From c100f720a767c1f9614ccf3ae68b4cede06c1a15 Mon Sep 17 00:00:00 2001
From: jeanrjc <jean.cury@normalesup.org>
Date: Tue, 9 Jan 2024 15:34:21 +0100
Subject: [PATCH] add relevantAbstract in frontmatter
---
content/3.defense-systems/abic.md | 3 +++
content/3.defense-systems/abid.md | 3 +++
content/3.defense-systems/abie.md | 4 ++++
content/3.defense-systems/abig.md | 3 +++
content/3.defense-systems/abii.md | 3 +++
content/3.defense-systems/abij.md | 3 +++
content/3.defense-systems/abik.md | 4 ++++
content/3.defense-systems/abin.md | 3 +++
content/3.defense-systems/abio.md | 3 +++
content/3.defense-systems/abip2.md | 4 ++++
content/3.defense-systems/abiq.md | 4 ++++
content/3.defense-systems/abir.md | 3 +++
content/3.defense-systems/abit.md | 3 +++
content/3.defense-systems/abiv.md | 3 +++
content/3.defense-systems/abiz.md | 3 +++
content/3.defense-systems/aditi.md | 2 ++
content/3.defense-systems/azaca.md | 2 ++
content/3.defense-systems/bsta.md | 2 ++
content/3.defense-systems/butters_gp57r.md | 2 ++
content/3.defense-systems/caprel.md | 2 ++
content/3.defense-systems/cbass.md | 7 +++++++
content/3.defense-systems/charlie_gp32.md | 2 ++
content/3.defense-systems/ddmde.md | 2 ++
content/3.defense-systems/disarm.md | 3 +++
content/3.defense-systems/dnd.md | 3 +++
content/3.defense-systems/dpd.md | 2 ++
content/3.defense-systems/druantia.md | 2 ++
content/3.defense-systems/dsr.md | 3 +++
content/3.defense-systems/eleos.md | 2 ++
content/3.defense-systems/fs_giy_yig.md | 2 ++
content/3.defense-systems/fs_hepn_tm.md | 2 ++
content/3.defense-systems/fs_hp_sdh_sah.md | 2 ++
content/3.defense-systems/fs_hsdr_like.md | 2 ++
content/3.defense-systems/fs_sma.md | 2 ++
content/3.defense-systems/gao_her.md | 2 ++
content/3.defense-systems/gao_iet.md | 2 ++
content/3.defense-systems/gao_ppl.md | 2 ++
content/3.defense-systems/gao_qat.md | 2 ++
content/3.defense-systems/gao_tery.md | 2 ++
content/3.defense-systems/gaps2.md | 2 ++
content/3.defense-systems/gaps4.md | 2 ++
content/3.defense-systems/gaps6.md | 2 ++
content/3.defense-systems/gasdermin.md | 4 ++--
content/3.defense-systems/hachiman.md | 2 ++
content/3.defense-systems/hna.md | 2 ++
content/3.defense-systems/isg15-like.md | 3 +++
content/3.defense-systems/jukab.md | 2 ++
content/3.defense-systems/mads.md | 2 ++
content/3.defense-systems/nlr.md | 2 ++
content/3.defense-systems/panchino_gp28.md | 2 ++
content/3.defense-systems/paris.md | 2 ++
content/3.defense-systems/pd-lambda-2.md | 2 ++
content/3.defense-systems/pd-lambda-4.md | 2 ++
content/3.defense-systems/pd-lambda-6.md | 2 ++
content/3.defense-systems/pd-t4-1.md | 2 ++
content/3.defense-systems/pd-t4-2.md | 2 ++
content/3.defense-systems/pd-t4-5.md | 2 ++
content/3.defense-systems/pd-t4-9.md | 2 ++
content/3.defense-systems/pd-t7-1.md | 2 ++
content/3.defense-systems/pd-t7-2.md | 2 ++
content/3.defense-systems/pd-t7-4.md | 2 ++
content/3.defense-systems/pd-t7-5.md | 2 ++
content/3.defense-systems/pfiat.md | 2 ++
content/3.defense-systems/pycsar.md | 2 ++
content/3.defense-systems/radar.md | 1 -
content/3.defense-systems/rexab.md | 2 ++
content/3.defense-systems/rloc.md | 3 +++
content/3.defense-systems/rnlab.md | 2 ++
content/3.defense-systems/rosmerta.md | 2 ++
content/3.defense-systems/rst_duf4238.md | 2 ++
content/3.defense-systems/rst_gop_beta_cll.md | 2 ++
content/3.defense-systems/rst_hydrolase-3tm.md | 2 ++
content/3.defense-systems/rst_rt-nitrilase-tm.md | 2 ++
content/3.defense-systems/septu.md | 4 ++++
content/3.defense-systems/sofic.md | 2 ++
content/3.defense-systems/spbk.md | 2 ++
content/3.defense-systems/sspbcde.md | 3 +++
content/3.defense-systems/stk2.md | 2 ++
content/3.defense-systems/thoeris.md | 3 +++
content/3.defense-systems/uzume.md | 2 ++
content/3.defense-systems/wadjet.md | 2 ++
content/3.defense-systems/zorya.md | 3 +++
82 files changed, 196 insertions(+), 3 deletions(-)
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index 6876763d..f0ad4e3f 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF16872
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiC
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index 6cf817e3..69670658 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiD
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index 706909d8..a7e06053 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkt1419
---
# AbiE
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index 87b0b196..f41b6ac6 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10899, PF16873
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiG
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index 97b709b0..e2349fd4 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiI
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 03b87ac9..46b1b9cc 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF14355
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiJ
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 607fec7f..5be8a8ce 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
# AbiK
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index b8033079..3eb41769 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiN
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 483e179b..5392e139 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF01443, PF09848
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiO
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index 83840172..e031cc40 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
# AbiP2
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index 2c65ede1..361f32e1 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13958
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1128/AEM.64.12.4748-4756.1998
---
