Molecular detection and in silico characterization of cold shock protein coding gene (cspA) from cold adaptive Pseudomonas koreensis
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Cold shock proteins (CSPs) are greatly conserved family of structurally related DNA binding proteins which are produced during temperature drift. A 213 bp long cspA gene was cloned and sequenced from Pseudomonas koreensis P2 in the present study. The expression analysis of the cspA showed > 2.5 folds increase in the mRNA level at 15 °C while the expression was almost on par at 30 °C and 5 °C indicating its role in moderately low temperature. In silico analyses of the gene showed that the gene codes for 7.69 kDa protein which was phylogenetically very similar to CspA present in Pseudomonads. Amino acid composition of the CspA from P. koreensis was different from that of mesophilic Pseudomonas and tiny/small amino varied significantly between CspA of cold adaptive and mesophilic species. The CspA from P. koreensis P2 contained RNP motifs involved in binding of DNA and RNA. Phylogenetic analyses revealed that the CspA protein of P. koreensis P2 was more close to CspA of distant subgroups of Pseudomonas like P. fluorescens and P. putida subgroup indicating a possible intra-specific gene transfer.
KeywordsCold shock protein Pseudomonas koreensis Psychrophiles Gene expression Molecular modeling
Cold shock proteins
Grand average hydropathy
Molecular evolutionary genetics analysis
Protein Data Bank
National Center for Biotechnology Information
Nucleic acid binding proteins
DNA Data Bank of Japan
Protein model database
Minimum information for publication of quantitative RT PCR experiments
The authors gratefully acknowledge the financial assistance under network project ‘Application of Microorganisms in Agriculture and Allied Sectors (AMAAS)’ and “CRP Genomics” from Indian Council of Agricultural Research (ICAR), India.
HC conceptualized the study. Primers were designed by KM. Molecular works were carried out by ASh and PS. SA performed all computational analyses. JY performed the gene expression experiment. AB performed statistical analyses. HC, KM, KP and ASi drafted and revised the manuscript. AKS, PLK and AKS helped in execution of the experiments.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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