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Ruma YN, Bu G, Gonen T. MicroED structure of the C11 cysteine protease Clostripain. bioRxiv 2024:2024.01.04.574240. [PMID: 38260293 PMCID: PMC10802345 DOI: 10.1101/2024.01.04.574240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Clostripain secreted from Clostridium histolyticum is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of C. histolyticum Clostripain determined at 3.6 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of Clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 to 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as Clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.
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2
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Mahmud ASM, Seers CA, Huq NL, Zhang L, Butler CA, Moore C, Cross KJ, Reynolds EC. Production and properties of adhesin-free gingipain proteinase RgpA. Sci Rep 2023; 13:10780. [PMID: 37402780 DOI: 10.1038/s41598-023-37534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
The Arg-specific gingipains of Porphyromonas gingivalis RgpA and RgpB have 97% identical sequences in their catalytic domains yet their propeptides are only 76% identical. RgpA isolates as a proteinase-adhesin complex (HRgpA) which hinders direct kinetic comparison of RgpAcat as a monomer with monomeric RgpB. We tested modifications of rgpA identifying a variant that enabled us to isolate histidine-tagged monomeric RgpA (rRgpAH). Kinetic comparisons between rRgpAH and RgpB used benzoyl-L-Arg-4-nitroanilide with and without cysteine and glycylglycine acceptor molecules. With no glycylglycine, values of Km, Vmax, kcat and kcat/Km for each enzyme were similar, but with glycylglycine Km decreased, Vmax increased and kcat increased ~ twofold for RgpB but ~ sixfold for rRgpAH. The kcat/Km for rRgpAH was unchanged whereas that of RgpB more than halved. Recombinant RgpA propeptide inhibited rRgpAH and RgpB with Ki 13 nM and 15 nM Ki respectively slightly more effectively than RgpB propeptide which inhibited rRgpAH and RgpB with Ki 22 nM and 29 nM respectively (p < 0.0001); a result that may be attributable to the divergent propeptide sequences. Overall, the data for rRgpAH reflected observations previously made by others using HRgpA, indicating rRgpAH fidelity and confirming the first production and isolation of functional affinity tagged RgpA.
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Affiliation(s)
- Abu Sayeed M Mahmud
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - N Laila Huq
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Catherine A Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Caroline Moore
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Fernández-Fernández ÁD, Stael S, Van Breusegem F. Mechanisms controlling plant proteases and their substrates. Cell Death Differ 2023; 30:1047-1058. [PMID: 36755073 PMCID: PMC10070405 DOI: 10.1038/s41418-023-01120-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 01/03/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
In plants, proteolysis is emerging as an important field of study due to a growing understanding of the critical involvement of proteases in plant cell death, disease and development. Because proteases irreversibly modify the structure and function of their target substrates, proteolytic activities are stringently regulated at multiple levels. Most proteases are produced as dormant isoforms and only activated in specific conditions such as altered ion fluxes or by post-translational modifications. Some of the regulatory mechanisms initiating and modulating proteolytic activities are restricted in time and space, thereby ensuring precision activity, and minimizing unwanted side effects. Currently, the activation mechanisms and the substrates of only a few plant proteases have been studied in detail. Most studies focus on the role of proteases in pathogen perception and subsequent modulation of the plant reactions, including the hypersensitive response (HR). Proteases are also required for the maturation of coexpressed peptide hormones that lead essential processes within the immune response and development. Here, we review the known mechanisms for the activation of plant proteases, including post-translational modifications, together with the effects of proteinaceous inhibitors.
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Affiliation(s)
- Álvaro Daniel Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zürich, Switzerland
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Uppsala BioCenter, Department of Molecular Sciences, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
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4
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Ramos-Guzmán CA, Ruiz-Pernía JJ, Zinovjev K, Tuñón I. Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1. ACS Catal 2023; 13:4348-4361. [PMID: 37066044 PMCID: PMC10088814 DOI: 10.1021/acscatal.3c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/27/2023] [Indexed: 03/17/2023]
Abstract
Caspases are cysteine proteases in charge of breaking a peptide bond next to an aspartate residue. Caspases constitute an important family of enzymes involved in cell death and inflammatory processes. A plethora of diseases, including neurological and metabolic diseases and cancer, are associated with the poor regulation of caspase-mediated cell death and inflammation. Human caspase-1 in particular carries out the transformation of the pro-inflammatory cytokine pro-interleukin-1β into its active form, a key process in the inflammatory response and then in many diseases, such as Alzheimer's disease. Despite its importance, the reaction mechanism of caspases has remained elusive. The standard mechanistic proposal valid for other cysteine proteases and that involves the formation of an ion pair in the catalytic dyad is not supported by experimental evidence. Using a combination of classical and hybrid DFT/MM simulations, we propose a reaction mechanism for the human caspase-1 that explains experimental observations, including mutagenesis, kinetic, and structural data. In our mechanistic proposal, the catalytic cysteine, Cys285, is activated after a proton transfer to the amide group of the scissile peptide bond, a process facilitated by hydrogen-bond interactions with Ser339 and His237. The catalytic histidine does not directly participate in any proton transfer during the reaction. After formation of the acylenzyme intermediate, the deacylation step takes place through the activation of a water molecule by the terminal amino group of the peptide fragment formed during the acylation step. The overall activation free energy obtained from our DFT/MM simulations is in excellent agreement with the value derived from the experimental rate constant, 18.7 vs 17.9 kcal·mol-1, respectively. Simulations of the H237A mutant support our conclusions and agree with the reported reduced activity observed for this caspase-1 variant. We propose that this mechanism can explain the reactivity of all cysteine proteases belonging to the CD clan and that differences with respect to other clans could be related to the larger preference showed by enzymes of the CD clan for charged residues at position P1. This mechanism would avoid the free energy penalty associated with the formation of an ion pair. Finally, our structural description of the reaction process can be useful to assist in the design of inhibitors of caspase-1, a target in the treatment of several human diseases.
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Affiliation(s)
- Carlos A. Ramos-Guzmán
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
- Instituto de Materiales Avanzados, Universitat Jaume I, 12071 Castelló, Spain
| | | | - Kirill Zinovjev
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
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5
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Movilla S, Martí S, Roca M, Moliner V. Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. J Chem Inf Model 2023; 63:950-958. [PMID: 36648276 PMCID: PMC10882967 DOI: 10.1021/acs.jcim.2c01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease represents one of the most ambitious challenges for biomedical sciences due to the growing number of cases worldwide in the elderly population and the lack of efficient treatments. One of the recent attempts to develop a treatment points to the cysteine protease RgpB as a promising drug target. In this attempt, several small-molecule covalent inhibitors of this enzyme have been proposed. Here, we report a computational study at the atomic level of the inhibition mechanism of the most promising reported compounds. Molecular dynamics simulations were performed on six of them, and their binding energies in the active site of the protein were computed. Contact maps and interaction energies were decomposed by residues to disclose those key interactions with the enzyme. Finally, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations were performed to evaluate the reaction mechanism by which these drug candidates lead to covalently bound complexes, inhibiting the RgpB protease. The results provide a guide for future re-design of prospective and efficient inhibitors for the treatment of Alzheimer's disease.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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Ajibola AA, Perveen F, Wojciechowska A, Sieroń L, Maniukiewicz W. MnII, ZnII and CdII Dinuclear Complexes Based on Mixed Benzoic Acid and Metronidazole Benzoate: Syntheses, Crystal structures, Spectroscopic, Hirshfeld surface analysis, and Molecular modelling of their potential activity against Porphyromas gingivalis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chow YC, Yam HC, Gunasekaran B, Lai WY, Wo WY, Agarwal T, Ong YY, Cheong SL, Tan SA. Implications of Porphyromonas gingivalis peptidyl arginine deiminase and gingipain R in human health and diseases. Front Cell Infect Microbiol 2022; 12:987683. [PMID: 36250046 PMCID: PMC9559808 DOI: 10.3389/fcimb.2022.987683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Porphyromonas gingivalis is a major pathogenic bacterium involved in the pathogenesis of periodontitis. Citrullination has been reported as the underlying mechanism of the pathogenesis, which relies on the interplay between two virulence factors of the bacterium, namely gingipain R and the bacterial peptidyl arginine deiminase. Gingipain R cleaves host proteins to expose the C-terminal arginines for peptidyl arginine deiminase to citrullinate and generate citrullinated proteins. Apart from carrying out citrullination in the periodontium, the bacterium is found capable of citrullinating proteins present in the host synovial tissues, atherosclerotic plaques and neurons. Studies have suggested that both virulence factors are the key factors that trigger distal effects mediated by citrullination, leading to the development of some non-communicable diseases, such as rheumatoid arthritis, atherosclerosis, and Alzheimer’s disease. Thus, inhibition of these virulence factors not only can mitigate periodontitis, but also can provide new therapeutic solutions for systematic diseases involving bacterial citrullination. Herein, we described both these proteins in terms of their unique structural conformations and biological relevance to different human diseases. Moreover, investigations of inhibitory actions on the enzymes are also enumerated. New approaches for identifying inhibitors for peptidyl arginine deiminase through drug repurposing and virtual screening are also discussed.