# AbiQ
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index 7edcc5ad..277c7ef9 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiR
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 6e79b4a1..4e4e2d8d 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18864
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
---
# AbiT
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index db416918..89e356c4 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF18728
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1128/AEM.00780-08
---
# AbiV
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index aa18e65a..68931ced 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Membrane disrupting
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1128/JB.00904-06
---
# AbiZ
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index 452259dc..5e539a1f 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
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 15ae31cb..50ea7855 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
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 58ea6fcc..882b9ead 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
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index 7279df46..4efd9095 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
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 63938fdd..2abb480e 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
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 3981e257..029e52c7 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -10,6 +10,13 @@ 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
+ - 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
+
---
# CBASS
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 397b2562..9c39da40 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
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index 9f9fe28f..2e3c30ec 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.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
---
# DdmDE
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index a1d2d802..100fac7a 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
+relevantAbstracts:
+ - doi: 10.1038/s41467-022-30673-1
+ - doi: 10.1038/s41564-017-0051-0
---
# DISARM
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index 2e06e4fa..7319afe1 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF00266, PF01507, PF01935, PF08870, PF13476, PF14072
+relevantAbstracts:
+ - doi: 10.1038/nchembio.2007.39
+ - doi: 10.1038/s41467-019-09390-9
---
# Dnd
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index 2301fb98..599a877b 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
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 835f6555..3f394efe 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
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 03e3cf23..12d240d9 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct
Effector: Nucleotide modifying
PFAM: PF13289
+relevantAbstracts:
+ - doi: 10.1038/s41564-022-01207-8
+ - doi: 10.1126/science.aba0372
---
# Dsr
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index 8220a15c..5370ae15 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
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 210603c6..ff41e101 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
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index c53fc9ff..0ccac65e 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
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 0334531a..5c0d6e5f 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
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index 90d07a4a..adaff9db 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
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 9931ce08..31120a93 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
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index c942058d..1f5cf399 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
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 5c0f1dd3..a2485e4d 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
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index a5aa0cc2..f88fe77c 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
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index c0129613..ecdaaaf4 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
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 21910352..d6278bb7 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
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 46a20217..528a69af 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
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index 4fe4db65..f1d8c806 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
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 3b218b60..f2258460 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
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 64bd8d76..792766c7 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -12,8 +12,8 @@ tableColumns:
contributors:
- Aude Bernheim
relevantAbstracts:
-- doi: 10.1126/science.abj8432
-- doi: 10.1101/2023.05.28.542683
+ - doi: 10.1126/science.abj8432
+ - doi: 10.1101/2023.05.28.542683
---
# GasderMIN
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index 5a8515cf..f2b53acd 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
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index 56a84f17..5134b844 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
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 314be5d1..242a75ed 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -9,6 +9,9 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Unknown
+relevantAbstracts:
+ - doi: 10.1016/j.chom.2022.09.017
+
---
