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Yimcharoen M, Saikaew S, Wattananandkul U, Phunpae P, Intorasoot S, Tayapiwatana C, Butr-Indr B. Mycobacterium tuberculosis Adaptation in Response to Isoniazid Treatment in a Multi-Stress System That Mimics the Host Environment. Antibiotics (Basel) 2023; 12:antibiotics12050852. [PMID: 37237755 DOI: 10.3390/antibiotics12050852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Isoniazid (INH) is an antibiotic that is widely used to treat tuberculosis (TB). Adaptation to environmental stress is a survival strategy for Mycobacterium tuberculosis and is associated with antibiotic resistance development. Here, mycobacterial adaptation following INH treatment was studied using a multi-stress system (MS), which mimics host-derived stress. Mtb H37Rv (drug-susceptible), mono-isoniazid resistant (INH-R), mono-rifampicin resistant (RIF-R), and multidrug-resistant (MDR) strains were cultivated in the MS with or without INH. The expression of stress-response genes (hspX, tgs1, icl1, and sigE) and lipoarabinomannan (LAM)-related genes (pimB, mptA, mptC, dprE1, dprE2, and embC), which play important roles in the host-pathogen interaction, were measured using real-time PCR. The different adaptations of the drug-resistant (DR) and drug-susceptible (DS) strains were presented in this work. icl1 and dprE1 were up-regulated in the DR strains in the MS, implying their roles as markers of virulence and potential drug targets. In the presence of INH, hspX, tgs1, and sigE were up-regulated in the INH-R and RIF-R strains, while icl1 and LAM-related genes were up-regulated in the H37Rv strain. This study demonstrates the complexity of mycobacterial adaptation through stress response regulation and LAM expression in response to INH under the MS, which could potentially be applied for TB treatment and monitoring in the future.
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Affiliation(s)
- Manita Yimcharoen
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sukanya Saikaew
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Usanee Wattananandkul
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ponrut Phunpae
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sorasak Intorasoot
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Bordin Butr-Indr
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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Prithviraj M, Kado T, Mayfield JA, Young DC, Huang AD, Motooka D, Nakamura S, Siegrist MS, Moody DB, Morita YS. Tuberculostearic Acid Controls Mycobacterial Membrane Compartmentalization. mBio 2023; 14:e0339622. [PMID: 36976029 PMCID: PMC10127668 DOI: 10.1128/mbio.03396-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
The intracellular membrane domain (IMD) is a laterally discrete region of the mycobacterial plasma membrane, enriched in the subpolar region of the rod-shaped cell. Here, we report genome-wide transposon sequencing to discover the controllers of membrane compartmentalization in Mycobacterium smegmatis. The putative gene cfa showed the most significant effect on recovery from membrane compartment disruption by dibucaine. Enzymatic analysis of Cfa and lipidomic analysis of a cfa deletion mutant (Δcfa) demonstrated that Cfa is an essential methyltransferase for the synthesis of major membrane phospholipids containing a C19:0 monomethyl-branched stearic acid, also known as tuberculostearic acid (TBSA). TBSA has been intensively studied due to its abundant and genus-specific production in mycobacteria, but its biosynthetic enzymes had remained elusive. Cfa catalyzed the S-adenosyl-l-methionine-dependent methyltransferase reaction using oleic acid-containing lipid as a substrate, and Δcfa accumulated C18:1 oleic acid, suggesting that Cfa commits oleic acid to TBSA biosynthesis, likely contributing directly to lateral membrane partitioning. Consistent with this model, Δcfa displayed delayed restoration of subpolar IMD and delayed outgrowth after bacteriostatic dibucaine treatment. These results reveal the physiological significance of TBSA in controlling lateral membrane partitioning in mycobacteria. IMPORTANCE As its common name implies, tuberculostearic acid is an abundant and genus-specific branched-chain fatty acid in mycobacterial membranes. This fatty acid, 10-methyl octadecanoic acid, has been an intense focus of research, particularly as a diagnostic marker for tuberculosis. It was discovered in 1934, and yet the enzymes that mediate the biosynthesis of this fatty acid and the functions of this unusual fatty acid in cells have remained elusive. Through a genome-wide transposon sequencing screen, enzyme assay, and global lipidomic analysis, we show that Cfa is the long-sought enzyme that is specifically involved in the first step of generating tuberculostearic acid. By characterizing a cfa deletion mutant, we further demonstrate that tuberculostearic acid actively regulates lateral membrane heterogeneity in mycobacteria. These findings indicate the role of branched fatty acids in controlling the functions of the plasma membrane, a critical barrier for the pathogen to survive in its human host.
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Affiliation(s)
- Malavika Prithviraj
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jacob A. Mayfield
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David C. Young
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Annie D. Huang
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - M. Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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53
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Sankey N, Merrick H, Singh P, Rogers J, Reddi A, Hartson SD, Mitra A. Role of the Mycobacterium tuberculosis ESX-4 Secretion System in Heme Iron Utilization and Pore Formation by PPE Proteins. mSphere 2023; 8:e0057322. [PMID: 36749044 PMCID: PMC10117145 DOI: 10.1128/msphere.00573-22] [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: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is transmitted through aerosols and primarily colonizes within the lung. The World Health Organization estimates that Mtb kills ~1.4 million people every year. A key aspect that makes Mtb such a successful pathogen is its ability to overcome iron limitation mounted by the host immune response. In our previous studies, we have shown that Mtb can utilize iron from heme, the largest source of iron in the human host, and that it uses two redundant heme utilization pathways. In this study, we show that the ESX-4 type VII secretion system (T7SS) is necessary for extracellular heme uptake into the Mtb cell through both heme utilization pathways. ESX-4 influences the secretion of the culture filtrate proteins Rv0125 and Rv1085c, which are also necessary for efficient heme utilization. We also discovered that deletion of the alternative sigma factor SigM significantly reduced Mtb heme utilization through both pathways and predict that SigM is a global positive regulator of core heme utilization genes of both pathways. Finally, we present the first direct evidence that some mycobacterial PPE (proline-proline-glutamate motif) proteins of the PPE protein family are pore-forming membrane proteins. Altogether, we identified core components of both Mtb Heme utilization pathways that were previously unknown and identified a novel channel-forming membrane protein of Mtb. IMPORTANCE M. tuberculosis (Mtb) is completely dependent on iron acquisition in the host to cause disease. The largest source of iron for Mtb in the human host is heme. Here, we show that the ancestral ESX-4 type VII secretion system is required for the efficient utilization of heme as a source of iron, which is an essential nutrient. This is another biological function identified for ESX-4 in Mtb, whose contribution to Mtb physiology is poorly understood. A most exciting finding is that some mycobacterial PPE (proline-proline-glutamate motif) proteins that have been implicated in the nutrient acquisition are membrane proteins that can form channels in a lipid bilayer. These observations have far-reaching implications because they support an emerging theme that PPE proteins can function as channel proteins in the outer mycomembrane for nutrient acquisition. Mtb has evolved a heme uptake system that is drastically different from all other known bacterial heme acquisition systems.
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Affiliation(s)
- November Sankey
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Haley Merrick
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Padam Singh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Amit Reddi
- School of Chemistry and Biochemistry, Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Steven D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Avishek Mitra
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Al-Jourani O, Benedict ST, Ross J, Layton AJ, van der Peet P, Marando VM, Bailey NP, Heunis T, Manion J, Mensitieri F, Franklin A, Abellon-Ruiz J, Oram SL, Parsons L, Cartmell A, Wright GSA, Baslé A, Trost M, Henrissat B, Munoz-Munoz J, Hirt RP, Kiessling LL, Lovering AL, Williams SJ, Lowe EC, Moynihan PJ. Identification of D-arabinan-degrading enzymes in mycobacteria. Nat Commun 2023; 14:2233. [PMID: 37076525 PMCID: PMC10115798 DOI: 10.1038/s41467-023-37839-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/31/2023] [Indexed: 04/21/2023] Open
Abstract
Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.
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Affiliation(s)
- Omar Al-Jourani
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Samuel T Benedict
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jennifer Ross
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Abigail J Layton
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Phillip van der Peet
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA The Koch Integrative Cancer Research Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas P Bailey
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tiaan Heunis
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Joseph Manion
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Francesca Mensitieri
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Aaron Franklin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Javier Abellon-Ruiz
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sophia L Oram
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Lauren Parsons
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alan Cartmell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Arnaud Baslé
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthias Trost
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Jose Munoz-Munoz
- Microbial Enzymology Group, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Robert P Hirt
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew L Lovering
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Mishra A, Das A, Banerjee T. Designing New Magic Bullets to Penetrate the Mycobacterial Shield: An Arduous Quest for Promising Therapeutic Candidates. Microb Drug Resist 2023; 29:213-227. [PMID: 37015080 DOI: 10.1089/mdr.2021.0441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Mycobacterium spp. intimidated mankind since time immemorial. The triumph over this organism was anticipated with the introduction of potent antimicrobials in the mid-20th century. However, the emergence of drug resistance in mycobacteria, Mycobacterium tuberculosis, in particular, caused great concern for the treatment. With the enemy growing stronger, there is an immediate need to equip the therapeutic arsenal with novel and potent chemotherapeutic agents. The task seems intricating as our understanding of the dynamic nature of the mycobacteria requires intense experimentation and research. Targeting the mycobacterial cell envelope appears promising, but its versatility allows it to escape the lethal effect of the molecules acting on it. The unique ability of hiding (inactivity during latency) also assists the bacterium to survive in a drug-rich environment. The drug delivery systems also require upgradation to allow better bioavailability and tolerance in patients. Although the resistance to the novel drugs is inevitable, our commitment to the research in this area will ensure the discovery of effective weapons against this formidable opponent.
