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Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts.

<div class='caption-title'>Structure of an Mtb RbpA/TIC with Fdx at 3.4 Å resolution.</div>
<div class='caption-title'>Abortive Transcription assays to determine IC50 for Fdx.</div>
<div class='caption-title'>Data processing pipeline for the cryo-EM movies of the Fdx/RbpA/σA-holo/us-fork complexes.</div>
Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA
OpenAccess logo Elife 7 (2018)
Related entries: 6bzo, 6c04, 6c06

Cited: 46 times
EuropePMC logo PMID: 29480804

Abstract

Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.

Reviews - 6c05 mentioned but not cited (5)

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Articles - 6c05 mentioned but not cited (4)

  1. Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein. Solano-Collado V, Ruiz-Cruz S, Lorenzo-Díaz F, Pluta R, Espinosa M, Bravo A. Front Mol Biosci 8 666504 (2021)
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Reviews citing this publication (2)

  1. RNA polymerases from low G+C gram-positive bacteria. Miller M, Oakley AJ, Lewis PJ. Transcription 12 92-102 (2021)
  2. [New inhibitors targeting bacterial RNA polymerase]. Shi J, Feng Y. Zhejiang Da Xue Xue Bao Yi Xue Ban 48 44-49 (2019)

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  10. A synthetic switch based on orange carotenoid protein to control blue-green light responses in chloroplasts. Piccinini L, Iacopino S, Cazzaniga S, Ballottari M, Giuntoli B, Licausi F. Plant Physiol 189 1153-1168 (2022)
  11. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Proc Natl Acad Sci U S A 120 e2220785120 (2023)
  12. Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis. Xu Z, Zhou A, Wu J, Zhou A, Li J, Zhang S, Wu W, Karakousis PC, Yao YF. Front Microbiol 9 2895 (2018)
  13. "Upcycling" known molecules and targets for drug-resistant TB. Roubert C, Fontaine E, Upton AM. Front Cell Infect Microbiol 12 1029044 (2022)
  14. An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence. Dutta E, DeJesus MA, Ruecker N, Zaveri A, Koh EI, Sassetti CM, Schnappinger D, Ioerger TR. PLoS One 16 e0257911 (2021)
  15. Association of ω with the C-Terminal Region of the β' Subunit Is Essential for Assembly of RNA Polymerase in Mycobacterium tuberculosis. Mao C, Zhu Y, Lu P, Feng L, Chen S, Hu Y. J. Bacteriol. 200 (2018)
  16. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. Nature 604 541-545 (2022)
  17. CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase. Jensen D, Manzano AR, Rammohan J, Stallings CL, Galburt EA. Nucleic Acids Res. 47 6685-6698 (2019)
  18. CueR activates transcription through a DNA distortion mechanism. Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y. Nat Chem Biol 17 57-64 (2021)
  19. Expression, Purification, and In Silico Characterization of Mycobacterium smegmatis Alternative Sigma Factor SigB. Singh RK, Jaiswal LK, Nayak T, Rawat RS, Kumar S, Rai SN, Gupta A. Dis Markers 2022 7475704 (2022)
  20. Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19. Wang B, Svetlov D, Bartikofsky D, Wobus CE, Artsimovitch I. Molecules 27 3815 (2022)
  21. High-throughput screening to discover inhibitors of the CarD·RNA polymerase protein-protein interaction in Mycobacterium tuberculosis. Stefan MA, Velazquez GM, Garcia GA. Sci Rep 10 21309 (2020)
  22. High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase. Jensen D, Ruiz Manzano A, Rector M, Tomko EJ, Record MT, Galburt EA. Nucleic Acids Res 51 e99 (2023)
  23. IM How the antibiotic fidaxomicin targets an intestinal pathogen. Nature (2022)
  24. Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria. Cheng A, Wan D, Ghatak A, Wang C, Feng D, Fondell JD, Ebright RH, Fan H. mBio 14 e0349922 (2023)
  25. Novel fidaxomicin antibiotics through site-selective catalysis. Dailler D, Dorst A, Schäfle D, Sander P, Gademann K. Commun Chem 4 59 (2021)
  26. Oxazinomycin arrests RNA polymerase at the polythymidine sequences. Prajapati RK, Rosenqvist P, Palmu K, Mäkinen JJ, Malinen AM, Virta P, Metsä-Ketelä M, Belogurov GA. Nucleic Acids Res. 47 10296-10312 (2019)
  27. Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. He D, You L, Wu X, Shi J, Wen A, Yan Z, Mu W, Fang C, Feng Y, Zhang Y. Nat Commun 13 4204 (2022)
  28. Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription. Brodolin K, Morichaud Z. J Biol Chem 296 100253 (2021)
  29. Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis. Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R. Mol Cell 83 1474-1488.e8 (2023)
  30. Structural basis for transcription antitermination at bacterial intrinsic terminator. You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y. Nat Commun 10 3048 (2019)
  31. Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis. Wan T, Li S, Beltran DG, Schacht A, Zhang L, Becker DF, Zhang L. Nucleic Acids Res. 48 501-516 (2020)
  32. The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase. Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Müller R, Mooney R, Landick R, Darst SA, Campbell EA. Proc Natl Acad Sci U S A 117 30423-30432 (2020)
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Related citations provided by authors (1)

  1. Structure of Mycobacterium Tuberculosis RNAP Holo Enzyme/RbpA in closed clamp conformation. Darst SA, Campbell EA, Boyaci Selcuk H, Chen J, Lilic M To be published -

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