Characterization of root-associated bacterial species of Leklek variety of common bean (Phaseolus sp.)

2021 ◽  
Vol 26 (5) ◽  
pp. 3008-3013
Author(s):  
DİLEK TEKDAL ◽  
◽  
İLKNUR AKÇA ◽  
ASLI KÜÇÜKRECEP ◽  
SELİM ÇETİNER ◽  
...  
Keyword(s):  
Common Bean ◽  
Ribosomal Rna ◽  
Root Nodules ◽  
Bacterial Species ◽  
Its Region ◽  
23S Rrna ◽  
Nodule Formation ◽  
Rrna Gene ◽  
Microbacterium Paraoxydans ◽  
23S Ribosomal Rna

The common bean is a valuable food source in the human diet. Leklek is a local variety of common bean (Phaseolus sp.) widely grown in Mersin's Gülnar district, but little is known about this variety. In the present study, bacterial species from root nodules of this common bean variety were identified by PCR-amplified 16S ribosomal RNA (rRNA) gene and 16S-23S ribosomal RNA (rRNA) Internal Transcribed Spacer (ITS) region and sequencing. The partial 16S rRNA gene and 16S-23S rRNA ITS region sequences were submitted to the NCBI database (accession numbers MT967369, MT968518, respectively). Amplified sequences were used to construct a phylogenetic tree. Phylogenetic analysis based on the identified sequences showed that the isolate belonged to the genus Microbacterium and was closely related to Microbacterium paraoxydans. The findings presented here will provide a clue for understanding this bacterium's role in nodule formation in Phaseolus sp. (variety Leklek).

scholarly journals Relatedness of Chromosomal and Plasmid DNAs of Erwinia pyrifoliae and Erwinia amylovora

2002 ◽  
Vol 68 (12) ◽  
pp. 6182-6192 ◽  
Author(s):  
Gayle C. McGhee ◽  
Elise L. Schnabel ◽  
Kimberly Maxson-Stein ◽  
Beatrix Jones ◽  
Verlyn K. Stromberg ◽  
...  
Keyword(s):  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Its Region ◽  
Nucleotide Composition ◽  
Molecular Properties ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Probe ◽  
Separate Species ◽  
Hybridization Data

ABSTRACT The plant pathogen Erwinia pyrifoliae has been classified as a separate species from Erwinia amylovora based in part on differences in molecular properties. In this study, these and other molecular properties were examined for E. pyrifoliae and for additional strains of E. amylovora, including strains from brambles (Rubus spp.). The nucleotide composition of the internal transcribed spacer (ITS) region was determined for six of the seven 16S-23S rRNA operons detected in these species with a 16S rRNA gene probe. Each species contained four operons with a tRNAGlu gene and two with tRNAIle and tRNAAla genes, and analysis of the operons from five strains of E. amylovora indicated a high degree of ITS variability among them. One tRNAGlu-containing operon from E. pyrifoliae Ep1/96 was identical to one in E. amylovora Ea110, but three tRNAGlu operons and two tRNAIle and tRNAAla operons from E. pyrifoliae contained unique nucleotide changes. When groEL sequences were used for species-specific identification, E. pyrifoliae and E. amylovora were the closest phylogenetic relatives among a set of 12 bacterial species. The placement of E. pyrifoliae distinct from E. amylovora corroborated molecular hybridization data indicating low DNA-DNA similarity between them. Determination of the nucleotide sequence of plasmid pEP36 from E. pyrifoliae Ep1/96 revealed a number of presumptive genes that matched genes previously found in pEA29 from E. amylovora and similar organization for the genes and origins of replication. Also, pEP36 and pEA29 were incompatible with clones containing the reciprocal origin regions. Finally, the ColE1-like plasmid pEP2.6 from strain Ep1/96 contained sequences found in small plasmids in E. amylovora strains IL-5 and IH3-1.

scholarly journals Helicobacter pylori eradication according to sequencing-based 23S ribosomal RNA point mutation associated with clarithromycin resistance

2019 ◽  
Author(s):  
Seung In Seo ◽  
Byoung Joo ◽  
Jin Gu Kang ◽  
Hyoung Su Kim ◽  
Myoung Kuk Jang ◽  
...  
Keyword(s):  
Point Mutation ◽  
Ribosomal Rna ◽  
Point Mutations ◽  
23S Rrna ◽  
Rrna Gene ◽  
Clarithromycin Resistance ◽  
Clinically Significant ◽  
H Pylori ◽  
23S Ribosomal Rna ◽  
Significant Point

