Cold Shock Protein Gene Family in Phaseolus vulgaris L.; Genome-Wide Insights and Expression Profiles

Cold shock proteins (CSPs) are evolutionarily conserved RNA-binding proteins that participate in transcriptional and post-transcriptional regulation during plant development and environmental adaptation. Despite their recognized roles in RNA metabolism, the CSP gene family has not been systematically characterized in Phaseolus vulgaris (common bean), a model legume and important food crop worldwide. To identify and characterize CSP genes in P. vulgaris, Arabidopsis thaliana CSP protein sequences were used as queries in BLASTP searches against the P. vulgaris genome. The PvCSP genes of interest were examined for protein domain, physiochemical properties, chromosome number, and subcellular localization predictions. The four PvCSP genes were found located on three different chromosomes, encoding cold shock domain, CCHC type zinc finger, and glycine-rich domain-containing proteins. The result of the neighbor-joining algorithm analysis indicated that the PvCSP2 and PvCSP4 clustered in the same group, which implied redundancy in their functions in plants. All PvCSPs possessed a single exon, shared two core conserved motifs, and displayed unique motif patterns indicative of subfunctionalization. The polyploid genome of the CSP subfamily was also validated, with each side of the gene having one exon, but the same core conserved motif, with the prospect of sub functionality between the four CSP subcellular localization predictions, located on one side of the CSP gene. The cis-element analysis revealed the presence of 488 cis-elements, including MeJA, ABA, and auxin response cis-elements, which was highly overrepresented in the PvCSP4 gene. The prediction of protein interactions revealed that the CSP subcellular localization predictions could possibly interact with the DEAD-box RNA helicases, mRNA decapping protein, and other predicted interactions with identical specificity profiles, with the likelihood of being sub functional because all subcellular localization predictions had the same specificity profiles, with 26% likelihood. Analysis conducted on the transcriptomics profile indicated that the PvCSP2 was ubiquitously expressed, while the PvCSP4 was predominantly found in the stem, roots, and developing pods.