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Bories P, Rima J, Tranier S, Marcoux J, Grimoire Y, Tomaszczyk M, Launay A, Fata K, Marrakchi H, Burlet‐Schiltz O, Mourey L, Ducoux‐Petit M, Bardou F, Bon C, Quémard A. HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function. Protein Sci 2024; 33:e4964. [PMID: 38501584 PMCID: PMC10949391 DOI: 10.1002/pro.4964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Worldwide, tuberculosis is the second leading infectious killer and multidrug resistance severely hampers disease control. Mycolic acids are a unique category of lipids that are essential for viability, virulence, and persistence of the causative agent, Mycobacterium tuberculosis (Mtb). Therefore, enzymes involved in mycolic acid biosynthesis represent an important class of drug targets. We previously showed that the (3R)-hydroxyacyl-ACP dehydratase (HAD) protein HadD is dedicated mainly to the production of ketomycolic acids and plays a determinant role in Mtb biofilm formation and virulence. Here, we discovered that HAD activity requires the formation of a tight heterotetramer between HadD and HadB, a HAD unit encoded by a distinct chromosomal region. Using biochemical, structural, and cell-based analyses, we showed that HadB is the catalytic subunit, whereas HadD is involved in substrate binding. Based on HadBDMtb crystal structure and substrate-bound models, we identified determinants of the ultra-long-chain lipid substrate specificity and revealed details of structure-function relationship. HadBDMtb unique function is partly due to a wider opening and a higher flexibility of the substrate-binding crevice in HadD, as well as the drastically truncated central α-helix of HadD hotdog fold, a feature described for the first time in a HAD enzyme. Taken together, our study shows that HadBDMtb , and not HadD alone, is the biologically relevant functional unit. These results have important implications for designing innovative antivirulence molecules to fight tuberculosis, as they suggest that the target to consider is not an isolated subunit, but the whole HadBD complex.
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Affiliation(s)
- Pascaline Bories
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Julie Rima
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Yasmina Grimoire
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Mathilde Tomaszczyk
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Anne Launay
- Service de TP de BiochimieUniversité de Toulouse, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Karine Fata
- Service de TP de BiochimieUniversité de Toulouse, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Odile Burlet‐Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Manuelle Ducoux‐Petit
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Fabienne Bardou
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, Université Toulouse III ‐ Paul Sabatier (UPS)ToulouseFrance
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2
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Ling X, Liu X, Wang K, Guo M, Ou Y, Li D, Xiang Y, Zheng J, Hu L, Zhang H, Li W. Lsr2 acts as a cyclic di-GMP receptor that promotes keto-mycolic acid synthesis and biofilm formation in mycobacteria. Nat Commun 2024; 15:695. [PMID: 38267428 PMCID: PMC10808224 DOI: 10.1038/s41467-024-44774-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a second messenger that promotes biofilm formation in several bacterial species, but the mechanisms are often unclear. Here, we report that c-di-GMP promotes biofilm formation in mycobacteria in a manner dependent on the nucleoid-associated protein Lsr2. We show that c-di-GMP specifically binds to Lsr2 at a ratio of 1:1. Lsr2 upregulates the expression of HadD, a (3R)-hydroxyacyl-ACP dehydratase, thus promoting the synthesis of keto-mycolic acid and biofilm formation. Thus, Lsr2 acts as a c-di-GMP receptor that links the second messenger's function to lipid synthesis and biofilm formation in mycobacteria.
