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Ahator SD, Hegstad K, Lentz CS, Johannessen M. Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins. mSystems 2024; 9:e0017924. [PMID: 38656122 PMCID: PMC11097646 DOI: 10.1128/msystems.00179-24] [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: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The utilization of ATP within cells plays a fundamental role in cellular processes that are essential for the regulation of host-pathogen dynamics and the subsequent immune response. This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during an intracellular infection. A snapshot of the various protein activity and function is provided using a desthiobiotin-ATP probe, which targets ATP-interacting proteins. In S. aureus, we observe enrichment in pathways required for nutrient acquisition, biosynthesis and metabolism of amino acids, and energy metabolism when located inside human cells. Additionally, the direct profiling of the protein activity revealed specific adaptations of S. aureus to the keratinocytes and macrophages. Mapping the differentially activated proteins to biochemical pathways in the human cells with intracellular bacteria revealed cell-type-specific adaptations to bacterial challenges where THP-1 cells prioritized immune defenses, autophagic cell death, and inflammation. In contrast, HaCaT cells emphasized barrier integrity and immune activation. We also observe bacterial modulation of host processes and metabolic shifts. These findings offer valuable insights into the dynamics of S. aureus-host cell interactions, shedding light on modulating host immune responses to S. aureus, which could involve developing immunomodulatory therapies. IMPORTANCE This study uses a chemoproteomic approach to target active ATP-interacting proteins and examines the dynamic proteomic interactions between Staphylococcus aureus and human cell lines THP-1 and HaCaT. It uncovers the distinct responses of macrophages and keratinocytes during bacterial infection. S. aureus demonstrated a tailored response to the intracellular environment of each cell type and adaptation during exposure to professional and non-professional phagocytes. It also highlights strategies employed by S. aureus to persist within host cells. This study offers significant insights into the human cell response to S. aureus infection, illuminating the complex proteomic shifts that underlie the defense mechanisms of macrophages and keratinocytes. Notably, the study underscores the nuanced interplay between the host's metabolic reprogramming and immune strategy, suggesting potential therapeutic targets for enhancing host defense and inhibiting bacterial survival. The findings enhance our understanding of host-pathogen interactions and can inform the development of targeted therapies against S. aureus infections.
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Affiliation(s)
- Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
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2
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Gwin CM, Gupta KR, Lu Y, Shao L, Rego EH. Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569614. [PMID: 38076906 PMCID: PMC10705497 DOI: 10.1101/2023.12.01.569614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.
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Affiliation(s)
- Celena M. Gwin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Kuldeepkumar R. Gupta
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Yao Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Lin Shao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
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3
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Shaku MT, Ocius KL, Apostolos AJ, Pires MM, VanNieuwenhze MS, Dhar N, Kana BD. Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking. Front Cell Infect Microbiol 2023; 13:1205829. [PMID: 37692163 PMCID: PMC10484409 DOI: 10.3389/fcimb.2023.1205829] [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: 04/14/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Mycobacteria assemble a complex cell wall with cross-linked peptidoglycan (PG) which plays an essential role in maintenance of cell wall integrity and tolerance to osmotic pressure. We previously demonstrated that various hydrolytic enzymes are required to remodel PG during essential processes such as cell elongation and septal hydrolysis. Here, we explore the chemistry associated with PG cross-linking, specifically the requirement for amidation of the D-glutamate residue found in PG precursors. Methods Synthetic fluorescent probes were used to assess PG remodelling dynamics in live bacteria. Fluorescence microscopy was used to assess protein localization in live bacteria and CRISPR-interference was used to construct targeted gene knockdown strains. Time-lapse microscopy was used to assess bacterial growth. Western blotting was used to assess protein phosphorylation. Results and discussion In Mycobacterium smegmatis, we confirmed the essentiality for D-glutamate amidation in PG biosynthesis by labelling cells with synthetic fluorescent PG probes carrying amidation modifications. We also used CRISPRi targeted knockdown of genes encoding the MurT-GatD complex, previously implicated in D-glutamate amidation, and demonstrated that these genes are essential for mycobacterial growth. We show that MurT-rseGFP co-localizes with mRFP-GatD at the cell poles and septum, which are the sites of cell wall synthesis in mycobacteria. Furthermore, time-lapse microscopic analysis of MurT-rseGFP localization, in fluorescent D-amino acid (FDAA)-labelled mycobacterial cells during growth, demonstrated co-localization with maturing PG, suggestive of a role for PG amidation during PG remodelling and repair. Depletion of MurT and GatD caused reduced PG cross-linking and increased sensitivity to lysozyme and β-lactam antibiotics. Cell growth inhibition was found to be the result of a shutdown of PG biosynthesis mediated by the serine/threonine protein kinase B (PknB) which senses uncross-linked PG. Collectively, these data demonstrate the essentiality of D-glutamate amidation in mycobacterial PG precursors and highlight the MurT-GatD complex as a novel drug target.
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Affiliation(s)
- Moagi T. Shaku
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis (TB) Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
| | - Karl L. Ocius
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | | | - Neeraj Dhar
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bavesh D. Kana
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis (TB) Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
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4
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Escobar-Salom M, Barceló IM, Jordana-Lluch E, Torrens G, Oliver A, Juan C. Bacterial virulence regulation through soluble peptidoglycan fragments sensing and response: knowledge gaps and therapeutic potential. FEMS Microbiol Rev 2023; 47:fuad010. [PMID: 36893807 PMCID: PMC10039701 DOI: 10.1093/femsre/fuad010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Given the growing clinical-epidemiological threat posed by the phenomenon of antibiotic resistance, new therapeutic options are urgently needed, especially against top nosocomial pathogens such as those within the ESKAPE group. In this scenario, research is pushed to explore therapeutic alternatives and, among these, those oriented toward reducing bacterial pathogenic power could pose encouraging options. However, the first step in developing these antivirulence weapons is to find weak points in the bacterial biology to be attacked with the goal of dampening pathogenesis. In this regard, during the last decades some studies have directly/indirectly suggested that certain soluble peptidoglycan-derived fragments display virulence-regulatory capacities, likely through similar mechanisms to those followed to regulate the production of several β-lactamases: binding to specific transcriptional regulators and/or sensing/activation of two-component systems. These data suggest the existence of intra- and also intercellular peptidoglycan-derived signaling capable of impacting bacterial behavior, and hence likely exploitable from the therapeutic perspective. Using the well-known phenomenon of peptidoglycan metabolism-linked β-lactamase regulation as a starting point, we gather and integrate the studies connecting soluble peptidoglycan sensing with fitness/virulence regulation in Gram-negatives, dissecting the gaps in current knowledge that need filling to enable potential therapeutic strategy development, a topic which is also finally discussed.
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Affiliation(s)
- María Escobar-Salom
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Isabel María Barceló
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Elena Jordana-Lluch
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
| | - Gabriel Torrens
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University. Försörjningsvägen 2A, SE-901 87 Umeå, Sweden
| | - Antonio Oliver
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Carlos Juan
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
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5
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Sun Y, Hürlimann S, Garner E. Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis. Nat Microbiol 2023; 8:469-480. [PMID: 36797487 DOI: 10.1038/s41564-023-01329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/13/2023] [Indexed: 02/18/2023]
Abstract
How bacteria link their growth rate to external nutrient conditions is unknown. To investigate how Bacillus subtilis cells alter the rate at which they expand their cell walls as they grow, we compared single-cell growth rates of cells grown under agar pads with the density of moving MreB filaments under a variety of growth conditions. MreB filament density increases proportionally with growth rate. We show that both MreB filament density and growth rate depend on the abundance of Lipid II and murAA, the first gene in the biosynthetic pathway creating the cell wall precursor Lipid II. Lipid II is sensed by the serine/threonine kinase PrkC, which phosphorylates RodZ and other proteins. We show that phosphorylated RodZ increases MreB filament density, which in turn increases cell growth rate. We also show that increasing the activity of this pathway in nutrient-poor media results in cells that elongate faster than wild-type cells, which means that B. subtilis contains spare 'growth capacity'. We conclude that PrkC functions as a cellular rheostat, enabling fine-tuning of cell growth rates in response to Lipid II in different nutrient conditions.
