Lv Haoxin, Tani Akio
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Japan.
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki 710-0046, Japan.
J Biosci Bioeng. 2018 Dec;126(6):667-675. doi: 10.1016/j.jbiosc.2018.05.023. Epub 2018 Jun 15.
Oharaeibacter diazotrophicus strain SM30, isolated from rice rhizosphere, is an aerobic, facultative lanthanide (Ln)-utilizing methylotroph and diazotroph that belongs to the Methylocystaceae family. In this research, the complete genome sequence of strain SM30 was determined, and its methylotrophy modules were characterized. The genome consists of one chromosome and two plasmids, comprising a total of 5,004,097 bp, and the GC content was 71.6 mol%. A total of 4497 CDSs, 67 tRNA, and 9 rRNA were encoded. Typical alpha-proteobacterial methylotrophy genes were found: pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) (mxaF and xoxF1-4), methylotrophy regulatory proteins (mxbDM and mxcQE), PQQ synthesis, HF pathway, HMPT pathway, formate oxidation, serine cycle, and ethylmalonyl-CoA pathway. SDS-PAGE and subsequent LC-MS analysis, and qPCR analysis revealed that MxaF and XoxF1 were the dominant MDH in the absence or presence of lanthanum (La), respectively. The growth of MDH gene-deletion mutants on alcohols and qPCR results indicated that mxaF and xoxF1 are also involved in ethanol and propanol oxidation, xoxF2 participates in methanol oxidation in the presence of La, while xoxF3 was associated with methanol and ethanol oxidation in the absence of La, implying that XoxF3 is a calcium (Ca)-binding XoxF. Four Ln such as La, cerium (Ce), praseodymium (Pr), and neodymium (Nd) served as cofactors for XoxF1 by supporting ΔmxaF growth on methanol. Some heavier lanthanides inhibited growth of SM30 on methanol. This study contributes to the understanding of the function of various XoxF-type MDHs and their roles in methylotrophs.
从水稻根际分离出的重氮营养大贺杆菌菌株SM30是一种需氧的、兼性利用镧系元素（Ln）的甲基营养菌和固氮菌，属于甲基孢囊菌科。在本研究中，测定了菌株SM30的全基因组序列，并对其甲基营养模块进行了表征。该基因组由一条染色体和两个质粒组成，总共5,004,097 bp，GC含量为71.6 mol%。共编码了4497个编码序列（CDS）、67个tRNA和9个rRNA。发现了典型的α-变形菌甲基营养基因：吡咯喹啉醌（PQQ）依赖性甲醇脱氢酶（MDH）（mxaF和xoxF1 - 4）、甲基营养调节蛋白（mxbDM和mxcQE）、PQQ合成、HF途径、HMPT途径、甲酸氧化、丝氨酸循环和乙基丙二酰辅酶A途径。SDS-PAGE及后续的LC-MS分析和qPCR分析表明，在不存在或存在镧（La）的情况下，MxaF和XoxF1分别是主要的MDH。MDH基因缺失突变体在醇类上的生长情况和qPCR结果表明，mxaF和xoxF1也参与乙醇和丙醇氧化，xoxF2在存在La的情况下参与甲醇氧化，而xoxF3在不存在La的情况下与甲醇和乙醇氧化有关，这意味着XoxF3是一种钙（Ca）结合型XoxF。镧（La）、铈（Ce）、镨（Pr）和钕（Nd）这四种镧系元素通过支持ΔmxaF在甲醇上的生长，作为XoxF1的辅因子。一些较重的镧系元素抑制了SM30在甲醇上的生长。本研究有助于理解各种XoxF型MDH的功能及其在甲基营养菌中的作用。
