An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism
Abstract
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis. One-fourth of the global population is estimated to be infected with Mtb, accounting for ~1.3 million deaths in 2017. As part of the immune response to Mtb infection, macrophages produce metabolites with the purpose of inhibiting or killing the bacterial cell. Itaconate is an abundant host metabolite thought to be both an antimicrobial agent and a modulator of the host inflammatory response. However, the exact mode of action of itaconate remains unclear. Here, we show that Mtb has an itaconate dissimilation pathway and that the last enzyme in this pathway, Rv2498c, also participates in l-leucine catabolism. Our results from phylogenetic analysis, in vitro enzymatic assays, X-ray crystallography, and in vivo Mtb experiments, identified Mtb Rv2498c as a bifunctional β-hydroxyacyl-CoA lyase and that deletion of the rv2498c gene from the Mtb genome resulted in attenuation in a mouse infection model. Altogether, this report describes an itaconate resistance mechanism in Mtb and an l-leucine catabolic pathway that proceeds via an unprecedented (R)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) stereospecific route in nature.
- Authors:
-
[1];
[1]
- Francis Crick Institute (United Kingdom)
- Albert Einstein College of Medicine, Bronx, NY (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1557314
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 116; Journal Issue: 32; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; biological sciences; biochemistry; enzyme function; carbon-carbon bond lyase; mycobacterium tuberculosis; itaconate catabolism; leucine catabolism
Citation Formats
Wang, Hua, Fedorov, Alexander A., Fedorov, Elena V., Hunt, Debbie M., Rodgers, Angela, Douglas, Holly L., Garza-Garcia, Acely, Bonanno, Jeffrey B., Almo, Steven C., and de Carvalho, Luiz Sório. An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism. United States: N. p., 2019.
Web. doi:10.1073/pnas.1906606116.
Wang, Hua, Fedorov, Alexander A., Fedorov, Elena V., Hunt, Debbie M., Rodgers, Angela, Douglas, Holly L., Garza-Garcia, Acely, Bonanno, Jeffrey B., Almo, Steven C., & de Carvalho, Luiz Sório. An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism. United States. https://doi.org/10.1073/pnas.1906606116
Wang, Hua, Fedorov, Alexander A., Fedorov, Elena V., Hunt, Debbie M., Rodgers, Angela, Douglas, Holly L., Garza-Garcia, Acely, Bonanno, Jeffrey B., Almo, Steven C., and de Carvalho, Luiz Sório. Thu .
"An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism". United States. https://doi.org/10.1073/pnas.1906606116. https://www.osti.gov/servlets/purl/1557314.
@article{osti_1557314,
title = {An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism},
author = {Wang, Hua and Fedorov, Alexander A. and Fedorov, Elena V. and Hunt, Debbie M. and Rodgers, Angela and Douglas, Holly L. and Garza-Garcia, Acely and Bonanno, Jeffrey B. and Almo, Steven C. and de Carvalho, Luiz Sório},
abstractNote = {Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis. One-fourth of the global population is estimated to be infected with Mtb, accounting for ~1.3 million deaths in 2017. As part of the immune response to Mtb infection, macrophages produce metabolites with the purpose of inhibiting or killing the bacterial cell. Itaconate is an abundant host metabolite thought to be both an antimicrobial agent and a modulator of the host inflammatory response. However, the exact mode of action of itaconate remains unclear. Here, we show that Mtb has an itaconate dissimilation pathway and that the last enzyme in this pathway, Rv2498c, also participates in l-leucine catabolism. Our results from phylogenetic analysis, in vitro enzymatic assays, X-ray crystallography, and in vivo Mtb experiments, identified Mtb Rv2498c as a bifunctional β-hydroxyacyl-CoA lyase and that deletion of the rv2498c gene from the Mtb genome resulted in attenuation in a mouse infection model. Altogether, this report describes an itaconate resistance mechanism in Mtb and an l-leucine catabolic pathway that proceeds via an unprecedented (R)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) stereospecific route in nature.},
doi = {10.1073/pnas.1906606116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 32,
volume = 116,
place = {United States},
year = {Thu Jul 18 00:00:00 EDT 2019},
month = {Thu Jul 18 00:00:00 EDT 2019}
}
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Works referenced in this record:
Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence
journal, September 2014
- Gouzy, Alexandre; Poquet, Yannick; Neyrolles, Olivier
- Nature Reviews Microbiology, Vol. 12, Issue 11
The Pathway of Itaconate Metabolism by Liver Mitochondria
journal, January 1961
- Wang, Shu-Fang; Adler, Julius; Lardy, Henry A.
