Gupta R S
Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada.
Mol Microbiol. 1998 Aug;29(3):695-707. doi: 10.1046/j.1365-2958.1998.00978.x.
The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/ protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G+C Gram-positive bacteria are phylogenetically distinct from the high-G+C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also show that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a Gram-negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria is not supported. These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal.
基于特征序列（定义为特定分类群共有的保守插入或缺失）以及源自不同蛋白质的系统发育关系，对原核生物内部的进化关系进行了研究。许多与信息传递过程相关的蛋白质表明古细菌是单系的。相比之下，对于其他几种高度保守的蛋白质，古细菌和革兰氏阳性菌中存在共同的特征序列，而革兰氏阴性菌则表现出明显的差异。对于这些蛋白质，古细菌并未形成一个系统发育上独特的分支，而是在革兰氏阳性菌中呈现多系分支。与革兰氏阴性菌相比，从大多数可用的基因/蛋白质序列来看，普遍认为古细菌与革兰氏阳性菌的关系更为密切。为了解释这些结果以及古细菌和革兰氏阳性菌都是被单一细胞膜包围的原核生物这一事实，我提出原核生物的主要划分是在单膜原核生物（被单一膜包围）和双膜原核生物（即所有真正的革兰氏阴性菌，包含内膜和外膜）之间。这一观点与细胞形态以及不同蛋白质中的特征序列均相符。对古细菌在某些基因上的单系性质以及其他人提出的它们在革兰氏阳性菌中的多系分支进行了严格审查，并提出了几种解释，包括古细菌因抗生素选择压力从革兰氏阳性菌演化而来。蛋白质中的特征序列还表明，低G + C含量的革兰氏阳性菌在系统发育上与高G + C含量的革兰氏阳性菌群不同，并且双膜原核生物（即革兰氏阴性菌）似乎是从后一组演化而来的。蛋白质系统发育和特征序列还表明，所有真核细胞都从一种古细菌和一种革兰氏阴性真细菌中获得了重要的基因贡献。因此，古细菌和真核生物共享一个排除真细菌的共同祖先这一假设并不成立。这些观察结果为不同于当前流行的三域学说的另一种生物进化关系观点提供了证据。
