Regulation of lanthanide-dependent methanol oxidation pathway in the legume symbiotic nitrogen-fixing bacterium Bradyrhizobium sp. strain Ce-3.

Viagian Pastawan, Soya Suganuma, Kosuke Mizuno, Lun Wang, Akio Tani, Ryoji Mitsui, Kohei Nakamura, Masaya Shimada, Takashi Hayakawa, Nanung Agus Fitriyanto, Tomoyuki Nakagawa

Journal of bioscience and bioengineering 2020 Dec

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Lanthanide (Ln)-dependent XoxF-type methanol dehydrogenase (MDH) genes can be found in bacteria that are not believed to be methylotrophs, and studies on their methylotrophic pathways and their use of Ln are now emerging. Ln-dependent methanol utilization in Bradyrhizobium sp. strain Ce-3, which belongs to the Bradyrhizobium elkanii superclade (clade II), was investigated in this study. Strain Ce-3 was able to grow in a media containing methanol as a sole carbon source and light Ln (L-Ln, i.e., La3+, Ce3+, Pr3+, and Nd3+), whereas the strain did not show any growth with Ca2+ or the heavy Ln, Sm3+. We found that the uptake of L-Ln is enhanced mainly by methanol and L-Ln species, and the strain incorporates each L-Ln species evenly into the cell. The genome of strain Ce-3 encodes the xox cluster for Ln-dependent methanol dehydrogenase (xoxF) and the enzymes participating in the methanol oxidation pathway (xoxG, fldA, and gfaA) and regulation (xoxR), but the gene encoding formate dehydrogenase (FDH) was not found in the cluster. MDH, formaldehyde dehydrogenase, and FDH activities were induced by methanol/Ln. Moreover, expression of the genes on the xox cluster was upregulated by methanol/Ln. Based on these results, we concluded that strain Ce-3 possesses a complete L-Ln-dependent methanol oxidation pathway, which is dissimilar to plant phyllospheric bacteria, Methylobacterium species, with a transport system for L-Ln species. Copyright © 2020 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Citation

Viagian Pastawan, Soya Suganuma, Kosuke Mizuno, Lun Wang, Akio Tani, Ryoji Mitsui, Kohei Nakamura, Masaya Shimada, Takashi Hayakawa, Nanung Agus Fitriyanto, Tomoyuki Nakagawa. Regulation of lanthanide-dependent methanol oxidation pathway in the legume symbiotic nitrogen-fixing bacterium Bradyrhizobium sp. strain Ce-3. Journal of bioscience and bioengineering. 2020 Dec;130(6):582-587