diff --git a/content/2.defense-systems/abi2.md b/content/2.defense-systems/abi2.md
index 7403ca3a6f6e1fde45a7f6a23d4fb2e14e44da27..d3c027315111e4c784e246358006c63a009d0ef0 100644
--- a/content/2.defense-systems/abi2.md
+++ b/content/2.defense-systems/abi2.md
@@ -7,7 +7,6 @@ tableColumns:
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
---
-# Abi2
# Abi2
The Abi2 system is composed of one protein: Abi_2.
diff --git a/content/2.defense-systems/abia.md b/content/2.defense-systems/abia.md
index 9061dfd6d46e667b9b165803d9f04eb913bed0b0..a7055ea9aa38800a9799c85d06b8c87c5fcd96f5 100644
--- a/content/2.defense-systems/abia.md
+++ b/content/2.defense-systems/abia.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiA
# AbiA
The AbiA system have been describe in a total of 2 subsystems.
diff --git a/content/2.defense-systems/abib.md b/content/2.defense-systems/abib.md
index 62da9295d03f1aa158574ed57792e008971a261c..1951d72efc0a0b40b11bb23a8c58971447be652a 100644
--- a/content/2.defense-systems/abib.md
+++ b/content/2.defense-systems/abib.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiB
# AbiB
The AbiB system is composed of one protein: AbiB.
diff --git a/content/2.defense-systems/abic.md b/content/2.defense-systems/abic.md
index efd2c8e3947da2ab82048370998c1cdf5830667d..cc1dd91ba157f8af529b4664d17099a62f998b45 100644
--- a/content/2.defense-systems/abic.md
+++ b/content/2.defense-systems/abic.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiC
# AbiC
The AbiC system is composed of one protein: AbiC.
diff --git a/content/2.defense-systems/abid.md b/content/2.defense-systems/abid.md
index 26d443aa4c31a72358114ac5a4baebd26d60f9bb..0ae3b82f26788b7f5a97a73874a17617d8b3fc6f 100644
--- a/content/2.defense-systems/abid.md
+++ b/content/2.defense-systems/abid.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiD
# AbiD
The AbiD system is composed of one protein: AbiD.
diff --git a/content/2.defense-systems/abie.md b/content/2.defense-systems/abie.md
index aa61f1dd6e96d275a0f4113494d8cff854be5924..23d85dda387ce193e3f5c53a1c5130013b9c9006 100644
--- a/content/2.defense-systems/abie.md
+++ b/content/2.defense-systems/abie.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiE
# AbiE
AbiE is a family of an anti-phage defense systems. They act through a Toxin-Antitoxin mechanism, and are comprised of a pair of genes, with one gene being toxic while the other confers immunity to this toxicity.Â
diff --git a/content/2.defense-systems/abig.md b/content/2.defense-systems/abig.md
index 8593fa97e5961328cadb67b5b381a7ced63f7f09..7a013fbdd847b28ff0544ade71147b31b6e1bd17 100644
--- a/content/2.defense-systems/abig.md
+++ b/content/2.defense-systems/abig.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiG
# AbiG
The AbiG system is composed of 2 proteins: AbiGi and, AbiGii.
diff --git a/content/2.defense-systems/abih.md b/content/2.defense-systems/abih.md
index 5fdab8fa0c8a883a94ec0bef354f4cafe86b3ad1..333517d5042eb0f1ed8dce5fa6aa8b1082d10360 100644
--- a/content/2.defense-systems/abih.md
+++ b/content/2.defense-systems/abih.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiH
# AbiH
## Example of genomic structure
diff --git a/content/2.defense-systems/abii.md b/content/2.defense-systems/abii.md
index c30ab04cf8918b5b36878b66f303fe6c95e37fcd..92b213f971c0feb2ef1c2c7dcb981056176ff1ef 100644
--- a/content/2.defense-systems/abii.md
+++ b/content/2.defense-systems/abii.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiI
# AbiI
## Example of genomic structure
diff --git a/content/2.defense-systems/abij.md b/content/2.defense-systems/abij.md
index 56e1d908a5d54d8f75f6f45a7e2da463375b5b17..83dfbe0e8a65e525d974ca05d55cd5790dbd3481 100644
--- a/content/2.defense-systems/abij.md
+++ b/content/2.defense-systems/abij.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiJ
# AbiJ
## Example of genomic structure
diff --git a/content/2.defense-systems/abik.md b/content/2.defense-systems/abik.md
index 3f5c36c34e8ab5c07f5b6a4413b7c29f075a640f..6923486b07b13395f5f6c452bd88fde67a4d05f3 100644
--- a/content/2.defense-systems/abik.md
+++ b/content/2.defense-systems/abik.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiK
# AbiK
## Example of genomic structure
diff --git a/content/2.defense-systems/abil.md b/content/2.defense-systems/abil.md
index 1841dd43f82d445436e5a69b125a5c4eb5fcbd64..3dee3534c6b119a70b0af4783f457f9590ebd3d8 100644
--- a/content/2.defense-systems/abil.md
+++ b/content/2.defense-systems/abil.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiL
# AbiL
## Example of genomic structure
diff --git a/content/2.defense-systems/abin.md b/content/2.defense-systems/abin.md
index cc2692a59916c3a06df4ae3723e638346a5a1e7d..466e2528e2532a76cd5309384012892150294908 100644
--- a/content/2.defense-systems/abin.md
+++ b/content/2.defense-systems/abin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiN
# AbiN
## Example of genomic structure
diff --git a/content/2.defense-systems/abio.md b/content/2.defense-systems/abio.md
index ab5f15f6844e38a13769ba4cc9d85b802e6ed17f..d89e1c5c2784760aaec1f17f97bbc44cd0d1b202 100644
--- a/content/2.defense-systems/abio.md
+++ b/content/2.defense-systems/abio.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiO
# AbiO
## Example of genomic structure
diff --git a/content/2.defense-systems/abip2.md b/content/2.defense-systems/abip2.md
index f9ea0dddbbd972f161349cbf8025b675322ec17f..1156872dbf26d58e2e9f42d39c0a04aaf5da238b 100644
--- a/content/2.defense-systems/abip2.md
+++ b/content/2.defense-systems/abip2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiP2
# AbiP2
## Example of genomic structure
diff --git a/content/2.defense-systems/abiq.md b/content/2.defense-systems/abiq.md
index 0b4e4c7965af44309e77b9fcb9c0c31ab62be160..f9438c7c79b84d43fd1a31009c8b76e8c0a5e876 100644
--- a/content/2.defense-systems/abiq.md
+++ b/content/2.defense-systems/abiq.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiQ
# AbiQ
## Example of genomic structure
diff --git a/content/2.defense-systems/abir.md b/content/2.defense-systems/abir.md
index 7004d5a1d13dbb03ca4627dff54e8483a3a7b01a..996b6ac528f089fc7aa74eaa31fd47d85858cf59 100644
--- a/content/2.defense-systems/abir.md
+++ b/content/2.defense-systems/abir.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiR
# AbiR
## Example of genomic structure
diff --git a/content/2.defense-systems/abit.md b/content/2.defense-systems/abit.md
index 5d32c87784e766b69ef045d3b2987cef394f5d74..b1865fe56fb285e6f9fa103db60070a4c81e7b85 100644
--- a/content/2.defense-systems/abit.md
+++ b/content/2.defense-systems/abit.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiT
# AbiT
## Example of genomic structure
diff --git a/content/2.defense-systems/abiu.md b/content/2.defense-systems/abiu.md
index c1b8e9b3bd37ecd398f106665fc3f26da93efca7..96aba14787a8a1e601be81671779506e62c7bde9 100644
--- a/content/2.defense-systems/abiu.md
+++ b/content/2.defense-systems/abiu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiU
# AbiU
## Example of genomic structure
diff --git a/content/2.defense-systems/abiv.md b/content/2.defense-systems/abiv.md
index 4b369c634933c7d619c3c6f78726b4e82f26a47b..eefbabd38f3d4422d3b459e1590563bdb79df06a 100644
--- a/content/2.defense-systems/abiv.md
+++ b/content/2.defense-systems/abiv.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# AbiV
# AbiV
## Example of genomic structure
diff --git a/content/2.defense-systems/abiz.md b/content/2.defense-systems/abiz.md
index 267a963e41654fdf34af62beed6b33742dcf24d3..b58ed7f172d5bfea10c12f482e526bf05e1317ad 100644
--- a/content/2.defense-systems/abiz.md
+++ b/content/2.defense-systems/abiz.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# AbiZ
# AbiZ
## Example of genomic structure
diff --git a/content/2.defense-systems/aditi.md b/content/2.defense-systems/aditi.md
index b3c286380e1226c462a9c22de9292542731dfa29..f458596ba7964950ee64c56a18a17686067d59da 100644
--- a/content/2.defense-systems/aditi.md
+++ b/content/2.defense-systems/aditi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Aditi
# Aditi
## Example of genomic structure
diff --git a/content/2.defense-systems/avs.md b/content/2.defense-systems/avs.md
index bc7e2b04eb8793b847a9e2138eede95ac03de1fd..5b66512b9d8ded9d8c8bd572c68f201faf8e1c9e 100644
--- a/content/2.defense-systems/avs.md
+++ b/content/2.defense-systems/avs.md
@@ -12,7 +12,7 @@ tableColumns:
---
# Avs
-# Avs
+
## Description
Avs (antiviral ATPases/NTPases of the STAND superfamily) is a group of anti-phage defense systems, active against some dsDNA phages.Â
diff --git a/content/2.defense-systems/azaca.md b/content/2.defense-systems/azaca.md
index 3b38e0a9f544bb9a5ea9c94f1533d42e04e74899..c106da473403bedbe39d5afeb62609e3ddb7dbb7 100644
--- a/content/2.defense-systems/azaca.md
+++ b/content/2.defense-systems/azaca.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Azaca
# Azaca
## Example of genomic structure
diff --git a/content/2.defense-systems/borvo.md b/content/2.defense-systems/borvo.md
index c17923bc7677fc9c26e56ea9e01d15a5218065ee..4f2b3b35fc3fe75471632d497a8ebaf09bd9a1b9 100644