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Affiliation(s)
- Anwita Mishra
- Department of Microbiology, Mahamana Pandit Madan Mohan Malviya Cancer Centre and Homi Bhabha Cancer Hospital, Varanasi, India
| | - Arghya Das
- Department of Microbiology, National Cancer Institute, All India Institute of Medical Sciences, New Delhi, India
| | - Tuhina Banerjee
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, India
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56
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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57
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Sparks IL, Nijjer J, Yan J, Morita YS. Lipoarabinomannan regulates septation in Mycobacterium smegmatis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534150. [PMID: 36993273 PMCID: PMC10055410 DOI: 10.1101/2023.03.26.534150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The growth and division of mycobacteria, which include several clinically relevant pathogens, deviate significantly from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. In addition to being structurally distinct, the molecular components of the mycobacterial envelope are also evolutionarily unique, including the phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM). LM and LAM modulate host immunity during infection, but their role outside of intracellular survival remains poorly understood, despite their widespread conservation among non-pathogenic and opportunistically pathogenic mycobacteria. Previously, Mycobacterium smegmatis and Mycobacterium tuberculosis mutants producing structurally altered LM and LAM were shown to grow slowly under certain conditions and to be more sensitive to antibiotics, suggesting that mycobacterial lipoglycans may support cellular integrity or growth. To test this, we constructed multiple biosynthetic lipoglycan mutants of M. smegmatis and determined the effect of each mutation on cell wall biosynthesis, envelope integrity, and division. We found that mutants deficient in LAM, but not LM, fail to maintain cell wall integrity in a medium-dependent manner, with envelope deformations specifically associated with septa and new poles. Conversely, a mutant producing abnormally large LAM formed multiseptated cells in way distinct from that observed in a septal hydrolase mutant. These results show that LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell envelope integrity and septal placement.
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Affiliation(s)
- Ian L. Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
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Mittal E, Roth AT, Seth A, Singamaneni S, Beatty W, Philips JA. Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions. eLife 2023; 12:e85416. [PMID: 36852737 PMCID: PMC9998084 DOI: 10.7554/elife.85416] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/11/2023] [Indexed: 03/01/2023] Open
Abstract
For decades, investigators have studied the interaction of Mycobacterium tuberculosis (Mtb) with macrophages, which serve as a major cellular niche for the bacilli. Because Mtb are prone to aggregation, investigators rely on varied methods to disaggregate the bacteria for these studies. Here, we examined the impact of routinely used preparation methods on bacterial cell envelope integrity, macrophage inflammatory responses, and intracellular Mtb survival. We found that both gentle sonication and filtering damaged the mycobacterial cell envelope and markedly impacted the outcome of infections in mouse bone marrow-derived macrophages. Unexpectedly, sonicated bacilli were hyperinflammatory, eliciting dramatically higher TLR2-dependent gene expression and elevated secretion of IL-1β and TNF-α. Despite evoking enhanced inflammatory responses, sonicated bacilli replicated normally in macrophages. In contrast, Mtb that had been passed through a filter induced little inflammatory response, and they were attenuated in macrophages. Previous work suggests that the mycobacterial cell envelope lipid, phthiocerol dimycocerosate (PDIM), dampens macrophage inflammatory responses to Mtb. However, we found that the impact of PDIM depended on the method used to prepare Mtb. In conclusion, widely used methodologies to disaggregate Mtb may introduce experimental artifacts in Mtb-host interaction studies, including alteration of host inflammatory signaling, intracellular bacterial survival, and interpretation of bacterial mutants.
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Affiliation(s)
- Ekansh Mittal
- Division of Infectious Diseases, Department of Medicine, Washington University School of MedicineSt LouisUnited States
- Department of Molecular Microbiology, Washington University School of MedicineSt LouisUnited States
| | - Andrew T Roth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of MedicineSt LouisUnited States
| | - Anushree Seth
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. LouisSt LouisUnited States
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. LouisSt LouisUnited States
- Siteman Cancer Center, Washington UniversitySt. LouisUnited States
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of MedicineSt LouisUnited States
| | - Jennifer A Philips
- Division of Infectious Diseases, Department of Medicine, Washington University School of MedicineSt LouisUnited States
- Department of Molecular Microbiology, Washington University School of MedicineSt LouisUnited States
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Exploring the Antitubercular Activity of Anthranilic Acid Derivatives: From MabA (FabG1) Inhibition to Intrabacterial Acidification. Pharmaceuticals (Basel) 2023; 16:ph16030335. [PMID: 36986435 PMCID: PMC10057394 DOI: 10.3390/ph16030335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Mycobacterium tuberculosis, the pathogen that causes tuberculosis, is responsible for the death of 1.5 million people each year and the number of bacteria resistant to the standard regimen is constantly increasing. This highlights the need to discover molecules that act on new M. tuberculosis targets. Mycolic acids, which are very long-chain fatty acids essential for M. tuberculosis viability, are synthesized by two types of fatty acid synthase (FAS) systems. MabA (FabG1) is an essential enzyme belonging to the FAS-II cycle. We have recently reported the discovery of anthranilic acids as MabA inhibitors. Here, the structure–activity relationships around the anthranilic acid core, the binding of a fluorinated analog to MabA by NMR experiments, the physico-chemical properties and the antimycobacterial activity of these inhibitors were explored. Further investigation of the mechanism of action in bacterio showed that these compounds affect other targets than MabA in mycobacterial cells and that their antituberculous activity is due to the carboxylic acid moiety which induces intrabacterial acidification.
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Valdemar-Aguilar CM, Manisekaran R, Acosta-Torres LS, López-Marín LM. Spotlight on mycobacterial lipid exploitation using nanotechnology for diagnosis, vaccines, and treatments. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 48:102653. [PMID: 36646193 PMCID: PMC9839462 DOI: 10.1016/j.nano.2023.102653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/24/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Tuberculosis (TB), historically the most significant cause of human morbidity and mortality, has returned as the top infectious disease worldwide, under circumstances worsened by the COVID-19 pandemic's devastating effects on public health. Although Mycobacterium tuberculosis, the causal agent, has been known of for more than a century, the development of tools to control it has been largely neglected. With the advancement of nanotechnology, the possibility of engineering tools at the nanoscale creates unique opportunities to exploit any molecular type. However, little attention has been paid to one of the major attributes of the pathogen, represented by the atypical coat and its abundant lipids. In this review, an overview of the lipids encountered in M. tuberculosis and interest in exploiting them for the development of TB control tools are presented. Then, the amalgamation of nanotechnology with mycobacterial lipids from both reported and future works are discussed.
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Affiliation(s)
- Carlos M. Valdemar-Aguilar
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico
| | - Ravichandran Manisekaran
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico.
| | - Laura S. Acosta-Torres
- Interdisciplinary Research Laboratory (LII), Nanostructures and Biomaterials Area, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Predio el Saucillo y el Potrero, Comunidad de los Tepetates, 37689 León, Mexico
| | - Luz M. López-Marín
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, 76230 Querétaro, Mexico,Corresponding authors
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Paiola M, Dimitrakopoulou D, Pavelka MS, Robert J. Amphibians as a model to study the role of immune cell heterogeneity in host and mycobacterial interactions. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 139:104594. [PMID: 36403788 DOI: 10.1016/j.dci.2022.104594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Mycobacterial infections represent major concerns for aquatic and terrestrial vertebrates including humans. Although our current knowledge is mostly restricted to Mycobacterium tuberculosis and mammalian host interactions, increasing evidence suggests common features in endo- and ectothermic animals infected with non-tuberculous mycobacteria (NTMs) like those described for M. tuberculosis. Importantly, most of the pathogenic and non-pathogenic NTMs detected in amphibians from wild, farmed, and research facilities represent, in addition to the potential economic loss, a rising concern for human health. Upon mycobacterial infection in mammals, the protective immune responses involving the innate and adaptive immune systems are highly complex and therefore not fully understood. This complexity results from the versatility and resilience of mycobacteria to hostile conditions as well as from the immune cell heterogeneity arising from the distinct developmental origins according with the concept of layered immunity. Similar to the differing responses of neonates versus adults during tuberculosis development, the pathogenesis and inflammatory responses are stage-specific in Xenopus laevis during infection by the NTM M. marinum. That is, both in human fetal and neonatal development and in tadpole development, responses are characterized by hypo-responsiveness and a lower capacity to contain mycobacterial infections. Similar to a mammalian fetus and neonates, T cells and myeloid cells in Xenopus tadpoles and axolotls are different from the adult immune cells. Fetal and amphibian larval T cells, which are characterized by a lower T cell receptor (TCR) repertoire diversity, are biased toward regulatory function, and they have distinct progenitor origins from those of the adult immune cells. Some early developing T cells and likely macrophage subpopulations are conserved in adult anurans and mammals, and therefore, they likely play an important role in the host-pathogen interactions from early stages of development to adulthood. Thus, we propose the use of developing amphibians, which have the advantage of being free-living early in their development, as an alternative and complementary model to study the role of immune cell heterogeneity in host-mycobacteria interactions.