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Affiliation(s)
- Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Sylvia Hürlimann
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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6
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Williams JT, Abramovitch RB. Molecular Mechanisms of MmpL3 Function and Inhibition. Microb Drug Resist 2023; 29:190-212. [PMID: 36809064 PMCID: PMC10171966 DOI: 10.1089/mdr.2021.0424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Mycobacteria species include a large number of pathogenic organisms such as Mycobacterium tuberculosis, Mycobacterium leprae, and various non-tuberculous mycobacteria. Mycobacterial membrane protein large 3 (MmpL3) is an essential mycolic acid and lipid transporter required for growth and cell viability. In the last decade, numerous studies have characterized MmpL3 with respect to protein function, localization, regulation, and substrate/inhibitor interactions. This review summarizes new findings in the field and seeks to assess future areas of research in our rapidly expanding understanding of MmpL3 as a drug target. An atlas of known MmpL3 mutations that provide resistance to inhibitors is presented, which maps amino acid substitutions to specific structural domains of MmpL3. In addition, chemical features of distinct classes of Mmpl3 inhibitors are compared to provide insights into shared and unique features of varied MmpL3 inhibitors.
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Affiliation(s)
- John T Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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7
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Wake Up! Resuscitation of Viable but Nonculturable Bacteria: Mechanism and Potential Application. Foods 2022; 12:foods12010082. [PMID: 36613298 PMCID: PMC9818539 DOI: 10.3390/foods12010082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
The viable but nonculturable (VBNC) state is a survival strategy for bacteria when encountered with unfavorable conditions. Under favorable environments such as nutrient supplementation, external stress elimination, or supplementation with resuscitation-promoting substances, bacteria will recover from the VBNC state, which is termed "resuscitation". The resuscitation phenomenon is necessary for proof of VBNC existence, which has been confirmed in different ways to exclude the possibility of culturable-cell regrowth. The resuscitation of VBNC cells has been widely studied for the purpose of risk control of recovered pathogenic or spoilage bacteria. From another aspect, the resuscitation of functional bacteria can also be considered a promising field to explore. To support this point, the resuscitation mechanisms were comprehensively reviewed, which could provide the theoretical foundations for the application of resuscitated VBNC cells. In addition, the proposed applications, as well as the prospects for further applications of resuscitated VBNC bacteria in the food industry are discussed in this review.
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8
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Garcia-Garcia T, Douché T, Giai Gianetto Q, Poncet S, El Omrani N, Smits WK, Cuenot E, Matondo M, Martin-Verstraete I. In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates. Mol Cell Proteomics 2022; 21:100428. [PMID: 36252736 PMCID: PMC9674922 DOI: 10.1016/j.mcpro.2022.100428] [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: 03/29/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile is the leading cause of postantibiotic diarrhea in adults. During infection, the bacterium must rapidly adapt to the host environment by using survival strategies. Protein phosphorylation is a reversible post-translational modification employed ubiquitously for signal transduction and cellular regulation. Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases have emerged as important players in bacterial cell signaling and pathogenicity. C. difficile encodes two STKs (PrkC and CD2148) and one phosphatase. We optimized a titanium dioxide phosphopeptide enrichment approach to determine the phosphoproteome of C. difficile. We identified and quantified 2500 proteins representing 63% of the theoretical proteome. To identify STK and serine/threonine phosphatase targets, we then performed comparative large-scale phosphoproteomics of the WT strain and isogenic ΔprkC, CD2148, Δstp, and prkC CD2148 mutants. We detected 635 proteins containing phosphorylated peptides. We showed that PrkC is phosphorylated on multiple sites in vivo and autophosphorylates in vitro. We were unable to detect a phosphorylation for CD2148 in vivo, whereas this kinase was phosphorylated in vitro only in the presence of PrkC. Forty-one phosphoproteins were identified as phosphorylated under the control of CD2148, whereas 114 proteins were phosphorylated under the control of PrkC including 27 phosphoproteins more phosphorylated in the ∆stp mutant. We also observed enrichment for phosphothreonine among the phosphopeptides more phosphorylated in the Δstp mutant. Both kinases targeted pathways required for metabolism, translation, and stress response, whereas cell division and peptidoglycan metabolism were more specifically controlled by PrkC-dependent phosphorylation in agreement with the phenotypes of the ΔprkC mutant. Using a combination of approaches, we confirmed that FtsK was phosphorylated in vivo under the control of PrkC and that Spo0A was a substrate of PrkC in vitro. This study provides a detailed mapping of kinase-substrate relationships in C. difficile, paving the way for the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Transito Garcia-Garcia
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,Hub de bioinformatique et biostatistiques, Departement de Biologie computationelle, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sandrine Poncet
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nesrine El Omrani
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elodie Cuenot
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France,Institut Universitaire de France, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
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9
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Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division. mBio 2022; 13:e0066922. [PMID: 35703435 PMCID: PMC9426605 DOI: 10.1128/mbio.00669-22] [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] [Indexed: 11/28/2022] Open
Abstract
Bacterial cell division is a complex process requiring the coordination of multiple components to allow the appropriate spatial and temporal control of septum formation and cell scission. Peptidoglycan (PG) is the major structural component of the septum, and our recent studies in the human pathogen Staphylococcus aureus have revealed a complex, multistage PG architecture that develops during septation. Penicillin-binding proteins (PBPs) are essential for the final steps of PG biosynthesis; their transpeptidase activity links the peptide side chains of nascent glycan strands. PBP1 is required for cell division in S. aureus, and here, we demonstrate that it has multiple essential functions associated with its enzymatic activity and as a regulator of division. Loss of PBP1, or just its C-terminal PASTA domains, results in cessation of division at the point of septal plate formation. The PASTA domains can bind PG and thereby potentially coordinate the cell division process. The transpeptidase activity of PBP1 is also essential, but its loss leads to a strikingly different phenotype of thickened and aberrant septa, which is phenocopied by the morphological effects of adding the PBP1-specific β-lactam, meropenem. Together, these results lead to a model for septal PG synthesis where PBP1 enzyme activity is required for the characteristic architecture of the septum and PBP1 protein molecules enable the formation of the septal plate.
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10
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Ren L, Shen D, Liu C, Ding Y. Protein Tyrosine and Serine/Threonine Phosphorylation in Oral Bacterial Dysbiosis and Bacteria-Host Interaction. Front Cell Infect Microbiol 2022; 11:814659. [PMID: 35087767 PMCID: PMC8787120 DOI: 10.3389/fcimb.2021.814659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023] Open
Abstract
The human oral cavity harbors approximately 1,000 microbial species, and dysbiosis of the microflora and imbalanced microbiota-host interactions drive many oral diseases, such as dental caries and periodontal disease. Oral microbiota homeostasis is critical for systemic health. Over the last two decades, bacterial protein phosphorylation systems have been extensively studied, providing mounting evidence of the pivotal role of tyrosine and serine/threonine phosphorylation in oral bacterial dysbiosis and bacteria-host interactions. Ongoing investigations aim to discover novel kinases and phosphatases and to understand the mechanism by which these phosphorylation events regulate the pathogenicity of oral bacteria. Here, we summarize the structures of bacterial tyrosine and serine/threonine kinases and phosphatases and discuss the roles of tyrosine and serine/threonine phosphorylation systems in Porphyromonas gingivalis and Streptococcus mutans, emphasizing their involvement in bacterial metabolism and virulence, community development, and bacteria-host interactions.
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Affiliation(s)
- Liang Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Daonan Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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11
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Progulske-Fox A, Chukkapalli SS, Getachew H, Dunn WA, Oliver JD. VBNC, previously unrecognized in the life cycle of Porphyromonas gingivalis?. J Oral Microbiol 2022; 14:1952838. [PMID: 35035782 PMCID: PMC8759725 DOI: 10.1080/20002297.2021.1952838] [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] [Indexed: 11/25/2022] Open
Abstract
Bacteria are exposed to stresses during their growth and multiplication in their ecological systems to which they respond in multiple ways as expert survivalists. One such response mechanism is to convert to a viable but not culturable (VBNC) state. As the name indicates, bacteria in the VBNC state have lost their ability to grow on routine growth medium. A large number of bacteria including many pathogenic species have been reported to be able to enter a VBNC state. VBNC differs from culturable cells in various physiological properties which may result in changes in chemical resistance, adhesion, cellular morphology, metabolism, gene expression, membrane and cell wall composition and/or virulence. The ability of VBNC bacteria to return to the culturable state or resuscitate, when the stressor is removed poses a considerable threat to public health. There have been few publications that overtly describe the ability of oral pathogenic species to enter the VBNC state. However, the presence of VBNCs among oral pathogens such as Porphyromonas gingivalis in human chronic infections may be an important virulence factor and have severe implications for therapy. In this review, we intend to i) define and summarize the significance of the VBNC state in general and ii) discuss the VBNC state of oral bacteria with regard to P. gingivalis. Future studies focused on this phenomenon of intraoral VBNC would provide novel molecular insights on the virulence and persistence of oral pathogens during chronic infections and identify potential novel therapies.