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Affiliation(s)
- Xiaocui Ling
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xiao Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Kun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Minhao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yanzhe Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Danting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yulin Xiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jiachen Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Hongyun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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3
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Kumar G, Kapoor S. Targeting mycobacterial membranes and membrane proteins: Progress and limitations. Bioorg Med Chem 2023; 81:117212. [PMID: 36804747 DOI: 10.1016/j.bmc.2023.117212] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Among the various bacterial infections, tuberculosis continues to hold center stage. Its causative agent, Mycobacterium tuberculosis, possesses robust defense mechanisms against most front-line antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. It is now well-established that bacteria change their membrane composition to optimize their environment to survive and elude drug action. Thus targeting membrane or membrane components is a promising avenue for exploiting the chemical space focussed on developing novel membrane-centric anti-bacterial small molecules. These approaches are more effective, non-toxic, and can attenuate resistance phenotype. We present the relevance of targeting the mycobacterial membrane as a practical therapeutic approach. The review highlights the direct and indirect targeting of membrane structure and function. Direct membrane targeting agents cause perturbation in the membrane potential and can cause leakage of the cytoplasmic contents. In contrast, indirect membrane targeting agents disrupt the function of membrane-associated proteins involved in cell wall biosynthesis or energy production. We discuss the chronological chemical improvements in various scaffolds targeting specific membrane-associated protein targets, their clinical evaluation, and up-to-date account of their ''mechanisms of action, potency, selectivity'' and limitations. The sources of anti-TB drugs/inhibitors discussed in this work have emerged from target-based identification, cell-based phenotypic screening, drug repurposing, and natural products. We believe this review will inspire the exploration of uncharted chemical space for informing the development of new scaffolds that can inhibit novel mycobacterial membrane targets.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Departemnt of Natural Products, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad 500037, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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4
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Singh V, Grzegorzewicz AE, Fienberg S, Müller R, Khonde LP, Sanz O, Alfonso S, Urones B, Drewes G, Bantscheff M, Ghidelli-Disse S, Ioerger TR, Angala B, Liu J, Lee RE, Sacchettini JC, Krieger IV, Jackson M, Chibale K, Ghorpade SR. 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:2315-2326. [PMID: 36325756 PMCID: PMC9673142 DOI: 10.1021/acsinfecdis.2c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 11/05/2022]
Abstract
Alternative mode-of-inhibition of clinically validated targets is an effective strategy for circumventing existing clinical drug resistance. Herein, we report 1,3-diarylpyrazolyl-acylsulfonamides as potent inhibitors of HadAB/BC, a 3-hydroxyl-ACP dehydratase complex required to iteratively elongate the meromycolate chain of mycolic acids in Mycobacterium tuberculosis (Mtb). Mutations in compound 1-resistant Mtb mutants mapped to HadC (Rv0637; K157R), while chemoproteomics confirmed the compound's binding to HadA (Rv0635), HadB (Rv0636), and HadC. The compounds effectively inhibited the HadAB and HadBC enzyme activities and affected mycolic acid biosynthesis in Mtb, in a concentration-dependent manner. Unlike known 3-hydroxyl-ACP dehydratase complex inhibitors of clinical significance, isoxyl and thioacetazone, 1,3-diarylpyrazolyl-acylsulfonamides did not require activation by EthA and thus are not liable to EthA-mediated resistance. Further, the crystal structure of a key compound in a complex with Mtb HadAB revealed unique binding interactions within the active site of HadAB, providing a useful tool for further structure-based optimization of the series.
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Affiliation(s)
- Vinayak Singh
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch7701, South Africa
| | - Anna E. Grzegorzewicz
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Stephen Fienberg
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Rudolf Müller
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Lutete Peguy Khonde
