Benachenhou-Lahfa N, Forterre P, Labedan B
Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France.
J Mol Evol. 1993 Apr;36(4):335-46. doi: 10.1007/BF00182181.
The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree.
通过对21条一级序列的比对以及对每对蛋白质之间相似性百分比的测定，推断出存在两个编码六聚体谷氨酸脱氢酶的基因家族。每个家族也可以通过特定的基序来表征。一个家族（家族I）由来自六种真细菌和六种低等真核生物（原始原生动物贾第虫、绿藻索氏小球藻以及几种真菌和酵母）的gdh基因组成。另一个家族（家族II）由来自两种真细菌、两种古细菌和五种高等真核生物（脊椎动物）的gdh基因组成。使用几种简约法和距离法重建系统发育树证实了这两个家族的存在。因此，这些结果强化了我们之前提出的假设，即在三个原界（真细菌、古细菌和真核生物）的最后一个共同祖先中存在两个相近但已不同的gdh基因。尽管根据分析区域略有不同，但无论采用何种树重建方法，家族I不同物种的分支顺序都是相同的。同样，家族II中真细菌和真核生物的拓扑位置与所使用的方法无关。然而，家族II中两种古细菌的分支情况似乎出乎意料：（1）嗜热嗜酸硫化叶菌在简约树和距离树中都与该家族的两种真细菌聚集在一起，这是最近提出的任何一个相互矛盾的树都没有预测到的情况；（2）嗜盐盐生盐杆菌的分支根据树构建方法而有所不同：在最大简约树中它更接近真细菌，而在距离树中更接近真核生物。因此，无论嗜盐物种的实际位置如何，在这些gdh基因树中古细菌似乎都不是单系的。这一结果质疑了目前对先前蛋白质树的公认解释的可靠性，这些蛋白质树本应明确地为生命的通用树确定根节点并将古细菌置于该树中。
