Update disarm.md

content/3.defense-systems/disarm.md

@@ -10,29 +10,34 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00145, PF00176, PF00271, PF04851, PF09369, PF13091
+contributors:
+  - Florian Tesson
+relevantAbstracts:
+    - doi: 10.1038/s41467-022-30673-1
+    - doi: 10.1038/s41564-017-0051-0
 ---
 
 # DISARM
 ## Description
 
-DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages (1,3).
+DISARM (Defense Island System Associated with Restriction-Modification) is a defense system widespread in prokaryotes, encoded by a 5-gene cassette. DISARM provides broad protection against double-stranded DNA phages, including siphophages, myophages, and podophages :ref{doi=10.1038/s41564-017-0051-0,10.1101/2021.12.28.474362}.
 
- It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination (1). This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism (1,2).
+ It was reported to restrict incoming phage DNA and methylate the bacterial host DNA, which could be responsible for self from non-self discrimination :ref{doi=10.1038/s41564-017-0051-0}. This suggests a [Restriction-Modification](/defense-systems/rm)-like (RM-like) mechanism, yet some pieces of experimental evidence hint that DISARM actually acts through a novel and uncharacterized molecular mechanism :ref{doi=10.1038/s41564-017-0051-0,10.1038/s41467-022-30673-1}.
 
 ## Molecular mechanism
 
-DISARM allows phage adsorption but prevents phage replication. DISARM is thought to cause intracellular phage DNA decay (1), but the molecular of this potential DNA degradation remains unknown.
+DISARM allows phage adsorption but prevents phage replication. DISARM is thought to cause intracellular phage DNA decay :ref{doi=10.1038/s41564-017-0051-0}, but the molecular of this potential DNA degradation remains unknown.
 
-The *drmMII* gene of DISARM system from *Bacillus paralicheniformis* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of *drmMII,* this DISARM system appears toxic to the cells (1). These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity. 
+The *drmMII* gene of DISARM system from *Bacillus paralicheniformis* was shown to methylate bacterial DNA at CCWGG motifs when expressed in Bacillus subtilis, and in the absence of *drmMII,* this DISARM system appears toxic to the cells :ref{doi=10.1038/s41564-017-0051-0}. These observations are consistent with an RM-like mechanism, where nucleic acid degradation targets specific DNA motifs, that are methylated in the bacterial chromosome to prevent auto-immunity. 
 
-Yet this system was also shown to protect against phages whose genomes are exempt of CCWGG motifs (1). Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a *Serratia sp.* does not result in autoimmunity (3). Both these results suggest additional phage DNA recognition mechanisms. 
+Yet this system was also shown to protect against phages whose genomes are exempt of CCWGG motifs :ref{doi=10.1038/s41564-017-0051-0}. Moreover, a recent study reports that the absence of methylases (DrmMI or DrmMII) of the DISARM system from a *Serratia sp.* does not result in autoimmunity :ref{doi=10.1101/2021.12.28.474362}. Both these results suggest additional phage DNA recognition mechanisms. 
 
-Hints of these additional mechanisms can be found in recent structural studies, which show that DrmA and DrmB form a complex that can bind single-stranded DNA (2). Moreover, the DrmAB complex seems to exhibit strong ATPase activity in presence of unmethylated DNA, and  reduced ATPase activity in the presence of a methylated DNA substrate (2). Finally, binding of unmethylated single-stranded DNA appears to mediate major conformational change of the complex, which was hypothesized to be responsible for downstream DISARM activation (2).
+Hints of these additional mechanisms can be found in recent structural studies, which show that DrmA and DrmB form a complex that can bind single-stranded DNA :ref{doi=10.1038/s41467-022-30673-1}. Moreover, the DrmAB complex seems to exhibit strong ATPase activity in presence of unmethylated DNA, and  reduced ATPase activity in the presence of a methylated DNA substrate :ref{doi=10.1038/s41467-022-30673-1}. Finally, binding of unmethylated single-stranded DNA appears to mediate major conformational change of the complex, which was hypothesized to be responsible for downstream DISARM activation :ref{doi=10.1038/s41467-022-30673-1}.
 
 
 ## Example of genomic structure
 
-DISARM is encoded by three core genes: *drmA* (encoding for a protein containing a putative helicase domain)*,* *drmB* (encoding for a protein containing a putative helicase-associated domain), and *drmC* (encoding for a protein containing a phospholipase D/nuclease domain) (1)
+DISARM is encoded by three core genes: *drmA* (encoding for a protein containing a putative helicase domain)*,* *drmB* (encoding for a protein containing a putative helicase-associated domain), and *drmC* (encoding for a protein containing a phospholipase D/nuclease domain) :ref{doi=10.1038/s41564-017-0051-0}
 
 These three core genes are accompanied by a methyltransferase, which can be either an adenine methylase (*drmMI*) for class 1 DISARM systems or a cytosine methylase (*drmMII*) for DISARM class 2. Both classes also encode an additional gene (*drmD* for class 1, and *drmE* for class 2). 
 
@@ -58,6 +63,97 @@ The system was detected in 201 different species.
 
 Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
+## structure
+### Experimentaly determined structure
+From :ref{doi=10.1038/s41586-023-06855-2} in *Serratia sp*:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/7s9v_DrmAB_1_1mer.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/7s9w_DrmAB_1_1mer_dna.pdb
+---
+::
+
+### DISARM_1
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_1,DISARM_1__drmD,0,DF-plddts_85.45851.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_1,DISARM_1__drmMI,0,DF-plddts_86.22485.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_1,DISARM__drmA,0,DF-plddts_88.08452.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_1,DISARM__drmB,0,DF-plddts_88.41231.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_1,DISARM__drmC,0,DF-plddts_93.3381.pdb
+---
+::
+
+### DISARM_2
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_2,DISARM_2__drmE,0,V-plddts_88.46395.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_2,DISARM_2__drmMII,0,V-plddts_92.6996.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_2,DISARM__drmA,0,V-plddts_87.64454.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_2,DISARM__drmB,0,V-plddts_89.69894.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /disarm/DISARM_2,DISARM__drmC,0,V-plddts_87.93933.pdb
+---
+::
+
 
 ## Experimental validation
 <mermaid>
@@ -120,14 +216,5 @@ 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: 10.1038/s41467-022-30673-1
-    - doi: 10.1038/s41564-017-0051-0
-
----
-::