scholarly journals Intraspecific Diversity of the 23S rRNA Gene and the Spacer Region Downstream in Escherichia coli

1999 ◽  
Vol 181 (9) ◽  
pp. 2703-2709 ◽  
Author(s):  
Ana I. Antón ◽  
Antonio J. Martínez-Murcia ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Escherichia Coli ◽  
Gene Families ◽  
Intraspecific Diversity ◽  
Rrna Genes ◽  
23S Rrna ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Enzyme Electrophoresis ◽  
Single Mutation ◽  
23S Rrna Gene

ABSTRACT The molecular microevolution of the 23S rRNA gene (rrl) plus the spacer downstream has been studied by sequencing of different operons from some representative strains of the Escherichia coli ECOR collection. The rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16S rRNA gene (rrs) in a previous study. The size of the gene was highly conserved (2902 to 2905 nucleotides). Most polymorphic sites were clustered in five secondary-structure helices. Those regions in a large number of operons were sequenced, and several variations were found. Sequences of the same helix from two different strains were often widely divergent, and no intermediate forms existed. Intercistronic variability was detected, although it seemed to be lower than for the rrs gene. The presence of two characteristic sequences was determined by PCR analysis throughout all of the strains of the ECOR collection, and some correlations with the multilocus enzyme electrophoresis clusters were detected. The mode of variation of the rrl gene seems to be quite similar to that of therrs gene. Homogenization of the gene families and transfer of sequences from different clonal lines could explain this pattern of variation detected; perhaps these factors are more relevant to evolution than single mutation. The spacer region between the 23S and 5S rRNA genes exhibited a highly polymorphic region, particularly at the 3′ end.

scholarly journals Intraspecific Diversity of the 23S rRNA Gene and the Spacer Region Downstream in Escherichia coli

1999 ◽  
Vol 181 (14) ◽  
pp. 4442-4442
Author(s):  
Ana I. Antón ◽  
Antonio J. Martínez-Murcia ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Escherichia Coli ◽  
Intraspecific Diversity ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene

scholarly journals Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21

2001 ◽  
Vol 183 (14) ◽  
pp. 4382-4385 ◽  
Author(s):  
Steven T. Gregory ◽  
Jamie H. D. Cate ◽  
Albert E. Dahlberg
Keyword(s):  
Genetic Manipulation ◽  
Thermus Thermophilus ◽  
Resistance Mutation ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
23S Rrna Gene ◽  
Resistant Mutants ◽  
23S Rrna Genes

ABSTRACT Spontaneous, erythromycin-resistant mutants of Thermus thermophilus IB-21 were isolated and found to carry the mutation A2058G in one of two 23S rRNA operons. The heterozygosity of these mutants indicates that A2058G confers a dominant or codominant phenotype in this organism. This mutation provides a valuable tool for the genetic manipulation of the 23S rRNA genes ofThermus.

scholarly journals Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis

2010 ◽  
Vol 60 (4) ◽  
pp. 737-748 ◽  
Author(s):  
Rafael R. de la Haba ◽  
David R. Arahal ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Group 2 ◽  
Group 1

A phylogenetic study of the family Halomonadaceae was carried out based on complete 16S rRNA and 23S rRNA gene sequences. Several 16S rRNA genes of type strains were resequenced, and 28 new sequences of the 23S rRNA gene were obtained. Currently, the family includes nine genera (Carnimonas, Chromohalobacter, Cobetia, Halomonas, Halotalea, Kushneria, Modicisalibacter, Salinicola and Zymobacter). These genera are phylogenetically coherent except Halomonas, which is polyphyletic. This genus comprises two clearly distinguished clusters: group 1 includes Halomonas elongata (the type species) and the species Halomonas eurihalina, H. caseinilytica, H. halmophila, H. sabkhae, H. almeriensis, H. halophila, H. salina, H. organivorans, H. koreensis, H. maura and H. nitroreducens. Group 2 comprises the species Halomonas aquamarina, H. meridiana, H. axialensis, H. magadiensis, H. hydrothermalis, H. alkaliphila, H. venusta, H. boliviensis, H. neptunia, H. variabilis, H. sulfidaeris, H. subterranea, H. janggokensis, H. gomseomensis, H. arcis and H. subglaciescola. Halomonas salaria forms a cluster with Chromohalobacter salarius and the recently described genus Salinicola, and their taxonomic affiliation requires further study. More than 20 Halomonas species are phylogenetically not within the core constituted by the Halomonas sensu stricto cluster (group 1) or group 2 and, since their positions on the different phylogenetic trees are not stable, they cannot be recognized as additional groups either. In general, there is excellent agreement between the phylogenies based on the two rRNA gene sequences, but the 23S rRNA gene showed higher resolution in the differentiation of species of the family Halomonadaceae.

scholarly journals Two New Point Mutations at A2062 Associated with Resistance to 16-Membered Macrolide Antibiotics in Mutant Strains ofMycoplasma hominis

