Masuda Sachiko, Suzuki Yutaka, Fujitani Yoshiko, Mitsui Ryoji, Nakagawa Tomoyuki, Shintani Masaki, Tani Akio
Institute of Plant Science and Resources, Okayama University, Okayama, Japan.
Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency, Tokyo, Japan.
mSphere. 2018 Jan 24;3(1). doi: 10.1128/mSphere.00462-17. eCollection 2018 Jan-Feb.
species are representative of methylotrophic bacteria. Their genomes usually encode two types of methanol dehydrogenases (MDHs): MxaF and XoxF. The former is a Ca-dependent enzyme, and the latter was recently determined to be a lanthanide-dependent enzyme that is necessary for the expression of . This finding revealed the unexpected and important roles of lanthanides in bacterial methylotrophy. In this study, we performed transcriptome sequencing (RNA-seq) analysis using strain 22A grown in the presence of different lanthanides. Expression of and genes showed a clear inverse correlation in response to La. 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 La; 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. Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by was recently found to be lanthanide dependent, while the classic-type is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. 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.
这些物种是甲基营养型细菌的代表。它们的基因组通常编码两种类型的甲醇脱氢酶（MDH）：MxaF和XoxF。前者是一种依赖钙的酶，而后者最近被确定为一种依赖镧系元素的酶，这对于……的表达是必需的。这一发现揭示了镧系元素在细菌甲基营养中的意外且重要的作用。在本研究中，我们使用在不同镧系元素存在下生长的22A菌株进行了转录组测序（RNA-seq）分析。响应镧（La）时，……和……基因的表达呈现出明显的负相关。我们观察到，在镧存在下生长的细胞进行反应时，甲醛氧化途径下调、甲醛脱氢酶活性高且甲醛积累量低；这可能是由于XoxF1将甲醇直接氧化为甲酸所致。镧系元素诱导了富含AT的基因（其中大多数功能未知）以及可能与细胞存活相关的基因和其他MDH同源物的转录。这些结果不仅揭示了对改变的初级甲醇氧化的代谢反应，还揭示了为更好地理解镧系元素存在下的甲基营养而需进一步研究的可能靶点。镧系元素一直被认为对生物过程不重要。然而，在甲基营养型细菌中，最近发现由……编码的一种甲醇脱氢酶（MDH）依赖镧系元素，而经典类型的则依赖钙。XoxF型MDH在不同细菌属中更为广泛，表明它们对甲基营养很重要。……物种是叶际中典型的甲基营养型和占主导地位的α-变形菌，同时包含这两种类型，并根据镧系元素的可用性调节它们的表达。RNA-seq分析表明，这种调节不仅发生在MDH基因上，还发生在随后的甲醛氧化途径和呼吸链上，这可能是由于XoxF将甲醇直接氧化为甲酸所致。此外，发现大量功能未知的基因，包括富含AT的基因，在镧系元素存在下上调。本研究首次深入了解了甲基营养型细菌对镧系元素存在的特定反应，强调了这种痕量金属的生物学相关性。
