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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
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certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
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or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
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Some devices are designed to deny users access to install or run
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The precise terms and conditions for copying, distribution and
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TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
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1. Source Code.
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The Corresponding Source for a work in source code form is that
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All rights granted under this License are granted for the term of
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Notwithstanding any other provision of this License, you have
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The Free Software Foundation may publish revised and/or new versions of
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
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EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
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17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) 2024 Remi PLANEL
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) 2024 Remi PLANEL
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.
content/3.defense-systems/caprel.md
View file @ c62a379c
......@@ -10,18 +10,21 @@ tableColumns:
Activator: Direct
Effector: Nucleic acid degrading (pyrophosphorylates tRNAs)
PFAM: PF04607
contributors:
- Héloïse Georjon
- Florian Tesson
relevantAbstracts:
- doi: 10.1038/s41586-022-05444-z
- doi: 10.1038/s41586-022-05444-z
---
# CapRel
## Description
CapRel is a fused toxin–antitoxin system that is active against diverse phages when expressed in *Escherichia coli*. CapRel belongs to the family of toxSAS toxin–antitoxin systems. CapRel is an Abortive infection system which is found in Cyanobacteria, Actinobacteria, and Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages.
CapRel is a fused toxin-antitoxin system that is active against diverse phages when expressed in *Escherichia coli* :ref{doi=10.1038/s41586-022-05444-z}. CapRel belongs to the family of toxSAS toxin-antitoxin systems. CapRel is an Abortive infection system which is found in Cyanobacteria, Actinobacteria, and Proteobacteria, Spirochetes, Bacteroidetes, and Firmicutes, as well as in some temperate phages.
## Molecular mechanism
The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
The CapRel system of Salmonella temperate phage SJ46 is normally found in a closed conformation, which is thought to maintain CapRel in an auto-inhibited state. However during phage SECPhi27 infection, binding of the major phage capsid protein (Gp57) to CapRel releases it from is inhibited state, allowing pyrophosphorylation of tRNAs by the toxin domain and resulting in translation inhibition :ref{doi=10.1038/s41586-022-05444-z}. Other phage capsid proteins can be recognized by CapRel, as observed during infection by phage Bas8.
Different CapRel homologues confer defense against different phages, suggesting variable phage specificity of CapRel system which seems to be mediated by the C-terminal region of CapRel.
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content/3.defense-systems/druantia.md
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Activator: Unknown
Effector: Unknown
PFAM: PF00145, PF00270, PF00271, PF04851, PF09369, PF14236
contributors:
- Lucas Paoli
relevantAbstracts:
- doi: 10.1126/science.aar4120
- doi: 10.1126/science.aar4120
---
# Druantia
## Description
The Druantia system was described by Doron et al. 2018 :ref{doi=10.1126/science.aar4120} and includes multiple subtypes, including type I (DruABCDE), type II (DruMFGE), and Type III (DruHE). Druantia is a particularly large system (~12 kb) and was named after the Gallic tree goddess. Type III was further tested by Wang et al. 2023 :ref{doi=10.1128/jvi.00599-23}.
## Molecular mechanisms
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
A total of 3 subsystems have been described for the Druantia system.
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content/3.defense-systems/gabija.md
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## Structure
### Experimentaly determined structure
From :ref{doi=10.1038/s41586-023-06855-2} in *Bacillus cereus* VD045:
::molstar-pdbe-plugin
---
height: 700
dataUrls:
- /gabija/8sm3_BcGajAB_4_4mer.pdb
- /gabija/8u7i_BcGajAB_4_4mer_gad1.pdb
---
::
### Gabija
##### Example 1
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content/3.defense-systems/gaps4.md
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doi: 10.1101/2023.03.28.534373
abstract: |
Bacteria are found in ongoing conflicts with rivals and predators, which lead to an evolutionary arms race and the development of innate and adaptive immune systems. Although diverse bacterial immunity mechanisms have been recently identified, many remain unknown, and their dissemination within bacterial populations is poorly understood. Here, we describe a widespread genetic element, defined by the Gamma-Mobile-Trio (GMT) proteins, that serves as a mobile bacterial weapons armory. We show that GMT islands have cargo comprising various combinations of secreted antibacterial toxins, anti-phage defense systems, and secreted anti-eukaryotic toxins. This finding led us to identify four new anti-phage defense systems encoded within GMT islands and reveal their active domains and mechanisms of action. We also find the phage protein that triggers the activation of one of these systems. Thus, we can identify novel toxins and defense systems by investigating proteins of unknown function encoded within GMT islands. Our findings imply that the concept of "defense islands" may be broadened to include other types of bacterial innate immunity mechanisms, such as antibacterial and anti-eukaryotic toxins that appear to stockpile with anti-phage defense systems within GMT weapon islands.
contributors:
- Hugo Vaysset
relevantAbstracts:
- doi: 10.1101/2023.03.28.534373
---
# GAPS4
## To do
## Description
GAPS4 is a two genes system (GAPS4a and GAPS4b). GAPS stands for GMT-encoded Anti-Phage System.
GAPS4 is present in both Gram positive and Gram negative
GAPS4 activity was assessed in *E. coli* and was shown to be active against T4, P1-vir and lambda-vir and to reduce lysis plaque size of T7 :ref{doi=10.1101/2023.03.28.534373}.
## Molecular mechanism
GAPS4a is a nuclease containing a domain from the PDDEXK clan (CL0236) suggesting that the GAPS4 defense system is acting via DNA degradation. Both genes are required for phage defense and were predicted to form a heterodimer. It was shown that the system works causes host DNA degradation upon infection by lambda-vir only, which would suggest that GAPS4 is an abortive infection system :ref{doi=10.1101/2023.03.28.534373}.
## Example of genomic structure
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## Structure
### GAPS4
##### Example 1
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content/3.defense-systems/pd-t7-1.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Hugo Vaysset
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
---
# PD-T7-1
## Description
PD-T7-1 is a single gene defense systems which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
## Example of genomic structure
The PD-T7-1 is composed of 1 protein: PD-T7-1.
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The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is composed of 1 protein: PD-T7-1 (WP_004150873.1)
## Distribution of the system among prokaryotes
<<<<<<< content/3.defense-systems/pd-t7-1.md
The PD-T7-1 system is present in a total of 136 different species.
=======
Among the 22,803 complete genomes of RefSeq, the PD-T7-1 is detected in 748 genomes (3.28 %).
>>>>>>> content/3.defense-systems/pd-t7-1.md
The system was detected in 146 different species.
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content/3.defense-systems/pd-t7-5.md
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Sensor: Unknown
Activator: Unknown
Effector: Unknown
contributors:
- Hugo Vaysset
relevantAbstracts:
- doi: 10.1038/s41564-022-01219-4
- doi: 10.1038/s41564-022-01219-4
---
# PD-T7-5
## Example of genomic structure
The PD-T7-5 is composed of 1 protein: PD-T7-5.
## Description
PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
## Molecular mechanism
As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
## Example of genomic structure
The PD-T7-5 system is composed of one protein: PD-T7-5.
Here is an example found in the RefSeq database:
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