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Affiliation(s)
- Yoke Chan Chow
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Kuala Lumpur, Malaysia
| | - Hok Chai Yam
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Weng Yeen Lai
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Weng Yue Wo
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Tarun Agarwal
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Yien Yien Ong
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Kuala Lumpur, Malaysia
| | - Siew Lee Cheong
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
- *Correspondence: Sheri-Ann Tan, ; Siew Lee Cheong,
| | - Sheri-Ann Tan
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University College, Kuala Lumpur, Malaysia
- *Correspondence: Sheri-Ann Tan, ; Siew Lee Cheong,
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8
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Saiki K, Urano-Tashiro Y, Yamanaka Y, Takahashi Y. Calcium ions and vitamin B 12 are growth factors for Porphyromonas gingivalis. J Oral Biosci 2022; 64:445-451. [PMID: 36103977 DOI: 10.1016/j.job.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Porphyromonas gingivalis is a causative agent of chronic periodontitis. Standard strains of P. gingivalis, such as W83 and ATCC 33277, proliferate in minimal medium when protein is added as the energy source and hemin and menadione are added as growth factors. Nevertheless, minimal medium containing bovine serum albumin sometimes fails to support growth. HIGHLIGHTS The proliferation of two W83 strains and seven ATCC 33277 strains in various minimal media was investigated. Previously, we determined that calcium chloride (CaCl2) was a growth factor for W83NM, a W83 strain. In this study, we found that vitamin B12 enhanced the proliferation of W83NM in a minimal medium with cultures from the fourth passage but not from the first to the third passage. Therefore, using fourth-passage cultures, we assessed the proliferation of two W83 and seven ATCC 33277 strains in minimal media and the effects of CaCl2 and vitamin B12. Surprisingly, the nine P. gingivalis strains all differed with respect to their proliferation in minimal media, and protein products used as energy sources showed product-to-product and lot-to-lot heterogeneity. Even though strains or protein products were different, we found CaCl2-dependent growth in nine strains and vitamin B12-dependent growth in seven strains. CONCLUSION These results suggest that calcium ions and vitamin B12 are novel growth factors for P. gingivalis.
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Affiliation(s)
- Keitarou Saiki
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yumiko Urano-Tashiro
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yuki Yamanaka
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yukihiro Takahashi
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
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9
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Moore C, Cheng Y, Tjokro N, Zhang B, Kerr M, Hayati M, Chang KCJ, Shah N, Chen C, Jokerst JV. A Photoacoustic-Fluorescent Imaging Probe for Proteolytic Gingipains Expressed by Porphyromonas gingivalis. Angew Chem Int Ed Engl 2022; 61:e202201843. [PMID: 35583940 PMCID: PMC9296565 DOI: 10.1002/anie.202201843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 11/07/2022]
Abstract
Porphyromonas gingivalis is a keystone pathogen in periodontal disease. We herein report a dual-modal fluorescent and photoacoustic imaging probe for the detection of gingipain proteases secreted by P. gingivalis. Upon proteolytic cleavage by Arg-specific gingipain (RgpB), five-fold photoacoustic enhancement and >100-fold fluorescence activation was measured with detection limits of 1.1 nM RgpB and 5.0E4 CFU mL-1 bacteria in vitro. RgpB activity was imaged in porcine jaws with low-nanomolar sensitivity. Diagnostic efficacy was evaluated in gingival crevicular fluid samples from subjects with and without periodontal disease, wherein activation was correlated to qPCR-based detection of P. gingivalis (Pearson's r=0.71). Finally, photoacoustic imaging of RgpB-cleaved probe was achieved in murine brains ex vivo, with relevance and potential utility for disease models of general infection by P. gingivalis, motivated by the recent biological link between gingipain and Alzheimer's disease.
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Affiliation(s)
- Colman Moore
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
| | - Yong Cheng
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
| | - Natalia Tjokro
- Herman Ostrow School of Dentistry, University of Southern California, 925 West 34 Street, Los Angeles, CA 90089. USA
| | - Brendan Zhang
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
| | - Matthew Kerr
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
| | - Mohammed Hayati
- Herman Ostrow School of Dentistry, University of Southern California, 925 West 34 Street, Los Angeles, CA 90089. USA
| | - Kai Chiao Joe Chang
- Herman Ostrow School of Dentistry, University of Southern California, 925 West 34 Street, Los Angeles, CA 90089. USA
| | - Nisarg Shah
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
| | - Casey Chen
- Herman Ostrow School of Dentistry, University of Southern California, 925 West 34 Street, Los Angeles, CA 90089. USA
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
- Materials Science Program, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
- Department of Radiology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093. USA
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10
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Moore C, Cheng Y, Tjokro N, Zhang B, Kerr M, Hayati M, Chang KCJ, Shah N, Chen C, Jokerst JV. A Photoacoustic‐Fluorescent Imaging Probe for Proteolytic Gingipains Expressed by
Porphyromonas gingivalis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Colman Moore
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
| | - Yong Cheng
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
| | - Natalia Tjokro
- Herman Ostrow School of Dentistry University of Southern California 925 West 34th Street Los Angeles CA 90089 USA
| | - Brendan Zhang
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
- Current address: Diazyme Laboratories Inc
| | - Matthew Kerr
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
| | - Mohammed Hayati
- Herman Ostrow School of Dentistry University of Southern California 925 West 34th Street Los Angeles CA 90089 USA
| | - Kai Chiao Joe Chang
- Herman Ostrow School of Dentistry University of Southern California 925 West 34th Street Los Angeles CA 90089 USA
| | - Nisarg Shah
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
| | - Casey Chen
- Herman Ostrow School of Dentistry University of Southern California 925 West 34th Street Los Angeles CA 90089 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
- Materials Science Program University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego 9500 Gilman Dr. La Jolla CA 92093 USA
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11
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Nowakowska Z, Madej M, Grad S, Wang T, Hackett M, Miller DP, Lamont RJ, Potempa J. Phosphorylation of major Porphyromonas gingivalis virulence factors is crucial for their processing and secretion. Mol Oral Microbiol 2021; 36:316-326. [PMID: 34569151 PMCID: PMC10148667 DOI: 10.1111/omi.12354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
The main etiological agent of periodontitis is the anaerobic bacterium Porphyromonas gingivalis. Virulence of this pathogen is controlled by various mechanisms and executed by major virulence factors including the gingipain proteases, peptidylarginine deiminase (PPAD), and RagB, an outer membrane macromolecular transport component. Although the structures and functions of these proteins are well characterized, little is known about their posttranslational maturation. Here, we determined the phosphoproteome of P. gingivalis in which phosphorylated tyrosine residues constitute over 80% of all phosphoresidues. Multiple phosphotyrosines were found in gingipains, PPAD, and RagB. Although mutation of phosphorylated residues in PPAD and RagB had no effect on secretion or activity, site-directed mutagenesis showed that phosphorylation in hemagglutinin/adhesin domains of RgpA and Kgp, and in the catalytic domain of RgpB, had a strong influence on secretion, processing, and enzymatic activity. Moreover, preventing phosphorylation of one gingipain influenced the others, suggesting multiple phosphorylation-dependent pathways of gingipain maturation in P. gingivalis. Various candidate kinases including Ptk1 BY kinase and ubiquitous bacterial kinase 1 (UbK1) may be involved, but their contribution to gingipain processing and activation remains to be confirmed.
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Affiliation(s)
- Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Grad
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Tiansong Wang
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Murray Hackett
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Daniel P. Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Richard J. Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
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12
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Mizgalska D, Goulas T, Rodríguez-Banqueri A, Veillard F, Madej M, Małecka E, Szczesniak K, Ksiazek M, Widziołek M, Guevara T, Eckhard U, Solà M, Potempa J, Gomis-Rüth FX. Intermolecular latency regulates the essential C-terminal signal peptidase and sortase of the Porphyromonas gingivalis type-IX secretion system. Proc Natl Acad Sci U S A 2021; 118:e2103573118. [PMID: 34593635 DOI: 10.1073/pnas.2103573118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Porphyromonas gingivalis is a keystone pathogen of the human dysbiotic oral microbiome that causes severe periodontitis. It employs a type-IX secretion system (T9SS) to shuttle proteins across the outer membrane (OM) for virulence. Uniquely, T9SS cargoes carry a C-terminal domain (CTD) as a secretion signal, which is cleaved and replaced with anionic lipopolysaccharide by transpeptidation for extracellular anchorage to the OM. Both reactions are carried out by PorU, the only known dual-function, C-terminal signal peptidase and sortase. PorU is itself secreted by the T9SS, but its CTD is not removed; instead, intact PorU combines with PorQ, PorV, and PorZ in the OM-inserted "attachment complex." Herein, we revealed that PorU transits between active monomers and latent dimers and solved the crystal structure of the ∼260-kDa dimer. PorU has an elongated shape ∼130 Å in length and consists of seven domains. The first three form an intertwined N-terminal cluster likely engaged in substrate binding. They are followed by a gingipain-type catalytic domain (CD), two immunoglobulin-like domains (IGL), and the CTD. In the first IGL, a long "latency β-hairpin" protrudes ∼30 Å from the surface to form an intermolecular β-barrel with β-strands from the symmetric CD, which is in a latent conformation. Homology modeling of the competent CD followed by in vivo validation through a cohort of mutant strains revealed that PorU is transported and functions as a monomer through a C690/H657 catalytic dyad. Thus, dimerization is an intermolecular mechanism for PorU regulation to prevent untimely activity until joining the attachment complex.