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Olalla Sanz
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Salvatore Alfonso
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Beatriz Urones
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Gerard Drewes
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | - Marcus Bantscheff
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | | | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas77843, United States
| | - Bhanupriya Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Jiuyu Liu
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - James C. Sacchettini
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Inna V. Krieger
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch7701, South Africa
| | - Sandeep R. Ghorpade
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
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5
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Di Capua CB, Belardinelli JM, Carignano HA, Buchieri MV, Suarez CA, Morbidoni HR. Unveiling the Biosynthetic Pathway for Short Mycolic Acids in Nontuberculous Mycobacteria: Mycobacterium smegmatis MSMEG_4301 and Its Ortholog Mycobacterium abscessus MAB_1915 Are Essential for the Synthesis of α'-Mycolic Acids. Microbiol Spectr 2022; 10:e0128822. [PMID: 35862962 PMCID: PMC9431677 DOI: 10.1128/spectrum.01288-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/09/2022] [Indexed: 11/20/2022] Open
Abstract
Mycolic acids, a hallmark of the genus Mycobacterium, are unique branched long-chain fatty acids produced by a complex biosynthetic pathway. Due to their essentiality and involvement in various aspects of mycobacterial pathogenesis, the synthesis of mycolic acids-and the identification of the enzymes involved-is a valuable target for drug development. Although most of the core pathway is comparable between species, subtle structure differences lead to different structures delineating the mycolic acid repertoire of tuberculous and some nontuberculous mycobacteria. We here report the characterization of an α'-mycolic acid-deficient Mycobacterium smegmatis mutant obtained by chemical mutagenesis. Whole-genome sequencing and bioinformatic analysis identified a premature stop codon in MSMEG_4301, encoding an acyl-CoA synthetase. Orthologs of MSMEG_4301 are present in all mycobacterial species containing α'-mycolic acids. Deletion of the Mycobacterium abscessus ortholog MAB_1915 abrogated synthesis of α'-mycolic acids; likewise, deletion of MSMEG_4301 in an otherwise wild-type M. smegmatis background also caused loss of these short mycolates. IMPORTANCE Mycobacterium abscessus is a nontuberculous mycobacterium responsible for an increasing number of hard-to-treat infections due to the impervious nature of its cell envelope, a natural barrier to several antibiotics. Mycolic acids are key components of that envelope; thus, their synthesis is a valuable target for drug development. Our results identify the first enzyme involved in α'-mycolic acids, a short-chain member of mycolic acids, loss of which greatly affects growth of this opportunistic pathogen.
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Affiliation(s)
- Cecilia B. Di Capua
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan M. Belardinelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo A. Carignano
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María V. Buchieri
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Cristian A. Suarez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor R. Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
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6
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Bailo R, Radhakrishnan A, Singh A, Nakaya M, Fujiwara N, Bhatt A. The mycobacterial desaturase DesA2 is associated with mycolic acid biosynthesis. Sci Rep 2022; 12:6943. [PMID: 35484172 PMCID: PMC9050676 DOI: 10.1038/s41598-022-10589-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Mycolic acids are critical for the survival and virulence of Mycobacterium tuberculosis, the causative agent of tuberculosis. Double bond formation in the merochain of mycolic acids remains poorly understood, though we have previously shown desA1, encoding an aerobic desaturase, is involved in mycolic acid desaturation. Here we show that a second desaturase encoded by desA2 is also involved in mycolate biosynthesis. DesA2 is essential for growth of the fast-growing Mycobacterium smegmatis in laboratory media. Conditional depletion of DesA2 led to a decrease in mycolic acid biosynthesis and loss of mycobacterial viability. Additionally, DesA2-depleted cells also accumulated fatty acids of chain lengths C19-C24. The complete loss of mycolate biosynthesis following DesA2 depletion, and the absence of any monoenoic derivatives (found to accumulate on depletion of DesA1) suggests an early role for DesA2 in the mycolic acid biosynthesis machinery, highlighting its potential as a drug target.
