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dc.contributor.authorSalvadó López, Baldiri
dc.contributor.authorVilaprinyo Terré, Ester
dc.contributor.authorSorribas Tello, Albert
dc.contributor.authorAlves, Rui
dc.date.accessioned2015-11-18T09:19:58Z
dc.date.available2015-11-18T09:19:58Z
dc.date.issued2015
dc.identifier.issn2167-8359
dc.identifier.urihttp://hdl.handle.net/10459.1/48983
dc.description.abstractTwo Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate howmuch more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect fromthe genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.ca_ES
dc.description.sponsorshipThis work was partially funded by Grant BFU2010-17704 from the Spanish MINECO and from small grants CMB and TR255 from University of Lleida to RA.
dc.language.isoengca_ES
dc.publisherPeerJca_ES
dc.relationMICINN/PN2008-2011/BFU2010-17704
dc.relation.isformatofReproducció del document publicat a https://doi.org/10.7717/peerj.1183ca_ES
dc.relation.ispartofPeerJ, 2015, vol. 3, p. 1-27ca_ES
dc.rightscc-by (c) Alves et al., 2015ca_ES
dc.subjectBiological organization principlesca_ES
dc.subjectMathematical modelingca_ES
dc.subjectSignal transductionca_ES
dc.subject.otherBioinformàticaca_ES
dc.titleA survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomesca_ES
dc.typearticleca_ES
dc.identifier.idgrec023762
dc.type.versionpublishedVersionca_ES
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessca_ES
dc.identifier.doihttps://doi.org/10.7717/peerj.1183


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