title: Coping with anoxia: a comprehensive proteomic and transcriptomic survey of denitrification.
abstract: Ralstonia eutropha H16 is a denitrifying microorganism able to use nitrate and nitrite as terminal electron acceptors under oxygen deprivation. To identify proteins showing an altered expression pattern in response to oxygen supply, R. eutropha cells grown aerobically and anaerobically were compared in a comprehensive proteome and transcriptome approach. Nearly 700 proteins involved in several processes including respiration, formation of cell appendages, and DNA and cofactor biosynthesis were found to be differentially expressed. A combination of 1D gel-LC and conventional 2D gel analysis of six consecutive sample points covering the entire denitrification sequence revealed a detailed view on the shifting abundance of the key proteins of denitrification. Denitrification- or anaerobiosis-induced alterations of the respiratory chain included a distinct expression pattern for multiple terminal oxidases. Alterations in the central carbon metabolism were restricted to a few key functions including the isoenzymes for aconitase and isocitrate dehydrogenase. Although R. eutropha is a strictly respiratory bacterium, the abundance of certain fermentation enzymes was increased. This work represents a comprehensive survey of denitrification on the proteomic and transcriptomic levels and provides unique insight into how R. eutropha adapts its metabolism to low oxygen conditions.
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin , Chausseestraße 117, 10115 Berlin, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Kohlmann
authors.forename: Anne
authors.initials: A
authors.lastname: Pohlmann
authors.forename: Edward
authors.initials: E
authors.lastname: Schwartz
authors.forename: Daniela
authors.initials: D
authors.lastname: Zühlke
authors.forename: Andreas
authors.initials: A
authors.lastname: Otto
authors.forename: Dirk
authors.initials: D
authors.lastname: Albrecht
authors.forename: Christina
authors.initials: C
authors.lastname: Grimmler
authors.forename: Armin
authors.initials: A
authors.lastname: Ehrenreich
authors.forename: Birgit
authors.initials: B
authors.lastname: Voigt
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Bärbel
authors.initials: B
authors.lastname: Friedrich
authors.forename: Rainer
authors.initials: R
authors.lastname: Cramm
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D020118:Cupriavidus necator / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D058440:Denitrification; D020869:Gene Expression Profiling; D010100:Oxygen / Q000378:metabolism*; D040901:Proteomics; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D010100:Oxygen
keywords: Ralstonia eutropha H16; anaerobiosis; denitrification; membrane proteins; spectral counting