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Affiliation(s)
- Rebeca Bailo
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Makoto Nakaya
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, Sakai City, Osaka, 599-8531, Japan
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Faculty of Contemporary Human Life Science, Tezukayama University, Nara City, Nara, 631-8585, Japan
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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7
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Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Proc Natl Acad Sci U S A 2022; 119:e2201632119. [PMID: 35380903 PMCID: PMC9169745 DOI: 10.1073/pnas.2201632119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Efforts to improve tuberculosis therapy include optimizing multidrug regimens to take advantage of drug–drug synergies. However, the complex host environment has a profound effect on bacterial metabolic state and drug activity, making predictions of optimal drug combinations difficult. In this study, we leverage a newly developed library of conditional knockdown Mycobacterium tuberculosis mutants in which genetic depletion of essential genes mimics the effect of drug therapy. This tractable system allowed us to assess the effect of growth condition on predicted drug–drug interactions. We found that these interactions can be differentially sensitive to the metabolic state, and select in vitro–defined interactions can be leveraged to accelerate bacterial killing during infection. These findings suggest strategies for optimizing tuberculosis therapy. Current chemotherapy against Mycobacterium tuberculosis (Mtb), an important human pathogen, requires a multidrug regimen lasting several months. While efforts have been made to optimize therapy by exploiting drug–drug synergies, testing new drug combinations in relevant host environments remains arduous. In particular, host environments profoundly affect the bacterial metabolic state and drug efficacy, limiting the accuracy of predictions based on in vitro assays alone. In this study, we utilized conditional Mtb knockdown mutants of essential genes as an experimentally tractable surrogate for drug treatment and probe the relationship between Mtb carbon metabolism and chemical–genetic interactions (CGIs). We examined the antitubercular drugs isoniazid, rifampicin, and moxifloxacin and found that CGIs are differentially responsive to the metabolic state, defining both environment-independent and -dependent interactions. Specifically, growth on the in vivo–relevant carbon source, cholesterol, reduced rifampicin efficacy by altering mycobacterial cell surface lipid composition. We report that a variety of perturbations in cell wall synthesis pathways restore rifampicin efficacy during growth on cholesterol, and that both environment-independent and cholesterol-dependent in vitro CGIs could be leveraged to enhance bacterial clearance in the mouse infection model. Our findings present an atlas of chemical–genetic–environmental interactions that can be used to optimize drug–drug interactions, as well as provide a framework for understanding in vitro correlates of in vivo efficacy.
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8
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Chen S, Teng T, Wen S, Zhang T, Huang H. The aceE involves in mycolic acid synthesis and biofilm formation in Mycobacterium smegmatis. BMC Microbiol 2020; 20:259. [PMID: 32811434 PMCID: PMC7437000 DOI: 10.1186/s12866-020-01940-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/11/2020] [Indexed: 11/26/2022] Open
Abstract
Background The integrity of cell wall structure is highly significant for the in vivo survival of mycobacteria. We hypothesized that changes in morphology may indicate changes in cell wall metabolism and identified an aceE gene mutant (aceE-mut) which presented a deficient colony morphology on 7H10 agar by screening transposon mutagenesis in Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis (M. smegmatis). This study aimed to identify the functional role of aceE gene in cell wall biosynthesis in M. smegmatis. Results We observed that the colony morphology of aceE-mut was quite different, smaller and smoother on the solid culture medium than the wild-type (WT) strain during the transposon library screening of M. smegmatis. Notably, in contrast with the WT, which aggregates and forms biofilm, the aceE-mut lost its ability of growing aggregately and biofilm formation, which are two very important features of mycobacteria. The morphological changes in the aceE-mut strain were further confirmed by electron microscopy which indicated smoother and thinner cell envelope images in contrast with the rough morphology of WT strains. Additionally, the aceE-mut was more fragile to acidic stress and exhibited a pronounced defects in entering the macrophages as compared to the WT. The analysis of mycolic acid (MA) using LC-MS indicated deficiency of alpha-MA and epoxy-MA in aceE-mut strain whereas complementation of the aceE-mut with a wild-type aceE gene restored the composition of MA. Conclusions Over all, this study indicates that aceE gene plays a significant role in the mycolic acid synthesis and affects the colony morphology, biofilm formation of M. smegmatis and bacteria invasion of macrophage.
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Affiliation(s)
- Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Tianlu Teng
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Shuan Wen
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Tingting Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, 101149, China.
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9
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Abstract
Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery.
