A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7

Abstract

Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O'Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a "hot topic" because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.

Keywords: 2DE; Exiguobacterium antarcticum B7; genomic; proteomic; transcriptomic.

Figure A1

(a) Fraction of a Differential Gel Electrophoresis (DIGE) comparing the proteome of E. antarcticum grown at 37 °C (green spots) and 0 °C (red spots). Each spot is indicated by its ID; (b) Three-dimensional view of the spots with their respective values of volume percentage.

Figure 1

Representation of the main molecular modifications presented by bacterial cells during cold adaptation. Four adaptations are presented: (1) production of unsaturated branched-chain fatty acids to maintain membrane fluidity; (2) destabilization of adverse RNA structures by cold shock proteins; (3) production of carotenoids to assist in the maintenance of membrane fluidity and prevent cell damage by UV radiation; and (4) transport of compatible solutes such as mannitol to stabilize the cytoplasmic environment and prevent ice formation.

Figure 2

Flowchart showing the omics strategies used to study cold adaptation of E. antarcticum B7. Each omic analysis contains the method used and the results achieved. This large amount of data can then be used to reconstruct metabolic models using top-down approaches of systems biology.