A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes

PeerJ
Baldiri SalvadoRui Alves

Abstract

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 how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is ...Continue Reading

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Citations

May 9, 2019·Future Microbiology·Aimee Rp Tierney, Philip N Rather
May 22, 2019·Nature Chemical Biology·Sebastian R SchmidlJeffrey J Tabor
Oct 21, 2017·Microbiology Spectrum·Brian P Landry, Jeffrey J Tabor
Aug 10, 2021·Frontiers in Microbiology·Josephine Z RappJody W Deming

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Methods Mentioned

BETA
phosphotransferases

Software Mentioned

BLAST
Mathematica
hmmbuild
house PERL script
displaystyle
PROSITE
HMMER
PERL script
Clustal X
MIST2

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