content/3.defense-systems/pd-t7-5.md

@@ -14,23 +14,24 @@ tableColumns:
 # PD-T7-5
 ## Example of genomic structure
 
-The PD-T7-5 system is composed of one protein: PD-T7-5.
+The PD-T7-5 is composed of 1 protein: PD-T7-5.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![pd-t7-5](/pd-t7-5/PD-T7-5.svg){max-width=750px}
 
-PD-T7-5 system in the genome of *Bacillus cereus* (GCF_001941885.1) is composed of 1 protein: PD-T7-5 (WP_075395673.1).
+The PD-T7-5 system in *Shewanella putrefaciens* (GCF_019599085.1, NZ_CP080633) is composed of 1 protein: PD-T7-5 (WP_220590848.1) 
 
 ## Distribution of the system among prokaryotes
 
-The PD-T7-5 system is present in a total of 128 different species.
+Among the 22,803 complete genomes of RefSeq, the PD-T7-5 is detected in 336 genomes (1.47 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 363 genomes (1.6 %).
+The system was detected in 129 different species.
 
 ![pd-t7-5](/pd-t7-5/Distribution_PD-T7-5.svg){max-width=750px}
 
-*Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/pfiat.md

@@ -15,23 +15,24 @@ tableColumns:
 # PfiAT
 ## Example of genomic structure
 
-The PfiAT system is composed of 2 proteins: PfiA and, PfiT.
+The PfiAT is composed of 2 proteins: PfiA and PfiT.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![pfiat](/pfiat/PfiAT.svg){max-width=750px}
 
-PfiAT system in the genome of *Pseudomonas amygdali* (GCF_023207855.1) is composed of 2 proteins: PfiT (WP_096134620.1)and, PfiA (WP_057431469.1).
+The PfiAT system in *Desulfoscipio gibsoniae* (GCF_000233715.2, NC_021184) is composed of 2 proteins PfiA (WP_006521270.1) PfiT (WP_006521271.1) 
 
 ## Distribution of the system among prokaryotes
 
-The PfiAT system is present in a total of 261 different species.
+Among the 22,803 complete genomes of RefSeq, the PfiAT is detected in 819 genomes (3.59 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 819 genomes (3.6 %).
+The system was detected in 308 different species.
 
 ![pfiat](/pfiat/Distribution_PfiAT.svg){max-width=750px}
 
-*Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/phrann_gp29_gp30.md

@@ -13,23 +13,24 @@ tableColumns:
 
 ## Example of genomic structure
 
-The phrann_gp29_gp30 system is composed of 2 proteins: gp30 and, gp29.
+The Phrann_gp29_gp30 is composed of 2 proteins: gp29 and gp30.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
-![phrann_gp29_gp30](/phrann_gp29_gp30/phrann_gp29_gp30.svg){max-width=750px}
+![phrann_gp29_gp30](/phrann_gp29_gp30/Phrann_gp29_gp30.svg){max-width=750px}
 
-phrann_gp29_gp30 system in the genome of *Mycobacterium tuberculosis* (GCF_002448055.1) is composed of 2 proteins: gp29 (WP_003407164.1)and, gp30 (WP_003407167.1).
+The Phrann_gp29_gp30 system in *Demequina sp. TMPB413* (GCF_020447105.2, NZ_CP096184) is composed of 2 proteins gp29 (WP_226094934.1) gp30 (WP_226094935.1) 
 
 ## Distribution of the system among prokaryotes
 
-The phrann_gp29_gp30 system is present in a total of 35 different species.
+Among the 22,803 complete genomes of RefSeq, the Phrann_gp29_gp30 is detected in 312 genomes (1.37 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 314 genomes (1.4 %).
+The system was detected in 35 different species.
 
-![phrann_gp29_gp30](/phrann_gp29_gp30/Distribution_phrann_gp29_gp30.svg){max-width=750px}
+![phrann_gp29_gp30](/phrann_gp29_gp30/Distribution_Phrann_gp29_gp30.svg){max-width=750px}
+
+Proportion of genome encoding the Phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
-*Proportion of genome encoding the phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
 ## Experimental validation
 <mermaid>

content/3.defense-systems/pif.md

@@ -10,28 +10,45 @@ tableColumns:
     Activator: Unknown
     Effector: Membrane disrupting (?)
     PFAM: PF07693
+contributors: 
+  - Lucas Paoli
+relevantAbstracts:
+  - doi: 10.1007/BF00327934
+  - doi: 10.1016/j.virol.2004.06.001
+  - doi: 10.1128/jb.173.20.6507-6514.1991
+  - doi: 10.1038/newbio231037a0
 ---
 
 # Pif
+
+## Description
+
+The Pif system (Phage Inhibition by F factors) was first described by Morisson & Malamy :ref{doi=10.1038/newbio231037a0}. The Pif region of the F plasmid inhibits the phage T7 through abortive infection :ref{doi=10.1038/newbio231037a0,10.1007/BF00327934}.  
+
+## Molecular mechanisms
+
+PifA was later identified as the effector of the abortive infection :ref{doi=10.1128/jb.173.20.6507-6514.1991,10.1016/j.virol.2004.06.001} through nucleotide depletion by increased membrane permeability (also known as "leakage").
+
 ## Example of genomic structure
 
-The Pif system is composed of 2 proteins: PifC and, PifA.
+The Pif is composed of 2 proteins: PifA and PifC.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![pif](/pif/Pif.svg){max-width=750px}
 
-Pif system in the genome of *Escherichia coli* (GCF_018628815.1) is composed of 2 proteins: PifA (WP_000698737.1)and, PifC (WP_000952217.1).
+The Pif system in *Shigella flexneri* (GCF_022353545.1, NZ_CP055168) is composed of 2 proteins PifC (WP_000952217.1) PifA (WP_000698737.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Pif system is present in a total of 28 different species.
+Among the 22,803 complete genomes of RefSeq, the Pif is detected in 140 genomes (0.61 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 143 genomes (0.6 %).
+The system was detected in 25 different species.
 