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Abstract
Alzheimer's disease represents one of the greatest medical concerns for today's population and health services. Its multifactorial inherent nature represents a challenge for its treatment and requires the development of a broad spectrum of drugs. Recently, the cysteine protease gingipain RgpB has been related to neurodegenerative diseases, including Alzheimer's disease, and its inhibition appears to be a promising neuroprotective strategy. Given these features, a computational study that integrates molecular dynamics (MD) simulations with classical and hybrid quantum mechanics/molecular mechanics (QM/MM) potentials was carried out to unravel the atomistic details of RgpB activity. First, a preliminary study based on principal component analysis (PCA), determined the protonation state of the Cys/His catalytic dyad, as well as the crucial role of a flexible loop that favors reactive interactions of the catalytic residues and the peptide in the precatalytic state in its closed conformation. Then, different mechanisms were explored by means of QM/MM MD simulations. The most favorable mechanism consists of two stages. First is an acylation stage that takes place in two steps where, initially, the sulfur atom of the C244 residue attacks the carbonylic carbon of the peptide and the proton of the C244 residue is transferred to the amino group of the peptide in a concerted manner. Subsequently, the peptide bond is broken, and a fragment of the peptide is released. After that, the deacylation stage takes place in a single step where a water molecule attacks the carbonylic carbon of the peptide and a proton of the water is transferred to the C244 residue. The free energy barrier of the rate limiting step is in very good agreement with available experimental data. The mechanism exhibits an unusual role of H211 residue compared with other cysteine proteases but a crucial role of the peptide in triggering the catalysis. Notably, the atomic and energetic particularities found represent a significant contribution to the comprehension of the reaction mechanism and a great opportunity for the design of efficient inhibitors of gingipain RgpB.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
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Okamura H, Hirota K, Yoshida K, Weng Y, He Y, Shiotsu N, Ikegame M, Uchida-Fukuhara Y, Tanai A, Guo J. Outer membrane vesicles of Porphyromonas gingivalis: Novel communication tool and strategy. Jpn Dent Sci Rev 2021; 57:138-146. [PMID: 34484474 PMCID: PMC8399048 DOI: 10.1016/j.jdsr.2021.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2021] [Accepted: 07/18/2021] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) have been recognized as a universal method of cellular communications and are reportedly produced in bacteria, archaea, and eukaryotes. Bacterial EVs are often called “Outer Membrane Vesicles” (OMVs) as they were the result of a controlled blebbing of the outer membrane of gram-negative bacteria such as Porphyromonas gingivalis (P. gingivalis). Bacterial EVs are natural messengers, implicated in intra- and inter-species cell-to-cell communication among microorganism populations present in microbiota. Bacteria can incorporate their pathogens into OMVs; the content of OMVs differs, depending on the type of bacteria. The production of distinct types of OMVs can be mediated by different factors and routes. A recent study highlighted OMVs ability to carry crucial molecules implicated in immune modulation, and, nowadays, they are considered as a way to communicate and transfer messages from the bacteria to the host and vice versa. This review article focuses on the current understanding of OMVs produced from major oral bacteria, P. gingivalis: generation, characteristics, and contents as well as the involvement in signal transduction of host cells and systemic diseases. Our recent study regarding the action of P. gingivalis OMVs in the living body is also summarized.
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Affiliation(s)
- Hirohiko Okamura
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Katsuhiko Hirota
- Department of Medical Hygiene, Dental Hygiene Course, Kochi Gakuen College, Kochi 780-0955, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Education, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8504, Japan
| | - Yao Weng
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Yuhan He
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Noriko Shiotsu
- Comprehensive Dental Clinic, Okayama University Hospital, Okayama University, Okayama, Japan
| | - Mika Ikegame
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Yoko Uchida-Fukuhara
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Airi Tanai
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan
| | - Jiajie Guo
- Department of Oral Morphology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata, Kitaku, Okayama 770-8525, Japan.,Department of Endodontics, School of Stomatology, China Medical University, Nanjing North Street 117, Shenyang 110002, China
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Rawat A, Roy M, Jyoti A, Kaushik S, Verma K, Srivastava VK. Cysteine proteases: Battling pathogenic parasitic protozoans with omnipresent enzymes. Microbiol Res 2021; 249:126784. [PMID: 33989978 DOI: 10.1016/j.micres.2021.126784] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023]
Abstract
Millions of people worldwide lie at the risk of parasitic protozoic infections that kill over a million people each year. The rising inefficacy of conventional therapeutics to combat these diseases, mainly due to the development of drug resistance to a handful of available licensed options contributes substantially to the rising burden of these ailments. Cysteine proteases are omnipresent enzymes that are critically implicated in the pathogenesis of protozoic infections. Despite their significance and druggability, cysteine proteases as therapeutic targets have not yet been translated into the clinic. The review presents the significance of cysteine proteases of members of the genera Plasmodium, Entamoeba, and Leishmania, known to cause Malaria, Amoebiasis, and Leishmaniasis, respectively, the protozoic diseases with the highest morbidity and mortality. Further, projecting them as targets for molecular tools like the CRISPR-Cas technology for favorable manipulation, exploration of obscure genomes, and achieving a better insight into protozoic functioning. Overcoming the hurdles that prevent us from gaining a better insight into the functioning of these enzymes in protozoic systems is a necessity. Managing the burden of parasitic protozoic infections pivotally depends upon the betterment of molecular tools and therapeutic concepts that will pave the path to an array of diagnostic and therapeutic applications.
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Affiliation(s)
- Aadish Rawat
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Mrinalini Roy
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Kuldeep Verma
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, India
| | - Vijay Kumar Srivastava
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India.
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Glew MD, Gorasia DG, McMillan PJ, Butler CA, Veith PD, Reynolds EC. Complementation in trans of Porphyromonas gingivalis Lipopolysaccharide Biosynthetic Mutants Demonstrates Lipopolysaccharide Exchange. J Bacteriol 2021; 203:e00631-20. [PMID: 33685973 DOI: 10.1128/JB.00631-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Porphyromonas gingivalis, a bacterial pathogen contributing to human periodontitis, exports and anchors cargo proteins to its surface, enabling the production of black pigmentation using a type IX secretion system (T9SS) and conjugation to anionic lipopolysaccharide (A-LPS). To determine whether T9SS components need to be assembled in situ for correct secretion and A-LPS modification of cargo proteins, combinations of nonpigmented mutants lacking A-LPS or a T9SS component were mixed to investigate in trans complementation. Reacquisition of pigmentation occurred only between an A-LPS mutant and a T9SS mutant, which coincided with A-LPS modification of cargo proteins detected by Western blotting and coimmunoprecipitation/quantitative mass spectrometry. Complementation also occurred using an A-LPS mutant mixed with outer membrane vesicles (OMVs) or purified A-LPS. Fluorescence experiments demonstrated that OMVs can fuse with and transfer lipid to P. gingivalis, leading to the conclusion that complementation of T9SS function occurred through A-LPS transfer between cells. None of the two-strain crosses involving only the five T9SS OM component mutants produced black pigmentation, implying that the OM proteins cannot be transferred in a manner that restores function and surface pigmentation, and hence, a more ordered temporal in situ assembly of T9SS components may be required. Our results show that LPS can be transferred between cells or between cells and OMVs to complement deficiencies in LPS biosynthesis and hemin-related pigmentation to reveal a potentially new mechanism by which the oral microbial community is modulated to produce clinical consequences in the human host.IMPORTANCE Porphyromonas gingivalis is a keystone pathogen contributing to periodontitis in humans, leading to tooth loss. The oral microbiota is essential in this pathogenic process and changes from predominantly Gram-positive (health) to predominantly Gram-negative (disease) species. P. gingivalis uses its type IX secretion system (T9SS) to secrete and conjugate virulence proteins to anionic lipopolysaccharide (A-LPS). This study investigated whether components of this secretion system could be complemented and found that it was possible for A-LPS biosynthetic mutants to be complemented in trans both by strains that had the A-LPS on the cell surface and by exogenous sources of A-LPS. This is the first known example of LPS exchange in a human bacterial pathogen which causes disease through complex microbiota-host interactions.
