Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.
Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.
复制标题
DOI：
10.1186/1471-2164-15-679
复制
发表时间：
2014-08-13
期刊：
影响因子：
4.4
通讯作者：
Brugère JF
中科院分区：
文献类型：
--
作者：
Borrel G;Parisot N;Harris HM;Peyretaillade E;Gaci N;Tottey W;Bardot O;Raymann K;Gribaldo S;Peyret P;O'Toole PW;Brugère JF
第七目的产甲烷菌，Methanomassiliicoccales，已被确定在不同的厌氧环境，包括胃肠道（GIT）的人类和其他动物，并可能显着贡献甲烷排放和全球变暖。产甲烷菌属是一个由非产甲烷古菌谱系组成的大的进化分支，如热浆菌目、深海热液喷口宽古菌2（DHVE-2，Aciduliprofundum boonei）和海洋古菌群II（MG-II）。为了更好地理解这种新的秩序及其与其他古菌的关系，我们手动策划并广泛比较了来自人类GIT微生物群的三种代表性的Methanomassiliicoccales的基因组序列，“Methanomethylophilus alvus”，“Methanomassiliicoccus alvus”和Methanomassiliicoccus luminyensis。比较分析显示了非典型的功能，如分散的核糖体RNA基因的基因组和真核生物样的组蛋白基因的情况下，否则存在于大多数的广古菌基因组。先前在热浆菌目基因组中鉴定的这些特征目前扩展到这个大的进化分支的几个完全测序的基因组，包括MG-II和DHVE 2。这三个Methanomassiliicoccales基因组共享一个独特的基因组成，参与能源节约，这表明先前在其他产甲烷菌中描述的两个主要能源节约过程的原始组合。它们还显示出彼此之间的实质性差异，例如它们的密码子使用，它们的CRISPR系统的性质和起源以及可能涉及特定环境适应的基因。分枝杆菌基因组Luminyensis编码了几个特征，以在土壤和沉积物条件下茁壮成长，表明其环境分布比GIT更大。相反，“Ca。M. alvus”和“Ca. M.“插件”不提供这些功能，在GIT上可能会受到更多的限制和专门化。预测的琥珀密码子的使用，无论是作为终止信号的翻译或编码吡咯赖氨酸揭示对比模式之间的三个基因组，并建议不同的处理的Pyl编码能力。这项研究代表了第七阶产甲烷菌的基因组组织和代谢特征的第一个见解。这表明对比的三个分析的Methanomassiliicoccales代表的进化历史，并提供信息的整体产甲烷菌和热浆菌之间的保守特征。本文的在线版本（doi：10.1186/1471-2164-15-679）包含补充材料，可供授权用户使用。
A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, “Candidatus Methanomethylophilus alvus", “Candidatus Methanomassiliicoccus intestinalis” and Methanomassiliicoccus luminyensis. Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, “Ca. M. alvus” and “Ca. M. intestinalis” do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata. The online version of this article (doi:10.1186/1471-2164-15-679) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
3.7
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
通讯作者：
Kyrpides N
影响因子：
12.2
作者：
Brugère JF;Borrel G;Gaci N;Tottey W;O'Toole PW;Malpuech-Brugère C
通讯作者：
Malpuech-Brugère C
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
4.8
作者：
Bäumer, S;Ide, T;Deppenmeier, U
通讯作者：
Deppenmeier, U
影响因子：
56.9
作者：
FRASER, CM;GOCAYNE, JD;VENTER, JC
通讯作者：
VENTER, JC