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Affiliation(s)
- Matthieu Paiola
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Dionysia Dimitrakopoulou
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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Conformational Dynamics and Stability of Bilayers Formed by Mycolic Acids from the Mycobacterium tuberculosis Outer Membrane. Molecules 2023; 28:molecules28031347. [PMID: 36771014 PMCID: PMC9921641 DOI: 10.3390/molecules28031347] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/16/2023] [Accepted: 01/21/2023] [Indexed: 02/04/2023] Open
Abstract
Bilayers of mycolic acids (MAs) form the outer membrane of Mycobacterium tuberculosis that has high strength and extremely low permeability for external molecules (including antibiotics). For the first time, we were able to study them using the all-atom long-term molecular dynamic simulations (from 300 ns up to 1.2 μs) in order to investigate the conformational changes and most favorable structures of the mycobacterial membranes. The structure and properties of the membranes are crucially dependent on the initial packing of the α-mycolic acid (AMA) molecules, as well as on the presence of the secondary membrane components, keto- and methoxy mycolic acids (KMAs and MMAs). In the case of AMA-based membranes, the most labile conformation is W while other types of conformations (sU as well as sZ, eU, and eZ) are much more stable. In the multicomponent membranes, the presence of the KMA and MMA components (in the W conformation) additionally stabilizes both the W and eU conformations of AMA. The membrane in which AMA prevails in the eU conformation is much thicker and, at the same time, much denser. Such a packing of the MA molecules promotes the formation of a significantly stronger outer mycobacterial membrane that should be much more resistant to the threatening external factors.
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Maranha A, Costa M, Ripoll-Rozada J, Manso JA, Miranda V, Mendes VM, Manadas B, Macedo-Ribeiro S, Ventura MR, Pereira PJB, Empadinhas N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 2023; 6:108. [PMID: 36707645 PMCID: PMC9883506 DOI: 10.1038/s42003-023-04448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) so far detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria such as Mycobacterium avium, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a previously undescribed α-endomannosidase that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1→4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, whose disruption affected mycobacterial growth rate at low temperature.
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Affiliation(s)
- Ana Maranha
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mafalda Costa
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jorge Ripoll-Rozada
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal ,grid.507090.b0000 0004 5303 6218Present Address: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, Spain
| | - José A. Manso
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vanessa Miranda
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Vera M. Mendes
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - M. Rita Ventura
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro José Barbosa Pereira
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Empadinhas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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65
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Ongwae GM, Lepori I, Chordia MD, Dalesandro BE, Apostolos AJ, Siegrist MS, Pires MM. Measurement of Small Molecule Accumulation into Diderm Bacteria. ACS Infect Dis 2023; 9:97-110. [PMID: 36530146 DOI: 10.1021/acsinfecdis.2c00435] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some of the most dangerous bacterial pathogens (Gram-negative and mycobacterial) deploy a formidable secondary membrane barrier to reduce the influx of exogenous molecules. For Gram-negative bacteria, this second exterior membrane is known as the outer membrane (OM), while for the Gram-indeterminate Mycobacteria, it is known as the "myco" membrane. Although different in composition, both the OM and mycomembrane are key structures that restrict the passive permeation of small molecules into bacterial cells. Although it is well-appreciated that such structures are principal determinants of small molecule permeation, it has proven to be challenging to assess this feature in a robust and quantitative way or in complex, infection-relevant settings. Herein, we describe the development of the bacterial chloro-alkane penetration assay (BaCAPA), which employs the use of a genetically encoded protein called HaloTag, to measure the uptake and accumulation of molecules into model Gram-negative and mycobacterial species, Escherichia coli and Mycobacterium smegmatis, respectively, and into the human pathogen Mycobacterium tuberculosis. The HaloTag protein can be directed to either the cytoplasm or the periplasm of bacteria. This offers the possibility of compartmental analysis of permeation across individual cell membranes. Significantly, we also showed that BaCAPA can be used to analyze the permeation of molecules into host cell-internalized E. coli and M. tuberculosis, a critical capability for analyzing intracellular pathogens. Together, our results show that BaCAPA affords facile measurement of permeability across four barriers: the host plasma and phagosomal membranes and the diderm bacterial cell envelope.
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Affiliation(s)
- George M Ongwae
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Irene Lepori
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brianna E Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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66
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Machine Learning Prediction of Mycobacterial Cell Wall Permeability of Drugs and Drug-like Compounds. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020633. [PMID: 36677691 PMCID: PMC9863426 DOI: 10.3390/molecules28020633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]
Abstract
The cell wall of Mycobacterium tuberculosis and related organisms has a very complex and unusual organization that makes it much less permeable to nutrients and antibiotics, leading to the low activity of many potential antimycobacterial drugs against whole-cell mycobacteria compared to their isolated molecular biotargets. The ability to predict and optimize the cell wall permeability could greatly enhance the development of novel antitubercular agents. Using an extensive structure-permeability dataset for organic compounds derived from published experimental big data (5371 compounds including 2671 penetrating and 2700 non-penetrating compounds), we have created a predictive classification model based on fragmental descriptors and an artificial neural network of a novel architecture that provides better accuracy (cross-validated balanced accuracy 0.768, sensitivity 0.768, specificity 0.769, area under ROC curve 0.911) and applicability domain compared with the previously published results.
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67
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Corrigan DT, Ishida E, Chatterjee D, Lowary TL, Achkar JM. Monoclonal antibodies to lipoarabinomannan/arabinomannan - characteristics and implications for tuberculosis research and diagnostics. Trends Microbiol 2023; 31:22-35. [PMID: 35918247 PMCID: PMC9771891 DOI: 10.1016/j.tim.2022.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022]
Abstract
Antibodies to the mycobacterial surface lipoglycan lipoarabinomannan (LAM) and its related capsular polysaccharide arabinomannan (AM) are increasingly important for investigations focused on both understanding mechanisms of protection against Mycobacterium tuberculosis (Mtb) and developing next-generation point-of-care tuberculosis (TB) diagnostics. We provide here an overview of the growing pipeline of monoclonal antibodies (mAbs) to LAM/AM. Old and new methodologies for their generation are reviewed and we outline and discuss their glycan epitope specificity and other features with implications for the TB field.
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Affiliation(s)
- Devin T Corrigan
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Elise Ishida
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jacqueline M Achkar
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
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68
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Nishimura N, Tomiyasu N, Torigoe S, Mizuno S, Fukano H, Ishikawa E, Katano H, Hoshino Y, Matsuo K, Takahashi M, Izumi Y, Bamba T, Akashi K, Yamasaki S. Mycobacterial mycolic acids trigger inhibitory receptor Clec12A to suppress host immune responses. Tuberculosis (Edinb) 2023; 138:102294. [PMID: 36542980 DOI: 10.1016/j.tube.2022.102294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Mycobacteria often cause chronic infection. To establish persistence in the host, mycobacteria need to evade host immune responses. However, the molecular mechanisms underlying the evasion strategy are not fully understood. Here, we demonstrate that mycobacterial cell wall lipids trigger an inhibitory receptor to suppress host immune responses. Mycolic acids are major cell wall components and are essential for survival of mycobacteria. By screening inhibitory receptors that react with mycobacterial lipids, we found that mycolic acids from various mycobacterial species bind to mouse Clec12A, and more potently to human Clec12A. Clec12A is a conserved inhibitory C-type lectin receptor containing immunoreceptor tyrosine-based inhibitory motif (ITIM). Innate immune responses, such as MCP-1 production, and PPD-specific recall T cell responses were augmented in Clec12A-deficient mice after infection. In contrast, human Clec12A transgenic mice were susceptible to infection with M. tuberculosis. These results suggest that mycobacteria dampen host immune responses by hijacking an inhibitory host receptor through their specific and essential lipids, mycolic acids. The blockade of this interaction might provide a therapeutic option for the treatment or prevention of mycobacterial infection.
