Roy Alankar, Ray Sujay
Amity Institute of Biotechnology, Amity University, Kolkata, India.
Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India.
Mol Biotechnol. 2025 Jan 8. doi: 10.1007/s12033-024-01333-0.
Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The K/ K ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.
在大肠杆菌冷休克结构域基因家族中已识别出九种同源冷休克蛋白（Csps）。这些Csps作为RNA伴侣发挥作用。本研究旨在通过识别和分类其旁系同源对应物来建立这些基因之间的进化关系。它专注于对基因进行物理化学、结构和功能分析，以探索Csp基因家族的系统发育。使用计算工具进行蛋白质分子建模、构象分析、功能研究和复制-分化评估。该研究还检查了氨基酸保守性、蛋白质突变、结构域-基序模式和进化残基群落，以更好地理解残基相互作用、进化偶联和共同进化。H33、M5、W11和F53残基在蛋白质家族中高度保守。进一步发现，残基M5、G17、G58、G61、P62、A64、V67对任何类型的突变都不耐受，而G3、D40、G41、Y42、S44、T54、T68、S69对取代最耐受。对残基群落的研究表明，在N13、F18、S27、F31和W11中观察到最强的残基偶联。据观察，除CspF/CspH外，所有基因对随着时间的推移都产生了新的基序。可以确定的是，所有基因对在复制后都经历了不对称表达分化。K/K比率还表明，所有残基都承受着中性和纯化选择压力。从新基序的产生可以明显看出，基因对中出现了新功能。Csps中新基序和功能的发现突出了它们的适应性多功能性，这对大肠杆菌抵御环境压力至关重要，对理解细菌应激反应机制也很有价值。这些发现将为未来对Csp进化的研究铺平道路，在微生物生态学和抗菌策略开发方面具有潜在应用。
