Jenkins C, Fuerst J A
Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA.
J Mol Evol. 2001 May;52(5):405-18. doi: 10.1007/s002390010170.
Sequences from the tuf gene coding for the elongation factor EF-Tu were amplified and sequenced from the genomic DNA of Pirellula marina and Isosphaera pallida, two species of bacteria within the order Planctomycetales. A near-complete (1140-bp) sequence was obtained from Pi. marina and a partial (759-bp) sequence was obtained for I. pallida. Alignment of the deduced Pi. marina EF-Tu amino acid sequence against reference sequences demonstrated the presence of a unique 11-amino acid sequence motif not present in any other division of the domain Bacteria. Pi. marina shared the highest percentage amino acid sequence identity with I. pallida but showed only a low percentage identity with other members of the domain Bacteria. This is consistent with the concept of the planctomycetes as a unique division of the Bacteria. Neither primary sequence comparison of EF-Tu nor phylogenetic analysis supports any close relationship between planctomycetes and the chlamydiae, which has previously been postulated on the basis of 16S rRNA. Phylogenetic analysis of aligned EF-Tu amino acid sequences performed using distance, maximum-parsimony, and maximum-likelihood approaches yielded contradictory results with respect to the position of planctomycetes relative to other bacteria. It is hypothesized that long-branch attraction effects due to unequal evolutionary rates and mutational saturation effects may account for some of the contradictions.
从浮霉菌目(Planctomycetales)中的两个细菌物种——海生梨形菌(Pirellula marina)和苍白等球藻(Isosphaera pallida)的基因组DNA中扩增并测序了编码延伸因子EF-Tu的tuf基因序列。从海生梨形菌中获得了一个近乎完整的(1140 bp)序列,从苍白等球藻中获得了一个部分(759 bp)序列。将推导的海生梨形菌EF-Tu氨基酸序列与参考序列进行比对,结果表明存在一个独特的11个氨基酸的序列基序,该基序在细菌域的任何其他分类中均不存在。海生梨形菌与苍白等球藻的氨基酸序列一致性百分比最高,但与细菌域的其他成员的一致性百分比仅较低。这与浮霉菌作为细菌的一个独特分类的概念是一致的。无论是EF-Tu的一级序列比较还是系统发育分析,都不支持浮霉菌与衣原体之间存在任何密切关系,而此前基于16S rRNA曾假定它们之间存在这种关系。使用距离法、最大简约法和最大似然法对排列好的EF-Tu氨基酸序列进行系统发育分析,得出了关于浮霉菌相对于其他细菌的位置的相互矛盾的结果。据推测,由于进化速率不均等导致的长枝吸引效应和突变饱和效应可能是造成部分矛盾的原因。