Gupta R S
Department of Biochemistry, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada.
Theor Popul Biol. 1998 Oct;54(2):91-104. doi: 10.1006/tpbi.1998.1376.
The three-domain proposal of Woese et al. (Proc. Natl. Acad. Sci. USA 87, 4576 (1990)) divides all living organisms into three primary groups or domains named Archaea (or archaebacteria), Bacteria (or eubacteria), and Eucarya (or eukaryotes), with Eucarya being relatives (or descendants) of Archaea. Although this proposal is currently widely accepted, sequence features and phylogenies derived from many highly conserved proteins are inconsistent with it and point to a close and specific relationship between archaebacteria and gram-positive bacteria, whereas gram-negative bacteria are indicated to be phylogenetically distinct. A closer relationship of archaebacteria to gram-positive bacteria in comparison to 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. 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, or that the ancestral eukaryotic cell directly descended from an archaea, is erroneous. These results call into question the validity of the currently popular three-domain proposal and the assignment of a domain status to archaebacteria. A new classifica- tion of organisms consistent with phenotype and macromolecular sequence data is proposed.
沃斯等人（《美国国家科学院院刊》87, 4576 (1990)）提出的三域学说将所有生物分为三个主要类别或域，即古菌（或古细菌）、细菌（或真细菌）和真核生物域（或真核生物），真核生物域是古菌的亲缘生物（或后代）。尽管这一学说目前已被广泛接受，但源自许多高度保守蛋白质的序列特征和系统发育关系与之并不相符，这些特征和关系表明古细菌与革兰氏阳性菌之间存在密切且特定的关系，而革兰氏阴性菌在系统发育上则有所不同。就大多数可用的基因/蛋白质序列而言，通常可以看到古细菌与革兰氏阳性菌的关系比与革兰氏阴性菌更为密切。为了解释这些结果，以及古细菌和革兰氏阳性菌都是被单层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（被单层膜包围）和双膜原核生物（即所有真正的革兰氏阴性菌，含有内膜和外膜）之间。这一划分与细胞形态和不同蛋白质中的特征序列均相符。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，认为古细菌和真核生物拥有一个排除真细菌的共同祖先，或者认为祖先真核细胞直接从古菌演化而来的假设是错误的。这些结果对当前流行的三域学说的有效性以及将古细菌归为一个域的分类提出了质疑。本文提出了一种与表型和大分子序列数据相一致的新的生物分类方法。
