Merge branch 'abernhei-main-patch-35933' into 'main'

Update rm.md

See merge request !77

content/3.defense-systems/rm.md

@@ -3,16 +3,36 @@ title: RM
 layout: article
 tableColumns:
     article:
-      doi: 10.1093/nar/gku734
+      doi: 10.1016/j.mib.2005.06.003
       abstract: |
-        The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
+        The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were first discovered five decades ago but have yielded only gradually to rigorous analysis. Work presented at the 5th New England Biolabs Meeting on Restriction-Modification (available on REBASE) and several recently published genetic, biochemical and biophysical analyses indicate that these fields continue to contribute significantly to basic science. Recently, there have been several studies that have shed light on the still developing field of restriction-modification and on the newly re-emerging field of anti-restriction.
     Sensor: Detecting invading nucleic acid
     Activator: Direct
     Effector: Nucleic acid degrading
     PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF18766
+contributors: 
+  - Aude Bernheim
+  - Florian Tesson
+relevantAbstracts:
+  - doi: 10.1016/j.mib.2005.06.003
+  - doi: 10.1093/nar/gku734
 ---
 
 # RM
+
+## Description
+Restriction modification systems are the most abundant antiphage systems. They already have their own [Wikipedia page](https://en.wikipedia.org/wiki/Restriction_modification_system)
+
+## Molecular Mechanisms
+Several reviews detail the molecular mechanisms of restriction modification systems. For example in :ref{doi=10.1016/j.mib.2005.06.003}:
+
+"Bacterial restriction-modification (R-M) systems function as prokaryotic immune systems that attack foreign DNA entering the cell :ref{doi=10.1128/jb.65.2.113-121.1953}. Typically, R-M systems have enzymes responsible for two opposing activities: a restriction endonuclease (REase) that recognizes a specific DNA sequence for cleavage and a cognate methyltransferase (MTase) that confers protection from cleavage by methylation of adenine or cytosine bases within the same recognition sequence. REases recognize ‘non-self’ DNA (Figure 1), such as that of phage and plasmids, by its lack of characteristic modification within specific recognition sites :ref{doi=10.1093/nar/29.18.3705}. Foreign DNA is then inactivated by endonucleolytic cleavage. Generally, methylation of a specific cytosine or adenine within the recognition sequence confers protection from restriction. Host DNA is normally methylated by the MTase following replication, whereas invading non-self DNA is not."
+
+![Figure_1](/rm/Figure_1_Tock_Dryden_2005.png){max-width=750px}
+
+Figure 1. The function of R-M systems, as illustrated by Type I R-M enzymes. From :ref{doi=10.1016/j.mib.2005.06.003}.
+
+
 ## Example of genomic structure
 
 A total of 5 subsystems have been described for the RM system.
@@ -52,103 +72,23 @@ Proportion of genome encoding the RM system for the 14 phyla with more than 50 g
 
 ## Structure
 
-### DISARM_1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM_1__drmD,0,DF-plddts_85.45851.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM_1__drmMI,0,DF-plddts_86.22485.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmA,0,DF-plddts_88.08452.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmB,0,DF-plddts_88.41231.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmC,0,DF-plddts_93.3381.pdb
----
-::
-
-### DISARM_2
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM_2__drmE,0,V-plddts_88.46395.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM_2__drmMII,0,V-plddts_92.6996.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmA,0,V-plddts_87.64454.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmB,0,V-plddts_89.69894.pdb
----
-::
+### Experimentaly determined structure
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmC,0,V-plddts_87.93933.pdb
----
-::
+Many structure for the different types of restriction-modification system are available on the [Protein Data Bank](https://www.rcsb.org).
 
 ### RM
+#### Restriction modification Type I Prr
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /rm/RM__Type_I_REases-plddts_86.33796.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/RM__Type_I_S-plddts_91.98582.pdb
+dataUrls:
+  - /rm/RM__Type_I_REases-plddts_86.33796.pdb
+  - /rm/RM__Type_I_S-plddts_91.98582.pdb
+  - /prrc/PrrC__EcoprrI-plddts_91.30003.pdb
 ---
 ::
 
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1093/nar/gku734
-
----
-::
+## Experimental validation
+Many RM systems defend against many phages, as such we cannot map this correctly.