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The Prokaryotic Antecedents of the Ubiquitin-Signaling System and the Early Evolution of Ubiquitin-Like β-Grasp Domains

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dc.contributor.author Iyer, Lakshminarayan M en_US
dc.contributor.author Burroughs, A Maxwell en_US
dc.contributor.author Aravind, L en_US
dc.date.accessioned 2012-01-09T14:44:45Z
dc.date.available 2012-01-09T14:44:45Z
dc.date.copyright 2006 en_US
dc.date.issued 2006-07-19 en_US
dc.identifier.citation Iyer, Lakshminarayan M, A Maxwell Burroughs, L Aravind. "The Prokaryotic Antecedents of the Ubiquitin-Signaling System and the Early Evolution of Ubiquitin-Like β-Grasp Domains" Genome Biology 7(7):R60. (2006) en_US
dc.identifier.issn 1465-6914 en_US
dc.identifier.uri http://hdl.handle.net/2144/2791
dc.description.abstract A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history. BACKGROUND. Ubiquitin (Ub)-mediated signaling is one of the hallmarks of all eukaryotes. Prokaryotic homologs of Ub (ThiS and MoaD) and E1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. However, there is no evidence for entire protein modification systems with Ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. Hence, the evolutionary assembly of the eukaryotic Ub-signaling apparatus remains unclear. RESULTS. We systematically analyzed prokaryotic Ub-related β-grasp fold proteins using sensitive sequence profile searches and structural analysis. Consequently, we identified novel Ub-related proteins beyond the characterized ThiS, MoaD, TGS, and YukD domains. To understand their functional associations, we sought and recovered several conserved gene neighborhoods and domain architectures. These included novel associations involving diverse sulfur metabolism proteins, siderophore biosynthesis and the gene encoding the transfer mRNA binding protein SmpB, as well as domain fusions between Ub-like domains and PIN-domain related RNAses. Most strikingly, we found conserved gene neighborhoods in phylogenetically diverse bacteria combining genes for JAB domains (the primary de-ubiquitinating isopeptidases of the proteasomal complex), along with E1-like adenylating enzymes and different Ub-related proteins. Further sequence analysis of other conserved genes in these neighborhoods revealed several Ub-conjugating enzyme/E2-ligase related proteins. Genes for an Ub-like protein and a JAB domain peptidase were also found in the tail assembly gene cluster of certain caudate bacteriophages. CONCLUSION. These observations imply that members of the Ub family had already formed strong functional associations with E1-like proteins, UBC/E2-related proteins, and JAB peptidases in the bacteria. Several of these Ub-like proteins and the associated protein families are likely to function together in signaling systems just as in eukaryotes. en_US
dc.description.sponsorship National Library of Medicine, National Institute of Health en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 2006 Iyer et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title The Prokaryotic Antecedents of the Ubiquitin-Signaling System and the Early Evolution of Ubiquitin-Like β-Grasp Domains en_US
dc.type article en_US
dc.identifier.doi 10.1186/gb-2006-7-7-r60 en_US
dc.identifier.pubmedid 16859499 en_US
dc.identifier.pmcid 1779556 en_US


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Copyright 2006 Iyer et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as Copyright 2006 Iyer et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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