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      Chloroplast biogenesis involves spatial coordination of nuclear and organellar gene expression in Chlamydomonas

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          Abstract

          The localization of translation can direct the polypeptide product to the proper intracellular compartment. Our results reveal translation by cytosolic ribosomes on a domain of the chloroplast envelope in the unicellular green alga Chlamydomonas ( Chlamydomonas reinhardtii). We show that this envelope domain of isolated chloroplasts retains translationally active ribosomes and mRNAs encoding chloroplast proteins. This domain is aligned with localized translation by chloroplast ribosomes in the translation zone, a chloroplast compartment where photosystem subunits encoded by the plastid genome are synthesized and assembled. Roles of localized translation in directing newly synthesized subunits of photosynthesis complexes to discrete regions within the chloroplast for their assembly are suggested by differences in localization on the chloroplast of mRNAs encoding either subunit of the light-harvesting complex II or the small subunit of Rubisco. Transcription of the chloroplast genome is spatially coordinated with translation, as revealed by our demonstration of a subpopulation of transcriptionally active chloroplast nucleoids at the translation zone. We propose that the expression of chloroplast proteins by the nuclear-cytosolic and organellar genetic systems is organized in spatially aligned subcompartments of the cytoplasm and chloroplast to facilitate the biogenesis of the photosynthetic complexes.

          Abstract

          The expression of chloroplast proteins occurs in spatially aligned subcompartments of the cytoplasm and chloroplast to facilitate the biogenesis of the photosynthetic complexes.

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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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            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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              Computer visualization of three-dimensional image data using IMOD.

              We have developed a computer software package, IMOD, as a tool for analyzing and viewing three-dimensional biological image data. IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions. The software allows image data to be visualized by several different methods. Models of the image data can be visualized by volume or contour surface rendering and can yield quantitative information.
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                Author and article information

                Contributors
                Journal
                Plant Physiol
                Plant Physiol
                plphys
                Plant Physiology
                Oxford University Press (US )
                0032-0889
                1532-2548
                September 2024
                06 May 2024
                06 May 2024
                : 196
                : 1
                : 112-123
                Affiliations
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Department of Anatomy and Cell Biology, McGill University , Montreal, Quebec, Canada, H3A 0C7
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Laboratory of Plant Molecular Genetics, Department of Botany, Graduate School of Sciences, Koyoto University , Oiwake-cho, Kita-Shirakawa, Kyoto-shi 606-8502, Japan
                School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University , Baoding, Hebei 071002, China
                Centre for Microscopy and Cell Imaging, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Department of Anatomy and Cell Biology, McGill University , Montreal, Quebec, Canada, H3A 0C7
                Department of Anatomy and Cell Biology, McGill University , Montreal, Quebec, Canada, H3A 0C7
                Department of Biology, Concordia University , Montreal, Quebec, Canada, H4B 1R6
                Author notes
                Author for correspondence: william.zerges@ 123456concordia.ca
                Present address: Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

                Yi Sun and Shiva Bakhtiari contributed equally to this work.

                The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors ( https://academic.oup.com/plphys/pages/General-Instructions) is William Zerges ( william.zerges@ 123456concordia.ca ).

                Conflict of interest statement. None declared.

                Author information
                https://orcid.org/0000-0002-2366-7153
                https://orcid.org/0000-0002-8737-3170
                https://orcid.org/0000-0001-8470-3739
                https://orcid.org/0009-0006-2226-5757
                https://orcid.org/0009-0007-3354-9023
                https://orcid.org/0000-0002-6946-8029
                https://orcid.org/0000-0001-8851-7562
                https://orcid.org/0000-0002-9973-0446
                https://orcid.org/0000-0003-2814-9889
                https://orcid.org/0000-0001-7227-2011
                Article
                kiae256
                10.1093/plphys/kiae256
                11376380
                38709497
                70bdf473-ecf2-4beb-9bfe-2b8c541b2e76
                © The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence ( https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.

                History
                : 04 December 2023
                : 12 April 2024
                : 29 May 2024
                Page count
                Pages: 12
                Funding
                Funded by: Natural Sciences and Engineering Research Council of Canada Discovery, DOI 10.13039/501100000038;
                Award ID: 217566
                Funded by: Japan Society for the Promotion of Science, DOI 10.13039/501100001691;
                Award ID: 22K19329
                Funded by: Scientific Research;
                Award ID: 21H02504
                Funded by: Transformative Research Areas;
                Award ID: 24H02275
                Funded by: Canadian Institutes of Health Research, DOI 10.13039/501100000024;
                Award ID: PJT-156354
                Categories
                Research Article
                Cell Biology
                AcademicSubjects/SCI01270
                AcademicSubjects/SCI01280
                AcademicSubjects/SCI02286
                AcademicSubjects/SCI02287
                AcademicSubjects/SCI02288

                Plant science & Botany
                Plant science & Botany

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