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Affiliation(s)
- A Progulske-Fox
- Department of Oral Biology, Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA.,Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA
| | - S S Chukkapalli
- Department of Oral Biology, Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA.,Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA
| | - H Getachew
- Department of Oral Biology, Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA.,Center for Molecular Microbiology, University of Florida, Gainesville, FL, USA
| | - W A Dunn
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL, USA
| | - J D Oliver
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, USA
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12
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Ulrych A, Fabrik I, Kupčík R, Vajrychová M, Doubravová L, Branny P. Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation. J Mol Biol 2021; 433:167319. [PMID: 34688688 DOI: 10.1016/j.jmb.2021.167319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that encodes a single eukaryotic-type Ser/Thr protein kinase StkP and its functional counterpart, the protein phosphatase PhpP. These signaling enzymes play critical roles in coordinating cell division and growth in pneumococci. In this study, we determined the proteome and phosphoproteome profiles of relevant mutants. Comparison of those with the wild-type provided a representative dataset of novel phosphoacceptor sites and StkP-dependent substrates. StkP phosphorylates key proteins involved in cell division and cell wall biosynthesis in both the unencapsulated laboratory strain Rx1 and the encapsulated virulent strain D39. Furthermore, we show that StkP plays an important role in triggering an adaptive response induced by a cell wall-directed antibiotic. Phosphorylation of the sensor histidine kinase WalK and downregulation of proteins of the WalRK core regulon suggest crosstalk between StkP and the WalRK two-component system. Analysis of proteomic profiles led to the identification of gene clusters regulated by catabolite control mechanisms, indicating a tight coupling of carbon metabolism and cell wall homeostasis. The imbalance of steady-state protein phosphorylation in the mutants as well as after antibiotic treatment is accompanied by an accumulation of the global Spx regulator, indicating a Spx-mediated envelope stress response. In summary, StkP relays the perceived signal of cell wall status to key cell division and regulatory proteins, controlling the cell cycle and cell wall homeostasis.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Rudolf Kupčík
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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13
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Nagarajan SN, Lenoir C, Grangeasse C. Recent advances in bacterial signaling by serine/threonine protein kinases. Trends Microbiol 2021; 30:553-566. [PMID: 34836791 DOI: 10.1016/j.tim.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been nearly three decades since the discovery of the first bacterial serine/threonine protein kinase (STPK). Since then, a blend of technological advances has led to the characterization of a multitude of STPKs and phosphorylation substrates in several bacterial species that finely regulate intricate signaling cascades. Years of intense research from several laboratories have demonstrated unexpected roles for serine/threonine phosphorylation, regulating not only bacterial growth and cell division but also antibiotic persistence, virulence and infection, metabolism, chromosomal biology, and cellular differentiation. This review aims to provide an account of the most recent and significant developments in this up and growing field in microbiology.
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Affiliation(s)
- Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
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14
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Efficacy of Ursolic Acid-Enriched Water-Soluble and Not Cytotoxic Nanoparticles against Enterococci. Pharmaceutics 2021; 13:pharmaceutics13111976. [PMID: 34834390 PMCID: PMC8625572 DOI: 10.3390/pharmaceutics13111976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Ursolic acid (UA), a pentacyclic triterpenoid acid found in many medicinal plants and aromas, is known for its antibacterial effects against multi-drug-resistant (MDR) Gram-positive bacteria, which seriously threaten human health. Unfortunately, UA water-insolubility, low bioavailability, and systemic toxicity limit the possibilities of its application in vivo. Consequently, the beneficial activities of UA observed in vitro lose their potential clinical relevance unless water-soluble, not cytotoxic UA formulations are developed. With a nano-technologic approach, we have recently prepared water-soluble UA-loaded dendrimer nanoparticles (UA-G4K NPs) non-cytotoxic on HeLa cells, with promising physicochemical properties for their clinical applications. In this work, with the aim of developing a new antibacterial agent based on UA, UA-G4K has been tested on different strains of the Enterococcus genus, including marine isolates, toward which UA-G4K has shown minimum inhibitory concentrations (MICs) very low (0.5-4.3 µM), regardless of their resistance to antibiotics. Time-kill experiments, in addition to confirming the previously reported bactericidal activity of UA against E. faecium, also established it for UA-G4K. Furthermore, cytotoxicity experiments on human keratinocytes revealed that nanomanipulation of UA significantly reduced the cytotoxicity of UA, providing UA-G4K NPs with very high LD50 (96.4 µM) and selectivity indices, which were in the range 22.4-192.8, depending on the enterococcal strain tested. Due to its physicochemical and biological properties, UA-G4K could be seriously evaluated as a novel oral-administrable therapeutic option for tackling difficult-to-treat enterococcal infections.
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15
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Kelliher JL, Grunenwald CM, Abrahams RR, Daanen ME, Lew CI, Rose WE, Sauer JD. PASTA kinase-dependent control of peptidoglycan synthesis via ReoM is required for cell wall stress responses, cytosolic survival, and virulence in Listeria monocytogenes. PLoS Pathog 2021; 17:e1009881. [PMID: 34624065 PMCID: PMC8528326 DOI: 10.1371/journal.ppat.1009881] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/20/2021] [Accepted: 09/27/2021] [Indexed: 02/01/2023] Open
Abstract
Pathogenic bacteria rely on protein phosphorylation to adapt quickly to stress, including that imposed by the host during infection. Penicillin-binding protein and serine/threonine-associated (PASTA) kinases are signal transduction systems that sense cell wall integrity and modulate multiple facets of bacterial physiology in response to cell envelope stress. The PASTA kinase in the cytosolic pathogen Listeria monocytogenes, PrkA, is required for cell wall stress responses, cytosolic survival, and virulence, yet its substrates and downstream signaling pathways remain incompletely defined. We combined orthogonal phosphoproteomic and genetic analyses in the presence of a β-lactam antibiotic to define PrkA phosphotargets and pathways modulated by PrkA. These analyses synergistically highlighted ReoM, which was recently identified as a PrkA target that influences peptidoglycan (PG) synthesis, as an important phosphosubstrate during cell wall stress. We find that deletion of reoM restores cell wall stress sensitivities and cytosolic survival defects of a ΔprkA mutant to nearly wild-type levels. While a ΔprkA mutant is defective for PG synthesis during cell wall stress, a double ΔreoM ΔprkA mutant synthesizes PG at rates similar to wild type. In a mouse model of systemic listeriosis, deletion of reoM in a ΔprkA background almost fully restored virulence to wild-type levels. However, loss of reoM alone also resulted in attenuated virulence, suggesting ReoM is critical at some points during pathogenesis. Finally, we demonstrate that the PASTA kinase/ReoM cell wall stress response pathway is conserved in a related pathogen, methicillin-resistant Staphylococcus aureus. Taken together, our phosphoproteomic analysis provides a comprehensive overview of the PASTA kinase targets of an important model pathogen and suggests that a critical role of PrkA in vivo is modulating PG synthesis through regulation of ReoM to facilitate cytosolic survival and virulence. Many antibiotics target bacterial cell wall biosynthesis, justifying continued study of this process and the ways bacteria respond to cell wall insults during infection. Penicillin-binding protein and serine/threonine-associated (PASTA) kinases are master regulators of cell wall stress responses in bacteria and are conserved in several major pathogens, including Listeria monocytogenes, Staphylococcus aureus, and Mycobacterium tuberculosis. We previously showed that the PASTA kinase in L. monocytogenes, PrkA, is essential for the response to cell wall stress and for virulence. In this work, we combined proteomic and genetic approaches to identify PrkA substrates in L. monocytogenes. We show that regulation of one candidate from both screens, ReoM, increases synthesis of the cell wall component peptidoglycan and that this regulation is required for pathogenesis. We also demonstrate that the PASTA kinase-ReoM pathway regulates cell wall stress responses in another significant pathogen, methicillin-resistant S. aureus. Additionally, we uncover a PrkA-independent role for ReoM in vivo in L. monocytogenes, suggesting a need for nuanced modulation of peptidoglycan synthesis during infection. Cumulatively, this study provides new insight into how bacterial pathogens control cell wall synthesis during infection.
