From 4bb362dc754e27726131b78f8aa57379ab1c2208 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Fri, 15 Dec 2023 21:25:24 +0100
Subject: [PATCH] Fix multiple typos
---
content/0.index.md | 4 ++--
content/3.defense-systems/abib.md | 2 +-
content/3.defense-systems/abiu.md | 4 ++--
content/3.defense-systems/pd-t4-4.md | 2 +-
4 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/content/0.index.md b/content/0.index.md
index a1c92a98..c2f4588d 100644
--- a/content/0.index.md
+++ b/content/0.index.md
@@ -18,13 +18,13 @@ relevantAbstracts:
## Introduction
-Bacteria and their phages have co-existed for billions of years. The pressure of phage infection is thought to be a major driver of bacterial evolution and has favored the development of a diversity of anti-phage weapons. These weapons, namely anti-phage defense systems can be defined as single genes or groups of genes that partially or fully inhibit phage infection. For reviews on anti-phage systems, see : :ref{doi=10.1038/s41586-019-1894-8, 10.1146/annurev-micro-020722-013730, 10.1016/j.mib.2005.06.006, 10.1038/s41579-023-00934-x}.
+Bacteria and their phages have co-existed for billions of years. The pressure of phage infection is thought to be a major driver of bacterial evolution and has favored the development of a diversity of anti-phage weapons. These weapons, namely anti-phage defense systems can be defined as single genes or groups of genes that partially or fully inhibit phage infection. For reviews on anti-phage systems, see : :ref{doi=10.1038/s41586-019-1894-8,10.1146/annurev-micro-020722-013730,10.1016/j.mib.2005.06.006,10.1038/s41579-023-00934-x}.
## A brief history of anti-phage systems
The first discovered anti-phage system, a Restriction-Modification (RM) system, was described in the early 1950s ref{doi=10.1128/jb.64.4.557-569.1952, 10.1128/jb.65.2.113-121.1953}. In the following decades, a handful of other systems were discovered :ref{doi=10.1016/j.mib.2005.06.006}. In 2007, CRISPR-Cas systems were discovered to be anti-phage systems :ref{doi=10.1126/science.1138140}. As CRISPR-Cas systems and RM systems are extremely prevalent in bacteria, it was thought for some years that the antiviral immune system of bacteria had been mostly elucidated.
-Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, it was revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11}. This led to a guilt-by-association hypothesis: if a gene or a set of genes is frequently found in bacterial genomes in close proximity to known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This hypothesis was tested systematically in a landarmark study in 2018 :ref{doi=10.1126/science.aar4120} leading to the discovery of 10 novel anti-phage systems. This started the uncovering of an impressive diversity of defense systems in a very short amount of time :ref{10.1038/s41579-023-00934-x}.
+Following these two major breakthroughs, knowledge of anti-phage systems remained scarce for some years. Yet, in 2011, it was revealed that anti-phage systems tend to colocalize on the bacterial genome in defense-islands :ref{doi=10.1128/JB.05535-11}. This led to a guilt-by-association hypothesis: if a gene or a set of genes is frequently found in bacterial genomes in close proximity to known defense systems, such as RM or CRISPR-Cas systems, then it might constitute a new defense system. This hypothesis was tested systematically in a landarmark study in 2018 :ref{doi=10.1126/science.aar4120} leading to the discovery of 10 novel anti-phage systems. This started the uncovering of an impressive diversity of defense systems in a very short amount of time :ref{doi=10.1038/s41579-023-00934-x}.
To date over 150 types of defense systems have been described, unveiling an unsuspected diversity of molecular mechanisms. The antiviral immune systems of bacteria therefore appear much more complex than previously envisioned, and new discoveries do not seem to be slowing down.
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index b137056a..baff8401 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -24,7 +24,7 @@ relevantAbstracts:
AbiB is a single-protein abortive infection defense system from *Lactococcus* that degrades mRNA.
## Molecular mechanism
-AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs:ref{doi=10.1046/j.1365-2958.1996.371896.x} that is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
+AbiB system is still poorly understood. It is a single-protein system that was described as an abortive infection system. Upon phage infection, AbiB activation leads to a strong degradation of mRNAs :ref{doi=10.1046/j.1365-2958.1996.371896.x} that is expected to be the mechanism of phage inhibition. AbiB expression is constitutive and does increase during phage infection. It is only activated during phage infection, most likely through the recognition of an early phage protein. Which protein, and whether this activation is direct or indirect remains to be elucidated.
## Example of genomic structure
The AbiB system is composed of one protein: AbiB.
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index 497cb4ce..3b5dd7b9 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -10,9 +10,9 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF10592
-contributor:
+contributors:
- Nathalie Bechon
-relevant-abstracts
+relevantAbstracts:
- doi: 10.1023/A:1002027321171
- doi: 10.1016/j.mib.2005.06.006
- doi: 10.1128/AEM.67.11.5225-5232.2001
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index 8eb17137..65ed8082 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -12,7 +12,7 @@ tableColumns:
PFAM: PF13175, PF13304
contributors:
- Nathalie Bechon
-relevantAbstracts
+relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
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