What is rpoB sequencing?
Sequencing of rpoB enables efficient estimation of bacterial G+C% content, DNA–DNA hybridization value and average nucleotide identity (percentage of the total genomic sequence shared between two strains) when taxonomic relation- ships have been firmly established.
What does the rpoB gene do?
The rpoB gene encodes the β subunit of bacterial RNA polymerase and the homologous plastid-encoded RNA polymerase (PEP). It codes for 1342 amino acids in E. coli, making it the second-largest polypeptide in the bacterial cell. It is targeted by the rifamycin family of antibacterials, such as rifampin.
How long is the rpoB gene?
The rpoB gene extends from 3411 bp (Staphylococcus aureus) to 4185 bp (Neisseria meningitidis) and is a monocopy gene, with the exception of that present in the RIF-R Nocardia farcinica strain [69].
What is inhA mutation?
inhA mutations cause low-level resistance to the drug, which means that high doses of INH may be effective against M. tuberculosis. 6,7. As ETH is a structural analogue of INH, cross-resistance occurs between INH and ETH.
What is the KatG gene?
tuberculosis catalase-peroxidase enzyme (KatG), encoded by the katG gene to generate a range of highly reactive species for bactericidal activity.
What is the function of beta subunit of RNA polymerase?
The β subunit is the second-largest subunit, and is encoded by the rpoB gene. The β subunit contains the rest of the active center responsible for RNA synthesis and contains the rest of the determinants for non-sequence-specific interactions with DNA and nascent RNA.
Why is LepA a good phylogenetic marker?
LepA has the unique function of back-translocating posttranslocational ribosomes, and the results suggest that it recognizes ribosomes after a defective translocation reaction and induces a back-translocation, thus giving EF-G a second chance to translocate the tRNAs correctly.
Is cyclophilin A housekeeping gene?
The results suggest that the cyclophilin A gene is the most suitable housekeeping gene analysed for expression studies utilising uncultured bronchial airway epithelial cells from healthy and asthmatic children, and highlight the importance of validating housekeeping genes for each experimental model.
Is there a method for strain identification without sequencing of rpoB?
In order to propose a method for strain identification which does not require sequencing of the complete rpoB sequence (approximately 3,500 bp), we identified an area with a high degree of polymorphism, bordered by conserved sequences that can be used as universal primers for PCR amplification and sequencing.
How similar are Corynebacterium rpoB sequences?
The almost complete rpoB sequences of 56 Corynebacterium species were determined by both PCR and genome walking methods. In all cases the percent similarities between different species were lower than those observed by 16S rRNA gene sequencing, even for those species with degrees of high similarity.
What does rpoB tell us about the taxonomic structure of mock communities?
rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota.
Which 16S rRNA markers are most useful for estimating bacterial diversity?
Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3 V4 hypervariable region of the 16S rRNA gene.