The origins and evolution of ubiquitination sites.

Protein ubiquitination is central to the regulation of various pathways in eukaryotes. The process of ubiquitination and its cellular outcome were investigated in hundreds of proteins to date. Despite this, the evolution of this regulatory mechanism has not yet been addressed comprehensively. Here, we quantify the rates of evolutionary changes of ubiquitination and SUMOylation (Small Ubiquitin-like MOdifier) sites. We estimate the time at which they first appeared, and compare them to acetylation and phosphorylation sites and to unmodified residues. We observe that the various modification sites studied exhibit similar rates. Mammalian ubiquitination sites are weakly more conserved than unmodified lysine residues, and a higher degree of relative conservation is observed when analyzing bona fide ubiquitination sites. Various reasons can be proposed for the limited level of excess conservation of ubiquitination, including shifts in locations of the sites, the presence of alternative sites, and changes in the regulatory pathways. We observe that disappearance of sites may be compensated by the presence of a lysine residue in close proximity, which is significant when compared to evolutionary patterns of unmodified lysine residues, especially in disordered regions. This emphasizes the importance of analyzing a window in the vicinity of functional residues, as well as the capability of the ubiquitination machinery to ubiquitinate residues in a certain region. Using prokaryotic orthologs of ubiquitinated proteins, we study how ubiquitination sites were formed, and observe that while sometimes sequence additions and rearrangements are involved, in many cases the ubiquitination machinery utilizes an already existing sequence without significantly changing it. Finally, we examine the evolution of ubiquitination, which is linked with other modifications, to infer how these complex regulatory modules have evolved. Our study gives initial insights into the formation of ubiquitination sites, their degree of conservation in various species, and their co-evolution with other posttranslational modifications.

[1]  F. Alt,et al.  Evolution of phosphorylation-dependent regulation of activation-induced cytidine deaminase. , 2008, Molecular cell.

[2]  E. Koonin.  The origin and early evolution of eukaryotes in the light of phylogenomics , 2010, Genome Biology.

[3]  A. Varshavsky.  The N‐end rule pathway and regulation by proteolysis , 2011, Protein science : a publication of the Protein Society.

[4]  Sixue Chen,et al.  Ubiquitin-like Small Archaeal Modifier Proteins (SAMPs) in Haloferax volcanii , 2010, Nature.

[5]  James E. Ferrell,et al.  A Mechanism for the Evolution of Phosphorylation Sites , 2011, Cell.

[6]  Jianzhi Zhang,et al.  Genome-wide evolutionary conservation of N-glycosylation sites. , 2011, Molecular biology and evolution.

[7]  P. Bork,et al.  Co-evolution of transcriptional and post-translational cell-cycle regulation , 2006, Nature.

[8]  S. Gygi,et al.  Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution , 2009, Science.

[9]  C. Landry,et al.  Weak functional constraints on phosphoproteomes. , 2009, Trends in genetics : TIG.

[10]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[11]  Burkhard Rost,et al.  The PredictProtein server , 2003, Nucleic Acids Res..

[12]  S. Miyamoto,et al.  Sequential Modification of NEMO/IKKγ by SUMO-1 and Ubiquitin Mediates NF-κB Activation by Genotoxic Stress , 2003, Cell.

[13]  Yaakov Levy,et al.  Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding , 2010, Proceedings of the National Academy of Sciences.

[14]  Geng Wu,et al.  Structure of a -TrCP1-Skp1--Catenin Complex , 2003 .

[15]  M. Kirschner,et al.  Mutagenic analysis of the destruction signal of mitotic cyclins and structural characterization of ubiquitinated intermediates. , 1996, Molecular biology of the cell.

[16]  Erik L. L. Sonnhammer,et al.  InParanoid 6: eukaryotic ortholog clusters with inparalogs , 2007, Nucleic Acids Res..

[17]  Roland L. Dunbrack,et al.  PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. , 2010, Biochimica et biophysica acta.

[18]  Tommer Ravid,et al.  Diversity of degradation signals in the ubiquitin–proteasome system , 2008, Nature Reviews Molecular Cell Biology.

[19]  P. Hieter,et al.  Subtle Alterations in PCNA-Partner Interactions Severely Impair DNA Replication and Repair , 2010, PLoS biology.

[20]  B. J. Roberts,et al.  HIF-1α and EPAS ubiquitination mediated by the VHL tumour suppressor involves flexibility in the ubiquitination mechanism, similar to other RING E3 ligases , 2007, Oncogene.

[21]  Vanessa E. Gray,et al.  Rampant purifying selection conserves positions with posttranslational modifications in human proteins. , 2011, Molecular biology and evolution.

[22]  C. Brown,et al.  Intrinsic protein disorder in complete genomes. , 2000, Genome informatics. Workshop on Genome Informatics.

[23]  M. Shirakawa,et al.  Crystal structure of SUMO-3-modified thymine-DNA glycosylase. , 2006, Journal of molecular biology.

[24]  S. Gygi,et al.  Ubiquitin-Like Protein Involved in the Proteasome Pathway of Mycobacterium tuberculosis , 2008, Science.

[25]  S. Jentsch,et al.  Principles of ubiquitin and SUMO modifications in DNA repair , 2009, Nature.

[26]  V. Vacic,et al.  Identification, analysis, and prediction of protein ubiquitination sites , 2010, Proteins.

