Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2.
Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2.
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DOI：
10.1371/journal.pone.0074767
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Liesack W
中科院分区：
文献类型：
--
作者：
Dam B;Dam S;Blom J;Liesack W
甲基孢囊菌SC2菌株对甲烷浓度的适应范围较宽。这是由于颗粒甲烷单加氧酶的两种同工酶的存在，表现出不同的甲烷氧化动力学。为了深入了解潜在的遗传信息，对其基因组进行了测序，发现其包含一条3.77 Mb的染色体和两个大质粒。我们报告了SC2菌株基因组的重要特征。它的序列与其他七个甲烷氧化菌基因组，包括成员的α-变形菌，γ-变形菌，和Verrucomicrobia进行比较。虽然所有八个甲烷氧化菌基因组的泛基因组总计19，358个CDS，但只有154个CDS是共享的。核心基因的数量随着系统发育相关性的增加而增加：328个CDS用于变形菌甲烷氧化菌，1，853个CDS用于三个α变形菌甲基囊菌科成员，甲基囊菌菌株SC 2和菌株Rockwell，以及发孢甲基弯菌OB 3b。通过比较研究和生理试验，验证了菌株SC 2具有多样的氮代谢能力。与涉及N2固定的34个基因的完整互补相对应，发现菌株SC2以大气N2作为唯一氮源生长，优选在低氧浓度下生长。反硝化介导的积累0.7纳摩尔30 N2/小时/毫克细胞干重缺氧条件下的示踪剂分析检测。N2的产生与质粒携带的一氧化氮和一氧化二氮还原酶的活性有关。菌株SC2中存在完整的反硝化途径，包括质粒编码的nosRZDFYX操纵子，在已知的甲烷氧化菌中是独特的。然而，这一途径的确切生理生态作用仍有待阐明。有毒的氮化合物的脱氮和在氧限制条件下的能量保存是可能的作用之一。可能刺激进一步研究的相关特征是，例如，菌株SC 2中不存在CRISPR/Cas系统，菌株OB 3b中大量的铁获取系统，以及菌株Rockwell中大量的转座酶。
Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol 30N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.
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影响因子：
3.3
作者：
Belova, Svetlana E.;Baani, Mohamed;Dedysh, Svetlana N.
通讯作者：
Dedysh, Svetlana N.
影响因子：
4.2
作者：
Braker, Gesche;Schwarz, Julia;Conrad, Ralf
通讯作者：
Conrad, Ralf
影响因子：
4.4
作者：
Dam, Bomba;Kube, Michael;Liesack, Werner
通讯作者：
Liesack, Werner
影响因子：
5.1
作者：
Chen, Yin;Dumont, Marc G.;Murrell, J. Colin
通讯作者：
Murrell, J. Colin
影响因子：
3.2
作者：
Chen, Yin;Crombie, Andrew;Dunfield, Peter F.
通讯作者：
Dunfield, Peter F.