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Affiliation(s)
- Jessica L. Kelliher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caroline M. Grunenwald
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rhiannon R. Abrahams
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - McKenzie E. Daanen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cassandra I. Lew
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Warren E. Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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16
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Shaku M, Ealand C, Kana BD. Cell Surface Biosynthesis and Remodeling Pathways in Mycobacteria Reveal New Drug Targets. Front Cell Infect Microbiol 2020; 10:603382. [PMID: 33282752 PMCID: PMC7688586 DOI: 10.3389/fcimb.2020.603382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains the leading cause of death from an infectious bacterium and is responsible for 1.8 million deaths annually. The emergence of drug resistance, together with the need for a shorter more effective regimen, has prompted the drive to identify novel therapeutics with the bacterial cell surface emerging as a tractable area for drug development. Mtb assembles a unique, waxy, and complex cell envelope comprised of the mycolyl-arabinogalactan-peptidoglycan complex and an outer capsule like layer, which are collectively essential for growth and pathogenicity while serving as an inherent barrier against antibiotics. A detailed understanding of the biosynthetic pathways required to assemble the polymers that comprise the cell surface will enable the identification of novel drug targets as these structures provide a diversity of biochemical reactions that can be targeted. Herein, we provide an overview of recently described mycobacterial cell wall targeting compounds, novel drug combinations and their modes of action. We anticipate that this summary will enable prioritization of the best pathways to target and triage of the most promising molecules to progress for clinical assessment.
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Affiliation(s)
- Moagi Shaku
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher Ealand
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Bavesh D Kana
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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17
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Stokas H, Rhodes HL, Purdy GE. Modulation of the M. tuberculosis cell envelope between replicating and non-replicating persistent bacteria. Tuberculosis (Edinb) 2020; 125:102007. [PMID: 33035766 DOI: 10.1016/j.tube.2020.102007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022]
Abstract
The success of Mycobacterium tuberculosis as a human pathogen depends on the bacterium's ability to persist in a quiescent form in oxygen and nutrient-poor host environments. In vitro studies have demonstrated that these restricting environments induce a shift from bacterial replication to non-replicating persistence (NRP). Entry into NRP involves changes in bacterial metabolism and remodeling of the cell envelope. Findings consistent with the phenotypes observed in vitro have been observed in patient and animal model samples. This review focuses on the cell envelope differences seen between replicating and NRP M. tuberculosis and summarizes the ways in which serine/threonine protein kinases (STPKs) may mediate this process.
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Affiliation(s)
- Haley Stokas
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States
| | - Heather L Rhodes
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States
| | - Georgiana E Purdy
- Oregon Health & Science University, Department of Molecular Microbiology & Immunology, Portland, OR, 97239, United States.
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18
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Djorić D, Minton NE, Kristich CJ. The enterococcal PASTA kinase: A sentinel for cell envelope stress. Mol Oral Microbiol 2020; 36:132-144. [PMID: 32945615 DOI: 10.1111/omi.12313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
Enterococci are Gram-positive, opportunistic pathogens that reside throughout the gastrointestinal tracts of most terrestrial organisms. Enterococci are resistant to many antibiotics, which makes enterococcal infections difficult to treat. Enterococci are also particularly hardy bacteria that can tolerate a variety of environmental stressors. Understanding how enterococci sense and respond to the extracellular environment to enact adaptive biological responses may identify new targets that can be exploited for development of treatments for enterococcal infections. Bacterial eukaryotic-like serine/threonine kinases (eSTKs) and cognate phosphatases (STPs) are important signaling systems that mediate biological responses to extracellular stimuli. Some bacterial eSTKs are transmembrane proteins that contain a series of extracellular repeats of the penicillin-binding and Ser/Thr kinase-associated (PASTA) domain, leading to their designation as "PASTA kinases." Enterococcal genomes encode a single PASTA kinase and its cognate phosphatase. Investigations of the enterococcal PASTA kinase revealed its importance in resistance to antibiotics and other cell wall stresses, in enterococcal colonization of the mammalian gut, clues about its mechanism of signal transduction, and its integration with other enterococcal signal transduction systems. In this review, we describe the current state of knowledge of PASTA kinase signaling in enterococci and describe important gaps that still need to be addressed to provide a better understanding of this important signaling system.
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Affiliation(s)
- Dušanka Djorić
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicole E Minton
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, WI, USA
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19
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Morales Angeles D, Macia-Valero A, Bohorquez LC, Scheffers DJ. The PASTA domains of Bacillus subtilis PBP2B strengthen the interaction of PBP2B with DivIB. MICROBIOLOGY (READING, ENGLAND) 2020; 166:826-836. [PMID: 32749956 PMCID: PMC7654742 DOI: 10.1099/mic.0.000957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cell division is mediated by a protein complex known as the divisome. Many protein-protein interactions in the divisome have been characterized. In this report, we analyse the role of the PASTA (Penicillin-binding protein And Serine Threonine kinase Associated) domains of Bacillus subtilis PBP2B. PBP2B itself is essential and cannot be deleted, but removing the PBP2B PASTA domains results in impaired cell division and a heat-sensitive phenotype. This resembles the deletion of divIB, a known interaction partner of PBP2B. Bacterial two-hybrid and co-immunoprecipitation analyses show that the interaction between PBP2B and DivIB is weakened when the PBP2B PASTA domains are removed. Combined, our results show that the PBP2B PASTA domains are required to strengthen the interaction between PBP2B and DivIB.
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Affiliation(s)
- Danae Morales Angeles
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Present address: Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Alicia Macia-Valero
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Laura C. Bohorquez
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Present address: BluSense Diagnostics ApS, Carrera 63 100-49, Bogota 111121, Colombia
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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20
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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21
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Sexton DL, Herlihey FA, Brott AS, Crisante DA, Shepherdson E, Clarke AJ, Elliot MA. Roles of LysM and LytM domains in resuscitation-promoting factor (Rpf) activity and Rpf-mediated peptidoglycan cleavage and dormant spore reactivation. J Biol Chem 2020; 295:9171-9182. [PMID: 32434927 PMCID: PMC7335776 DOI: 10.1074/jbc.ra120.013994] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/15/2020] [Indexed: 11/06/2022] Open
Abstract
Bacterial dormancy can take many forms, including formation of Bacillus endospores, Streptomyces exospores, and metabolically latent Mycobacterium cells. In the actinobacteria, including the streptomycetes and mycobacteria, the rapid resuscitation from a dormant state requires the activities of a family of cell-wall lytic enzymes called resuscitation-promoting factors (Rpfs). Whether Rpf activity promotes resuscitation by generating peptidoglycan fragments (muropeptides) that function as signaling molecules for spore germination or by simply remodeling the dormant cell wall has been the subject of much debate. Here, to address this question, we used mutagenesis and peptidoglycan binding and cleavage assays to first gain broader insight into the biochemical function of diverse Rpf enzymes. We show that their LysM and LytM domains enhance Rpf enzyme activity; their LytM domain and, in some cases their LysM domain, also promoted peptidoglycan binding. We further demonstrate that the Rpfs function as endo-acting lytic transglycosylases, cleaving within the peptidoglycan backbone. We also found that unlike in other systems, Rpf activity in the streptomycetes is not correlated with peptidoglycan-responsive Ser/Thr kinases for cell signaling, and the germination of rpf mutant strains could not be stimulated by the addition of known germinants. Collectively, these results suggest that in Streptomyces, Rpfs have a structural rather than signaling function during spore germination, and that in the actinobacteria, any signaling function associated with spore resuscitation requires the activity of additional yet to be identified enzymes.
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Affiliation(s)
- Danielle L Sexton
- Michael G. DeGroote Institute for Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Canada
| | - Francesca A Herlihey
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Ashley S Brott
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - David A Crisante
- Michael G. DeGroote Institute for Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Canada
| | - Evan Shepherdson
- Michael G. DeGroote Institute for Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Marie A Elliot
- Michael G. DeGroote Institute for Infectious Disease Research and Department of Biology, McMaster University, Hamilton, Canada.
