1. The Sumo proteome of proliferating and neuronal-differentiating cells reveals Utf1 among key Sumo targets involved in neurogenesis
- Author
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Sina V. Barysch, Pablo García-Gutiérrez, Francisco Juárez-Vicente, Juan F. Correa-Vázquez, Mario García-Domínguez, Frauke Melchior, [Correa-Vázquez,JF, Juárez-Vicente,F, García-Gutiérrez,P, García-Domínguez,M] Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain. [Barysch,SV, Melchior,F] Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, DKFZ-ZMBH Alliance, Heidelberg, Germany., This work was supported by grants BFU2015-64721-P and PGC2018-094232-B-I00 from the Ministry of Science, Innovation and Universities (MICIU), Spain, to M.G.-D., and also received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project Number 278001972-TRR 186 to F.M., Ministerio de Economía y Competitividad (España), and Consejo Superior de Investigaciones Científicas (España)
- Subjects
Neurogénesis ,Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Differentiation [Medical Subject Headings] ,Cancer Research ,Proteome ,Organisms::Eukaryota::Animals::Chordata::Vertebrates [Medical Subject Headings] ,Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Differentiation::Neurogenesis [Medical Subject Headings] ,Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Expression Regulation::Protein Modification, Translational::Protein Processing, Post-Translational::Ubiquitination::Sumoylation [Medical Subject Headings] ,SUMO protein ,Neural tube ,Aminoácidos, péptidos y proteínas ,Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings] ,Anatomy::Cells::Cells, Cultured::Cell Line [Medical Subject Headings] ,Stable isotope labeling by amino acids in cell culture ,Organisms::Eukaryota::Animals [Medical Subject Headings] ,Disciplines and Occupations::Natural Science Disciplines::Chemistry::Biochemistry::Proteomics [Medical Subject Headings] ,Anatomy::Embryonic Structures::Neural Tube [Medical Subject Headings] ,Proteoma ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Nuclear Proteins [Medical Subject Headings] ,lcsh:Cytology ,Neurogenesis ,Nuclear Proteins ,Cell Differentiation ,Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Expression Regulation::Protein Modification, Translational::Protein Processing, Post-Translational [Medical Subject Headings] ,Chromatin ,Cell biology ,ARN ,P19 cell ,Enzyme mechanisms ,Small Ubiquitin-Related Modifier Proteins ,Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Isotope Labeling [Medical Subject Headings] ,Cell signalling ,Cell signaling ,Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Culture Techniques::Cell Culture Techniques [Medical Subject Headings] ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Ubiquitins::Small Ubiquitin-Related Modifier Proteins [Medical Subject Headings] ,Immunology ,Biology ,Article ,Cellular and Molecular Neuroscience ,Humans ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Peptides [Medical Subject Headings] ,lcsh:QH573-671 ,Phenomena and Processes::Cell Physiological Phenomena::Cell Physiological Processes::Cell Growth Processes::Cell Proliferation [Medical Subject Headings] ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Amino Acids [Medical Subject Headings] ,Tubo neural ,Amino acids, peptides, and proteins ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Transcription Factors::Trans-Activators [Medical Subject Headings] ,Sumoylation ,Cell Biology ,Chemicals and Drugs::Nucleic Acids, Nucleotides, and Nucleosides::Nucleic Acids::RNA::RNA, Messenger [Medical Subject Headings] ,Trans-Activators ,Anatomy::Nervous System [Medical Subject Headings] ,RNA ,Protein Processing, Post-Translational ,Function (biology) ,Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Proteome [Medical Subject Headings] - Abstract
Post-translational modification by covalent attachment of the Small ubiquitin-like modifier (Sumo) polypeptide regulates a multitude of processes in vertebrates. Despite demonstrated roles of Sumo in the development and function of the nervous system, the identification of key factors displaying a sumoylation-dependent activity during neurogenesis remains elusive. Through a SILAC (stable isotope labeling by/with amino acids in cell culture)-based proteomic approach, we have identified the Sumo proteome of the model cell line P19 under proliferation and neuronal differentiation conditions. More than 300 proteins were identified as putative Sumo targets differentially associated with one or the other condition. A group of proteins of interest were validated and investigated in functional studies. Among these, Utf1 was revealed as a new Sumo target. Gain-of-function experiments demonstrated marked differences between the effects on neurogenesis of overexpressing wild-type and sumoylation mutant versions of the selected proteins. While sumoylation of Prox1, Sall4a, Trim24, and Utf1 was associated with a positive effect on neurogenesis in P19 cells, sumoylation of Kctd15 was associated with a negative effect. Prox1, Sall4a, and Kctd15 were further analyzed in the vertebrate neural tube of living embryos, with similar results. Finally, a detailed analysis of Utf1 showed the sumoylation dependence of Utf1 function in controlling the expression of bivalent genes. Interestingly, this effect seems to rely on two mechanisms: sumoylation modulates binding of Utf1 to the chromatin and mediates recruitment of the messenger RNA-decapping enzyme Dcp1a through a conserved SIM (Sumo-interacting motif). Altogether, our results indicate that the combined sumoylation status of key proteins determines the proper progress of neurogenesis., J.F.C.-V. and F.J.-V. were the recipients of FPI (MICIU, BES-2016-076500) and JAE Ph.D. (CSIC) fellowships, respectively. We acknowledge the ZMBH Core Facility for Mass Spectrometry and Proteomics. We thank Dr. Annette Flotho for help with data analysis. We also acknowledge L.M. Buch and A. Romero-Franco for preliminary results on Kctd15 and Sall4, respectively.
- Published
- 2021