--- a/content/2.defense-systems/borvo.md
+++ b/content/2.defense-systems/borvo.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Borvo
# Borvo
## Example of genomic structure
diff --git a/content/2.defense-systems/brex.md b/content/2.defense-systems/brex.md
index 71046b353e7f306340d48dffa0dd8fc500a26d51..e9cb8dd08afcf7da22e9d7d8aaec988cc90f5059 100644
--- a/content/2.defense-systems/brex.md
+++ b/content/2.defense-systems/brex.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# BREX
# BREX
## Description
diff --git a/content/2.defense-systems/bsta.md b/content/2.defense-systems/bsta.md
index 1fa1c169541fd04caab491006034012834fe0a35..3b06e7f678675390648c33eee58022f074783c08 100644
--- a/content/2.defense-systems/bsta.md
+++ b/content/2.defense-systems/bsta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# BstA
# BstA
## Description
diff --git a/content/2.defense-systems/bunzi.md b/content/2.defense-systems/bunzi.md
index e747f3f44e2c35be9d9311a68ad346f21798dee2..8b1612a2339da71206d410ab416f7ff14d5639cb 100644
--- a/content/2.defense-systems/bunzi.md
+++ b/content/2.defense-systems/bunzi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Bunzi
# Bunzi
## Example of genomic structure
diff --git a/content/2.defense-systems/butters_gp30_gp31.md b/content/2.defense-systems/butters_gp30_gp31.md
new file mode 100644
index 0000000000000000000000000000000000000000..6f03ec356a475f5d3fefdcc9be8a029562e06729
--- /dev/null
+++ b/content/2.defense-systems/butters_gp30_gp31.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp30_gp31
+tableColumns:
+ article:
+ doi: 10.1128/mSystems.00534-20
+ abstract: |
+ Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance., A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems., IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
+---
+
+# Butters_gp30_gp31
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1128/mSystems.00534-20
+
+---
+::
diff --git a/content/2.defense-systems/butters_gp57r.md b/content/2.defense-systems/butters_gp57r.md
new file mode 100644
index 0000000000000000000000000000000000000000..520d08dd6ba5461d8674e8a32e7b1cddad0dbafb
--- /dev/null
+++ b/content/2.defense-systems/butters_gp57r.md
@@ -0,0 +1,21 @@
+---
+title: Butters_gp57r
+tableColumns:
+ article:
+ doi: 10.1101/2023.01.03.522681
+ abstract: |
+ During lysogeny temperate phages establish a truce with the bacterial host. In this state, the phage genome (prophage) is maintained within the host environment. Consequently, many prophages have evolved systems to protect the host from heterotypic viral attack. This phenomenon of prophages mediating defense of their host against competitor phages is widespread among temperate mycobacteriophages. We previously showed that the Mycobacterium phage Butters prophage encodes a two-component system (gp30/31) that inhibits infection from a subset of mycobacteriophages that include PurpleHaze, but not Island3. Here we show that Butters gp57r is both necessary and sufficient to inhibit infection by Island3 and other phages. Gp57r acts post-DNA injection and its antagonism results in the impairment of Island3 DNA amplification. Gp57r inhibition of Island3 is absolute with no defense escape mutants. However, mutations mapping to minor tail proteins allow PurpleHaze to overcome gp57r defense. Gp57r has a HEPN domain which is present in many proteins involved in inter-genomic conflicts, suggesting that gp57r may inhibit heterotypic phage infections via its HEPN domain. We also show that Butters gp57r has orthologues in clinical isolates of Mycobacterium abscessus sp. including the phage therapy candidate strain GD91 which was found to be resistant to the panel of phages tested. It is conceivable that this GD91 orthologue of gp57r may mediate resistance to the subset of phages tested. Challenges of this nature underscore the importance of elucidating mechanisms of antiphage systems and mutations that allow for escape from inhibition. IMPORTANCE The evolutionary arms race between phages and their bacteria host is ancient. During lysogeny, temperate phages establish a ceasefire with the host where they do not kill the host but derive shelter from it. Within the phenomenon of prophage-mediated defense, some temperate phages contribute genes that make their host more fit and resistant to infections by other phages. This arrangement has significance for both phage and bacterial evolutionary dynamics. Further, the prevalence of such antiphage systems poses a challenge to phage therapy. Thus, studies aimed at elucidating antiphage systems will further our understanding of phage-bacteria evolution as well as help with efforts to engineer therapeutic phages that circumvent antiphage systems.
+---
+
+# Butters_gp57r
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.01.03.522681
+
+---
+::
diff --git a/content/2.defense-systems/caprel.md b/content/2.defense-systems/caprel.md
index ee88be4fac12e211b0dec51d1976a1274d727c80..1ad554427596fd8dfaa6c18dbb6646d25ef76208 100644
--- a/content/2.defense-systems/caprel.md
+++ b/content/2.defense-systems/caprel.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
---
-# CapRel
# CapRel
## Description
diff --git a/content/2.defense-systems/card_nlr.md b/content/2.defense-systems/card_nlr.md
new file mode 100644
index 0000000000000000000000000000000000000000..8cc15bd768d3272b59b50fd50cb7e5feb3dc122b
--- /dev/null
+++ b/content/2.defense-systems/card_nlr.md
@@ -0,0 +1,21 @@
+---
+title: CARD_NLR
+tableColumns:
+ article:
+ doi: 10.1101/2023.05.28.542683
+ abstract: |
+ Caspase recruitment domains (CARDs) and pyrin domains are important facilitators of inflammasome activity and pyroptosis. Upon pathogen recognition by NLR proteins, CARDs recruit and activate caspases, which, in turn, activate gasdermin pore forming proteins to and induce pyroptotic cell death. Here we show that CARD-like domains are present in defense systems that protect bacteria against phage. The bacterial CARD is essential for protease-mediated activation of certain bacterial gasdermins, which promote cell death once phage infection is recognized. We further show that multiple anti-phage defense systems utilize CARD-like domains to activate a variety of cell death effectors. We find that these systems are triggered by a conserved immune evasion protein that phages use to overcome the bacterial defense system RexAB, demonstrating that phage proteins inhibiting one defense system can activate another. We also detect a phage protein with a predicted CARD-like structure that can inhibit the CARD-containing bacterial gasdermin system. Our results suggest that CARD domains represent an ancient component of innate immune systems conserved from bacteria to humans, and that CARD-dependent activation of gasdermins is conserved in organisms across the tree of life.
+---
+
+# CARD_NLR
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.05.28.542683
+
+---
+::
diff --git a/content/2.defense-systems/cbass.md b/content/2.defense-systems/cbass.md
index 12d4998c34b4e159fa1979e362985886160706f6..8a16ae01939a5a288b07b23689154c921dacc82b 100644
--- a/content/2.defense-systems/cbass.md
+++ b/content/2.defense-systems/cbass.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Divers (Nucleic acid degrading, Nucleotide modifying, Membrane disrupting)
---
-# CBASS
# CBASS
## Example of genomic structure
diff --git a/content/2.defense-systems/charlie_gp32.md b/content/2.defense-systems/charlie_gp32.md
new file mode 100644
index 0000000000000000000000000000000000000000..39c1703a5407cddf35c48368bf0ce73e2110b2a5
--- /dev/null
+++ b/content/2.defense-systems/charlie_gp32.md
@@ -0,0 +1,21 @@
+---
+title: Charlie_gp32
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# Charlie_gp32
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/dartg.md b/content/2.defense-systems/dartg.md
index ce8d8989c31016297127dae7b409c4c53cdfcc06..ebe19f6df71ef743989b66528321bdaaa21a2305 100644
--- a/content/2.defense-systems/dartg.md
+++ b/content/2.defense-systems/dartg.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (ADP-ribosylation)
---
-# DarTG
# DarTG
## Example of genomic structure
diff --git a/content/2.defense-systems/dazbog.md b/content/2.defense-systems/dazbog.md
index 349869bc031c8e68aaa135e9780f7d5d9b88ed9c..8bd4c17ffa9b1a2d19e21dd194b1c5e4d56b07c1 100644
--- a/content/2.defense-systems/dazbog.md
+++ b/content/2.defense-systems/dazbog.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Dazbog
# Dazbog
## Example of genomic structure
diff --git a/content/2.defense-systems/dctpdeaminase.md b/content/2.defense-systems/dctpdeaminase.md
index f4747904f0cccbd61ff53960abd93676bb37f3b4..563e14d05c447dbd287abd0c33b39af16cfaf96b 100644
--- a/content/2.defense-systems/dctpdeaminase.md
+++ b/content/2.defense-systems/dctpdeaminase.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# dCTPdeaminase
# dCTPdeaminase
## Description
dCTPdeaminase is a family of systems. dCTPdeaminase from Escherichia coli has been shown to provide resistance against various lytic phages when express heterologously in another Escherichia coli.