 ![pif](/pif/Distribution_Pif.svg){max-width=750px}
 
-*Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -75,15 +92,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1007/BF00327934
-    - doi: 10.1016/j.virol.2004.06.001
-    - doi: 10.1128/jb.173.20.6507-6514.1991
-
----
-::
-

content/3.defense-systems/prrc.md

@@ -10,28 +10,45 @@ tableColumns:
     Activator: Direct
     Effector: Nucleic acid degrading
     PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF13166, PF18766
+contributors:
+    - Ernest Mordret
+relevant abstracts:
+    - doi: 10.1186/1743-422X-7-360
+    - doi: 10.1006/jmbi.1995.0343
 ---
 
 # PrrC
+
+## Description
+
+The PrrC system protects bacteria against phages via an abortive infection. It is composed of a single effector protein, but relies on the presence of a full type Ic restriction-modification system in the vicinity. PrrC proteins are therefore typically found embedded in a larger RM system.
+
+## Molecular mechanism
+The effector protein prrC complements a RM system by cutting tRNALys in the anticodon loop, upstream of the wobble nucleotide and causes the arrest of phage protein synthesis and phage growth.
+prrC serves as a guardian of the acrivity of EcoprrI, which can be inactivated by the Stp peptide of phage T4 at the beginning of infection. Inactivation of EcoprrI by Stp induces a conformation change that in turn activates PrrC, releasing its nuclease activity and stalling host and phage growth :ref{doi=10.1006/jmbi.1995.0343}.
+Because it sabotages the host's translation machinery, prrC is considered to be an abortive infection system. 
+
+
 ## Example of genomic structure
 
-The PrrC system is composed of 4 proteins: EcoprrI, Type_I_S, PrrC and, Type_I_REases.
+The PrrC is composed of the PrrC protein and a type I restriction modification system.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![prrc](/prrc/PrrC.svg){max-width=750px}
 
-PrrC system in the genome of *Streptococcus canis* (GCF_900636575.1) is composed of 4 proteins: Type_I_REases (WP_003046543.1), PrrC (WP_003046540.1), Type_I_S (WP_129544911.1)and, Type_I_MTases (WP_003046534.1).
+The PrrC system in *Parazoarcus communis* (GCF_003111645.1, NZ_CP022187) is composed of 4 proteins Type_I_REases (WP_108949925.1) Type_I_S (WP_108949926.1) PrrC (WP_108949927.1) Type_I_MTases (WP_108949929.1) 
 
 ## Distribution of the system among prokaryotes
 
-The PrrC system is present in a total of 285 different species.
+Among the 22,803 complete genomes of RefSeq, the PrrC is detected in 705 genomes (3.09 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 705 genomes (3.1 %).
+The system was detected in 309 different species.
 
 ![prrc](/prrc/Distribution_PrrC.svg){max-width=750px}
 
-*Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -78,14 +95,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1006/jmbi.1995.0343
-    - doi: 10.1186/1743-422X-7-360
-
----
-::
-

content/3.defense-systems/psyrta.md

@@ -10,28 +10,61 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00270, PF00271, PF02481, PF04851, PF18306
+contributors:
+    - Ernest Mordret
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.09.017
+    - doi: 10.1016/j.molcel.2013.02.002
+    - doi: 10.1371/journal.ppat.1005317
 ---
 
 # PsyrTA
+
+## Description
+
+Originally found in a high throughput shotgun cloning of bacterial fragments in E. coli looking for Toxin-Antitoxin pairs. PsyrTA is composed of two proteins, PsyrT, the toxin, is a RecQ family DNA helicase, and PsyrA, the antitoxin, was shown to be a Nucleotide-binding protein. Note that that system is sometimes called RqlHI :ref{doi=10.1371/journal.ppat.1005317}, where RqlH refers to PsyrT and RqlI to PsyrA
+
+## Molecular mechanisms
+
+from :ref{doi=10.1016/j.molcel.2013.02.002} :
+
+> The psyrT shares homology with domains of the RecQ helicase,
+> a family of proteins implicated in DNA repair (Bernstein et al.,
+> 2010); and the antitoxin of the same system, psyrA, has a nucle-
+> otide binding domain (COG0758) that was previously described
+> in proteins involved in DNA uptake
+
+
+from :ref{doi=10.1016/j.chom.2022.09.017} :
+
+> Both systems encode an antitoxin
+> with homology to DprA, a single-stranded DNA (ssDNA)-binding
+> protein known to be involved in DNA transformation (Mortier-
+> Barrière et al., 2007). The toxin contains a phosphoribosyl trans-
+> ferase (PRTase) domain, which was previously found in effectors
+> of retron abortive infection systems "
+
+
 ## Example of genomic structure
 
-The PsyrTA system is composed of 2 proteins: PsyrT and, PsyrA.
+The PsyrTA is composed of 2 proteins: PsyrA and PsyrT.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![psyrta](/psyrta/PsyrTA.svg){max-width=750px}
 
-PsyrTA system in the genome of *Photorhabdus laumondii* (GCF_003343225.1) is composed of 2 proteins: PsyrT (WP_109791883.1)and, PsyrA (WP_113049635.1).
+The PsyrTA system in *Providencia rettgeri* (GCF_013702265.1, NZ_CP059348) is composed of 2 proteins PsyrT (WP_049246657.1) PsyrA (WP_001103168.1) 
 
 ## Distribution of the system among prokaryotes
 
-The PsyrTA system is present in a total of 281 different species.
+Among the 22,803 complete genomes of RefSeq, the PsyrTA is detected in 629 genomes (2.76 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1435 genomes (6.3 %).
+The system was detected in 132 different species.
 
