A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes
MetadataShow full item record
Two 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.
Is part ofPeerJ, 2015, vol. 3, p. 1-27
European research projects
Showing items related by title, author, creator and subject.
Salvadó López, Baldiri; Karathia, Hiren; Usié Chimenos, Anabel; Vilaprinyo Terré, Ester; Omholt, Stig; Sorribas Tello, Albert; Alves, Rui (Elsevier, 2011)Most aspects of molecular biology can be understood in terms of biological design principles. These principles can be loosely defined as qualitative and quantitative features that emerge in evolution and recur more ...
Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling Comas, Jorge; Benfeitas, Rui; Vilaprinyo Terré, Ester; Sorribas Tello, Albert; Solsona Tehàs, Francesc; Farré Martinez, Gemma; Berman Quintana, Judit; Zorrilla López, Uxue; Capell Capell, Teresa; Sandmann, Gerhard; Zhu, Changfu; Christou, Paul; Alves, Rui (Wiley online library, 2016)Plant synthetic biology is still in its infancy. However, synthetic biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops such as rice, potato and maize. With ...
Salvadó López, Baldiri; Vilaprinyo Terré, Ester; Karathia, Hiren; Sorribas Tello, Albert; Alves, Rui (Public Library of Science, 2012)Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal transduction is often done through Two Component Systems (TCS). These TCS are phosphotransfer ...