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Jones BS, Pareek V, Hu DD, Weaver SD, Syska C, Galfano G, Champion MM, Champion PA. N - acetyl-transferases required for iron uptake and aminoglycoside resistance promote virulence lipid production in M. marinum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602253. [PMID: 39005365 PMCID: PMC11245092 DOI: 10.1101/2024.07.05.602253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Phagosomal lysis is a key aspect of mycobacterial infection of host macrophages. Acetylation is a protein modification mediated enzymatically by N-acetyltransferases (NATs) that impacts bacterial pathogenesis and physiology. To identify NATs required for lytic activity, we leveraged Mycobacterium marinum, a nontubercular pathogen and an established model for M. tuberculosis. M. marinum hemolysis is a proxy for phagolytic activity. We generated M. marinum strains with deletions in conserved NAT genes and screened for hemolytic activity. Several conserved lysine acetyltransferases (KATs) contributed to hemolysis. Hemolysis is mediated by the ESX-1 secretion system and by phthiocerol dimycocerosate (PDIM), a virulence lipid. For several strains, the hemolytic activity was restored by the addition of second copy of the ESX-1 locus. Using thin-layer chromatography (TLC), we found a single NAT required for PDIM and phenolic glycolipid (PGL) production. MbtK is a conserved KAT required for mycobactin siderophore synthesis and virulence. Mycobactin J exogenously complemented PDIM/PGL production in the Δ mbtK strain. The Δ mbtK M. marinum strain was attenuated in macrophage and Galleria mellonella infection models. Constitutive expression of either eis or papA5, which encode a KAT required for aminoglycoside resistance and a PDIM/PGL biosynthetic enzyme, rescued PDIM/PGL production and virulence of the Δ mbtK strain. Eis N-terminally acetylated PapA5 in vitro , supporting a mechanism for restored lipid production. Overall, our study establishes connections between the MbtK and Eis NATs, and between iron uptake and PDIM and PGL synthesis in M. marinum . Our findings underscore the multifunctional nature of mycobacterial NATs and their connection to key virulence pathways. Significance Statement Acetylation is a modification of protein N-termini, lysine residues, antibiotics and lipids. Many of the enzymes that promote acetylation belong to the GNAT family of proteins. M. marinum is a well-established as a model to understand how M. tuberculosis causes tuberculosis. In this study we sought to identify conserved GNAT proteins required for early stages of mycobacterial infection. Using M. marinum, we determined that several GNAT proteins are required for the lytic activity of M. marinum. We uncovered previously unknown connections between acetyl-transferases required for iron uptake and antimicrobial resistance, and the production of the unique mycobacterial lipids, PDIM and PGLOur data support that acetyl-transferases from the GNAT family are interconnected, and have activities beyond those previously reported.
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Maure A, Lawarée E, Fiorentino F, Pawlik A, Gona S, Giraud-Gatineau A, Eldridge MJG, Danckaert A, Hardy D, Frigui W, Keck C, Gutierrez C, Neyrolles O, Aulner N, Mai A, Hamon M, Barreiro LB, Brodin P, Brosch R, Rotili D, Tailleux L. A host-directed oxadiazole compound potentiates antituberculosis treatment via zinc poisoning in human macrophages and in a mouse model of infection. PLoS Biol 2024; 22:e3002259. [PMID: 38683873 PMCID: PMC11081512 DOI: 10.1371/journal.pbio.3002259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 05/09/2024] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Antituberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multiresistant strains of Mycobacterium tuberculosis (MTB) are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high-content imaging, we identified novel 1,2,4-oxadiazole-based compounds, which allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, MTB became even more sensitive to antituberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.