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Abrão F, Silva TS, Moura CL, Ambrósio SR, Veneziani RCS, de Paiva REF, Bastos JK, Martins CHG. Oleoresins and naturally occurring compounds of Copaifera genus as antibacterial and antivirulence agents against periodontal pathogens. Sci Rep 2021; 11:4953. [PMID: 33654123 DOI: 10.1038/s41598-021-84480-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Invasion of periodontal tissues by Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans can be associated with aggressive forms of periodontitis. Oleoresins from different copaifera species and their compounds display various pharmacological properties. The present study evaluates the antibacterial and antivirulence activity of oleoresins obtained from different copaifera species and of ten isolated compounds against two causative agents of periodontitis. The following assays were performed: determination of the minimum inhibitory concentration (MIC), determination of the minimum bactericidal concentration (MBC), and determination of the antibiofilm activity by inhibition of biofilm formation and biofilm eradication tests. The antivirulence activity was assessed by hemagglutination, P. gingivalis Arg-X and Lis-X cysteine protease inhibition assay, and A. actinomycetemcomitans leukotoxin inhibition assay. The MIC and MBC of the oleoresins and isolated compounds 1, 2, and 3 ranged from 1.59 to 50 μg/mL against P. gingivalis (ATCC 33277) and clinical isolates and from 6.25 to 400 μg/mL against A. actinomycetemcomitans (ATCC 43717) and clinical isolates. About the antibiofilm activity, the oleoresins and isolated compounds 1, 2, and 3 inhibited biofilm formation by at least 50% and eradicated pre-formed P. gingivalis and A. actinomycetemcomitans biofilms in the monospecies and multispecies modes. A promising activity concerning cysteine protease and leucotoxin inhibition was also evident. In addition, molecular docking analysis was performed. The investigated oleoresins and their compounds may play an important role in the search for novel sources of agents that can act against periodontal pathogens.
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Mu W, Jia Y, Chen X, Li H, Wang Z, Cheng B. Intracellular Porphyromonas gingivalis Promotes the Proliferation of Colorectal Cancer Cells via the MAPK/ERK Signaling Pathway. Front Cell Infect Microbiol 2020; 10:584798. [PMID: 33425779 PMCID: PMC7785964 DOI: 10.3389/fcimb.2020.584798] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Porphyromonas gingivalis (P. gingivalis) is a keystone pathogen in periodontitis. However, several clinical studies have revealed an enrichment of P. gingivalis in the stool samples and colorectal mucosa of colorectal cancer patients. Thus, the goal of this study was to determine whether P. gingivalis can promote colorectal cancer progression in vitro. We established an acute infection model (24 h, multiplicity of infection =100) of P. gingivalis invasion of colorectal cancer cells to study the alterations induced by P. gingivalis in the proliferation and cell cycle of colorectal cancer cells. We observed that P. gingivalis can adhere and invade host cells a few hours after infection. Once invaded, P. gingivalis significantly promoted colorectal cancer cell proliferation, and the percentage of S phase cells was increased in the cell cycle assay. However, KDP136, a gingipain-deficient mutant of P. gingivalis 33277, showed a decreased ability to promote colorectal cancer cell proliferation, indicating that gingipain is associated with colorectal cancer cell proliferation. Furthermore, we extracted RNA from colorectal cancer cells for high-throughput sequencing analysis and reconfirmed the results by quantitative polymerase chain reaction and western blot analyses. The results suggested that the MAPK/ERK signaling pathway is significantly activated by P. gingivalis, while these changes were not observed for KDP136. In conclusion, P. gingivalis can invade cells and promote the proliferation of colorectal cancer cells by activating the MAPK/ERK signaling pathway. Gingipain is an essential virulence factor in this interaction.
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Affiliation(s)
- Wenxin Mu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Yiqun Jia
- Stomatology Center, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Xiaobing Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Haoyu Li
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Zhi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
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19
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Abstract
Protein domains exist by themselves or in combination with other domains to form complex multidomain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β-sheet is known to be particularly troublesome for automatic structure-based domain decomposition pipelines. Here, we study edge-to-edge β-strand interactions between domains in a protein chain, to help define the boundaries for some more difficult cases where a single β-sheet spanning over two domains gives an appearance of one. We give a number of examples where β-strands belonging to a single β-sheet do not belong to a single domain and highlight the difficulties of automatic domain parsers on these examples. This work can be used as a baseline for defining domain boundaries in homologous proteins or proteins with similar domain interactions in the future.
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Affiliation(s)
- Archana S. Bhat
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
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He Z, Zhang X, Song Z, Li L, Chang H, Li S, Zhou W. Quercetin inhibits virulence properties of Porphyromas gingivalis in periodontal disease. Sci Rep 2020; 10:18313. [PMID: 33110205 DOI: 10.1038/s41598-020-74977-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023] Open
Abstract
Porphyromonas gingivalis is a causative agent in the onset and progression of periodontal disease. This study aims to investigate the effects of quercetin, a natural plant product, on P. gingivalis virulence properties including gingipain, haemagglutinin and biofilm formation. Antimicrobial effects and morphological changes of quercetin on P. gingivalis were detected. The effects of quercetin on gingipains activities and hemolytic, hemagglutination activities were evaluated using chromogenic peptides and sheep erythrocytes. The biofilm biomass and metabolism with different concentrations of quercetin were assessed by the crystal violet and MTT assay. The structures and thickness of the biofilms were observed by confocal laser scanning microscopy. Bacterial cell surface properties including cell surface hydrophobicity and aggregation were also evaluated. The mRNA expression of virulence and iron/heme utilization was assessed using real time-PCR. Quercetin exhibited antimicrobial effects and damaged the cell structure. Quercetin can inhibit gingipains, hemolytic, hemagglutination activities and biofilm formation at sub-MIC concentrations. Molecular docking analysis further indicated that quercetin can interact with gingipains. The biofilm became sparser and thinner after quercetin treatment. Quercetin also modulate cell surface hydrophobicity and aggregation. Expression of the genes tested was down-regulated in the presence of quercetin. In conclusion, our study demonstrated that quercetin inhibited various virulence factors of P. gingivalis.
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Peng HY, Chen SY, Siao SH, Chang JT, Xue TY, Lee YH, Jan MS, Tsay GJ, Zouali M. Targeting a cysteine protease from a pathobiont alleviates experimental arthritis. Arthritis Res Ther 2020; 22:114. [PMID: 32410713 PMCID: PMC7222327 DOI: 10.1186/s13075-020-02205-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/29/2020] [Indexed: 01/05/2023] Open
Abstract
Background Several lines of evidence suggest that the pathobiont Porphyromonas gingivalis is involved in the development and/or progression of auto-inflammatory diseases. This bacterium produces cysteine proteases, such as gingipain RgpA, endowed with the potential to induce significant bone loss in model systems and in patients. Objective We sought to gain further insight into the role of this pathobiont in rheumatoid arthritis (RA) and to identify novel therapeutic targets for auto-inflammatory diseases. Methods We profiled the antibody response to RgPA-specific domains in patient sera. We also tested the potential protective effects of RgpA domains in an experimental arthritis model. Results Pre-immunization of rats with purified recombinant RgpA domains alleviated arthritis in the joints of the rodents and reduced bone erosion. Using a functional genomics approach at both the mRNA and protein levels, we report that the pre-immunizations reduced arthritis severity by impacting a matrix metalloprotease characteristic of articular injury, a chemokine known to be involved in recruiting inflammatory cells, and three inflammatory cytokines. Finally, we identified an amino acid motif in the RgpA catalytic domain of P. gingivalis that shares sequence homology with type II collagen. Conclusion We conclude that pre-immunization against gingipain domains can reduce the severity of experimentally induced arthritis. We suggest that targeting gingipain domains by pre-immunization, or, possibly, by small-molecule inhibitors, could reduce the potential of P. gingivalis to translocate to remote tissues and instigate and/or exacerbate pathology in RA, but also in other chronic inflammatory diseases.