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10
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Grzegorzewicz AE, Gee C, Das S, Liu J, Belardinelli JM, Jones V, McNeil MR, Lee RE, Jackson M. Mechanisms of Resistance Associated with the Inhibition of the Dehydration Step of Type II Fatty Acid Synthase in Mycobacterium tuberculosis. ACS Infect Dis 2020; 6:195-204. [PMID: 31775512 DOI: 10.1021/acsinfecdis.9b00162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Isoxyl (ISO) and thiacetazone (TAC) are two antitubercular prodrugs that abolish mycolic acid biosynthesis and kill Mycobacterium tuberculosis (Mtb) through the inhibition of the essential type II fatty acid synthase (FAS-II) dehydratase HadAB. While mutations preventing ISO and TAC either from being converted to their active form or from covalently modifying their target are the most frequent spontaneous mutations associated with high-level resistance to both drugs, the molecular mechanisms underlying the high-level ISO and TAC resistance of Mtb strains harboring missense mutations in the second, nonessential, FAS-II dehydratase HadBC have remained unexplained. Using a combination of genetic, biochemical, and biophysical approaches and molecular dynamics simulation, we here show that all four reported resistance mutations in the HadC subunit of HadBC alter the stability and/or specific activity of the enzyme, allowing it in two cases (HadBCV85I and HadBCK157R) to compensate for a deficiency in HadAB in whole Mtb bacilli. The analysis of the mycolic acid profiles of Mtb strains expressing the mutated forms of HadC further points to alterations in the activity of the mycolic acid biosynthetic complex and suggests an additional contributing resistance mechanism whereby HadC mutations may reduce the accessibility of HadAB to ISO and TAC. Collectively, our results highlight the importance of developing optimized inhibitors of the dehydration step of FAS-II capable of inhibiting both dehydratases simultaneously, a goal that may be achievable given the structural resemblance of the two enzymes and their reliance on the same catalytic subunit HadB.
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Affiliation(s)
- Anna E. Grzegorzewicz
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, Wroclaw PL-53-114, Poland
| | - Clifford Gee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Sourav Das
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jiuyu Liu
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Juan Manuel Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Victoria Jones
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Michael R. McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
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11
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Discovery of a novel dehydratase of the fatty acid synthase type II critical for ketomycolic acid biosynthesis and virulence of Mycobacterium tuberculosis. Sci Rep 2020; 10:2112. [PMID: 32034201 PMCID: PMC7005898 DOI: 10.1038/s41598-020-58967-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023] Open
Abstract
The fatty acid synthase type II (FAS-II) multienzyme system builds the main chain of mycolic acids (MAs), important lipid pathogenicity factors of Mycobacterium tuberculosis (Mtb). Due to their original structure, the identification of the (3 R)-hydroxyacyl-ACP dehydratases, HadAB and HadBC, of Mtb FAS-II complex required in-depth work. Here, we report the discovery of a third dehydratase protein, HadDMtb (Rv0504c), whose gene is non-essential and sits upstream of cmaA2 encoding a cyclopropane synthase dedicated to keto- and methoxy-MAs. HadDMtb deletion triggered a marked change in Mtb keto-MA content and size distribution, deeply impacting the production of full-size molecules. Furthermore, abnormal MAs, likely generated from 3-hydroxylated intermediates, accumulated. These data strongly suggest that HadDMtb catalyzes the 3-hydroxyacyl dehydratation step of late FAS-II elongation cycles during keto-MA biosynthesis. Phenotyping of Mtb hadD deletion mutant revealed the influence of HadDMtb on the planktonic growth, colony morphology and biofilm structuration, as well as on low temperature tolerance. Importantly, HadDMtb has a strong impact on Mtb virulence in the mouse model of infection. The effects of the lack of HadDMtb observed both in vitro and in vivo designate this protein as a bona fide target for the development of novel anti-TB intervention strategies.
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12
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Belardinelli JM, Stevens CM, Li W, Tan YZ, Jones V, Mancia F, Zgurskaya HI, Jackson M. The MmpL3 interactome reveals a complex crosstalk between cell envelope biosynthesis and cell elongation and division in mycobacteria. Sci Rep 2019; 9:10728. [PMID: 31341202 PMCID: PMC6656915 DOI: 10.1038/s41598-019-47159-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/08/2019] [Indexed: 01/19/2023] Open
Abstract
Integral membrane transporters of the Mycobacterial Membrane Protein Large (MmpL) family and their interactome play important roles in the synthesis and export of mycobacterial outer membrane lipids. Despite the current interest in the mycolic acid transporter, MmpL3, from the perspective of drug discovery, the nature and biological significance of its interactome remain largely unknown. We here report on a genome-wide screening by two-hybrid system for MmpL3 binding partners. While a surprisingly low number of proteins involved in mycolic acid biosynthesis was found to interact with MmpL3, numerous enzymes and transporters participating in the biogenesis of peptidoglycan, arabinogalactan and lipoglycans, and the cell division regulatory protein, CrgA, were identified among the hits. Surface plasmon resonance and co-immunoprecipitation independently confirmed physical interactions for three proteins in vitro and/or in vivo. Results are in line with the focal localization of MmpL3 at the poles and septum of actively-growing bacilli where the synthesis of all major constituents of the cell wall core are known to occur, and are further suggestive of a role for MmpL3 in the coordination of new cell wall deposition during cell septation and elongation. This novel aspect of the physiology of MmpL3 may contribute to the extreme vulnerability and high therapeutic potential of this transporter.
