
A system from *Thiomonas sp. FB-6* in *Escherichia coli* has an anti-phage effect against SECphi27 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index 0aec5c30..729b9e3e 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF13099
+relevantAbstracts:
+ - doi: 10.1101/2022.09.17.508391
---
# JukAB
@@ -31,12 +33,3 @@ dataUrl: /jukab/JukAB__JukB-plddts_67.28863.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2022.09.17.508391
-
----
-::
-
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 2c6e98b1..09ba636f 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF16162
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Kiwa
@@ -57,13 +59,3 @@ Kiwa systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Doron et al., 2018)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index 296df2a8..ce520675 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
PFAM: PF00753, PF02463, PF05057, PF12532, PF13175, PF13289, PF13476, PF14130
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Lamassu-Fam
@@ -340,24 +342,3 @@ Subsystem LmuA+LmuC+LmuB with a system from *Janthinobacterium agaricidamnosum*
Subsystem DdmABC with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Jaskólska et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
- - doi: 10.1038/s41586-022-04546-y
- - doi: 10.1126/science.aar4120
-
----
-::
-
-
-## References
-
-1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
-
-2. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. *Nucleic Acids Res*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883
-
-3. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447
-
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index 55ddaf31..b360721b 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Other (Cleaves an elongation factor, inhibiting cellular translation
PFAM: PF10463
+relevantAbstracts:
+ - doi: 10.1073/pnas.91.2.802
---
# Lit
@@ -50,15 +52,3 @@ Lit systems were experimentally validated using:
A system from *Escherichia coli defective prophage e14* in *Escherichia coli* has an anti-phage effect against T4 (Yu and Snyder, 1994)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1073/pnas.91.2.802
- - doi: 10.1074/jbc.M002546200
- - doi: 10.1186/1743-422X-7-360
-
----
-::
-
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index ae2362ba..d5a33031 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF00069, PF01170, PF02384, PF07714, PF08378, PF12728, PF13304, PF13588
+relevantAbstracts:
+ - doi: 10.1101/2023.03.30.534895
---
# MADS
@@ -66,12 +68,3 @@ dataUrl: /mads/MADS__mad8-plddts_82.23514.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2023.03.30.534895
-
----
-::
-
diff --git a/content/3.defense-systems/mazef.md b/content/3.defense-systems/mazef.md
index 2ca8dee2..61096d36 100644
--- a/content/3.defense-systems/mazef.md
+++ b/content/3.defense-systems/mazef.md
@@ -7,18 +7,11 @@ tableColumns:
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.
PFAM: PF02452, PF04014
+relevantAbstracts:
+ - doi: 10.1007/s00438-004-1048-y
---
# MazEF
## To do
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1007/s00438-004-1048-y
-
----
-::
-
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index 85131b62..2a7f2b67 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF03235, PF05973, PF12476, PF13175, PF13304, PF13476
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Menshen
@@ -66,13 +68,3 @@ A system from *Solibacillus silvestris* in *Escherichia coli* has an anti-phage
A system from *Solibacillus silvestris* in *Bacillus subtilis* has an anti-phage effect against Fado (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index 8be0aab3..97cb93ed 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -6,6 +6,8 @@ tableColumns:
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.
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# MMB_gp29_gp30
@@ -30,11 +32,3 @@ dataUrl: /mmb_gp29_gp30/MMB_gp29_gp30__gp30-plddts_65.6043.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
-
----
-::
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index 3e6c4834..56be8725 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01848
+relevantAbstracts:
+ - doi: 10.1128/jb.178.7.2044-2050.1996
---
# Mok_Hok_Sok
@@ -50,13 +52,3 @@ Mok_Hok_Sok systems were experimentally validated using:
A system from *R1 plasmid of Salmonella paratyphi* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir (Pecota and Wood, 1996)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1128/jb.178.7.2044-2050.1996
-
----
-::
-
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index 45a48f56..512835e4 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00069, PF07714, PF08378, PF13086, PF13087, PF13091, PF13245, PF13604
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Mokosh
@@ -88,13 +90,3 @@ Subsystem Type I with a system from *Escherichia coli* in *Escherichia coli* has
Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/mqsrac.md b/content/3.defense-systems/mqsrac.md
index dfb6b3cf..df3252af 100644
--- a/content/3.defense-systems/mqsrac.md
+++ b/content/3.defense-systems/mqsrac.md
@@ -6,6 +6,7 @@ tableColumns:
doi: 10.1101/2023.02.25.529695
abstract: |
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.