diff --git a/content/2.defense-systems/detocs.md b/content/2.defense-systems/detocs.md
new file mode 100644
index 0000000000000000000000000000000000000000..4fa1a73724b3cda0543109fb71fe807c0420f6c8
--- /dev/null
+++ b/content/2.defense-systems/detocs.md
@@ -0,0 +1,21 @@
+---
+title: Detocs
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2023.07.020
+ abstract: |
+ During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
+---
+
+# Detocs
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2023.07.020
+
+---
+::
diff --git a/content/2.defense-systems/dgtpase.md b/content/2.defense-systems/dgtpase.md
index 9c2c4b66c59d0d8df45b8c6bfaed44dde6179e69..8226a1a385d3f3d24ef4677a721c061f8d9cd91e 100644
--- a/content/2.defense-systems/dgtpase.md
+++ b/content/2.defense-systems/dgtpase.md
@@ -10,9 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# dGTPase
-# dGTPase
-# dGTPase
# dGTPase
## Example of genomic structure
diff --git a/content/2.defense-systems/disarm.md b/content/2.defense-systems/disarm.md
index 6f04047978a519d8e13e60f4e68cf6fa63bd6e13..0ad07b78686b94f68e924f004d04cb6edaeba713 100644
--- a/content/2.defense-systems/disarm.md
+++ b/content/2.defense-systems/disarm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# DISARM
# DISARM
## Description
diff --git a/content/2.defense-systems/dmdde.md b/content/2.defense-systems/dmdde.md
index b77c8a641232d59a637704e040ebf4af8ea90f0c..1aa12aa14d24f65d1851f88af2ba19dcaa0aef08 100644
--- a/content/2.defense-systems/dmdde.md
+++ b/content/2.defense-systems/dmdde.md
@@ -4,10 +4,9 @@ tableColumns:
article:
doi: 10.1038/s41586-022-04546-y
abstract: |
- Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2–4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
+ Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability of bacteria. Nevertheless, invasive mobile genetic elements can also present grave risks to the host; bacteria have therefore evolved a vast array of defences against these elements1. Here we identify two plasmid defence systems conserved in the Vibrio cholerae El Tor strains responsible for the ongoing seventh cholera pandemic2-4. These systems, termed DdmABC and DdmDE, are encoded on two major pathogenicity islands that are a hallmark of current pandemic strains. We show that the modules cooperate to rapidly eliminate small multicopy plasmids by degradation. Moreover, the DdmABC system is widespread and can defend against bacteriophage infection by triggering cell suicide (abortive infection, or Abi). Notably, we go on to show that, through an Abi-like mechanism, DdmABC increases the burden of large low-copy-number conjugative plasmids, including a broad-host IncC multidrug resistance plasmid, which creates a fitness disadvantage that counterselects against plasmid-carrying cells. Our results answer the long-standing question of why plasmids, although abundant in environmental strains, are rare in pandemic strains; have implications for understanding the dissemination of antibiotic resistance plasmids; and provide insights into how the interplay between two defence systems has shaped the evolution of the most successful lineage of pandemic V. cholerae.
---
-# DmdDE
# DmdDE
## Example of genomic structure
diff --git a/content/2.defense-systems/dnd.md b/content/2.defense-systems/dnd.md
index 1c5201d9f5383b45e8e1871eb47f6a4f27ef21d8..79d1ed31087122466a7cea1ad2c3762949c7ac25 100644
--- a/content/2.defense-systems/dnd.md
+++ b/content/2.defense-systems/dnd.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# Dnd
# Dnd
## Example of genomic structure
diff --git a/content/2.defense-systems/dodola.md b/content/2.defense-systems/dodola.md
index 8e4cddbba34e716bc8ddae0abef4e96662eaa9c5..367f760dbceba13869fcb0574ffead60ba018a2e 100644
--- a/content/2.defense-systems/dodola.md
+++ b/content/2.defense-systems/dodola.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Dodola
# Dodola
## Example of genomic structure
diff --git a/content/2.defense-systems/dpd.md b/content/2.defense-systems/dpd.md
index 76d7220211ffc678b38f119aed70b495b2be70c9..ff62362fd14a5e73f89b9d8dc1d96970c44b3d9f 100644
--- a/content/2.defense-systems/dpd.md
+++ b/content/2.defense-systems/dpd.md
@@ -4,10 +4,9 @@ tableColumns:
article:
doi: 10.1073/pnas.1518570113
abstract: |
- The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction–modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
+ The discovery of ?20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2’-deoxy-preQ0 and 2’-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S. Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ?150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis. Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2’-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.
---
-# Dpd
# Dpd
## Example of genomic structure
diff --git a/content/2.defense-systems/drt.md b/content/2.defense-systems/drt.md
index 1b7ae8106ea9d21beeedbce194e5b27b451f5964..8430ad290c2cf7e55d7daebb2d270738440e2f36 100644
--- a/content/2.defense-systems/drt.md
+++ b/content/2.defense-systems/drt.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# DRT
# DRT
## Example of genomic structure
diff --git a/content/2.defense-systems/druantia.md b/content/2.defense-systems/druantia.md
index 80e690cdcc0a9b47f667569b212b124a236a6231..88068ad1fb51a5c40796e35651ca504c860ab97f 100644
--- a/content/2.defense-systems/druantia.md
+++ b/content/2.defense-systems/druantia.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Druantia
# Druantia
## Example of genomic structure
diff --git a/content/2.defense-systems/dsr.md b/content/2.defense-systems/dsr.md
index 908c36bcd8e43e718f98ed57e1fad26f9b95d5f2..b4b959f9b47fa43340c6d96afcaf6db480da7387 100644
--- a/content/2.defense-systems/dsr.md
+++ b/content/2.defense-systems/dsr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Dsr
# Dsr
## Example of genomic structure
diff --git a/content/2.defense-systems/eleos.md b/content/2.defense-systems/eleos.md
index b9710709ed4706c8e4caa087abccfeb2734c320f..9c114b958f23c5d8b1459a42651ebbb4b3ee9a8e 100644
--- a/content/2.defense-systems/eleos.md
+++ b/content/2.defense-systems/eleos.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Eleos
# Eleos
The Eleos system was previously described as the Dynamins-like system in (Millman et al, 2022).