 ![psyrta](/psyrta/Distribution_PsyrTA.svg){max-width=750px}
 
-*Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -77,14 +110,5 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.chom.2022.09.017
-    - doi: 10.1016/j.molcel.2013.02.002
-
----
 ::
 

content/3.defense-systems/pycsar.md

@@ -15,23 +15,26 @@ tableColumns:
 # Pycsar
 ## Example of genomic structure
 
-The Pycsar system is composed of 2 proteins: AG_cyclase and, Effector_TIR.
+The Pycsar is composed of at least 2 proteins: a Cyclase and Effector.
 
-Here is an example found in the RefSeq database: 
+Like the CBASS system, it can encode for a variety of different effectors.
+
+Here is an example found in the RefSeq database:
 
 ![pycsar](/pycsar/Pycsar.svg){max-width=750px}
 
-Pycsar system in the genome of *Staphylococcus aureus* (GCF_003186105.1) is composed of 2 proteins: AG_cyclase (WP_065316016.1)and, 2TM_5 (WP_000073144.1).
+The Pycsar system in *Nocardioides sambongensis* (GCF_006494815.1, NZ_CP041091) is composed of 2 proteins 2TM_5 (WP_141014207.1) AG_cyclase (WP_141014208.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Pycsar system is present in a total of 276 different species.
+Among the 22,803 complete genomes of RefSeq, the Pycsar is detected in 552 genomes (2.42 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 559 genomes (2.5 %).
+The system was detected in 295 different species.
 
 ![pycsar](/pycsar/Distribution_Pycsar.svg){max-width=750px}
 
-*Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/radar.md

@@ -23,27 +23,28 @@ RADAR mediates growth arrest upon infection and is therefore considered to be an
 
 ## Example of genomic structure
 
-The RADAR system have been describe in a total of 2 subsystems.
+A total of 2 subsystems have been described for the RADAR system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![radar](/radar/radar_I.svg){max-width=750px}
+![radar_i](/radar/radar_I.svg){max-width=750px}
 
-radar_I subsystem in the genome of *Dickeya dianthicola* (GCF_014893095.1) is composed of 2 proteins: rdrB_I (WP_192988590.1)and, rdrA_I (WP_192988591.1).
+The radar_I system in *Vibrio splendidus* (GCF_022812155.1, NZ_CP089205) is composed of 2 proteins rdrA_I (WP_243585344.1) rdrB_I (WP_243585345.1) 
 
-![radar](/radar/radar_II.svg){max-width=750px}
+![radar_ii](/radar/radar_II.svg){max-width=750px}
 
-radar_II subsystem in the genome of *Klebsiella aerogenes* (GCF_008693885.1) is composed of 3 proteins: rdrD_II (WP_015705078.1), rdrB_II (WP_015705077.1)and, rdrA_II (WP_015705076.1).
+The radar_II system in *Enterobacter sp. JH25* (GCF_021725435.1, NZ_CP091319) is composed of 3 proteins rdrD_II (WP_022649082.1) rdrB_II (WP_227746616.1) rdrA_II (WP_022649084.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RADAR system is present in a total of 39 different species.
+Among the 22,803 complete genomes of RefSeq, the RADAR is detected in 135 genomes (0.59 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 135 genomes (0.6 %).
+The system was detected in 44 different species.
 
 ![radar](/radar/Distribution_RADAR.svg){max-width=750px}
 
-*Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/retron.md

@@ -10,88 +10,118 @@ tableColumns:
     Activator: Unknown
     Effector: Diverse
     PFAM: PF00078, PF00089, PF01381, PF01582, PF12686, PF12844, PF13175, PF13304, PF13365, PF13476, PF13560, PF13676
+contributors: 
+  - Adi Millman
+  - Héloïse Georjon
+  - Aude Bernheim
+relevantAbstracts:
+  - doi: 10.1016/j.cell.2020.09.065
+  - doi: 10.1093/nar/gkaa1149
+  - doi: 10.1038/s41586-022-05091-4
+  - doi: 10.1126/science.aba0372
+  - doi: 10.1038/s41564-022-01197-7
+  - doi: 10.1093/nar/gkaa1149
+  - doi: 10.1038/s41589-021-00927-y
+  - doi: 10.1093/femsre/fuab025
+  - doi: 10.1371/journal.pone.0285274
+  - doi: 10.1038/s41596-023-00819-6
+  - doi: 10.1093/nar/gkac177
+  - doi: 10.1080/15476286.2019.1639310
+  - doi: 10.1101/2023.08.16.553469
+
 ---
 
 # Retron
 ## Description
 
-Retrons are genetic elements constituted of a non-coding RNA (ncRNA) associated with a reverse-transcriptase (RT). The RT reverse-transcribes part of the ncRNA to generate an RNA-DNA hybrid molecule. Although the existence of retrons have been known for decades, their biological functions were unknown. Recent studies revealed that most retrons could in fact be anti-phage systems (1,2). 
+Retrons are distinct genetic elements found in bacterial genomes that code for a reverse transcriptase (RT) and a non-coding RNA (ncRNA). These elements generate a unique satellite DNA/RNA hybrid in the cell termed multicopy single-stranded DNA (msDNA). Retrons were recently found to function as anti-phage defense systems protecting bacteria against phage infection :ref{doi=10.1016/j.cell.2020.09.065}. Their defensive unit is composed of three components: the reverse transcriptase, the non-coding RNA, and an effector protein. 
 
-![retron](/retron/Retron_mestre_et_al_fig_1.jpg)
+### Discovery
+Discovery
+Retrons were originally discovered in 1984 in Myxococcus xanthus, when Yee et al. :ref{doi=10.1016/0092-8674(84)90541-5} identified a high copy, short, single-stranded linear ex-chromosomal DNA fragment in the gram-negative bacterium, Myxococcus xanthus. These multi-copy single-stranded DNA fragments were termed msDNA. Further studies showed that this single-stranded DNA (ssDNA) is covalently linked to an RNA molecule :ref{doi=10.1016/0092-8674(87)90596-4}. Although at the time reverse transcriptases were only known from Eukaryotes and viruses, Inouye and colleagues hypothesized that msDNA must be a product of a reverse transcription reaction :ref{doi=10.1016/j.gene.2016.10.031}. Five years later an RT was shown to be associated with the biosynthesis of msDNA :ref{doi=10.1016/0092-8674(89)90593-X,10.1016/0092-8674(89)90592-8}, this was the first discovery of an RT in bacteria.
 
