Carbon Monoxide Dehydrogenase Activity in Bradyrhizobium japonicum

146

227

Isolates belonging to six genera not previously known to oxidize CO were obtained from enrichments with aquatic and terrestrial plants. DNA from these and other isolates was used in PCR assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxL). CoxL and putative coxL fragments were amplified from known CO oxidizers (e.g., Oligotropha carboxidovorans and Bradyrhizobium japonicum), from novel COoxidizing isolates (e.g., Aminobacter sp. strain COX, Burkholderia sp. strain LUP, Mesorhizobium sp. strain NMB1, Stappia strains M4 and M8, Stenotrophomonas sp. strain LUP, and Xanthobacter sp. strain COX), and from several well-known isolates for which the capacity to oxidize CO is reported here for the first time (e.g., Burkholderia fungorum LB400, Mesorhizobium loti, Stappia stellulata, and Stappia aggregata). PCR products from several taxa, e.g., O. carboxidovorans, B. japonicum, and B. fungorum, yielded sequences with a high degree (>99.6%) of identity to those in GenBank or genome databases. Aligned sequences formed two phylogenetically distinct groups. Group OMP contained sequences from previously known CO oxidizers, including O. carboxidovorans and Pseudomonas thermocarboxydovorans, plus a number of closely related sequences. Group BMS was dominated by putative coxL sequences from genera in the Rhizobiaceae and other ␣-Proteobacteria. PCR analyses revealed that many CO oxidizers contained two coxL sequences, one from each group. CO oxidation by M. loti, for which whole-genome sequencing has revealed a single BMS-group putative coxL gene, strongly supports the notion that BMS sequences represent functional CO dehydrogenase proteins that are related to but distinct from previously characterized aerobic CO dehydrogenases.Carbon monoxide occurs in nonurban atmospheres at about 60 to 300 ppb (11,33,43). In spite of these low concentrations, CO participates in a number of chemical reactions that determine the oxidative state of the troposphere as well as the residence times of many organic species, including greenhouse gases such as methane (11,12,20,34). Atmospheric CO also serves as a substrate for soil microbes, which remove as much as 15% of the annual CO flux to the atmosphere (7, 21). Although soil microbes play an important role in the global CO budget, the populations involved remain poorly known (7,8). Limited evidence indicates that fungi, actinomycetes, and bacteria actively consume CO but that "classic" carboxydotrophs play a minimal role in situ (3, 10). However, the role of such carboxydotrophs has only been inferred from laboratory studies that may not accurately reflect capabilities expressed in situ.Carboxydotrophic bacteria constitute a small but diverse group of aerobes (31), primarily within the ␣-Proteobacteria and the Firmicutes, that utilize CO as sole carbon and energy sources at high (much higher than 1%) concentrations while expressing relatively low-affinity CO uptake systems (apparent K m , Ն500 ppm). While the ecological roles of these organisms need clarification, seve...

Section: Discussionmentioning

confidence: 99%

Molecular andCulture-Based Analyses of Aerobic Carbon Monoxide OxidizerDiversity†

King

2003

146

227

“…Also, N. winogradskyi lacks the capacity to produce cytochrome b 561 , a key electron transfer chain component typically associated with carbon monoxide-dependent growth of aerobic carboxidotrophic bacteria (61,62). Utilization of carbon monoxide as a sole carbon and energy source to support growth has been demonstrated for the closest relative to N. winogradskyi, B. japonicum USDA110 (57). However, the B. japonicum USDA110 genome possesses multiple copies of putative CODH-encoding genes, including three cox/cutSML clusters, and at least two ORFs putatively encoding cytochrome b 561 .…”