diff --git a/content/2.defense-systems/fs_giy_yig.md b/content/2.defense-systems/fs_giy_yig.md
new file mode 100644
index 0000000000000000000000000000000000000000..5d946fe1bbe40c98bb385700bec9b443d90601fe
--- /dev/null
+++ b/content/2.defense-systems/fs_giy_yig.md
@@ -0,0 +1,21 @@
+---
+title: FS_GIY_YIG
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_GIY_YIG
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hepn_tm.md b/content/2.defense-systems/fs_hepn_tm.md
new file mode 100644
index 0000000000000000000000000000000000000000..239eb07f319d77e65904350b3c0dc8d65ebaff11
--- /dev/null
+++ b/content/2.defense-systems/fs_hepn_tm.md
@@ -0,0 +1,21 @@
+---
+title: FS_HEPN_TM
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HEPN_TM
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp.md b/content/2.defense-systems/fs_hp.md
new file mode 100644
index 0000000000000000000000000000000000000000..7e66e331292194c3a965fd2a1d1c3312beec077f
--- /dev/null
+++ b/content/2.defense-systems/fs_hp.md
@@ -0,0 +1,21 @@
+---
+title: FS_HP
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HP
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hp_sdh_sah.md b/content/2.defense-systems/fs_hp_sdh_sah.md
new file mode 100644
index 0000000000000000000000000000000000000000..8e64de232827829c855be1ffa05435c9d8ecdcbe
--- /dev/null
+++ b/content/2.defense-systems/fs_hp_sdh_sah.md
@@ -0,0 +1,21 @@
+---
+title: FS_HP_SDH_sah
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HP_SDH_sah
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_hsdr_like.md b/content/2.defense-systems/fs_hsdr_like.md
new file mode 100644
index 0000000000000000000000000000000000000000..3f668c217e7fa8f2ea42ecbec4b0f772deb81132
--- /dev/null
+++ b/content/2.defense-systems/fs_hsdr_like.md
@@ -0,0 +1,21 @@
+---
+title: FS_HsdR_like
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_HsdR_like
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/fs_sma.md b/content/2.defense-systems/fs_sma.md
new file mode 100644
index 0000000000000000000000000000000000000000..de46a35048268e3781e3824dbd2ecdcb1c1af331
--- /dev/null
+++ b/content/2.defense-systems/fs_sma.md
@@ -0,0 +1,21 @@
+---
+title: FS_Sma
+tableColumns:
+ article:
+ doi: 10.1016/j.cell.2022.07.014
+ abstract: |
+ Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
+---
+
+# FS_Sma
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.cell.2022.07.014
+
+---
+::
diff --git a/content/2.defense-systems/gabija.md b/content/2.defense-systems/gabija.md
index 2f0dbf0d4f93ede5f1a99b6349ff0ed46a1c1323..97410e3c8b2dab6ddbc71d9b63571e119f36bd6f 100644
--- a/content/2.defense-systems/gabija.md
+++ b/content/2.defense-systems/gabija.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Degrading nucleic acids
---
-# Gabija
# Gabija
## Description
diff --git a/content/2.defense-systems/gao_ape.md b/content/2.defense-systems/gao_ape.md
index db2e7fc37fd622be9a7ca18b34f025defc2990d6..c104f609e95d84fcf1a450160a6edd41de7a14d8 100644
--- a/content/2.defense-systems/gao_ape.md
+++ b/content/2.defense-systems/gao_ape.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ape
# Gao_Ape
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_her.md b/content/2.defense-systems/gao_her.md
index 62c7d6db8b56a46fee5f13035f90a2e9c5cb1841..1d848a7e5b750cbd0bb4fd61eacc481ba8309f69 100644
--- a/content/2.defense-systems/gao_her.md
+++ b/content/2.defense-systems/gao_her.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Her
# Gao_Her
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_hhe.md b/content/2.defense-systems/gao_hhe.md
index 078ea6d6582e21088cc651dc371b14bc19caf54f..9df0702d41652f0ed0a856b53dde16db53805c78 100644
--- a/content/2.defense-systems/gao_hhe.md
+++ b/content/2.defense-systems/gao_hhe.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Hhe
# Gao_Hhe
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_iet.md b/content/2.defense-systems/gao_iet.md
index bf817a950409ff92b12200ea8a0f9bbd57e6d8c2..8b7957a0dade05f188086ee16bc50f9fd20b4429 100644
--- a/content/2.defense-systems/gao_iet.md
+++ b/content/2.defense-systems/gao_iet.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Iet
# Gao_Iet
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_mza.md b/content/2.defense-systems/gao_mza.md
index 668ce15d2070c1aaa3047e5b2352634f60796e1e..87a59887b9d8c381a5117713bed30581c5236dbc 100644
--- a/content/2.defense-systems/gao_mza.md
+++ b/content/2.defense-systems/gao_mza.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Mza
# Gao_Mza
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_ppl.md b/content/2.defense-systems/gao_ppl.md
index 107aaf340df6e4f4960e37ec0830af5bde22db31..068702079641ba082b485ae5e80f8bfa8aa5d4f9 100644
--- a/content/2.defense-systems/gao_ppl.md
+++ b/content/2.defense-systems/gao_ppl.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Ppl
# Gao_Ppl
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_qat.md b/content/2.defense-systems/gao_qat.md
index 131275c5dccc7253176fc3546453117e7453e9af..aa56459f5e5277cef78287dce016a87ccb4a5fa6 100644
--- a/content/2.defense-systems/gao_qat.md
+++ b/content/2.defense-systems/gao_qat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Qat
# Gao_Qat
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_rl.md b/content/2.defense-systems/gao_rl.md
index c639d8243b4445af334721a3012231e312cdec20..7f4ec5d51ca278182192528f5fb0e4e64511cf3e 100644
--- a/content/2.defense-systems/gao_rl.md
+++ b/content/2.defense-systems/gao_rl.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_RL
# Gao_RL
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_tery.md b/content/2.defense-systems/gao_tery.md
index 1c2611ad5639a251c3ecfb14d3645f3e17e02a67..c00fc534ec8bb29c804a0a618eafcb8dd433b82b 100644
--- a/content/2.defense-systems/gao_tery.md
+++ b/content/2.defense-systems/gao_tery.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_TerY
# Gao_TerY
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_tmn.md b/content/2.defense-systems/gao_tmn.md
index bc179c0876e04b0a070bd80797813e30aaf8220e..948e84902afaf93fce27596e11843b98768c1c23 100644
--- a/content/2.defense-systems/gao_tmn.md
+++ b/content/2.defense-systems/gao_tmn.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Tmn
# Gao_Tmn
## Example of genomic structure
diff --git a/content/2.defense-systems/gao_upx.md b/content/2.defense-systems/gao_upx.md
index 4469dd3f89411df7cac04d27c66ea34a9919a252..6380af64eb4242b87c2431076b7c2dbde7a82639 100644
--- a/content/2.defense-systems/gao_upx.md
+++ b/content/2.defense-systems/gao_upx.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Gao_Upx
# Gao_Upx
## Example of genomic structure
diff --git a/content/2.defense-systems/gaps1.md b/content/2.defense-systems/gaps1.md
new file mode 100644
index 0000000000000000000000000000000000000000..317126a9db10acc5fef56a3d0ecb802aa01106b4
--- /dev/null
+++ b/content/2.defense-systems/gaps1.md
@@ -0,0 +1,21 @@
+---
+title: GAPS1
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS1
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps2.md b/content/2.defense-systems/gaps2.md
new file mode 100644
index 0000000000000000000000000000000000000000..4b63ea07ff902f0b4d488315128deba3aed03443
--- /dev/null
+++ b/content/2.defense-systems/gaps2.md
@@ -0,0 +1,21 @@
+---
+title: GAPS2
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS2
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps4.md b/content/2.defense-systems/gaps4.md
new file mode 100644
index 0000000000000000000000000000000000000000..982c9a601913e2927e6d05027822906000b07c05
--- /dev/null
+++ b/content/2.defense-systems/gaps4.md
@@ -0,0 +1,21 @@
+---
+title: GAPS4
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS4
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gaps6.md b/content/2.defense-systems/gaps6.md
new file mode 100644
index 0000000000000000000000000000000000000000..36906584cd9f29574c09a095c45e534795f862d8
--- /dev/null
+++ b/content/2.defense-systems/gaps6.md
@@ -0,0 +1,21 @@
+---
+title: GAPS6
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.28.534373
+ abstract: |
+ Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of defense islands may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
+---
+
+# GAPS6
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.28.534373
+
+---
+::
diff --git a/content/2.defense-systems/gasdermin.md b/content/2.defense-systems/gasdermin.md
index 24e06d7844df34a70bb8884fbafd42a2d26d45dc..0f0fa0d5b04617036dc9f9bac469c700911f8687 100644
--- a/content/2.defense-systems/gasdermin.md
+++ b/content/2.defense-systems/gasdermin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# GasderMIN
# GasderMIN
## Example of genomic structure
diff --git a/content/2.defense-systems/hachiman.md b/content/2.defense-systems/hachiman.md
index f893d7779f2cfb3be9c82350704383315dba0cd3..71b90a84b0360b8d0823de001b78c4937d4b4463 100644
--- a/content/2.defense-systems/hachiman.md
+++ b/content/2.defense-systems/hachiman.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Hachiman
# Hachiman
## Description
diff --git a/content/2.defense-systems/hna.md b/content/2.defense-systems/hna.md
