Abstract
BackgroundExiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0°C and 37°C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS).ResultsWe found expression of 2,058 transcripts in all replicates from both platforms and differential expression of 564 genes (absolute log2FC ≥1, P-value <0.001) comparing the two temperatures by RNA-Seq. A total of 73 spots were differentially expressed between the two temperatures on 2D-DIGE, 25 of which were identified by MS/MS. Some proteins exhibited patterns of dispersion in the gel that are characteristic of post-translational modifications.ConclusionsOur findings suggest that the two sequencing platforms yielded similar results and that different omic approaches may be used to improve the understanding of gene expression. To adapt to low temperatures, E. antarcticum B7 expresses four of the six cold-shock proteins present in its genome. The cold-shock proteins were the most abundant in the bacterial proteome at 0°C. Some of the differentially expressed genes are required to preserve transcription and translation, while others encode proteins that contribute to the maintenance of the intracellular environment and appropriate protein folding. The results denote the complexity intrinsic to the adaptation of psychrotrophic organisms to cold environments and are based on two omic approaches. They also unveil the lifestyle of a bacterial species isolated in Antarctica.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-986) contains supplementary material, which is available to authorized users.
Highlights
Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica
The noncoding RNA (ncRNA) reads were filtered from our data set, and the remaining reads that aligned to mRNA regions were used for the gene expression estimate (Table 1 and Additional file 3: Table S1)
The gene sigD, which is related to a regulon of genes involved in flagellar synthesis, is one of 31 genes included in an operon, all of which participate in flagellar synthesis and bacterial chemotaxis [43]. All those genes comprising the SigW regulon, including the sigW gene, were upregulated at cold (Additional file 4: Table S4). These findings suggest that bacterial motility might be significant at low temperatures and that these genes, which were annotated as organized in an operon in the E. antarcticum B7 genome, are expressed as a polycistronic mRNA molecule
Summary
Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. This bacteria has been poorly studied, its genome has already been sequenced. It is an appropriate model for the study of thermal adaptation. Prokaryotes are able to adapt to a wide range of environmental conditions, including extreme variations in temperature, pressure, salinity, pH and radiation [1,2]. Microorganisms adapted to cold conditions are classified as psychrophiles when their optimal temperature for growth is approximately 15°C or lower and as psychrotrophic when their optimal temperature for growth is above that level [2,5]. Several adaptive mechanisms are activated to maintain membrane fluidity, transport, transcription, translation, cell division, metabolism and enzyme activity and to avoid intracellular ice formation [8,9]
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