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Affiliation(s)
- Alexandra Maure
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Emeline Lawarée
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Alexandre Pawlik
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Saideep Gona
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | | | | | - Anne Danckaert
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - David Hardy
- Institut Pasteur, Université Paris Cité, Histopathology Platform, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Camille Keck
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aulner
- Institut Pasteur, Université Paris Cité, UTechS BioImaging-C2RT, Paris, France
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci-bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Mélanie Hamon
- Institut Pasteur, Université Paris Cité, Chromatine et Infection unit, Paris, France
| | - Luis B. Barreiro
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Priscille Brodin
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Ludovic Tailleux
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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3
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Anand C, Santoshi M, Singh PR, Nagaraja V. Rv0802c is an acyltransferase that succinylates and acetylates Mycobacterium tuberculosis nucleoid-associated protein HU. MICROBIOLOGY-SGM 2021; 167. [PMID: 34224344 DOI: 10.1099/mic.0.001058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Among the nucleoid-associated proteins (NAPs), HU is the most conserved in eubacteria, engaged in overall chromosome organization and regulation of gene expression. Unlike other bacteria, HU from Mycobacterium tuberculosis (MtHU), has a long carboxyl terminal domain enriched in basic amino acids, resembling eukaryotic histone N-terminal tails. As with histones, MtHU undergoes post-translational modifications and we have previously identified interacting kinases, methyltransferases, an acetyltransferase and a deacetylase. Here we show that Rv0802c interacts and succinylates MtHU. Although categorized as a succinyltransferase, we show that this GNAT superfamily member can catalyse both succinylation and acetylation of MtHU with comparable kinetic parameters. Like acetylation of MtHU, succinylation of MtHU caused reduced interaction of the NAP with DNA, determined by electrophoretic mobility shift assay and surface plasmon resonance. However, in vivo expression of Rv0802c did not significantly alter the nucleoid architecture. Although such succinylation of NAPs is rare, these modifications of the archetypal NAP may provide avenues to the organism to compensate for the underrepresentation of NAPs in its genome to control the dynamics of nucleoid architecture and cellular functions.
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Affiliation(s)
- Chinmay Anand
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Meghna Santoshi
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Prakruti R Singh
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell biology, Indian Institute of Science, Bengaluru, Karnataka 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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4
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Sugiyama K, Iijima K, Yoshino M, Dohra H, Tokimoto Y, Nishikawa K, Idogaki H, Yoshida N. Nicotinamide mononucleotide production by fructophilic lactic acid bacteria. Sci Rep 2021; 11:7662. [PMID: 33828213 PMCID: PMC8027369 DOI: 10.1038/s41598-021-87361-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Nicotinamide mononucleotide (NMN), an intermediate in nicotinamide adenine dinucleotide biosynthesis, is recently attracting much attention for its pharmacological and anti-aging efficacies. However, current commercial products containing NMN are very high-priced because efficient and facile methods for industrial NMN production are limited. In this study, aiming for its nutraceutical application, we attempted to screen lactic acid bacteria for intracellular and/or extracellular NMN production. Using a bioassay system with an auxotrophic yeast that requires nicotinamide riboside (NR; dephosphorylated NMN), three candidates were obtained from a library of 174 strains of facultative anaerobic lactic acid bacteria. All three candidates belonged to the genus Fructobacillus and produced NR in the culture media (0.8–1.5 mg/l). Lactic acid bacteria of the genus Fructobacillus are known to use d-fructose as an electron acceptor in anaerobic lactic acid fermentation; addition of d-fructose to the medium caused intracellular accumulation of NMN and NR, but no extracellular production of these compounds was observed. Draft genome sequencing for one of the candidates suggested that nicotinamide phosphoribosyltransferase, which exists commonly in mammals but is less reported in microorganisms, is a key enzyme for NMN and NR production in the fructophilic bacteria.
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Affiliation(s)
- Kazane Sugiyama
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| | - Kana Iijima
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| | - Miyako Yoshino
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| | - Hideo Dohra
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yuji Tokimoto
- Osaka Soda Co., Ltd., 12-18 Awaza 1-chome, Nishi-ku, Osaka, 550-0011, Japan
| | - Koji Nishikawa
- Osaka Soda Co., Ltd., 12-18 Awaza 1-chome, Nishi-ku, Osaka, 550-0011, Japan
| | - Hideaki Idogaki
- Osaka Soda Co., Ltd., 12-18 Awaza 1-chome, Nishi-ku, Osaka, 550-0011, Japan
| | - Nobuyuki Yoshida
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan.
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5
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Rohde KH, Sorci L. The Prospective Synergy of Antitubercular Drugs With NAD Biosynthesis Inhibitors. Front Microbiol 2021; 11:634640. [PMID: 33584600 PMCID: PMC7873932 DOI: 10.3389/fmicb.2020.634640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022] Open
Abstract
Given the upsurge of drug-resistant tuberculosis worldwide, there is much focus on developing novel drug combinations allowing shorter treatment duration and a lower toxicity profile. Nicotinamide adenine dinucleotide (NAD) biosynthesis targeting is acknowledged as a promising strategy to combat drug-susceptible, drug-resistant, and latent tuberculosis (TB) infections. In this review, we describe the potential synergy of NAD biosynthesis inhibitors with several TB-drugs in prospective novel combination therapy. Despite not directly targeting the essential NAD cofactor's biosynthesis, several TB prodrugs either require a NAD biosynthesis enzyme to be activated or form a toxic chemical adduct with NAD(H) itself. For example, pyrazinamide requires the action of nicotinamidase (PncA), often referred to as pyrazinamidase, to be converted into its active form. PncA is an essential player in NAD salvage and recycling. Since most pyrazinamide-resistant strains are PncA-defective, a combination with downstream NAD-blocking molecules may enhance pyrazinamide activity and possibly overcome the resistance mechanism. Isoniazid, ethionamide, and delamanid form NAD adducts in their active form, partly perturbing the redox cofactor metabolism. Indeed, NAD depletion has been observed in Mycobacterium tuberculosis (Mtb) during isoniazid treatment, and activation of the intracellular NAD phosphorylase MbcT toxin potentiates its effect. Due to the NAD cofactor's crucial role in cellular energy production, additional synergistic correlations of NAD biosynthesis blockade can be envisioned with bedaquiline and other drugs targeting energy-metabolism in mycobacteria. In conclusion, future strategies targeting NAD metabolism in Mtb should consider its potential synergy with current and other forthcoming TB-drugs.
