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      p97/VCP Promotes the Recycling of Endocytic Cargo

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          Abstract

          The endocytic pathway is of central importance for eukaryotic cells, as it enables uptake of extracellular materials, membrane protein quality control and recycling, as well as modulation of receptor signaling. While the ATPase p97 (VCP, Cdc48) has been found to be involved in the fusion of early endosomes and endolysosomal degradation, its role in endocytic trafficking is still incompletely characterized. Here, we identify myoferlin (MYOF), a ferlin family member with functions in membrane trafficking and repair, as a hitherto unknown p97 interactor. The interaction of MYOF with p97 depends on the cofactor PLAA previously linked to endosomal sorting. Besides PLAA, shared interactors of p97 and MYOF comprise several proteins involved in endosomal recycling pathways, including Rab11, Rab14, and the transferrin receptor CD71. Accordingly, a fraction of p97 and PLAA localizes to MYOF-, Rab11-, and Rab14-positive endosomal compartments. Pharmacological inhibition of p97 delays transferrin recycling, indicating that p97 promotes not only the lysosomal degradation, but also the recycling of endocytic cargo.

          Abstract

          • The ATPase p97/VCP has been linked to endosomal trafficking in the past, but the full range of its involvement in endosomal processes is still unknown.

          • The authors used crosslinking-assisted mass spectrometry to identify MYOF as novel p97 binding partner.

          • Using immunofluorescence microscopy, they found that a subpopulation of p97 and MYOF localizes to recycling endosomes and that chemical inhibition of p97 delays the recycling of transferrin to the plasma membrane.

          • These findings suggest that p97 possesses functions beyond the endolysosomal degradation of endocytic cargo and implicate p97 in MYOF-dependent membrane trafficking and repair pathways.

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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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            MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

            Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
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              The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

              The PRoteomics IDEntifications (PRIDE) database ( https://www.ebi.ac.uk/pride/ ) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.
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                Author and article information

                Contributors
                Role: Monitoring Editor
                Journal
                Mol Biol Cell
                Mol Biol Cell
                molbiolcell
                mboc
                Molecular Biology of the Cell
                The American Society for Cell Biology
                1059-1524
                1939-4586
                01 December 2023
                13 November 2023
                : 34
                : 13
                : ar126
                Affiliations
                [a ]Chair of Biochemistry I, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
                [b ]Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
                University of California, Berkeley
                Author notes

                Conflict of interest: The authors declare no competing interests.

                Author contributions: M.Ka. and A.B. conceived the project and wrote the manuscript; M.Ka. and M.Kö. performed experiments; M.Ka., M.Kö., A.S. and A.B. analyzed the data.

                Additional information: Correspondence and requests for materials should be addressed to A.B.

                ORCID ID: Alexander Buchberger, 0000-0002-2836-0820

                *Address correspondence to: Alexander Buchberger ( alexander.buchberger@ 123456uni-wuerzburg.de ).
                Article
                E23-06-0237
                10.1091/mbc.E23-06-0237
                10848945
                37756124
                ff7b7915-5a69-4b60-a9dc-5d7ebe62cdd1
                © 2023 Kawan et al. “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology.

                This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial-Share Alike 4.0 International Creative Commons License.

                History
                : 20 June 2023
                : 11 September 2023
                : 20 September 2023
                Categories
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                Molecular biology
                Molecular biology

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