-_Fig 1. (Mestre et al., 2020) Structure and organisation of a retron_ . The two non-coding contiguous inverted sequences (named msr and msd) are transcribed as a single RNA. The RT recognizes its specific structure and reverse-transcribes it, generating an RNA-DNA hybrid
+Although retrons were biochemically well studied and characterized, it was only 36 years after msDNA discovery, when their biological function was discovered :ref{doi=10.1126/science.abf6127}. In a systematic screen for the discovery of novel anti-phage defense systems in bacterial genomes :ref{doi=10.1016/j.chom.2022.09.017}, Millman et al. discovered a new defense system that contained a retron element (Retron-Eco8), further analysis showed that retrons are enriched in bacterial defense islands and together with their accessory proteins many were shown to confer defense against phage infection :ref{doi=10.1016/j.cell.2020.09.065}. An independent screen for defense systems, later that same year, also reported similar conclusions showing retrons function in antiphage defense :ref{doi=10.1126/science.aba0372}.
 
+Due to their ability to produce high copy of DNA within the cell, since their discovery retrons have served as a fertile ground for biotechnological applications :ref{doi=10.1073/pnas.2018181118,10.1038/s41589-021-00927-y,10.1038/s41596-023-00819-6}
 
-The majority of retrons are encoded on a gene cassette that encodes the retron and one or two additional proteins, which act as the retrons effectors. Bioinformatic prediction reveals that these effectors are very diverse and include transmembrane proteins, proteases, Cold-shock proteins, TIR domains proteins, ATPase, endonucleases, etc. Interestingly, several of these effector domains have already been described in other defense systems, including CBASS and Septu. Most retrons appear to act through an Abortive infection strategy (1).
 
 ## Molecular mechanisms
 
-The *E.coli* retron system Ec48 mediates growth arrest upon sensing the inactivation of the bacterial RecBCD complex, a key element of the bacterial DNA repair system and immunity (1). Another study demonstrates that several retrons are part of Toxin-Antitoxin systems, where the RT-msDNA complex acts as an antitoxin that binds to and inhibits its cognate toxin. The tempering of the RT-msDNA, possibly by phage-encoded anti-RM systems, abolishes the antitoxin properties of the retron element, resulting in cell death mediated by the toxin activity (2). 
+### General
+When the retron ncRNA (msr-msd) is transcribed it folds into a typical structure that is recognized by the RT :ref{doi=10.1016/S0021-9258(18)83336-1}. The RT then reverse transcribes a portion of the ncRNA (msd), starting from the 2′-end of a conserved guanosine residue found immediately after a double-stranded RNA structure within the ncRNA :ref{doi=10.1016/0092-8674(89)90592-8}. During reverse transcription, cellular RNase H degrades the segment of the ncRNA that serves as template, but not other parts of the ncRNA (msr), yielding the mature RNA-DNA hybrid (msDNA) :ref{doi=10.1016/0092-8674(89)90592-8}. In some cases cellular nucleases have been shown to further process the msDNA :ref{doi=10.1111/j.1365-2958.1992.tb01788.x,10.1006/plas.1997.1298,10.1007/s12275-015-5304-0}.
+
+### Retron-Eco6 (Ec48)
+The Retron-Eco6 system encodes in addition to the retron an effector protein containing 2 transmembrane domains (2TM). Retron-Eco6 was shown to protect bacteria against phage through abortive infection (Abi) by guarding the integrity of the RecBCD complex in the cell. Many phages inhibit RecBCD in order to successfully infect the cell. Upon inhibition of RecBCD, the effector protein turns the membrane permeable and the cells lyse within 45 minutes post infection :ref{doi=10.1016/j.cell.2020.09.065}.
+
+### Retron-Sen2 (St85), Retron-Eco9
+The Retron-Sen2 system was shown to function as a three-partite toxin-antitoxin (TA) system. The accessory gene RcaT acts as a bona fide toxin and ectopically inhibits growth. The Retron-RT-msDNA complex acts as an antitoxin alleviating RcaT toxicity.
+Several triggers were identified for the Sen2-TA system, including Dam that was shown to methylate the mature msDNA and thus likely disrupt the RcaT–RT–msDNA complex, and RecE that degrades mature msDNA and reduces the RT-msDNA antitoxin levels :ref{doi=10.1038/s41586-022-05091-4}
 
 
 ## Example of genomic structure
 
-The Retron system have been describe in a total of 16 subsystems.
+A total of 16 subsystems have been described for the Retron system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![retron](/retron/Retron_II.svg){max-width=750px}
+![retron_ii](/retron/Retron_II.svg){max-width=750px}
 
-Retron_II subsystem in the genome of *Klebsiella pneumoniae* (GCF_904866255.1) is composed of 2 proteins: NDT2 (WP_057222224.1)and, RT_Tot (WP_048289034.1).
+The Retron_II system in *Agrobacterium tumefaciens* (GCF_017726655.1, NZ_CP072309) is composed of 2 proteins NDT (WP_209089758.1) RT_Tot (WP_209089760.1) 
 
-![retron](/retron/Retron_IV.svg){max-width=750px}
+![retron_iii](/retron/Retron_III.svg){max-width=750px}
 
-Retron_IV subsystem in the genome of *Aliivibrio fischeri* (GCF_000011805.1) is composed of 2 proteins: RT_Tot (WP_011261677.1)and, 2TM (WP_236727775.1).
+The Retron_III system in *Dokdonia sp. 4H-3-7-5* (GCF_000212355.1, NC_015496) is composed of 3 proteins PRTase (WP_148236012.1) WH (WP_013752369.1) RT_Tot (WP_013752370.1) 
 
