Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria

Campbell, Mark; Nyerges, G; Kozlowski, Jessica A.; Poret-Peterson, Amisha T.; Stein, Lisa Y.; Klotz, Martin G.

doi:10.1111/j.1574-6968.2011.02340.x

Cited by 93 publications

(83 citation statements)

References 29 publications

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“…Many of these organisms harbor at least one HAO-like protein that has an elusive role. It was suggested that these HAO-like proteins could either oxidize hydroxylamine to nitrite or NO or alternatively reduce nitrite to NO (61,62). Despite substantial sequence divergence, HAO-like proteins from methane oxidizers have two prominent features in common with kustc1061 and its homologs in anammox bacteria: they do contain the tyrosine involved in the covalent binding of the catalytic heme that favors oxidative reactions and lack the tyrosine present in NeHAO (Tyr 358 ; supplemental Fig.…”

Section: Discussionmentioning

confidence: 99%

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

Maalcke

Dietl

Marritt

et al. 2014

Journal of Biological Chemistry

157

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Background: Multiheme proteins have crucial roles in diverse nitrogen cycle processes. Results: The kustc1061 octaheme protein from anaerobic ammonium-oxidizing (anammox) bacteria specifically oxidizes hydroxylamine to NO. Conclusion: Enzyme specificity derives from subtle amino acid changes near the P 460 catalytic heme. Significance: The presence of kustc1061 homologs in anammox and other bacteria enables the detoxification of hydroxylamine, thereby generating NO for respiratory purposes.

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Section: Discussionmentioning

confidence: 99%

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

Maalcke

Dietl

Marritt

et al. 2014

Journal of Biological Chemistry

157

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“…Genes for nitrite reduction (nirS) and nitric oxide reduction (norB) were predicted. A gene encoding cytochrome P460 was predicted, indicating a potential for hydroxylamine detoxification (4,6).…”

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confidence: 99%

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

et al. 2011

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Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.Methylomonas methanica (11,21) is one of four recognized species within the genus Methylomonas in the Gammaproteobacteria, which includes M. aurantiaca (3, 12), M. fodinarum (3,12), and M. scandinavica (13,14). Several other Methylomonas species without validly published names have also been described, including "M. clara" (8) and "M. rubra" (18). All members of the genus use methane as the sole carbon and energy source. The majority of known strains were obtained from terrestrial environments; however, M. methanica MC09 was isolated from a methane enrichment culture inoculated with seawater obtained from the coast of Penarth, United Kingdom (lat 51.43, long Ϫ3.17) (M. Cunliffe and J. C. Murrell, unpublished data). Methylomonas spp. are prevalent in various marine and estuarine environments (5,9,16,19,20). The complete genome sequence of M. methanica MC09 is the first available for a marine methanotroph, providing insights into methane cycling in marine environments.The genome (5.05 Mbp) of M. methanica MC09 was assembled using VELVET (22) and Newbler from an Illumina GAii (2) shotgun library (74,177,086 reads; 2.67 Gbp) and 454 Titanium (15) standard (215,708 reads) and paired-end (154 Mbp) libraries representing 24.3ϫ coverage. Gaps were closed by PCR and Bubble PCR primer walks (350 reactions and 1 shatter library) using Consed (7). The genome is a single circular replicon with 4,494 candidate protein-encoding genes, as predicted by Prodigal (10) and GenePrimp (17). The mean GC content of the sequence was 51.3 mol%.Synthetic pathways for tRNAs of all 20 structural amino acids were accounted for, along with a single rRNA operon. Three terminal oxidases were predicted: aa 3 , o-quinol, and bd-quinol.All genes for the 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase variant of the ribulose monophosphate (RuMP) pathway of formaldehyde fixation were predicted, consistent with experimental data for Methylomonas spp. (1). All genes of the pentose phosphate and Embden-Meyerhof-Parnas pathways were predicted. Genes for all enzymes of Krebs' cycle, with the exception of fumarase, were predicted. Genes for RubisCO were not found. The mxaFJGIRSACKLDEK cluster encoding methanol dehydrogenase was predicted, along with the cluster pqqBCDE for biosynthesis of the cofactor pyrroloquinoline quinone. Both particulate (pmoCAB) and soluble (mmoXYBZDCGR) methane monooxygenases were predicted. Acetate kinase and acetyl coenzyme A synthase were predicted, potentially allowing C 2 -compound assimilation.All genes required for dinitrogen fixation were predicted, as were those for nitrate/nitrite transport (nasFED), ammonification (nasCA, nasB, and nirBD), direct ammonium uptake (amtB), and nitrogen assimilation (glnA, gltB, and ald). Urea metabolism genes were predicted (...

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“…A gene homologous to hydroxylamine oxidoreductase (hao), possibly handling hydroxylamine toxicity arising from oxidation of ammonia by pMMO, is present (2).…”

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confidence: 99%

Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z

et al. 2012

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Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.A erobic methanotrophy, widespread within the bacterial world, is commonly found in Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia (3,8,10). Methylomicrobium alcaliphilum 20Z represents a methanotrophic clade adapted to high-pH and high-salinity ecosystems (4, 6, 13).The assembled genome sequence of M. alcaliphilum 20Z was determined at Genoscope. A mate-paired GSflx 454 library with 3-kb insert size was constructed (22 Mbp; Ϸ4.6-fold coverage) and combined with 454 Titanium reads (71 Mbp; Ϸ15-fold coverage) for assembly using Newbler (version 2.0.01.14) with validation via the Consed interface (www.phrap.org). For gap closure, 1,163 PCRs between contigs were performed and sequenced. Potential base errors were corrected by mapping a total of 1,3497,122 Illumina 36-bp reads onto the whole genome sequence using SOAP (http://soap.genomics.org.cn) as described previously (1) to finalize the 4.8-Mb assembly. Sequence annotation and comparative genome analysis are under way using the MicroScope platform at Genoscope (14).M. alcaliphilum 20Z features a relatively large circular chromosome of 4.67 Mb, with an average GC content of 48.75%, three complete rRNA operons, 44 tRNAs, and 4,083 predicted proteincoding sequences in the initial annotation. The genome also features a circular plasmid of 128 kb of very similar GC content (48.70%) encoding putative systems for replication and conjugation transfer. To our knowledge, this is the first reported plasmid for a methanotrophic bacterium with a known genome sequence.The C 1 metabolism gene inventory in M. alcaliphilum 20Z includes a single copy of the membrane-associated methane monooxygenase gene cluster (pmoCAB) (12), pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (mxaFI) and an associated cytochrome c, genes for MDH assembly and PQQ biosynthesis, tetrahydromethanopterin-and tetrahydrofolatelinked C 1 transfer pathways, aldehyde ferredoxin oxidoreductase (aorAB), membrane-associated quinoprotein formaldehyde dehydrogenase (adh), two formate dehydrogenases, and the ribulose monophosphate (RuMP) pathway. Although serine cycle enzyme activities have not been previously detected in strain 20Z (6), genes encoding glyA, sga, hpr, gck, mclA, and mtkAB are present. Key enzymes of the Calvin-Benson-Bassham cycle (5) are missing. Complete sets of genes for function of the Embden-MeyerhofParnas pathway, the Entner-Doudoroff pathway, and the pentose phosphate pathway were identified. Similar ...

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Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria

Cited by 93 publications

References 29 publications

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

Structural Basis of Biological NO Generation by Octaheme Oxidoreductases

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z

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