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Affiliation(s)
- Naoya Nishimura
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan; Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Noriyuki Tomiyasu
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shota Torigoe
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan; Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan; Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Satoru Mizuno
- Research and Development Department, Japan BCG Laboratory, Tokyo, 204-0022, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan
| | - Eri Ishikawa
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Disease, Tokyo, 162-8640, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan
| | - Kazuhiro Matsuo
- Research and Development Department, Japan BCG Laboratory, Tokyo, 204-0022, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 812-8582, Japan; Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 812-8582, Japan; Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 812-8582, Japan; Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University (CiDER), Suita, 565-0871, Japan; Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan; Division of Molecular Design, Research Center for Systems Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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69
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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70
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Yan MY, Zheng D, Li SS, Ding XY, Wang CL, Guo XP, Zhan L, Jin Q, Yang J, Sun YC. Application of combined CRISPR screening for genetic and chemical-genetic interaction profiling in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eadd5907. [PMID: 36417506 PMCID: PMC9683719 DOI: 10.1126/sciadv.add5907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/05/2022] [Indexed: 05/30/2023]
Abstract
CRISPR screening, including CRISPR interference (CRISPRi) and CRISPR-knockout (CRISPR-KO) screening, has become a powerful technology in the genetic screening of eukaryotes. In contrast with eukaryotes, CRISPR-KO screening has not yet been applied to functional genomics studies in bacteria. Here, we constructed genome-scale CRISPR-KO and also CRISPRi libraries in Mycobacterium tuberculosis (Mtb). We first examined these libraries to identify genes essential for Mtb viability. Subsequent screening identified dozens of genes associated with resistance/susceptibility to the antitubercular drug bedaquiline (BDQ). Genetic and chemical validation of the screening results suggested that it provided a valuable resource to investigate mechanisms of action underlying the effects of BDQ and to identify chemical-genetic synergies that can be used to optimize tuberculosis therapy. In summary, our results demonstrate the potential for efficient genome-wide CRISPR-KO screening in bacteria and establish a combined CRISPR screening approach for high-throughput investigation of genetic and chemical-genetic interactions in Mtb.
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Affiliation(s)
- Mei-Yi Yan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Dandan Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Si-Shang Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xin-Yuan Ding
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Chun-Liang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiao-Peng Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Lingjun Zhan
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yi-Cheng Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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Pohane AA, Moore DJ, Lepori I, Gordon RA, Nathan TO, Gepford DM, Kavunja HW, Gaidhane IV, Swarts BM, Siegrist MS. A Bifunctional Chemical Reporter for in Situ Analysis of Cell Envelope Glycan Recycling in Mycobacteria. ACS Infect Dis 2022; 8:2223-2231. [PMID: 36288262 PMCID: PMC9924612 DOI: 10.1021/acsinfecdis.2c00396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In mycobacteria, the glucose-based disaccharide trehalose cycles between the cytoplasm, where it is a stress protectant and carbon source, and the cell envelope, where it is released as a byproduct of outer mycomembrane glycan biosynthesis and turnover. Trehalose recycling via the LpqY-SugABC transporter promotes virulence, antibiotic recalcitrance, and efficient adaptation to nutrient deprivation. The source(s) of trehalose and the regulation of recycling under these and other stressors are unclear. A key technical gap in addressing these questions has been the inability to trace trehalose recycling in situ, directly from its site of liberation from the cell envelope. Here we describe a bifunctional chemical reporter that simultaneously marks mycomembrane biosynthesis and subsequent trehalose recycling with alkyne and azide groups. Using this probe, we discovered that the recycling efficiency for trehalose increases upon carbon starvation, concomitant with an increase in LpqY-SugABC expression. The ability of the bifunctional reporter to probe multiple, linked steps provides a more nuanced understanding of mycobacterial cell envelope metabolism and its plasticity under stress.
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Affiliation(s)
- Amol Arunrao Pohane
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003 USA
| | - Devin J. Moore
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Irene Lepori
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003 USA
| | - Rebecca A. Gordon
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003 USA
| | - Temitope O. Nathan
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Dana M. Gepford
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Herbert W. Kavunja
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Ishani V. Gaidhane
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
| | - Benjamin M. Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859 USA
- Biochemistry, Cell, and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI, 48859 United States
| | - M. Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003 USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003 USA
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72
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Poulton NC, Rock JM. Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:997283. [PMID: 36325467 PMCID: PMC9618640 DOI: 10.3389/fcimb.2022.997283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/30/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis (TB) is among the most difficult infections to treat, requiring several months of multidrug therapy to produce a durable cure. The reasons necessitating long treatment times are complex and multifactorial. However, one major difficulty of treating TB is the resistance of the infecting bacterium, Mycobacterium tuberculosis (Mtb), to many distinct classes of antimicrobials. This review will focus on the major gaps in our understanding of intrinsic drug resistance in Mtb and how functional and chemical-genetics can help close those gaps. A better understanding of intrinsic drug resistance will help lay the foundation for strategies to disarm and circumvent these mechanisms to develop more potent antitubercular therapies.
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73
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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74
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Poulton NC, Azadian ZA, DeJesus MA, Rock JM. Mutations in rv0678 Confer Low-Level Resistance to Benzothiazinone DprE1 Inhibitors in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2022; 66:e0090422. [PMID: 35920665 PMCID: PMC9487612 DOI: 10.1128/aac.00904-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death from any bacterial infection, causing 1.5 million deaths worldwide each year. Due to the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) there have been significant efforts aimed at developing novel drugs to treat TB. One promising drug target in Mtb is the arabinogalactan biosynthetic enzyme DprE1, and there have been over a dozen unique chemical scaffolds identified which inhibit the activity of this protein. Among the most promising lead compounds are the benzothiazinones BTZ043 and PBTZ169, both of which are currently in or have completed phase IIa clinical trials. Due to the potential clinical utility of these drugs, we sought to identify potential synergistic interactions and new mechanisms of resistance using a genome-scale CRISPRi chemical-genetic screen with PBTZ169. We found that knockdown of rv0678, the negative regulator of the mmpS5/L5 drug efflux pump, confers resistance to PBTZ169. Mutations in rv0678 are the most common form of resistance to bedaquiline and there is already abundant evidence of these mutations emerging in bedaquiline-treated patients. We confirmed that rv0678 mutations from clinical isolates confer low level cross-resistance to BTZ043 and PBTZ169. While it is yet unclear whether rv0678 mutations would render benzothiazinones ineffective in treating TB, these results highlight the importance of monitoring for clinically prevalent rv0678 mutations during ongoing BTZ043 and PBTZ169 clinical trials.
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Affiliation(s)
- Nicholas C. Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Zachary A. Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Jeremy M. Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
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75
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Rudraraju RS, Daher SS, Gallardo-Macias R, Wang X, Neiditch MB, Freundlich JS. Mycobacterium tuberculosis KasA as a drug target: Structure-based inhibitor design. Front Cell Infect Microbiol 2022; 12:1008213. [PMID: 36189349 PMCID: PMC9519891 DOI: 10.3389/fcimb.2022.1008213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have reported the β-ketoacyl-acyl carrier protein KasA as a druggable target for Mycobacterium tuberculosis. This review summarizes the current status of major classes of KasA inhibitors with an emphasis on significant contributions from structure-based design methods leveraging X-ray crystal structures of KasA alone and in complex with inhibitors. The issues addressed within each inhibitor class are discussed while detailing the characterized interactions with KasA and structure-activity relationships. A critical analysis of these findings should lay the foundation for new KasA inhibitors to study the basic biology of M. tuberculosis and to form the basis of new antitubercular molecules of clinical significance with activity against drug-sensitive and drug-resistant infections.
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Affiliation(s)
- Reshma S. Rudraraju
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Samer S. Daher
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Ricardo Gallardo-Macias
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard University T.H. Chan School of Public Health, Boston, MA, United States
| | - Matthew B. Neiditch
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, United States,*Correspondence: Matthew B. Neiditch, ; Joel S. Freundlich,
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, United States,Department of Medicine, Center for Emerging and Re-emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, United States,*Correspondence: Matthew B. Neiditch, ; Joel S. Freundlich,
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76
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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77
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Romano GE, Silva-Pereira TT, de Melo FM, Sisco MC, Banari AC, Zimpel CK, Soler-Camargo NC, Guimarães AMDS. Unraveling the metabolism of Mycobacterium caprae using comparative genomics. Tuberculosis (Edinb) 2022; 136:102254. [PMID: 36126496 DOI: 10.1016/j.tube.2022.102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022]
Abstract
In our laboratory, Mycobacterium caprae has poor growth in standard medium (SM) 7H9-OADC supplemented with pyruvate and Tween-80. Our objectives were to identify mutations affecting M. caprae metabolism and use this information to design a culture medium to improve its growth. We selected 77 M. caprae genomes and sequenced M. caprae NLA000201913 used in our experiments. Mutations present in >95% of the strains compared to Mycobacterium tuberculosis H37Rv were analyzed in silico for their deleterious effects on proteins of metabolic pathways. Apart from the known defect in the pyruvate kinase, M. caprae has important lesions in enzymes of the TCA cycle, methylmalonyl cycle, B12 metabolism, and electron-transport chain. We provide evidence of enzymatic redundancy elimination and epistatic mutations, and possible production of toxic metabolites hindering M. caprae growth in vitro. A newly designed SM supplemented with l-glutamate allowed faster growth and increased final microbial mass of M. caprae. However, possible accumulation of metabolic waste-products and/or nutritional limitations halted M. caprae growth prior to a M. tuberculosis-like stationary phase. Our findings suggest that M. caprae relies on GABA and/or glyoxylate shunts for in vitro growth in routine media. The newly developed medium will improve experiments with this bacterium by allowing faster growth in vitro.
