Lanthanide-dependent methanol dehydrogenase from the legume symbiotic nitrogen-fixing bacterium Bradyrhizobium diazoefficiens strain USDA110

Biological Function of Lanthanide in Plant-Symbiotic Bacteria: Lanthanide-Dependent Methanol Oxidation System

“…2A). Kawai et al, 2007Hibi et al, 2011Nakagawa et al, 2012Fitriyanto et al, 2011aWang et al, 2019Pastawan et al, 2020Fitriyanto et al, 2011bPol et al, 2014Wehrmann et al, 2020 In the case of Mr. extorquens AM1, MxaFI is encoded on the mxa cluster ( Fig. 2B) and the gene cluster includes several genes for methanol oxidation; mxaF and mxaI, encoding subunits α and β of MDH, respectively (Nunn and Lidstrom, 1986a;1986b); mxaG, encoding cytochrome cL, which is electron acceptor for MxaFI (Amaratunga et al, 1997); mxaJ, encoding a putative chaperone for MxaFI (Featherston et al, 2019); mxaA, encoding a putative chaperone for Ca 2+ insertion to MxaF (Morris et al, 1995); and many other genes of unknown function (Anderson et al, 1990;Toyama et al, 1998).…”

“…Since Fitriyanto et al (2011a) reported that Bradyrhizobium sp. Ce-3 (= MAFF211645) grown on methanol with Ce 3+ possessed Ln-dependent MDH, the enzymatic properties of XoxFs including the recombinant form have been indicated in genus Bradyrhizobium (Wang et al, 2019;Huang et al, 2019), and the physiological functions of XoxF and the Ln-dependent methanol metabolic pathway, in which XoxF participates, have become one of the targets for the study in the field of C1 microbiology.…”

“…Ce-3 and USDA110 grown on methanol with L-Ln species possessed Lndependent MDH (Fitriyanto et al, 2011a;Wang et al, 2019) and showed methanol utilization with supplementation of L-Ln species in the methanol medium (Wang et al, 2019;Pastawan et al, 2020). Both purified Ln-dependent MDHs exhibited sufficient methanol-oxidizing activities and contained L-Ln species as a cofactor in their subunits, similarly to XoxFs from strains in the Methylobacterium group (Fitriyanto et al, 2011a;Wang et al, 2019;Huang et al, 2019). Moreover, in the solution structure of the XoxF from strain USDA110 was analyzed by small angle Xray scattering (SAXS) analysis, suggesting that XoxF adopts a dimer structure in solution (Wang et al, 2019).…”

Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and function

“…These enzymes are aptly referred to as Ln-dependent alcohol dehydrogenases (Ln-ADHs) and their discovery has added Ln 3+ to the biological table of the elements (7,8,(10)(11)(12). A number of XoxF-type MDHs have been studied from methylotrophic bacteria, with analyses including X-ray crystallography and enzyme kinetics (7,9,(13)(14)(15)(16). ExaF EDH from the model methylotroph Methylorubrum (formerly Methylobacterium (17)) extorquens AM1 is currently the only representative reported from a methylotroph, though genes encoding putative ExaF homologs have been identified in a diverse set of organisms (8,18,19).…”

“…Phylogenetic analyses of XoxF-coding genes indicate they are wide-spread in the environment and can be grouped into at least 5 distinct clades with representatives in Alpha-, Beta-, and Gammaproteobacteria; Verrucomicrobia, and the NC10 phylum bacterium Candidatus "Methylomirabilis oxyfera" (20). Importantly, phylogenetic consideration of potential Ln 3+related genes led to two discoveries: 1 -bacteria previously reported to be non-methylotrophic, such as Bradyrhizobium diazoefficiens USDA110, can indeed grow methylotrophically using XoxF-type MDHs (15), and 2 -Ln-ADHs metabolize multicarbon compounds in methylotrophs and nonmethylotrophs, such as Pseudomonas putida KT2440 (8,21). These relatively recent discoveries underscore the relevance of Ln 3+ to microbial diversity and emphasize the importance of metal bioavailability on plant, soil, aquatic, and marine ecosystems-complex environments where Lnutilizing bacteria are major constituents (22)(23)(24)(25).…”