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      FinO/ProQ-family proteins: an evolutionary perspective

      review-article
      ,
      Bioscience Reports
      Portland Press Ltd.
      evolution, FinO, ProQ, RNA chaperone, RNA-binding proteins

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          Abstract

          RNA-binding proteins are key actors of post-transcriptional networks. Almost exclusively studied in the light of their interactions with RNA ligands and the associated functional events, they are still poorly understood as evolutionary units. In this review, we discuss the FinO/ProQ family of bacterial RNA chaperones, how they evolve and spread across bacterial populations and what properties and opportunities they provide to their host cells. We reflect on major conserved and divergent themes within the family, trying to understand how the same ancestral RNA-binding fold, augmented with additional structural elements, could yield either highly specialised proteins or, on the contrary, globally acting regulatory hubs with a pervasive impact on gene expression. We also consider dominant convergent evolutionary trends that shaped their RNA chaperone activity and recurrently implicated the FinO/ProQ-like proteins in bacterial DNA metabolism, translation and virulence. Finally, we offer a new perspective in which FinO/ProQ-family regulators emerge as active evolutionary players with both negative and positive roles, significantly impacting the evolutionary modes and trajectories of their bacterial hosts.

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          AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

          The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk ) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.
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            UniProt: the universal protein knowledgebase in 2021

            Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
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              Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae.

              The mammalian gut harbors a dense microbial community interacting in multiple ways, including horizontal gene transfer (HGT). Pangenome analyses established particularly high levels of genetic flux between Gram-negative Enterobacteriaceae. However, the mechanisms fostering intraenterobacterial HGT are incompletely understood. Using a mouse colitis model, we found that Salmonella-inflicted enteropathy elicits parallel blooms of the pathogen and of resident commensal Escherichia coli. These blooms boosted conjugative HGT of the colicin-plasmid p2 from Salmonella enterica serovar Typhimurium to E. coli. Transconjugation efficiencies of ~100% in vivo were attributable to high intrinsic p2-transfer rates. Plasmid-encoded fitness benefits contributed little. Under normal conditions, HGT was blocked by the commensal microbiota inhibiting contact-dependent conjugation between Enterobacteriaceae. Our data show that pathogen-driven inflammatory responses in the gut can generate transient enterobacterial blooms in which conjugative transfer occurs at unprecedented rates. These blooms may favor reassortment of plasmid-encoded genes between pathogens and commensals fostering the spread of fitness-, virulence-, and antibiotic-resistance determinants.
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                Author and article information

                Contributors
                Role: Data curationRole: Writing—original draft
                Role: ConceptualizationRole: SupervisionRole: Funding acquisitionRole: VisualizationRole: Project administrationRole: Writing—review & editing
                Journal
                Biosci Rep
                Biosci Rep
                bsr
                Bioscience Reports
                Portland Press Ltd.
                0144-8463
                1573-4935
                31 March 2023
                01 March 2023
                : 43
                : 3
                : BSR20220313
                Affiliations
                [1 ]UMR7156 - Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, France
                [2 ]University of Strasbourg Institute for Advanced Study (USIAS), France
                Author notes
                Correspondence: Alexandre Smirnov ( alexandresmirnov@ 123456unistrs.fr )
                Author information
                https://orcid.org/0000-0002-9142-7979
                Article
                BSR20220313
                10.1042/BSR20220313
                9977716
                36787218
                b7c5cd5f-e054-4519-86d3-1dad11d46b48
                © 2023 The Author(s).

                This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY).

                History
                : 30 October 2022
                : 02 February 2023
                : 14 February 2023
                : 14 February 2023
                Page count
                Pages: 21
                Categories
                Evolutionary Biology
                Gene Expression & Regulation
                Microbiology
                Molecular Interactions
                RNA
                Review Articles

                Life sciences
                evolution,fino,proq,rna chaperone,rna-binding proteins
                Life sciences
                evolution, fino, proq, rna chaperone, rna-binding proteins

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