- Journal of Biological Chemistry, Vol. 236, Issue 1
Cysteine Is the General Base That Serves in Catalysis by Isocitrate Lyase and in Mechanism-Based Inhibition by 3-Nitropropionate
journal, December 2013
- Moynihan, Margaret M.; Murkin, Andrew S.
- Biochemistry, Vol. 53, Issue 1
Acetyl-CoA-Dependent Cleavage of Citrate on Inactivated Citrate Lyase
journal, August 1973
- Buckel, Wolfgang; Ziegert, Kathrin; Eggerer, Hermann
- European Journal of Biochemistry, Vol. 37, Issue 2
A Novel Mammalian Homologue of a Bacterial Citrate-Metabolizing Enzyme
journal, June 2002
- SÖDerberg, Charlotte; Lind, Peter
- Annals of the New York Academy of Sciences, Vol. 967, Issue 1
The Pfam protein families database: towards a more sustainable future
journal, December 2015
- Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
- Nucleic Acids Research, Vol. 44, Issue D1
FATCAT: a web server for flexible structure comparison and structure similarity searching
journal, July 2004
- Ye, Y.; Godzik, A.
- Nucleic Acids Research, Vol. 32, Issue Web Server
The Structure and Computational Analysis of Mycobacterium tuberculosis Protein CitE Suggest a Novel Enzymatic Function
journal, January 2007
- Goulding, Celia W.; Bowers, Peter M.; Segelke, Brent
- Journal of Molecular Biology, Vol. 365, Issue 2
CitE Enzymes Are Essential for Mycobacterium tuberculosis to Establish Infection in Macrophages and Guinea Pigs
journal, November 2018
- Arora, Garima; Chaudhary, Deepika; Kidwai, Saqib
- Frontiers in Cellular and Infection Microbiology, Vol. 8
The Apparent Malate Synthase Activity of Rhodobacter sphaeroides Is Due to Two Paralogous Enzymes, (3S)-Malyl-Coenzyme A (CoA)/ -Methylmalyl-CoA Lyase and (3S)- Malyl-CoA Thioesterase
journal, January 2010
- Erb, T. J.; Frerichs-Revermann, L.; Fuchs, G.
- Journal of Bacteriology, Vol. 192, Issue 5
Origin, Spread and Demography of the Mycobacterium tuberculosis Complex
journal, September 2008
- Wirth, Thierry; Hildebrand, Falk; Allix-Béguec, Caroline
- PLoS Pathogens, Vol. 4, Issue 9
Investigation of Conserved Acidic Residues in 3-Hydroxy-3-methylglutaryl-CoA Lyase: IMPLICATIONS FOR HUMAN DISEASE AND FOR FUNCTIONAL ROLES IN A FAMILY OF RELATED PROTEINS
journal, July 2003
- Tuinstra, Robbyn L.; Miziorko, Henry M.
- Journal of Biological Chemistry, Vol. 278, Issue 39
The Global Burden of Latent Tuberculosis Infection: A Re-estimation Using Mathematical Modelling
journal, October 2016
- Houben, Rein M. G. J.; Dodd, Peter J.
- PLOS Medicine, Vol. 13, Issue 10
The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases
journal, January 2013
- Zarzycki, Jan; Kerfeld, Cheryl A.
- BMC Structural Biology, Vol. 13, Issue 1
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG
journal, November 2017
- Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W.
- Protein Science, Vol. 27, Issue 1
Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1
journal, March 2018
- Mills, Evanna L.; Ryan, Dylan G.; Prag, Hiran A.
