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.

Figure 1

Phylogenetic relationship of HKs from Arabidopsis, rice and soybean. The bar indicates the relative divergence of the sequences examined. Bootstrap values higher than 50% are displayed next to the branch.

Figure 2

Phylogenetic relationship of phosphotransfer (HPt) proteins from Arabidopsis, rice and soybean. The bar indicates the relative divergence of the sequences examined. Bootstrap values higher than 50% are displayed next to the branch.

Figure 3

Phylogenetic relationship of response regulator proteins from Arabidopsis, rice and soybean. The bar indicates the relative divergence of the sequences examined. Bootstrap values higher than 50% are displayed next to the branch.

Figure 4

Graphical representation of locations for putative TCS genes on soybean chromosomes. The (+) and (−) indicate the sense and antisense strands, respectively. Number displayed next to each gene ID indicates the position of the annotation start for each TCS gene in bases.

Figure 5

Heat map representation for tissue-specific expression of soybean and Arabidopsis TCS genes. Heat map representation for the tissue-specific expression of 9 HK, 6 HPt and 24 RR encoding soybean TCS genes (A). Heat map representation for the tissue-specific expression of Arabidopsis TCS genes (B). Elevated expression levels are indicated by increasing intensities of blue colour expressed in log2 scale.