diff --git a/content/2.general-concepts/0.index.md b/content/2.general-concepts/0.index.md index 255c3d7f997c61900c2b0280f3cc9fcf0090b874..7451bf80353327542cd32d6b1b8a9f8016ab8a88 100644 --- a/content/2.general-concepts/0.index.md +++ b/content/2.general-concepts/0.index.md @@ -3,5 +3,3 @@ title: General Concepts layout: article --- - -This section is empty. You can help by adding to it. \ No newline at end of file diff --git a/content/2.general-concepts/3.phage_trigger.md b/content/2.general-concepts/3.defense-systems_trigger.md similarity index 100% rename from content/2.general-concepts/3.phage_trigger.md rename to content/2.general-concepts/3.defense-systems_trigger.md diff --git a/content/2.general-concepts/4.defense-systems_effector.md b/content/2.general-concepts/4.defense-systems_effector.md new file mode 100644 index 0000000000000000000000000000000000000000..2e5c1975b13f8ef5dca161a567840a8bb6c8820b --- /dev/null +++ b/content/2.general-concepts/4.defense-systems_effector.md @@ -0,0 +1,12 @@ +--- +title: Abortive Infection +layout: article +toc: true +--- + + +This section is empty. You can help by adding to it. + + +## test article + diff --git a/content/2.general-concepts/5.defense-systems-discovery.md b/content/2.general-concepts/5.defense-systems-discovery.md new file mode 100644 index 0000000000000000000000000000000000000000..c5a661a2252bb6baba9aa827e994fb50c7cfbb85 --- /dev/null +++ b/content/2.general-concepts/5.defense-systems-discovery.md @@ -0,0 +1,7 @@ +--- +title: Discovery of defense systems +layout: article +toc: true +--- + +Defense systems are known since the birth of molecular biology. Then, more were discovered. diff --git a/content/2.general-concepts/6.defensive-domains.md b/content/2.general-concepts/6.defensive-domains.md new file mode 100644 index 0000000000000000000000000000000000000000..08c06c5ae19a314f9fe4cdbd2fac83731751fb94 --- /dev/null +++ b/content/2.general-concepts/6.defensive-domains.md @@ -0,0 +1,7 @@ +--- +title: Defensive Domains +layout: article +toc: true +--- + +Among proteins involved in defense systems, a few domains appear to be frequent. diff --git a/content/2.general-concepts/7.MGE-defense-systems.md b/content/2.general-concepts/7.MGE-defense-systems.md new file mode 100644 index 0000000000000000000000000000000000000000..4ee41cda91ea1914fc0abb040a065aef3e016d9b --- /dev/null +++ b/content/2.general-concepts/7.MGE-defense-systems.md @@ -0,0 +1,8 @@ +--- +title: Defense Systems and MGE +layout: article +toc: true +--- + +Defense systems help bacteria against mobile genetic elements (MGE), such as phage or plasmids. +Yet, some defense systems favor certain MGE, or some MGE carry defense systems. \ No newline at end of file diff --git a/content/2.general-concepts/8.anti-defense-systems.md b/content/2.general-concepts/8.anti-defense-systems.md new file mode 100644 index 0000000000000000000000000000000000000000..05462fbff9d4a5adb8d924a5dbda30b915067bd9 --- /dev/null +++ b/content/2.general-concepts/8.anti-defense-systems.md @@ -0,0 +1,8 @@ +--- +title: Anti Defense Systems +layout: article +toc: true +--- + +Anti defense systems are systems that act against defense system, and thus help bypass the defense mechanism. + diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md index 09df1a0e85735d0c3da77613c14924c731c4c66e..e2eb4fc99e384c62e3182be94d6776b1fe7d0deb 100644 --- a/content/3.defense-systems/gasdermin.md +++ b/content/3.defense-systems/gasdermin.md @@ -6,12 +6,27 @@ tableColumns: doi: 10.1126/science.abj8432 abstract: | Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death. Structures of bacterial gasdermins revealed a conserved pore-forming domain that was stabilized in the inactive state with a buried lipid modification. Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide. Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity. Thus, pyroptosis is an ancient form of regulated cell death shared between bacteria and animals. - Sensor: Unknown + Sensor: Phage protein Activator: Unknown Effector: Membrane disrupting +contributors: + - Aude Bernheim +relevantAbstracts: +- doi: 10.1126/science.abj8432 +- doi: 10.1101/2023.05.28.542683 --- # GasderMIN + + +## Description + +Gasdermin proteins were initially discovered in humans. Recently there were shown to be present in multiple bacteria, where they are almost always encoded in an operon together with a protease. The experimental validation of the antiphage activity of bacterial gasdermins was demonstrated through the heterologous experession of a 4-genes operon from Lysobacter in E. coli :ref{doi=10.1126/science.abj8432} :ref{doi=10.1101/2023.05.28.542683}. + +## Molecular Mechanism + +Akin to their human counterparts, bacterial gasdermins encode a C-terminal inhibotry domain. Following phage infection, proteases associated to bacterial gasdermin cleave this domain triggering oligomerization of gasdermins into large, membrane-breaching pores :ref{doi=10.1126/science.abj8432} leading to cell death:ref{doi=10.1101/2023.05.28.542683}. As such gasdermins containing systems are abortive infection systems. rIIB, a protein allowing T6 to overcome RexAB system was shown to activate gasdermin. It was further shown that CARD domain are also essential in bacterial gasdermins defense :ref{doi=10.1101/2023.05.28.542683}. + ## Example of genomic structure The GasderMIN system is composed of one protein: bGSDM. @@ -105,12 +120,4 @@ 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: 10.1126/science.abj8432 ---- -:: diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md index 2651d6c2116bb0ac1498d0d927a2cd6db54e1b53..b4d528a67c07faa3aed277d6142af69d4e2e1131 100644 --- a/content/3.defense-systems/retron.md +++ b/content/3.defense-systems/retron.md @@ -12,9 +12,23 @@ tableColumns: PFAM: PF00078, PF00089, PF01381, PF01582, PF12686, PF12844, PF13175, PF13304, PF13365, PF13476, PF13560, PF13676 contributors: - Adi Millman + - Héloïse Georjon + - Aude Bernheim relevantAbstracts: - doi: 10.1016/j.cell.2020.09.065 - doi: 10.1093/nar/gkaa1149 + - doi: 10.1038/s41586-022-05091-4 + - doi: 10.1126/science.aba0372 + - doi: 10.1038/s41564-022-01197-7 + - doi: 10.1093/nar/gkaa1149 + - doi: 10.1038/s41589-021-00927-y + - doi: 10.1093/femsre/fuab025 + - doi: 10.1371/journal.pone.0285274 + - doi: 10.1038/s41596-023-00819-6 + - doi: 10.1093/nar/gkac177 + - doi: 10.1080/15476286.2019.1639310 + - doi: 10.1101/2023.08.16.553469 + --- # Retron