Using Cryo-EM to Understand Antimycobacterial Resistance in the Catalase-peroxidase (KatG) from Mycobacterium Tuberculosis

Overview

Journal Structure

Publisher Cell Press

Specialties Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Date 2021 Jan 14

PMID 33444527

Citations 14

Authors

Asma Munir

Michael T Wilson

Steven W Hardwick

Dimitri Y Chirgadze

Jonathan A R Worrall

Tom L Blundell

Amanda K Chaplin

Affiliations

Soon will be listed here.

Abstract

Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance.

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References

Zhao X, Yu H, Yu S, Wang F, Sacchettini J, Magliozzo R . Hydrogen peroxide-mediated isoniazid activation catalyzed by Mycobacterium tuberculosis catalase-peroxidase (KatG) and its S315T mutant. Biochemistry. 2006; 45(13):4131-40. DOI: 10.1021/bi051967o. View

Gajhede M, Schuller D, Henriksen A, Smith A, Poulos T . Crystal structure of horseradish peroxidase C at 2.15 A resolution. Nat Struct Biol. 1997; 4(12):1032-8. DOI: 10.1038/nsb1297-1032. View

Pierattelli R, Banci L, Eady N, Bodiguel J, Jones J, Moody P . Enzyme-catalyzed mechanism of isoniazid activation in class I and class III peroxidases. J Biol Chem. 2004; 279(37):39000-9. DOI: 10.1074/jbc.M402384200. View

Kamachi S, Hirabayashi K, Tamoi M, Shigeoka S, Tada T, Wada K . The crystal structure of isoniazid-bound KatG catalase-peroxidase from Synechococcus elongatus PCC7942. FEBS J. 2014; 282(1):54-64. DOI: 10.1111/febs.13102. View

Kim J, Tan Y, Wicht K, Erramilli S, Dhingra S, Okombo J . Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature. 2019; 576(7786):315-320. PMC: 6911266. DOI: 10.1038/s41586-019-1795-x. View

Wong W, Bai X, Brown A, Fernandez I, Hanssen E, Condron M . Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Elife. 2014; 3. PMC: 4086275. DOI: 10.7554/eLife.03080. View

Jakopitsch C, Auer M, Ivancich A, Ruker F, Furtmuller P, Obinger C . Total conversion of bifunctional catalase-peroxidase (KatG) to monofunctional peroxidase by exchange of a conserved distal side tyrosine. J Biol Chem. 2003; 278(22):20185-91. DOI: 10.1074/jbc.M211625200. View

Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis M . Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Cell. 2016; 165(7):1698-1707. PMC: 4931924. DOI: 10.1016/j.cell.2016.05.040. View

Jagielski T, Bakula Z, Roeske K, Kaminski M, Napiorkowska A, Augustynowicz-Kopec E . Detection of mutations associated with isoniazid resistance in multidrug-resistant Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother. 2014; 69(9):2369-75. DOI: 10.1093/jac/dku161. View

10.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

11.

Metcalfe C, Daltrop O, Ferguson S, Raven E . Tuning the formation of a covalent haem-protein link by selection of reductive or oxidative conditions as exemplified by ascorbate peroxidase. Biochem J. 2007; 408(3):355-61. PMC: 2267360. DOI: 10.1042/BJ20071041. View

12.

Punjani A, Rubinstein J, Fleet D, Brubaker M . cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017; 14(3):290-296. DOI: 10.1038/nmeth.4169. View

13.

Santoni E, Jakopitsch C, Obinger C, Smulevich G . Manipulating the covalent link between distal side tryptophan, tyrosine, and methionine in catalase-peroxidases: an electronic absorption and resonance Raman study. Biopolymers. 2004; 74(1-2):46-50. DOI: 10.1002/bip.20041. View

14.

Yu S, Girotto S, Zhao X, Magliozzo R . Rapid formation of compound II and a tyrosyl radical in the Y229F mutant of Mycobacterium tuberculosis catalase-peroxidase disrupts catalase but not peroxidase function. J Biol Chem. 2003; 278(45):44121-7. DOI: 10.1074/jbc.M304757200. View

15.

Ceska T, Chung C, Cooke R, Phillips C, Williams P . Cryo-EM in drug discovery. Biochem Soc Trans. 2019; 47(1):281-293. DOI: 10.1042/BST20180267. View

16.

BEERS Jr R, SIZER I . A spectrophotometric method for measuring the breakdown of hydrogen peroxide by catalase. J Biol Chem. 1952; 195(1):133-40. View

17.

Torres M, Garcia-Garcia L, Cruz-Hervert P, Guio H, Carranza C, Ferreyra-Reyes L . Effect of isoniazid on antigen-specific interferon-γ secretion in latent tuberculosis. Eur Respir J. 2014; 45(2):473-82. PMC: 4318657. DOI: 10.1183/09031936.00123314. View

18.

SOUCHON H, Wilming M, Johnsson K, Alzari P, Cole S . Use of site-directed mutagenesis to probe the structure, function and isoniazid activation of the catalase/peroxidase, KatG, from Mycobacterium tuberculosis. Biochem J. 1999; 338 ( Pt 3):753-60. PMC: 1220113. View

19.

Torres J, Paul L, Rodwell T, Victor T, Amallraja A, Elghraoui A . Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerg Microbes Infect. 2015; 4(7):e42. PMC: 4522615. DOI: 10.1038/emi.2015.42. View

20.

Hameed A, Shahina M, Lai W, Stothard P, Young L, Lin S . Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex. J Glob Antimicrob Resist. 2019; 20:28-30. DOI: 10.1016/j.jgar.2019.11.017. View