title: Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707.
abstract: The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H(+)-dependent F(0)F(1) type, one Na(+)-dependent V type).
authors.affiliation: Department of Biology, University of Louisville, 139 Life Science Building, Louisville, KY 40292, USA. aem@mgklotz.com
authors.forename: Martin G
authors.initials: MG
authors.lastname: Klotz
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Arp
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.forename: Amal F
authors.initials: AF
authors.lastname: El-Sheikh
authors.forename: Loren J
authors.initials: LJ
authors.lastname: Hauser
authors.forename: Norman G
authors.initials: NG
authors.lastname: Hommes
authors.forename: Frank W
authors.initials: FW
authors.lastname: Larimer
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Malfatti
authors.forename: Jeanette M
authors.initials: JM
authors.lastname: Norton
authors.forename: Amisha T
authors.initials: AT
authors.lastname: Poret-Peterson
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Vergez
authors.forename: Bess B
authors.initials: BB
authors.lastname: Ward
mesh_terms: D000255:Adenosine Triphosphate / Q000096:biosynthesis; D000596:Amino Acids / Q000378:metabolism; D000641:Ammonia / Q000378:metabolism*; D001482:Base Composition; D002244:Carbon / Q000378:metabolism; D002841:Chromatiaceae / Q000235:genetics* / Q000378:metabolism* / Q000648:ultrastructure; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004579:Electron Transport; D004734:Energy Metabolism; D016680:Genome, Bacterial; D005964:Glucosyltransferases / Q000235:genetics / Q000378:metabolism; D008854:Microscopy, Electron; D008954:Models, Biological; D008969:Molecular Sequence Data; D005810:Multigene Family; D009584:Nitrogen / Q000378:metabolism; D009711:Nucleotides / Q000378:metabolism; D009876:Operon; D010084:Oxidation-Reduction; D010758:Phosphorus / Q000378:metabolism; D010957:Plasmids / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D012623:Seawater / Q000382:microbiology; D013455:Sulfur / Q000378:metabolism
chemical_list: D000596:Amino Acids; D004269:DNA, Bacterial; D009711:Nucleotides; D010758:Phosphorus; D013455:Sulfur; D002244:Carbon; D000641:Ammonia; D000255:Adenosine Triphosphate; D005964:Glucosyltransferases; C022699:sucrose synthase; C022698:sucrose-phosphate synthase; D009584:Nitrogen