Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

Abstract

A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with Methylocystis sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of Methylocystis sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that Methylocystis sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated.

Marker Exchange Mutagenesis of mxaF , Encoding the Large Subunit of the Mxa Methanol Dehydrogenase, in Methylosinus trichosporium OB3b

“…Methylene tetrahydromethanopterin is oxidized to formate, which can be either converted to carbon dioxide via formate dehydrogenase or reduced to methylene tetrahydrofolate. It is speculated that such redundancy for the conversion of formaldehyde exists to control the buildup of this toxic intermediate (1)(2)(3)(4)(5)(6)(7)(8)(9).What is less readily discerned from this simple pathway, however, is that substantial redundancy exists for many steps of the transformation of methane to carbon dioxide and not just the condensation of formaldehyde with either methylene tetrahydrofolate or methylene tetrahydromethanopterin. For example, the first step of methane oxidation (conversion of methane to methanol) can be carried out by two different forms of MMO that are regulated by the availability of copper, i.e., the copper switch.…”

“…Methylene tetrahydromethanopterin is oxidized to formate, which can be either converted to carbon dioxide via formate dehydrogenase or reduced to methylene tetrahydrofolate. It is speculated that such redundancy for the conversion of formaldehyde exists to control the buildup of this toxic intermediate (1)(2)(3)(4)(5)(6)(7)(8)(9).…”

Biosynthesis of secondary metabolites in methanotrophs: Biochemical and genetic aspects (Review)

“…That is why a detailed study of the structural and functional organization and regulation of primary and central metabolic pathways in methanotrophic produc ers is required. The results of genome and transcriptome analysis of a new group of facultative methanotrophs able to use methane and/or polycarbon compounds are of special interest [72].…”

Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands

“…strain SB2, which has proven ability to grow on acetate or ethanol (Im et al. 2011; Vorobev et al. 2014).…”