scholarly journals Genetic Diversity and Phylogenetic Relationship of Clinical Isolates of Brucella melitensis Based on Gene Polymorphism of β Subunit of RNA Polymerase (rpoB) Gene in Iran

2020 ◽  
Vol 14 (5) ◽  
pp. 425-440
Author(s):  
Nasim Bazrgari ◽  
Ghasem Ali Garosi ◽  
Maryam Dadar ◽  
◽  
◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Polymorphism ◽  
Rna Polymerase ◽  
Phylogenetic Relationship ◽  
Brucella Melitensis ◽  
Rpob Gene ◽  
Clinical Isolates ◽  
Β Subunit ◽  
Relationship Of

scholarly journals Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka

2021 ◽  
Vol 15 (12) ◽  
pp. e0009917
Author(s):  
Himali S. Jayasinghearachchi ◽  
Enoka M. Corea ◽  
Kumari I. Jayaratne ◽  
Regina A. Fonseka ◽  
Thilini A. Muthugama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Southeast Asia ◽  
Burkholderia Pseudomallei ◽  
Evolutionary Relationship ◽  
Type A ◽  
Clinical Isolates ◽  
Sri Lankan ◽  
Evolutionary Analysis ◽  
Relationship Of

Background Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in SoutheastAsia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. Methods The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast t Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. Results The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC Clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. Conclusion This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania.

scholarly journals Investigation of Mutations in the Rifampin-Resistance-Determining Region of the rpoB Gene of Brucella melitensis by Gene Analysis

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Maryam Dadar ◽  
Nasim Bazrgari ◽  
Ghasem Ali Garosi ◽  
Sameer Hassan
Keyword(s):  
Genetic Diversity ◽  
Synovial Fluid ◽  
Binding Sites ◽  
Brucella Melitensis ◽  
Gene Sequencing ◽  
Rpob Gene ◽  
Gene Analysis ◽  
Disk Diffusion ◽  
Rifampin Resistance ◽  
Susceptibility Tests

Background: RNA polymerase beta subunit (rpoB) gene analysis in bacterial communities is known as a method for determining rifampin sensitivity and genetic diversity among Brucella spp. Detection of antibiotic resistance among Brucella isolates can be a critical approach to control brucellosis. However, rpoB gene analysis of Brucella melitensis for assessing rifampicin resistance has not yet been performed in Iran, which is considered an endemic area for brucellosis. Objectives: The aim of this study was to analyze the whole sequence of rpoB genes of different B. melitensis isolates from humans to identify the single-nucleotide polymorphisms (SNPs) and mutations related to rifampin resistance and to analyze the genetic diversity of these bacteria in Iran. Methods: Between 2017 and 2019, a total of 156 blood samples along with 12 synovial fluid specimens were collected from brucellosis patients in different Iranian provinces and subjected to bacterial culture in Brucella selective media. Brucella identification was carried out using classical biotyping and molecular examinations. Polymerase chain reaction (PCR)-based amplification of the rpoB gene was performed by specific rpoB primers for whole gene sequencing. The antimicrobial susceptibility of Brucella isolates was assessed using disk diffusion susceptibility tests and minimal inhibitory concentration (MIC) methods. The presence of rifampin-binding sites and SNPs were investigated through rpoB whole gene sequencing. Results: Clinical B. melitensis isolates were obtained from blood (13) and synovial fluid (1) samples of patients from different regions of Iran. The results of MIC and disk diffusion susceptibility tests showed that all the isolates were sensitive to rifampin except for one isolate showing intermediate rifampin resistance based on the standards defined for slow-growing bacteria by the Clinical and Laboratory Standards Institute (CLSI). Gene analysis for identifying the mutations related to rifampin resistance and investigating genetic diversity showed that none of the B. melitensis isolates had missense mutations, confirming the susceptibility of all the studied isolates to rifampin. Conclusions: The present study revealed that rpoB gene analysis could be used for the efficient and precise identifying of the mutations related to rifampin resistance, investigating rifampin binding sites, and genotyping Brucella species. Furthermore, the identification of B. melitensis isolates with intermediate resistance to rifampicin highlighted the importance of periodically carrying out antibiotic susceptibility testing. The molecular detection of rpoB mutations in different Brucella isolates may help to prevent the spread of rifampin-resistant Brucella spp. among humans and livestock.