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Affiliation(s)
- Juan Manuel Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Casey M Stevens
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Victoria Jones
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA.
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13
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Nontuberculous Mycobacteria Persistence in a Cell Model Mimicking Alveolar Macrophages. Microorganisms 2019; 7:microorganisms7050113. [PMID: 31035520 PMCID: PMC6560506 DOI: 10.3390/microorganisms7050113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
Nontuberculous Mycobacteria (NTM) respiratory infections have been gradually increasing. Here, THP-1 cells were used as a model to evaluate intracellular persistence of three NTM species (reference and clinical strains) in human alveolar macrophages. The contribution of phagosome acidification, nitric oxide (NO) production and cell dead on NTM intracellular fate was assessed. In addition, strains were characterized regarding their repertoire of virulence factors by whole-genome sequencing. NTM experienced different intracellular fates: M. smegmatis and M. fortuitum ATCC 6841 were cleared within 24h. In contrast, M. avium strains (reference/clinical) and M. fortuitum clinical strain were able to replicate. Despite this fact, unexpectedly high percentages of acidified phagosomes were found harbouring rab7, but not CD63. All NTM were able to survive in vitro at acidic pHs, with the exception of M. smegmatis. Our data further suggested a minor role for NO in intracellular persistence and that apoptosis mediated by caspase 8 and 3/7, but not necrosis, is triggered during NTM infection. Insights regarding the bacteria genomic backbone corroborated the virulence potential of M. avium and M. fortuitum. In conclusion, the phenotypic traits detected contrast with those described for M. tuberculosis, pointing out that NTM adopt distinct strategies to manipulate the host immune defense and persist intracellularly.
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14
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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15
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Di Capua CB, Belardinelli JM, Buchieri MV, Bortolotti A, Franceschelli JJ, Morbidoni HR. Deletion of MSMEG_1350 in Mycobacterium smegmatis causes loss of epoxy-mycolic acids, fitness alteration at low temperature and resistance to a set of mycobacteriophages. MICROBIOLOGY-SGM 2018; 164:1567-1582. [PMID: 30311878 DOI: 10.1099/mic.0.000734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mycobacterium smegmatis is intrinsically resistant to thiacetazone, an anti-tubercular thiourea; however we report here that it causes a mild inhibition in growth in liquid medium. Since mycolic acid biosynthesis was affected, we cloned and expressed Mycobacterium smegmatis mycolic acid methyltransferases, postulated as targets for thiacetazone in other mycobacterial species. During this analysis we identified MSMEG_1350 as the methyltransferase involved in epoxy mycolic acid synthesis since its deletion led to their total loss. Phenotypic characterization of the mutant strain showed colony morphology alterations at all temperatures, reduced growth and a slightly increased susceptibility to SDS, lipophilic and large hydrophilic drugs at 20 °C with little effect at 37 °C. No changes were detected between parental and mutant strains in biofilm formation, sliding motility or sedimentation rate. Intriguingly, we found that several mycobacteriophages severely decreased their ability to form plaques in the mutant strain. Taken together our results prove that, in spite of being a minor component of the mycolic acid pool, epoxy-mycolates are required for a proper assembly and functioning of the cell envelope. Further studies are warranted to decipher the role of epoxy-mycolates in the M. smegmatis cell envelope.
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Affiliation(s)
- Cecilia B Di Capua
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan M Belardinelli
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina.,‡Present address: Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - María V Buchieri
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ana Bortolotti
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina J Franceschelli
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor R Morbidoni
- Laboratorio de Microbiología Molecular, Cátedra de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
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