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Affiliation(s)
- Kyle H. Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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6
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Bonds AC, Yuan T, Werman JM, Jang J, Lu R, Nesbitt NM, Garcia-Diaz M, Sampson NS. Post-translational Succinylation of Mycobacterium tuberculosis Enoyl-CoA Hydratase EchA19 Slows Catalytic Hydration of Cholesterol Catabolite 3-Oxo-chol-4,22-diene-24-oyl-CoA. ACS Infect Dis 2020; 6:2214-2224. [PMID: 32649175 DOI: 10.1021/acsinfecdis.0c00329] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cholesterol is a major carbon source for Mycobacterium tuberculosis (Mtb) during infection, and cholesterol utilization plays a significant role in persistence and virulence within host macrophages. Elucidating the mechanism by which cholesterol is degraded may permit the identification of new therapeutic targets. Here, we characterized EchA19 (Rv3516), an enoyl-CoA hydratase involved in cholesterol side-chain catabolism. Steady-state kinetics assays demonstrated that EchA19 preferentially hydrates cholesterol enoyl-CoA metabolite 3-oxo-chol-4,22-diene-24-oyl-CoA, an intermediate of side-chain β-oxidation. In addition, succinyl-CoA, a downstream catabolite of propionyl-CoA that forms during cholesterol degradation, covalently modifies targeted mycobacterial proteins, including EchA19. Inspection of a 1.9 Å resolution X-ray crystallography structure of Mtb EchA19 suggests that succinylation of Lys132 and Lys139 may perturb enzymatic activity by modifying the entrance to the substrate binding site. Treatment of EchA19 with succinyl-CoA revealed that these two residues are hotspots for succinylation. Replacement of these specific lysine residues with negatively charged glutamate reduced the rate of catalytic hydration of 3-oxo-chol-4,22-diene-24-oyl-CoA by EchA19, as does succinylation of EchA19. Our findings suggest that succinylation is a negative feedback regulator of cholesterol metabolism, thereby adding another layer of complexity to Mtb physiology in the host. These regulatory pathways are potential noncatabolic targets for antimicrobial drugs.
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Affiliation(s)
- Amber C. Bonds
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
| | - Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Jungwon Jang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Rui Lu
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Natasha M. Nesbitt
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
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7
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Acetylation of lysine 182 inhibits the ability of Mycobacterium tuberculosis DosR to bind DNA and regulate gene expression during hypoxia. Emerg Microbes Infect 2018; 7:108. [PMID: 29899473 PMCID: PMC5999986 DOI: 10.1038/s41426-018-0112-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/11/2018] [Accepted: 05/16/2018] [Indexed: 11/08/2022]
Abstract
The DosR regulon is believed to be a key factor in latency adaptation of Mycobacterium tuberculosis and is strongly induced by multiple stresses, including hypoxia. Previous studies have revealed reversible acetylation of the conserved core DNA-binding lysine residue 182 (K182) of DosR in M. tuberculosis. In this study, we demonstrated that acetylated K182 plays an important role in the DNA-binding ability of DosR and that acetylation of K182 completely abolished the affinity of DosR for DNA in vitro. Antibodies that specifically recognized acetyllysine at position 182 of DosR were used to monitor DosR acetylation. We found that in vitro acetylation of K182 could be removed by deacetylase Rv1151c and that either the deacetylase-deletion strain ∆npdA or treatment with a deacetylase inhibitor resulted in increased levels of K182 acetylation in vivo. The physiological significance of DosR acetylation was demonstrated by decreased levels of acetylated K182 in M. tuberculosis in response to hypoxia and by the effects of K182 acetylation on the transcript levels of DosR regulon genes. Since the DosR regulon plays a critical role during host infection by M. tuberculosis, our findings suggest that targeting DosR acetylation may be a viable strategy for antituberculosis drug development.