Identification and phylogenetic relationship of Mannheimia varigena using the 16S rRNA subunit and the rpoB gene

2014 ◽  
Vol 65 (3) ◽  
pp. 1781-1787
Author(s):  
Zaydy Suástegui-Urquijo ◽  
Carlos Julio Jaramillo-Arango ◽  
Fernando Martínez-Hernández ◽  
Elizabeth Ureta ◽  
Francisco Trigo-Tavera ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Relationship ◽  
Rpob Gene ◽  
Relationship Of

Mapping of sequences required for the translation of the β subunit of Escherichia coli RNA polymerase

1997 ◽  
Vol 43 (9) ◽  
pp. 819-826
Author(s):  
Luciano Passador ◽  
Thomas Linn
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Translational Regulation ◽  
Rpob Gene ◽  
Β Subunit ◽  
E Coli ◽  
Lacz Fusions ◽  
Translational Start ◽  
Genetic Constructs ◽  
Expression Plasmids

Previous experiments using expression plasmids which overproduce the β and β′ subunits of Escherichia coli RNA polymerase suggested that regions considerably upstream of the start of the rpoB gene, which encodes the β subunit, are required for its efficient synthesis. To further delineate the required regions, a collection of genetic constructs that contained varying amounts of the region either upstream or downstream of the translational start of rpoB was assembled. Measurements of β and β′ synthesis and rpoB mRNA production from a series of rpoBC expression plasmids indicated that sequences extending more than 43 bp but less than 79 bp upstream of rpoB are required for the efficient translation of rpoB mRNA. This result was confirmed by β-galactosidase measurements from a series of rpoB-lacZ fusions that have the same set of end points upstream of rpoB as the expression plasmids. A second set of gene fusions containing differing amounts of the sequence distal to the start of rpoB fused in frame to lacZ revealed that more than 29 bp but less than 70 bp of rpoB was required for efficient translation.Key words: RNA polymerase, E. coli, translational regulation.

scholarly journals Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers

2021 ◽  
Vol 64 (1) ◽  
pp. 7-16
Author(s):  
Qing Xia ◽  
Xiangyu Wang ◽  
Zhangyuan Pan ◽  
Rensen Zhang ◽  
Caihong Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Pair Group ◽  
Introduced Populations ◽  
Unbiased Gene ◽  
Relationship Of ◽  
Hu Sheep

Abstract. The objective of this study was to assess the genetic diversity and phylogenetic relationship of nine sheep populations, including two famous high prolific populations and seven popular mutton populations raised in China. Overall, these sheep populations in this study exhibited a rich genetic diversity. Both the expected heterozygosity and Nei's unbiased gene diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not display the expected diversity; therefore more attention should be paid to the maintenance of diversity during management of these populations. The results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the nine investigated populations can be divided into two groups. Suffolk (SUF) and DST were clustered in one group, and the other group can be further divided into three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is consistent with sheep breeding history. TreeMix analysis also hinted at the possible gene flow from GMM to SUF. Together, an in-depth view of genetic diversity and genetic relationship will have important implications for breed-specific management.

scholarly journals In silico mutational analysis in RNA polymerase β subunit (rpoB) gene of rifampicin-resistant in Mycobacterium tuberculosis from Malaysia

2021 ◽  
pp. 47-58
Author(s):  
Ernie Zuraida Ali ◽  
Nurul Hamizah Hamidon ◽  
Rahizan Issa
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rna Polymerase ◽  
Protein Interactions ◽  
Mutational Analysis ◽  
Public Health Problem ◽  
Rpob Gene ◽  
Drug Susceptibility ◽  
Β Subunit ◽  
Mutant Proteins ◽  
Information Sequence

Tuberculosis (TB) is mainly caused by Mycobacterium tuberculosis (MTB) and remains as a key public health problem worldwide. Most of MTB clinical strains are resistant to rifampicin (RIF), the first-line anti-tuberculosis drug. RIF resistance to MTB is due to mutations that mainly found in RIF resistance-determining region (RRDR) in drug target gene, RNA polymerase β subunit (rpoB). Therefore, the aim of the study is to extend the identification of variants in rpoB gene and to elucidate the effect of variants to the RIF resistance. Four of the strains, MTBR1/09, MTBR2/09, MTBR3/09 and MTB221/11 were subjected to drug susceptibility test (DST). All of the strains sequenced and submitted to the National Center for Biotechnology Information Sequence Read Archive were analyzed to identify the variants in the rpoB gene. The identified new variants were then subjected to docking to examine the drug-protein interactions. DST analysis revealed MTBR1/09, MTBR2/09 and MTBR3/09 were resistant to the RIF drug, while MTB221/11 was a presumptive susceptible strain. Two new variants were observed, the deletion (Phe433_Met434delinsLeu in MTBR1/09) and missense (Lys37Arg in MTBR3/09) variants. Meanwhile, the His445Leu, Ser450Leu, Asp103Asp, Ala1075Ala were reported variants. Docking of RIF to MTBR1/09 and MTBR3/09 mutant models revealed the RIF bound to the RIF binding site at different binding affinity and conformation. Concurrently, the new variants caused the RIF to bind to the different active site and neighboring residues. Findings from DST and docking analyses indicate that new variants potentially disturb the RIF inhibition in RpoB mutant proteins, and thus might be responsible to cause the RIF resistance.

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