- Nature, Vol. 556, Issue 7699
The utilization of itaconate by Pseudomonas sp
journal, April 1964
- Cooper, Ra; Kornberg, Hl
- Biochemical Journal, Vol. 91, Issue 1
Kinetic and Chemical Mechanism of Malate Synthase from Mycobacterium tuberculosis
journal, August 2011
- Quartararo, Christine E.; Blanchard, John S.
- Biochemistry, Vol. 50, Issue 32
Bacterial l-leucine catabolism as a source of secondary metabolites
journal, October 2015
- Díaz-Pérez, Alma L.; Díaz-Pérez, César; Campos-García, Jesús
- Reviews in Environmental Science and Bio/Technology, Vol. 15, Issue 1
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
journal, June 1998
- Cole, S. T.; Brosch, R.; Parkhill, J.
- Nature, Vol. 393, Issue 6685
Irg1 expression in myeloid cells prevents immunopathology during M. tuberculosis infection
journal, March 2018
- Nair, Sharmila; Huynh, Jeremy P.; Lampropoulou, Vicky
- The Journal of Experimental Medicine, Vol. 215, Issue 4
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
journal, November 2004
- Krissinel, E.; Henrick, K.
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence
journal, May 2005
- Muñoz-Elías, Ernesto J.; McKinney, John D.
- Nature Medicine, Vol. 11, Issue 6
Bacterial itaconate degradation promotes pathogenicity
journal, March 2014
- Sasikaran, Jahminy; Ziemski, Michał; Zadora, Piotr K.
- Nature Chemical Biology, Vol. 10, Issue 5
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus
journal, December 2009
- Zarzycki, Jan; Brecht, Volker; Müller, Michael
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 50, p. 21317-21322
Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis
journal, June 2009
- Smith, Noel H.; Hewinson, R. Glyn; Kremer, Kristin
- Nature Reviews Microbiology, Vol. 7, Issue 7
TubercuList – 10 years after
journal, January 2011
- Lew, Jocelyne M.; Kapopoulou, Adamandia; Jones, Louis M.
- Tuberculosis, Vol. 91, Issue 1
Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation
journal, July 2016
- Lampropoulou, Vicky; Sergushichev, Alexey; Bambouskova, Monika
- Cell Metabolism, Vol. 24, Issue 1
The Utilization of Aconate and Itaconate by Micrococcus sp.
journal, January 1965
- Cooper, Ra; Itiaba, K.; Kornberg, Hl
- Biochemical Journal, Vol. 94, Issue 1
Food Fight: Role of Itaconate and Other Metabolites in Antimicrobial Defense
journal, September 2016
- Luan, Harding H.; Medzhitov, Ruslan
- Cell Metabolism, Vol. 24, Issue 3
Itaconate, an isocitrate lyase-directed inhibitor in Pseudomonas indigofera.
journal, January 1977
- McFadden, B. A.; Purohit, S.
- Journal of Bacteriology, Vol. 131, Issue 1
Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase
journal, August 2000
- McKinney, John D.; zu Bentrup, Kerstin Höner; Muñoz-Elías, Ernesto J.
- Nature, Vol. 406, Issue 6797
Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis
journal, March 2017
- Puckett, Susan; Trujillo, Carolina; Wang, Zhe
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 11
The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes
journal, January 2011
- Kapopoulou, Adamandia; Lew, Jocelyne M.; Cole, Stewart T.
- Tuberculosis, Vol. 91, Issue 1
Mycobacteria, metals, and the macrophage
journal, February 2015
- Neyrolles, Olivier; Wolschendorf, Frank; Mitra, Avishek
- Immunological Reviews, Vol. 264, Issue 1
Metabolic anticipation in Mycobacterium tuberculosis
journal, May 2017
- Eoh, Hyungjin; Wang, Zhe; Layre, Emilie
- Nature Microbiology, Vol. 2, Issue 8
Itaconate reduces visceral fat by inhibiting fructose 2,6-bisphosphate synthesis in rat liver
journal, November 2004
- Sakai, Akiko; Kusumoto, Aki; Kiso, Yoshinobu
- Nutrition, Vol. 20, Issue 11-12
A Methylaspartate Cycle in Haloarchaea
journal, January 2011
- Khomyakova, M.; Bukmez, O.; Thomas, L. K.
