Molecular characterization of rpoB gene encoding the RNA polymerase β subunit in rifampin-resistant Mycobacterium tuberculosis strains from south India

2012 ◽  
Vol 11 (13) ◽  
Author(s):  
A. Nisha
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rna Polymerase ◽  
Molecular Characterization ◽  
South India ◽  
Rpob Gene ◽  
Β Subunit ◽  
Gene Encoding

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.

Multiple mutations in RNA polymerase β-Subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory

2021 ◽  
Author(s):  
Saori Ogawa ◽  
Hitomi Shimidzu ◽  
Koji Fukuda ◽  
Naoki Tsunekawa ◽  
Toshiyuki Hirano ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Rna Polymerase ◽  
Density Functional ◽  
Rpob Gene ◽  
Complex Model ◽  
Dynamics Simulation ◽  
Β Subunit ◽  
Negative Effects ◽  
Gene Encoding ◽  
Functional Theory

Abstract Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, anti-protozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y made moderate or even negative effects. To identify why the rif-cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The four residues were located near the mRNA strand. Density functional theory-based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.

scholarly journals Activation of Antibiotic Biosynthesis by Specified Mutations in the rpoB Gene (Encoding the RNA Polymerase β Subunit) of Streptomyces lividans

2002 ◽  
Vol 184 (14) ◽  
pp. 3984-3991 ◽  
Author(s):  
Haifeng Hu ◽  
Qin Zhang ◽  
Kozo Ochi
Keyword(s):  
Rna Polymerase ◽  
Point Mutations ◽  
Normal Growth ◽  
Rpob Gene ◽  
Growth Conditions ◽  
Streptomyces Lividans ◽  
Regulatory Genes ◽  
Antibiotic Biosynthesis ◽  
Β Subunit ◽  
Gene Encoding

ABSTRACT We found that the biosynthesis of actinorhodin (Act), undecylprodigiosin (Red), and calcium-dependent antibiotic (CDA) are dramatically activated by introducing certain mutations into the rpoB gene that confer resistance to rifampin to Streptomyces lividans 66, which produces less or no antibiotics under normal growth conditions. Activation of Act and/or Red biosynthesis by inducing mutations in the rpoB gene was shown to be dependent on the mutation's position and the amino acid species substituted in the β-subunit of the RNA polymerase. Mutation analysis identified 15 different kinds of point mutations, which are located in region I, II, or III of the rpoB gene and, in addition, two novel mutations (deletion of nucleotides 1287 to 1289 and a double substitution at nucleotides 1309 and 1310) were also found. Western blot analyses and S1 mapping analyses demonstrated that the expression of actII-ORF4 and redD, which are pathway-specific regulatory genes for Act and Red, respectively, was activated in the mutants able to produce Act and Red. The ActIV-ORF1 protein (an enzyme for Act biosynthesis) and the RedD protein were produced just after the upregulation of ActII-ORF4 and RedZ, respectively. These results indicate that the mutation in the rpoB gene of S. lividans, resulting in the activation of Act and/or Red biosynthesis, functions at the transcription level by activating directly or indirectly the key regulatory genes, actII-ORF4 and redD. We propose that the mutated RNA polymerase may function by mimicking the ppGpp-bound form in activating the onset of secondary metabolism in Streptomyces.

scholarly journals Molecular Characterization of Clinical Isolates to Study rpoB Gene in Mycobacterium tuberculosis Complex

2019 ◽  
Vol 11 (2) ◽  
Author(s):  
Shilpa Rana ◽  
Yusra Ahmad ◽  
Narotam Sharma ◽  
Vijay Kumar ◽  
Satish Chandra Nautiyal
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Molecular Characterization ◽  
Mycobacterium Tuberculosis Complex ◽  
Rpob Gene ◽  
Clinical Isolates ◽  
Tuberculosis Complex

scholarly journals Molecular characterization of the rpoB gene mutations of Mycobacterium tuberculosis isolated from China

2013 ◽  
Vol 01 (01) ◽  
pp. 1-8 ◽  
Author(s):  
Shengfen Wang ◽  
Bing Zhao ◽  
Yuanyuan Song ◽  
Yang Zhou ◽  
Yu Pang ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Molecular Characterization ◽  
Gene Mutations ◽  
Rpob Gene

scholarly journals The Spectrum of Spontaneous Rifampin Resistance Mutations in the rpoB Gene of Bacillussubtilis 168 Spores Differs from That of Vegetative Cells and Resembles That of Mycobacterium tuberculosis

2002 ◽  
Vol 184 (17) ◽  
pp. 4936-4940 ◽  
Author(s):  
Wayne L. Nicholson ◽  
Heather Maughan
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Bacillus Subtilis ◽  
Rpob Gene ◽  
Β Subunit ◽  
Resistance Mutations ◽  
New Mutation ◽  
Gene Encoding ◽  
Vegetative Cells ◽  
Dormant Cells ◽  
Rifampin Resistance

ABSTRACT Mutations causing rifampin resistance in vegetative cells of Bacillus subtilis 168 have thus far been mapped to a rather restricted set of alterations at either Q469 or H482 within cluster I of the rpoB gene encoding the β subunit of RNA polymerase. In this study, we demonstrated that spores of B. subtilis 168 exhibit a spectrum of spontaneous rifampin resistance mutations distinct from that of vegetative cells. In addition to the rpoB mutations Q469K, Q469R, and H482Y previously characterized in vegetative cells, we isolated a new mutation of rpoB, H482R, from vegetative cells. Additional new rifampin resistance mutations arising from spores were detected at A478N and most frequently at S487L. The S487L change is the predominant change found in rpoB mutations sequenced from rifampin-resistant clinical isolates of Mycobacterium tuberculosis. The observations are discussed in terms of the underlying differences of the DNA environment within dormant cells and vegetatively growing cells.

scholarly journals Characterization of the putative tryptophan synthase β-subunit from Mycobacterium tuberculosis

2009 ◽  
Vol 41 (5) ◽  
pp. 379-388 ◽  
Author(s):  
Hongbo Shen ◽  
Yanping Yang ◽  
Feifei Wang ◽  
Ying Zhang ◽  
Naihao Ye ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tryptophan Synthase ◽  
Β Subunit
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