Abstract Background Clarithromycin resistance in Helicobacter pylori (H. pylori) is associated with point mutations in the 23S ribosomal RNA (rRNA) gene. A sequencing-based method can detect more point mutations than a polymerase chain reaction (PCR)-based method. We investigated the point mutations in the 23S rRNA genes of patients infected with clarithromycin-resistant H. pylori and compared the H. pylori eradication rates based on the identified clinically significant point mutations. Methods A total of 431 adult patients with H. pylori infection were retrospectively recruited in Kangdong Sacred Heart Hospital in 2017 and 2018. Patients who did not have point mutations related to clarithromycin resistance and/or had clinically insignificant point mutations were treated with PAC (proton pump inhibitor, amoxicillin, clarithromycin) for 7 days, while patients with clinically significant point mutations were treated with PAM (proton pump inhibitor, amoxicillin, metronidazole) for 7 days. H. pylori eradication rates were compared between the two groups. Results Sequencing-based detection of point mutations identified four mutations that were considered clinically significant (A2142G, A2142C, A2143G, A2143C), while all the other mutations were considered clinically insignificant. The clarithromycin resistance rate was 21.3% in the overall group of patients. A2143G was the most clinically significant point mutation (84/431, 19.5%), while T2182C was the most clinically insignificant point mutation (283/431, 65.7%). The H. pylori eradication rate in the overall group of patients was 83.7%, and the 7-day PAM-treated clarithromycin-resistance group showed a significantly lower eradication rate than the 7-day PAC-treated nonresistance group [ITT; 55.4% (51/92) vs. 74.3% (252/339), P=0.001, PP; 66.2% (51/77) vs. 88.4% (252/285), P=0.0001]. Conclusions There were significantly lower eradication rates in the patients with clarithromycin-resistant H. pylori as identified by the sequencing of point mutations in the 23S rRNA gene when treated with PAM for 7 days. A future study comparing treatment regimens in clarithromycin-resistant H. pylori-infected patients may be necessary.

scholarly journals Mycoplasma genitalium in Symptomatic Male Urethritis: Macrolide Use Is Associated With Increased Resistance

2019 ◽  
Vol 70 (5) ◽  
pp. 805-810 ◽  
Author(s):  
Yang Li ◽  
Xiaohong Su ◽  
Wenjing Le ◽  
Sai Li ◽  
Zhaoyan Yang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Mycoplasma Genitalium ◽  
Macrolide Resistance ◽  
Rrna Genes ◽  
Fluoroquinolone Resistance ◽  
23S Rrna ◽  
Transmitted Infection ◽  
Sexually Transmitted ◽  
23S Ribosomal Rna ◽  
The Impact

Abstract Background Mycoplasma genitalium (MG) causes symptomatic urethritis in men, and can infect alone or together with other sexually transmitted infection (STI) agents. Methods The prevalence of MG and other STIs was determined in 1816 men with symptomatic urethritis. Resistance of MG to macrolides and fluoroquinolones was determined by sequencing; the impact of recent antimicrobial usage on the distribution of MG single or mixed infections was determined. Results Overall, prevalence of MG infection was 19.7% (358/1816). Fifty-four percent (166/307) of MG infections occurred alone in the absence of other STI agents. Men with single MG infection self-administered or were prescribed antibiotics more often in the 30 days prior to enrollment than subjects with urethritis caused by MG coinfection (P < .0001). Higher rates (96.7%) of infection with macrolide resistance in MG were identified in men who had taken macrolides prior to enrollment (P < .03). Overall, 88.9% (303/341) of 23S ribosomal RNA (rRNA) genes contained mutations responsible for macrolide resistance; 89.5% (308/344) of parC and 12.4% (42/339) of gyrA genes had mutations responsible for fluoroquinolone resistance. Approximately 88% (270/308) of MG had combined mutations in 23S rRNA and parC genes; 10.4% (32/308) had mutations in all 3 genes. Conclusions MG was the single pathogen identified in 11% of men with symptomatic urethritis. Overall, nearly 90% of MG infections were resistant to macrolides and fluoroquinolones. Men who took macrolides in the 30 days prior to enrollment had higher rates (97%) of macrolide-resistant MG. Resistance was associated with numerous mutations in 23SrRNA, parC, and gyrA genes.

scholarly journals Sequence specific detection of bacterial 23S ribosomal RNA by TLR13

eLife ◽  
2012 ◽  
Vol 1 ◽  
Author(s):  
Xiao-Dong Li ◽  
Zhijian J Chen
Keyword(s):  
Ribosomal Rna ◽  
Single Point ◽  
Point Mutations ◽  
Peptide Bond ◽  
Interleukin 1Β ◽  
23S Rrna ◽  
Sequence Specificity ◽  
Bacterial Rna ◽  
Microbial Infections ◽  
23S Ribosomal Rna

Toll-like receptors (TLRs) detect microbial infections and trigger innate immune responses. Among vertebrate TLRs, the role of TLR13 and its ligand are unknown. Here we show that TLR13 detects the 23S ribosomal RNA of both gram-positive and gram-negative bacteria. A sequence containing 13 nucleotides near the active site of 23S rRNA ribozyme, which catalyzes peptide bond synthesis, was both necessary and sufficient to trigger TLR13-dependent interleukin-1β production. Single point mutations within this sequence destroyed the ability of the 23S rRNA to stimulate the TLR13 pathway. Knockout of TLR13 in mice abolished the induction of interleukin-1β and other cytokines by the 23S rRNA sequence. Thus, TLR13 detects bacterial RNA with exquisite sequence specificity.