Section: Discussionmentioning

confidence: 99%

Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

Starkenburg

Chain

Sayavedra-Soto

et al. 2006

160

134

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 C 2 to C 4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C 6 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 aerobictype 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.Nitrification, the microbiological process by which ammonia is converted to nitrate, is a major component of the global nitrogen cycle, plays a crucial role in transformation of fertilizer nitrogen in agricultural systems, and is a key component of nitrogen removal in wastewater treatment. Excess production of soluble nitrogen by nitrification results in the contamination of potable water and eutrophication of aquatic and terrestrial ecosystems, while the gaseous by-products of nitrification, nitric oxide and nitrous oxide, are two of the most potent greenhouse gases. As anthropogenic inputs of fixed nitrogen continue to expand to meet the demands of a growing global population, intimate knowledge of the nitrification process and the microorganisms that control this process will be necessary to address environmental nitrogen imbalances.Nitrobacter winogradskyi Nb-255 and other nitrite-oxidizing bacteria participate in nitrification by converting nitrite, the end product of ammonia oxidation, into nitrate according to the reaction NO 2 Ϫ ϩ H 2 O 3 NO 3 Ϫ ϩ 2H ϩ ϩ 2e Ϫ . Nitrite functions as an electron donor for the reduction of NAD via reverse electron flow and the generation of ATP by oxidative phosphorylation (36).As a facultative chemolithoautotroph, N. winogradskyi gains energy from nitrite oxidation, and fix...

“…H 2 uptake-positive (Hup ϩ ) strains of B. japonicum USDA122 (13) and USDA110 (6) carrying hup genes can grow chemolithoautotrophically in mineral salts medium with H 2 , CO 2 , and low concentrations of O 2 . B. japonicum USDA110 is also reportedly able to grow chemolithotrophically with carbon monoxide as an electron donor (27). Thus, it is possible that B. japonicum USDA110 may utilize an inorganic sulfur compound, thiosulfate, as an electron donor and CO 2 as a carbon source for chemolithoautotrophic growth.…”

mentioning

confidence: 99%

“…japonicum is known to grow chemolithoautotrophically using the gaseous electron donors H 2 and CO (6,13,27). H 2 uptake-positive (Hup ϩ ) strains of B. japonicum USDA122 (13) and USDA110 (6) carrying hup genes can grow chemolithoautotrophically in mineral salts medium with H 2 , CO 2 , and low concentrations of O 2 .…”

mentioning

confidence: 99%

Thiosulfate-Dependent Chemolithoautotrophic Growth of Bradyrhizobium japonicum

Masuda

Eda

Ikeda

et al. 2010

Thiosulfate-oxidizing sox gene homologues were found at four loci (I, II, III, and IV) on the genome of Bradyrhizobium japonicum USDA110, a symbiotic nitrogen-fixing bacterium in soil. In fact, B. japonicum USDA110 can oxidize thiosulfate and grow under a chemolithotrophic condition. The deletion mutation of the soxY 1 gene at the sox locus I, homologous to the sulfur-oxidizing (Sox) system in Alphaproteobacteria, left B. japonicum unable to oxidize thiosulfate and grow under chemolithotrophic conditions, whereas the deletion mutation of the soxY 2 gene at sox locus II, homologous to the Sox system in green sulfur bacteria, produced phenotypes similar to those of wild-type USDA110. Thiosulfate-dependent O 2 respiration was observed only in USDA110 and the soxY 2 mutant and not in the soxY 1 mutant. In the cells, 1 mol of thiosulfate was stoichiometrically converted to approximately 2 mol of sulfate and consumed approximately 2 mol of O 2 . B. japonicum USDA110 showed 14 CO 2 fixation under chemolithotrophic growth conditions. The CO 2 fixation of resting cells was significantly dependent on thiosulfate addition. These results show that USDA110 is able to grow chemolithoautotrophically using thiosulfate as an electron donor, oxygen as an electron acceptor, and carbon dioxide as a carbon source, which likely depends on sox locus I including the soxY 1 gene on USDA110 genome. Thiosulfate oxidation capability is frequently found in members of the Bradyrhizobiaceae, which phylogenetic analysis showed to be associated with the presence of sox locus I homologues, including the soxY 1 gene of B. japonicum USDA110.