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Affiliation(s)
- Giovanni Emiddio Romano
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Filipe Menegatti de Melo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Maria Carolina Sisco
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Alexandre Campos Banari
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Ana Marcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University. 625 Harrison Street, West Lafayette, IN, 47907, USA.
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78
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Nguyen PP, Kado T, Prithviraj M, Siegrist MS, Morita YS. Inositol acylation of phosphatidylinositol mannosides: a rapid mass response to membrane fluidization in mycobacteria. J Lipid Res 2022; 63:100262. [PMID: 35952902 PMCID: PMC9490103 DOI: 10.1016/j.jlr.2022.100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Mycobacteria share an unusually complex, multilayered cell envelope, which contributes to adaptation to changing environments. The plasma membrane is the deepest layer of the cell envelope and acts as the final permeability barrier against outside molecules. There is an obvious need to maintain the plasma membrane integrity, but the adaptive responses of the plasma membrane to stress exposure remain poorly understood. Using chemical treatment and heat stress to fluidize the membrane, we show here that phosphatidylinositol (PI)-anchored plasma membrane glycolipids known as PI mannosides (PIMs) are rapidly remodeled upon membrane fluidization in Mycobacterium smegmatis. Without membrane stress, PIMs are predominantly in a triacylated form: two acyl chains of the PI moiety plus one acyl chain modified at one of the mannose residues. Upon membrane fluidization, we determined the fourth fatty acid is added to the inositol moiety of PIMs, making them tetra-acylated variants. Additionally, we show that PIM inositol acylation is a rapid response independent of de novo protein synthesis, representing one of the fastest mass conversions of lipid molecules found in nature. Strikingly, we found that M. smegmatis is more resistant to the bactericidal effect of a cationic detergent after benzyl alcohol pre-exposure. We further demonstrate that fluidization-induced PIM inositol acylation is conserved in pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. Our results demonstrate that mycobacteria possess a mechanism to sense plasma membrane fluidity change. We suggest that inositol acylation of PIMs is a novel membrane stress response that enables mycobacterial cells to resist membrane fluidization.
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Affiliation(s)
- Peter P Nguyen
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA.
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79
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Li YY, Liu HM, Wang D, Lu Y, Ding C, Zhou LS, Wu XY, Zhou ZW, Xu SQ, Lin C, Qin LH, Li Y, Liu J, Liu HP, Zhang L. Arabinogalactan enhances Mycobacterium marinum virulence by suppressing host innate immune responses. Front Immunol 2022; 13:879775. [PMID: 36090984 PMCID: PMC9459032 DOI: 10.3389/fimmu.2022.879775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022] Open
Abstract
Arabinogalactan (AG) participates in forming the cell wall core of mycobacteria, a structure known as the mAGP complex. Few studies have reported the virulence of inartificial AG or its interaction with the host immune system. Using clustered regularly interspaced short palindromic repeats interference gene editing technology, conditional Mycobacterium marinum mutants were constructed with a low expression of embA or glfT2 (EmbA_KD or GlfT2_KD), which are separately involved in the biosynthesis of AG arabinose and galactose domains. High-performance gel permeation chromatography and high-performance liquid chromatography assays confirmed that the EmbA_KD strain showed a remarkable decrease in AG content with fragmentary arabinose chains, and the GlfT2_KD strain displayed less reduction in content with cut-down galactose chains. Based on transmission and scanning electron microscopy observations, the cell walls of the two mutants were found to be dramatically thickened, and the boundaries of different layers were more distinct. Phenotypes including the over-secretion of extracellular substances and enhanced spreading motility with a concomitant decreased resistance to ethambutol appeared in the EmbA_KD strain. The EmbA_KD and GlfT2_KD strains displayed limited intracellular proliferation after infecting murine J774A.1 macrophages. The disease progression infected with the EmbA_KD or GlfT2_KD strain significantly slowed down in zebrafish/murine tail infection models as well. Through transcriptome profiling, macrophages infected by EmbA_KD/GlfT2_KD strains showed enhanced oxidative metabolism. The cell survival measured using the CCK8 assay of macrophages exposed to the EmbA_KD strain was upregulated and consistent with the pathway enrichment analysis of differentially expressed genes in terms of cell cycle/apoptosis. The overexpression of C/EBPβ and the increasing secretion of proinflammatory cytokines were validated in the macrophages infected by the EmbA_KD mutant. In conclusion, the AG of Mycobacterium appears to restrain the host innate immune responses to enhance intracellular proliferation by interfering with oxidative metabolism and causing macrophage death. The arabinose chains of AG influence the Mycobacterium virulence and pathogenicity to a greater extent.
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Affiliation(s)
- Ye-yu Li
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Han-Mei Liu
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Decheng Wang
- School of Medicine, China Three Gorges University, Yichang, China
| | - Yan Lu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, China
| | - Cairong Ding
- School of Medicine, China Three Gorges University, Yichang, China
| | - Li-Shuang Zhou
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, China
| | - Xiang-Yang Wu
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zi-Wei Zhou
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
| | - Shu-qin Xu
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
| | - Chen Lin
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
| | - Lian-Hua Qin
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Jun Liu, ; Hai-Peng Liu, ; Lu Zhang,
| | - Hai-Peng Liu
- Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Jun Liu, ; Hai-Peng Liu, ; Lu Zhang,
| | - Lu Zhang
- Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- *Correspondence: Jun Liu, ; Hai-Peng Liu, ; Lu Zhang,
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80
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Bongaerts N, Edoo Z, Abukar AA, Song X, Sosa-Carrillo S, Haggenmueller S, Savigny J, Gontier S, Lindner AB, Wintermute EH. Low-cost anti-mycobacterial drug discovery using engineered E. coli. Nat Commun 2022; 13:3905. [PMID: 35798732 PMCID: PMC9262897 DOI: 10.1038/s41467-022-31570-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/23/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-cell screening for Mycobacterium tuberculosis (Mtb) inhibitors is complicated by the pathogen's slow growth and biocontainment requirements. Here we present a synthetic biology framework for assaying Mtb drug targets in engineered E. coli. We construct Target Essential Surrogate E. coli (TESEC) in which an essential metabolic enzyme is deleted and replaced with an Mtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model for Mtb alanine racemase (Alr) revealed benazepril as a targeted inhibitor, a result validated in whole-cell Mtb. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical Alr inhibitors. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets.
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Affiliation(s)
- Nadine Bongaerts
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Zainab Edoo
- Sorbonne Université, Université Paris Cité, Inserm, Centre de Recherche des Cordeliers (CRC), Paris, France
| | - Ayan A Abukar
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Xiaohu Song
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sebastián Sosa-Carrillo
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- Institut Pasteur, Inria de Paris, Université Paris Cité, InBio, Paris, France
| | - Sarah Haggenmueller
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Juline Savigny
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Sophie Gontier
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- CRI, Paris, France
| | - Ariel B Lindner
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
| | - Edwin H Wintermute
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France.
- CRI, Paris, France.
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81
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Shamma F, Rego EH, Boutte CC. Mycobacterial serine/threonine phosphatase PstP is phosphoregulated and localized to mediate control of cell wall metabolism. Mol Microbiol 2022; 118:47-60. [PMID: 35670057 PMCID: PMC10070032 DOI: 10.1111/mmi.14951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
The mycobacterial cell wall is profoundly regulated in response to environmental stresses, and this regulation contributes to antibiotic tolerance. The reversible phosphorylation of different cell wall regulatory proteins is a major mechanism of cell wall regulation. Eleven serine/threonine protein kinases phosphorylate many critical cell wall-related proteins in mycobacteria. PstP is the sole serine/ threonine phosphatase, but few proteins have been verified as PstP substrates. PstP is itself phosphorylated, but the role of its phosphorylation in regulating its activity has been unclear. In this study, we aim to discover novel substrates of PstP in Mycobacterium tuberculosis (Mtb). We show in vitro that PstP dephosphorylates two regulators of peptidoglycan in Mtb, FhaA, and Wag31. We also show that a phosphomimetic mutation of T137 on PstP negatively regulates its catalytic activity against the cell wall regulators FhaA, Wag31, CwlM, PknB, and PknA, and that the corresponding mutation in Mycobacterium smegmatis causes misregulation of peptidoglycan in vivo. We show that PstP is localized to the septum, which likely restricts its access to certain substrates. These findings on the regulation of PstP provide insight into the control of cell wall metabolism in mycobacteria.