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Affiliation(s)
- Hsin-Yi Peng
- Division of Immunology and Rheumatology, China Medical University Hospital, Taichung, Taiwan
| | - Shih-Yao Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Shih-Hong Siao
- Graduate Institute of Immunology, National Taiwan University, Taipei, Taiwan
| | | | - Ting-Yin Xue
- Division of Immunology and Rheumatology, China Medical University Hospital, Taichung, Taiwan
| | - Yi-Hsuan Lee
- Division of Immunology and Rheumatology, China Medical University Hospital, Taichung, Taiwan
| | - Ming-Shiou Jan
- Institute of Biochemistry, Microbiology, Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Gregory J Tsay
- Division of Immunology and Rheumatology, China Medical University Hospital, Taichung, Taiwan. .,College of Medicine, China Medical University, Taichung, Taiwan.
| | - Moncef Zouali
- Inserm UMR 1132, F-75475, Paris, France. .,University Paris Diderot, Sorbonne Paris Cité, F-75475, Paris, France. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
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Gabarrini G, Grasso S, van Winkelhoff AJ, van Dijl JM. Gingimaps: Protein Localization in the Oral Pathogen Porphyromonas gingivalis. Microbiol Mol Biol Rev 2020; 84:e00032-19. [PMID: 31896547 DOI: 10.1128/MMBR.00032-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porphyromonas gingivalis is an oral pathogen involved in the widespread disease periodontitis. In recent years, however, this bacterium has been implicated in the etiology of another common disorder, the autoimmune disease rheumatoid arthritis. Periodontitis and rheumatoid arthritis were known to correlate for decades, but only recently a possible molecular connection underlying this association has been unveiled. P. gingivalis possesses an enzyme that citrullinates certain host proteins and, potentially, elicits autoimmune antibodies against such citrullinated proteins. These autoantibodies are highly specific for rheumatoid arthritis and have been purported both as a symptom and a potential cause of the disease. The citrullinating enzyme and other major virulence factors of P. gingivalis, including some that were implicated in the etiology of rheumatoid arthritis, are targeted to the host tissue as secreted or outer-membrane-bound proteins. These targeting events play pivotal roles in the interactions between the pathogen and its human host. Accordingly, the overall protein sorting and secretion events in P. gingivalis are of prime relevance for understanding its full disease-causing potential and for developing preventive and therapeutic approaches. The aim of this review is therefore to offer a comprehensive overview of the subcellular and extracellular localization of all proteins in three reference strains and four clinical isolates of P. gingivalis, as well as the mechanisms employed to reach these destinations.
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Sato K, Kakuda S, Yukitake H, Kondo Y, Shoji M, Takebe K, Narita Y, Naito M, Nakane D, Abiko Y, Hiratsuka K, Suzuki M, Nakayama K. Immunoglobulin‐like domains of the cargo proteins are essential for protein stability during secretion by the type IX secretion system. Mol Microbiol 2018; 110:64-81. [DOI: 10.1111/mmi.14083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Keiko Sato
- Department of Microbiology and Oral Infection Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
| | - Shinji Kakuda
- Institute for Protein Research Osaka University Yamadaoka, Suita Osaka 565‐0871Japan
| | - Hideharu Yukitake
- Department of Microbiology and Oral Infection Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
| | - Yoshio Kondo
- Department of Pediatric Dentistry Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
| | - Mikio Shoji
- Department of Microbiology and Oral Infection Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
| | - Katsuki Takebe
- Institute for Protein Research Osaka University Yamadaoka, Suita Osaka 565‐0871Japan
| | - Yuka Narita
- Department of Functional Bioscience, Infection Biology Fukuoka Dental College Matsudo, Tamura, Sawara, Fukuoka 814‐0913Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
| | - Daisuke Nakane
- Department of Physics, Faculty of Science Gakushuin University Toshima‐ku, Tokyo 171‐8588Japan
| | - Yoshimitsu Abiko
- Department of Biochemistry and Molecular Biology Nihon University School of Dentistry at Matsudo Matsudo Chiba 271‐8587Japan
| | - Koichi Hiratsuka
- Department of Biochemistry and Molecular Biology Nihon University School of Dentistry at Matsudo Matsudo Chiba 271‐8587Japan
| | - Mamoru Suzuki
- Institute for Protein Research Osaka University Yamadaoka, Suita Osaka 565‐0871Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 852‐8588Japan
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Zhang L, Veith PD, Huq NL, Chen YY, Seers CA, Cross KJ, Gorasia DG, Reynolds EC. Porphyromonas gingivalis Gingipains Display Transpeptidation Activity. J Proteome Res 2018; 17:2803-2818. [PMID: 29984580 DOI: 10.1021/acs.jproteome.8b00286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors, and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The reaction kinetics suggested that GlyGly may function as an acceptor molecule for gingipain-catalyzed transpeptidation. Purified gingipains and P. gingivalis whole cells were used to digest selected substrates including human hemoglobin in the presence or absence of peptide acceptors. Mass spectrometric analysis of the substrates digested with gingipains in the presence of GlyGly showed that transpeptidation outcompeted hydrolysis, whereas the trypsin-digested controls exhibited predominantly hydrolysis activity. The transpeptidation levels increased with increasing concentration of GlyGly. Purified gingipains and whole cells exhibited extensive transpeptidation activities on human hemoglobin. All hemoglobin cleavage sites were found to be suitable for GlyGly transpeptidation, and this transpeptidation enhanced hemoglobin digestion. The transpeptidation products were often more abundant than the corresponding hydrolysis products. In the absence of GlyGly, hemoglobin peptides produced during digestion were utilized as acceptors leading to the detection of up to 116 different transpeptidation products in a single reaction. P. gingivalis cells were able to digest hemoglobin faster when acceptor peptides derived from human serum albumin were included in the reaction, suggesting that gingipain-catalyzed transpeptidation may be relevant for substrates encountered in vivo. The transpeptidation of host proteins in vivo may potentially lead to the breakdown of immunological tolerance, culminating in autoimmune reactions.
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Affiliation(s)
- Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Paul D Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - N Laila Huq
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Yu-Yen Chen
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Dhana G Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
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Luo S, Tong L. Structural biology of the separase-securin complex with crucial roles in chromosome segregation. Curr Opin Struct Biol 2018; 49:114-122. [PMID: 29452922 DOI: 10.1016/j.sbi.2018.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/26/2017] [Accepted: 01/22/2018] [Indexed: 11/15/2022]
Abstract
The cysteine protease separase opens the cohesin ring by cleaving its kleisin subunit and is a pivotal cell cycle factor for the transition from metaphase to anaphase. It is inhibited by forming a complex with the chaperone securin, and in vertebrates, also by the Cdk1-cyclin B1 complex. Separase is activated upon the destruction of securin or cyclin B1 by the proteasome, after ubiquitination by the anaphase-promoting complex/cyclosome (APC/C). Here we review recent structures of the active protease segment of Chaetomium thermophilum separase in complex with a substrate-mimic inhibitor and full-length Saccharomyces cerevisiae and Caenorhabditis elegans separase in complex with securin. These structures define the mechanism for substrate recognition and catalysis by separase, and show that securin has extensive contacts with separase, consistent with its chaperone function. They confirm that securin inhibits separase by binding as a pseudo substrate.
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Affiliation(s)
- Shukun Luo
- Department of Biological Sciences Columbia University New York, NY 10027, USA
| | - Liang Tong
- Department of Biological Sciences Columbia University New York, NY 10027, USA.
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26
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Veith PD, Glew MD, Gorasia DG, Reynolds EC. Type IX secretion: the generation of bacterial cell surface coatings involved in virulence, gliding motility and the degradation of complex biopolymers. Mol Microbiol 2017; 106:35-53. [DOI: 10.1111/mmi.13752] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Paul D. Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute; The University of Melbourne; Melbourne Australia
| | - Michelle D. Glew
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute; The University of Melbourne; Melbourne Australia
| | - Dhana G. Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute; The University of Melbourne; Melbourne Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute; The University of Melbourne; Melbourne Australia
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27
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Melcher RL, Neumann M, Fuenzalida Werner JP, Gröhn F, Moerschbacher BM. Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain. Sci Rep 2017; 7:44115. [PMID: 28327560 DOI: 10.1038/srep44115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 02/06/2017] [Indexed: 01/02/2023] Open
Abstract
Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.
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Dashper SG, Mitchell HL, Seers CA, Gladman SL, Seemann T, Bulach DM, Chandry PS, Cross KJ, Cleal SM, Reynolds EC. Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors. Front Microbiol 2017; 8:48. [PMID: 28184216 PMCID: PMC5266723 DOI: 10.3389/fmicb.2017.00048] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P. gingivalis strains sourced from international locations over a 25-year period and to determine if variability in surface virulence factors has a phylogenetic basis. Whole genome sequencing was performed on 13 strains and comparison made to 10 previously sequenced strains. A single nucleotide polymorphism-based phylogenetic analysis demonstrated a shallow tri-lobed phylogeny. There was a high level of reticulation in the phylogenetic network, demonstrating extensive horizontal gene transfer between the strains. Two highly conserved variants of the catalytic domain of the major virulence factor the Kgp proteinase (KgpcatI and KgpcatII) were found. There were three variants of the fourth Kgp C-terminal cleaved adhesin domain. Specific variants of the cell surface proteins FimA, FimCDE, MfaI, RagAB, Tpr, and PrtT were also identified. The occurrence of all these variants in the P. gingivalis strains formed a mosaic that was not related to the SNP-based phylogeny. In conclusion P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors.
