Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

Rustad, Tige R.; Minch, K; Ma, Shuyi; Winkler, Jessica K.; Hobbs, Samuel J.; Hickey, Mark J.; Brabant, William; Turkarslan, Serdar; Price, Nathan D.; Baliga, Nitin S.; Sherman, David R.

doi:10.1186/preaccept-1701638048134699

Cited by 85 publications

(157 citation statements)

References 36 publications

Supporting

Mentioning

152

Contrasting

Unclassified

Order By: Relevance

“…Transcript profiling of the M. tuberculosis cmr mutant compared with the same strain transformed with an integrated plasmid expressing cmr resulted in extensive complementation of the mutant transcription profile, indicating that the observed changes in transcription were mediated by disruption of the cmr gene (Table 1). Previous transcript profiling data obtained by 6-fold over-expression of cmr suggested that no genes were significantly regulated (≥2-fold, P ≤ 0.01) (25), hence, the cmr mutant to parent comparison undertaken here has revealed components of the Cmr regulon under laboratory conditions for the first time. Although the changes in transcript abundance reported by Rustad et al .…”

Section: Resultsmentioning

confidence: 55%

See 1 more Smart Citation

Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence

Smith

Bochkareva

Rolfe

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

Mycobacterium tuberculosis (MTb) is the causative agent of pulmonary tuberculosis (TB). MTb colonizes the human lung, often entering a non-replicating state before progressing to life-threatening active infections. Transcriptional reprogramming is essential for TB pathogenesis. In vitro, Cmr (a member of the CRP/FNR super-family of transcription regulators) bound at a single DNA site to act as a dual regulator of cmr transcription and an activator of the divergent rv1676 gene. Transcriptional profiling and DNA-binding assays suggested that Cmr directly represses dosR expression. The DosR regulon is thought to be involved in establishing latent tuberculosis infections in response to hypoxia and nitric oxide. Accordingly, DNA-binding by Cmr was severely impaired by nitrosation. A cmr mutant was better able to survive a nitrosative stress challenge but was attenuated in a mouse aerosol infection model. The complemented mutant exhibited a ∼2-fold increase in cmr expression, which led to increased sensitivity to nitrosative stress. This, and the inability to restore wild-type behaviour in the infection model, suggests that precise regulation of the cmr locus, which is associated with Region of Difference 150 in hypervirulent Beijing strains of Mtb, is important for TB pathogenesis.

show abstract

Section: Resultsmentioning

confidence: 55%

“…Although the changes in transcript abundance reported by Rustad et al . did not meet the statistical criteria to be considered significant, nine Cmr-repressed genes ( rv0080, rv1738, rv2007c, rv2031c, rv2032, rv2623, rv2626c, rv3130c, rv3131 ) detected here were also repressed by Cmr when cmr was over-expressed (25). …”

Section: Resultsmentioning

confidence: 94%

Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence

Smith

Bochkareva

Rolfe

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Out of the TF perturbations simulated, MTB PROM 2.0 identified Rv0880 as a knockout that would exploit the drug-specific vulnerabilities, yielding a strong defect when knocked out in the presence of bedaquiline, but not in its absence (see Table S3 for full results). Rv0880 , under standard culture conditions, modulates the expression of 23 genes 17 , 17 of which were significantly differentially expressed when treated with bedaquiline (Figure 1B). The Rv0880 bedaquiline-response regulon also contains a notable number of upregulated genes (8 out of 17, Figure 1b ).…”

Section: Resultsmentioning

confidence: 99%

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

Peterson

Sherman

et al. 2016

Nat Microbiol

Self Cite

View full text Add to dashboard Cite

Resilience of Mycobacterium tuberculosis (MTB) emerges from its ability to effectively counteract immunological, environmental, and antitubercular challenges. Here, we demonstrate that MTB can tolerate drug treatment by adopting a tolerant state that can be deciphered through systems analysis of its transcriptional responses. Specifically, we demonstrate how treatment with the antitubercular drug bedaquiline activates a regulatory network that coordinates multiple resistance mechanisms to push MTB into a tolerant state. Disruption of this network, by knocking out its predicted transcription factors, Rv0324 and Rv0880, significantly increased bedaquiline killing and enabled the discovery of a second drug pretomanid that potentiated killing by bedaquiline. We demonstrate that the synergistic effect of this combination emerges, in part, through disruption of the tolerance network. We discuss how this network strategy also predicts drug combinations with antagonistic interactions, potentially accelerating the discovery of new effective combination drug regimens for TB.

show abstract

“…9a). The promoter regions encompass all identified promoter and transcription factor binding elements identified525354. These regions were subcloned into TOPO vector by TA cloning (TOPO TA cloning kit, Life Technologies), propagated in TOP10 chemically competent E. coli , and sequenced to select for vectors that correctly amplified the PCR fragment.…”

Section: Methodsmentioning

confidence: 99%

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence

et al. 2016

View full text Add to dashboard Cite

Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria.

show abstract

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

Cited by 85 publications

References 36 publications

Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence

Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence

Contact Info

Product

Resources

About