-![retron](/retron/Retron_I_A.svg){max-width=750px}
+![retron_iv](/retron/Retron_IV.svg){max-width=750px}
 
-Retron_I_A subsystem in the genome of *Vibrio harveyi* (GCF_009184745.1) is composed of 3 proteins: RT_Tot (WP_152163686.1), ATPase_TypeIA (WP_152163687.1)and, HNH_TIGR02646 (WP_152163688.1).
+The Retron_IV system in *Pseudomonas lurida* (GCF_001708485.1, NZ_CP015639) is composed of 2 proteins RT_Tot (WP_081327059.1) 2TM (WP_145980332.1) 
 
-![retron](/retron/Retron_I_B.svg){max-width=750px}
+![retron_i_a](/retron/Retron_I_A.svg){max-width=750px}
 
-Retron_I_B subsystem in the genome of *Vibrio vulnificus* (GCF_009665475.1) is composed of 2 proteins: ATPase_TOPRIM_COG3593 (WP_103277404.1)and, RT_Tot (WP_043877188.1).
+The Retron_I_A system in *Hafnia alvei* (GCF_902387815.1, NZ_LR699008) is composed of 3 proteins RT_Tot (WP_197737714.1) ATPase_TypeIA (WP_111329110.1) HNH_TIGR02646 (WP_111329111.1) 
 
-![retron](/retron/Retron_I_C.svg){max-width=750px}
+![retron_i_b](/retron/Retron_I_B.svg){max-width=750px}
 
-Retron_I_C subsystem in the genome of *Listeria monocytogenes* (GCF_905219385.1) is composed of 1 protein: RT_1_C2 (WP_003726410.1).
+The Retron_I_B system in *Dickeya zeae* (GCF_012278555.1, NZ_CP033622) is composed of 2 proteins ATPase_TOPRIM_COG3593 (WP_168363308.1) RT_Tot (WP_168363309.1) 
 
-![retron](/retron/Retron_V.svg){max-width=750px}
+![retron_i_c](/retron/Retron_I_C.svg){max-width=750px}
 
-Retron_V subsystem in the genome of *Proteus terrae* (GCF_013171285.1) is composed of 2 proteins: CSD (WP_004244726.1)and, RT_Tot (WP_109418979.1).
+The Retron_I_C system in *Proteus vulgaris* (GCF_009931275.1, NZ_CP034668) is composed of 1 protein: RT_1_C1 (WP_017628371.1) 
 
-![retron](/retron/Retron_VI.svg){max-width=750px}
+![retron_vi](/retron/Retron_VI.svg){max-width=750px}
 
-Retron_VI subsystem in the genome of *Pseudomonas eucalypticola* (GCF_013374995.1) is composed of 2 proteins: HTH (WP_245217789.1)and, RT_Tot (WP_176571652.1).
+The Retron_VI system in *Enterobacter roggenkampii* (GCF_013728935.1, NZ_CP056148) is composed of 2 proteins HTH (WP_008499884.1) RT_Tot (WP_016243639.1) 
 
-![retron](/retron/Retron_VII_1.svg){max-width=750px}
+![retron_vii_1](/retron/Retron_VII_1.svg){max-width=750px}
 
-Retron_VII_1 subsystem in the genome of *Pseudoxanthomonas mexicana* (GCF_014397415.1) is composed of 1 protein: RT_7_A1 (WP_187572543.1).
+The Retron_VII_1 system in *Hypericibacter terrae* (GCF_008728855.1, NZ_CP042906) is composed of 1 protein: RT_7_A1 (WP_151178207.1) 
 
-![retron](/retron/Retron_VII_2.svg){max-width=750px}
+![retron_vii_2](/retron/Retron_VII_2.svg){max-width=750px}
 
-Retron_VII_2 subsystem in the genome of *Bacillus mycoides* (GCF_018742105.1) is composed of 2 proteins: DUF3800 (WP_215564565.1)and, RT_Tot (WP_215564572.1).
+The Retron_VII_2 system in *Sideroxydans lithotrophicus* (GCF_000025705.1, NC_013959) is composed of 2 proteins RT_Tot (WP_013028226.1) DUF3800 (WP_013028227.1) 
 
-![retron](/retron/Retron_XI.svg){max-width=750px}
+![retron_xi](/retron/Retron_XI.svg){max-width=750px}
 
-Retron_XI subsystem in the genome of *Planococcus kocurii* (GCF_001465835.2) is composed of 1 protein: RT_11 (WP_058386256.1).
+The Retron_XI system in *Sphingopyxis granuli* (GCF_022637755.1, NZ_CP093335) is composed of 1 protein: RT_11 (WP_241940850.1) 
 
-![retron](/retron/Retron_XII.svg){max-width=750px}
+![retron_xii](/retron/Retron_XII.svg){max-width=750px}
 
-Retron_XII subsystem in the genome of *Stenotrophomonas acidaminiphila* (GCF_014109845.1) is composed of 1 protein: RT_12 (WP_182333825.1).
+The Retron_XII system in *Tenuifilum thalassicum* (GCF_013265555.1, NZ_CP041345) is composed of 1 protein: RT_12 (WP_173072943.1) 
 
-![retron](/retron/Retron_XIII.svg){max-width=750px}
+![retron_xiii](/retron/Retron_XIII.svg){max-width=750px}
 
-Retron_XIII subsystem in the genome of *Delftia acidovorans* (GCF_016026535.1) is composed of 3 proteins: ARM (WP_197944577.1), WHSWIM (WP_197944578.1)and, RT_Tot (WP_065344905.1).
+The Retron_XIII system in *Clostridium saccharobutylicum* (GCF_002003365.1, NZ_CP016091) is composed of 3 proteins ARM (WP_022745963.1) WHSWIM (WP_022745966.1) RT_Tot (WP_022745969.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Retron system is present in a total of 731 different species.
+Among the 22,803 complete genomes of RefSeq, the Retron is detected in 2537 genomes (11.13 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 2601 genomes (11.4 %).
+The system was detected in 840 different species.
 