+relevantAbstracts:
---
# MqsRAC
@@ -29,5 +30,3 @@ Among the 22k complete genomes of RefSeq, this system is present in 26 genomes (
*Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.*
-## Relevant abstracts
-
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index 44b87275..9d4160df 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading (?)
PFAM: PF01443, PF09848, PF13604
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.03.001
---
# Nhi
@@ -58,13 +60,3 @@ A system from *Staphylococcus aureus* in *Staphylococcus aureus* has an anti-pha
A system from *Vibrio vulnificus* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.03.001
-
----
-::
-
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 0058acc8..443e7110 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading
+relevantAbstracts:
+ - doi: 10.1101/2021.07.12.452122
---
# NixI
@@ -49,12 +51,3 @@ NixI systems were experimentally validated using:
A system from *Vibrio cholerae* in *Vibrio cholerae* has an anti-phage effect against ICP1 (Legault et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2021.07.12.452122
-
----
-::
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index 930fd169..934e074f 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF05729
+relevantAbstracts:
+ - doi: 10.1101/2022.07.19.500537
---
# NLR
@@ -79,13 +81,3 @@ Subsystem bNACHT67 with a system from *Klebsiella michiganensis* in *Escherichia
Subsystem bNACHT09 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, LambdaVir, T3, T7 (Kibby et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1101/2022.07.19.500537
-
----
-::
-
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index 185ea8ba..77ce0f34 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -10,6 +10,7 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304
+relevantAbstracts:
---
# Old_exonuclease
@@ -50,9 +51,3 @@ Old_exonuclease systems were experimentally validated using:
A system from *Enterobacteria phage P2* in *Escherichia coli* has an anti-phage effect against Lambda, T4, LF82_P8, Al505_P2 (Rousset et al., 2022)
-## Relevant abstracts
-
-**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).**
-Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
-
-
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 92aa955a..0860e23a 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Olokun
@@ -56,12 +58,3 @@ Olokun systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 911f122f..a7300f4a 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Diverse (Nucleotide modifyingn, Membrane disrupting)
PFAM: PF02171, PF13289, PF13676, PF14280, PF18742
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2022.03.012
---
# pAgo
@@ -128,18 +130,3 @@ Subsystem Sir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia
Subsystem SiAgo/Aga1/Aga2 with a system from *Sulfolobus islandicus* in *Sulfolobus islandicus* has an anti-phage effect against SMV1 (Zeng et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2022.03.012
- - doi: 10.1016/j.chom.2022.04.015
- - doi: 10.1038/s41564-022-01207-8
- - doi: 10.1038/s41586-020-2605-1
- - doi: 10.1186/1745-6150-4-29
- - doi: 10.1038/s41564-022-01239-0
-
----
-::
-
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index c6d2ad59..3a31b33d 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF01170, PF02384, PF13588
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# Panchino_gp28
@@ -24,12 +26,3 @@ dataUrl: /panchino_gp28/Panchino_gp28__gp28-plddts_90.80762.pdb
---
::
-## Relevant abstract
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
-
----
-::
-
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index afc2c846..d9ab8582 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Sensing of phage protein
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Paris
@@ -111,13 +113,3 @@ Subsystem Paris 1 with a system from *Escherichia coli (P4 loci)* in *Escherichi
Subsystem Paris 2 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
-
----
-::
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index 042701a1..80984b55 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10544, PF13250, PF13455
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-1
@@ -50,13 +52,3 @@ PD-Lambda-1 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index 15237efb..2f819e0b 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF06114, PF09907, PF14350
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-2
@@ -64,13 +66,3 @@ PD-Lambda-2 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi17, SECphi18, SECphi27, T3 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index d592552a..46a4f35f 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF09509
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-3
@@ -64,13 +66,3 @@ PD-Lambda-3 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 8583dd0b..cd86cc76 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-4
@@ -56,12 +58,3 @@ PD-Lambda-4 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir, SECphi27, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index 2ed43850..42bf9dd5 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02086
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-5