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Affiliation(s)
- Stuart G Dashper
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
| | - Helen L Mitchell
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
| | - Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
| | - Simon L Gladman
- Victorian Life Sciences Computation Initiative Carlton, VIC, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative Carlton, VIC, Australia
| | - Dieter M Bulach
- Victorian Life Sciences Computation Initiative Carlton, VIC, Australia
| | | | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
| | - Steven M Cleal
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, University of Melbourne VIC, Australia
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Song Q, Zhang X, Li N, Shen J, Cheng J. A propeptide-independent protease from Tannerella sp.6_1_58FAA_CT1 displays trypsin-like specificity. J Basic Microbiol 2016; 57:50-56. [PMID: 27714828 DOI: 10.1002/jobm.201600486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/18/2016] [Indexed: 11/06/2022]
Abstract
Despite the absence of any homologs of Tannerella forsythia KLIKK proteases in Tannerella sp.6_1_58FAA_CT1, the strain possesses a putative cysteine protease (G9S4N1) closely related to RgpB of Porphyromonas gingivalis. G9S4N1 lacks obvious propeptide that behaves as inhibitor of proteases and was proven to be a propeptide-independent protease. Unlike RgpB, which exclusively cleaves ArgXaa bonds, G9S4N1 exhibits both arginine- and citrulline-specific activities. Mutations of Asp177, a potential P1-Arg binding site, to uncharged or positively charged residues did not alter the substrate specificity of G9S4N1 significantly. Moreover, a group of arginine-specific proteases from different species including porcine trypsin, bovine thrombin, and a trypsin-like serine protease of dengue 2 virus CF40-Gly-NS3pro185 also display different specificity toward citrulline residue, suggesting that citrulline-modified protein might have different roles and destiny in biological processes involving various proteases.
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Affiliation(s)
- Qitao Song
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Xiaoyue Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Na Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Jie Shen
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
| | - Jiansong Cheng
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, P. R. China
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Taniguchi M, Matsuhashi Y, Abe TK, Ishiyama Y, Saitoh E, Kato T, Ochiai A, Tanaka T. Contribution of cationic amino acids toward the inhibition of Arg-specific cysteine proteinase (Arg-gingipain) by the antimicrobial dodecapeptide, CL(14-25), from rice protein. Biopolymers 2016; 102:379-89. [PMID: 25046435 DOI: 10.1002/bip.22525] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/11/2014] [Accepted: 06/28/2014] [Indexed: 11/11/2022]
Abstract
CL(14-25), a dodecapeptide, exhibits antimicrobial activity against Porphyromonas gingivalis with the 50% growth-inhibitory concentration (IC50 ) value of 145 µM, and arginine-specific gingipain (Rgp)-inhibitory activity. Kinetic analysis revealed that CL(14-25) is a mixed-type inhibitor, with inhibition constants (Ki and Ki ' values) of 1.4 × 10(-6) M and 4.3 × 10(-6) M, respectively. To elucidate the contributions of four cationic amino acid residues at the N- and C-termini of CL(14-25) toward Rgp-inhibitory activity, we investigated the Rgp-inhibitory activities of truncated and alanine-substituted analogs of CL(14-25). Rgp-inhibitory activities significantly decreased by truncated analogs, CL(15-25) and CL(16-25), whereas those of CL(14-24) and CL(14-23) were almost as high as that of CL(14-25). Rgp-inhibitory activities of alanine-substituted analogs, CL(R14A) and CL(R14A, R15A) also significantly decreased, whereas those of CL(K25A) and CL(R24A, K25A) were higher than that of CL(14-25). These results suggest that the arginine residue at position 15 substantially contributes to the Rgp-inhibitory activity and that the arginine residue at position 14 plays important roles in exerting Rgp-inhibitory activity. In this study, we demonstrated that CL(K25A) was a potent, dual function, peptide inhibitor candidate, exhibiting Rgp-inhibitory activity with Ki and Ki ' of 9.6 × 10(-7) M and 1.9 × 10(-6) M, respectively, and antimicrobial activity against P. gingivalis with an IC50 value of 51 µM.
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Affiliation(s)
- Masayuki Taniguchi
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan; Center for Transdisciplinary Research, Niigata University, Niigata, 950-2181, Japan
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31
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Bachmann G, Richards MW, Winter A, Beuron F, Morris E, Bayliss R. A closed conformation of the Caenorhabditis elegans separase-securin complex. Open Biol 2016; 6:160032. [PMID: 27249343 PMCID: PMC4852461 DOI: 10.1098/rsob.160032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/18/2016] [Indexed: 11/12/2022] Open
Abstract
The protease separase plays a key role in sister chromatid disjunction and centriole disengagement. To maintain genomic stability, separase activity is strictly regulated by binding of an inhibitory protein, securin. Despite its central role in cell division, the separase and securin complex is poorly understood at the structural level. This is partly owing to the difficulty of generating a sufficient quantity of homogeneous, stable protein. Here, we report the production of Caenorhabditis elegans separase-securin complex, and its characterization using biochemical methods and by negative staining electron microscopy. Single particle analysis generated a density map at a resolution of 21-24 Å that reveals a close, globular structure of complex connectivity harbouring two lobes. One lobe matches closely a homology model of the N-terminal HEAT repeat domain of separase, whereas the second lobe readily accommodates homology models of the separase C-terminal death and caspase-like domains. The globular structure of the C. elegans separase-securin complex contrasts with the more elongated structure previously described for the Homo sapiens complex, which could represent a different functional state of the complex, suggesting a mechanism for the regulation of separase activity through conformational change.
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Affiliation(s)
- Gudrun Bachmann
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Mark W Richards
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK Department of Molecular and Cell Biology, University of Leicester, Leicester LE2 9HN, UK Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anja Winter
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE2 9HN, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Edward Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Richard Bayliss
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK Department of Molecular and Cell Biology, University of Leicester, Leicester LE2 9HN, UK Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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de Diego I, Ksiazek M, Mizgalska D, Koneru L, Golik P, Szmigielski B, Nowak M, Nowakowska Z, Potempa B, Houston JA, Enghild JJ, Thøgersen IB, Gao J, Kwan AH, Trewhella J, Dubin G, Gomis-Rüth FX, Nguyen KA, Potempa J. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain. Sci Rep 2016; 6:23123. [PMID: 27005013 DOI: 10.1038/srep23123] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/26/2016] [Indexed: 12/31/2022] Open
Abstract
In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway.
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33
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McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC. Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome. J Biol Chem 2016; 291:9482-91. [PMID: 26940874 PMCID: PMC4850288 DOI: 10.1074/jbc.m115.706143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 11/21/2022] Open
Abstract
Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys147, resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.
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Affiliation(s)
- Karen McLuskey
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Jaspreet S Grewal
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Debanu Das
- the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Adam Godzik
- the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, the Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Scott A Lesley
- the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, the Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, and
| | - Ashley M Deacon
- the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Graham H Coombs
- the Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Marc-André Elsliger
- the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Ian A Wilson
- the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037,
| | - Jeremy C Mottram
- From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom,
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Smalley JW, Olczak T. Heme acquisition mechanisms of Porphyromonas gingivalis - strategies used in a polymicrobial community in a heme-limited host environment. Mol Oral Microbiol 2016; 32:1-23. [PMID: 26662717 DOI: 10.1111/omi.12149] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 01/14/2023]
Abstract
Porphyromonas gingivalis, a main etiologic agent and key pathogen responsible for initiation and progression of chronic periodontitis requires heme as a source of iron and protoporphyrin IX for its survival and the ability to establish an infection. Porphyromonas gingivalis is able to accumulate a defensive cell-surface heme-containing pigment in the form of μ-oxo bisheme. The main sources of heme for P. gingivalis in vivo are hemoproteins present in saliva, gingival crevicular fluid, and erythrocytes. To acquire heme, P. gingivalis uses several mechanisms. Among them, the best characterized are those employing hemagglutinins, hemolysins, and gingipains (Kgp, RgpA, RgpB), TonB-dependent outer-membrane receptors (HmuR, HusB, IhtA), and hemophore-like proteins (HmuY, HusA). Proteins involved in intracellular heme transport, storage, and processing are less well characterized (e.g. PgDps). Importantly, P. gingivalis may also use the heme acquisition systems of other bacteria to fulfill its own heme requirements. Porphyromonas gingivalis displays a novel paradigm for heme acquisition from hemoglobin, whereby the Fe(II)-containing oxyhemoglobin molecule must first be oxidized to methemoglobin to facilitate heme release. This process not only involves P. gingivalis arginine- and lysine-specific gingipains, but other proteases (e.g. interpain A from Prevotella intermedia) or pyocyanin produced by Pseudomonas aeruginosa. Porphyromonas gingivalis is then able to fully proteolyze the more susceptible methemoglobin substrate to release free heme or to wrest heme from it directly through the use of the HmuY hemophore.
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Affiliation(s)
- J W Smalley
- School of Dentistry, University of Liverpool, Liverpool, UK
| | - T Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Abstract
As our knowledge of host-microbial interactions within the oral cavity increases, future treatments are likely to be more targeted. For example, efforts to target a single species or key virulence factors that they produce, while maintaining the natural balance of the resident oral microbiota that acts to modulate the host immune response would be an advantage. Targeted approaches may be directed at the black-pigmented anaerobes, Porphyromonas gingivalis and Prevotella intermedia, associated with periodontitis. Such pigments provide an opportunity for targeted phototherapy with high-intensity monochromatic light. Functional inhibition approaches, including the use of enzyme inhibitors, are also being explored to control periodontitis. More general disruption of dental plaque through the use of enzymes and detergents, alone and in combination, shows much promise. The use of probiotics and prebiotics to improve gastrointestinal health has now led to an interest in using these approaches to control oral disease. More recently the potential of antimicrobial peptides and nanotechnology, through the application of nanoparticles with biocidal, anti-adhesive and delivery capabilities, has been explored. The aim of this review is to consider the current status as regards non-conventional treatment approaches for oral infections with particular emphasis on the plaque-related diseases.
