Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

Abstract

The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

FIG. 1.

Chromosome of Nitrobacter winogradskyi Nb-255 (ATCC 25391). The outer two circles indicate the locations of key energetic and metabolic features. The third and fourth circles depict predicted protein-encoding and structural RNA genes on the plus and minus strands, respectively (green, energy metabolism; red, DNA replication; magenta, transcription; yellow, translation; orange, amino acid metabolism; dark blue, carbohydrate metabolism; pale red, nucleotide metabolism; black, coenzyme metabolism; cyan, lipid metabolism; light blue, cellular processes; brown, general function; gray, hypothetical and conserved hypothetical genes; pale green, structural RNAs). The fifth and sixth circles depict the location of IS elements and phage regions (gray bars) on the plus and minus strands, respectively. The seventh circle indicates GC bias; and the eighth circle indicates GC skew.

FIG. 2.

Organization of N. winogradskyi gene clusters. Each arrow represents one gene. The N. winogradskyi locus numbers are indicated within the arrows and putative gene names are above each arrow. In panel D, a gene cluster from N. europaea (ATCC 19718) is shown for comparison.

FIG. 3.

N. winogradskyi cell diagram. Cellular processes depicted are based on putative gene annotations. Roman numerals refer to electron transport components of enzyme complex I (NADH-ubiquinone reductase), complex II (succinate dehydrogenase), complex III (ubiquinol-cytochrome c reductase), and complex IV (cytochrome c oxidase).