@@ -57,13 +59,3 @@ PD-Lambda-5 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 5983f9ae..a9103b09 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-Lambda-6
@@ -49,12 +51,3 @@ PD-Lambda-6 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, T5 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 6ec543d1..840f5ec6 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13020
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# PD-T4-1
@@ -50,13 +52,3 @@ PD-T4-1 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1371/journal.pgen.1010065
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 09bba3f5..29fa88cb 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# PD-T4-10
@@ -56,12 +58,3 @@ PD-T4-10 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1371/journal.pgen.1010065
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 9c3e67fd..742afc4e 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF03235, PF18735
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-2
@@ -57,13 +59,3 @@ PD-T4-2 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index d5739ccb..502fc227 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-3
@@ -49,12 +51,3 @@ PD-T4-3 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index 8a6550d7..8cf52247 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-4
@@ -57,13 +59,3 @@ PD-T4-4 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi17 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index aab0d33d..ded3b89c 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-5
@@ -50,13 +52,3 @@ PD-T4-5 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T6, LambdaVir, T5 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 7734d40a..5225f75c 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00069, PF03793, PF07714
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-6
@@ -50,13 +52,3 @@ PD-T4-6 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index 8c40ef4b..e9fdef12 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-7
@@ -49,12 +51,3 @@ PD-T4-7 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index ebacb14a..3b682d7f 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14082
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-8
@@ -50,13 +52,3 @@ PD-T4-8 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi18, SECphi27 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index bf220afd..b4c224be 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02556
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T4-9
@@ -64,13 +66,3 @@ PD-T4-9 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index 0323f458..049bc842 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-1
@@ -49,12 +51,3 @@ PD-T7-1 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7(Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index 69f5f63e..5ff80db6 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01935, PF13289
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-2
@@ -57,13 +59,3 @@ PD-T7-2 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index 873cfafc..fc376bf8 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-3
@@ -49,12 +51,3 @@ PD-T7-3 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi17, T3, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 0fba1c7c..81403504 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13643
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-4
@@ -50,13 +52,3 @@ PD-T7-4 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
-
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index a6f14af8..f6ca3d73 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01219-4
---
# PD-T7-5
@@ -49,12 +51,3 @@ PD-T7-5 systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17, T3, T7 (Vassallo et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41564-022-01219-4
-
----
-::
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index c5debcb8..88338192 100644
--- a/content/3.defense-systems/pfiat.md
+++ b/content/3.defense-systems/pfiat.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02604, PF05016
+relevantAbstracts:
+ - doi: 10.1111/1751-7915.13570
---
# PfiAT
@@ -51,13 +53,3 @@ dataUrl: /pfiat/PfiAT,PfiAT__PfiT,0,V-plddts_94.1034.pdb
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1111/1751-7915.13570
-
----
-::
-
diff --git a/content/3.defense-systems/phrann_gp29_gp30.md b/content/3.defense-systems/phrann_gp29_gp30.md
index 8a874385..8d595a89 100644
--- a/content/3.defense-systems/phrann_gp29_gp30.md
+++ b/content/3.defense-systems/phrann_gp29_gp30.md
@@ -7,6 +7,8 @@ tableColumns:
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.
PFAM: PF04607
+relevantAbstracts:
+ - doi: 10.1038/nmicrobiol.2016.251
---
# Phrann_gp29_gp30
@@ -31,13 +33,3 @@ Among the 22k complete genomes of RefSeq, this system is present in 314 genomes
*Proportion of genome encoding the phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/nmicrobiol.2016.251
-
----
-::
-
diff --git a/content/3.defense-systems/pif.md b/content/3.defense-systems/pif.md
index 7cbf6e9a..df25f117 100644
--- a/content/3.defense-systems/pif.md
+++ b/content/3.defense-systems/pif.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Membrane disrupting (?)
