Unusual biology across a group comprising more than 15% of domain Bacteria
Unusual biology across a group comprising more than 15% of domain Bacteria
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DOI：
10.1038/nature14486
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发表时间：
2015-07-09
期刊：
影响因子：
64.8
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
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作者：
Brown, Christopher T.;Hug, Laura A.;Banfield, Jillian F.
细菌域的一个突出特征是被定义为候选门的主要谱系的辐射，因为它们缺乏孤立的代表。来自这些门的细菌存在于不同的环境中（1），并被认为介导碳和氢循环（2）。一些代表的基因组分析表明，代谢限制阻止了他们的培养（2-6）。在这里，我们重建了8个完整的基因组和789个来自细菌的基因组草案，代表了>35个门，并记录了将这些生物体与其他细菌区分开来的特征。我们推断，这组，其中可能包括>（1）5%的细菌域，有共同的进化历史，并描述为候选门辐射（CPR）。所有CPR基因组都很小，大多数缺乏许多生物合成途径。由于不同的16 S核糖体RNA（rRNA）基因序列，50-100%的生物样品从特定的门将逃避检测，在典型的培养无关的调查。CPR生物体通常在其rRNA基因中编码有自我剪接内含子和蛋白质，这在细菌中很少报道。此外，它们具有不寻常的核糖体组成。所有这些都缺少一种核糖体蛋白，这种蛋白在共生体中通常不存在，而特定的谱系缺少核糖体蛋白和被认为在细菌中普遍存在的生物发生因子。这意味着不同的核糖体结构和生物发生机制，并强调了细菌大部分领域的不寻常生物学。
A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments(1) and are thought to mediate carbon and hydrogen cycles(2). Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation(2-6). Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >(1)5% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.