Dr. Jeremy Rock - Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis Dr. Jeremy Rock - Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis
Vendredi 18 juillet 2025, 11h00 Tremenet
Jeremy Rock The Rockefeller University, New York
Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors. Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy. However, RifR Mtb accounts for one-fifth of all deaths due to drug-resistant bacteria. We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli, Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA. We find this pro-pausing NusG–RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG–RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb.
Selected publications
Eckartt KA, Delbeau M, Munsamy-Govender V, DeJesus MA, Azadian ZA, Reddy AK, Chandanani J, Poulton NC, Quiñones-Garcia S, Bosch B, Landick R, Campbell EA, Rock JM. Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis. Nature
Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature
Poulton NC, DeJesus MA, Munsamy-Govender V, Kanai M, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: The whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. Cell Chem Biol
Wong AI, Beites T, Planck KA, Fieweger RA, Eckartt KA, Li S, Poulton NC, VanderVen BC, Rhee KY, Schnappinger D, Ehrt S, Rock J. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis. Elife
Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell
Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA, Ruecker N, Zimmerman MD, Eckartt KA, Bosch B, Engelhart CA, Sullivan DF, Gengenbacher M, Dartois VA, Schnappinger D, Rock JM. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol
d'Andrea FB, Poulton NC, Froom R, Tam K, Campbell EA, Rock JM. The essential M. tuberculosis Clp protease is functionally asymmetric in vivo. Sci Adv
Dr. Jeremy Rock - Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis Dr. Jeremy Rock - Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis
Vendredi 18 juillet 2025, 11h00 Tremenet
Jeremy Rock The Rockefeller University, New York
Compensatory evolution in NusG improves fitness of drug-resistant Mycobacterium tuberculosis Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors. Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy. However, RifR Mtb accounts for one-fifth of all deaths due to drug-resistant bacteria. We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli, Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA. We find this pro-pausing NusG–RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG–RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb.
Selected publications
Eckartt KA, Delbeau M, Munsamy-Govender V, DeJesus MA, Azadian ZA, Reddy AK, Chandanani J, Poulton NC, Quiñones-Garcia S, Bosch B, Landick R, Campbell EA, Rock JM. Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis. Nature
Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature
Poulton NC, DeJesus MA, Munsamy-Govender V, Kanai M, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: The whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. Cell Chem Biol
Wong AI, Beites T, Planck KA, Fieweger RA, Eckartt KA, Li S, Poulton NC, VanderVen BC, Rhee KY, Schnappinger D, Ehrt S, Rock J. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis. Elife
Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell
Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA, Ruecker N, Zimmerman MD, Eckartt KA, Bosch B, Engelhart CA, Sullivan DF, Gengenbacher M, Dartois VA, Schnappinger D, Rock JM. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol
d'Andrea FB, Poulton NC, Froom R, Tam K, Campbell EA, Rock JM. The essential M. tuberculosis Clp protease is functionally asymmetric in vivo. Sci Adv
