Update lamassu-fam.md

#219 (closed)

content/3.defense-systems/lamassu-fam.md

@@ -9,21 +9,32 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Diverse (Nucleic acid degrading (?), Nucleotide modifying (?), Membrane disrupting (?))
-    PFAM: PF00753, PF02463, PF05057, PF12532, PF13175, PF13289, PF13476, PF14130
+    PFAM: PF00753, PF02463, PF05057, PF12532, PF13175, PF13289, PF13476, PF14130  
+contributors: 
+    - Matthieu Haudiquet
+    - Aude Bernheim
+relevantAbstracts:
+    - doi: 10.1126/science.aar4120
+    - doi: 10.1016/j.chom.2022.09.017
+    - doi: 10.1093/nar/gkab883
+    - doi: 10.1038/s41586-022-04546-y 
+    - doi: 10.1101/2022.11.18.517080 
 ---
 
 # Lamassu-Fam
 ## Description
 
-The original types of Lamassu systems are Lamassu Type 1 and 2. They both necessarily comprise two genes *lmuA* and *lmuB*, to which a third gene (*lmuC*) is added in the case of Lamassu Type 2.  
+The original types of Lamassu systems are Lamassu Type 1 :ref{doi=10.1126/science.aar4120} and Type 2 :ref{doi=10.1016/j.chom.2022.09.017}. They both necessarily comprise two genes *lmuA* and *lmuB*, to which a third gene (*lmuC*) is added in the case of Lamassu Type 2.  
 
-More recently, Lamassu has been suggested to be a large family of defense systems, that can be classified into multiple subtypes. 
+Lamassu has been suggested to be a large family of defense systems, that can be classified into multiple subtypes :ref{doi=10.1016/j.chom.2022.09.017}. 
 
-These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC.* In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein (3). This effector  can not only be LmuA (Lamassu Type1 and 2) but also proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains (3). Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes (3).
+These systems all encode the *lmuB* gene, and in most cases also comprise *lmuC*. In addition to these two core genes, Lamassu systems of various subtypes encode a third protein, hypothesized to be the Abi effector protein :ref{doi=10.1101/2022.05.11.491447}. This effector  can be proteins encoding endonuclease domains, SIR2-domains, or even hydrolase domains :ref{doi=10.1016/j.chom.2022.09.017}. Systems of the extended Lamassu-family can be found in 10% of prokaryotic genomes :ref{doi=10.1016/j.chom.2022.09.017}.
+
+Lamassu were also described as DdmABC in *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y, 10.1101/2022.11.18.517080}. They were found to be antiplasmids and thus to eliminate plasmids from seventh pandemic *Vibrio cholerae* :ref{doi=10.1038/s41586-022-04546-y}.
 
 ## Molecular mechanism
 
-Lamassu systems function through abortive infection (Abi), but their molecular mechanism remains to be described.
+Lamassu systems function through abortive infection (Abi), but the molecular mechanism remains to be described. It was shown that, in Vibrio cholerae palindromic DNA sequences that are predicted to form stem-loop hairpin trigger the system :ref{doi=10.1101/2022.11.18.517080}. 
 
 ## Example of genomic structure
 
@@ -33,11 +44,11 @@ Here is an example of a Lamassu-Fam_Cap4_nuclease found in the RefSeq database:
 
 ![lamassu-fam](/lamassu-fam/Lamassu-Fam_Cap4_nuclease.svg){max-width=750px}
 
-Lamassu-Fam_Cap4_nuclease subsystem in the genome of *Pseudomonas sp.* (GCF_016925675.1) is composed of 3 proteins: LmuB_SMC_Hydrolase_protease (WP_205519025.1), LmuC_acc_Cap4_nuclease (WP_205478326.1)and, LmuA_effector_Cap4_nuclease_II (WP_205478325.1).
+Lamassu-Fam_Cap4_nuclease subsystem in the genome of *Pseudomonas sp.* (GCF_016925675.1) is composed of 3 proteins: LmuB_SMC_Hydrolase_protease (WP_205519025.1), LmuC_acc_Cap4_nuclease (WP_205478326.1) and, LmuA_effector_Cap4_nuclease_II (WP_205478325.1).
 
 ![lamassu-fam](/lamassu-fam/Lamassu-Fam_Mrr.svg){max-width=750px}
 
-Lamassu-Fam_Mrr subsystem in the genome of *Escherichia coli* (GCF_011404895.1) is composed of 2 proteins: LmuA_effector_Mrr (WP_044864610.1)and, LmuB_SMC_Cap4_nuclease_II (WP_226199836.1).
+Lamassu-Fam_Mrr subsystem in the genome of *Escherichia coli* (GCF_011404895.1) is composed of 2 proteins: LmuA_effector_Mrr (WP_044864610.1) and, LmuB_SMC_Cap4_nuclease_II (WP_226199836.1).
 
 ![lamassu-fam](/lamassu-fam/Lamassu-Fam_Hydrolase.svg){max-width=750px}
 
@@ -427,24 +438,3 @@ 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: 10.1016/j.chom.2022.09.017
-    - doi: 10.1038/s41586-022-04546-y
-    - doi: 10.1126/science.aar4120
-
----
-::
-
-
-## References
-
-1. Doron S, Melamed S, Ofir G, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. *Science*. 2018;359(6379):eaar4120. doi:10.1126/science.aar4120
-
-2. Payne LJ, Todeschini TC, Wu Y, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. *Nucleic Acids Res*. 2021;49(19):10868-10878. doi:10.1093/nar/gkab883
-
-3. Millman, A., Melamed, S., Leavitt, A., Doron, S., Bernheim, A., Hör, J., Lopatina, A., Ofir, G., Hochhauser, D., Stokar-Avihail, A., Tal, N., Sharir, S., Voichek, M., Erez, Z., Ferrer, J.L.M., Dar, D., Kacen, A., Amitai, G., Sorek, R., 2022. An expanding arsenal of immune systems that protect bacteria from phages. bioRxiv. https://doi.org/10.1101/2022.05.11.491447
-