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      A dynamic bactofilin cytoskeleton cooperates with an M23 endopeptidase to control bacterial morphogenesis

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          Abstract

          Bactofilins have emerged as a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, but their precise mode of action is still incompletely understood. In this study, we identify the bactofilin cytoskeleton as a key regulator of cell growth in the stalked budding alphaproteobacterium Hyphomonas neptunium. We show that, in this species, bactofilin polymers localize dynamically to the stalk base and the bud neck, with their absence leading to unconstrained growth of the stalk and bud compartments, indicating a central role in the spatial regulation of cell wall biosynthesis. Database searches reveal that bactofilin genes are often clustered with genes for cell wall hydrolases of the M23 peptidase family, suggesting a functional connection between these two types of proteins. In support of this notion, we find that the H. neptunium M23 peptidase homolog LmdC interacts directly with bactofilin in vitro and is required for proper cell shape in vivo. Complementary studies in the spiral-shaped alphaproteobacterium Rhodospirillum rubrum again reveal a close association of its bactofilin and LmdC homologs, which co-localize at the inner curve of the cell, modulating the degree of cell curvature. Collectively, these findings demonstrate that bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis, thereby driving cell shape determination in morphologically complex bacteria.

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            Highly accurate protein structure prediction with AlphaFold

            Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1 – 4 , the structures of around 100,000 unique proteins have been determined 5 , but this represents a small fraction of the billions of known protein sequences 6 , 7 . Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’ 8 —has been an important open research problem for more than 50 years 9 . Despite recent progress 10 – 14 , existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14) 15 , demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.
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              Basic local alignment search tool.

              A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                31 January 2024
                2024
                : 12
                : RP86577
                Affiliations
                [1 ] Department of Biology, University of Marburg, Marburg, Germany ( https://ror.org/01rdrb571) Marburg Germany
                [2 ] Max Planck Institute for Terrestrial Microbiology ( https://ror.org/05r7n9c40) Marburg Germany
                [3 ] Department of Chemistry, University of Marburg ( https://ror.org/01rdrb571) Marburg Germany
                [4 ] Center for Synthetic Microbiology (SYNMIKRO) ( https://ror.org/04e209f39) Marburg Germany
                [5 ] Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University ( https://ror.org/01kj2bm70) Newcastle upon Tyne United Kingdom
                [6 ] Institute for Molecular Bioscience, The University of Queensland ( https://ror.org/00rqy9422) Brisbane Australia
                University of Freiburg ( https://ror.org/0245cg223) Germany
                University of Geneva ( https://ror.org/01swzsf04) Switzerland
                University of Freiburg Germany
                University of Marburg Marburg Germany
                University of Marburg Marburg Germany
                University of Marburg Marburg Germany
                University of Marburg Marburg Germany
                University of Marburg Marburg Germany
                Newcastle University Newcastle upon Tyne United Kingdom
                University of Marburg Marburg Germany
                Newcastle University Newcastle upon Tyne United Kingdom
                University of Marburg Marburg Germany
                Philipp University of Marburg Marburg Germany
                Author notes
                [†]

                These authors contributed equally to this work.

                [‡]

                Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, United States.

                [§]

                Faculty of Sciences and Technologies, Université de Lorraine, Nancy, France.

                Author information
                https://orcid.org/0000-0002-5048-116X
                https://orcid.org/0000-0003-4666-3929
                https://orcid.org/0000-0002-1286-6851
                https://orcid.org/0000-0003-0408-8567
                https://orcid.org/0000-0002-1303-1442
                Article
                86577
                10.7554/eLife.86577
                10945521
                38294932
                265d345b-b465-4f17-83a1-f59614f46d2d
                © 2023, Pöhl, Osorio-Valeriano, Cserti et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 26 February 2023
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100008967, University of Marburg;
                Award ID: Core funding
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;
                Award ID: Max Planck Fellowship
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: 450420164
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: 26942323 - TRR 174
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/W013630/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004189, Max-Planck-Gesellschaft;
                Award ID: PhD fellowship of the IMPRS for Environmental, Cellular and Molecular Microbiology
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Open access funding provided by Max Planck Society.
                Categories
                Research Article
                Microbiology and Infectious Disease
                Custom metadata
                Analyses of the stalked budding bacterium Hyphomonas neptunium and its spiral-shaped relative Rhodospirillum rubrum reveal a conserved morphogenetic module that controls the establishment of complex bacterial cell shapes.
                prc

                Life sciences
                cell shape,bactofilin,m23 endopeptidase,rodz,elongasome,crispri,hyphomonas neptunium,rhodospirillum rubrum,other

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