Fax +41 61 306 12 34 E-Mail karger@karger.ch www.karger.com J Mol Microbiol Biotechnol 2009;16:38–52 DOI: 10.1159/000142893 Genomic View of Energy Metabolism in Ralstonia eutropha H16 Rainer Cramm Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany Introduction Ralstonia eutropha is a strictly respiratory facultative lithoautotrophic soil and freshwater bacterium of the - subgroup of proteobacteria [Aragno and Schlegel, 1992]. Strain H16 is one of the best-studied model organisms for lithoautotrophic growth on molecular hydrogen and car- bon dioxide [Friedrich and Schwartz, 1993]. Under con- ditions of anoxia, the bacterium can switch to denitrifica- tion by using nitrate as alternative electron acceptor [Rö- mermann and Friedrich, 1985]. Organic carbon and energy sources for heterotrophic growth include TCA cy- cle intermediates, sugar acids, fatty acids, amino acids, alcohols, and aromatic compounds, while utilization of sugars is restricted to fructose and N-acetylglucosamine [Johnson and Stanier, 1971; Kersters and De Ley, 1984]. Fructose is catabolized via the Entner-Doudoroff path- way [Gottschalk et al., 1964]. Activities of the key en- zymes of the Embden-Meyerhoff-Parnas and the oxida- tive pentose phosphate pathways, phosphofructokinase and 6-phosphogluconate dehydrogenase, were not de- tected. Recently, the complete nucleotide sequence of strain H16 was determined [Pohlmann et al., 2006; Schwartz et al., 2003]. The genome consists of three circular rep- licons: chromosome 1 (4,052,032 bp), chromosome 2 (2,912,490 bp), and megaplasmid pHG1 (452,156 bp). Both the genomic size of 7.42 Mbp and a total of 6,626 genes lie within the upper range of proteobacterial ge- Key Words Energy metabolism  Ralstonia eutropha  Lithoautotrophy  Hydrogen oxidation  Denitrification  Electron transport pathways Abstract Ralstonia eutropha is a strictly respiratory facultative lithoau- totrophic -proteobacterium. In the absence of organic sub- strates, H 2 and CO 2 are used as sole sources of energy and carbon. In the absence of oxygen, the organism can respire by denitrification. The recent determination of the complete genome sequence of strain H16 provides the opportunity to reconcile the results of previous physiological and biochem- ical studies in light of the coding capacity. These analyses revealed genes for several isoenzymes, permit assignment of well-known physiological functions to previously uniden- tified genes, and suggest the presence of unknown compo- nents of energy metabolism. The respiratory chain is fueled by two NADH dehydrogenases, two uptake hydrogenases and at least three formate dehydrogenases. The presence of genes for five quinol oxidases and three cytochrome oxidas- es indicates that the aerobic respiration chain adapts to vary- ing concentrations of dioxygen. Several additional compo- nents may act in balancing or dissipation of redox energy. Paralogous sets of nitrate reductase and nitric oxide reduc- tase genes result in enzymatic redundancy for denitrifica- tion. Copyright © 2008 S. Karger AG, Basel Published online: October 29, 2008 Rainer Cramm Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin Chausseestrasse 117 DE–10115 Berlin (Germany) Tel. +49 30 2093 8111, Fax +49 30 2093 8102, E Mail rainer.cramm@rz.hu-berlin.de © 2008 S. Karger AG, Basel 1464–1801/09/0162–0038$26.00/0 Accessible online at: www.karger.com/mmb