Structural Basis of Mycobacterium Tuberculosis Transcription and Transcription Inhibition

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2017 Apr 11

PMID 28392175

Citations 82

Authors

Wei Lin

Soma Mandal

David Degen

Yu Liu

Yon W Ebright

Shengjian Li

Yu Feng

Yu Zhang

Sukhendu Mandal

Yi Jiang

Shuang Liu

Matthew Gigliotti

Meliza Talaue

Nancy Connell

Kalyan Das

Eddy Arnold

Richard H Ebright

Affiliations

Soon will be listed here.

Abstract

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds-Nα-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.

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References

Srivastava A, Degen D, Ebright Y, Ebright R . Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus. Antimicrob Agents Chemother. 2012; 56(12):6250-5. PMC: 3497154. DOI: 10.1128/AAC.01060-12. View

Artsimovitch I, Vassylyeva M, Svetlov D, Svetlov V, Perederina A, Igarashi N . Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell. 2005; 122(3):351-63. DOI: 10.1016/j.cell.2005.07.014. View

Stewart F, Gordon D, Levin B . Fluctuation analysis: the probability distribution of the number of mutants under different conditions. Genetics. 1990; 124(1):175-85. PMC: 1203904. DOI: 10.1093/genetics/124.1.175. View

Jacques J, Rodrigue S, Brzezinski R, Gaudreau L . A recombinant Mycobacterium tuberculosis in vitro transcription system. FEMS Microbiol Lett. 2006; 255(1):140-7. DOI: 10.1111/j.1574-6968.2005.00071.x. View

Artsimovitch I, Chu C, Lynch A, Landick R . A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science. 2003; 302(5645):650-4. DOI: 10.1126/science.1087526. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Horrevorts A, Michel M, Kerrebijn K . Antibiotic interaction: interpretation of fractional inhibitory and fractional bactericidal concentration indices. Eur J Clin Microbiol. 1987; 6(4):502-3. DOI: 10.1007/BF02013128. View

Aristoff P, Garcia G, Kirchhoff P, Showalter H . Rifamycins--obstacles and opportunities. Tuberculosis (Edinb). 2010; 90(2):94-118. DOI: 10.1016/j.tube.2010.02.001. View

Bae B, Davis E, Brown D, Campbell E, Wigneshweraraj S, Darst S . Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proc Natl Acad Sci U S A. 2013; 110(49):19772-7. PMC: 3856789. DOI: 10.1073/pnas.1314576110. View

10.

Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis A . Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 2002; 108(5):599-614. DOI: 10.1016/s0092-8674(02)00667-0. View

11.

Srivastava A, Talaue M, Liu S, Degen D, Ebright R, Sineva E . New target for inhibition of bacterial RNA polymerase: 'switch region'. Curr Opin Microbiol. 2011; 14(5):532-43. PMC: 3196380. DOI: 10.1016/j.mib.2011.07.030. View

12.

Weinzierl R . The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol. 2010; 8:134. PMC: 2988716. DOI: 10.1186/1741-7007-8-134. View

13.

Rothstein D . Rifamycins, Alone and in Combination. Cold Spring Harb Perspect Med. 2016; 6(7). PMC: 4930915. DOI: 10.1101/cshperspect.a027011. View

14.

Hubin E, Fay A, Xu C, Bean J, Saecker R, Glickman M . Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. Elife. 2017; 6. PMC: 5302886. DOI: 10.7554/eLife.22520. View

15.

Stols L, Millard C, Dementieva I, Donnelly M . Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J Struct Funct Genomics. 2004; 5(1-2):95-102. DOI: 10.1023/B:JSFG.0000029196.87615.6e. View

16.

Murphy K, Papavinasasundaram K, Sassetti C . Mycobacterial recombineering. Methods Mol Biol. 2015; 1285:177-99. DOI: 10.1007/978-1-4939-2450-9_10. View

17.

Hein P, Landick R . The bridge helix coordinates movements of modules in RNA polymerase. BMC Biol. 2010; 8:141. PMC: 2993669. DOI: 10.1186/1741-7007-8-141. View

18.

Jokerst R, Weeks J, Zehring W, Greenleaf A . Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol Gen Genet. 1989; 215(2):266-75. DOI: 10.1007/BF00339727. View

19.

Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho M, Arnold E . Structural basis of transcription initiation. Science. 2012; 338(6110):1076-80. PMC: 3593053. DOI: 10.1126/science.1227786. View

20.

Davis E, Chen J, Leon K, Darst S, Campbell E . Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Res. 2014; 43(1):433-45. PMC: 4288152. DOI: 10.1093/nar/gku1231. View