Discovery of a potential regulatory transcription factor upon redox alterations in Shewanella oneidensis MR-1
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Shewanella oneidensis is a model organism for bioremediation studies because of its diverse respiratory capabilities and the regulatory mechanisms underlying the ability of S. oneidensis to survive and adapt to various environmental stresses is poorly understood. This work describes the discovery and characterization of a potential -proteobacerial regulatory transcription factor, SO3363p, of the mesophile Shewanella oneidensis. An integrated approach was used including genomics, proteomics and bioinformatics. A DNA affinity protein capture experiment was employed to capture transcription factors responsible for the observed gene regulation in DNA microarray expression profiles of the transcriptional response of S. oneidensis to growth in the presence or absence of oxygen (O2). The recombinant SO3363p was verified to bind specifically to promoters by electrophoretic mobility shift assay (EMSA) and the recognized DNA-binding motif was determined by SELEX. In order to understand the role of SO3363 in S. oneidensis, SO3363 deletion strain was constructed and subjected to both physiological characterization and microarray analysis. The phenotypic microarray revealed that the mutant exhibited a defect in utilizing uridine, 2-deoxy adenosine, pyruvic acid, etc. compared with the wild type MR-1; Growth assays showed that the deletion mutant is more resistant to H2O2; Whole genome DNA microarray analyses showed that a number of genes’ expression was +altered in mutant strain under the conditions tested, including nqr regulon involved in Na translocation, three chemotaxis proteins responding to the change in chemical concentration with anaerobic growth condition; cys regulon related to cysteine biosynthesis, pur regulon involved in de novo synthesis of purine with H2O2 growth condition.