title: Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.
abstract: BACKGROUND
  Exiguobacterium 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).
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Our 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.
authors.forename: Hivana P M B
authors.initials: HP
authors.lastname: Dall'Agnol
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Baraúna
authors.forename: Pablo H C G
authors.initials: PH
authors.lastname: de Sá
authors.forename: Rommel T J
authors.initials: RT
authors.lastname: Ramos
authors.forename: Felipe
authors.initials: F
authors.lastname: Nóbrega
authors.forename: Catarina I P
authors.initials: CI
authors.lastname: Nunes
authors.forename: Diego A
authors.initials: DA
authors.lastname: das Graças
authors.forename: Adriana R
authors.initials: AR
authors.lastname: Carneiro
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Santos
authors.forename: Adriano M C
authors.initials: AM
authors.lastname: Pimenta
authors.forename: Marta S P
authors.initials: MS
authors.lastname: Carepo
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.forename: Vivian H
authors.initials: VH
authors.lastname: Pellizari
authors.forename: Maria P C
authors.initials: MP
authors.lastname: Schneider
authors.affiliation: Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brasil. asilva@ufpa.br.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001406:Bacillaceae / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D002462:Cell Membrane / Q000378:metabolism; D057773:Cold Shock Proteins and Peptides / Q000378:metabolism; D003080:Cold Temperature; D015180:Electrophoresis, Gel, Two-Dimensional; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics / Q000379:methods*; D013058:Mass Spectrometry; D014176:Protein Biosynthesis; D017510:Protein Folding; D020543:Proteome / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D057773:Cold Shock Proteins and Peptides; D020543:Proteome