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      Evolution and functional cross‐talk of protein post‐translational modifications

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          Abstract

          Protein post‐translational modifications ( PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post‐translational regulation and progress made in the large‐scale functional characterization of PTM function.

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          Systematic and quantitative assessment of the ubiquitin-modified proteome.

          Woong Kim, Eric J. Bennett, Edward L. Huttlin … (2011)
          Despite the diverse biological pathways known to be regulated by ubiquitylation, global identification of substrates that are targeted for ubiquitylation has remained a challenge. To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides following trypsin digestion. We identify ~19,000 diGly-modified lysine residues within ~5000 proteins. Using quantitative proteomics we monitored temporal changes in diGly site abundance in response to both proteasomal and translational inhibition, indicating both a dependence on ongoing translation to observe alterations in site abundance and distinct dynamics of individual modified lysines in response to proteasome inhibition. Further, we demonstrate that quantitative diGly proteomics can be utilized to identify substrates for cullin-RING ubiquitin ligases. Interrogation of the ubiquitinome allows for not only a quantitative assessment of alterations in protein homeostasis fidelity, but also identification of substrates for individual ubiquitin pathway enzymes. Copyright © 2011 Elsevier Inc. All rights reserved.
          Article 0 comments Cited 599 times – based on 0 reviews     Review now
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            Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.

            Liam Holt, Brian B. Tuch, Judit Villén … (2009)
            To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae. We combined specific chemical inhibition of Cdk1 with quantitative mass spectrometry to identify the positions of 547 phosphorylation sites on 308 Cdk1 substrates in vivo. Comparisons of these substrates with orthologs throughout the ascomycete lineage revealed that the position of most phosphorylation sites is not conserved in evolution; instead, clusters of sites shift position in rapidly evolving disordered regions. We propose that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions. The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.
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              Nonproteolytic functions of ubiquitin in cell signaling.

              Zhijian Chen, Lijun J Sun (2009)
              The small protein ubiquitin is a central regulator of a cell's life and death. Ubiquitin is best known for targeting protein destruction by the 26S proteasome. In the past few years, however, nonproteolytic functions of ubiquitin have been uncovered at a rapid pace. These functions include membrane trafficking, protein kinase activation, DNA repair, and chromatin dynamics. A common mechanism underlying these functions is that ubiquitin, or polyubiquitin chains, serves as a signal to recruit proteins harboring ubiquitin-binding domains, thereby bringing together ubiquitinated proteins and ubiquitin receptors to execute specific biological functions. Recent advances in understanding ubiquitination in protein kinase activation and DNA repair are discussed to illustrate the nonproteolytic functions of ubiquitin in cell signaling.
              Article 0 comments Cited 270 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mol Syst Biol
                Journal ID (iso-abbrev): Mol. Syst. Biol
                Journal ID (doi): 10.1002/(ISSN)1744-4292
                Journal ID (publisher-id): MSB
                Journal ID (hwp): msb
                Title: Molecular Systems Biology
                Publisher: European Molecular Biology Organization
                ISSN (Electronic): 1744-4292
                Publication date (Electronic): 20 December 2013
                Publication date Collection: 2013
                Volume: 9
                Issue: ( doiID: 10.1002/msb.v9.1 )
                Electronic Location Identifier: 714
                Affiliations
                [ 1 ] European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI) CambridgeUK
                [ 2 ] Structural and Computational Biology UnitEuropean Molecular Biology Laboratory HeidelbergGermany
                [ 3 ]Max‐Delbruck‐Centre for Molecular Medicine Berlin‐BuchGermany
                [ 4 ] Department of Cellular and Molecular PharmacologyUniversity of California San Francisco CaliforniaUSA
                [ 5 ]California Institute for Quantitative Biosciences San Francisco CaliforniaUSA
                [ 6 ]J. David Gladstone Institutes San Francisco CaliforniaUSA
                Author notes
                [*] [* ] Corresponding author. E‐mail: pbeltrao@ 123456ebi.ac.uk

                Corresponding author. E‐mail: bork@ 123456embl.de

                Corresponding author. E‐mail: nevan.krogan@ 123456ucsf.edu

                Corresponding author. E‐mail: vera.vannoort@ 123456embl.de

                Article
                Publisher ID: MSB134521
                DOI: 10.1002/msb.201304521
                PMC ID: 4019982
                PubMed ID: 24366814
                SO-VID: 8a1a10fe-b418-4578-bc5a-2d3596be59df
                Copyright © © 2013 EMBO© 2013 The Authors
                License:

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 30 April 2013
                Date revision received : 18 November 2013
                Date accepted : 22 November 2013
                Page count
                Pages: 13
                Funding
                Funded by: US National Institutes of Health
                Award ID: P50GM082250
                Award ID: R01GM084448
                Award ID: P01AI090935
                Award ID: P50GM081879
                Award ID: R01GM098101
                Award ID: R01GM084279
                Award ID: P01AI091575
                Funded by: Defense Advanced Research Projects Agency
                Award ID: DARPA‐10‐93‐Prophecy‐PA‐008
                Funded by: Human Frontier Science Program
                Award ID: CDA00069/2013‐C
                Categories
                Subject: Embo017
                Subject: Embo031
                Subject: Review
                Subject: Reviews
                Custom metadata
                source-schema-version-number 2.0
                component-id msb134521
                cover-date 2013
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLM version:4.0.5 mode:remove_FC converted:12.05.2014

                ScienceOpen disciplines: Quantitative & Systems biology
                Keywords: acetylation,evolution,phosphorylation,post‐translational modifications,ptm cross‐talk
                Data availability:
                ScienceOpen disciplines: Quantitative & Systems biology
                Keywords: acetylation, evolution, phosphorylation, post‐translational modifications, ptm cross‐talk

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