Lanthanide-Dependent Regulation of Methylotrophy in Methylobacteriumaquaticum Strain 22A

Sachiko Masuda; Yutaka Suzuki; Yoshiko Fujitani; Ryoji Mitsui; Tomoyuki Nakagawa; Masaki Shintani; Akio Tani

doi:10.1128/mSphere.00462-17

Lanthanide-Dependent Regulation of Methylotrophy in Methylobacteriumaquaticum Strain 22A

mSphere. 2018 Jan 24;3(1):e00462-17. doi: 10.1128/mSphere.00462-17. eCollection 2018 Jan-Feb.

Authors

Sachiko Masuda^{1

2}, Yutaka Suzuki³, Yoshiko Fujitani¹, Ryoji Mitsui⁴, Tomoyuki Nakagawa⁵, Masaki Shintani⁶, Akio Tani¹

Affiliations

¹ Institute of Plant Science and Resources, Okayama University, Okayama, Japan.
² Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency, Tokyo, Japan.
³ Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, Japan.
⁴ Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama, Japan.
⁵ Faculty of Applied Biological Science, Gifu University, Gifu, Japan.
⁶ Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.

Abstract

Methylobacterium species are representative of methylotrophic bacteria. Their genomes usually encode two types of methanol dehydrogenases (MDHs): MxaF and XoxF. The former is a Ca²⁺-dependent enzyme, and the latter was recently determined to be a lanthanide-dependent enzyme that is necessary for the expression of mxaF. This finding revealed the unexpected and important roles of lanthanides in bacterial methylotrophy. In this study, we performed transcriptome sequencing (RNA-seq) analysis using M. aquaticum strain 22A grown in the presence of different lanthanides. Expression of mxaF and xoxF1 genes showed a clear inverse correlation in response to La³⁺. We observed downregulation of formaldehyde oxidation pathways, high formaldehyde dehydrogenase activity, and low accumulation of formaldehyde in the reaction with cells grown in the presence of La³⁺; this might be due to the direct oxidation of methanol to formate by XoxF1. Lanthanides induced the transcription of AT-rich genes, the function of most of which was unknown, and genes possibly related to cellular survival, as well as other MDH homologues. These results revealed not only the metabolic response toward altered primary methanol oxidation, but also the possible targets to be investigated further in order to better understand methylotrophy in the presence of lanthanides. IMPORTANCE Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by xoxF was recently found to be lanthanide dependent, while the classic-type mxaFI is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. Methylobacterium species, representative methylotrophic and predominating alphaproteobacteria in the phyllosphere, contain both types and regulate their expression depending on the availability of lanthanides. RNA-seq analysis showed that the regulation takes place not only for MDH genes but also the subsequent formaldehyde oxidation pathways and respiratory chain, which might be due to the direct oxidation of methanol to formate by XoxF. In addition, a considerable number of genes of unknown function, including AT-rich genes, were found to be upregulated in the presence of lanthanides. This study provides first insights into the specific reaction of methylotrophic bacteria to the presence of lanthanides, emphasizing the biological relevance of this trace metal.

Keywords: lanthanide; methanol dehydrogenase; methylotrophs; xoxF.