DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens

Abstract

The regulon of the sigma factor RpoS was defined in Geobacter sulfurreducens by using a combination of DNA microarray expression profiles and proteomics. An rpoS mutant was examined under steady-state conditions with acetate as an electron donor and fumarate as an electron acceptor and with additional transcriptional profiling using Fe(III) as an electron acceptor. Expression analysis revealed that RpoS acts as both a positive and negative regulator. Many of the RpoS-dependent genes determined play roles in energy metabolism, including the tricarboxylic acid cycle, signal transduction, transport, protein synthesis and degradation, and amino acid metabolism and transport. As expected, RpoS activated genes involved in oxidative stress resistance and adaptation to nutrient limitation. Transcription of the cytochrome c oxidase operon, necessary for G. sulfurreducens growth using oxygen as an electron acceptor, and expression of at least 13 c-type cytochromes, including one previously shown to participate in Fe(III) reduction (MacA), were RpoS dependent. Analysis of a subset of the rpoS mutant proteome indicated that 15 major protein species showed reproducible differences in abundance relative to those of the wild-type strain. Protein identification using mass spectrometry indicated that the expression of seven of these proteins correlated with the microarray data. Collectively, these results indicate that RpoS exerts global effects on G. sulfurreducens physiology and that RpoS is vital to G. sulfurreducens survival under conditions typically encountered in its native subsurface environments.

Deletion of thioredoxin-interacting protein in mice impairs mitochondrial function but protects the myocardium from ischemia-reperfusion injury

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Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

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Analysis of the RpoS regulon in Borrelia burgdorferi in response to mammalian host signals provides insight into RpoS function during the enzootic cycle

“…Microarrays have proven to be a valuable tool for delineating the RpoS regulons of other microorganisms (Lacour and Landini, 2004; Patten et al ., 2004; Schuster et al ., 2004; Yildiz et al ., 2004; Weber et al ., 2005; Nunez et al ., 2006; Rahman et al ., 2006). While microarray technology has been used to examine differential gene expression in Bb cultivated under different environmental conditions (Liang et al ., 2002; Revel et al ., 2002; Brooks et al ., 2003; Ojaimi et al ., 2003; Tokarz et al ., 2004; Fisher et al ., 2005; Hyde et al ., 2006), only one study (Fisher et al ., 2005) has examined the contribution of alternative sigma factors to gene expression in Bb on a genome‐wide scale, and then, only under standard in vitro growth conditions.…”