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

Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa Cuernavaca, Morelos 62210, Mexico.
Journal of Bacteriology (Impact Factor: 2.81). 05/2006; 188(8):2792-800. DOI: 10.1128/JB.188.8.2792-2800.2006
Source: PubMed


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.

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    • "This was reflected by increased abundances of enzymes related to the utilization of alternative electron acceptors, signal transduction and protection against oxidative stress (Fig. 5). In G. sulfurreducens, some of these homologous proteins were also found to belong to the regulon of sigma RpoS, a master regulator of the general stress response [29]. Such physiology is advantageous for Geobactereaceae to survive in natural habitats with energy limitation , heavy metals, or oxidative stress. "
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    • "microarray techniques) since mRNAs are not inherently part of the ECM, and not all proteins that contribute to the formation of skeletal elements are produced in the vicinity of these elements. In addition, mRNA abundance has been shown to correlate poorly to the protein content [7], [8], [9], and does not take into account the wide variety of post-translational modifications which are critical to protein functions [10]. This makes proteomics an essential tool for characterizing the composition of the skeletal ECM. "
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    • "RpoS regulated genes and proteins were identified in Geobacter sulfurreducens and Burkholderia pseudomallei (Nunez et al., 2006; Osiriphun et al., 2009). As expected, most of the RpoS regulated genes and proteins are related to stress responses, but many of the RpoS regulated genes and proteins are involved in the expression of diverse physiological traits, such as general metabolism, transcription, translation, cell motility and secretions (Nunez et al., 2006; Osiriphun et al., 2009). "
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