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8
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Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
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Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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9
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Birhanu AG, Yimer SA, Holm-Hansen C, Norheim G, Aseffa A, Abebe M, Tønjum T. N ε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. J Proteome Res 2017; 16:4045-4059. [PMID: 28920697 DOI: 10.1021/acs.jproteome.7b00429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of three Mtb isolates: two lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses, and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interactions, and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb and open a new avenue of research for exploring the role of protein acetylation in Mtb physiology.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Addis Ababa University , Institute of Biotechnology, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Carol Holm-Hansen
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Gunnstein Norheim
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Abraham Aseffa
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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10
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Anand C, Garg R, Ghosh S, Nagaraja V. A Sir2 family protein Rv1151c deacetylates HU to alter its DNA binding mode in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2017; 493:1204-1209. [PMID: 28935371 DOI: 10.1016/j.bbrc.2017.09.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 11/29/2022]
Abstract
Till recently, knowledge about epigenetic regulation in bacterial world confined largely to DNA methylation. Lysine acetylation/deacetylation of histones is a major contributor for chromatin dynamics in eukaryotes. However, little is known about such epigenetic changes brought about by post-translational modifications in bacteria. Here, we describe an example of such mechanism occurring in a histone like protein, HU from Mycobacterium tuberculosis (Mtb). Previously, we demonstrated the interaction and acetylation of Mtb HU (MtHU) by one of the acetyl transferases, Eis. In this work, we demonstrate the deacetylation of acetylated HU (MtHUAc) by Rv1151c, the only Sir2 like protein discovered in Mtb. The DNA binding properties of MtHU are significantly altered upon acetylation but reversed consequent to deacetylation by the deacetylase. Deacetylated HU (MtHUdAc) bound to relaxed DNA leading to the formation of looped and dense molecules as compared to open structures formed by its acetylated form. Interaction of MtHUdAc with linear DNA modifies its organization leading to formation of highly bridged compact structures while binding of MtHUAc leads to the formation of stiff and straight rods. That a nucleoid associated protein can undergo acetylation/deacetylation to alter its DNA binding and architectural role opens up a new dimension of investigation of epigenetic regulation in mycobacteria.
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Affiliation(s)
- Chinmay Anand
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Rajni Garg
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, 560064, India
| | - Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, 560064, India.
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11
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Yadav GS, Ravala SK, Malhotra N, Chakraborti PK. Phosphorylation Modulates Catalytic Activity of Mycobacterial Sirtuins. Front Microbiol 2016; 7:677. [PMID: 27242704 PMCID: PMC4860497 DOI: 10.3389/fmicb.2016.00677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
Sirtuins are NAD+-dependent deacetylases involved in the regulation of diverse cellular processes and are conserved throughout phylogeny. Here we report about in vitro transphosphorylation of the only NAD+-dependent deacetylase (mDAC) present in the genome of Mycobacterium tuberculosis by eukaryotic-type Ser/Thr kinases, particularly PknA. The phosphorylated mDAC displayed decreased deacetylase activity compared to its unphosphorylated counterpart. Mass-spectrometric study identified seven phosphosites in mDAC; however, mutational analysis highlighted major contribution of Thr-214 for phosphorylation of the protein. In concordance to this observation, variants of mDAC substituting Thr-214 with either Ala (phospho-ablated) or Glu (phosphomimic) exhibited significantly reduced deacetylase activity suggesting phosphorylation mediated control of enzymatic activity. To assess the role of phosphorylation towards functionality of mDAC, we opted for a sirtuin knock-out strain of Escherichia coli (Δdac), where interference of endogenous mycobacterial kinases could be excluded. The Δdac strain in nutrient deprived acetate medium exhibited compromised growth and complementation with mDAC reversed this phenotype. The phospho-ablated or phosphomimic variant, on the other hand, was unable to restore the functionality of mDAC indicating the role of phosphorylation per se in the process. We further over-expressed mDAC or mDAC-T214A as His-tagged protein in M. smegmatis, where endogenous eukaryotic-type Ser/Thr kinases are present. Anti-phosphothreonine antibody recognized both mDAC and mDAC-T214A proteins in western blotting. However, the extent of phosphorylation as adjudged by scanning the band intensity, was significantly low in the mutant protein (mDAC-T214A) compared to that of the wild-type (mDAC). Furthermore, expression of PknA in the mDAC complemented Δdac strain was able to phosphorylate M. tuberculosis sirtuin. The growth profile of this culture in acetate medium was slow compared to that transformed with only vector. On the other hand, use of a kinase dead variant, PknA-K42N instead of PknA, did not display such behavior, which again supported phosphorylation mediated control of mDAC protein. Thus, our results ostensibly render evidence for cross-talk between two distinct post-translational modifications, phosphorylation and deacetylation, in any bacteria. Bioinformatic analysis further indicated conservation of Thr-214 among different mDAC orthologs, thereby arguing the event as mycobacteria specific.
