diff --git a/content/2.general-concepts/1.abortive-infection.md b/content/2.general-concepts/1.abortive-infection.md index 44d6b82a1c48494e28ac1877bbe2ebf85e33984b..51ce4c4cf75ef6cafe8de0cca8b0715041b01a62 100644 --- a/content/2.general-concepts/1.abortive-infection.md +++ b/content/2.general-concepts/1.abortive-infection.md @@ -19,6 +19,7 @@ relevantAbstracts: - doi: 10.1038/s41579-023-00934-x --- +# Abortive Infection The term abortive infection was coined in the 1950s :ref{doi=10.1128/jb.68.1.36-42.1954} to describe the observations that a fraction of the bacterial population did not support phage replication. diff --git a/content/2.general-concepts/6.defensive-domains.md b/content/2.general-concepts/6.defensive-domains.md index 44960e31f74bd4b074e10d1feff9797832a35945..28fc16d4d3d051f6066638a9e7d996444438de7b 100644 --- a/content/2.general-concepts/6.defensive-domains.md +++ b/content/2.general-concepts/6.defensive-domains.md @@ -5,8 +5,9 @@ toc: true contributors: - Hugo Vaysset --- +# Defensive Domains -# What are protein domains ? +## What are protein domains ? Proteins can typically be decomposed into a set of structural or functional units called "domains" where each individual domain has a specific biological function (e.g. catalyzing a chemical reaction or binding to another protein). The combination of one or several protein domains within a protein determines its biological function. @@ -14,10 +15,10 @@ Proteins can typically be decomposed into a set of structural or functional unit To examplify this idea, the figure is a depiction of the ThsA protein involved in the [Thoeris](/defense-systems/thoeris) defense system in *Bacillus cereus*. The protein is composed of two domains : a SIR2-like domain (blue) and a SLOG domain (green). The SLOG domain of ThsA is able to bind to cyclic Adenosine Diphosphate Ribose (cADPR), a signalling molecule produced by ThsB upon phage infection. Binding of cADPR activates the Nicotinamide Adenine Dinucleotide (NAD) depletion activity of the SIR2-like domain which causes abortive infection. This shows how the presence of two domains in this protein allows it to be activated by the sensor component of the system (ThsB) and to trigger the immune response mechanism :ref{doi=10.1038/s41586-021-04098-7}. -# Domain characterization helps to understand the biological function of a protein +## Domain characterization helps to understand the biological function of a protein Although a considerable diversity of molecular mechanisms have been described for defense systems, it is striking to observe that some functional domains are recurrently involved in antiphage defense :ref{doi=10.1038/s41586-021-04098-7}. When studying the presence of a new defense system, the *in silico* characterization of the domains present in the system can provide valuable information regarding the molecular mechanism of the system. If one protein of the system contains for example a TerB domain, this might indicate that the system is involved in membrane integrity surveillance as this domain was previously shown to be associated with the periplasmic membrane :ref{doi=10.1016/j.chom.2022.09.017}. If a protein of the system contains a TIR domain this might indicate that the system possess a NAD degradation activity or that the protein could multimerize as both functions have been shown for this domain in the past :ref{doi=10.3389/fimmu.2021.784484}. -# Domains can be conserved throughout evolution +## Domains can be conserved throughout evolution It is clear that some defense systems can be conserved among different clades of bacteria but it was also observed that the unit of evolutionary conservation can be the protein domain :ref{doi=10.1038/s41467-022-30269-9}. As a consequence, it is frequent to find the same domain associated with a wide range of distinct other domains in different defense systems :ref{doi=10.1016/j.mib.2023.102312}. This is well illustrated by defense systems such [Avs](/defense-systems/avs) or [CBASS](/defense-systems/cbass) that can be constituted of diverse effector proteins which differ from each other based on the specific domains that compose them :ref{doi=10.1126/science.aba0372}, :ref{doi=10.1038/s41564-022-01239-0}, :ref{doi=10.1038/s41564-020-0777-y}. The modular aspect of protein domains fits with the concept of "evolution as tinkering" stating that already existing objects (here protein domains) can often be repurposed in new manners, allowing the efficient development of novel functions :ref{doi=10.1126/science.860134}. diff --git a/content/2.general-concepts/7.mge-defense-systems.md b/content/2.general-concepts/7.mge-defense-systems.md index 634fc571d8fca3118e1c13e719cc6f3409bbb25c..4d78a0b0e571a77d91c24d1278a4eb9a671b51b9 100644 --- a/content/2.general-concepts/7.mge-defense-systems.md +++ b/content/2.general-concepts/7.mge-defense-systems.md @@ -4,5 +4,6 @@ contributors: - Marian Dominguez-Mirazo layout: article --- +# Defense Systems and Mobile Genetic Elements Mobile genetic elements (MGEs), such as plasmids, bacteriophages, and phage satellites, facilitate horizontal gene transfer (HGT) within microbial populations, playing a crucial role in the genetic diversity and genomic evolution of bacteria :ref{doi=10.1098/rstb.2020.0460}. These elements expedite the exchange of genetic material among bacterial cells, promoting the dissemination of advantageous traits like antibiotic resistance, virulence factors, and metabolic capabilities, allowing bacteria to adapt to dynamic environments :ref{doi=10.1098/rstb.2020.0460}. However, the presence of MGEs can impose a substantial fitness cost on the bacterial host, as in the case of lytic phage infections. To counteract parasitic genomic elements, including viruses and other MGEs, bacteria have evolved defense systems. These defense systems are often disadvantageous under low parasite pressure, leading to their occasional loss. However, as the pressure from parasites increases, these defense systems become advantageous. Consequently, defense systems in bacteria exhibit high mobility and transfer rates :ref{doi=10.1038/s41576-019-0172-9}. Interestingly, a large fraction of defense systems in bacteria are encoded by MGEs :ref{doi=10.1038/s41467-022-30269-9,10.1371/journal.pbio.3001514}. While sometimes the fitness interests of MGEs and the bacterial host are aligned, these systems are likely to be selected because they benefit the MGE encoding it rather than the host cell who :ref{doi=10.1371/journal.pbio.3001514,10.1038/s41576-019-0172-9}. This benefit may include preventing other mobile elements from infecting the same cell and competing for essential resources. The presence of defense systems can, in turn, have an effect in gene flow who :ref{doi=10.1371/journal.pbio.3001514}.