Martínez-Murcia A J, Antón A I, Rodríguez-Valera F
Centro de Biología Molecular y Celular, Facultad de Medicina, Universidad Miguel Hernández, Alicante, Spain.
Int J Syst Bacteriol. 1999 Apr;49 Pt 2:601-10. doi: 10.1099/00207713-49-2-601.
Sequence heterogeneities of variable positions located at regions V1 and V6 of 56 cloned 16S rRNA genes were determined from six Escherichia coli strains. These nucleotides were involved in secondary structure base-pairing of stem-loops. Compensatory and single mutations have occurred but secondary structure was conserved. Eight different sequences were found in the stem at region V1 indicating that in these sites mutation rates are higher than those of homogenizatin processes. Region V6 showed two different structures (V6-I and V6-II) although heterogeneities were determined in nine sites. Strains ECOR52 and ECOR56 only showed the V6-I sequence, ECOR35 showed V6-II, whereas clones from ECOR42 and ECOR49 showed both types of V6 structures. Results were confirmed by PCR using V6 sequence-specific probes. Stem V6-II was also found in 16S rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6-II seems to be homogenized in all rrn operons of the multigene family of strain ECOR35 producing effects of distortion in the molecular clock, similar to those that homoplasies could produce. V6 sequence-specific probes were applied to the 72 ECOR strains: half showed both V6-I and V6-II, and the rest had one or another. Only strain ECOR24 did not yield products in the PCR test and sequencing of 12 cloned 16S rRNA genes revealed a third form, V6-III, also found in the RDP. Concerted evolution by homogenization of the rRNA family may induce chronometric distortions responsible for a loss of ultrametricity in phylogenetic trees, particularly, of very closely related micro-organisms.
从6株大肠杆菌菌株中测定了56个克隆的16S rRNA基因V1和V6区域可变位置的序列异质性。这些核苷酸参与茎环的二级结构碱基配对。发生了补偿性和单突变，但二级结构得以保留。在V1区域的茎中发现了8种不同的序列，表明这些位点的突变率高于均一化过程的突变率。V6区域显示出两种不同的结构（V6-I和V6-II），尽管在9个位点测定了异质性。菌株ECOR52和ECOR56仅显示V6-I序列，ECOR35显示V6-II，而来自ECOR42和ECOR49的克隆显示两种类型的V6结构。使用V6序列特异性探针通过PCR证实了结果。在属于远缘分类群的RDP（核糖体数据库项目）中保存的16S rRNA序列中也发现了茎V6-II；祖先序列V6-II似乎在菌株ECOR35多基因家族的所有rrn操纵子中均一化，从而在分子钟中产生扭曲效应，类似于同塑性可能产生的效应。将V6序列特异性探针应用于72株ECOR菌株：一半显示V6-I和V6-II，其余的具有其中一种。只有菌株ECOR24在PCR测试中未产生产物，对12个克隆的16S rRNA基因进行测序揭示了第三种形式V6-III，在RDP中也有发现。rRNA家族通过均一化的协同进化可能会导致计时扭曲，从而导致系统发育树中失去超度量性，特别是对于密切相关的微生物。