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Affiliation(s)
| | | | - Neha Malhotra
- CSIR-Institute of Microbial Technology Chandigarh, India
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12
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Tan Y, Xu Z, Tao J, Ni J, Zhao W, Lu J, Yao YF. A SIRT4-like auto ADP-ribosyltransferase is essential for the environmental growth of Mycobacterium smegmatis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:145-52. [PMID: 26685303 DOI: 10.1093/abbs/gmv121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 09/26/2015] [Indexed: 01/12/2023] Open
Abstract
SIRT family proteins are highly conserved both in the structure and function among all the organisms, and are involved in gene silencing, DNA damage repair, cell growth and metabolism. Here, a SIRT4 homologue MSMEG_4620 was identified and characterized in Mycobacterium smegmatis. MSMEG_4620 exhibits deacetylase activity that can be activated by fatty acids. Interestingly, MSMEG_4620 also possesses auto ADP-ribosylation activity. MSMEG_4620 is modified on arginine residues as revealed by a chemical stability assay. Moreover, the auto ADP-ribosylation activity of MSMEG_4620 was found to be enhanced by ferric ion. Notably, the SIRT4 homologues are widely distributed in the genomes of environmental mycobacterial species instead of pathogenic mycobacterial species. When MSMEG_4620 was deleted in M. smegmatis, the mutant strain showed a growth defect in 7H9 minimal medium compared with the parental strain. Taken together, these results provided the characteristics of a SIRT4 homologue in prokaryotes and implicated its critical roles in the growth of environmental mycobacterial species.
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Affiliation(s)
- Yongcong Tan
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Tao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhao
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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13
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Gu L, Chen Y, Wang Q, Li X, Mi K, Deng H. Functional Characterization of Sirtuin-like Protein in Mycobacterium smegmatis. J Proteome Res 2015; 14:4441-9. [PMID: 26375486 DOI: 10.1021/acs.jproteome.5b00359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD)-dependent deacetylases (sirtuins) are well conserved from prokaryotes to eukaryotes. Functions and regulations of mammalian sirtuins have been extensively studied and indicate that sirtuins play an important role in regulation of biological processes, whereas functions of mycobacterial sirtuins were less explored. To examine functions of the sirtuin-like protein in mycobacteria, a Mycobacterium smegmatis sirtuin, MSMEG_5175, was overexpressed in a M. smegmatis strain mc(2)155 to generate an MSMEG_5175-overexpression strain (mc(2)155-MS5175) in the present study. The physiological aspects of mc(2)155-MS5175 strain were characterized showing that they had a lower intracellular NAD level and a higher resistance to isoniazid (INH) as compared to mc(2)155 containing empty pMV261 plasmid (mc(2)155-pMV261). Quantitative proteomic analysis was carried out to determine differentially expressed proteins between mc(2)155-pMV261 and mc(2)155-MS5175. Among 3032 identified proteins, overexpression of MSMEG_5175 results in up-regulation of 34 proteins and down-regulation of 72 proteins, which involve in diverse cellular processes including metabolic activation, transcription and translation, antioxidant, and DNA repair. Down-regulation of catalase peroxidase (KatG) expression in both mRNA and protein levels were observed in mc(2)155-MS5175 strain, suggesting that a decrease in cellular NAD content and down-regulation of KatG expression contribute to the higher resistance to INH in mc(2)155-MS5175. Using a combination of immunoprecipitation and proteomic analysis, we found that acetylation in 27 proteins was decreased in mc(2)155-MS5175 as compared to those in mc(2)155-pMV261, suggesting that these proteins including the beta prime subunit of RNA polymerase (rpoC), ribosomal proteins, and metabolic enzymes were substrates of MSMEG_5175. Acetylation changes in rpoC may affect its function and cause changes in global gene transcription. Taken together, these results suggest that MSMEG_5175 regulates diverse cellular processes resulting in an increase in INH resistance in mycobacteria, and provide a useful resource to further biological exploration into functions of protein acetylation in mycobacteria.
