Identification of proteins involved in formaldehyde metabolism by Rhodobacter sphaeroides

Abstract

Formaldehyde is an intermediate formed during the metabolism of methanol or other methylated compounds. Many Gram-negative bacteria generate formaldehyde from methanol via a periplasmic pyrroloquinoline quinone (PQQ)-dependent dehydrogenase in which the a subunit of an a 2 b 2 tetramer has catalytic activity. The genome of the facultative formaldehyde-oxidizing bacterium Rhodobacter sphaeroides encodes XoxF, a homologue of the catalytic subunit of a proposed PQQ-containing dehydrogenase of Paracoccus denitrificans. R. sphaeroides xoxF is part of a gene cluster that encodes periplasmic c-type cytochromes, including CycI, isocytochrome c 2 and CycB (a cyt c 553i homologue), as well as adhI, a glutathione-dependent formaldehyde dehydrogenase (GSH-FDH), and gfa, a homologue of a glutathione-formaldehyde activating enzyme (Gfa). To test the roles of XoxF, CycB and Gfa in formaldehyde metabolism by R. sphaeroides, we monitored photosynthetic growth with methanol as a source of formaldehyde and whole-cell methanol-dependent oxygen uptake. Our data show that R. sphaeroides cells lacking XoxF or CycB do not exhibit methanol-dependent oxygen uptake and lack the capacity to utilize methanol as a sole photosynthetic carbon source. These results suggest that both proteins are required for formaldehyde metabolism. R. sphaeroides Gfa is not essential to activate formaldehyde, as cells lacking gfa are capable of both methanol-dependent oxygen uptake and growth with methanol as a photosynthetic carbon source.

Characterization of a Novel Methanol Dehydrogenase in Representatives of Burkholderiales : Implications for Environmental Detection of Methylotrophy and Evidence for Convergent Evolution

“…However, this polypeptide was even more closely related to XoxF polypeptides found in a variety of proteobacterial species including both methylotrophs and nonmethylotrophs (6,7,16,38,45). xoxF genes have been previously mutated in two methylotrophs, M. extorquens and Paracoccus denitrificans, without resulting in any visible effect on methanol-oxidizing capability (7,16).…”

Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact

“…The presence of Rhodobacter-related clone sequences is not surprising, as Rhodobacter spp. are capable of growth on methanol (Wilson et al, 2008). The detection of a singleton OTU (CH 3 OH_B7) clustering closely with Halomonas sp.…”

Seasonal variability in microbial methanol utilisation in coastal waters of the western English Channel

“…When the analysis is confined to using values from June 2011 to March 2012, a statistically significant correlation is found, suggesting that Rhodobacterales may be contributing to rates of microbial methanol assimilation into cell biomass, at least in some 10 circumstances (Wilson et al 2008, Chen 2012 …”

“…Methylophaga thiooxidans DMS010, Boden et al 2010, Neufeld et al 2007, Schäfer 2007. The successful design of 15 new primer sets targeting xoxF an alternative methanol dehydrogenase like XoxF (Giovannoni et al 2008, Wilson et al 2008 will enable future studies to investigate the prevalence and role of xoxF at station L4.…”

“…Rhodobacterales have been shown to metabolise methanol: for example, Rhodobacter sphaeroides possesses a xoxF gene (Wilson et al 2008) which has also been identified in 40 genomes of the marine Roseobacter clade (Chen 2012). Newly designed primers targeting xoxF have demonstrated the widespread presence of this gene in coastal waters, including station L4 where some of the most abundant xoxF sequences detected were related to xoxF of 20 members of the Rhodobactaceae family .…”