Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli

Abstract

Sequence heterogeneities of variable positions located a t 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 a t region V1 indicating that in these sites mutation rates are higher than those of homogenization processes. Region V6 showed two different structures (V6-I and V6-ll) although heterogeneities were determined in nine sites. Strains ECOR52 and ECOR56 only showed the V6-I sequence, ECOR35 showed V6-ll, whereas clones from ECOR42 and ECOR49 showed both types of V6 structures. Results were confirmed b y PCR using V6 sequence-specific probes. Stem V6-ll was also found in 165 rRNA sequences deposited in the RDP (Ribosomal Database Project) belonging to distantly related taxa; ancestral sequence V6-II seems to be homogenized in all rm 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-specif ic probes were applied to the 72 ECOR strains: half showed both V6-I and V6-ll, and the rest had one or another. Only strain ECOR24 did not yield products in the PCR test and sequencing of 12 cloned 165 rRNA genes revealed a third form, V6-Ill, 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.

Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies

“…Furthermore, intragenomic heterogeneity in the form of nucleotide differences between 16S rDNA copies, so-called microheterogeneity, has been described in few cases. For example, microheterogeneity has been identified in Escherichia coli (7,31), Mycobacterium terrae (34), Paenibacillus polymyxa (36), members of the class Mollicutes (14,23,39), and the Actinomycetales Thermomonospora chromogena (53), Thermobispora bispora (38), and Streptomyces spp. (49).…”

Aeromonas bivalvium sp. nov., isolated from bivalve molluscs

“…Oligonucleotide primers used for PCR amplification and sequencing of the 16S rRNA gene were those described by Martínez-Murcia et al (1999). DNA was subjected to PCR amplification in a total volume of 50 ml that contained 50 mM KCl, 15 mM Tris/ HCl (pH 8.0), 1.5 mM MgCl 2 , 0.2 mM each dNTP (Amersham Biosciences), 1.25 U AmpliTaq Gold DNA polymerase (Applera) and 25 pmol each primer.…”

Aeromonas molluscorum sp. nov., isolated from bivalve molluscs

“…Oligonucleotide primers used for PCR amplification and sequencing of the 16S rRNA gene were those described by Martínez-Murcia et al (1999). DNA was subjected to PCR amplification in a total volume of 50 ml that contained 50 mM KCl, 15 mM Tris/HCl (pH 8?0), 1?5 mM MgCl 2 , 0?2 mM each deoxyribonucleotide (dATP, dCTP, dGTP, dTTP; Amersham Biosciences), 1?25 U AmpliTaq Gold DNA polymerase (Applera) and 25 pmol each primer.…”