- Science, Vol. 331, Issue 6015
Structural insights into RipC, a putative citrate lyase β subunit from a Yersinia pestis virulence operon
journal, December 2011
- Torres, Rodrigo; Chim, Nicholas; Sankaran, Banumathi
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 68, Issue 1
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production
journal, April 2013
- Michelucci, A.; Cordes, T.; Ghelfi, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 19
Itaconic Acid Is a Mammalian Metabolite Induced during Macrophage Activation
journal, October 2011
- Strelko, Cheryl L.; Lu, Wenyun; Dufort, Fay J.
- Journal of the American Chemical Society, Vol. 133, Issue 41
The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
journal, November 2017
- Shen, Hongying; Campanello, Gregory C.; Flicker, Daniel
- Cell, Vol. 171, Issue 4
Bacterial citrate lyase
journal, October 1984
- Subramanian, Subhalakshmi; Sivaraman, C.
- Journal of Biosciences, Vol. 6, Issue 4
Mycobacterial persistence requires the utilization of host cholesterol
journal, March 2008
- Pandey, A. K.; Sassetti, C. M.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 11
Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation
journal, July 2016
- Lampropoulou, Vicky; Sergushichev, Alexey; Bambouskova, Monika
- Cell Metabolism, Vol. 24, Issue 1
Food Fight: Role of Itaconate and Other Metabolites in Antimicrobial Defense
journal, September 2016
- Luan, Harding H.; Medzhitov, Ruslan
- Cell Metabolism, Vol. 24, Issue 3
The Structure and Computational Analysis of Mycobacterium tuberculosis Protein CitE Suggest a Novel Enzymatic Function
journal, January 2007
- Goulding, Celia W.; Bowers, Peter M.; Segelke, Brent
- Journal of Molecular Biology, Vol. 365, Issue 2
A new BEACON of hope for the treatment of inflammation? The endogenous metabolite itaconate as an alternative activator of the KEAP1-Nrf2 system
journal, October 2018
- Perico, Luca; Wyatt, Christina M.; Benigni, Ariela
- Kidney International, Vol. 94, Issue 4
The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes
journal, January 2011
- Kapopoulou, Adamandia; Lew, Jocelyne M.; Cole, Stewart T.
- Tuberculosis, Vol. 91, Issue 1
TubercuList – 10 years after
journal, January 2011
- Lew, Jocelyne M.; Kapopoulou, Adamandia; Jones, Louis M.
- Tuberculosis, Vol. 91, Issue 1
Kinetic and Chemical Mechanism of Malate Synthase from Mycobacterium tuberculosis
journal, August 2011
- Quartararo, Christine E.; Blanchard, John S.
- Biochemistry, Vol. 50, Issue 32
Cysteine Is the General Base That Serves in Catalysis by Isocitrate Lyase and in Mechanism-Based Inhibition by 3-Nitropropionate
journal, December 2013
- Moynihan, Margaret M.; Murkin, Andrew S.
- Biochemistry, Vol. 53, Issue 1
Itaconic Acid Is a Mammalian Metabolite Induced during Macrophage Activation
journal, October 2011
- Strelko, Cheryl L.; Lu, Wenyun; Dufort, Fay J.
- Journal of the American Chemical Society, Vol. 133, Issue 41
Bacterial itaconate degradation promotes pathogenicity
journal, March 2014
- Sasikaran, Jahminy; Ziemski, Michał; Zadora, Piotr K.
- Nature Chemical Biology, Vol. 10, Issue 5
Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence
journal, May 2005
- Muñoz-Elías, Ernesto J.; McKinney, John D.
