Abstract
BackgroundThe Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene.ResultsTo understand the role of ArcA in S. oneidensis, an arcA deletion strain was constructed and subjected to both physiological characterization and microarray analysis. Compared to the wild-type MR-1, the mutant exhibited impaired aerobic growth and a defect in utilizing DMSO in the absence of O2. Microarray analyses on cells grown aerobically and anaerobically on fumarate revealed that expression of 1009 genes was significantly affected (p < 0.05) by the mutation. In contrast to E. coli ArcA, the protein appears to be dispensable in regulation of the TCA cycle in S. oneidensis. To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map. By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.ConclusionThese results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.
Highlights
The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli
Screening for target operons of ArcA(-P) by electrophoretic motility shift assay (EMSA) The analyses presented far clearly showed that S. oneidensis ArcA differs substantially from its E. coli counterpart in its physiological role and regulates a large number of genes
This study provides the first comprehensive profile to elucidate the functions of the atypical Arc system in S. oneidensis, compared to the canonical one in E. coli
Summary
The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 is a facultative gram-negative anaerobe with remarkable anaerobic respiration abilities that allow the use of a diverse array of terminal electron acceptors. These acceptors include fumarate, nitrate, nitrite, thiosulfate, elemental sulfur, trimethylamine N-. Oxide (TMAO), dimethyl sulfoxide (DMSO), Fe(III), Mn(III) and (IV), Cr(VI), and U(VI) [1] Because of this exceptional metabolic flexibility and the potential use of this organism for the bioremediation of metal/radionuclide contaminants in the environment, S. oneidensis MR1 has been extensively studied and its genome has been (page number not for citation purposes). In Escherichia coli, the global regulator Fnr (fumarate nitrate regulator) plays a major role in altering gene expression between aerobic and anaerobic conditions. S. oneidensis MR-1 appears to employ Crp (cyclic-AMP receptor protein) rather than EtrA (electron transport regulator, S. oneidensis analog to E. coli Fnr) and possibly other unidentified proteins in regulating anaerobic respiration [3,4,5]
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