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

Baldiri Salvado,Ester Vilaprinyo,Albert Sorribas,Rui Alves

doi:10.7717/peerj.1183

Baldiri Salvado, Ester Vilaprinyo + Show 2 more

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https://doi.org/10.7717/peerj.1183

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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 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.

Highlights

Two Component Systems and Phosphorelays (TCS/PR) have been considered primary environmental signal transduction cascades in prokaryotes (Wolanin, Thomason & Stock, 2002; Cheung & Hendrickson, 2010)
Survey of proteomes containing proteins with domains involved in internal signal transduction (IST) in TCS/PR cascades Bacteria Table 1 summarizes the full set of results for bacteria
Proteins with Histidine Kinase (HK) and RR domains are present in the proteome of 100% of the species analyzed from the following bacterial phyla: Aquificae, Chlorobi, Verrucomicrobia, Chloroflexi, Cyanobacteria, Deferribacteres, Deinococcus-Thermus, Dictyoglomi, Acidobacteria, Nitrospirae, Planctomycetes, Epsilonproteobacteria, Spirochaetes, Thermodesulfobacteria, and Thermotogae

Summary

Introduction

Two Component Systems and Phosphorelays (TCS/PR) have been considered primary environmental signal transduction cascades in prokaryotes (Wolanin, Thomason & Stock, 2002; Cheung & Hendrickson, 2010). In TCS this sensor transfers its phosphate to a response regulator, which will in turn directly regulate the relevant cellular responses to the signal. In PR, additional phosphotransfer steps may happen before the phosphate reaches the response regulator protein(s) that directly controls cellular responses (Fig. 1). PR are considered to be a main form of signal transduction in bacteria (Parkinson, 1993; Hoch & Silhavy, 1995). They are less frequently present in eukaryotes and absent in animals (Chang et al, 1993; Maeda, Wurgler-Murphy & Saito, 1994; Appleby, Parkinson & Bourret, 1996; Thomason & Kay, 2000)

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