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Affiliation(s)
- Lixiao Gu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Qingtao Wang
- Beijing Chaoyang Hospital, Capital Medical University , Beijing 100020, China
| | - Xiaojing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing 100084, China
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Singhal A, Arora G, Virmani R, Kundu P, Khanna T, Sajid A, Misra R, Joshi J, Yadav V, Samanta S, Saini N, Pandey AK, Visweswariah SS, Hentschker C, Becher D, Gerth U, Singh Y. Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase. J Biol Chem 2015; 290:26218-34. [PMID: 26350458 DOI: 10.1074/jbc.m115.687269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 02/02/2023] Open
Abstract
Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.
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Affiliation(s)
- Anshika Singhal
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Gunjan Arora
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India, the Translational Health Science and Technology Institute, Faridabad 121001, India
| | - Richa Virmani
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Parijat Kundu
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Tanya Khanna
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Andaleeb Sajid
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Richa Misra
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Jayadev Joshi
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Vikas Yadav
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Sintu Samanta
- the Indian Institute of Science, Bangalore 560012, India, and
| | - Neeru Saini
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Amit K Pandey
- the Translational Health Science and Technology Institute, Faridabad 121001, India,
| | | | - Christian Hentschker
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Dörte Becher
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Ulf Gerth
- the Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany
| | - Yogendra Singh
- From the CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India,
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15
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Stehr M, Elamin AA, Singh M. Pyrazinamide: the importance of uncovering the mechanisms of action in mycobacteria. Expert Rev Anti Infect Ther 2015; 13:593-603. [PMID: 25746054 DOI: 10.1586/14787210.2015.1021784] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pyrazinamide (PZA) is still one of the key drugs used in current therapeutic regimens for tuberculosis (TB). Despite its importance for TB therapy, the mode of action of PZA remains unknown. PZA has to be converted to its active form pyrazinoic acid (POA) by the nicotinamidase PncA and is then excreted by an unknown efflux pump. At acidic conditions, POA is protonated to HPOA and is reabsorbed into the cell where it causes cellular damage. For a long time, it has been thought that PZA/POA has no defined target of action, but recent studies have shown that both PZA and POA have several different targets interfering with diverse biochemical pathways, especially in the NAD(+) and energy metabolism. PZA resistance seems to depend not only on a defective pyrazinamidase but is also rather a result of the interplay of many different enzyme targets and transport mechanisms.
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Affiliation(s)
- Matthias Stehr
- LIONEX Diagnostics and Therapeutics GmbH, Salzdahlumer Straße 196, D-38126, Braunschweig, Germany
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16
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Yang M, Wang Y, Chen Y, Cheng Z, Gu J, Deng J, Bi L, Chen C, Mo R, Wang X, Ge F. Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis. Mol Cell Proteomics 2015; 14:796-811. [PMID: 25605462 DOI: 10.1074/mcp.m114.045922] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, remains one of the most prevalent human pathogens and a major cause of mortality worldwide. Metabolic network is a central mediator and defining feature of the pathogenicity of Mtb. Increasing evidence suggests that lysine succinylation dynamically regulates enzymes in carbon metabolism in both bacteria and human cells; however, its extent and function in Mtb remain unexplored. Here, we performed a global succinylome analysis of the virulent Mtb strain H37Rv by using high accuracy nano-LC-MS/MS in combination with the enrichment of succinylated peptides from digested cell lysates and subsequent peptide identification. In total, 1545 lysine succinylation sites on 626 proteins were identified in this pathogen. The identified succinylated proteins are involved in various biological processes and a large proportion of the succinylation sites are present on proteins in the central metabolism pathway. Site-specific mutations showed that succinylation is a negative regulatory modification on the enzymatic activity of acetyl-CoA synthetase. Molecular dynamics simulations demonstrated that succinylation affects the conformational stability of acetyl-CoA synthetase, which is critical for its enzymatic activity. Further functional studies showed that CobB, a sirtuin-like deacetylase in Mtb, functions as a desuccinylase of acetyl-CoA synthetase in in vitro assays. Together, our findings reveal widespread roles for lysine succinylation in regulating metabolism and diverse processes in Mtb. Our data provide a rich resource for functional analyses of lysine succinylation and facilitate the dissection of metabolic networks in this life-threatening pathogen.