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Affiliation(s)
- Robert P Allaker
- a Oral Microbiology; Barts and The London School of Medicine & Dentistry; Queen Mary University of London ; London, UK
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36
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Veillard F, Potempa B, Guo Y, Ksiazek M, Sztukowska MN, Houston JA, Koneru L, Nguyen KA, Potempa J. Purification and characterisation of recombinant His-tagged RgpB gingipain from Porphymonas gingivalis. Biol Chem 2015; 396:377-84. [PMID: 25720118 DOI: 10.1515/hsz-2014-0304] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/02/2015] [Indexed: 12/16/2022]
Abstract
Gingipain proteases are important virulence factors from the periodontal pathogen Porphyromonas gingivalis and are the target of many in vitro studies. Due to their close biochemical properties, purification of individual gingipains is difficult and requires multiple chromatographic steps. In this study, we demonstrate that insertion of a hexahistidine affinity tag upstream of a C-terminal outer membrane translocation signal in RgpB gingipain leads to the secretion of a soluble, mature form of RgpB bearing the affinity tag that can easily be purified by nickel-chelating affinity chromatography. The final product obtained high yielding high purity is biochemically indistinguishable from the native RgpB enzyme.
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Abstract
The strategies of pathogens to evade the human immune system are highly sophisticated and modulate a variety of inflammatory pathways. The similarities in the demands for modulation of inflammatory responses during disease treatment and during pathogenic infection provide opportunities to use pathogenic virulence factors to develop a new class of therapeutic materials that control inflammation. In this work, we harness a strategy from Porphyromonas gingivalis by transforming its major virulence factor, an arginine-specific cysteine protease, into self-assembled protease-inorganic hybrid supraparticles. The cysteine protease degrades the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-α). It is an irreversible inhibition of TNF-α, which avoids some of the adverse effects of current TNF-α antagonists. We fabricated self-assembled porous supraparticles that specifically incorporate the pathogen-derived protease and showed improved inactivation of TNF-α over soluble enzyme, creating a potential therapeutic for various autoimmune diseases or other sources of inflammation.
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Affiliation(s)
- Won Min Park
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA 30332, USA.
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Winter A, Schmid R, Bayliss R. Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains. PLoS Comput Biol 2015; 11:e1004548. [PMID: 26513470 PMCID: PMC4626109 DOI: 10.1371/journal.pcbi.1004548] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022] Open
Abstract
Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes. They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains. However, unlike other well-characterized groups of clan CD peptidases, there are no high-resolution structures of separases and the details of their regulation and substrate recognition are poorly understood. Here we undertook an in-depth bioinformatical analysis of separases from different species with respect to their similarity in amino acid sequence and protein fold in comparison to caspases, MALT-1 proteins (mucosa-associated lymphoidtissue lymphoma translocation protein 1) and gingipain-R. A comparative model of the single C-terminal caspase-like domain in separase from C. elegans suggests similar binding modes of substrate peptides between these protein subfamilies, and enables differences in substrate specificity of separase proteins to be rationalised. We also modelled a newly identified putative death domain, located N-terminal to the caspase-like domain. The surface features of this domain identify potential sites of protein-protein interactions. Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif. We envisage that findings from our study will guide structural and functional studies of this important protein family. The separation of sister chromatids is a crucial step in cell division and is triggered by the activation of separase, a protease that cleaves the proteins that maintain the cohesion between sister chromatids. Knowledge of the molecular structure and activation mechanism of separase is limited by the difficulty of obtaining structural information on this large and flexible protein. Sequence conservation between separase homologues from diverse species is limited to the C-terminal region that contains the catalytically active protease domain. We conducted an in-depth bioinformatical analysis of separase and generated structural models of the two conserved domains that comprise the C-terminal region: a caspase-like domain and a putative death domain. This analysis provided insights into substrate recognition and identified potential sites of protein-protein interactions. Both the death domain and caspase-like domain are well-conserved in separases, which suggests an evolutionary pressure to keep these two domains together, perhaps to enable separase activity and/or provide stability. Insights into the molecular structures of separase gained in this study may provide a starting point for experimental structural studies on this protein and may aid therapeutic development against cancers where chromosomes are improperly segregated.
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Affiliation(s)
- Anja Winter
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Ralf Schmid
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Richard Bayliss
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Gorasia DG, Veith PD, Chen D, Seers CA, Mitchell HA, Chen YY, Glew MD, Dashper SG, Reynolds EC. Porphyromonas gingivalis Type IX Secretion Substrates Are Cleaved and Modified by a Sortase-Like Mechanism. PLoS Pathog 2015; 11:e1005152. [PMID: 26340749 DOI: 10.1371/journal.ppat.1005152] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022] Open
Abstract
The type IX secretion system (T9SS) of Porphyromonas gingivalis secretes proteins possessing a conserved C-terminal domain (CTD) to the cell surface. The C-terminal signal is essential for these proteins to translocate across the outer membrane via the T9SS. On the surface the CTD of these proteins is cleaved prior to extensive glycosylation. It is believed that the modification on these CTD proteins is anionic lipopolysaccharide (A-LPS), which enables the attachment of CTD proteins to the cell surface. However, the exact site of modification and the mechanism of attachment of CTD proteins to the cell surface are unknown. In this study we characterized two wbaP (PG1964) mutants that did not synthesise A-LPS and accumulated CTD proteins in the clarified culture fluid (CCF). The CTDs of the CTD proteins in the CCF were cleaved suggesting normal secretion, however, the CTD proteins were not glycosylated. Mass spectrometric analysis of CTD proteins purified from the CCF of the wbaP mutants revealed the presence of various peptide/amino acid modifications from the growth medium at the C-terminus of the mature CTD proteins. This suggested that modification occurs at the C-terminus of T9SS substrates in the wild type P. gingivalis. This was confirmed by analysis of CTD proteins from wild type, where a 648 Da linker was identified to be attached at the C-terminus of mature CTD proteins. Importantly, treatment with proteinase K released the 648 Da linker from the CTD proteins demonstrating a peptide bond between the C-terminus and the modification. Together, this is suggestive of a mechanism similar to sortase A for the cleavage and modification/attachment of CTD proteins in P. gingivalis. PG0026 has been recognized as the CTD signal peptidase and is now proposed to be the sortase-like protein in P. gingivalis. To our knowledge, this is the first biochemical evidence suggesting a sortase-like mechanism in Gram-negative bacteria. Chronic periodontitis, associated with the pathogen Porphyromonas gingivalis, is a major public health problem. P. gingivalis secretes virulence factors including the gingipains via the type IX secretion system (T9SS). These proteins contain a C-terminal signal that allows their secretion through the T9SS and it is cleaved by the protein PG0026 at the cell surface. Here we identify a mechanism by which gingipains and other proteins attach to the cell surface of this bacterium. We found that after removal of the C-terminal signal, the proteins were modified via a peptide linkage to either a putative component of anionic lipopolysaccharide (A-LPS) in the wild type or peptides from the growth medium in mutants lacking A-LPS, which has been suggested to anchor the proteins to the cell surface. Results from this study provide evidence for the exact site of modification of these proteins with A-LPS. Furthermore, our results also demonstrate for the first time that the anchoring mechanism of this secretion system involves a substitution between the signal and the anchor (A-LPS) which can be explained by the action of a single enzyme known as a sortase, which we believe is PG0026. This is the first evidence for a sortase-like mechanism in Gram-negative bacteria.
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Goulas T, Mizgalska D, Garcia-Ferrer I, Kantyka T, Guevara T, Szmigielski B, Sroka A, Millán C, Usón I, Veillard F, Potempa B, Mydel P, Solà M, Potempa J, Gomis-Rüth FX. Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Sci Rep 2015; 5:11969. [PMID: 26132828 DOI: 10.1038/srep11969] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/12/2015] [Indexed: 01/08/2023] Open
Abstract
Citrullination is a post-translational modification of higher organisms that deiminates arginines in proteins and peptides. It occurs in physiological processes but also pathologies such as multiple sclerosis, fibrosis, Alzheimer’s disease and rheumatoid arthritis (RA). The reaction is catalyzed by peptidylarginine deiminases (PADs), which are found in vertebrates but not in lower organisms. RA has been epidemiologically associated with periodontal disease, whose main infective agent is Porphyromonas gingivalis. Uniquely among microbes, P. gingivalis secretes a PAD, termed PPAD (Porphyromonas peptidylarginine deiminase), which is genetically unrelated to eukaryotic PADs. Here, we studied function of PPAD and its substrate-free, substrate-complex, and substrate-mimic-complex structures. It comprises a flat cylindrical catalytic domain with five-fold α/β-propeller architecture and a C-terminal immunoglobulin-like domain. The PPAD active site is a funnel located on one of the cylinder bases. It accommodates arginines from peptide substrates after major rearrangement of a “Michaelis loop” that closes the cleft. The guanidinium and carboxylate groups of substrates are tightly bound, which explains activity of PPAD against arginines at C-termini but not within peptides. Catalysis is based on a cysteine-histidine-asparagine triad, which is shared with human PAD1-PAD4 and other guanidino-group modifying enzymes. We provide a working mechanism hypothesis based on 18 structure-derived point mutants.