- Nature Medicine, Vol. 11, Issue 6
Metabolic anticipation in Mycobacterium tuberculosis
journal, May 2017
- Eoh, Hyungjin; Wang, Zhe; Layre, Emilie
- Nature Microbiology, Vol. 2, Issue 8
The utilization of itaconate by Pseudomonas sp
journal, April 1964
- Cooper, Ra; Kornberg, Hl
- Biochemical Journal, Vol. 91, Issue 1
The Utilization of Aconate and Itaconate by Micrococcus sp.
journal, January 1965
- Cooper, Ra; Itiaba, K.; Kornberg, Hl
- Biochemical Journal, Vol. 94, Issue 1
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus
journal, December 2009
- Zarzycki, Jan; Brecht, Volker; Müller, Michael
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 50, p. 21317-21322
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production
journal, April 2013
- Michelucci, A.; Cordes, T.; Ghelfi, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 19
Functional Insights into Human HMG-CoA Lyase from Structures of Acyl-CoA-containing Ternary Complexes
journal, June 2010
- Fu, Zhuji; Runquist, Jennifer A.; Montgomery, Christa
- Journal of Biological Chemistry, Vol. 285, Issue 34
Biochemical and Structural Studies of Malate Synthase from Mycobacterium tuberculosis
journal, October 2002
- Smith, Clare V.; Huang, Chih-chin; Miczak, Andras
- Journal of Biological Chemistry, Vol. 278, Issue 3
Crystal Structures of Two Bacterial 3-Hydroxy-3-methylglutaryl-CoA Lyases Suggest a Common Catalytic Mechanism among a Family of TIM Barrel Metalloenzymes Cleaving Carbon-Carbon Bonds
journal, December 2005
- Forouhar, Farhad; Hussain, Munif; Farid, Ramy
- Journal of Biological Chemistry, Vol. 281, Issue 11
The Key Role of Anaplerosis and Cataplerosis for Citric Acid Cycle Function
journal, June 2002
- Owen, Oliver E.; Kalhan, Satish C.; Hanson, Richard W.
- Journal of Biological Chemistry, Vol. 277, Issue 34
Irg1 expression in myeloid cells prevents immunopathology during M. tuberculosis infection
journal, March 2018
- Nair, Sharmila; Huynh, Jeremy P.; Lampropoulou, Vicky
- The Journal of Experimental Medicine, Vol. 215, Issue 4
FATCAT: a web server for flexible structure comparison and structure similarity searching
journal, July 2004
- Ye, Y.; Godzik, A.
- Nucleic Acids Research, Vol. 32, Issue Web Server
The Pfam protein families database: towards a more sustainable future
journal, December 2015
- Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
- Nucleic Acids Research, Vol. 44, Issue D1
Mycobacteria, metals, and the macrophage
journal, February 2015
- Neyrolles, Olivier; Wolschendorf, Frank; Mitra, Avishek
- Immunological Reviews, Vol. 264, Issue 1
Acetyl-CoA-Dependent Cleavage of Citrate on Inactivated Citrate Lyase
journal, August 1973
- Buckel, Wolfgang; Ziegert, Kathrin; Eggerer, Hermann
- European Journal of Biochemistry, Vol. 37, Issue 2
The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases
journal, January 2013
- Zarzycki, Jan; Kerfeld, Cheryl A.
- BMC Structural Biology, Vol. 13, Issue 1
The Global Burden of Latent Tuberculosis Infection: A Re-estimation Using Mathematical Modelling
journal, October 2016
- Houben, Rein M. G. J.; Dodd, Peter J.
- PLOS Medicine, Vol. 13, Issue 10
Origin, Spread and Demography of the Mycobacterium tuberculosis Complex
journal, September 2008
- Wirth, Thierry; Hildebrand, Falk; Allix-Béguec, Caroline
- PLoS Pathogens, Vol. 4, Issue 9
Disorders of branched chain amino acid metabolism
journal, November 2016
- Manoli, I.; Venditti, C. P.
- Translational Science of Rare Diseases, Vol. 1, Issue 2
Corrigendum: CitE Enzymes Are Essential for Mycobacterium tuberculosis to Establish Infection in Macrophages and Guinea Pigs
journal, October 2020
- Arora, Garima; Chaudhary, Deepika; Kidwai, Saqib
- Frontiers in Cellular and Infection Microbiology, Vol. 10
Works referencing / citing this record:
Crystal structure of cis -aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis
journal, September 2019
- Chen, Fangfang; Lukat, Peer; Iqbal, Azeem Ahmed
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 41