[27]  Peter B. McGarvey,et al.  Infrastructure for the life sciences: design and implementation of the UniProt website , 2009, BMC Bioinformatics.

[28]  M. Hattori,et al.  Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group , 2010, Nucleic acids research.

[29]  Alejandro Garcia,et al.  UbiProt: a database of ubiquitylated proteins , 2007, BMC Bioinformatics.

[30]  B. D. Freudenthal,et al.  Crystal structure of SUMO-modified proliferating cell nuclear antigen. , 2011, Journal of molecular biology.

[31]  J. F. Storz,et al.  Evolutionary origins of oxygen sensing in animals , 2011, EMBO reports.

[32]  B. J. Roberts,et al.  Role of the von Hippel-Lindau tumour suppressor protein in the regulation of HIF-1α and its oxygen-regulated transactivation domains at high cell density , 2005, Oncogene.

[33]  M. Hochstrasser,et al.  Origin and function of ubiquitin-like proteins , 2009, Nature.

[34]  G. Dittmar,et al.  Cell Cycle–Regulated Modification of the Ribosome by a Variant Multiubiquitin Chain , 2000, Cell.

[35]  Dan S. Tawfik,et al.  Slow protein evolutionary rates are dictated by surface–core association , 2011, Proceedings of the National Academy of Sciences.

[36]  A. Ciechanover,et al.  Mechanism of processing of the NF-κB2 p100 precursor: identification of the specific polyubiquitin chain-anchoring lysine residue and analysis of the role of NEDD8-modification on the SCFβ-TrCP ubiquitin ligase , 2004, Oncogene.

[37]  R. Deshaies,et al.  Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. , 2003, Molecular cell.

[38]  Alan M. Moses,et al.  Evolution of characterized phosphorylation sites in budding yeast. , 2010, Molecular biology and evolution.

[39]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[40]  David Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[41]  Alexander Varshavsky,et al.  The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis , 1989, Nature.

[42]  J. Gsponer.  Who initiates proteasomal degradation? , 2011, Journal of molecular biology.

[43]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.

[44]  David C. Jones,et al.  Assessing the impact of secondary structure and solvent accessibility on protein evolution. , 1998, Genetics.

[45]  Á. Tóth-Petróczy,et al.  Intrinsic disorder in ubiquitination substrates. , 2011, Journal of molecular biology.

[46]  Tzong-Yi Lee,et al.  Incorporating Distant Sequence Features and Radial Basis Function Networks to Identify Ubiquitin Conjugation Sites , 2011, PloS one.

[47]  Chunaram Choudhary,et al.  Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation , 2011, Science Signaling.

[48]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[49]  A. Bielinsky,et al.  Defects in DNA Ligase I Trigger PCNA Ubiquitination at Lysine 107 , 2009, Nature Cell Biology.

[50]  L. Aravind,et al.  The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains , 2006, Genome Biology.

[51]  A. Ciechanover,et al.  The ubiquitin system. , 1998, Annual review of biochemistry.

[52]  J. Kornhauser,et al.  PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation , 2004, Proteomics.

[53]  B. Schierwater,et al.  The hypoxia‐inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens , 2011, EMBO reports.

[54]  J. Nilsson,et al.  Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins , 2011, Genome Biology.

[55]  W. Lim,et al.  Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS biology.

[56]  B. Dye,et al.  Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. , 2007, Annual review of biophysics and biomolecular structure.

[57]  Jaime Prilusky,et al.  FoldIndex copyright: a simple tool to predict whether a given protein sequence is intrinsically unfolded , 2005, Bioinform..

[58]  Ivan Mijakovic,et al.  MATERIALS AND METHODS , 1981, Green Corrosion Inhibitors: Reviews and Applications.

[59]  C. Landry,et al.  Molecular characterization of the evolution of phagosomes , 2010, Molecular systems biology.

[60]  Luca Freschi,et al.  Phosphorylation network rewiring by gene duplication , 2011, Molecular systems biology.

[61]  Ivan Dikic,et al.  The spatial and temporal organization of ubiquitin networks , 2011, Nature Reviews Molecular Cell Biology.

[62]  Richard Durbin,et al.  Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites , 2007, Proceedings of the National Academy of Sciences.

[63]  R. Poon,et al.  The N-terminal Regulatory Domain of Cyclin A Contains Redundant Ubiquitination Targeting Sequences and Acceptor Sites , 2005, Cell cycle.

[64]  G. Vriend,et al.  Molecular docking using surface complementarity , 1996, Proteins.

[65]  Zhihao Zhuang,et al.  Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. , 2010, Nature chemical biology.

[66]  Mark Gerstein,et al.  Measuring the Evolutionary Rewiring of Biological Networks , 2011, PLoS Comput. Biol..

[67]  Yoshio Tateno,et al.  Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. , 2011, Molecular biology and evolution.

[68]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[69]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[70]  A. Varshavsky.  The N-end rule , 1992, Cell.

[71]  Itay Mayrose,et al.  Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues , 2002, ISMB.

[72]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[73]  Alexander Varshavsky,et al.  Regulated protein degradation. , 2005, Trends in biochemical sciences.

[74]  G. Lienhard,et al.  Non-functional phosphorylations? , 2008, Trends in biochemical sciences.