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Affiliation(s)
- Mingkun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yan Wang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ying Chen
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhongyi Cheng
- §Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
| | - Jing Gu
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jiaoyu Deng
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lijun Bi
- ‖Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuangbin Chen
- **Jingjie PTM Biolabs (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Ran Mo
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xude Wang
- ¶Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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17
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Zhou Y, Chen T, Zhou L, Fleming J, Deng J, Wang X, Wang L, Wang Y, Zhang X, Wei W, Bi L. Discovery and characterization of Ku acetylation in Mycobacterium smegmatis. FEMS Microbiol Lett 2014; 362:fnu051. [DOI: 10.1093/femsle/fnu051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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18
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Xie L, Liu W, Li Q, Chen S, Xu M, Huang Q, Zeng J, Zhou M, Xie J. First succinyl-proteome profiling of extensively drug-resistant Mycobacterium tuberculosis revealed involvement of succinylation in cellular physiology. J Proteome Res 2014; 14:107-19. [PMID: 25363132 DOI: 10.1021/pr500859a] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein lysine succinylation, an emerging protein post-translational modification widespread among eukaryotic and prokaryotic cells, represents an important regulator of cellular processes. However, the extent and function of lysine succinylation in Mycobacterium tuberculosis, especially extensively drug-resistant strain, remain elusive. Combining protein/peptide prefractionation, immunoaffinity enrichment, and LC-MS/MS analysis, a total of 686 succinylated proteins and 1739 succinylation sites of M. tuberculosis were identified, representing the first global profiling of M. tuberculosis lysine succinylation. The identified succinylated proteins are involved in a variety of cellular functions such as metabolic processes, transcription, translation, and stress responses and exhibit different subcellular localization via GO, protein interaction network, and other bioinformatic analysis. Notably, proteins involved in protein biosynthesis and carbon metabolism are preferred targets of lysine succinylation. Moreover, two prevalent sequence patterns: EK(suc) and K*****K(suc), can be found around the succinylation sites. There are 109 lysine-succinylated homologues in E. coli, suggesting highly conserved succinylated proteins. Succinylation was found to occur at the active sites predicted by Prosite signature including Rv0946c, indicating that lysine succinylation may affect their activities. There is extensive overlapping between acetylation sites and succinylation sites in M. tuberculosis. Many M. tuberculosis metabolic enzymes and antibiotic resistance proteins were succinylated. This study provides a basis for further characterization of the pathophysiological role of lysine succinylation in M. tuberculosis.
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Affiliation(s)
- Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715, China
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19
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Liu F, Yang M, Wang X, Yang S, Gu J, Zhou J, Zhang XE, Deng J, Ge F. Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. Mol Cell Proteomics 2014; 13:3352-66. [PMID: 25180227 DOI: 10.1074/mcp.m114.041962] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The lysine acetylation of proteins is a reversible post-translational modification that plays a critical regulatory role in both eukaryotes and prokaryotes. Mycobacterium tuberculosis is a facultative intracellular pathogen and the causative agent of tuberculosis. Increasing evidence shows that lysine acetylation may play an important role in the pathogenesis of M. tuberculosis. However, only a few acetylated proteins of M. tuberculosis are known, presenting a major obstacle to understanding the functional roles of reversible lysine acetylation in this pathogen. We performed a global acetylome analysis of M. tuberculosis H37Ra by combining protein/peptide prefractionation, antibody enrichment, and LC-MS/MS. In total, we identified 226 acetylation sites in 137 proteins of M. tuberculosis H37Ra. The identified acetylated proteins were functionally categorized into an interaction map and shown to be involved in various biological processes. Consistent with previous reports, a large proportion of the acetylation sites were present on proteins involved in glycolysis/gluconeogenesis, the citrate cycle, and fatty acid metabolism. A NAD(+)-dependent deacetylase (MRA_1161) deletion mutant of M. tuberculosis H37Ra was constructed and its characterization showed a different colony morphology, reduced biofilm formation, and increased tolerance of heat stress. Interestingly, lysine acetylation was found, for the first time, to block the immunogenicity of a peptide derived from a known immunogen, HspX, suggesting that lysine acetylation plays a regulatory role in immunogenicity. Our data provide the first global survey of lysine acetylation in M. tuberculosis. The dataset should be an important resource for the functional analysis of lysine acetylation in M. tuberculosis and facilitate the clarification of the entire metabolic networks of this life-threatening pathogen.
