Survey of the transcriptome of Brevibacillus borstelensis exposed to low temperature shock S. Tripathy a , R. Sen a , S.K. Padhi a , D.K. Sahu b , S. Nandi b , S. Mohanty a , N.K. Maiti a, ⁎ a Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India b Division of Fish Genetics and Biotechnology, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India abstract article info Article history: Received 29 April 2014 Received in revised form 14 August 2014 Accepted 17 August 2014 Available online 21 August 2014 Keywords: Thermophile Brevibacillus borstelensis Low temperature Transcriptome Molecular mechanisms underlying the ability of Brevibacillus borstelensis to survive and adapt to various environ- mentally relevant stresses are poorly understood. To define organism's molecular response to low temperature, gene expression profile of B. borstelensis at 20 °C was carried out by high-throughput sequencing technology. A total of 4579 transcripts with a maximum transcript length of 9919 bp were annotated. Gene expression profiling identified 712 genes that were significantly up- or down-regulated during cold shock. Functional categorization of the differentially expressed genes revealed that response to stress, regulation of transcription, transport, signal transduction and cytoplasm were the differentially regulated processes. The microbial stress responsive genes (hsp90, hslU, grpE, dnaK, dnaJ, hslV) and genes under regulatory adaptive responses (rpoN) were identified. The gene encoding cold shock protein purine nucleoside phosphorylase was found to be remarkably up-regulated. RT-PCR experiments carried out on genes expressed under cold shock independently verified the transcriptome data results. In addition, a large number of genes encoding hypothetical protein were identified. The brief survey of the transcripts obtained in response to cold shock underlines the survival strategy of thermophilic bacteria ex- posed to low temperature environment, which is further helpful in generating genetic information associated with this bacteria. © 2014 Elsevier B.V. All rights reserved. 1. Introduction Temperature is a fundamental factor that affects all living organisms. It is a common environmental factor, and virtually all organisms elicit a cellular response to an increase or decrease in temperature (Gao et al., 2006). Adaptations to fluctuations in temperature are common because of the impact of temperature on the biochemical reactions of the cell. The major impact of reduced temperatures on any system is the reduc- tion of molecular motion, which causes the rate of biological or chemical reactions to slow down (Grout and Morris, 1987). Living organisms typ- ically encounter temperature changes throughout their life cycle and particularly, microbes can tolerate a variety of changing conditions and stresses in their surrounding environment. They possess several defense mechanisms to survive under temperature stresses. This is essential because the temperature in aquatic environments changes seasonally, requiring the microorganisms to carry out long-term tem- perature adaptation. One such example of microorganism with the abil- ity of adapting to wide fluctuations in temperature is the Gram-positive thermophilic bacteria Brevibacillus borstelensis. The potentiality of B. borstelensis as a polythene degrading bacteria and capability of utilizing polyethylene as the sole carbon and energy source have been previously reported (Hadad et al., 2005). In recent years, degradation of low-density polythene has become a major con- cern for protection of environment against pollution and particularly, this has been more challenging in colder environments compared to the hotter ones. Generally, the ability of the bacteria to grow under multiple extreme conditions makes them a good candidate for biodeg- radation of synthetic wastes in different environments. Even though B. borstelensis is widely distributed in nature still the mechanisms by which the bacteria adapt to various environmental conditions especially to low temperature remain largely unexplored. Moreover, until date, most of the reports about the adaptation mechanism of thermophiles are focused on their adaptation to the increasing temperature. Even though few studies have been carried out with respect to low tempera- ture response in thermophiles like Streptococcus thermophilus (Wouters et al., 1999) and Rhodothermus sp. (Ruan et al., 2007), reports describing the transcriptional response of thermophilic bacteria with respect to cold shock are still in its infancy. Gene 550 (2014) 207–213 Abbreviations: cDNA, complementary DNA; CIFA, Central Institute of Freshwater Aquaculture; BLAST, Basic Local Alignment Search Tool; NR, non-redundant; GO, gene on- tology; KEGG, Kyoto Encyclopedia of Genes and Genomes; GIP, genetic information pro- cessing; EIP, environmental information processing; °C, degree centigrade; mRNA, messenger ribonucleic acid; rRNA, ribosomal RNA; KO, KEGG orthology; DGE, differential gene expression; DEPC, diethylpyrocarbonate; ANOVA, analysis of variance; CSP, cold shock protein; HSP, heat shock protein; FDR, false discovery rate. ⁎ Corresponding author. E-mail address: maitink@yahoo.co.in (N.K. Maiti). http://dx.doi.org/10.1016/j.gene.2014.08.030 0378-1119/© 2014 Elsevier B.V. All rights reserved. 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