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Affiliation(s)
- Farah Shamma
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - E Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cara C Boutte
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
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82
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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83
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Gupta S, Mishra DK, Khan MZ, Saini V, Mehta D, Kumar S, Yadav A, Mitra M, Rani P, Singh M, Nandi CK, Das P, Ahuja V, Nandicoori VK, Bajaj A. Development of a Highly Specific, Selective, and Sensitive Fluorescent Probe for Detection of Mycobacteria in Human Tissues. Adv Healthc Mater 2022; 11:e2102640. [PMID: 35038229 DOI: 10.1002/adhm.202102640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/07/2022] [Indexed: 11/08/2022]
Abstract
Tuberculosis (TB), including extrapulmonary TB, is responsible for more than one million deaths in a year worldwide. Existing methods of mycobacteria detection have poor sensitivity, selectivity, and specificity, especially in human tissues. Herein, the synthesis of a cholic acid-derived fluorescent probe (P4) that can specifically stain the mycobacterium species is presented. It is shown that P4 probe specifically binds with mycobacterial lipids, trehalose monomycolate, and phosphatidylinositol mannoside 6. P4 probe can detect mycobacteria in polymicrobial planktonic cultures and biofilms with high specificity, selectivity, and sensitivity. Moreover, it can detect a single mycobacterium in the presence of 10 000 other bacilli. Unlike the probes that depend on active mycobacterial enzymes, the membrane-specific P4 probe can detect mycobacteria even in formalin-fixed paraffin-embedded mice and human tissue sections. Therefore, the ability of the P4 probe to detect mycobacteria in different biological milieu makes it a potential candidate for diagnostic and prognostic applications in clinical settings.
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Affiliation(s)
- Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Deepak Kumar Mishra
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Mehak Zahoor Khan
- National Institute of Immunology Aruna Asaf Ali Marg New Delhi 110067 India
| | - Varsha Saini
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Devashish Mehta
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Aditya Yadav
- School of Basic Sciences Indian Institute of Technology Mandi Mandi HP 175005 India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Parul Rani
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
| | - Mukesh Singh
- Department of Gastroenterology All India Institute of Medical Sciences New Delhi 110029 India
| | - Chayan Kanti Nandi
- School of Basic Sciences Indian Institute of Technology Mandi Mandi HP 175005 India
| | - Prasenjit Das
- Department of Pathology All India Institute of Medical Sciences New Delhi 110029 India
| | - Vineet Ahuja
- Department of Gastroenterology All India Institute of Medical Sciences New Delhi 110029 India
| | | | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad‐Gurgaon Expressway Faridabad Haryana 121001 India
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84
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Menon AP, Dong W, Lee TH, Aguilar MI, Duan M, Kapoor S. Mutually Exclusive Interactions of Rifabutin with Spatially Distinct Mycobacterial Cell Envelope Membrane Layers Offer Insights into Membrane-Centric Therapy of Infectious Diseases. ACS BIO & MED CHEM AU 2022; 2:395-408. [PMID: 35996474 PMCID: PMC9389580 DOI: 10.1021/acsbiomedchemau.2c00010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjana P. Menon
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Wanqian Dong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Tzong-Hsien Lee
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Marie-Isabel Aguilar
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Mojie Duan
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IITB-Monash Academy, 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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85
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Cardoso NC, Chibale K, Singh V. Implications of Mycobacterium tuberculosis Metabolic Adaptability on Drug Discovery and Development. ACS Infect Dis 2022; 8:414-421. [PMID: 35175727 DOI: 10.1021/acsinfecdis.1c00627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tuberculosis remains a global health threat that is being exacerbated by the increase in infections attributed to drug resistant Mycobacterium tuberculosis. To combat this, there has been a surge in drug discovery programs to develop new, potent compounds and identify promising drug targets in the pathogen. Two areas of M. tuberculosis biology that have emerged as rich sources of potential novel drug targets are cell wall biosynthesis and energy metabolism. Both processes are important for survival of M. tuberculosis under replicating and nonreplicating conditions. However, both processes are also inherently adaptable under different conditions. Furthermore, cell wall biosynthesis is energy intensive and, thus, reliant on an efficiently functioning energy production system. This Perspective focuses on the interplay between cell wall biosynthesis and energy metabolism in M. tuberculosis, how adaptations in one pathway may affect the other, and what consequences this could have for drug discovery and development and the identification of novel drug targets.
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Affiliation(s)
- Nicole C. Cardoso
- Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, 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, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, 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, Rondebosch 7701, South Africa
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86
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Babu Sait MR, Koliwer-Brandl H, Stewart JA, Swarts BM, Jacobsen M, Ioerger TR, Kalscheuer R. PPE51 mediates uptake of trehalose across the mycomembrane of Mycobacterium tuberculosis. Sci Rep 2022; 12:2097. [PMID: 35136132 PMCID: PMC8826857 DOI: 10.1038/s41598-022-06109-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/19/2022] [Indexed: 01/07/2023] Open
Abstract
The disaccharide trehalose is essential for viability of Mycobacterium tuberculosis, which synthesizes trehalose de novo but can also utilize exogenous trehalose. The mycobacterial cell wall encompasses two permeability barriers, the cytoplasmic membrane and the outer mycolic acid-containing mycomembrane. The ABC transporter LpqY-SugA-SugB-SugC has previously been demonstrated to mediate the specific uptake of trehalose across the cytoplasmic membrane. However, it is still unclear how the transport of trehalose molecules across the mycomembrane is mediated. In this study, we harnessed the antimycobacterial activity of the analogue 6-azido trehalose to select for spontaneous resistant M. tuberculosis mutants in a merodiploid strain harbouring two LpqY-SugA-SugB-SugC copies. Mutations mediating resistance to 6-azido trehalose mapped to the proline-proline-glutamate (PPE) family member PPE51 (Rv3136), which has recently been shown to be an integral mycomembrane protein involved in uptake of low-molecular weight compounds. A site-specific ppe51 gene deletion mutant of M. tuberculosis was unable to grow on trehalose as the sole carbon source. Furthermore, bioorthogonal labelling of the M. tuberculosis Δppe51 mutant incubated with 6-azido trehalose corroborated the impaired internalization. Taken together, the results indicate that the transport of trehalose and trehalose analogues across the mycomembrane of M. tuberculosis is exclusively mediated by PPE51.
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Affiliation(s)
- Mohammed Rizwan Babu Sait
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hendrik Koliwer-Brandl
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Jessica A Stewart
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, 48859, USA
| | - Marc Jacobsen
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX, 77843, USA
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225, Düsseldorf, Germany.
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87
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Modak B, Girkar S, Narayan R, Kapoor S. Mycobacterial Membranes as Actionable Targets for Lipid-Centric Therapy in Tuberculosis. J Med Chem 2022; 65:3046-3065. [PMID: 35133820 DOI: 10.1021/acs.jmedchem.1c01870] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Infectious diseases remain significant health concerns worldwide, and resistance is particularly common in patients with tuberculosis caused by Mycobacterium tuberculosis. The development of anti-infectives with novel modes of action may help overcome resistance. In this regard, membrane-active agents, which modulate membrane components essential for the survival of pathogens, present attractive antimicrobial agents. Key advantages of membrane-active compounds include their ability to target slow-growing or dormant bacteria and their favorable pharmacokinetics. Here, we comprehensively review recent advances in the development of membrane-active chemotypes that target mycobacterial membranes and discuss clinically relevant membrane-active antibacterial agents that have shown promise in counteracting bacterial infections. We discuss the relationship between the membrane properties and the synthetic requirements within the chemical scaffold, as well as the limitations of current membrane-active chemotypes. This review will lay the chemical groundwork for the development of membrane-active antituberculosis agents and will foster the discovery of more effective antitubercular agents.