 ![retron](/retron/Distribution_Retron.svg){max-width=750px}
 
-*Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -534,14 +564,5 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
 
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.cell.2020.09.065
-    - doi: 10.1093/nar/gkaa1149
-
----
-::
 

content/3.defense-systems/rexab.md

@@ -15,23 +15,24 @@ tableColumns:
 # RexAB
 ## Example of genomic structure
 
-The RexAB system is composed of 2 proteins: RexA and, RexB.
+The RexAB is composed of 2 proteins: RexA and RexB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rexab](/rexab/RexAB.svg){max-width=750px}
 
-RexAB system in the genome of *Escherichia coli* (GCF_008033315.1) is composed of 2 proteins: RexA (WP_000788349.1)and, RexB (WP_001245922.1).
+The RexAB system in *Klebsiella pneumoniae* (GCF_016780145.1, NZ_CP068798) is composed of 2 proteins RexB (WP_032749558.1) RexA (WP_077270569.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RexAB system is present in a total of 17 different species.
+Among the 22,803 complete genomes of RefSeq, the RexAB is detected in 73 genomes (0.32 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 73 genomes (0.3 %).
+The system was detected in 18 different species.
 
 ![rexab](/rexab/Distribution_RexAB.svg){max-width=750px}
 
-*Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the RexAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rloc.md

@@ -15,23 +15,24 @@ tableColumns:
 # RloC
 ## Example of genomic structure
 
-The RloC system is composed of one protein: RloC.
+The RloC is composed of 1 protein: RloC.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rloc](/rloc/RloC.svg){max-width=750px}
 
-RloC system in the genome of *Flavobacterium arcticum* (GCF_003344925.1) is composed of 1 protein: RloC (WP_114676820.1).
+The RloC system in *Pseudomonas aeruginosa* (GCF_000981825.1, NZ_CP011317) is composed of 1 protein: RloC (WP_010794466.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RloC system is present in a total of 803 different species.
+Among the 22,803 complete genomes of RefSeq, the RloC is detected in 1944 genomes (8.53 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 1961 genomes (8.6 %).
+The system was detected in 919 different species.
 
 ![rloc](/rloc/Distribution_RloC.svg){max-width=750px}
 
-*Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the RloC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rm.md

@@ -15,39 +15,40 @@ tableColumns:
 # RM
 ## Example of genomic structure
 
-The RM system have been describe in a total of 5 subsystems.
+A total of 5 subsystems have been described for the RM system.
 
-Here is some example found in the RefSeq database:
+Here is some examples found in the RefSeq database:
 
-![rm](/rm/RM_Type_I.svg){max-width=750px}
+![rm_type_i](/rm/RM_Type_I.svg){max-width=750px}
 
-RM_Type_I subsystem in the genome of *Aeromonas veronii* (GCF_014169835.1) is composed of 4 proteins: Type_I_MTases (WP_182963881.1), Type_I_MTases (WP_182963881.1), Type_I_S (WP_182963883.1)and, Type_I_REases (WP_182963884.1).
+The RM_Type_I system in *Tessaracoccus flavescens* (GCF_001998865.1, NZ_CP019607) is composed of 3 proteins Type_I_MTases (WP_237268350.1) Type_I_S (WP_077346826.1) Type_I_REases (WP_237268249.1) 
 
-![rm](/rm/RM_Type_II.svg){max-width=750px}
+![rm_type_ii](/rm/RM_Type_II.svg){max-width=750px}
 
-RM_Type_II subsystem in the genome of *Mannheimia haemolytica* (GCF_007965905.1) is composed of 2 proteins: Type_II_MTases (WP_006248352.1)and, Type_II_REases (WP_006253295.1).
+The RM_Type_II system in *Aeromonas caviae* (GCF_000783775.2, NZ_CP026055) is composed of 2 proteins Type_II_MTases (WP_042865101.1) Type_II_REases (WP_042865102.1) 
 
-![rm](/rm/RM_Type_IIG.svg){max-width=750px}
+![rm_type_iig](/rm/RM_Type_IIG.svg){max-width=750px}
 
-RM_Type_IIG subsystem in the genome of *Spirochaeta africana* (GCF_000242595.2) is composed of 1 protein: Type_IIG (WP_014455422.1).
+The RM_Type_IIG system in *Microbacterium wangchenii* (GCF_004564355.1, NZ_CP038266) is composed of 1 protein: Type_IIG (WP_135067980.1) 
 
-![rm](/rm/RM_Type_III.svg){max-width=750px}
+![rm_type_iii](/rm/RM_Type_III.svg){max-width=750px}
 
-RM_Type_III subsystem in the genome of *Pannonibacter phragmitetus* (GCF_001484065.1) is composed of 2 proteins: Type_III_MTases (WP_058898889.1)and, Type_III_REases (WP_058898890.1).
+The RM_Type_III system in *Sphingobacterium spiritivorum* (GCF_016725325.1, NZ_CP068083) is composed of 2 proteins Type_III_REases (WP_139420208.1) Type_III_MTases (WP_139420206.1) 
 
-![rm](/rm/RM_Type_IV.svg){max-width=750px}
+![rm_type_iv](/rm/RM_Type_IV.svg){max-width=750px}
 
-RM_Type_IV subsystem in the genome of *Clostridioides difficile* (GCF_018884605.1) is composed of 1 protein: Type_IV_REases (WP_021364579.1).
+The RM_Type_IV system in *Halobaculum rubrum* (GCF_019880225.1, NZ_CP082284) is composed of 1 protein: Type_IV_REases (WP_222915961.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RM system is present in a total of 4699 different species.
+Among the 22,803 complete genomes of RefSeq, the RM is detected in 18264 genomes (80.09 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 19087 genomes (83.7 %).
+The system was detected in 6137 different species.
 
