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PMID: 19325621 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Origin and function of ubiquitin-like proteins.

Nature ·Vol. 458 ·No. 7237 ·2009-03-26 ·Pages 422-9

Hochstrasser M

Abstract

Eukaryotic proteins can be modified through attachment to various small molecules and proteins. One such modification is conjugation to ubiquitin and ubiquitin-like proteins (UBLs), which controls an enormous range of physiological processes. Bound UBLs mainly regulate the interactions of proteins with other macromolecules, for example binding to the proteasome or recruitment to chromatin. The various UBL systems use related enzymes to attach specific UBLs to proteins (or other molecules), and most of these attachments are transient. There is increasing evidence suggesting that such UBL-protein modification evolved from prokaryotic sulphurtransferase systems or related enzymes. Moreover, proteins similar to UBL-conjugating enzymes and UBL-deconjugating enzymes seem to have already been widespread at the time of the last common ancestor of eukaryotes, suggesting that UBL-protein conjugation did not first evolve in eukaryotes.

MeSH Terms
Evolution, Molecular Humans Peptide Hydrolases/metabolism Proteasome Endopeptidase Complex/metabolism Sulfur/metabolism Ubiquitination Ubiquitins/chemistry,metabolism
Chemicals
Ubiquitins Sulfur Peptide Hydrolases Proteasome Endopeptidase Complex
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Hochstrasser Mark
Yale University, Department of Molecular Biophysics & Biochemistry, 266 Whitney Avenue, PO Box 208114, New Haven, Connecticut 06520, USA. mark.hochstrasser@yale.edu
References (74)
74 references, click to expand
  1. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation.
    J Biol Chem. 2005 Dec 2;280(48):40122-9 PMID: 16204249
  2. New type of polyubiquitin-like genes with intein-like autoprocessing domains.
    Trends Genet. 2004 Nov;20(11):538-42 PMID: 15475112
  3. Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes.
    Cell. 2008 Jul 25;134(2):268-78 PMID: 18662542
  4. Ubiquitin-like protein activation.
    Oncogene. 2004 Mar 15;23(11):1958-71 PMID: 15021884
  5. Recognition of the polyubiquitin proteolytic signal.
    EMBO J. 2000 Jan 4;19(1):94-102 PMID: 10619848
  6. Solution conformation of Lys63-linked di-ubiquitin chain provides clues to functional diversity of polyubiquitin signaling.
    J Biol Chem. 2004 Feb 20;279(8):7055-63 PMID: 14645257
  7. The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins.
    Biochemistry. 2008 Jun 17;47(24):6479-89 PMID: 18491921
  8. The basis for selective E1-E2 interactions in the ISG15 conjugation system.
    J Biol Chem. 2008 Aug 29;283(35):23895-902 PMID: 18583345
  9. Cofactor biosynthesis: an organic chemist's treasure trove.
    Nat Prod Rep. 2006 Feb;23(1):15-25 PMID: 16453030
  10. Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
    Biol Direct. 2007 Jul 02;2:18 PMID: 17605815
  11. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.
    Biol Direct. 2008 Nov 03;3:45 PMID: 18980670
  12. N-terminal ubiquitination: more protein substrates join in.
    Trends Cell Biol. 2004 Mar;14(3):103-6 PMID: 15055197
  13. Quantitative SUMO-1 modification of a vaccinia virus protein is required for its specific localization and prevents its self-association.
    Mol Biol Cell. 2005 Jun;16(6):2822-35 PMID: 15800065
  14. A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2.
    Cell. 1997 Jan 10;88(1):97-107 PMID: 9019411
  15. ISG15 inhibits Nedd4 ubiquitin E3 activity and enhances the innate antiviral response.
    J Biol Chem. 2008 Apr 4;283(14):8783-7 PMID: 18287095
  16. How to activate a damage-tolerant polymerase: consequences of PCNA modifications by ubiquitin and SUMO.
    Cell Cycle. 2004 Jan;3(1):15-8 PMID: 14657656
  17. UBA 1: an essential yeast gene encoding ubiquitin-activating enzyme.
    EMBO J. 1991 Jan;10(1):227-36 PMID: 1989885
  18. Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.
    J Struct Biol. 2008 May;162(2):205-18 PMID: 18276160