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Affiliation(s)
- Biswabrata Modak
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Siddhali Girkar
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Goa 403110, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Goa 403110, 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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88
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Yimcharoen M, Saikaew S, Wattananandkul U, Phunpae P, Intorasoot S, Kasinrerk W, Tayapiwatana C, Butr-Indr B. The Regulation of ManLAM-Related Gene Expression in Mycobacterium tuberculosis with Different Drug Resistance Profiles Following Isoniazid Treatment. Infect Drug Resist 2022; 15:399-412. [PMID: 35153492 PMCID: PMC8828085 DOI: 10.2147/idr.s346869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) remains a global health concern because of the development of drug resistance. The adaptability of MTB in response to a variety of environmental stresses is a crucial strategy that supports their survival and evades host defense mechanisms. Stress regulates gene expression, particularly virulence genes, leading to the development of drug tolerance. Mannose-capped lipoarabinomannan (ManLAM) is a critical component of the cell wall, functions as a virulence factor and influences host defense mechanisms. Purpose This study focuses on the effect of isoniazid (INH) stress on the regulation of ManLAM-related genes, to improve our understanding of virulence and drug resistance development in MTB. Materials and Methods MTB with distinct drug resistance profiles were used for gene expression analysis. Multiplex-real time PCR assay was performed to monitor stress-related genes (hspX, tgs1, and sigE). The expression levels of ManLAM-related genes (pimB, mptA, mptC, dprE1, dprE2, and embC) were quantified by qRT-PCR. Sequence analysis of drug resistance-associated genes (inhA, katG, and rpoB) and ManLAM-related genes were performed to establish a correlation between genetic variation and gene expression. Results INH treatment activates the stress response mechanism in MTB, resulting in a distinct gene expression pattern between drug resistance and drug-sensitive TB. In response to INH, hspX was up-regulated in RIF-R and MDR. tgs1 was strongly up-regulated in MDR, whereas sigE was dramatically up-regulated in the drug-sensitive TB. Interestingly, ManLAM-related genes were most up-regulated in drug resistance, notably MDR (pimB, mptA, dprE1, and embC), implying a role for drug resistance and adaptability of MTB via ManLAM modulation. Conclusion This study establishes a relationship between the antibiotic stress response mechanism and the expression of ManLAM-related genes in MTB samples with diverse drug resistance profiles. The novel gene expression pattern in this work is valuable knowledge that can be applied for TB monitoring and treatment in the future.
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Affiliation(s)
- Manita Yimcharoen
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sukanya Saikaew
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Usanee Wattananandkul
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Ponrut Phunpae
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sorasak Intorasoot
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Watchara Kasinrerk
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at The Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at The Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Bordin Butr-Indr
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Correspondence: Bordin Butr-Indr, Tel +66 53945086 ext. 15, Fax +66 53217143, Email ;
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89
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Structural basis for safe and efficient energy conversion in a respiratory supercomplex. Nat Commun 2022; 13:545. [PMID: 35087070 PMCID: PMC8795186 DOI: 10.1038/s41467-022-28179-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022] Open
Abstract
Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa3 oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa3 (III2-IV2) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Qc site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis. Aerobic energy metabolism is driven by proton-pumping respiratory supercomplexes. The study reports the structural basis for energy conversion in such supercomplex. It may aid metabolic engineering and drug design against diphtheria and tuberculosis.
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90
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Allué-Guardia A, Garcia-Vilanova A, Olmo-Fontánez AM, Peters J, Maselli DJ, Wang Y, Turner J, Schlesinger LS, Torrelles JB. Host- and Age-Dependent Transcriptional Changes in Mycobacterium tuberculosis Cell Envelope Biosynthesis Genes after Exposure to Human Alveolar Lining Fluid. Int J Mol Sci 2022; 23:ijms23020983. [PMID: 35055170 PMCID: PMC8780516 DOI: 10.3390/ijms23020983] [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: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis (M.tb), resulted in almost 1.4 million deaths in 2019, and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M.tb comes into close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic, innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M.tb upon contact, defining subsequent M.tb-host cell interactions and infection outcomes in vitro and in vivo. We also demonstrated that ALF from 60+ year old elders (E-ALF) vs. healthy 18- to 45-year-old adults (A-ALF) is dysfunctional, with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay shows that M.tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M.tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M.tb exposure to E-ALF shows a lesser transcriptional response, with most of the M.tb genes unchanged or downregulated. Overall, this study indicates that M.tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status, determined by factors such as age, might play an important role in determining infection outcome.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Andreu Garcia-Vilanova
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
| | - Angélica M. Olmo-Fontánez
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jay Peters
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Diego J. Maselli
- Division of Pulmonary and Critical Care Medicine, School of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA; (J.P.); (D.J.M.)
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA;
| | - Joanne Turner
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Larry S. Schlesinger
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (J.T.); (L.S.S.)
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (A.G.-V.); (A.M.O.-F.)
- Correspondence: (A.A.-G.); (J.B.T.)
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91
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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92
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Carlier M, Lesur E, Baron A, Lemétais A, Guitot K, Roupnel L, Dietrich C, Doisneau G, Urban D, Bayan N, Beau JM, Guianvarc'h D, Vauzeilles B, Bourdreux Y. Synthesis of chemical tools to label the mycomembrane of corynebacteria using a modified Iron (III) chloride-mediated protection of trehalose. Org Biomol Chem 2022; 20:1974-1981. [DOI: 10.1039/d2ob00107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trehalose-based probes are useful tools allowing the detection of the mycomembrane of Mycobacteria through the metabolic labeling approach. Some of them are trehalose analogues conjugated to fluorescent probes and others...
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93
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Yang F, Xu L, Liang L, Liang W, Li J, Lin D, Dai M, Zhou D, Li Y, Chen Y, Zhao H, Tian GB, Feng S. The Involvement of Mycobacterium Type III-A CRISPR-Cas System in Oxidative Stress. Front Microbiol 2021; 12:774492. [PMID: 34956138 PMCID: PMC8696179 DOI: 10.3389/fmicb.2021.774492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Type I and type II CRISPR-Cas systems are employed to evade host immunity by targeting interference of bacteria’s own genes. Although Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, possesses integrated type III-A CRISPR-Cas system, its role in mycobacteria remains obscure. Here, we observed that seven cas genes (csm2∼5, cas10, cas6) were upregulated in Mycobacterium bovis BCG under oxidative stress treatment, indicating the role of type III-A CRISPR-Cas system in oxidative stress. To explore the functional role of type III-A CRISPR-Cas system, TCC (Type III-A CRISPR-Cas system, including cas6, cas10, and csm2-6) mutant was generated. Deletion of TCC results in increased sensitivity in response to hydrogen peroxide and reduced cell envelope integrity. Analysis of RNA-seq dataset revealed that TCC impacted on the oxidation-reduction process and the composition of cell wall which is essential for mycobacterial envelop integrity. Moreover, disrupting TCC led to poor intracellular survival in vivo and in vitro. Finally, we showed for the first time that TCC contributed to the regulation of regulatory T cell population, supporting a role of TCC in modulating host immunity. Our finding reveals the important role of TCC in cell envelop homeostasis. Our work also highlights type III-A CRISPR-Cas system as an important factor for intracellular survival and host immunoregulation in mycobacteria, thus may be a potential target for therapy.
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Affiliation(s)
- Fan Yang
- Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Lingqing Xu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lujie Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Wanfei Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiachen Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Daixi Lin
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Dianrong Zhou
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yaxin Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yong Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Hui Zhao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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94
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Spatiotemporal localization of proteins in mycobacteria. Cell Rep 2021; 37:110154. [PMID: 34965429 PMCID: PMC8861988 DOI: 10.1016/j.celrep.2021.110154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 01/10/2023] Open
Abstract
Although prokaryotic organisms lack traditional organelles, they must still organize cellular structures in space and time, challenges that different species solve differently. To systematically define the subcellular architecture of mycobacteria, we perform high-throughput imaging of a library of fluorescently tagged proteins expressed in Mycobacterium smegmatis and develop a customized computational pipeline, MOMIA and GEMATRIA, to analyze these data. Our results establish a spatial organization network of over 700 conserved mycobacterial proteins and reveal a coherent localization pattern for many proteins of known function, including those in translation, energy metabolism, cell growth and division, as well as proteins of unknown function. Furthermore, our pipeline exploits morphologic proxies to enable a pseudo-temporal approximation of protein localization and identifies previously uncharacterized cell-cycle-dependent dynamics of essential mycobacterial proteins. Collectively, these data provide a systems perspective on the subcellular organization of mycobacteria and provide tools for the analysis of bacteria with non-standard growth characteristics. Zhu et al. develop a two-stage image analysis pipeline, MOMIA and GEMATRIA, that efficiently models the spatial and temporal dynamics of over 700 conserved proteins in M. smegmatis. Through the analysis they report spatial constraints of mycobacterial ribosomes and membrane complexes and reconstruct temporal dynamics from still image data.