2001 ◽  
Vol 45 (10) ◽  
pp. 2958-2960 ◽  
Author(s):  
Pio Maria Furneri ◽  
Giancarlo Rappazzo ◽  
Maria Pia Musumarra ◽  
Patrizia Di Pietro ◽  
Lucrezia S. Catania ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Point Mutations ◽  
Mycoplasma Hominis ◽  
23S Rrna ◽  
Macrolide Antibiotics ◽  
Rrna Gene ◽  
In Vitro Exposure ◽  
Mutant Strains ◽  
23S Rrna Gene

ABSTRACT We describe two mutants of Mycoplasma hominis PG-21 which show resistance to 16-membered macrolides but susceptibility to lincosamides, obtained by in vitro exposure to increasing doses of josamycin. The 23S rRNA gene showed that each had a mutation (A2062G and A2062T) corresponding to nucleotide 2062 in Escherichia coli, which was associated with the acquired phenotype.

scholarly journals Reassessment of the phylogenetic relationships of Thiomonas cuprina

2007 ◽  
Vol 57 (11) ◽  
pp. 2720-2724 ◽  
Author(s):  
Donovan P. Kelly ◽  
Yoshihito Uchino ◽  
Harald Huber ◽  
Ricardo Amils ◽  
Ann P. Wood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Significant Similarity ◽  
23S Rrna Gene ◽  
The 16S Rrna Gene

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.

scholarly journals Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China

2013 ◽  
Vol 62 (4) ◽  
pp. 351-358
Author(s):  
Xueling Wu ◽  
Hong Duan ◽  
Hongwei Fan ◽  
Zhenzhen Zhang ◽  
Lili Liu
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Intergenic Spacers ◽  
Acidithiobacillus Caldus ◽  
Pcr Fingerprinting ◽  
23S Rrna Gene

Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity respectively. In contrast, according to the analysis of bacterial diversity based on rep-PCR and AP-PCR fingerprinting, they produced highly discriminatory banding patterns, and the similarity values between them varied from 61.97% to 71.64%. RAPD analysis showed that banding profiles of their genomic DNA exhibited obvious differences from each other with 53.44-75% similarity. These results suggested that in contrast to 16S rRNA genes and 16S-23S rRNA gene intergenic spacers sequencing analysis, rep-PCR, AP-PCR fingerprinting and RAPD analysis possessed higher discriminatory power in identifying these closely related strains. And they could be used as rapid and highly discriminatory typing techniques in studying bacterial diversity, especially in differentiating bacteria within Acidithiobacillus caldus.

scholarly journals Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia

2005 ◽  
Vol 55 (4) ◽  
pp. 1439-1452 ◽  
Author(s):  
Endalkachew Wolde-meskel ◽  
Zewdu Terefework ◽  
Åsa Frostegård ◽  
Kristina Lindström
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Genes ◽  
Partial Sequence ◽  
23S Rrna ◽  
Southern Ethiopia ◽  
Rrna Gene ◽  
Pcr Rflp ◽  
23S Rrna Gene

The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR–RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100 % similar to those of previously described species and 34 were novel sequences with 94–99 % similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.

scholarly journals Mutations in a 23S rRNA Gene of Chlamydia trachomatis Associated with Resistance to Macrolides

2004 ◽  
Vol 48 (4) ◽  
pp. 1347-1349 ◽  
Author(s):  
O. Y. Misyurina ◽  
E. V. Chipitsyna ◽  
Y. P. Finashutina ◽  
V. N. Lazarev ◽  
T. A. Akopian ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Chlamydia Trachomatis ◽  
Gene Mutations ◽  
Clinical Isolates ◽  
23S Rrna ◽  
Rrna Gene ◽  
In Vitro Susceptibility ◽  
23S Rrna Gene ◽  
Mixed Populations

ABSTRACT For six clinical isolates of Chlamydia trachomatis, in vitro susceptibility to erythromycin, azithromycin, and josamycin has been determined. Four isolates were resistant to all the antibiotics and had the mutations A2058C and T2611C (Escherichia coli numbering) in the 23S rRNA gene. All the isolates had mixed populations of bacteria that did and did not carry 23S rRNA gene mutations.

scholarly journals Rapid Detection and Estimation by Pyrosequencing of 23S rRNA Genes with a Single Nucleotide Polymorphism Conferring Linezolid Resistance in Enterococci

2003 ◽  
Vol 47 (11) ◽  
pp. 3620-3622 ◽  
Author(s):  
Alistair Sinclair ◽  
Catherine Arnold ◽  
Neil Woodford
Keyword(s):  
Fragment Length Polymorphism ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Linezolid Resistance ◽  
Gene Copies ◽  
23S Rrna Gene ◽  
23S Rrna Genes

ABSTRACT Pyrosequencing was used to detect rapidly and estimate the number of 23S rRNA genes with a G2576T mutation in 43 linezolid-resistant and -susceptible clinical isolates of enterococci. The method showed 100% concordance with PCR-restriction fragment length polymorphism for detecting isolates homozygous for either G2576 or T2576 or heterozygous for this mutation. A good correlation was found between linezolid MICs and the number of 23S rRNA gene copies carrying the mutation.

Sign in / Sign up

Export Citation Format

Share Document