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Characterization of Lipoyl Synthase from Mycobacterium tuberculosis

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† ‡ § Department of Biochemistry and Molecular Biology, Department of Chemistry, and §The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
*(C.K.) E-mail: [email protected]. Phone: 814-865-6089. Fax: 814-865-5325.
*(S.J.B.) E-mail: [email protected]. Phone: 814-865-0119. Fax: 814-865-5325.
Cite this: Biochemistry 2016, 55, 9, 1372–1383
Publication Date (Web):February 3, 2016
https://doi.org/10.1021/acs.biochem.5b01216
Copyright © 2016 American Chemical Society

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    Abstract

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    The prevalence of multiple and extensively drug-resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is on the rise, necessitating the identification of new targets to combat an organism that has infected one-third of the world’s population, according to the World Health Organization. The biosynthesis of the lipoyl cofactor is one possible target, given its critical importance in cellular metabolism and the apparent lack of functional salvage pathways in Mtb that are found in humans and many other organisms. The lipoyl cofactor is synthesized de novo in two committed steps, involving the LipB-catalyzed transfer of an octanoyl chain derived from fatty acid biosynthesis to a lipoyl carrier protein and the LipA-catalyzed insertion of sulfur atoms at C6 and C8 of the octanoyl chain. A number of in vitro studies of lipoyl synthases from Escherichia coli, Sulfolobus solfataricus, and Thermosynechococcus elongatus have been conducted, but the enzyme from Mtb has not been characterized. Herein, we show that LipA from Mtb contains two [4Fe–4S] clusters and converts an octanoyl peptide substrate to the corresponding lipoyl peptide product via the same C6-monothiolated intermediate as that observed in the E. coli LipA reaction. In addition, we show that LipA from Mtb forms a complex with the H protein of the glycine cleavage system and that the strength of association is dependent on the presence of S-adenosyl-l-methionine. We also show that LipA from Mtb can complement a lipA mutant of E. coli, demonstrating the commonalities of the two enzymes. Lastly, we show that the substrate for LipA, which normally acts on a post-translationally modified protein, can be reduced to carboxybenzyl-octanoyllysine.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.biochem.5b01216.

    • 1H NMR, LC-MS, MtLipA purification, Mössbauer, EPR, size-exclusion chromatography, E. coli complementation, elution profile, and activity data as well as additional methods (PDF)

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    2. Christian J. Suess, Floriane L. Martins, Anna K. Croft, Christof M. Jäger. Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. Journal of Chemical Information and Modeling 2019, 59 (12) , 5111-5125. https://doi.org/10.1021/acs.jcim.9b00017
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    4. Jian-qiang Jin, Takaaki Sato, Shin-ichi Hachisuka, Haruyuki Atomi, . A Lipoate-Protein Ligase Is Required for De Novo Lipoyl-Protein Biosynthesis in the Hyperthermophilic Archaeon Thermococcus kodakarensis. Applied and Environmental Microbiology 2022, 88 (13) https://doi.org/10.1128/aem.00644-22
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    6. Karen L. F. Alvarez-Eraso, Laura M. Muñoz-Martínez, Juan F. Alzate, Luis F. Barrera, Andres Baena. Modulatory Impact of the sRNA Mcr11 in Two Clinical Isolates of Mycobacterium tuberculosis. Current Microbiology 2022, 79 (2) https://doi.org/10.1007/s00284-021-02733-0
    7. Vivian Robert Jeyachandran, Jay V. Pendyala, Erin L. McCarthy, Amie K. Boal, Squire J. Booker. Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis. 2021, 307-332. https://doi.org/10.1007/978-1-0716-1605-5_16
    8. Jian-qiang Jin, Shin-ichi Hachisuka, Takaaki Sato, Tsuyoshi Fujiwara, Haruyuki Atomi, . A Structurally Novel Lipoyl Synthase in the Hyperthermophilic Archaeon Thermococcus kodakarensis. Applied and Environmental Microbiology 2020, 86 (23) https://doi.org/10.1128/AEM.01359-20
    9. Erin L. McCarthy, Squire J. Booker. The Biosynthesis of Lipoic Acid. 2020, 3-23. https://doi.org/10.1016/B978-0-12-409547-2.14861-9
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    11. Piero Zanello. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins. Journal of Structural Biology 2018, 202 (3) , 250-263. https://doi.org/10.1016/j.jsb.2018.01.010
    12. Christof M. Jäger, Anna K. Croft. Anaerobic Radical Enzymes for Biotechnology. ChemBioEng Reviews 2018, 5 (3) , 143-162. https://doi.org/10.1002/cben.201800003
    13. Geng Dong, Lili Cao, Ulf Ryde. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. JBIC Journal of Biological Inorganic Chemistry 2018, 23 (2) , 221-229. https://doi.org/10.1007/s00775-017-1522-8
    14. Katherine M. Davis, Amie K. Boal. Mechanism-Based Strategies for Structural Characterization of Radical SAM Reaction Intermediates. 2017, 331-359. https://doi.org/10.1016/bs.mie.2017.07.008
    15. Martin I. McLaughlin, Nicholas D. Lanz, Peter J. Goldman, Kyung-Hoon Lee, Squire J. Booker, Catherine L. Drennan. Crystallographic snapshots of sulfur insertion by lipoyl synthase. Proceedings of the National Academy of Sciences 2016, 113 (34) , 9446-9450. https://doi.org/10.1073/pnas.1602486113

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