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95
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Mycobacterial MCE proteins as transporters that control lipid homeostasis of the cell wall. Tuberculosis (Edinb) 2021; 132:102162. [PMID: 34952299 DOI: 10.1016/j.tube.2021.102162] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023]
Abstract
Mammalian cell entry (mce) genes are not only present in genomes of pathogenic mycobacteria, including Mycobacterium tuberculosis (the causative agent of tuberculosis), but also in saprophytic and opportunistic mycobacterial species. MCE are conserved cell-wall proteins encoded by mce operons, which maintain an identical structure in all mycobacteria: two yrbE genes (A and B) followed by six mce genes (A, B, C, D, E and F). Although these proteins are known to participate in the virulence of pathogenic mycobacteria, the presence of the operons in nonpathogenic mycobacteria and other bacteria indicates that they play another role apart from host cell invasion. In this respect, more recent studies suggest that they are functionally similar to ABC transporters and form part of lipid transporters in Actinobacteria. To date, most reviews on mce operons in the literature discuss their role in virulence. However, according to data from transcriptional studies, mce genes, particularly the mce1 and mce4 operons, modify their expression according to the carbon source and upon hypoxia, starvation, surface stress and oxidative stress; which suggests a role of MCE proteins in the response of Mycobacteria to external stressors. In addition to these data, this review also summarizes the studies demonstrating the role of MCE proteins as lipid transporters as well as the relevance of their transport function in the interaction of pathogenic Mycobacteria with the hosts. Altogether, the evidence to date would indicate that MCE proteins participate in the response to the stress conditions that mycobacteria encounter during infection, by participating in the cell wall remodelling and possibly contributing to lipid homeostasis.
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96
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Passot FM, Cantlay S, Flärdh K. Protein phosphatase SppA regulates apical growth and dephosphorylates cell polarity determinant DivIVA in Streptomyces coelicolor. Mol Microbiol 2021; 117:411-428. [PMID: 34862689 DOI: 10.1111/mmi.14856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/23/2021] [Accepted: 12/02/2021] [Indexed: 11/27/2022]
Abstract
Members of the Actinobacteria, including mycobacteria and streptomycetes, exhibit a distinctive mode of polar growth, with cell wall synthesis occurring in zones at cell poles and directed by the essential cell polarity determinant DivIVA. Streptomyces coelicolor modulates polar growth via the Ser/Thr protein kinase AfsK, which phosphorylates DivIVA. Here, we show that the phosphoprotein phosphatase SppA has strong effects on polar growth and cell shape and that it reverses the AfsK-mediated phosphorylation of DivIVA. SppA affects hyphal branching and the rate of tip extension. The sppA mutant hyphae also exhibit a high frequency of spontaneous growth arrests, indicating problems with maintenance of tip extension. The phenotypic effects are partially suppressed in an afsK sppA double mutant, indicating that AfsK and SppA to some extent share target proteins. Strains with a nonphosphorylatable mutant DivIVA confirm that the effect of afsK on hyphal branching during normal growth is mediated by DivIVA phosphorylation. However, the phenotypic effects of sppA deletion are independent of DivIVA phosphorylation and must be mediated via other substrates. This study adds a PPP-family protein phosphatase to the proteins involved in the control of polar growth and cell shape determination in S. coelicolor.
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Affiliation(s)
| | | | - Klas Flärdh
- Department of Biology, Lund University, Lund, Sweden
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97
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De Maio F, Salustri A, Battah B, Palucci I, Marchionni F, Bellesi S, Palmieri V, Papi M, Kramarska E, Sanguinetti M, Sali M, Berisio R, Delogu G. PE_PGRS3 ensures provision of the vital phospholipids cardiolipin and phosphatidylinositols by promoting the interaction between M. tuberculosis and host cells. Virulence 2021; 12:868-884. [PMID: 33757409 PMCID: PMC8007152 DOI: 10.1080/21505594.2021.1897247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/23/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
PE_PGRS proteins of Mycobacterium tuberculosis (Mtb) constitute a large family of complex modular proteins whose role is still unclear. Among those, we have previously shown, using the heterologous expression in Mycobacterium smegmatis, that PE_PGRS3 containing a unique arginine-rich C-terminal domain, promotes adhesion to host cells. In this study, we investigate the role of PE_PGRS3 and its C-terminal domain directly in Mtb using functional deletion mutants. The results obtained here show that PE_PGRS3 is localized on the mycobacterial cell wall and its arginine-rich C-terminal region protrudes from the mycobacterial membrane and mediates Mtb entry into epithelial cells. Most importantly, this positively charged helical domain specifically binds phosphorylated phosphatidylinositols and cardiolipin, whereas it is unable to bind other phospholipids. Interestingly, administration of cardiolipin and phosphatidylinositol but no other phospholipids was able to turn-off expression of pe_pgrs3 activated by phosphate starvation conditions. These findings suggest that PE_PGRS3 has the key role to serve as a bridge between mycobacteria and host cells by interacting with specific host phospholipids and extracting them from host cells, for their direct integration or as a source of phosphate, during phases of TB pathogenesis when Mtb is short of phosphate supply.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro Salustri
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Basem Battah
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ivana Palucci
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Federica Marchionni
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Silvia Bellesi
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Valentina Palmieri
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Massimiliano Papi
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Roma, Italy
- Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
| | - Eliza Kramarska
- Institute of Biostructures and Bioimaging - CNR-IBB, Naples, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
- Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie – Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging - CNR-IBB, Naples, Italy
| | - Giovanni Delogu
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli”, Rome, Italy
- Mater Olbia Hospital, Olbia, Italy
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98
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Amoroso M, Langgartner D, Lowry CA, Reber SO. Rapidly Growing Mycobacterium Species: The Long and Winding Road from Tuberculosis Vaccines to Potent Stress-Resilience Agents. Int J Mol Sci 2021; 22:ijms222312938. [PMID: 34884743 PMCID: PMC8657684 DOI: 10.3390/ijms222312938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory diseases and stressor-related psychiatric disorders, for which inflammation is a risk factor, are increasing in modern Western societies. Recent studies suggest that immunoregulatory approaches are a promising tool in reducing the risk of suffering from such disorders. Specifically, the environmental saprophyte Mycobacterium vaccae National Collection of Type Cultures (NCTC) 11659 has recently gained attention for the prevention and treatment of stress-related psychiatric disorders. However, effective use requires a sophisticated understanding of the effects of M. vaccae NCTC 11659 and related rapidly growing mycobacteria (RGMs) on microbiome–gut–immune–brain interactions. This historical narrative review is intended as a first step in exploring these mechanisms and provides an overview of preclinical and clinical studies on M. vaccae NCTC 11659 and related RGMs. The overall objective of this review article is to increase the comprehension of, and interest in, the mechanisms through which M. vaccae NCTC 11659 and related RGMs promote stress resilience, with the intention of fostering novel clinical strategies for the prevention and treatment of stressor-related disorders.
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Affiliation(s)
- Mattia Amoroso
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
| | - Dominik Langgartner
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
| | - Christopher A. Lowry
- Department of Integrative Physiology, Center for Neuroscience and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO 80309, USA;
- Department of Physical Medicine and Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), The Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA
- Senior Fellow, inVIVO Planetary Health, of the Worldwide Universities Network (WUN), West New York, NJ 07093, USA
| | - Stefan O. Reber
- Laboratory for Molecular Psychosomatics, Department of Psychosomatic Medicine and Psychotherapy, University of Ulm, 89081 Ulm, Germany; (M.A.); (D.L.)
- Correspondence:
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99
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Shen K, Bai B, Liu YH, Lowary TL. Synthesis of a Tridecasaccharide Lipooligosaccharide Antigen from the Opportunistic Pathogen Mycobacterium kansasii. Angew Chem Int Ed Engl 2021; 60:24859-24863. [PMID: 34553821 DOI: 10.1002/anie.202111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 11/06/2022]
Abstract
The outer surfaces of mycobacteria, including the organism that causes tuberculosis, are decorated with an array of immunomodulatory glycans. Among these are lipooligosaccharides (LOSs), a class of molecules for which the function remains poorly understood. We describe the chemical synthesis of the glycan portion of a tridecasaccharide LOS from the opportunistic pathogen Mycobacterium kansasii. The target contains a number of unusual structural motifs that complicate its assembly and is the most complex mycobacterial LOS glycan to be synthesized to date when considering size and number of unique monosaccharides and glycosidic linkages. These studies not only provide a roadmap for the preparation of additional members of this family of glycans, but also provides a valuable probe for use in structure-activity relationship investigations.
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Affiliation(s)
- Ke Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Bing Bai
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yu-Hsuan Liu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.,Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National (Taiwan) University, Roosevelt Road, Section 4, #1, Taipei, 10617, Taiwan
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100
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Shen K, Bai B, Liu Y, Lowary TL. Synthesis of a Tridecasaccharide Lipooligosaccharide Antigen from the Opportunistic Pathogen
Mycobacterium kansasii. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ke Shen
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Bing Bai
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Yu‐Hsuan Liu
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Todd L. Lowary
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
- Institute of Biological Chemistry Academia Sinica Academia Road, Section 2, #128 Nangang Taipei 11529 Taiwan
- Institute of Biochemical Sciences National (Taiwan) University Roosevelt Road, Section 4, #1 Taipei 10617 Taiwan
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