XoxF Acts as the Predominant Methanol Dehydrogenase in the Type I Methanotroph Methylomicrobium buryatense

Abstract

Many methylotrophic taxa harbor two distinct methanol dehydrogenase (MDH) systems for oxidizing methanol to formaldehyde: the well-studied calcium-dependent MxaFI type and the more recently discovered lanthanide-containing XoxF type. MxaFI has traditionally been accepted as the major functional MDH in bacteria that contain both enzymes. However, in this study, we present evidence that, in a type I methanotroph, Methylomicrobium buryatense, XoxF is likely the primary functional MDH in the environment. The addition of lanthanides increases xoxF expression and greatly reduces mxa expression, even under conditions in which calcium concentrations are almost 100-fold higher than lanthanide concentrations. Mutations in genes encoding the MDH enzymes validate our finding that XoxF is the major functional MDH, as XoxF mutants grow more poorly than MxaFI mutants under unfavorable culturing conditions. In addition, mutant and transcriptional analyses demonstrate that the lanthanide-dependent MDH switch operating in methanotrophs is mediated in part by the orphan response regulator MxaB, whose gene transcription is itself lanthanide responsive. IMPORTANCEAerobic methanotrophs, bacteria that oxidize methane for carbon and energy, require a methanol dehydrogenase enzyme to convert methanol into formaldehyde. The calcium-dependent enzyme MxaFI has been thought to primarily carry out methanol oxidation in methanotrophs. Recently, it was discovered that XoxF, a lanthanide-containing enzyme present in most methanotrophs, can also oxidize methanol. In a methanotroph with both MxaFI and XoxF, we demonstrate that lanthanides transcriptionally control genes encoding the two methanol dehydrogenases, in part by controlling expression of the response regulator MxaB. Lanthanides are abundant in the Earth's crust, and we demonstrate that micromolar amounts of lanthanides are sufficient to suppress MxaFI expression. Thus, we present evidence that XoxF acts as the predominant methanol dehydrogenase in a methanotroph.A n increasing surplus in the global methane budget exists due to human activity. The industrial use of microorganisms to convert methane into useful chemicals or biofuels represents one way to mitigate atmospheric methane (1, 2). Methanotrophs, or methane-oxidizing bacteria, utilize methane as their carbon and energy source and are prime candidates for the industrial bioconversion of methane (1). Renewed interest in the industrial use of methanotrophs has come about partially because of the discovery of rapidly growing strains and new tools for genetic manipulation, allowing for fast-paced metabolic engineering (3, 4). The success of metabolic engineering strategies in these methanotrophs depends upon a strong foundation of knowledge concerning the metabolic pathways that methanotrophs employ, both in the laboratory and in their natural environments, and an understanding of how various branches of metabolic pathways are regulated.The majority of methanotrophs have two systems for oxidizing methane to methanol: the parti...

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

“…In line with previous findings with other methanotrophs (26,27), we provide evidence that in pure culture in the presence of lanthanum the XoxF-type (Fig. 3A) is the predominant MDH in M. tundripaludum 31/32.…”

“…In the two type I strains tested so far (ref. 26 and this study), in pure cultures, the amount of lanthanum added was sufficient to repress expression of the genes for the MxaF-type MDH throughout the course of the experiment, even in the presence of copper.…”

“…Before RNA was extracted, samples were flushed and incubated as described above for 2 h to ensure that samples were obtained at the onset of the micro-oxic phase of the experiment. The procedure was performed as described (26) except that FastPrep Lysing Matrix E tubes (MP Biomedicals) were used. The purified RNA was tested for DNA contamination using 16S PCR.…”

“…The expression of the methanotroph MxaF-type MDH in the cocultures was unexpected because 30 μM lanthanum was included in all cultures, and recent studies with other methanotrophs have shown that the XoxF-type MDH should be the dominant MDH expressed in the presence of lanthanum (26,27). To verify these observations, we repeated this experiment with an independent set of cultures and used qRT-PCR to analyze the gene expression of xoxF and mxaF in the methanotroph with and without a co-occurring species (Fig.…”

“…Traditionally, this reaction was thought to be catalyzed by a calciumdependent MDH (MxaF). However, recent findings identified an additional, lanthanide-dependent MDH (XoxF), that is widespread in bacterial methylotrophs and dominates under some growth conditions (26)(27)(28).…”