PFAM: PF07693
+relevantAbstracts:
+ - doi: 10.1007/BF00327934
---
# Pif
@@ -57,15 +59,3 @@ Pif systems were experimentally validated using:
A system from *Escherichia coli F-plasmid* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2004)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1007/BF00327934
- - doi: 10.1016/j.virol.2004.06.001
- - doi: 10.1128/jb.173.20.6507-6514.1991
-
----
-::
-
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index ecc2ad47..754be886 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF13166, PF18766
+relevantAbstracts:
+ - doi: 10.1006/jmbi.1995.0343
---
# PrrC
@@ -57,14 +59,3 @@ PrrC systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T4 Dec8 (Jabbar and Snyder, 1984)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1006/jmbi.1995.0343
- - doi: 10.1186/1743-422X-7-360
-
----
-::
-
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index 5efe4704..f0d2e66f 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00270, PF00271, PF02481, PF04851, PF18306
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# PsyrTA
@@ -57,14 +59,3 @@ PsyrTA systems were experimentally validated using:
A system from *Bacillus sp. FJAT-29814* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
- - doi: 10.1016/j.molcel.2013.02.002
-
----
-::
-
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index 7a5e184a..daaf2916 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Signaling molecules
Effector: Membrane disrupting, Nucleotides modifying
PFAM: PF00004, PF00027, PF00211, PF00899, PF01734, PF10137, PF14461, PF14464, PF18145, PF18153, PF18303, PF18967
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2021.09.031
---
# Pycsar
@@ -75,13 +77,3 @@ A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect
A system from *Xanthomonas perforans* in *Escherichia coli* has an anti-phage effect against T7 (Tal et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2021.09.031
-
----
-::
-
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index 55a39eca..69e05eea 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading
+relevantAbstracts:
+ - doi: 10.1126/science.aba0372
---
# RADAR
@@ -96,17 +98,3 @@ A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect
A system from *Streptococcus suis* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T6 (Duncan-Lowey et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aba0372
-
----
-::
-
-
-## References
-
-1. Gao L, Altae-Tran H, Böhning F, et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. *Science*. 2020;369(6507):1077-1084. doi:10.1126/science.aba0372
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index e977224e..8166ece0 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Diverse
PFAM: PF00078, PF00089, PF01381, PF01582, PF12686, PF12844, PF13175, PF13304, PF13365, PF13476, PF13560, PF13676
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2020.09.065
---
# Retron
@@ -339,14 +341,3 @@ Subsystem Retron-Eco9 with a system from *Escherichia coli* in *Escherichia coli
Subsystem Retron-Eco1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Bobonis et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2020.09.065
- - doi: 10.1093/nar/gkaa1149
-
----
-::
-
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index 332b7ab4..170f507c 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Membrane disrupting
PFAM: PF15968, PF15969
+relevantAbstracts:
+ - doi: 10.1101/gad.6.3.497
---
# RexAB
@@ -57,13 +59,3 @@ RexAB systems were experimentally validated using:
A system from *Escherichia coli lambda prophage* in *Escherichia coli* has an anti-phage effect against T4, Lamboid phages (Parma et al., 1992)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1101/gad.6.3.497
-
----
-::
-
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index cf96c958..0274b760 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF13166
+relevantAbstracts:
+ - doi: 10.1111/j.1365-2958.2008.06387.x
---
# RloC
@@ -50,14 +52,3 @@ RloC systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Penner et al., 1995)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1111/j.1365-2958.2008.06387.x
- - doi: 10.1111/mmi.13074
-
----
-::
-
diff --git a/content/3.defense-systems/rm.md b/content/3.defense-systems/rm.md
index bf3a3f6a..922ca847 100644
--- a/content/3.defense-systems/rm.md
+++ b/content/3.defense-systems/rm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF18766
+relevantAbstracts:
+ - doi: 10.1093/nar/gku734
---
# RM
@@ -141,13 +143,3 @@ dataUrl: /rm/RM__Type_I_S-plddts_91.98582.pdb
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1093/nar/gku734
-
----
-::
-
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 575b7b3d..79b0567f 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF15933, PF15935, PF18869, PF19034
+relevantAbstracts:
+ - doi: 10.1534/genetics.110.121798
---
# RnlAB
@@ -57,13 +59,3 @@ RnlAB systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Koga et al., 2011)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1534/genetics.110.121798
-
----
-::
-
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index 4664af1f..37e9a409 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01381, PF06114, PF12844, PF13443, PF13560
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# RosmerTA
@@ -57,13 +59,3 @@ RosmerTA systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, LambdaVir (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/rst_2tm_1tm_tir.md b/content/3.defense-systems/rst_2tm_1tm_tir.md
index 15dc322c..a36c7953 100644
--- a/content/3.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/3.defense-systems/rst_2tm_1tm_tir.md
@@ -7,6 +7,8 @@ tableColumns:
abstract: |
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.