new file mode 100644
index 0000000000000000000000000000000000000000..1717a49b839fc5cb9f3008739c75574e1581dfb4
--- /dev/null
+++ b/content/2.defense-systems/hna.md
@@ -0,0 +1,21 @@
+---
+title: Hna
+tableColumns:
+ article:
+ doi: 10.1016/j.chom.2023.01.010
+ abstract: |
+ There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
+---
+
+# Hna
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1016/j.chom.2023.01.010
+
+---
+::
diff --git a/content/2.defense-systems/isg15-like.md b/content/2.defense-systems/isg15-like.md
index aac319fdd3022bbe548d4c8c9bcfe24565e1d78c..d5894b86ca712c93733e9549d16448b7496cc79d 100644
--- a/content/2.defense-systems/isg15-like.md
+++ b/content/2.defense-systems/isg15-like.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# ISG15-like
# ISG15-like
## Example of genomic structure
diff --git a/content/2.defense-systems/jukab.md b/content/2.defense-systems/jukab.md
new file mode 100644
index 0000000000000000000000000000000000000000..e4c71ee11880e0f754cb714a48bbd5fdc472f91e
--- /dev/null
+++ b/content/2.defense-systems/jukab.md
@@ -0,0 +1,21 @@
+---
+title: JukAB
+tableColumns:
+ article:
+ doi: 10.1101/2022.09.17.508391
+ abstract: |
+ Jumbo bacteriophages of the ?KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the "jumbo phage killer"(Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist PhiKZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific antiPhiKZ activity when expressed in P. aeruginosa. Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
+---
+
+# JukAB
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2022.09.17.508391
+
+---
+::
diff --git a/content/2.defense-systems/kiwa.md b/content/2.defense-systems/kiwa.md
index e5826c2847154dcb32d49af70231f16d849b13ce..044f267bc40050700721dd9b2f078a2bcfe529f0 100644
--- a/content/2.defense-systems/kiwa.md
+++ b/content/2.defense-systems/kiwa.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Kiwa
# Kiwa
## Example of genomic structure
diff --git a/content/2.defense-systems/lamassu-fam.md b/content/2.defense-systems/lamassu-fam.md
index edf177a6f34c504d7fee673a8f9b19fa2c64a981..628f2f7b7771e798310561c22ebb52f168d3153f 100644
--- a/content/2.defense-systems/lamassu-fam.md
+++ b/content/2.defense-systems/lamassu-fam.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
---
-# Lamassu-Fam
# Lamassu-Fam
## Description
diff --git a/content/2.defense-systems/lit.md b/content/2.defense-systems/lit.md
index f3b1f40494f066faf821eb8da8341d72eb5ec683..63950ee2217dcb775df273e9bbebecba2fadb887 100644
--- a/content/2.defense-systems/lit.md
+++ b/content/2.defense-systems/lit.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Other (Cleaves an elongation factor, inhibiting cellular translation
---
-# Lit
# Lit
## Example of genomic structure
diff --git a/content/2.defense-systems/mads.md b/content/2.defense-systems/mads.md
new file mode 100644
index 0000000000000000000000000000000000000000..77782681ce6e6022db8157633d542e0c232e03c0
--- /dev/null
+++ b/content/2.defense-systems/mads.md
@@ -0,0 +1,21 @@
+---
+title: MADS
+tableColumns:
+ article:
+ doi: 10.1101/2023.03.30.534895
+ abstract: |
+ The constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5-9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot in Pseudomonas aeruginosa and distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome of P. aeruginosa SMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
+---
+
+# MADS
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1101/2023.03.30.534895
+
+---
+::
diff --git a/content/2.defense-systems/mazef.md b/content/2.defense-systems/mazef.md
new file mode 100644
index 0000000000000000000000000000000000000000..1ee0682eededf5b81ba98809b209f546f1e01144
--- /dev/null
+++ b/content/2.defense-systems/mazef.md
@@ -0,0 +1,21 @@
+---
+title: MazEF
+tableColumns:
+ article:
+ doi: 10.1007/s00438-004-1048-y
+ abstract: |
+ The Escherichia coli gene pair mazEF is a regulatable chromosomal toxin-antitoxin module: mazF encodes a stable toxin and mazE encodes for a labile antitoxin that overcomes the lethal effect of MazF. Because MazE is labile, inhibition of mazE expression results in cell death. We studied the effect of mazEF on the development of bacteriophage P1 upon thermoinduction of the prophage P1CM c1ts and upon infection with virulent phage particles (P1vir). In several E. coli strains, we showed that the ?mazEF derivative strains produced significantly more phages than did the parent strain. In addition, upon induction of K38(P1CM c1ts), nearly all of the ?mazEF mutant cells lysed; in contrast, very few of the parental mazEF + K38 cells underwent lysis. However, most of these cells did not remain viable. Thus, while the ?mazEF cells die as a result of the lytic action of the phage, most of the mazEF + cells are killed by a different mechanism, apparently through the action of the chromosomal mazEF system itself. Furthermore, the introduction of lysogens into a growing non-lysogenic culture is lethal to ?mazEF but not for mazEF + cultures. Thus, although mazEF action causes individual cells to die, upon phage growth this is generally beneficial to the bacterial culture because it causes P1 phage exclusion from the bacterial population. These results provide additional support for the view that bacterial cultures may share some of the characteristics of multicellular organisms.
+---
+
+# MazEF
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1007/s00438-004-1048-y
+
+---
+::
diff --git a/content/2.defense-systems/menshen.md b/content/2.defense-systems/menshen.md
index b219cfe8e0afe50b30c038c1b756c7943c7c5d64..ec508e9f4cd0201a85dd6c7f2cfa617375a68641 100644
--- a/content/2.defense-systems/menshen.md
+++ b/content/2.defense-systems/menshen.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Menshen
# Menshen
## Example of genomic structure
diff --git a/content/2.defense-systems/mmb_gp29_gp30.md b/content/2.defense-systems/mmb_gp29_gp30.md
new file mode 100644
index 0000000000000000000000000000000000000000..4003dd632eacb44a505d6c70e60406877467e5c6
--- /dev/null
+++ b/content/2.defense-systems/mmb_gp29_gp30.md
@@ -0,0 +1,21 @@
+---
+title: MMB_gp29_gp30
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# MMB_gp29_gp30
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/mok_hok_sok.md b/content/2.defense-systems/mok_hok_sok.md
index 414f643a1294fbc42df8613961298c2074637373..33a83651774df7934c5bc901084870f5d7a1772e 100644
--- a/content/2.defense-systems/mok_hok_sok.md
+++ b/content/2.defense-systems/mok_hok_sok.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Mok_Hok_Sok
# Mok_Hok_Sok
## Example of genomic structure
diff --git a/content/2.defense-systems/mokosh.md b/content/2.defense-systems/mokosh.md
index e46e8009cb7646414506c2ebb24d039a375c3463..d455ce34bf0fc2eb22358dacf270560595ed476d 100644
--- a/content/2.defense-systems/mokosh.md
+++ b/content/2.defense-systems/mokosh.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Mokosh
# Mokosh
## Example of genomic structure
diff --git a/content/2.defense-systems/mqsrac.md b/content/2.defense-systems/mqsrac.md
index 934810f74c7fafa3caf968b00572a504d8da0eef..a4c93c5c0ac05f6fdef6c9a4f60116147ed5ad19 100644
--- a/content/2.defense-systems/mqsrac.md
+++ b/content/2.defense-systems/mqsrac.md
@@ -7,7 +7,6 @@ tableColumns:
Myriad bacterial anti-phage systems have been described and often the mechanism of programmed cell death is invoked for phage inhibition. However, there is little evidence of ‘suicide’ under physiological conditions for these systems. Instead of death to stop phage propagation, we show here that persister cells, i.e., transiently-tolerant, dormant, antibiotic-insensitive cells, are formed and survive using the Escherichia coli C496_10 tripartite toxin/antitoxin system MqsR/MqsA/MqsC to inhibit T2 phage. Specifically, MqsR/MqsA/MqsC inhibited T2 phage by one million-fold and reduced T2 titers by 500-fold. During T2 phage attack, in the presence of MqsR/MqsA/MqsC, evidence of persistence include the single-cell physiological change of reduced metabolism (via flow cytometry), increased spherical morphology (via transmission electron microscopy), and heterogeneous resuscitation. Critically, we found restriction-modification systems (primarily EcoK McrBC) work in concert with the toxin/antitoxin system to inactivate phage, likely while the cells are in the persister state. Phage attack also induces persistence in Klebsiella and Pseudomonas spp. Hence, phage attack invokes a stress response similar to antibiotics, starvation, and oxidation, which leads to persistence, and this dormant state likely allows restriction/modification systems to clear phage DNA.
---
-# MqsRAC
# MqsRAC
## Example of genomic structure
diff --git a/content/2.defense-systems/nhi.md b/content/2.defense-systems/nhi.md
index d3ed4b73874c4889279504685e66f2213104d140..0f2ce7478a3b363eed5fed92892cf085c75c9adf 100644
--- a/content/2.defense-systems/nhi.md
+++ b/content/2.defense-systems/nhi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading (?)
