Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis

Ahmad, Ezaz; Mitra, Anirban P.; Ahmed, Wareed; Mahapatra, Varsha; Hegde, Shubhada R.; Sala, Claudia; Cole, Stewart T.; Nagaraja, Valakunja

doi:10.1016/j.bbagrm.2023.194923

Cited by 4 publications

(2 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…smegmatis, and M. tuberculosis RNAPs. − To measure the transcription elongation rates, we immobilized the biotinylated DNA. RNAP and a mixture of rGTP and rATP were added to the immobilized DNA to initiate the transcription and to synthesize a SEC with 19-mer RNA.…”

Section: Resultsmentioning

confidence: 99%

Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time

Tare,

Bhowmick,

Katagi

et al. 2023

ACS Omega

Self Cite

View full text Add to dashboard Cite

RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter–polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis , Mycobacterium smegmatis , and Escherichia coli , which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.

show abstract

Section: Resultsmentioning

confidence: 99%

Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time

Tare,

Bhowmick,

Katagi

et al. 2023

ACS Omega

Self Cite

View full text Add to dashboard Cite

show abstract

“…The absence of ribosomes adjacent to the RNA polymerase therefore sensitizes transcripts to premature Rho-mediated transcriptional termination (reviewed in [73]). Rho-dependent termination is prevalent in the mycobacteria [76][77][78], and translational block by B11 binding is therefore expected to lead to premature transcriptional termination and thereby lower steady-state mRNA abundance of many B11 targets. Transcription of B11 target genes is therefore expected to be higher in the ΔB11 strain.…”

Section: Plos Pathogensmentioning

confidence: 99%

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence

Bar-Oz,

Martini,

Alonso

et al. 2023

PLoS Pathog

View full text Add to dashboard Cite

Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.

show abstract

Common Features of Environmental Mycobacterium chelonae from Colorado Using Partial and Whole Genomic Sequence Analyses

Glauser,

Kelley,

Leonard

et al. 2024

Curr Microbiol

View full text Add to dashboard Cite

Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that cause chronic lung disease in susceptible individuals. While presumed to be ubiquitous in built and natural environments, NTM environmental studies are limited. While environmental sampling campaigns have been performed in geographic areas of high NTM disease burden, NTM species diversity is less defined among areas of lower disease burden like Colorado. In Colorado, metals such as molybdenum have been correlated with increased risk for NTM infection, yet environmental NTM species diversity has not yet been widely studied. Based on prior regression modeling, three areas of predicted high, moderate, and low NTM risk were identified for environmental sampling in Colorado. Ice, plumbing biofilms, and sink tap water samples were collected from publicly accessible freshwater sources. All samples were microbiologically cultured and NTM were identified using partial rpoB gene sequencing. From these samples, areas of moderate risk were more likely to be NTM positive. NTM recovery from ice was more common than recovery from plumbing biofilms or tap water. Overall, nine different NTM species were identified, including clinically important Mycobacterium chelonae. MinION technology was used to whole genome sequence and compare mutational differences between six M. chelonae genomes, representing three environmental isolates from this study and three other M. chelonae isolates from other sources. Drug resistance genes and prophages were common findings among environmentally derived M. chelonae, promoting the need for expanded environmental sampling campaigns to improve our current understanding of NTM species abundance while opening new avenues for improved targeted drug therapies.

show abstract

Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis

Cited by 4 publications

References 69 publications

Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time

Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence

Common Features of Environmental Mycobacterium chelonae from Colorado Using Partial and Whole Genomic Sequence Analyses

Contact Info

Product

Resources

About