PFAM: PF13676
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_2TM_1TM_TIR
@@ -55,13 +57,3 @@ dataUrl: /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR,Rst_2TM_1TM_TIR__Rst_TIR_tm,0,V-plddts
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index f57a036e..72d3019e 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_3HP
@@ -63,12 +65,3 @@ Rst_3HP systems were experimentally validated using:
A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against P1 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index af72cbfd..28bd6a50 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14022
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_DUF4238
@@ -50,13 +52,3 @@ Rst_DUF4238 systems were experimentally validated using:
A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index f7e32190..d09bb37c 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14350
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_gop_beta_cll
@@ -64,13 +66,3 @@ Rst_gop_beta_cll systems were experimentally validated using:
A system from *Enterobacteria phage P4* in *Escherichia coli* has an anti-phage effect against Lambda, P1 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index 8e94dd2d..6c9cc66c 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10053, PF13538
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_HelicaseDUF2290
@@ -57,13 +59,3 @@ Rst_HelicaseDUF2290 systems were experimentally validated using:
A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index 34c3d7c5..9f4b0fa6 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13242, PF13419
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_Hydrolase-3Tm
@@ -57,13 +59,3 @@ Rst_Hydrolase-3Tm systems were experimentally validated using:
A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index ef862c48..8ec61df1 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_RT-nitrilase-Tm
@@ -57,13 +59,3 @@ Rst_RT-nitrilase-Tm systems were experimentally validated using:
A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Al505_P2 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index a1bb04a2..86c906c7 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13676
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.02.018
---
# Rst_TIR-NLR
@@ -50,13 +52,3 @@ Rst_TIR-NLR systems were experimentally validated using:
A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T4, P1, CLB_P2, LF82_P8, AL505_P2, T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.02.018
-
----
-::
-
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index a054e42c..cbc1bc42 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08843
+relevantAbstracts:
+ - doi: 10.1016/j.molcel.2013.02.002
---
# SanaTA
@@ -57,13 +59,3 @@ SanaTA systems were experimentally validated using:
A system from *Shewanella sp. ANA-3* in *Escherichia coli* has an anti-phage effect against T7 (Sberro et al., 2013)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.molcel.2013.02.002
-
----
-::
-
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index 6137599b..ce8e7098 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08357, PF13676
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# SEFIR
@@ -58,18 +60,3 @@ SEFIR systems were experimentally validated using:
A system from *Bacillus sp. NIO-1130* in *Bacillus subtilis* has an anti-phage effect against phi29 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
-
-## References
-[1] Millman, A. et al. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 30, 1556-1569.e5 (2022).
-[2] Novatchkova, M., Leibbrandt, A., Werzowa, J., Neubüser, A., & Eisenhaber, F. (2003). The STIR-domain superfamily in signal transduction, development and immunity. _Trends in biochemical sciences_, _28_(5), 226-229.
-
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index ee3f9144..bedcda27 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304, PF13476
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2020.09.065
---
# Septu
@@ -75,15 +77,3 @@ A system from *Bacillus thuringiensis* in *Bacillus subtilis* has an anti-phage
A system from *Bacillus weihenstephanensis* in *Bacillus subtilis* has an anti-phage effect against SBSphiC, SpBeta (Doron et al., 2018)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.cell.2020.09.065
- - doi: 10.1093/nar/gkab883
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index 3314b5d7..8d67d12c 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00270, PF00271, PF05099, PF10923, PF13208, PF15615
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Shango
@@ -77,23 +79,3 @@ Shango systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
-
-## References
-Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J. Bondy-Denomy (UCSF).
-
-[1] Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Garb, J., Bechon, N., Brandis, A., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J. L. M., Dar, D., … Sorek, R. (2022). An expanded arsenal of immune systems that protect bacteria from phages. _Cell Host & Microbe_, _30_(11), 1556-1569.e5. [https://doi.org/10.1016/j.chom.2022.09.017](https://doi.org/10.1016/j.chom.2022.09.017)
-
-[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.