# ISG15-like
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index b650585e..c153378b 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
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index e13fcc40..4c44664d 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
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index c463d483..9fb50ad8 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
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index e197f1d8..b526b528 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
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index c9b25cc4..06b902d5 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
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index a6d47cfc..e39dc537 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
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 2890057b..7dc2f86c 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
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 70128d2a..76136adc 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
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 5f5d9c36..5b22a947 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
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 289fd9cb..1d2a11f3 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
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index dd2b3118..37d1c023 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
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index 8a6b8a36..ee080a2e 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
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index c0953753..2ea58ee0 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
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index bd62bba0..39a84ff6 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
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 6658dba5..3d1085e1 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
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index 564c4bfe..34db3bbb 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
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index c21eec60..ebfbe341 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
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index f33d2091..6a6469e0 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
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index dffd65f8..0510cece 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -9,7 +9,6 @@ tableColumns:
Sensor: Unknown
Activator: Unknown
Effector: Nucleic acid degrading
-
contributors:
- Hugo Vaysset
- Aude Bernheim
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index ee6c0c51..e02d4414 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
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index 3bb39164..273ede06 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Nucleic acid degrading
PFAM: PF13166
+relevantAbstracts:
+ - doi: 10.1111/j.1365-2958.2008.06387.x
+ - doi: 10.1111/mmi.13074
---
# RloC
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 7aec609f..282a7875 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
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index c59f85c1..ee968724 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
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index c96e888d..cda9b5f6 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
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index 44af6c64..6a49f423 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
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index 3f777d18..ecf86fe5 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
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index 286a6be9..c1112119 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
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index 232f9b3c..2addac55 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -10,6 +10,10 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF13175, PF13304, PF13476
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2020.09.065
+ - doi: 10.1093/nar/gkab883
+ - doi: 10.1126/science.aar4120
---
# Septu
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 3988f556..9b38dbc4 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
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 6377138a..8b3f25f7 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
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index fabced18..acb6b9bb 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading
PFAM: PF01507, PF01580, PF03235, PF07510, PF13182
+relevantAbstracts:
+ - doi: 10.1128/mBio.00613-21
+ - doi: 10.1128/mBio.00613-21
---
# SspBCDE
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index ce9a908e..b90aff23 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
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 3f8baaf0..37cc0da5 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Signaling
Effector: Nucleotide modifying
PFAM: PF08937, PF13289, PF18185
+relevantAbstracts:
+ - doi: 10.1038/s41586-021-04098-7
+ - doi: 10.1126/science.aar4120
---
# Thoeris
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index 4bdf5245..eb205809 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
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index 8d55567a..a4c099ba 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
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index ae950966..a83c1d3c 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -10,6 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00176, PF00271, PF00691, PF04851, PF15611
+relevantAbstracts:
+ - doi: 10.1093/nar/gkab883
+ - doi: 10.1126/science.aar4120
---
# Zorya
--
GitLab