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22
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Regulation of virulence and antibiotic resistance in Gram-positive microbes in response to cell wall-active antibiotics. Curr Opin Infect Dis 2020; 32:217-222. [PMID: 31021953 DOI: 10.1097/qco.0000000000000542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Antibiotic stress can evoke considerable genotypic and phenotypic changes in Gram-positive bacteria. Here, we review recent studies describing altered virulence expression in response to cell wall-acting antibiotics and discuss mechanisms that coordinate regulation of the antibiotic response. RECENT FINDINGS Pleiotropic effects induced by antibiotic exposure include alterations to bacterial metabolism, cell wall structure and antibiotic resistance. In addition, subinhibitory concentrations of cell wall-active (CWA) antibiotics have increasingly been shown to induce the production of exotoxins and biofilm formation that may influence virulence. Remarkably, phenotypes associated with comparable antibiotic stresses can vary considerably, emphasizing the need to better understand the response to CWA antibiotics. Recent studies support both direct antibiotic recognition and recognition of antibiotic-induced stress to the bacterial cell wall. Specifically, bacterial two-component systems, penicillin-binding protein and serine/threonine kinase-associated kinases and conserved oxidative-stress sensors each contribute to modulating the antibiotic stress response. SUMMARY Bacterial sensory systems and global regulators coordinate signaling in response to CWA antibiotics. Regulation of the antibiotic response is complex and involves integration of signals from multiple response pathways. A better definition of the antibiotic stress response among Gram-positive pathogens may yield novel therapeutic targets to counter antibiotic resistance and virulence factor expression.
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23
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Wamp S, Rutter ZJ, Rismondo J, Jennings CE, Möller L, Lewis RJ, Halbedel S. PrkA controls peptidoglycan biosynthesis through the essential phosphorylation of ReoM. eLife 2020; 9:56048. [PMID: 32469310 PMCID: PMC7286690 DOI: 10.7554/elife.56048] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Peptidoglycan (PG) is the main component of bacterial cell walls and the target for many antibiotics. PG biosynthesis is tightly coordinated with cell wall growth and turnover, and many of these control activities depend upon PASTA-domain containing eukaryotic-like serine/threonine protein kinases (PASTA-eSTK) that sense PG fragments. However, only a few PG biosynthetic enzymes are direct kinase substrates. Here, we identify the conserved ReoM protein as a novel PASTA-eSTK substrate in the Gram-positive pathogen Listeria monocytogenes. Our data show that the phosphorylation of ReoM is essential as it controls ClpCP-dependent proteolytic degradation of the essential enzyme MurA, which catalyses the first committed step in PG biosynthesis. We also identify ReoY as a second novel factor required for degradation of ClpCP substrates. Collectively, our data imply that the first committed step of PG biosynthesis is activated through control of ClpCP protease activity in response to signals of PG homeostasis imbalance.
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Affiliation(s)
- Sabrina Wamp
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Zoe J Rutter
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Jeanine Rismondo
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Claire E Jennings
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Newcastle upon Tyne, United Kingdom
| | - Lars Möller
- ZBS 4 - Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sven Halbedel
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
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24
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Shaku M, Ealand C, Matlhabe O, Lala R, Kana BD. Peptidoglycan biosynthesis and remodeling revisited. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:67-103. [PMID: 32762868 DOI: 10.1016/bs.aambs.2020.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The bacterial peptidoglycan layer forms a complex mesh-like structure that surrounds the cell, imparting rigidity to withstand cytoplasmic turgor and the ability to tolerate stress. As peptidoglycan has been the target of numerous clinically successful antimicrobials such as penicillin, the biosynthesis, remodeling and recycling of this polymer has been the subject of much interest. Herein, we review recent advances in the understanding of peptidoglycan biosynthesis and remodeling in a variety of different organisms. In order for bacterial cells to grow and divide, remodeling of cross-linked peptidoglycan is essential hence, we also summarize the activity of important peptidoglycan hydrolases and how their functions differ in various species. There is a growing body of evidence highlighting complex regulatory mechanisms for peptidoglycan metabolism including protein interactions, phosphorylation and protein degradation and we summarize key recent findings in this regard. Finally, we provide an overview of peptidoglycan recycling and how components of this pathway mediate resistance to drugs. In the face of growing antimicrobial resistance, these recent advances are expected to uncover new drug targets in peptidoglycan metabolism, which can be used to develop novel therapies.
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Affiliation(s)
- Moagi Shaku
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Christopher Ealand
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Ofentse Matlhabe
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Rushil Lala
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh D Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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Zeng J, Platig J, Cheng TY, Ahmed S, Skaf Y, Potluri LP, Schwartz D, Steen H, Moody DB, Husson RN. Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility. PLoS Pathog 2020; 16:e1008452. [PMID: 32255801 PMCID: PMC7164672 DOI: 10.1371/journal.ppat.1008452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/17/2020] [Accepted: 03/03/2020] [Indexed: 01/28/2023] Open
Abstract
The Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB are essential for growth and have been proposed as possible drug targets. We used a titratable conditional depletion system to investigate the functions of these kinases. Depletion of PknA or PknB or both kinases resulted in growth arrest, shortening of cells, and time-dependent loss of acid-fast staining with a concomitant decrease in mycolate synthesis and accumulation of trehalose monomycolate. Depletion of PknA and/or PknB resulted in markedly increased susceptibility to β-lactam antibiotics, and to the key tuberculosis drug rifampin. Phosphoproteomic analysis showed extensive changes in protein phosphorylation in response to PknA depletion and comparatively fewer changes with PknB depletion. These results identify candidate substrates of each kinase and suggest specific and coordinate roles for PknA and PknB in regulating multiple essential physiologies. These findings support these kinases as targets for new antituberculosis drugs and provide a valuable resource for targeted investigation of mechanisms by which protein phosphorylation regulates pathways required for growth and virulence in M. tuberculosis.
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Affiliation(s)
- Jumei Zeng
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Saima Ahmed
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Yara Skaf
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Lakshmi-Prasad Potluri
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Robert N. Husson
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
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26
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Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
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Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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Dong K, Pan H, Yang D, Rao L, Zhao L, Wang Y, Liao X. Induction, detection, formation, and resuscitation of viable but non‐culturable state microorganisms. Compr Rev Food Sci Food Saf 2019; 19:149-183. [DOI: 10.1111/1541-4337.12513] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/21/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Kai Dong
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Hanxu Pan
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Dong Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Lei Rao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Liang Zhao
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Yongtao Wang
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Xiaojun Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
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28
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Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Sci Rep 2019; 9:18043. [PMID: 31792329 PMCID: PMC6888817 DOI: 10.1038/s41598-019-54646-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
When nutrients run out, bacteria enter a dormant metabolic state. This low or undetectable metabolic activity helps bacteria to preserve their scant reserves for the future needs, yet it also diminishes their ability to scan the environment for new growth-promoting substrates. However, neighboring microbial growth is a reliable indicator of a favorable environment and can thus serve as a cue for exiting dormancy. Here we report that for Escherichia coli and Pseudomonas aeruginosa this cue is provided by the basic peptidoglycan unit (i.e. muropeptide). We show that several forms of muropeptides from a variety of bacterial species can stimulate growth resumption of dormant cells and the sugar – peptide bond is crucial for this activity. These results, together with previous research that identifies muropeptides as a germination signal for bacterial spores, and their detection by mammalian immune cells, show that muropeptides are a universal cue for bacterial growth.
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29
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh Davandra Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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30
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Park EJ, Kwon YM, Lee JW, Kang HY, Oh JI. Dual control of RegX3 transcriptional activity by SenX3 and PknB. J Biol Chem 2019; 294:11023-11034. [PMID: 31160336 DOI: 10.1074/jbc.ra119.008232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The mycobacterial SenX3-RegX3 two-component system consists of the SenX3 sensor histidine kinase and its cognate RegX3 response regulator. This system is a phosphorelay-based regulatory system involved in sensing environmental Pi levels and induction of genes required for Pi acquisition under Pi-limiting conditions. Here we demonstrate that overexpression of the kinase domain of Mycobacterium tuberculosis PknB (PknB-KDMtb) inhibits the transcriptional activity of RegX3 of both M. tuberculosis and Mycobacterium smegmatis (RegX3Mtb and RegX3Ms, respectively). Mass spectrometry results, along with those of in vitro phosphorylation and complementation analyses, revealed that PknB kinase activity inhibits the transcriptional activity of RegX3Mtb through phosphorylation events at Thr-100, Thr-191, and Thr-217. Electrophoretic mobility shift assays disclosed that phosphorylation of Thr-191 and Thr-217 abolishes the DNA-binding ability of RegX3Mtb and that Thr-100 phosphorylation likely prevents RegX3Mtb from being activated through conformational changes induced by SenX3-mediated phosphorylation. We propose that the convergence of the PknB and SenX3-RegX3 signaling pathways might enable mycobacteria to integrate environmental Pi signals with the cellular replication state to adjust gene expression in response to Pi availability.