---
-# Nhi
# Nhi
## Example of genomic structure
diff --git a/content/2.defense-systems/nixi.md b/content/2.defense-systems/nixi.md
index 0befa10ab77e6909bd74b7a14984b2a120727e94..5b44630e971a6496d2e68c1ff5c34a5a9fe58fb1 100644
--- a/content/2.defense-systems/nixi.md
+++ b/content/2.defense-systems/nixi.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# NixI
# NixI
## Example of genomic structure
diff --git a/content/2.defense-systems/nlr.md b/content/2.defense-systems/nlr.md
index 8b997d621d88c01166e2e0780fca3c52bb493c35..d8a572cf49d374c532a128beef9079a98aaa9c41 100644
--- a/content/2.defense-systems/nlr.md
+++ b/content/2.defense-systems/nlr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# NLR
# NLR
## Example of genomic structure
diff --git a/content/2.defense-systems/old_exonuclease.md b/content/2.defense-systems/old_exonuclease.md
index 01c94eb824142b612755ffd0c4eeb65057ddadbe..069b112f0e66ed7f173c18d52d62b7df798159d2 100644
--- a/content/2.defense-systems/old_exonuclease.md
+++ b/content/2.defense-systems/old_exonuclease.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Old_exonuclease
# Old_exonuclease
## Example of genomic structure
diff --git a/content/2.defense-systems/olokun.md b/content/2.defense-systems/olokun.md
index e3c07e3a266769379a83d284d8caa60cbcdcac92..5b4693f442e5541e286bf01be1c6a9bec5160870 100644
--- a/content/2.defense-systems/olokun.md
+++ b/content/2.defense-systems/olokun.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Olokun
# Olokun
## Example of genomic structure
diff --git a/content/2.defense-systems/pago.md b/content/2.defense-systems/pago.md
index eae655759d495515eec2bd93c05b5ba223c9aed8..bf67ee0606e071464f9dcd53afc2bcf10f9c6488 100644
--- a/content/2.defense-systems/pago.md
+++ b/content/2.defense-systems/pago.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse (Nucleotide modifyingn, Membrane disrupting)
---
-# pAgo
# pAgo
## Example of genomic structure
diff --git a/content/2.defense-systems/panchino_gp28.md b/content/2.defense-systems/panchino_gp28.md
new file mode 100644
index 0000000000000000000000000000000000000000..b1d1891b8baf8e5b038e32c5430954435a0ebcbf
--- /dev/null
+++ b/content/2.defense-systems/panchino_gp28.md
@@ -0,0 +1,21 @@
+---
+title: Panchino_gp28
+tableColumns:
+ article:
+ doi: 10.1038/nmicrobiol.2016.251
+ abstract: |
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
+---
+
+# Panchino_gp28
+
+## To do
+
+## Relevant abstract
+::article-doi-list
+---
+items:
+ - doi: 10.1038/nmicrobiol.2016.251
+
+---
+::
diff --git a/content/2.defense-systems/paris.md b/content/2.defense-systems/paris.md
index 8a1a858eaa94444626fb5f8d4069cf4d94598f32..6a881f784e5fb744e7a579bead124a0fead2694f 100644
--- a/content/2.defense-systems/paris.md
+++ b/content/2.defense-systems/paris.md
@@ -11,7 +11,7 @@ tableColumns:
---
# Paris
-# Paris
+
## Description
PARIS (for Phage Anti-Restriction-Induced System) is a novel anti-phage system. PARIS is found in 4% of prokaryotic genomes. It comprises an ATPase associated with a DUF4435 protein, which can be found either as a two-gene cassette or a single-gene fusion (1).
diff --git a/content/2.defense-systems/pd-lambda-1.md b/content/2.defense-systems/pd-lambda-1.md
index e0894156a35fdd46bcb4c5ad60c2c027fa1c51ca..7eda7e6d39b8336bddd0b4a302215472399f0a57 100644
--- a/content/2.defense-systems/pd-lambda-1.md
+++ b/content/2.defense-systems/pd-lambda-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-1
# PD-Lambda-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-2.md b/content/2.defense-systems/pd-lambda-2.md
index 063ee69f212deacd5d2e7a0bdad9c97d11762053..44c4f60edd0aed20be918b9e9e3665df1e542215 100644
--- a/content/2.defense-systems/pd-lambda-2.md
+++ b/content/2.defense-systems/pd-lambda-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-2
# PD-Lambda-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-3.md b/content/2.defense-systems/pd-lambda-3.md
index a79919bd35561b5e751f003c06d952887efed984..7000431905faf729922ffa8e3ca5eca2b17f65c1 100644
--- a/content/2.defense-systems/pd-lambda-3.md
+++ b/content/2.defense-systems/pd-lambda-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-3
# PD-Lambda-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-4.md b/content/2.defense-systems/pd-lambda-4.md
index cbc0f346bcb7711f0ffbabac021955b92e429831..416d993896d9b5308722185df5d4e2fe30ab61e2 100644
--- a/content/2.defense-systems/pd-lambda-4.md
+++ b/content/2.defense-systems/pd-lambda-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-4
# PD-Lambda-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-5.md b/content/2.defense-systems/pd-lambda-5.md
index a13d1c07beb80c9f811be2b99623870ea78e590c..eef05860ef8ee1b7f1bfa5bfaedc13b5ce8e4890 100644
--- a/content/2.defense-systems/pd-lambda-5.md
+++ b/content/2.defense-systems/pd-lambda-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-5
# PD-Lambda-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-lambda-6.md b/content/2.defense-systems/pd-lambda-6.md
index 190e8c01a91943ce1ab5d4eb33305e733848404b..6fe30c0b3b07af60c54accfba95ac1e22dbb0d56 100644
--- a/content/2.defense-systems/pd-lambda-6.md
+++ b/content/2.defense-systems/pd-lambda-6.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-Lambda-6
# PD-Lambda-6
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-1.md b/content/2.defense-systems/pd-t4-1.md
index bf19377788bb32a61ae898092ef4e5d5d81e6d01..7d9cdb3052fbf4f139cb4d11a449c7dfe70d2508 100644
--- a/content/2.defense-systems/pd-t4-1.md
+++ b/content/2.defense-systems/pd-t4-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-1
# PD-T4-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-10.md b/content/2.defense-systems/pd-t4-10.md
index 30e0935337b416c84524c43e22651a8cbbc69ff6..703a26ad7bc0f5e56ff0b326d348609d3746e5da 100644
--- a/content/2.defense-systems/pd-t4-10.md
+++ b/content/2.defense-systems/pd-t4-10.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-10
# PD-T4-10
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-2.md b/content/2.defense-systems/pd-t4-2.md
index 4c058c11fbb90f4105bf8d5d0348ad2b89cd7dce..2dd4523eeb405689a70ddaf68b31018b0b196412 100644
--- a/content/2.defense-systems/pd-t4-2.md
+++ b/content/2.defense-systems/pd-t4-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-2
# PD-T4-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-3.md b/content/2.defense-systems/pd-t4-3.md
index c61bcf03247240e41028b754cc5228f68c1ed2cc..49c94b69c65de83fdf47b32e942de047f2c5a754 100644
--- a/content/2.defense-systems/pd-t4-3.md
+++ b/content/2.defense-systems/pd-t4-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-3
# PD-T4-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-4.md b/content/2.defense-systems/pd-t4-4.md
index 7fafa2ee769bb4c3233061ae4efa1ce8a13c65c3..d0b68a43a46421c0d2b5e034ee50e9fdb5320365 100644
--- a/content/2.defense-systems/pd-t4-4.md
+++ b/content/2.defense-systems/pd-t4-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-4
# PD-T4-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-5.md b/content/2.defense-systems/pd-t4-5.md
index c7e600d2fc136b1babd417394d2ccf167b40d8cc..856b8818ba002994dd22af14b4cc9c3859e4908d 100644
--- a/content/2.defense-systems/pd-t4-5.md
+++ b/content/2.defense-systems/pd-t4-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-5
# PD-T4-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-6.md b/content/2.defense-systems/pd-t4-6.md
index 0a63138b84a079364694155a4fac51c28a57b4f9..b47fb45ac31df2301509661aa4f664712dd6a03b 100644
--- a/content/2.defense-systems/pd-t4-6.md
+++ b/content/2.defense-systems/pd-t4-6.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-6
# PD-T4-6
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-7.md b/content/2.defense-systems/pd-t4-7.md
index 7279ce0a4f4fb3fb72ddd1afc353cd26eb934f6f..8042bc4c3469270ada86625f5fd77a213739ffbb 100644
--- a/content/2.defense-systems/pd-t4-7.md
+++ b/content/2.defense-systems/pd-t4-7.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-7
# PD-T4-7
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-8.md b/content/2.defense-systems/pd-t4-8.md
index 99dde5a14d7ae079da7b51f838963cd105c43fa1..34c7eccf97b4950ff6595c7a64cf2d8c7a5637f5 100644
--- a/content/2.defense-systems/pd-t4-8.md
+++ b/content/2.defense-systems/pd-t4-8.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-8
# PD-T4-8
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t4-9.md b/content/2.defense-systems/pd-t4-9.md
index c7425ba907370a781d481e9cb734a0be989cac5a..23424c29bb2f6a50a7c0fa9f981e91be69f387d2 100644
--- a/content/2.defense-systems/pd-t4-9.md
+++ b/content/2.defense-systems/pd-t4-9.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T4-9
# PD-T4-9
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-1.md b/content/2.defense-systems/pd-t7-1.md
index aea267edc4e7e8c435aedca8c3c2800c0a6b9a55..7374c6a0d4e660da7b62e69c57efbdb450bd5989 100644
--- a/content/2.defense-systems/pd-t7-1.md
+++ b/content/2.defense-systems/pd-t7-1.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-1
# PD-T7-1
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-2.md b/content/2.defense-systems/pd-t7-2.md
index 936f9bd2e704375ff7508701218f23c46f73241f..e2890ee347f0045102928e94e929dbef5d8ed75c 100644
--- a/content/2.defense-systems/pd-t7-2.md
+++ b/content/2.defense-systems/pd-t7-2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-2
# PD-T7-2
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-3.md b/content/2.defense-systems/pd-t7-3.md
index 68a80228d9751b6d215f01fbf35d5bc1957988e6..f7451c726d7676563dff39f0bdd699f7bce82158 100644
--- a/content/2.defense-systems/pd-t7-3.md
+++ b/content/2.defense-systems/pd-t7-3.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-3
# PD-T7-3
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-4.md b/content/2.defense-systems/pd-t7-4.md
index f819d8a29f25753de34a1f53158a5744e8fc23ce..c7693137a922e2d0f81ba2d3e3cd6d0eedc032d7 100644
--- a/content/2.defense-systems/pd-t7-4.md
+++ b/content/2.defense-systems/pd-t7-4.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-4
# PD-T7-4
## Example of genomic structure
diff --git a/content/2.defense-systems/pd-t7-5.md b/content/2.defense-systems/pd-t7-5.md
index 859515e92b53a4049d98e9d668e30032c59542d9..908910e3c9f9abecae778f174b37d6d4aad06bb4 100644
--- a/content/2.defense-systems/pd-t7-5.md
+++ b/content/2.defense-systems/pd-t7-5.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PD-T7-5
# PD-T7-5
## Example of genomic structure
diff --git a/content/2.defense-systems/pfiat.md b/content/2.defense-systems/pfiat.md
index 29b87685f5debcd99780b53b5f7a91264d60a330..7638ef7de124497dc41a5565385b06872277eb48 100644
--- a/content/2.defense-systems/pfiat.md
+++ b/content/2.defense-systems/pfiat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PfiAT
# PfiAT
## Example of genomic structure
diff --git a/content/2.defense-systems/phrann_gp29_gp30.md b/content/2.defense-systems/phrann_gp29_gp30.md
index 26f84206f396ea5dde18454ba485545aca08b53d..3149e458b2c4c41282039053255b414a3c14e079 100644
--- a/content/2.defense-systems/phrann_gp29_gp30.md
+++ b/content/2.defense-systems/phrann_gp29_gp30.md
@@ -1,14 +1,14 @@
---
-title: phrann_gp29_gp30
+title: Phrann_gp29_gp30
tableColumns:
article:
doi: 10.1038/nmicrobiol.2016.251
abstract: |
- Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.
+ Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
---
-# phrann_gp29_gp30
-# phrann_gp29_gp30
+# Phrann_gp29_gp30
+
## Example of genomic structure
The phrann_gp29_gp30 system is composed of 2 proteins: gp30 and, gp29.
diff --git a/content/2.defense-systems/pif.md b/content/2.defense-systems/pif.md
index 4c3fbfacd3f1f36f46a97ce604c052c3ced28bff..58444a2c4ad0d2b0cdd8beeb3335a991fc5fa827 100644
--- a/content/2.defense-systems/pif.md
+++ b/content/2.defense-systems/pif.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting (?)
---
-# Pif
# Pif
## Example of genomic structure
diff --git a/content/2.defense-systems/prrc.md b/content/2.defense-systems/prrc.md
index 39e3b19c7095128589d3d3b0b0f45587bde43507..317ff23baa45d36a7b27312a8ee19e30c8933a18 100644
--- a/content/2.defense-systems/prrc.md
+++ b/content/2.defense-systems/prrc.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# PrrC
# PrrC
## Example of genomic structure
diff --git a/content/2.defense-systems/psyrta.md b/content/2.defense-systems/psyrta.md
index 2bba747f3ba4e065aca0d9da4dccf0cf3ffce1e3..616000fa4fa341d15b4c1436bca1106732365b5d 100644
--- a/content/2.defense-systems/psyrta.md
+++ b/content/2.defense-systems/psyrta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# PsyrTA
# PsyrTA
## Example of genomic structure
diff --git a/content/2.defense-systems/pycsar.md b/content/2.defense-systems/pycsar.md
index 1bbf925fc36ed282875864872d2bcec7276dad83..7888ee671958969f5c981c1fb16268bdafcfd02f 100644
--- a/content/2.defense-systems/pycsar.md
+++ b/content/2.defense-systems/pycsar.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting, Nucleotides modifying
---
-# Pycsar
# Pycsar
## Example of genomic structure
diff --git a/content/2.defense-systems/radar.md b/content/2.defense-systems/radar.md
index 191d0d5165b96fe19b2b45f23789226c20888327..4305d7154cedd3daadfb15e6b2c13660e0a6a3d0 100644
--- a/content/2.defense-systems/radar.md
+++ b/content/2.defense-systems/radar.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RADAR
# RADAR
## Description
diff --git a/content/2.defense-systems/retron.md b/content/2.defense-systems/retron.md
index 9fd21f64d363b4f87b9c4e781ac8efe04db15380..ab9d432b8cff85aedbb13adedc8207d38137ebe3 100644
--- a/content/2.defense-systems/retron.md
+++ b/content/2.defense-systems/retron.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Diverse
---
-# Retron
# Retron
## Description
diff --git a/content/2.defense-systems/rexab.md b/content/2.defense-systems/rexab.md
index fbc34b388d9ed32c633d3b554e329f88bc338121..46cff76a02f6f19ccc87c9bc87b77fd91cd1cccc 100644
--- a/content/2.defense-systems/rexab.md
+++ b/content/2.defense-systems/rexab.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Membrane disrupting
---
-# RexAB
# RexAB
## Example of genomic structure
diff --git a/content/2.defense-systems/rloc.md b/content/2.defense-systems/rloc.md
index 68d1fc32471e6a31772a69ea96dfc3bdf6f7def6..a413fe3a7c81adcdf703a7293b6b0b8c95f4a780 100644
--- a/content/2.defense-systems/rloc.md
+++ b/content/2.defense-systems/rloc.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RloC
# RloC
## Example of genomic structure
diff --git a/content/2.defense-systems/rm.md b/content/2.defense-systems/rm.md
index 70abce918f14627e978ced621637f6c67bfae8ed..60dd9da788929826ee041b84a6ec09f1f5417d1d 100644
--- a/content/2.defense-systems/rm.md
+++ b/content/2.defense-systems/rm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# RM
# RM
## Example of genomic structure
diff --git a/content/2.defense-systems/rnlab.md b/content/2.defense-systems/rnlab.md
index c011da5f5e2a8344efd86b148c7d50caadc7f1f3..0f9acc42f4f8410981c2cd389339f002138a7df4 100644
--- a/content/2.defense-systems/rnlab.md
+++ b/content/2.defense-systems/rnlab.md
@@ -4,13 +4,12 @@ tableColumns:
article:
doi: 10.1534/genetics.110.121798
abstract: |
- RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA–rnlB define a new toxin–antitoxin (TA) system.
+ RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Ectopic expression of RnlA caused inhibition of cell growth and rapid degradation of mRNAs in ?rnlAB cells. On the other hand, RnlB neutralized these RnlA effects. Furthermore, overexpression of RnlB in wild-type cells could completely suppress the growth defect of a T4 dmd mutant, that is, excess RnlB inhibited RNase LS activity. Pull-down analysis showed a specific interaction between RnlA and RnlB. Compared to RnlA, RnlB was extremely unstable, being degraded by ClpXP and Lon proteases, and this instability may increase RNase LS activity after T4 infection. All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.
