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      A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli

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          SUMMARY

          Nucleus-forming jumbo phages establish an intricate subcellular organization, enclosing phage genomes within a proteinaceous shell called the phage nucleus. During infection in Pseudomonas, some jumbo phages assemble a bipolar spindle of tubulin-like PhuZ filaments that positions the phage nucleus at midcell and drives its intracellular rotation. This facilitates the distribution of capsids on its surface for genome packaging. Here we show that the Escherichia coli jumbo phage Goslar assembles a phage nucleus surrounded by an array of PhuZ filaments resembling a vortex instead of a bipolar spindle. Expression of a mutant PhuZ protein strongly reduces Goslar phage nucleus rotation, demonstrating that the PhuZ cytoskeletal vortex is necessary for rotating the phage nucleus. While vortex-like cytoskeletal arrays are important in eukaryotes for cytoplasmic streaming and nucleus alignment, this work identifies a coherent assembly of filaments into a vortex-like structure driving intracellular rotation within the prokaryotic cytoplasm.

          In brief

          The phage nucleus was recently discovered, and the diversity and ubiquity of this phage replication pathway is unclear. Birkholz et al. identify a nucleus-forming E. coli phage and show that tubulin (PhuZ) filaments form a vortex-like structure driving intracellular rotation of the phage nucleus within the prokaryotic cytoplasm.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            UCSF ChimeraX : Structure visualization for researchers, educators, and developers

            UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
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              Automated electron microscope tomography using robust prediction of specimen movements.

              A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction. The method uses changes in specimen position at previous tilt angles to predict the position at the current tilt angle. Actual measurement of the position or focus is skipped if the statistical error of the prediction is low enough. This method allows a tilt series to be acquired rapidly when conditions are good but falls back toward the traditional approach of taking focusing and tracking images when necessary. The method has been implemented in a program, SerialEM, that provides an efficient environment for data acquisition. This program includes control of an energy filter as well as a low-dose imaging mode, in which tracking and focusing occur away from the area of interest. The program can automatically acquire a montage of overlapping frames, allowing tomography of areas larger than the field of the CCD camera. It also includes tools for navigating between specimen positions and finding regions of interest.
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                Author and article information

                Journal
                101573691
                39703
                Cell Rep
                Cell Rep
                Cell reports
                2211-1247
                10 January 2023
                16 August 2022
                01 February 2023
                : 40
                : 7
                : 111179
                Affiliations
                [1 ]Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
                [2 ]Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
                [3 ]Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
                [4 ]Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
                [5 ]Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
                [6 ]Lead contact
                Author notes

                AUTHOR CONTRIBUTIONS

                E.A.B., T.G.L., S.S., E.A., and J.L. conducted experiments and analyzed data.

                E.A.B. and J.P. conceptualized the original manuscript. J.W. provided the phage for study. E.A.B., T.G.L., E.A., J.W., K.D.C., E.V., and J.P. contributed to editing the manuscript.

                [* ]Correspondence: evilla@ 123456ucsd.edu (E.V.), jpogliano@ 123456ucsd.edu (J.P.)
                Article
                NIHMS1830640
                10.1016/j.celrep.2022.111179
                9891218
                35977483
                5eb9129b-8937-4bec-a4ec-1415b97aaaac

                This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/).

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                Cell biology
                Cell biology

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