The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification
复制标题
DOI：
10.1099/00207713-52-1-7
复制
发表时间：
2002-01-01
影响因子：
2.8
通讯作者：
Cavalier-Smith, T
中科院分区：
文献类型：
--
作者：
Cavalier-Smith, T
原核生物构成一个单一的界，细菌，在这里分为两个新的亚界：负细菌，具有两种不同的遗传膜的细胞被膜，和单细菌，包括新的门古细菌和Posibacteria，只有一个。其他新的细菌分类群建立在一个修订的更高级别的分类，承认只有8门和29类。形态学，古生物学和分子数据被整合到一个统一的图片大规模的细菌细胞进化，尽管偶尔横向基因转移。古细菌和真核生物包括进化枝neomura，具有许多共同特征，特别是N-连接糖蛋白的专性共翻译分泌，具有75个RNA和抑制-停滞结构域的信号识别颗粒，蛋白质剪接的tRNA内含子，八亚基伴侣蛋白，前折叠蛋白，核心组蛋白，小核仁核糖核蛋白（snoRNP），外泌体和类似的复制，修复，转录和翻译机制。真细菌（Posibacteria和Negibacteria）是并系的，新穆拉菌（neomura）起源于新亚门放线菌（Actinobacteria）中的Posibacteria（可能来自新的Arabobacteria纲，真核生物胆固醇的生物合成可能来自该纲）。真细菌肽聚糖被糖蛋白取代和嗜热性适应是新小鼠起源的关键。所有19种常见的新穆拉特征套件可能基本上是在放线菌的激进修改过程中同时出现的。至少有11个可以说是适应嗜热性。最独特的古细菌特征（异戊二烯醚脂质;鞭毛轴的糖蛋白，而不是鞭毛蛋白; DNA结合蛋白10 b;特别修饰的tRNA;缺乏热休克蛋白90）是随后的第二次适应hyperthermophily和/或hyperacidic。蛋白质剪接的tRNA内含子的插入起源和质子泵ATP酶的插入也支持neomura来自真细菌。组蛋白和DNA处理蛋白之间的分子协同进化，以及在新的蛋白质起始和分泌机制中，引起了干新尾类中它们的性质的量子进化转变。蛋白酶体可能起源于新尾菌和放线菌的直接共同祖先。主要的基因丢失（如肽聚糖合成，热休克蛋白90，secA）和基因组减少的核心古细菌的起源。祖先的古细菌可能是异养，厌氧，硫依赖hyperthermoacidophiles;甲烷和嗜盐是次要的衍生。来自真细菌的多个横向基因转移有助于次级古细菌适应中温性和基因组再扩增。从一个急剧改变的新村放线菌的起源，以及紧接着的古细菌和真核生物的同时起源，是自细胞开始以来量子进化的最极端和最重要的案例。这三个特征都惊人地支持了De Beer的马赛克进化原理：在重大的进化转变过程中，一些有机体特征具有高度的创新性，变化非常迅速，而另一些则基本上是静态的，在自然界中保持保守的祖先。这种表型镶嵌现象在分类群中创造了特征分布，这对于那些错误地期望特征和谱系之间具有统一进化速率的人来说是令人困惑的。古细菌中新的（新穆拉或古细菌）和祖先真细菌样特征的混合物主要反映了这种垂直镶嵌进化，而不是通过横向基因转移的嵌合进化。基本的新穆拉特征的量子进化，以及基因复制树中姐妹旁系同源物之间的量子进化，使得许多序列树大大夸大了古细菌的表观年龄。化石证据是令人信服的真细菌的极端古老[超过35亿年（My）]，但是，像他们的真核生物姐妹篇一样，古细菌可能只出现在850 My前。阴性杆菌是最古老的;迅速辐射成六门。从分子序列、超微结构、光合作用的进化、包膜结构和化学以及运动机制等方面的证据表明，cenortistic细胞是一种光合负杆菌属，特别是一种厌氧绿色非硫细菌，而且通用树植根于硫细菌和非硫绿色细菌之间的分歧。负细菌的外膜在生命的历史上只丢失过一次，那是在大约2800万年前Posibacteria从蓝细菌分化出来后出现的。
Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms: Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 75 RNA and translation-arrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids; flagellar shaft of glycoprotein, not flagellin; DNA-binding protein 10b; specially modified tRNA; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution: the fact that, during major evolutionary transformations, some organismal characters are highly innovative and change remarkably swiftly, whereas others are largely static, remaining conservatively ancestral in nature. This phenotypic mosaicism creates character distributions among taxa that are puzzling to those mistakenly expecting uniform evolutionary rates among characters and lineages. The mixture of novel (neomuran or archaebacterial) and ancestral eubacteria-like characters in archaebacteria primarily reflects such vertical mosaic evolutionnot chimaeric evolution by lateral gene transfer. No symbiogenesis occurred.Quantum evolution of the basic neomuran characters, and between sister paralogues in gene duplication trees, makes many sequence trees exaggerate greatly the apparent age of archaebacteria. Fossil evidence is compelling for the extreme antiquity of eubacteria [over 3500 million years (My)] but, like their eukaryote sisters, archaebacteria probably arose only 850 My ago. Negibacteria are the most ancient; radiating rapidly into six phyla. Evidence from molecular sequences, ultrastructure, evolution of photosynthesis, envelope structure and chemistry and motility mechanisms fits the view that the cenancestral cell was a photosynthetic negibacterium, specifically an anaerobic green non-sulphur bacterium, and that the universal tree is rooted at the divergence between sulphur and non-sulphur green bacteria. The negibacterial outer membrane was lost once only in the history of life, when Posibacteria arose about 2800 My ago after their ancestors diverged from Cyanobacteria.