RNA-Seq-Based Analysis of Cold Shock Response in <i>Thermoanaerobacter tengcongensis</i>, a Bacterium Harboring a Single Cold Shock Protein Encoding Gene

Abstract

<div><p>Background</p><p>Although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. <i>Thermoanaerobacter tengcongensis</i> MB4, a thermophile harboring only one known cold shock protein gene (<i>TtescpC</i>), can survive from 50° to 80°C, but has poor natural competence under cold shock at 50°C. We therefore examined cold shock responses and their effect on natural competence in this bacterium.</p><p>Results</p><p>The transcriptomes of <i>T. tengcongensis</i> before and after cold shock were analyzed by RNA-seq and over 1200 differentially expressed genes were successfully identified. These genes were involved in a wide range of biological processes, including modulation of DNA replication, recombination, and repair; energy metabolism; production of cold shock protein; synthesis of branched amino acids and branched-chain fatty acids; and sporulation. RNA-seq analysis also suggested that <i>T. tengcongensis</i> initiates cell wall and membrane remodeling processes, flagellar assembly, and sporulation in response to low temperature. Expression profiles of <i>TtecspC</i> and failed attempts to produce a <i>TtecspC</i> knockout strain confirmed the essential role of <i>Tte</i>CspC in the cold shock response, and also suggested a role of this protein in survival at optimum growth temperature. Repression of genes encoding ComEA and ComEC and low energy metabolism levels in cold-shocked cells are the likely basis of poor natural competence at low temperature.</p><p>Conclusion</p><p>Our study demonstrated changes in global gene expression under cold shock and identified several candidate genes related to cold shock in <i>T. tengcongensis</i>. At the same time, the relationship between cold shock response and poor natural competence at low temperature was preliminarily elucidated. These findings provide a foundation for future studies on genetic and molecular mechanisms associated with cold shock and acclimation at low temperature.</p></div