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Affiliation(s)
- Eun-Jin Park
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Yu-Mi Kwon
- Biomedical Research Institute, Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea, and; Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Ho-Young Kang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea,.
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31
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Microbes Infect 2019; 21:222-229. [PMID: 31254628 DOI: 10.1016/j.micinf.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation is known to be one of the keystones of signal sensing and transduction in all living organisms. Once thought to be essentially confined to the eukaryotic kingdoms, reversible phosphorylation on serine, threonine and tyrosine residues, has now been shown to play a major role in many prokaryotes, where the number of Ser/Thr protein kinases (STPKs) equals or even exceeds that of two component systems. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the most studied organisms for the role of STPK-mediated signaling in bacteria. Driven by the interest and tractability of these enzymes as potential therapeutic targets, extensive studies revealed the remarkable conservation of protein kinases and their cognate phosphatases across evolution, and their involvement in bacterial physiology and virulence. Here, we present an overview of the current knowledge of mycobacterial STPKs structures and kinase activation mechanisms, and we then focus on PknB and PknG, two well-characterized STPKs that are essential for the intracellular survival of the bacillus. We summarize the mechanistic evidence that links PknB to the regulation of peptidoglycan synthesis in cell division and morphogenesis, and the major findings that establishes PknG as a master regulator of central carbon and nitrogen metabolism. Two decades after the discovery of STPKs in M. tuberculosis, the emerging landscape of O-phosphosignaling is starting to unveil how eukaryotic-like kinases can be engaged in unique, non-eukaryotic-like, signaling mechanisms in mycobacteria.
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Affiliation(s)
- Marco Bellinzoni
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Anne Marie Wehenkel
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo 11400, Uruguay
| | - Pedro M Alzari
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France.
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32
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Labbe BD, Hall CL, Kellogg SL, Chen Y, Koehn O, Pickrum AM, Mirza SP, Kristich CJ. Reciprocal Regulation of PASTA Kinase Signaling by Differential Modification. J Bacteriol 2019; 201:e00016-19. [PMID: 30858297 PMCID: PMC6482931 DOI: 10.1128/jb.00016-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022] Open
Abstract
Transmembrane Ser/Thr kinases containing extracellular PASTA (penicillin-binding protein [PBP] and Ser/Thr-associated) domains are ubiquitous among Actinobacteria and Firmicutes species. Such PASTA kinases regulate critical bacterial processes, including antibiotic resistance, cell division, cell envelope homeostasis, and virulence, and are sometimes essential for viability. Previous studies of purified PASTA kinase fragments revealed they are capable of autophosphorylation in vitro, typically at multiple sites on the kinase domain. Autophosphorylation of a specific structural element of the kinase known as the activation loop is thought to enhance kinase activity in response to stimuli. However, the role of kinase phosphorylation at other sites is largely unknown. Moreover, the mechanisms by which PASTA kinases are deactivated once their stimulus has diminished are poorly understood. Enterococcus faecalis is a Gram-positive intestinal bacterium and a major antibiotic-resistant opportunistic pathogen. In E. faecalis, the PASTA kinase IreK drives intrinsic resistance to cell wall-active antimicrobials, and such antimicrobials trigger enhanced phosphorylation of IreK in vivo Here we identify multiple sites of phosphorylation on IreK and evaluate their function in vivo and in vitro While phosphorylation of the IreK activation loop is required for kinase activity, we found that phosphorylation at a site distinct from the activation loop reciprocally modulates IreK activity in vivo, leading to diminished activity (and diminished antimicrobial resistance). Moreover, this site is important for deactivation of IreK in vivo upon removal of an activating stimulus. Our results are consistent with a model in which phosphorylation of IreK at distinct sites reciprocally regulates IreK activity in vivo to promote adaptation to cell wall stresses.IMPORTANCE Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes species and regulate critical processes, including antibiotic resistance, cell division, and cell envelope homeostasis. Previous studies of PASTA kinase fragments revealed autophosphorylation at multiple sites. However, the functional role of autophosphorylation and the relative impacts of phosphorylation at distinct sites are poorly understood. The PASTA kinase of Enterococcus faecalis, IreK, regulates intrinsic resistance to antimicrobials. Here we identify multiple sites of phosphorylation on IreK and show that modification of IreK at distinct sites reciprocally regulates IreK activity and antimicrobial resistance in vivo Thus, these results provide new insights into the mechanisms by which PASTA kinases can regulate critical physiological processes in a wide variety of bacterial species.
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Affiliation(s)
- Benjamin D Labbe
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Cherisse L Hall
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Stephanie L Kellogg
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Yao Chen
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Olivia Koehn
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Adam M Pickrum
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Shama P Mirza
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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Irazoki O, Hernandez SB, Cava F. Peptidoglycan Muropeptides: Release, Perception, and Functions as Signaling Molecules. Front Microbiol 2019; 10:500. [PMID: 30984120 PMCID: PMC6448482 DOI: 10.3389/fmicb.2019.00500] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Peptidoglycan (PG) is an essential molecule for the survival of bacteria, and thus, its biosynthesis and remodeling have always been in the spotlight when it comes to the development of antibiotics. The peptidoglycan polymer provides a protective function in bacteria, but at the same time is continuously subjected to editing activities that in some cases lead to the release of peptidoglycan fragments (i.e., muropeptides) to the environment. Several soluble muropeptides have been reported to work as signaling molecules. In this review, we summarize the mechanisms involved in muropeptide release (PG breakdown and PG recycling) and describe the known PG-receptor proteins responsible for PG sensing. Furthermore, we overview the role of muropeptides as signaling molecules, focusing on the microbial responses and their functions in the host beyond their immunostimulatory activity.
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Affiliation(s)
- Oihane Irazoki
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Sara B Hernandez
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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34
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Kaur P, Rausch M, Malakar B, Watson U, Damle NP, Chawla Y, Srinivasan S, Sharma K, Schneider T, Jhingan GD, Saini D, Mohanty D, Grein F, Nandicoori VK. LipidII interaction with specific residues of Mycobacterium tuberculosis PknB extracytoplasmic domain governs its optimal activation. Nat Commun 2019; 10:1231. [PMID: 30874556 PMCID: PMC6428115 DOI: 10.1038/s41467-019-09223-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/28/2019] [Indexed: 02/08/2023] Open
Abstract
The Mycobacterium tuberculosis kinase PknB is essential for growth and survival of the pathogen in vitro and in vivo. Here we report the results of our efforts to elucidate the mechanism of regulation of PknB activity. The specific residues in the PknB extracytoplasmic domain that are essential for ligand interaction and survival of the bacterium are identified. The extracytoplasmic domain interacts with mDAP-containing LipidII, and this is abolished upon mutation of the ligand-interacting residues. Abrogation of ligand-binding or sequestration of the ligand leads to aberrant localization of PknB. Contrary to the prevailing hypothesis, abrogation of ligand-binding is linked to activation loop hyperphosphorylation, and indiscriminate hyperphosphorylation of PknB substrates as well as other proteins, ultimately causing loss of homeostasis and cell death. We propose that the ligand-kinase interaction directs the appropriate localization of the kinase, coupled to stringently controlled activation of PknB, and consequently the downstream processes thereof. The Mycobacterium tuberculosis kinase PknB regulates essential cell functions via interactions with muropeptides. Here the authors identify interaction sites in the extracytoplasmic PASTA domain and show that abrogation of ligand binding leads to a hyper-activated kinase, causing loss of homeostasis and cell death.
