Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.
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DOI：
10.1186/1745-6150-3-26
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发表时间：
2008-07-01
期刊：
影响因子：
5.5
通讯作者：
Alam M
中科院分区：
文献类型：
--
作者：
Hou S;Makarova KS;Saw JH;Senin P;Ly BV;Zhou Z;Ren Y;Wang J;Galperin MY;Omelchenko MV;Wolf YI;Yutin N;Koonin EV;Stott MB;Mountain BW;Crowe MA;Smirnova AV;Dunfield PF;Feng L;Wang L;Alam M
疣微菌门是一个分布广泛但特征不明确的细菌分支。尽管独立于培养的方法可以在多种环境中检测到该门的代表，包括土壤、海水、温泉和人类胃肠道，但在纯培养中仅分离出少数。我们最近报道了从新西兰地狱之门地热区分离出的疣微菌属极度嗜酸甲烷氧化菌菌株 V4 的培养和初步表征。类似的生物体是从意大利和俄罗斯的地热系统中独立分离出来的。我们报告了菌株 V4 的完整基因组序列，这是疣微菌属代表的第一个菌株。分离株 V4 最初被命名为“Mmethylokorus infernorum”（最近更名为 Mmethylacidiphilum infernorum），是一种自养细菌，其基因组精简为约 2.3 Mbp，编码简单的信号转导途径，并且调节基因表达的潜力有限。与其他已知的甲基营养生物相比，M. infernorum 的中央代谢几乎完全重建，并揭示了自养中央代谢的高度互连途径和 C1 利用途径的修改。 M. infernorum 基因组不编码先前在 Prosthecobacter 属细菌中发现的微管蛋白，也不编码任何其他标志性真核蛋白的密切同源物。核糖体蛋白和 RNA 聚合酶亚基的系统发育分析明确支持将浮霉菌、疣微菌和衣原体归为一个进化枝，即 PVC 超门，尽管这三个组的成员的基因含量显着不同。比较基因组分析表明，M. infernorum 谱系的进化涉及与多种细菌的广泛水平基因交换。地狱火的基因组表现出明显的适应极端酸性条件的能力，包括蛋白质等电点的大幅上移。 M. infernorum 的基因组分析结果支持 PVC 超门的单系性。地狱火拥有精简的基因组，但似乎已经获得了许多基因，包括通过水平基因转移（特别是来自变形菌）的甲基营养途径酶的基因。本文由 John A. Fuerst、Ludmila Chistoserdova 和 Radhey S. Gupta 审阅。
The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
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影响因子：
9.8
作者：
Devos D;Dokudovskaya S;Alber F;Williams R;Chait BT;Sali A;Rout MP
通讯作者：
Rout MP
DOI：
10.1099/00221287-143-5-1729
发表时间：
1997-05-01
期刊：
MICROBIOLOGY-UK
影响因子：
--
作者：
Chistoserdova, L;Lidstrom, ME
通讯作者：
Lidstrom, ME
影响因子：
4.4
作者：
Fuchsman, Clara A.;Rocap, Gabrielle
通讯作者：
Rocap, Gabrielle
影响因子：
10.7
作者：
Bapteste, E.;Susko, E.;Doolittle, W. F.
通讯作者：
Doolittle, W. F.
影响因子：
3.9
作者：
Bauer, M;Lombardot, T;Glöckner, F
通讯作者：
Glöckner, F