Genome-Wide Analysis of Two-Component Systems and Prediction of Stress-Responsive Two-Component System Members in Soybean

Abstract

In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms.

Characterization of Genes Involved in Cytokinin Signaling and Metabolism from Rice

“…No additional families of response regulators were found unique to rice or Arabidopsis. These results confirm and expand on previous analyses (Pareek et al, 2006;Pils and Heyl, 2009;Mochida et al, 2010), with minor differences likely due to our analyses being performed on a larger complement of signaling elements and/or being based on the conserved domains rather than the entire sequence.…”

Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

“…Protein sequences of all known plant TCS genes, particularly 56, 52, 51, 98, 62, and 85 members in the genome of Arabidopsis , rice, maize, soybean, Lotus japonicus , Physcomitrella patens , wheat, and Chinese cabbage, respectively, were downloaded from Phytozome [44] and then used as queries to perform BLASTP searches in the SGN database () with E -value of 1 × 10 −5 as the threshold [9,30]. Meanwhile, the tomato genome protein sequences were downloaded from SGN database and Hidden Markov Model (HMM) profiles of TCS characteristic domains, i.e., HisK (PF00512), HATPase (PF02518), HPt (PF01627), and REC (PF00072) were downloaded from Pfam ().…”

Arabidopsis AHP2, AHP3, and AHP5 histidine phosphotransfer proteins function as redundant negative regulators of drought stress response

“…Although the subcellular localization of these AHPs is independent of CK and CK-receptor AHKs (14), AHP gene expression is induced by CK (15,16). All five AHPs, as well as those in rice and soybean, contain a consensus sequence of HQXKGSSXS with a highly conserved His residue (17,18). Analyses of ahp multiple mutants indicated that with the exception of AHP4, for which consistent evidence is lacking, all remaining AHPs function as redundant positive regulators of CK signaling and affect many aspects of plant development (13).…”