Sensor: Monitor the integrity of the bacterial cell machinery
Activator: Direct
Effector: Nucleic acid degrading
---
-# RnlAB
# RnlAB
## Example of genomic structure
diff --git a/content/2.defense-systems/rosmerta.md b/content/2.defense-systems/rosmerta.md
index 89ad12cb9ad75226f67ea5bfb960d40a49b6bc57..d9ffb12f10f0b7a9fbfe689b7d3cb95f420ce18a 100644
--- a/content/2.defense-systems/rosmerta.md
+++ b/content/2.defense-systems/rosmerta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# RosmerTA
# RosmerTA
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_2tm_1tm_tir.md b/content/2.defense-systems/rst_2tm_1tm_tir.md
index bcdaa38960f6864f40bc11512f6a82fbe507b0a4..761b4a4f64b1a7e4bf76a98e93ab265c5ce25ade 100644
--- a/content/2.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/2.defense-systems/rst_2tm_1tm_tir.md
@@ -7,7 +7,6 @@ tableColumns:
Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
---
-# Rst_2TM_1TM_TIR
# Rst_2TM_1TM_TIR
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_3hp.md b/content/2.defense-systems/rst_3hp.md
index c10986546e46dbdacec03d0e691f7c535ce8c83a..b31ab1f89df8f1b96b4e0979738f51ed0a3a7de4 100644
--- a/content/2.defense-systems/rst_3hp.md
+++ b/content/2.defense-systems/rst_3hp.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_3HP
# Rst_3HP
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_duf4238.md b/content/2.defense-systems/rst_duf4238.md
index bb1671511d1c57233aff2837a653f4ec32b62532..262546f1f66aa8381f376027323710022bcdc9b7 100644
--- a/content/2.defense-systems/rst_duf4238.md
+++ b/content/2.defense-systems/rst_duf4238.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_DUF4238
# Rst_DUF4238
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_gop_beta_cll.md b/content/2.defense-systems/rst_gop_beta_cll.md
index c6049f36b62d2c7d11e0bcf53761b9bc3c8504de..220806795da0e6cc4faea652e88de1855d8279a2 100644
--- a/content/2.defense-systems/rst_gop_beta_cll.md
+++ b/content/2.defense-systems/rst_gop_beta_cll.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_gop_beta_cll
# Rst_gop_beta_cll
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_helicaseduf2290.md b/content/2.defense-systems/rst_helicaseduf2290.md
index 51a229be4f321b7d9e1a10198f13f48778da0f55..d935ef2d8a120c5408fcdce2d064216b34b35860 100644
--- a/content/2.defense-systems/rst_helicaseduf2290.md
+++ b/content/2.defense-systems/rst_helicaseduf2290.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_HelicaseDUF2290
# Rst_HelicaseDUF2290
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_hydrolase-3tm.md b/content/2.defense-systems/rst_hydrolase-3tm.md
index be86ec803569b9cc0e0cfcce7faf9dc56a84e24c..00edbe611de878ae1d141cabe0759504882a1c8a 100644
--- a/content/2.defense-systems/rst_hydrolase-3tm.md
+++ b/content/2.defense-systems/rst_hydrolase-3tm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_Hydrolase-3Tm
# Rst_Hydrolase-3Tm
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_rt-nitrilase-tm.md b/content/2.defense-systems/rst_rt-nitrilase-tm.md
index 5522003e962c147deeb06e1f38556fb843ec8205..a4453e14c587f23d62db4acfa1a500b56896a652 100644
--- a/content/2.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/2.defense-systems/rst_rt-nitrilase-tm.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_RT-nitrilase-Tm
# Rst_RT-nitrilase-Tm
## Example of genomic structure
diff --git a/content/2.defense-systems/rst_tir-nlr.md b/content/2.defense-systems/rst_tir-nlr.md
index 59f5c281415d98e517e5479b338b9505d8630d66..c7e52d931a81317937f80433b0df3024463a31c7 100644
--- a/content/2.defense-systems/rst_tir-nlr.md
+++ b/content/2.defense-systems/rst_tir-nlr.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Rst_TIR-NLR
# Rst_TIR-NLR
## Example of genomic structure
diff --git a/content/2.defense-systems/sanata.md b/content/2.defense-systems/sanata.md
index 54a92cf671663f04a7da08554f081e7f1984cfd5..d3867a55115b17a154a8b8be5f27188ba34f00b2 100644
--- a/content/2.defense-systems/sanata.md
+++ b/content/2.defense-systems/sanata.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SanaTA
# SanaTA
## Example of genomic structure
diff --git a/content/2.defense-systems/sefir.md b/content/2.defense-systems/sefir.md
index e299110e980a2338651e255c224a5291fb4bb2c1..b6b8479006094309d74236b780d94e40520d10c1 100644
--- a/content/2.defense-systems/sefir.md
+++ b/content/2.defense-systems/sefir.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SEFIR
# SEFIR
## Description
The SEFIR defense system is composed of a single bacterial SEFIR (bSEFIR)-domain protein. bSEFIR-domain genes were identified in bacterial genomes, were shown to be enriched in defense islands and the activity of the defense system was first experimentally validated in *Bacillus sp.* NIO-1130 against phage phi29 [1].
diff --git a/content/2.defense-systems/septu.md b/content/2.defense-systems/septu.md
index 487f76c7bc296b8e031c79a648eb9728aa48c879..17e4a741116f99d3bea3d3bb72a08f939abc4a37 100644
--- a/content/2.defense-systems/septu.md
+++ b/content/2.defense-systems/septu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Septu
# Septu
## Example of genomic structure
diff --git a/content/2.defense-systems/shango.md b/content/2.defense-systems/shango.md
index 399734e0eca8a1149130aa6b8d8f684323ca69c0..0ce65b4317aa6635842ecdaa5a782dcdf2a0b9e5 100644
--- a/content/2.defense-systems/shango.md
+++ b/content/2.defense-systems/shango.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Shango
# Shango
## Description
@@ -67,4 +66,4 @@ Shango was discovered in parallel by Adi Millman (Sorek group) and the team of J
[2] Johnson, Matthew, Laderman, Eric, Huiting, Erin, Zhang, Charles, Davidson, Alan, & Bondy-Denomy, Joseph. (2022). _Core Defense Hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems_. [https://doi.org/10.5281/ZENODO.7254690](https://doi.org/10.5281/ZENODO.7254690)
-[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
\ No newline at end of file
+[3] Alekhina, O., Valkovicova, L., & Turna, J. (2011). Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. _General physiology and biophysics_, _30_(3), 286-292.
diff --git a/content/2.defense-systems/shedu.md b/content/2.defense-systems/shedu.md
index d775b45102902e08e3684a0bbe7206060c6bab70..6b939d8718a6b71c9c58c7274e976ae90f5e70d8 100644
--- a/content/2.defense-systems/shedu.md
+++ b/content/2.defense-systems/shedu.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Shedu
# Shedu
## Example of genomic structure
diff --git a/content/2.defense-systems/shosta.md b/content/2.defense-systems/shosta.md
index 9c1c779c4ce0db7655d806fe20634609fb7fef90..f4b0e62d836031ba0386c4c514b7b323d8eb87da 100644
--- a/content/2.defense-systems/shosta.md
+++ b/content/2.defense-systems/shosta.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# ShosTA
# ShosTA
## Example of genomic structure
diff --git a/content/2.defense-systems/sofic.md b/content/2.defense-systems/sofic.md
index 3d1ca7e59b480aa165175bd442c4786637084783..b8d6f66dd993693cf05d68558fb11782daee647a 100644
--- a/content/2.defense-systems/sofic.md
+++ b/content/2.defense-systems/sofic.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SoFIC
# SoFIC
## Example of genomic structure
diff --git a/content/2.defense-systems/spbk.md b/content/2.defense-systems/spbk.md
index d7b93c1725028873dd962de0885dab9a54bc52fb..221db9e4040a62b7b72934d3023cc6a05e70444d 100644
--- a/content/2.defense-systems/spbk.md
+++ b/content/2.defense-systems/spbk.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# SpbK
# SpbK
## Example of genomic structure
diff --git a/content/2.defense-systems/sspbcde.md b/content/2.defense-systems/sspbcde.md
index fc7e586545095935207fd3ce3f38a495d74f5d0e..38618b531f256479107329630e1447db90d1e574 100644
--- a/content/2.defense-systems/sspbcde.md
+++ b/content/2.defense-systems/sspbcde.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# SspBCDE
# SspBCDE
## Example of genomic structure
diff --git a/content/2.defense-systems/stk2.md b/content/2.defense-systems/stk2.md
index 3a1fa18fbfb474e0aac73a0e622c049871f1a452..0cd7d51e1aa4520a137ab36e052635783c3ddb68 100644
--- a/content/2.defense-systems/stk2.md
+++ b/content/2.defense-systems/stk2.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Other (protein modifying)
---
-# Stk2
# Stk2
## Description
diff --git a/content/2.defense-systems/thoeris.md b/content/2.defense-systems/thoeris.md
index 51772f36b9a87283e78b2d742d2d883c36d6b458..8ccf5b662570c39e4e6966335a9664bef49f4a3f 100644
--- a/content/2.defense-systems/thoeris.md
+++ b/content/2.defense-systems/thoeris.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Thoeris
# Thoeris
## Example of genomic structure
diff --git a/content/2.defense-systems/tiamat.md b/content/2.defense-systems/tiamat.md
index 169abf12a873e98059be7f959d5dd5c195c20565..0959ef39d2d762428cb66b959ef1d886f39e9290 100644
--- a/content/2.defense-systems/tiamat.md
+++ b/content/2.defense-systems/tiamat.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Tiamat
# Tiamat
## Example of genomic structure
diff --git a/content/2.defense-systems/uzume.md b/content/2.defense-systems/uzume.md
index 167eb495d27e5880fd2b2dc7b8da861ae5bf9ba4..11e72a49b3f82fe039c68673dbf1bd97c6a3e444 100644
--- a/content/2.defense-systems/uzume.md
+++ b/content/2.defense-systems/uzume.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Uzume
# Uzume
## Example of genomic structure
diff --git a/content/2.defense-systems/viperin.md b/content/2.defense-systems/viperin.md
index 8bf85a847b9f1e2e0531d0928c89f8f043e2e6d2..46a2fdf95f29332e2a2b18f7216d38fabf50bc69 100644
--- a/content/2.defense-systems/viperin.md
+++ b/content/2.defense-systems/viperin.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleotide modifying
---
-# Viperin
# Viperin
## Description
diff --git a/content/2.defense-systems/wadjet.md b/content/2.defense-systems/wadjet.md
index 1b77a8a716685a0f3663daa8c56f4d17ff67671a..8fa050f0e5294c211ec6d8ab5d6d46b029896870 100644
--- a/content/2.defense-systems/wadjet.md
+++ b/content/2.defense-systems/wadjet.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Nucleic acid degrading
---
-# Wadjet
# Wadjet
## Example of genomic structure
diff --git a/content/2.defense-systems/zorya.md b/content/2.defense-systems/zorya.md
index f5acde756c7b50e63e2cc655edc598df6458ae12..6cb8efbec5d72455f183d7b2538566e834523e53 100644
--- a/content/2.defense-systems/zorya.md
+++ b/content/2.defense-systems/zorya.md
@@ -10,7 +10,6 @@ tableColumns:
Effector: Unknown
---
-# Zorya
# Zorya
## Example of genomic structure