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

Bo Liu,Wei Zhang,Yuhong Zhang,Jacob Guy Bundy

doi:10.1371/journal.pone.0093289

Bo Liu, Wei Zhang + Show 2 more

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https://doi.org/10.1371/journal.pone.0093289

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Abstract

BackgroundAlthough 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.ResultsThe 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.ConclusionOur 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.

Highlights

Rapid temperature downshifts of more than 15–20uC can cause global alterations in gene expression that result in broad physiological changes collectively referred to as cold shock responses
There was a 4-h lag in T. tengcongensis growth upon shift to cold temperature, and growth resumed at a slower rate. This finding was similar to the classical cold shock response of E. coli described by Jones et al [20], and indicates that a cold shock response exists in T. tengcongensis
Cold shock in T. tengcongensis caused global alterations in gene expression that led to multiple physiological changes

Summary

Introduction

Rapid temperature downshifts of more than 15–20uC can cause global alterations in gene expression that result in broad physiological changes collectively referred to as cold shock responses. These include changes in cell wall/membrane composition, protein synthesis rates, energy metabolism, and others [1]. The major cold shock protein in Escherichia coli (EcoCspA) and some of its homologs in other bacterial species play critical roles in cold shock and acclimation of cells, and act as RNA chaperones to destabilize RNA secondary structures at low temperature [9,10]. We examined cold shock responses and their effect on natural competence in this bacterium

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