scholarly journals Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

2013 ◽  
Vol 79 (13) ◽  
pp. 3974-3985 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Andreas Teske
Keyword(s):  
Gulf Of California ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genetic Exchange ◽  
23S Rrna ◽  
Rrna Gene ◽  
Homing Endonucleases ◽  
Guaymas Basin ◽  
Content Type ◽  
Group I

ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

scholarly journals Comparison of Genospecies and Antimicrobial Resistance Profiles of Isolates in the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex from Various Clinical Specimens

2012 ◽  
Vol 56 (12) ◽  
pp. 6267-6271 ◽  
Author(s):  
Ni Tien ◽  
Bang-Jau You ◽  
Hui-Lan Chang ◽  
Hsiu-Shen Lin ◽  
Chin-Yi Lee ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Restriction Analysis ◽  
Acinetobacter Calcoaceticus ◽  
Its Region ◽  
Clinical Isolates ◽  
23S Rrna ◽  
Rrna Gene ◽  
Genotype 3 ◽  
Content Type

ABSTRACTThis study was conducted to compare the prevalences of antimicrobial resistance profiles of clinical isolates in theAcinetobacter calcoaceticus-Acinetobacter baumanniicomplex from sterile and nonsterile sites and to further study the relationship of antimicrobial resistance profiles and genospecies by amplified rRNA gene restriction analysis (ARDRA). A total of 1,381 isolates were tested with 12 different antibiotics to show their antimicrobial susceptibility profiles. A total of 205 clinical isolates were further analyzed by ARDRA of the intergenic spacer (ITS) region of the 16S-23S rRNA gene. It was found that the overall percentage of isolates from nonsterile sites (urine, sputum, pus, or catheter tip) that were resistant to the 12 antibiotics tested was significantly higher than that of isolates from sterile sites (cerebrospinal fluid [CSF], ascites fluid, and bloodstream) (46% versus 22%;P< 0.05). After ARDRA, it was found that 97% of the 62 isolates resistant to all antibiotics tested were theA. baumanniigenospecies, which was identified in only 31% of the isolates susceptible to all antibiotics tested. More genospecies diversity was identified in the isolates susceptible to all antibiotics tested, including genospecies of 13TU (34%), genotype 3 (29%), andA. calcoaceticus(5%). Furthermore, as 91% (10/11) of the isolates from CSF were susceptible to all antibiotics tested, theA. calcoaceticus-A. baumanniicomplex isolates with multidrug resistance could be less invasive than the more susceptible isolates. This study also indicated current emergence of carbapenem-, fluoroquinolone-, aminoglycoside-, and cephalosporin-resistantA. calcoaceticus-A. baumanniicomplex isolates in Taiwan.

Nature of the genome of the saprophytic spirochete Spirochaeta aurantia and its ribosomal RNA operons

2004 ◽  
Vol 50 (11) ◽  
pp. 967-971 ◽  
Author(s):  
Richard McLaughlin ◽  
David M Secko ◽  
Catherine J Paul ◽  
Andrew M Kropinski
Keyword(s):  
Ribosomal Rna ◽  
Gel Electrophoresis ◽  
Large Subunit ◽  
Complete Sequence ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pulsed Field ◽  
23S Rrna Gene ◽  
Intergenic Regions

Using restriction endonucleases DraI, AseI, and I-CeuI in conjunction with pulsed-field gel electrophoresis, we have shown that Spirochaeta aurantia M1 possesses a circular 3.98-Mb genome. This is the second largest spirochete chromosome yet analyzed. The observation that the latter enzyme cuts in 3 places suggests the presence of 3 copies of the large subunit (23S) rRNA gene (rrl), which was confirmed by Southern hybridizations. The complete sequence of 2 of the ribosomal RNA operons was determined, revealing that their structure resembled that of the typical member of the bacterial superkingdom: rrs (16S; 1561 bp), tRNA, rrl (23S; 2972 bp), and rrf (5S; 110 bp). The S. aurantia rrs–rrl intergenic regions, as with Treponema denticola, contain genes specifying a 73-nt tRNAAla (anticodon TGC) and a 77-nt tRNAIle (anticodon GAT).Key words: spirochete, pulsed-field gel electrophoresis, ribosomal RNA, operon, Spirochaeta aurantia.

Variations in the 16S–23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen

2011 ◽  
Vol 57 (7) ◽  
pp. 617-622 ◽  
Author(s):  
Kirsti E. Præsteng ◽  
Roderick I. Mackie ◽  
Isaac K.O. Cann ◽  
Svein D. Mathiesen ◽  
Monica A. Sundset
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rangifer Tarandus ◽  
Its Region ◽  
16S Rrna Gene Sequencing ◽  
23S Rrna ◽  
Rrna Gene ◽  
Its Sequence ◽  
Neighbor Joining ◽  
Phylogenetic Neighbor

Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.

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