 ![rm](/rm/Distribution_RM.svg){max-width=750px}
 
-*Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
+Proportion of genome encoding the RM system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rnlab.md

@@ -15,23 +15,24 @@ tableColumns:
 # RnlAB
 ## Example of genomic structure
 
-The RnlAB system is composed of 2 proteins: RnlA and, RnlB.
+The RnlAB is composed of 2 proteins: RnlA and RnlB.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rnlab](/rnlab/RnlAB.svg){max-width=750px}
 
-RnlAB system in the genome of *Escherichia coli* (GCF_014338505.1) is composed of 2 proteins: RnlA (WP_000155570.1)and, RnlB (WP_000461704.1).
+The RnlAB system in *Bacteroides caecimuris* (GCF_001688725.2, NZ_CP015401) is composed of 2 proteins RnlA (WP_004327332.1) RnlB (WP_004327330.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RnlAB system is present in a total of 71 different species.
+Among the 22,803 complete genomes of RefSeq, the RnlAB is detected in 279 genomes (1.22 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 284 genomes (1.2 %).
+The system was detected in 68 different species.
 
 ![rnlab](/rnlab/Distribution_RnlAB.svg){max-width=750px}
 
-*Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the RnlAB system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rosmerta.md

@@ -15,23 +15,24 @@ tableColumns:
 # RosmerTA
 ## Example of genomic structure
 
-The RosmerTA system is composed of 2 proteins: RmrA_2634932349 and, RmrT_2634932349.
+The RosmerTA is composed of 2 proteins: RmrT and RmrA.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rosmerta](/rosmerta/RosmerTA.svg){max-width=750px}
 
-RosmerTA system in the genome of *Acinetobacter indicus* (GCF_002953575.2) is composed of 2 proteins: RmrT_2641389401 (WP_045796188.1)and, RmrA_2641389401 (WP_045796189.1).
+The RosmerTA system in *Paucibacter sp. KCTC 42545* (GCF_001477625.1, NZ_CP013692) is composed of 2 proteins RmrT_2662548665 (WP_231741552.1) RmrA_2662548665 (WP_058719324.1) 
 
 ## Distribution of the system among prokaryotes
 
-The RosmerTA system is present in a total of 540 different species.
+Among the 22,803 complete genomes of RefSeq, the RosmerTA is detected in 2080 genomes (9.12 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 2124 genomes (9.3 %).
+The system was detected in 613 different species.
 
 ![rosmerta](/rosmerta/Distribution_RosmerTA.svg){max-width=750px}
 
-*Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the RosmerTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rst_2tm_1tm_tir.md

@@ -12,23 +12,24 @@ tableColumns:
 # Rst_2TM_1TM_TIR
 ## Example of genomic structure
 
-The Rst_2TM_1TM_TIR system is composed of 3 proteins: Rst_TIR_tm, Rst_1TM_TIR and, Rst_2TM_TIR.
+The Rst_2TM_1TM_TIR is composed of 3 proteins: Rst_2TM_TIR, Rst_TIR_tm and Rst_1TM_TIR.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rst_2tm_1tm_tir](/rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.svg){max-width=750px}
 
-Rst_2TM_1TM_TIR system in the genome of *Escherichia coli* (GCF_001900375.1) is composed of 3 proteins: Rst_TIR_tm (WP_023140578.1), Rst_1TM_TIR (WP_001534953.1)and, Rst_2TM_TIR (WP_023140577.1).
+The Rst_2TM_1TM_TIR system in *Escherichia coli* (GCF_004006575.1, NZ_CP034787) is composed of 3 proteins Rst_TIR_tm (WP_023140578.1) Rst_1TM_TIR (WP_001534953.1) Rst_2TM_TIR (WP_023140577.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_2TM_1TM_TIR system is present in a total of 1 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_2TM_1TM_TIR is detected in 2 genomes (0.01 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 2 genomes (0.0 %).
+The system was detected in 1 different species.
 
 ![rst_2tm_1tm_tir](/rst_2tm_1tm_tir/Distribution_Rst_2TM_1TM_TIR.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rst_3hp.md

@@ -9,28 +9,43 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+    PFAM: Unknown
+contributors:
+    - Alba Herrero del Valle
+relevantAbstracts:
+    - doi: 10.1016/j.chom.2022.02.018
 ---
 
 # Rst_3HP
+
+## Description
+
+The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3. These proteins do not have clear predicted domains but they confer resistance against the phage P1 in *Escherichia coli* E1114 :ref{doi=10.1016/j.chom.2022.02.018}.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
-The Rst_3HP system is composed of 3 proteins: Hp1, Hp2 and, Hp3.
+The Rst_3HP is composed of 3 proteins: Hp1, Hp2 and Hp3.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rst_3hp](/rst_3hp/Rst_3HP.svg){max-width=750px}
 
-Rst_3HP system in the genome of *Klebsiella pneumoniae* (GCF_016403065.1) is composed of 3 proteins: Hp3 (WP_004151009.1), Hp2 (WP_004151008.1)and, Hp1 (WP_004151007.1).
+The Rst_3HP system in *Aquitalea denitrificans* (GCF_009856625.1, NZ_CP047241) is composed of 3 proteins Hp1 (WP_159879082.1) Hp2 (WP_159879084.1) Hp3 (WP_159879086.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_3HP system is present in a total of 83 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_3HP is detected in 417 genomes (1.83 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 420 genomes (1.8 %).
+The system was detected in 89 different species.
 