  19. Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase.
    Science. 2005 Jul 1;309(5731):127-30 PMID: 15994556
  20. Budding yeast Dsk2p is a polyubiquitin-binding protein that can interact with the proteasome.
    Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):745-50 PMID: 11805328
  21. Dissecting the ubiquitin pathway by mass spectrometry.
    Biochim Biophys Acta. 2006 Dec;1764(12):1940-7 PMID: 17055348
  22. Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation.
    Nat Struct Biol. 2001 Jan;8(1):42-6 PMID: 11135669
  23. Solution structure of ThiS and implications for the evolutionary roots of ubiquitin.
    Nat Struct Biol. 2001 Jan;8(1):47-51 PMID: 11135670
  24. Characterization of Escherichia coli MoeB and its involvement in the activation of molybdopterin synthase for the biosynthesis of the molybdenum cofactor.
    J Biol Chem. 2001 Sep 14;276(37):34695-701 PMID: 11463785
  25. Biosynthesis of the thioquinolobactin siderophore: an interesting variation on sulfur transfer.
    J Bacteriol. 2007 Apr;189(7):2941-4 PMID: 17209031
  26. Modification of proteins by ubiquitin and ubiquitin-like proteins.
    Annu Rev Cell Dev Biol. 2006;22:159-80 PMID: 16753028
  27. Mechanisms underlying ubiquitination.
    Annu Rev Biochem. 2001;70:503-33 PMID: 11395416
  28. Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3.
    J Cell Biol. 2007 May 21;177(4):613-24 PMID: 17502423
  29. Maturation of an Escherichia coli ribosomal peptide antibiotic by ATP-consuming N-P bond formation in microcin C7.
    J Am Chem Soc. 2008 Mar 19;130(11):3603-9 PMID: 18290647
  30. SUMO junction-what's your function? New insights through SUMO-interacting motifs.
    EMBO Rep. 2007 Jun;8(6):550-5 PMID: 17545995
  31. Molecular evolution of ubiquitin genes.
    Trends Ecol Evol. 1987 Nov;2(11):328-32 PMID: 21227875
  32. Interferon-inducible ubiquitin E2, Ubc8, is a conjugating enzyme for protein ISGylation.
    Mol Cell Biol. 2004 Nov;24(21):9592-600 PMID: 15485925
  33. Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems.
    J Biol Chem. 2008 Oct 10;283(41):27469-27476 PMID: 18664566
  34. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis.
    Science. 2008 Nov 14;322(5904):1104-7 PMID: 18832610
  35. A proteomics approach to understanding protein ubiquitination.
    Nat Biotechnol. 2003 Aug;21(8):921-6 PMID: 12872131
  36. Mechanism and function of deubiquitinating enzymes.
    Biochim Biophys Acta. 2004 Nov 29;1695(1-3):189-207 PMID: 15571815
  37. Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue.
    Nat Cell Biol. 2007 Apr;9(4):422-7 PMID: 17310239
  38. Biosynthesis and processing of the molybdenum cofactors.
    Biochem Soc Trans. 1997 Aug;25(3):757-61 PMID: 9388540
  39. Functionality of human thymine DNA glycosylase requires SUMO-regulated changes in protein conformation.
    Curr Biol. 2005 Apr 12;15(7):616-23 PMID: 15823533
  40. A genomic and functional inventory of deubiquitinating enzymes.
    Cell. 2005 Dec 2;123(5):773-86 PMID: 16325574
  41. Thiamin biosynthesis in Escherichia coli. Identification of ThiS thiocarboxylate as the immediate sulfur donor in the thiazole formation.
    J Biol Chem. 1998 Jun 26;273(26):16555-60 PMID: 9632726
  42. Trafficking in persulfides: delivering sulfur in biosynthetic pathways.
    Nat Chem Biol. 2006 Apr;2(4):185-94 PMID: 16547481
  43. IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses.
    Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1371-6 PMID: 17227866
  44. A 26 S protease subunit that binds ubiquitin conjugates.
    J Biol Chem. 1994 Mar 11;269(10):7059-61 PMID: 8125911
  45. Evolution and function of ubiquitin-like protein-conjugation systems.
    Nat Cell Biol. 2000 Aug;2(8):E153-7 PMID: 10934491
  46. Physical and functional interactions of monoubiquitylated transactivators with the proteasome.
    J Biol Chem. 2008 Aug 1;283(31):21789-98 PMID: 18515799
  47. Regulation of monoubiquitinated PCNA by DUB autocleavage.
    Nat Cell Biol. 2006 Apr;8(4):339-47 PMID: 16531995
