Sequence heterogeneities of variable positions located at regions V1 and V6 56 cloned 16S rRNA genes were determined from six strain These nucleotides were involved in secondary structure base-pairing of stem-loops. Compensatory and single mutations have occurred but seconat structure was conserved. Eight different sequences were found in the stem a region V1 indicating that in these sites mutation rates are higher than those homogenization 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 structre Results were confirmed by PCR using V6 sequence-specific probes. Stem V6-I was also found in 16S rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6 seems to be homogenized in all operons of the multigene family of ECOR35 producing effects of distortion in the molecular clock, similar to tho 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 fami may induce chronometric distortions responsible for a loss of ultrametricity phylogenetic trees, particularly, of very closely related micro-organisms.


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