Transcriptomics

Dataset Information

19

Pyruvate vs Lactate as electron donor in Sulfate reduction


ABSTRACT: In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2. The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies. Keywords: Growth protocol Overall design: Desulfovibrio vulgaris Hildenborough was cultured at 37°C with pyruvate as the only electron donor (with sulfate as the electron acceptor) to mid-log phase. Cultures were also cultivated similarly using lactate as the sole electron donor to mid-log phase. Gene expression profiles of cultures grown with pyruvate as the electron donor were compared with those of the cultures grown with lactate as the electron donor for sulfate reduction. Total RNA was harvested from three replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (dye swap).

INSTRUMENT(S): ORNL-ESD Desulfovibrio vulgaris 70mer oligo-array

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough  

SUBMITTER: Qiang He   

PROVIDER: GSE8071 | GEO | 2008-05-31

SECONDARY ACCESSION(S): PRJNA105401

REPOSITORIES: GEO

altmetric image

Publications

Sorry, this publication's infomation has not been loaded in the Indexer, please go directly to PUBMED or Altmetric.

Similar Datasets

2008-05-31 | GSE8037 | GEO
2014-05-02 | E-GEOD-8037 | ArrayExpress
2014-05-02 | E-GEOD-8071 | ArrayExpress
2008-05-31 | GSE8072 | GEO
2014-05-02 | E-GEOD-8072 | ArrayExpress
2014-05-02 | E-GEOD-8069 | ArrayExpress
2008-05-31 | GSE8015 | GEO
2014-05-02 | E-GEOD-8015 | ArrayExpress
2010-04-25 | GSE21287 | GEO
2011-06-10 | E-GEOD-21287 | ArrayExpress