  48. A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal.
    Nature. 2002 Apr 18;416(6882):763-7 PMID: 11961560
  49. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis.
    J Am Chem Soc. 2005 Aug 24;127(33):11602-3 PMID: 16104727
  50. The Aspergillus nidulans cnxF gene and its involvement in molybdopterin biosynthesis. Molecular characterization and analysis of in vivo generated mutants.
    J Biol Chem. 1998 Jun 12;273(24):14869-76 PMID: 9614089
  51. Proteasome subunit Rpn13 is a novel ubiquitin receptor.
    Nature. 2008 May 22;453(7194):481-8 PMID: 18497817
  52. A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae.
    RNA. 2008 Oct;14(10):2183-94 PMID: 18755837
  53. The UbcH8 ubiquitin E2 enzyme is also the E2 enzyme for ISG15, an IFN-alpha/beta-induced ubiquitin-like protein.
    Proc Natl Acad Sci U S A. 2004 May 18;101(20):7578-82 PMID: 15131269
  54. The interferon-inducible 15-kDa ubiquitin homolog conjugates to intracellular proteins.
    J Biol Chem. 1992 Apr 15;267(11):7806-13 PMID: 1373138
  55. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.
    Nature. 2005 Jun 2;435(7042):687-92 PMID: 15931224
  56. Proteolysis, proteasomes and antigen presentation.
    Nature. 1992 Jun 4;357(6377):375-9 PMID: 1317508
  57. Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p.
    Eukaryot Cell. 2003 Oct;2(5):930-6 PMID: 14555475
  58. A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes.
    J Biol Chem. 2000 Mar 17;275(11):7462-5 PMID: 10713047
  59. Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology.
    Annu Rev Pharmacol Toxicol. 2009;49:73-96 PMID: 18834306
  60. Influenza B virus NS1 protein inhibits conjugation of the interferon (IFN)-induced ubiquitin-like ISG15 protein.
    EMBO J. 2001 Feb 1;20(3):362-71 PMID: 11157743
  61. The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility.
    Cell. 2002 Oct 18;111(2):209-18 PMID: 12408865
  62. Interferon induces a 15-kilodalton protein exhibiting marked homology to ubiquitin.
    J Biol Chem. 1987 Aug 15;262(23):11315-23 PMID: 2440890
  63. The ubiquitin system for protein degradation.
    Annu Rev Biochem. 1992;61:761-807 PMID: 1323239
  64. Ubiquitin-binding domains.
    Biochem J. 2006 Nov 1;399(3):361-72 PMID: 17034365
  65. Structural analysis of Escherichia coli ThiF.
    J Mol Biol. 2005 Jun 17;349(4):774-86 PMID: 15896804
  66. Rooting the tree of life by transition analyses.
    Biol Direct. 2006 Jul 11;1:19 PMID: 16834776
  67. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.
    Genome Biol. 2006;7(7):R60 PMID: 16859499
  68. Proteasome-independent functions of ubiquitin in endocytosis and signaling.
    Science. 2007 Jan 12;315(5809):201-5 PMID: 17218518
  69. ISG15 inhibits Ebola VP40 VLP budding in an L-domain-dependent manner by blocking Nedd4 ligase activity.
    Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3974-9 PMID: 18305167
  70. Rad23 promotes the targeting of proteolytic substrates to the proteasome.
    Mol Cell Biol. 2002 Jul;22(13):4902-13 PMID: 12052895
  71. Molecular dissection of autophagy: two ubiquitin-like systems.
    Nat Rev Mol Cell Biol. 2001 Mar;2(3):211-6 PMID: 11265251
  72. Molecular evolution of proteasomes.
    Curr Top Microbiol Immunol. 2002;268:1-22 PMID: 12083003
  73. Multiple interactions of rad23 suggest a mechanism for ubiquitylated substrate delivery important in proteolysis.
    Mol Biol Cell. 2004 Jul;15(7):3357-65 PMID: 15121879
  74. Ubiquitin-dependent protein degradation.
    Annu Rev Genet. 1996;30:405-39 PMID: 8982460
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature07958
Email
mark.hochstrasser@yale.edu
Published
2009-03-26
Pages
422-9
Language
English
Region
England
NLM ID
0410462
PMCID
PMC2819001
Subset
IM
Grants
NIGMS NIH HHS · R01 GM046904 · United States
NIGMS NIH HHS · R01 GM046904-18 · United States
NIGMS NIH HHS · R01 GM053756 · United States
NIGMS NIH HHS · R01 GM053756-15 · United States
External Links
PubMed source DOI: 10.1038/nature07958 PMC Full Text View journal details
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