From 49298b16af39b9ba8295a64870c201f301567c5f Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Tue, 19 Dec 2023 15:23:06 +0100
Subject: [PATCH] typo: change name system dmdde -> ddmde
---
content/3.defense-systems/{dmdde.md => ddmde.md} | 12 ++++++------
.../DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb | 0
.../DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb | 0
public/{dmdde => ddmde}/DdmDE.svg | 0
public/{dmdde => ddmde}/Distribution_DmdDE.svg | 0
5 files changed, 6 insertions(+), 6 deletions(-)
rename content/3.defense-systems/{dmdde.md => ddmde.md} (91%)
rename public/{dmdde => ddmde}/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb (100%)
rename public/{dmdde => ddmde}/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb (100%)
rename public/{dmdde => ddmde}/DdmDE.svg (100%)
rename public/{dmdde => ddmde}/Distribution_DmdDE.svg (100%)
diff --git a/content/3.defense-systems/dmdde.md b/content/3.defense-systems/ddmde.md
similarity index 91%
rename from content/3.defense-systems/dmdde.md
rename to content/3.defense-systems/ddmde.md
index 582a1782..d09c53d7 100644
--- a/content/3.defense-systems/dmdde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -1,5 +1,5 @@
---
-title: DmdDE
+title: DdmDE
layout: article
tableColumns:
article:
@@ -8,26 +8,26 @@ tableColumns:
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
+# DdmDE
## Example of genomic structure
The DmdDE is composed of 2 proteins: DdmE and DdmD.
Here is an example found in the RefSeq database:
-{max-width=750px}
+{max-width=750px}
The DdmDE system in *Vibrio coralliilyticus* (GCF_000772065.1, NZ_CP009617) is composed of 2 proteins DdmD (WP_043007104.1) DdmE (WP_043007106.1)
## Distribution of the system among prokaryotes
-Among the 22,803 complete genomes of RefSeq, the DmdDE is detected in 135 genomes (0.59 %).
+Among the 22,803 complete genomes of RefSeq, the DdmDE is detected in 135 genomes (0.59 %).
The system was detected in 50 different species.
-{max-width=750px}
+{max-width=750px}
-Proportion of genome encoding the DmdDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
+Proportion of genome encoding the DdmDE system for the 14 phyla with more than 50 genomes in the RefSeq database.
## Structure
diff --git a/public/dmdde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb b/public/ddmde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb
similarity index 100%
rename from public/dmdde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb
rename to public/ddmde/DdmDE,DdmDE__DdmD,0,V-plddts_86.22213.pdb
diff --git a/public/dmdde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb b/public/ddmde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
similarity index 100%
rename from public/dmdde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
rename to public/ddmde/DdmDE,DdmDE__DdmE,0,V-plddts_90.70804.pdb
diff --git a/public/dmdde/DdmDE.svg b/public/ddmde/DdmDE.svg
similarity index 100%
rename from public/dmdde/DdmDE.svg
rename to public/ddmde/DdmDE.svg
diff --git a/public/dmdde/Distribution_DmdDE.svg b/public/ddmde/Distribution_DmdDE.svg
similarity index 100%
rename from public/dmdde/Distribution_DmdDE.svg
rename to public/ddmde/Distribution_DmdDE.svg
--
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