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

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.

Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature

“…The upregulation of BCAA transporters at cooler temperatures was proved to transfer exogenous BCAA into cell for BCFA synthesis. Therefore, promoting BCFA portion could help to maintain the membrane fluidity of bacteria, which is a conventional strategy in cold adaptation [63]. The induction of BCAA transportation system in L .…”

A generation-time effect on the rate of molecular evolution in bacteria

“…) and therefore was predicted to be able to sporulate in this and a previous study (Traag et al ). Although T. tengcongensis has not been observed to sporulate when it was first identified (Xue et al ), RNA‐seq has shown that a cold‐shock protein induces expression of sporulation genes in response to low temperatures (Liu et al ). We note that misclassification of SFF or NSFF will reduce the power to detect generation‐time effect.…”

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

“…Moreover, M. prima (grown at 35°C) contained branched, mono-unsaturated, and saturated fatty acids, while K. olearia (grown at 55°C) contained only saturated fatty acids (Nesbø et al 2012). Fatty acid composition is also part of the immediate coldshock response with genes involved in the production of, for instance, branched fatty acids being upregulated in the thermophile Thermoanaerobacter tengcongensis when grown at suboptimal temperatures (Liu et al 2014). Increase of branched fatty acids is a common response to lower temperatures (Suutari and Laakso 1994), and in Listeria monocytogenes this is due to temperaturedependent substrate selectivity of FabH, the enzyme responsible for the first condensation reaction in fatty acid biosynthesis (Singh et al 2009).…”