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Affiliation(s)
- Fengying Liu
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Mingkun Yang
- §Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xude Wang
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shanshan Yang
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jing Gu
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jie Zhou
- ¶Foshan Fourth People's Hospital, Foshan, China
| | - Xian-En Zhang
- ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaoyu Deng
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;
| | - Feng Ge
- §Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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20
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Hayden JD, Brown LR, Gunawardena HP, Perkowski EF, Chen X, Braunstein M. Reversible acetylation regulates acetate and propionate metabolism in Mycobacterium smegmatis. MICROBIOLOGY-SGM 2013; 159:1986-1999. [PMID: 23813678 DOI: 10.1099/mic.0.068585-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Carbon metabolic pathways are important to the pathogenesis of Mycobacterium tuberculosis, the causative agent of tuberculosis. However, extremely little is known about metabolic regulation in mycobacteria. There is growing evidence for lysine acetylation being a mechanism of regulating bacterial metabolism. Lysine acetylation is a post-translational modification in which an acetyl group is covalently attached to the side chain of a lysine residue. This modification is mediated by acetyltransferases, which add acetyl groups, and deacetylases, which remove the acetyl groups. Here we set out to test whether lysine acetylation and deacetylation impact acetate metabolism in the model mycobacteria Mycobacterium smegmatis, which possesses 25 candidate acetyltransferases and 3 putative lysine deacetylases. Using mutants lacking predicted acetyltransferases and deacetylases we showed that acetate metabolism in M. smegmatis is regulated by reversible acetylation of acetyl-CoA synthetase (Ms-Acs) through the action of a single pair of enzymes: the acetyltransferase Ms-PatA and the sirtuin deacetylase Ms-SrtN. We also confirmed that the role of Ms-PatA in regulating Ms-Acs regulation depends on cAMP binding. We additionally demonstrated a role for Ms-Acs, Ms-PatA and Ms-SrtN in regulating the metabolism of propionate in M. smegmatis. Finally, along with Ms-Acs, we identified a candidate propionyl-CoA synthetase, Ms5404, as acetylated in whole-cell lysates. This work lays the foundation for studying the regulatory circuit of acetylation and deacetylation in the cellular context of mycobacteria.
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Affiliation(s)
- Jennifer D Hayden
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lanisha R Brown
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ellen F Perkowski
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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21
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Zheng W. Sirtuins as emerging anti-parasitic targets. Eur J Med Chem 2013; 59:132-40. [DOI: 10.1016/j.ejmech.2012.11.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 10/16/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
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22
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A novel metabolite of antituberculosis therapy demonstrates host activation of isoniazid and formation of the isoniazid-NAD+ adduct. Antimicrob Agents Chemother 2011; 56:28-35. [PMID: 22037847 DOI: 10.1128/aac.05486-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most effective and widely used antituberculosis (anti-TB) drugs is isoniazid (INH), a prodrug activated via oxidation that forms an adduct with NAD(+) to inhibit NADH-dependent targets of Mycobacterium tuberculosis, such as enoyl-acyl carrier protein reductase (InhA). The metabolic by-products and potentially toxic intermediates resulting from INH therapy have been identified through a large body of work. However, an INH-NAD adduct or structures related to this adduct have not been identified in specimens from human TB patients or animal models of TB. Analyses by mass spectrometry of urine collected from TB patients in a study conducted by the NIAID-funded Tuberculosis Research Unit identified 4-isonicotinoylnicotinamide (C(12)H(9)N(3)O(2)) as a novel metabolite of INH therapy. This compound was formed by M. tuberculosis strains in a KatG-dependent manner but could also be produced by mice treated with INH independent of an M. tuberculosis infection. Thus, the 4-isonicotinoylnicotinamide observed in human urine samples is likely derived from the degradation of oxidized INH-NAD adducts and provides direct evidence of host INH activation.
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23
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Hirsch BM, Zheng W. Sirtuin mechanism and inhibition: explored with N(ε)-acetyl-lysine analogs. MOLECULAR BIOSYSTEMS 2010; 7:16-28. [PMID: 20842312 DOI: 10.1039/c0mb00033g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Silent information regulator 2 (Sir2) enzymes or sirtuins are a family of intracellular protein deacetylases that can catalyze the β-nicotinamide adenine dinucleotide (β-NAD(+))-dependent deacetylation of N(ε)-acetyl-lysine on protein substrates, with the formation of lysine N(ε)-deacetylated protein species and small molecule products, i.e. nicotinamide and 2'-O-acetyl-ADP-ribose (2'-O-AADPR). These enzymes are evolutionarily conserved among all the three kingdoms of life, with the yeast Sir2 being the founding family member. In humans, seven sirtuins, i.e. SIRT1-7, have been identified. The past a few years have witnessed a tremendous interest in investigating the unique mechanism for the sirtuin-catalyzed deacetylation reaction. We have also seen a lot of research employing different strategies to identify different types of the inhibitors for this enzymatic deacetylation reaction. These inhibitors hold great potential toward a fuller exploration of sirtuin biology and pharmacology as well as toward developing novel therapeutics for metabolic and age-related diseases and cancer. Here we would like to review the significant contributions that the judicious use of a variety of N(ε)-acetyl-lysine analogs has been able to make toward our enhanced mechanistic understanding and capability of pharmacological exploitation of the sirtuin-catalyzed deacetylation reaction.
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Affiliation(s)
- Brett M Hirsch
- Department of Chemistry, University of Akron, 190 E. Buchtel Commons, Akron, OH 44325, USA
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