-
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index 25062ee6..b517bb27 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14082
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Shedu
@@ -50,13 +52,3 @@ Shedu systems were experimentally validated using:
A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi105, rho14, SPP1, phi29 (Doron et al., 2018)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 93b01cfd..4eaf68d3 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02481
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# ShosTA
@@ -59,15 +61,3 @@ A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect
A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T7 (Rousset et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
- - doi: 10.1016/j.chom.2022.09.017
- - doi: 10.1101/gr.133850.111
-
----
-::
-
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 38e1c8de..2ea2460f 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF02661, PF13784
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# SoFIC
@@ -50,13 +52,3 @@ SoFIC systems were experimentally validated using:
A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 50aaf76e..c6141af9 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13676
+relevantAbstracts:
+ - doi: 10.1371/journal.pgen.1010065
---
# SpbK
@@ -50,13 +52,3 @@ SpbK systems were experimentally validated using:
A system from *Bacillus subtilis* in *Bacillus subtilis* has an anti-phage effect against SPbeta (Johnson et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1371/journal.pgen.1010065
-
----
-::
-
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index 499b6653..ede3eb43 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
+relevantAbstracts:
+ - doi: 10.1128/mBio.00613-21
---
# SspBCDE
@@ -121,14 +123,3 @@ Subsystem SspBCD+SspE with a system from *Streptomyces yokosukanensis* in *Strep
Subsystem SspBCD+SspFGH with a system from *Vibrio anguillarum* in *Escherichia coli* has an anti-phage effect against T1, JMPW2, T4, EEP (Wang et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1128/mBio.00613-21
- - doi: 10.1128/mBio.00613-21
-
----
-::
-
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index 0ef68de6..a9c2f320 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Other (protein modifying)
PFAM: PF00069, PF07714
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2016.08.010
---
# Stk2
@@ -61,13 +63,3 @@ A system from *Staphylococcus epidermidis* in *Staphylococcus epidermidis* has a
A system from *Staphylococcus epidermidis* in *Staphylococcus aureus* has an anti-phage effect against phage 80alpha, phage 85, phiNM1, phiNM2, phiNM4 (Depardieu et al., 2016)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2016.08.010
-
----
-::
-
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 66b69abe..f7fdad37 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Signaling
Effector: Nucleotide modifying
PFAM: PF08937, PF13289, PF18185
+relevantAbstracts:
+ - doi: 10.1038/s41586-021-04098-7
---
# Thoeris
@@ -81,14 +83,3 @@ A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect
A system from *Bacillus dafuensis* in *Bacillus subtilis* has an anti-phage effect against phi3T, SPBeta, SPR, SBSphi11, SBSphi13, phi29, SBSphiJ, SPO1 (Ofir et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-021-04098-7
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index 0324f6c6..1d1fb729 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00656, PF13020
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Tiamat
@@ -50,13 +52,3 @@ Tiamat systems were experimentally validated using:
A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T6, T5 (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
-
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index c8f0aabf..eff6ed45 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -9,6 +9,8 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
---
# Uzume
@@ -49,12 +51,3 @@ Uzume systems were experimentally validated using:
A system from *Bacillus sp. FJAT-27231* in *Bacillus subtilis* has an anti-phage effect against SPO1, SP82G, SBSphiC (Millman et al., 2022)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1016/j.chom.2022.09.017
-
----
-::
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index b2cf1ae9..65de655f 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF04055, PF13353
+relevantAbstracts:
+ - doi: 10.1038/s41586-020-2762-2
---
# Viperin
@@ -101,13 +103,3 @@ Subsystem pVip62 with a system from *Fibrobacteria bacterium* in *Escherichia co
Subsystem pVip63 with a system from *Pseudoalteromonas sp. XI10* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1038/s41586-020-2762-2
-
----
-::
-
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index e0a469df..0ac11a29 100644
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF09660, PF09661, PF09664, PF09983, PF11795, PF11796, PF11855, PF13555, PF13558, PF13835
+relevantAbstracts:
+ - doi: 10.1126/science.aar4120
---
# Wadjet
@@ -133,13 +135,3 @@ dataUrl: /wadjet/Wadjet_III,Wadjet__JetD_III,0,V-plddts_91.07357.pdb
---
::
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1126/science.aar4120
-
----
-::
-
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index 77310bbe..b68419eb 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -10,6 +10,8 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
+relevantAbstracts:
+ - doi: 10.1093/nar/gkab883
---
# Zorya
@@ -102,14 +104,3 @@ Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* ha
Subsystem Type III with a system from *Stenotrophomonas nitritireducens* in *Escherichia coli* has an anti-phage effect against T1, T4, T7, LambdaVir, PVP-SE1 (Payne et al., 2021)
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
- - doi: 10.1093/nar/gkab883
- - doi: 10.1126/science.aar4120
-
----
-::
-
--
GitLab