Genomic characterization of methanomicrobiales reveals three classes of methanogens.
Genomic characterization of methanomicrobiales reveals three classes of methanogens.
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DOI：
10.1371/journal.pone.0005797
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发表时间：
2009-06-04
期刊：
影响因子：
3.7
通讯作者：
Kyrpides N
中科院分区：
文献类型：
--
作者：
Anderson I;Ulrich LE;Lupa B;Susanti D;Porat I;Hooper SD;Lykidis A;Sieprawska-Lupa M;Dharmarajan L;Goltsman E;Lapidus A;Saunders E;Han C;Land M;Lucas S;Mukhopadhyay B;Whitman WB;Woese C;Bristow J;Kyrpides N
甲烷微生物目是研究最少的产甲烷菌目。虽然在基于核糖体的系统发育分析中，这些生物似乎与甲烷肉芽胞菌目的亲缘关系更近，但它们在代谢上更接近I类产甲烷菌。为了提高我们对这一谱系的了解，我们对该目的两个成员--拉伯氏甲烷螺杆菌Z和马里斯尼格雷甲烷螺杆菌JR1的基因组进行了完整的测序，并将其与第三个成员--洪氏甲烷螺杆菌JF-1的基因组进行了比较。与I类产甲烷菌类似，甲烷微生物利用部分还原柠檬酸循环合成2-氧戊二酸，它们具有EHA能量转换氢酶。与甲烷假单胞菌一样，甲烷微生物假单胞菌具有Ech氢酶，它们中的至少一部分可能会将甲酰基甲烷呋喃的形成和异二硫化物还原与跨膜离子梯度偶联。独特的是，拉伯氏支原体和亨加特氏支原体含有类似于呋喃热链球菌MBH氢酶的氢酶，并且这三种甲烷微生物都含有其他产甲烷菌中没有的抗西格玛因子和抗西格玛因子调节蛋白。基于产甲烷和辅因子生物合成的7个核心蛋白的系统发育分析表明，甲烷微生物群与I类产甲烷菌和甲烷腐生菌等距离。我们的结果表明，甲烷微生物群不是类似于I类产甲烷菌或甲烷微生物群，而是具有两者的一些特征和一些独特的性质。我们发现有三类不同的产甲烷菌：第一类产甲烷菌、第二类甲烷微生物和第三类甲烷腐生菌。
Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).
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