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Affiliation(s)
- Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
| | - Basanti Malakar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uchenna Watson
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, 560012, India
| | - Nikhil P Damle
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,BIOSS, Center for Biological Signaling Studies, University of Freiburg, Freiburg, 79104, Germany
| | - Yogesh Chawla
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Sandhya Srinivasan
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Kanika Sharma
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
| | - Gagan Deep Jhingan
- Vproteomics, Valerian Chem Private Limited, Green Park Main, New Delhi, 110016, India
| | - Deepak Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, 560012, India
| | - Debasisa Mohanty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, 53105, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, 53105, Germany
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Turapov O, Forti F, Kadhim B, Ghisotti D, Sassine J, Straatman-Iwanowska A, Bottrill AR, Moynihan PJ, Wallis R, Barthe P, Cohen-Gonsaud M, Ajuh P, Vollmer W, Mukamolova GV. Two Faces of CwlM, an Essential PknB Substrate, in Mycobacterium tuberculosis. Cell Rep 2018; 25:57-67.e5. [PMID: 30282038 PMCID: PMC6180346 DOI: 10.1016/j.celrep.2018.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/11/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis claims >1 million lives annually, and its causative agent Mycobacterium tuberculosis is a highly successful pathogen. Protein kinase B (PknB) is reported to be critical for mycobacterial growth. Here, we demonstrate that PknB-depleted M. tuberculosis can replicate normally and can synthesize peptidoglycan in an osmoprotective medium. Comparative phosphoproteomics of PknB-producing and PknB-depleted mycobacteria identify CwlM, an essential regulator of peptidoglycan synthesis, as a major PknB substrate. Our complementation studies of a cwlM mutant of M. tuberculosis support CwlM phosphorylation as a likely molecular basis for PknB being essential for mycobacterial growth. We demonstrate that growing mycobacteria produce two forms of CwlM: a non-phosphorylated membrane-associated form and a PknB-phosphorylated cytoplasmic form. Furthermore, we show that the partner proteins for the phosphorylated and non-phosphorylated forms of CwlM are FhaA, a fork head-associated domain protein, and MurJ, a proposed lipid II flippase, respectively. From our results, we propose a model in which CwlM potentially regulates both the biosynthesis of peptidoglycan precursors and their transport across the cytoplasmic membrane.
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Affiliation(s)
- Obolbek Turapov
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - Francesca Forti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Baleegh Kadhim
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK; Biology Department, College of Science, University of Al-Qadisiyah, Al-Diwaniyah 58002, Iraq
| | - Daniela Ghisotti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Jad Sassine
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Anna Straatman-Iwanowska
- Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester LE1 7RH, UK
| | - Andrew R Bottrill
- Protein Nucleic Acid Laboratory, University of Leicester, Leicester LE1 7RH, UK
| | - Patrick J Moynihan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Russell Wallis
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK; The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, UK
| | - Philippe Barthe
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, Montpellier 34090, France
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, Montpellier 34090, France
| | - Paul Ajuh
- Gemini Biosciences, Liverpool Science Park, Liverpool L3 5TF, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Galina V Mukamolova
- Leicester Tuberculosis Research Group, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK.
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Raghavendra T, Patil S, Mukherjee R. Peptidoglycan in Mycobacteria: chemistry, biology and intervention. Glycoconj J 2018; 35:421-432. [DOI: 10.1007/s10719-018-9842-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 09/05/2018] [Indexed: 01/07/2023]
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Golichenari B, Velonia K, Nosrati R, Nezami A, Farokhi-Fard A, Abnous K, Behravan J, Tsatsakis AM. Label-free nano-biosensing on the road to tuberculosis detection. Biosens Bioelectron 2018; 113:124-135. [DOI: 10.1016/j.bios.2018.04.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/14/2018] [Accepted: 04/28/2018] [Indexed: 12/16/2022]
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Calvanese L, Falcigno L, Squeglia F, Berisio R, D’Auria G. PASTA sequence composition is a predictive tool for protein class identification. Amino Acids 2018; 50:1441-1450. [DOI: 10.1007/s00726-018-2621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022]
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Khan MZ, Kaur P, Nandicoori VK. Targeting the messengers: Serine/threonine protein kinases as potential targets for antimycobacterial drug development. IUBMB Life 2018; 70:889-904. [DOI: 10.1002/iub.1871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/22/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
| | - Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
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40
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Global proteome and phosphoproteome dynamics indicate novel mechanisms of vitamin C induced dormancy in Mycobacterium smegmatis. J Proteomics 2018; 180:1-10. [DOI: 10.1016/j.jprot.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/20/2017] [Accepted: 10/10/2017] [Indexed: 01/30/2023]
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41
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Puffal J, García-Heredia A, Rahlwes KC, Siegrist MS, Morita YS. Spatial control of cell envelope biosynthesis in mycobacteria. Pathog Dis 2018; 76:4953754. [DOI: 10.1093/femspd/fty027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/25/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Julia Puffal
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - 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
| | - Yasu S Morita
- 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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42
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Takada H, Yoshikawa H. Essentiality and function of WalK/WalR two-component system: the past, present, and future of research. Biosci Biotechnol Biochem 2018. [PMID: 29514560 DOI: 10.1080/09168451.2018.1444466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The WalK/WalR two-component system (TCS), originally identified in Bacillus subtilis, is very highly conserved in gram-positive bacteria, including several important pathogens. The WalK/WalR TCS appears to be involved in the growth of most bacterial species encoding it. Previous studies have indicated conserved functions of this system, defining this signal transduction pathway as a crucial regulatory system for cell wall metabolism. Because of such effects on essential functions, this system is considered a potential target for anti-infective therapeutics. In this review, we discuss the role of WalK/WalR TCS in different bacterial cells, focusing on the function of the genes in its regulon as well as the variations in walRK operon structure, its auxiliary proteins, and the composition of its regulon. We also discuss recent experimental data addressing its essential function and the potential type of signal being sensed by B. subtilis. This review also focuses on the potential future research.
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Affiliation(s)
- Hiraku Takada
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan.,Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio 2018; 9:mBio.02333-17. [PMID: 29511081 PMCID: PMC5845002 DOI: 10.1128/mbio.02333-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis is the leading killer among infectious diseases worldwide. Increasing multidrug resistance has prompted new approaches for tuberculosis drug development, including targeted inhibition of virulence determinants and of signaling cascades that control many downstream pathways. We used a multisystem approach to determine the effects of a potent small-molecule inhibitor of the essential Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB. We observed differential levels of phosphorylation of many proteins and extensive changes in levels of gene expression, protein abundance, cell wall lipids, and intracellular metabolites. The patterns of these changes indicate regulation by PknA and PknB of several pathways required for cell growth, including ATP synthesis, DNA synthesis, and translation. These data also highlight effects on pathways for remodeling of the mycobacterial cell envelope via control of peptidoglycan turnover, lipid content, a SigE-mediated envelope stress response, transmembrane transport systems, and protein secretion systems. Integrated analysis of phosphoproteins, transcripts, proteins, and lipids identified an unexpected pathway whereby threonine phosphorylation of the essential response regulator MtrA decreases its DNA binding activity. Inhibition of this phosphorylation is linked to decreased expression of genes for peptidoglycan turnover, and of genes for mycolyl transferases, with concomitant changes in mycolates and glycolipids in the cell envelope. These findings reveal novel roles for PknA and PknB in regulating multiple essential cell functions and confirm that these kinases are potentially valuable targets for new antituberculosis drugs. In addition, the data from these linked multisystems provide a valuable resource for future targeted investigations into the pathways regulated by these kinases in the M. tuberculosis cell. Tuberculosis is the leading killer among infectious diseases worldwide. Increasing drug resistance threatens efforts to control this epidemic; thus, new antitubercular drugs are urgently needed. We performed an integrated, multisystem analysis of Mycobacterium tuberculosis responses to inhibition of its two essential serine/threonine protein kinases. These kinases allow the bacterium to adapt to its environment by phosphorylating cellular proteins in response to extracellular signals. We identified differentially phosphorylated proteins, downstream changes in levels of specific mRNA and protein abundance, and alterations in the metabolite and lipid content of the cell. These results include changes previously linked to growth arrest and also reveal new roles for these kinases in regulating essential processes, including growth, stress responses, transport of proteins and other molecules, and the structure of the mycobacterial cell envelope. Our multisystem data identify PknA and PknB as promising targets for drug development and provide a valuable resource for future investigation of their functions.
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Phosphorylation-dependent activation of the cell wall synthase PBP2a in Streptococcus pneumoniae by MacP. Proc Natl Acad Sci U S A 2018; 115:2812-2817. [PMID: 29487215 DOI: 10.1073/pnas.1715218115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Most bacterial cells are surrounded by an essential cell wall composed of the net-like heteropolymer peptidoglycan (PG). Growth and division of bacteria are intimately linked to the expansion of the PG meshwork and the construction of a cell wall septum that separates the nascent daughter cells. Class A penicillin-binding proteins (aPBPs) are a major family of PG synthases that build the wall matrix. Given their central role in cell wall assembly and importance as drug targets, surprisingly little is known about how the activity of aPBPs is controlled to properly coordinate cell growth and division. Here, we report the identification of MacP (SPD_0876) as a membrane-anchored cofactor of PBP2a, an aPBP synthase of the Gram-positive pathogen Streptococcus pneumoniae We show that MacP localizes to the division site of S. pneumoniae, forms a complex with PBP2a, and is required for the in vivo activity of the synthase. Importantly, MacP was also found to be a substrate for the kinase StkP, a global cell cycle regulator. Although StkP has been implicated in controlling the balance between the elongation and septation modes of cell wall synthesis, none of its substrates are known to modulate PG synthetic activity. Here we show that a phosphoablative substitution in MacP that blocks StkP-mediated phosphorylation prevents PBP2a activity without affecting the MacP-PBP2a interaction. Our results thus reveal a direct connection between PG synthase function and the control of cell morphogenesis by the StkP regulatory network.
