Transcriptomics,Genomics

Dataset Information

35

G. sulfurreducens growth with acetate as limiting electron donor versus fumarate as limiting electron acceptor


ABSTRACT: Microbially-mediated uranium bioremediation has been demonstrated in uranium contaminated aquifers when acetate was artificially supplied and growth of the natural population of Geobacteraceae was stimulated. In order to mimic the environmental response to acetate, steady-state cells of G. sulfureducens were cultured in chemostats under conditions of either 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor or 2) acetate was supplied in excess with fumarate as sole electron acceptor and limiting factor. In silico fluxome modeling and transcriptome analysis were used as tools for investigating the cell response to the acetate availability. For global gene expression profiling, a DNA microarray of the complete G. sulfurreducens genome was used. Statistically significant results were obtained from two-color, dye swap hybridizations produced from a total of three biological replicates. Eight technical replicates were tested from two of the biological replicates and six technical replicates were tested from the third biological replicate. Major findings from this study are given as follows. The in silico model successfully predicted a higher TCA-cycle flux (ca. 2-fold) under acetate-excess conditions, suggesting that catabolism of acetate is favored with respect to anabolism, and thus more electrons are available for metal reduction. Transcriptome analyses offered a comprehensive picture of the regulation points subjected to the acetate availability. Under acetate-excess conditions, acetate transporters in the G. sulfurreducens genome were down-regulated. In addition the oxidation-related acetyl-CoA transferase was up-regulated approximately three-fold and the assimilatory-related acetate kinase was down-regulated approximately two-fold, respectively, indicating that the transcriptional regulation of acetate activation may be the key point for coping with the excess of acetate and increasing the TCA flux. The level of transcription for 10 c-type cytochromes was significantly increased in cells cultured with an excess of acetate. OmcS, an outer-membrane cytochrome which actively participates in electron transfer to Fe(III)-oxides and graphite electrodes from fuel cells, showed one of the highest fold increases in transcription. The integration of in silico modeling and genome-wide analysis shows for first time how G. sulffureducens adapts its metabolic flux and transcriptional network for optimizing the use of acetate as an electron donor for exocellular respiration instead of for use as a carbon source for biomass production. Keywords: Geobacter, gene expression, acetate limitation, fumarate limitation Overall design: RNA was extracted and used for hybridizations from three identically treated chemostat cultures (biological replicates) of Geobacter sulfurreducens DL1 at steady state. The two conditions tested were 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor and 2) acetate was supplied in excess with fumarate supplied as the sole electron acceptor and limiting factor. A two-color hybridization strategy was used to produce a total of twenty two technical replicates (hybridizations) from three biological replicates as follows. Eight technical replicates were completed from the two biological replicate of which four of the technical replicates were in the opposite or “flip dye” configuration and six technical replicates were produced from the third biological replicate of which three were “flip dyes” .

INSTRUMENT(S): Geobacter sulfurreducens PCA cDNA array (IAS_GGS3)

SUBMITTER: Chun-Hua Wan  

PROVIDER: GSE9830 | GEO | 2008-12-09

SECONDARY ACCESSION(S): PRJNA103799

REPOSITORIES: GEO

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