 ![rst_3hp](/rst_3hp/Distribution_Rst_3HP.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -82,12 +97,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.chom.2022.02.018
 
----
-::

content/3.defense-systems/rst_duf4238.md

@@ -15,23 +15,24 @@ tableColumns:
 # Rst_DUF4238
 ## Example of genomic structure
 
-The Rst_DUF4238 system is composed of one protein: DUF4238_Pers.
+The Rst_DUF4238 is composed of 1 protein: DUF4238.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rst_duf4238](/rst_duf4238/Rst_DUF4238.svg){max-width=750px}
 
-Rst_DUF4238 system in the genome of *Enterobacter kobei* (GCF_008365235.1) is composed of 1 protein: DUF4238_Pers (WP_058689834.1).
+The Rst_DUF4238 system in *Novosphingobium pentaromativorans* (GCF_000767465.1, NZ_CP009291) is composed of 1 protein: DUF4238_Pers (WP_007011908.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_DUF4238 system is present in a total of 34 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_DUF4238 is detected in 46 genomes (0.2 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 46 genomes (0.2 %).
+The system was detected in 37 different species.
 
 ![rst_duf4238](/rst_duf4238/Distribution_Rst_DUF4238.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rst_gop_beta_cll.md

@@ -15,23 +15,24 @@ tableColumns:
 # Rst_gop_beta_cll
 ## Example of genomic structure
 
-The Rst_gop_beta_cll system is composed of 3 proteins: gop, beta and, cll.
+The Rst_gop_beta_cll is composed of 3 proteins: beta, cll and gop.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rst_gop_beta_cll](/rst_gop_beta_cll/Rst_gop_beta_cll.svg){max-width=750px}
 
-Rst_gop_beta_cll system in the genome of *Escherichia coli* (GCF_003018615.1) is composed of 3 proteins: cll (WP_001357997.1), beta (WP_001357996.1)and, gop (WP_000931915.1).
+The Rst_gop_beta_cll system in *Klebsiella grimontii* (GCF_019334465.1, NZ_CP079754) is composed of 3 proteins gop (WP_189095150.1) beta (WP_189095151.1) cll (WP_219192256.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_gop_beta_cll system is present in a total of 14 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_gop_beta_cll is detected in 37 genomes (0.16 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 37 genomes (0.2 %).
+The system was detected in 15 different species.
 
 ![rst_gop_beta_cll](/rst_gop_beta_cll/Distribution_Rst_gop_beta_cll.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 

content/3.defense-systems/rst_helicaseduf2290.md

@@ -10,28 +10,44 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF10053, PF13538
+
+contributors: 
+  - Ernest Mordret
+relevantAbstracts:
+  - doi: 10.1016/j.chom.2022.02.018
+
 ---
 
 # Rst_HelicaseDUF2290
+
+## Description
+
+The Rst_HelicaseDUF2290 system was discovered during a screen for defense systems targeted at hotspots of antiphage activity in phages and phage-satellites. It is composed of 2 proteins, an helicase and a protein with the domain DUF2290.
+
+## Molecular mechanism
+
+The molecular mechanism of the Rst_HelicaseDUF2290 is unkown.
+
 ## Example of genomic structure
 
-The Rst_HelicaseDUF2290 system is composed of 2 proteins: Helicase and, DUF2290.
+The Rst_HelicaseDUF2290 is composed of 2 proteins: Helicase and DUF2290.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
 ![rst_helicaseduf2290](/rst_helicaseduf2290/Rst_HelicaseDUF2290.svg){max-width=750px}
 
-Rst_HelicaseDUF2290 system in the genome of *Xylella fastidiosa* (GCF_021459885.1) is composed of 2 proteins: Helicase (WP_012338122.1)and, DUF2290 (WP_004084731.1).
+The Rst_HelicaseDUF2290 system in *Klebsiella quasipneumoniae* (GCF_003020825.1, NZ_CP023478) is composed of 2 proteins Helicase (WP_046623504.1) DUF2290_Pers (WP_046623503.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_HelicaseDUF2290 system is present in a total of 124 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_HelicaseDUF2290 is detected in 207 genomes (0.91 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 211 genomes (0.9 %).
+The system was detected in 123 different species.
 
 ![rst_helicaseduf2290](/rst_helicaseduf2290/Distribution_Rst_HelicaseDUF2290.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure
 
@@ -75,13 +91,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.chom.2022.02.018
-
----
-::
 

content/3.defense-systems/rst_hydrolase-3tm.md

@@ -15,23 +15,24 @@ tableColumns:
 # Rst_Hydrolase-3Tm
 ## Example of genomic structure
 
-The Rst_Hydrolase-3Tm system is composed of 2 proteins: Hydrolase and, Hydrolase-Tm.
+The Rst_Hydrolase-3Tm is composed of 2 proteins: Hydrolase and Hydrolase-Tm.
 
-Here is an example found in the RefSeq database: 
+Here is an example found in the RefSeq database:
 
-![rst_hydrolase-3tm](/rst_hydrolase-3tm/Rst_Hydrolase-Tm.svg){max-width=750px}
+![rst_hydrolase-tm](/rst_hydrolase-3tm/Rst_Hydrolase-Tm.svg){max-width=750px}
 
-Rst_Hydrolase-Tm subsystem in the genome of *Escherichia coli* (GCF_004792495.1) is composed of 2 proteins: Hydrolase-Tm (WP_000998640.1)and, Hydrolase (WP_000754434.1).
+The Rst_Hydrolase-Tm system in *Pectobacterium versatile* (GCF_003031305.1, NZ_CP024842) is composed of 2 proteins Hydrolase (WP_107333258.1) Hydrolase-Tm (WP_107333259.1) 
 
 ## Distribution of the system among prokaryotes
 
-The Rst_Hydrolase-3Tm system is present in a total of 34 different species.
+Among the 22,803 complete genomes of RefSeq, the Rst_Hydrolase-3Tm is detected in 42 genomes (0.18 %).
 
-Among the 22k complete genomes of RefSeq, this system is present in 42 genomes (0.2 %).
+The system was detected in 34 different species.
 
 ![rst_hydrolase-3tm](/rst_hydrolase-3tm/Distribution_Rst_Hydrolase-3Tm.svg){max-width=750px}
 
-*Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
+Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with more than 50 genomes in the RefSeq database.
+
 
 ## Structure