title: RNA-Seq-based analysis of cold shock response in Thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene.
abstract: BACKGROUND
  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. Thermoanaerobacter tengcongensis MB4, a thermophile harboring only one known cold shock protein gene (TtescpC), 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.
  
  
  RESULTS
  The transcriptomes of T. tengcongensis 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 T. tengcongensis initiates cell wall and membrane remodeling processes, flagellar assembly, and sporulation in response to low temperature. Expression profiles of TtecspC and failed attempts to produce a TtecspC knockout strain confirmed the essential role of TteCspC 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.
  
  
  CONCLUSIONS
  Our study demonstrated changes in global gene expression under cold shock and identified several candidate genes related to cold shock in T. tengcongensis. 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.
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D057773:Cold Shock Proteins and Peptides / Q000235:genetics*; D058639:Cold-Shock Response / Q000235:genetics*; D004260:DNA Repair; D004261:DNA Replication; D015964:Gene Expression Regulation, Bacterial; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D014176:Protein Biosynthesis; D011995:Recombination, Genetic; D017423:Sequence Analysis, RNA; D046968:Thermoanaerobacter / Q000235:genetics* / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D057773:Cold Shock Proteins and Peptides