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      Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth

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          Abstract

          Pizzinga et al. show that mRNAs encoding a range of translation factors are localized to granules that get transported into the yeast daughter cell using the She2p/She3p machinery. This likely supports an intensification of protein synthetic activity to facilitate apical polarized growth.

          Abstract

          mRNA localization serves key functions in localized protein production, making it critical that the translation machinery itself is present at these locations. Here we show that translation factor mRNAs are localized to distinct granules within yeast cells. In contrast to many messenger RNP granules, such as processing bodies and stress granules, which contain translationally repressed mRNAs, these granules harbor translated mRNAs under active growth conditions. The granules require Pab1p for their integrity and are inherited by developing daughter cells in a She2p/She3p-dependent manner. These results point to a model where roughly half the mRNA for certain translation factors is specifically directed in granules or translation factories toward the tip of the developing daughter cell, where protein synthesis is most heavily required, which has particular implications for filamentous forms of growth. Such a feedforward mechanism would ensure adequate provision of the translation machinery where it is to be needed most over the coming growth cycle.

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          Stress granules: the Tao of RNA triage.

          Cytoplasmic RNA structures such as stress granules (SGs) and processing bodies (PBs) are functional byproducts of mRNA metabolism, sharing substrate mRNA, dynamic properties and many proteins, but also housing separate components and performing independent functions. Each can exist independently, but when coordinately induced they are often tethered together in a cytosolic dance. Although both self-assemble in response to stress-induced perturbations in translation, several recent reports reveal novel proteins and RNAs that are components of these structures but also perform other cellular functions. Proteins that mediate splicing, transcription, adhesion, signaling and development are all integrated with SG and PB assembly. Thus, these ephemeral bodies represent more than just the dynamic sorting of mRNA between translation and decay.
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            Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

            We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about approximately 5,600 ( approximately 540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.
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              Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

              Although subcellular mRNA trafficking has been demonstrated as a mechanism to control protein distribution, it is generally believed that most protein localization occurs subsequent to translation. To address this point, we developed and employed a high-resolution fluorescent in situ hybridization procedure to comprehensively evaluate mRNA localization dynamics during early Drosophila embryogenesis. Surprisingly, of the 3370 genes analyzed, 71% of those expressed encode subcellularly localized mRNAs. Dozens of new and striking localization patterns were observed, implying an equivalent variety of localization mechanisms. Tight correlations between mRNA distribution and subsequent protein localization and function, indicate major roles for mRNA localization in nucleating localized cellular machineries. A searchable web resource documenting mRNA expression and localization dynamics has been established and will serve as an invaluable tool for dissecting localization mechanisms and for predicting gene functions and interactions.
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                Author and article information

                Journal
                J Cell Biol
                J. Cell Biol
                jcb
                jcb
                The Journal of Cell Biology
                Rockefeller University Press
                0021-9525
                1540-8140
                06 May 2019
                15 March 2019
                15 March 2019
                : 218
                : 5
                : 1564-1581
                Affiliations
                [1 ]Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
                [2 ]Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
                [3 ]Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY
                Author notes
                Correspondence to Mark P. Ashe: mark.p.ashe@ 123456manchester.ac.uk

                M. Pizzinga’s present address is Medical Research Council Toxicology Unit, University of Cambridge, Leicester, UK.

                Author information
                http://orcid.org/0000-0002-0585-7578
                http://orcid.org/0000-0002-9578-7701
                http://orcid.org/0000-0002-7695-3081
                http://orcid.org/0000-0002-5425-7800
                http://orcid.org/0000-0002-3388-7723
                http://orcid.org/0000-0003-2906-4182
                http://orcid.org/0000-0002-4457-7851
                Article
                201704019
                10.1083/jcb.201704019
                6504908
                30877141
                f744054e-a88f-44b8-a860-67bb057f53b4
                © 2019 Pizzinga et al.

                This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).

                History
                : 05 April 2017
                : 12 November 2018
                : 28 February 2019
                Page count
                Pages: 18
                Funding
                Funded by: Wellcome Trust, DOI https://doi.org/10.13039/100010269;
                Award ID: 099732/Z/12/Z
                Award ID: 210002/Z/17/Z
                Award ID: 210004/Z/17/Z
                Award ID: 109330//Z/15/Z
                Funded by: Biotechnology and Biological Sciences Research Council, DOI https://doi.org/10.13039/501100000268;
                Award ID: BB/K005979/1
                Funded by: Comisión Nacional de Investigación Científica y Tecnológica;
                Award ID: 72140307
                Funded by: Biotechnology and Biological Sciences Research Council, DOI https://doi.org/10.13039/501100000268;
                Funded by: Wellcome Trust, DOI https://doi.org/10.13039/100010269;
                Funded by: University of Manchester Strategic Fund
                Categories
                Research Articles
                Article
                31
                40

                Cell biology
                Cell biology

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