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Pompeo F, Byrne D, Mengin-Lecreulx D, Galinier A. Dual regulation of activity and intracellular localization of the PASTA kinase PrkC during Bacillus subtilis growth. Sci Rep 2018; 8:1660. [PMID: 29374241 PMCID: PMC5786024 DOI: 10.1038/s41598-018-20145-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
The activity of the PrkC protein kinase is regulated in a sophisticated manner in Bacillus subtilis cells. In spores, in the presence of muropeptides, PrkC stimulates dormancy exit. The extracellular region containing PASTA domains binds peptidoglycan fragments to probably enhance the intracellular kinase activity. During exponential growth, the cell division protein GpsB interacts with the intracellular domain of PrkC to stimulate its activity. In this paper, we have reinvestigated the regulation of PrkC during exponential and stationary phases. We observed that, during exponential growth, neither its septal localization nor its activity are influenced by the addition of peptidoglycan fragments or by the deletion of one or all PASTA domains. However, Dynamic Light Scattering experiments suggest that peptidoglycan fragments bind specifically to PrkC and induce its oligomerization. In addition, during stationary phase, PrkC appeared evenly distributed in the cell wall and the deletion of one or all PASTA domains led to a non-activated kinase. We conclude that PrkC activation is not as straightforward as previously suggested and that regulation of its kinase activity via the PASTA domains and peptidoglycan fragments binding occurs when PrkC is not concentrated to the bacterial septum, but all over the cell wall in non-dividing bacillus cells.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France.
| | - Deborah Byrne
- Protein Expression Facility, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France
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Abstract
Cell elongation occurs primarily at the mycobacterial cell poles, but the molecular mechanisms governing this spatial regulation remain elusive. We recently reported the presence of an intracellular membrane domain (IMD) that was spatially segregated from the conventional plasma membrane in Mycobacterium smegmatis. The IMD is enriched in the polar region of actively elongating cells and houses many essential enzymes involved in envelope biosynthesis, suggesting its role in spatially restricted elongation at the cell poles. Here, we examined reorganization of the IMD when the cells are no longer elongating. To monitor the IMD, we used a previously established reporter strain expressing fluorescent IMD markers and grew it to the stationary growth phase or exposed the cells to nutrient starvation. In both cases, the IMD was delocalized from the cell pole and distributed along the sidewall. Importantly, the IMD could still be isolated biochemically by density gradient fractionation, indicating its maintenance as a membrane domain. Chemical and genetic inhibition of peptidoglycan biosynthesis led to the delocalization of the IMD, suggesting the suppression of peptidoglycan biosynthesis as a trigger of spatial IMD rearrangement. Starved cells with a delocalized IMD can resume growth upon nutrient repletion, and polar enrichment of the IMD coincides with the initiation of cell elongation. These data reveal that the IMD is a membrane domain with the unprecedented capability of subcellular repositioning in response to the physiological conditions of the mycobacterial cell. Mycobacteria include medically important species, such as the human tuberculosis pathogen Mycobacterium tuberculosis. The highly impermeable cell envelope is a hallmark of these microbes, and its biosynthesis is a proven chemotherapeutic target. Despite the accumulating knowledge regarding the biosynthesis of individual envelope components, the regulatory mechanisms behind the coordinated synthesis of the complex cell envelope remain elusive. We previously reported the presence of a metabolically active membrane domain enriched in the elongating poles of actively growing mycobacteria. However, the spatiotemporal dynamics of the membrane domain in response to stress have not been examined. Here, we show that the membrane domain is spatially reorganized when growth is inhibited in the stationary growth phase, under nutrient starvation, or in response to perturbation of peptidoglycan biosynthesis. Our results suggest that mycobacteria have a mechanism to spatiotemporally coordinate the membrane domain in response to metabolic needs under different growth conditions.
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Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities. Curr Top Microbiol Immunol 2018; 420:1-21. [PMID: 30406866 DOI: 10.1007/82_2018_128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.
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48
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Genome-Wide Screens Reveal New Gene Products That Influence Genetic Competence in Streptococcus mutans. J Bacteriol 2017; 200:JB.00508-17. [PMID: 29109185 DOI: 10.1128/jb.00508-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/26/2017] [Indexed: 12/11/2022] Open
Abstract
A network of genes and at least two peptide signaling molecules tightly control when Streptococcus mutans becomes competent to take up DNA from its environment. Widespread changes in the expression of genes occur when S. mutans is presented with competence signal peptides in vitro, including the increased production of the alternative sigma factor, ComX, which activates late competence genes. Still, the way that gene products that are regulated by competence peptides influence DNA uptake and cellular physiology are not well understood. Here, we developed and employed comprehensive transposon mutagenesis of the S. mutans genome, with a screen to identify mutants that aberrantly expressed comX, coupled with transposon sequencing (Tn-seq) to gain a more thorough understanding of the factors modulating comX expression and progression to the competent state. The screens effectively identified genes known to affect competence, e.g., comR, comS, comD, comE, cipB, clpX, rcrR, and ciaH, but disclosed an additional 20 genes that were not previously competence associated. The competence phenotypes of mutants were characterized, including by fluorescence microscopy to determine at which stage the mutants were impaired for comX activation. Among the novel genes studied were those implicated in cell division, the sensing of cell envelope stress, cell envelope biogenesis, and RNA stability. Our results provide a platform for determining the specific chemical and physical cues that are required for genetic competence in S. mutans, while highlighting the effectiveness of using Tn-seq in S. mutans to discover and study novel biological processes.IMPORTANCE Streptococcus mutans acquires DNA from its environment by becoming genetically competent, a physiologic state triggered by cell-cell communication using secreted peptides. Competence is important for acquiring novel genetic traits and has a strong influence on the expression of virulence-associated traits of S. mutans Here, we used transposon mutagenesis and genomic technologies to identify novel genes involved in competence development. In addition to identifying genes previously known to be required for comX expression, 20 additional genes were identified and characterized. The findings create opportunities to diminish the pathogenic potential of S. mutans, while validating technologies that can rapidly advance our understanding of the physiology, biology, and genetics of S. mutans and related pathogens.
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49
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Squeglia F, Ruggiero A, Berisio R. Chemistry of Peptidoglycan in Mycobacterium tuberculosis
Life Cycle: An off-the-wall Balance of Synthesis and Degradation. Chemistry 2017; 24:2533-2546. [DOI: 10.1002/chem.201702973] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
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50
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Righino B, Galisson F, Pirolli D, Vitale S, Réty S, Gouet P, De Rosa MC. Structural model of the full-length Ser/Thr protein kinase StkP from S. pneumoniae and its recognition of peptidoglycan fragments. J Biomol Struct Dyn 2017; 36:3666-3679. [PMID: 29057709 DOI: 10.1080/07391102.2017.1395767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The unique eukaryotic-like Ser/Thr protein kinases of Streptococcus pneumoniae, StkP, plays a primary role in the cell division process. It is composed of an intracellular kinase domain, a transmembrane helix and four extracellular PASTA subunits. PASTA domains were shown to interact with cell wall fragments but the key questions related to the molecular mechanism governing ligand recognition remain unclear. To address this issue, the full-length structural model of StkP was generated by combining small-angle X-ray scattering data with the results of computer simulations. Docking and molecular dynamics studies on the generated three-dimensional model structure reveal the possibility of peptidoglycan fragment binding at the hinge regions between PASTA subunits with a preference for a bent hinge between PASTA3 and PASTA4.
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Affiliation(s)
- Benedetta Righino
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Frédéric Galisson
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Davide Pirolli
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy.,c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
| | - Serena Vitale
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Stéphane Réty
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Patrice Gouet
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Maria Cristina De Rosa
- c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
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