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Schmuch J, Beckert S, Brandt S, Löhr G, Hermann F, Schmidt TJ, Beikler T, Hensel A. Extract from Rumex acetosa L. for prophylaxis of periodontitis: inhibition of bacterial in vitro adhesion and of gingipains of Porphyromonas gingivalis by epicatechin-3-O-(4β→8)-epicatechin-3-O-gallate (procyanidin-B2-Di-gallate). PLoS One 2015; 10:e0120130. [PMID: 25803708 PMCID: PMC4372542 DOI: 10.1371/journal.pone.0120130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/19/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The aerial parts of Rumex acetosa L. have been used in traditional European medicine for inflammatory diseases of the mouth epithelial tissue. The following study aimed to investigate the influence of a proanthocyanidin-enriched extract from R. acetosa extract against the adhesion of Porphyromonas gingivalis (P. gingivalis), a pathogen strongly involved in chronic and aggressive periodontitis. A further goal was to define the bioactive lead structures responsible for a potential antiadhesive activity and to characterize the underlying molecular mechanisms of the antiadhesive effects. METHODOLOGY An extract of R. acetosa (RA1) with a defined mixture of flavan-3-ols, oligomeric proanthocyanidins and flavonoids, was used. Its impact on P. gingivalis adhesion to KB cells was studied by flow cytometry, confocal laser scanning microscopy and in situ adhesion assay using murine buccal tissue. RA1 and its compounds 1 to 15 were further investigated for additional effects on gingipain activity, hemagglutination and gene expression by RT-PCR. PRINCIPAL FINDINGS RA1 (5 to 15 μg/mL) reduced P. gingivalis adhesion in a dose-dependent manner to about 90%. Galloylated proanthocyanidins were confirmed to be responsible for this antiadhesive effect with epicatechin-3-O-gallate-(4β,8)-epicatechin-3'-O-gallate (syn. procyanidin B2-di-gallate) being the lead compound. Ungalloylated flavan-3-ols and oligomeric proanthocyanidins were inactive. RA1 and the galloylated proanthocyanidins strongly interact with the bacterial virulence factor Arg-gingipain, while the corresponding Lys-gingipain was hardly influenced. RA1 inhibited also hemagglutination. In silico docking studies indicated that epicatechin-3-O-gallate-(4β,8)-epicatechin-3'-O-gallate interacts with the active side of Arg-gingipain and hemaglutinin from P. gingivalis; the galloylation of the molecule seems to be responsible for fixation of the ligand to the protein. In conclusion, the proanthocyanidin-enriched extract RA1 and its main active constituent procyanidin B2-di-gallate protect cells from P. gingivalis infection by inhibiting bacterial adhesion to the host cell. RA1 and procyanidin B2-di-gallate appear to be promising candidates for future cytoprotective preparations for oral mouth care products.
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Affiliation(s)
- Jana Schmuch
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Sabine Beckert
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Simone Brandt
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Gesine Löhr
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Fabian Hermann
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Thomas J. Schmidt
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Thomas Beikler
- Heinrich-Heine-University, Department of Operative Dentistry, Periodontics and Endodontics, Düsseldorf, Germany
| | - Andreas Hensel
- University of Münster, Institute for Pharmaceutical Biology and Phytochemistry, Münster, Germany
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McLuskey K, Mottram J. Comparative structural analysis of the caspase family with other clan CD cysteine peptidases. Biochem J 2015; 466:219-32. [PMID: 25697094 PMCID: PMC4357240 DOI: 10.1042/bj20141324] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
Abstract
Clan CD forms a structural group of cysteine peptidases, containing seven individual families and two subfamilies of structurally related enzymes. Historically, it is most notable for containing the mammalian caspases, on which the structures of the clan were founded. Interestingly, the caspase family is split into two subfamilies: the caspases, and a second subfamily containing both the paracaspases and the metacaspases. Structural data are now available for both the paracaspases and the metacaspases, allowing a comprehensive structural analysis of the entire caspase family. In addition, a relative plethora of structural data has recently become available for many of the other families in the clan, allowing both the structures and the structure-function relationships of clan CD to be fully explored. The present review compares the enzymes in the caspase subfamilies with each other, together with a comprehensive comparison of all the structural families in clan CD. This reveals a diverse group of structures with highly conserved structural elements that provide the peptidases with a variety of substrate specificities and activation mechanisms. It also reveals conserved structural elements involved in substrate binding, and potential autoinhibitory functions, throughout the clan, and confirms that the metacaspases are structurally diverse from the caspases (and paracaspases), suggesting that they should form a distinct family of clan CD peptidases.
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Key Words
- caspase
- clan cd
- crystallography
- metacaspase
- peptidase
- protein structure
- ap, activation peptide
- card, caspase recruitment domain
- chf, caspase/haemoglobinase fold
- cpd, cysteine peptidase domain
- csd, c-terminal subdomain
- dd, death domain
- ded, death effector domain
- insp6, myo-inositol hexakisphosphate
- lsam, legumain stabilization and activity modulation
- lsd1, lesion-simulating disease 1
- malt1, mucosa-associated lymphoid tissue translocation protein 1
- martx, multi-functional, autoprocessing repeat in toxin
- rmsd, root-mean-square deviation
- sse, secondary structural element
- xiap, x-linked inhibitor of apoptosis
- z-vrpr-fmk, benzoxycarbonyl-val-arg-pro-arg-fluoromethylketone
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Affiliation(s)
- Karen McLuskey
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Jeremy C. Mottram
- *Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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Gorman MA, Seers CA, Michell BJ, Feil SC, Huq NL, Cross KJ, Reynolds EC, Parker MW. Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health. Protein Sci 2014; 24:162-6. [PMID: 25327141 DOI: 10.1002/pro.2589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Abstract
The oral pathogen Porphyromonas gingivalis is a keystone pathogen in the development of chronic periodontitis. Gingipains, the principle virulence factors of P. gingivalis are multidomain, cell-surface proteins containing a cysteine protease domain. The lysine specific gingipain, Kgp, is a critical virulence factor of P. gingivalis. We have determined the X-ray crystal structure of the lysine-specific protease domain of Kgp to 1.6 Å resolution. The structure provides insights into the mechanism of substrate specificity and catalysis.
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Affiliation(s)
- Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
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de Diego I, Veillard F, Sztukowska MN, Guevara T, Potempa B, Pomowski A, Huntington JA, Potempa J, Gomis-Rüth FX. Structure and mechanism of cysteine peptidase gingipain K (Kgp), a major virulence factor of Porphyromonas gingivalis in periodontitis. J Biol Chem 2014; 289:32291-32302. [PMID: 25266723 DOI: 10.1074/jbc.m114.602052] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine peptidases are key proteolytic virulence factors of the periodontopathogen Porphyromonas gingivalis, which causes chronic periodontitis, the most prevalent dysbiosis-driven disease in humans. Two peptidases, gingipain K (Kgp) and R (RgpA and RgpB), which differ in their selectivity after lysines and arginines, respectively, collectively account for 85% of the extracellular proteolytic activity of P. gingivalis at the site of infection. Therefore, they are promising targets for the design of specific inhibitors. Although the structure of the catalytic domain of RgpB is known, little is known about Kgp, which shares only 27% sequence identity. We report the high resolution crystal structure of a competent fragment of Kgp encompassing the catalytic cysteine peptidase domain and a downstream immunoglobulin superfamily-like domain, which is required for folding and secretion of Kgp in vivo. The structure, which strikingly resembles a tooth, was serendipitously trapped with a fragment of a covalent inhibitor targeting the catalytic cysteine. This provided accurate insight into the active site and suggested that catalysis may require a catalytic triad, Cys(477)-His(444)-Asp(388), rather than the cysteine-histidine dyad normally found in cysteine peptidases. In addition, a 20-Å-long solvent-filled interior channel traverses the molecule and links the bottom of the specificity pocket with the molecular surface opposite the active site cleft. This channel, absent in RgpB, may enhance the plasticity of the enzyme, which would explain the much lower activity in vitro toward comparable specific synthetic substrates. Overall, the present results report the architecture and molecular determinants of the working mechanism of Kgp, including interaction with its substrates.
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Affiliation(s)
- Iñaki de Diego
- Proteolysis Lab, Molecular Biology Institute of Barcelona, Spanish Research Council (Consejo Superior de Investigaciones Cientificas), Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Florian Veillard
- Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Maryta N Sztukowska
- Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Tibisay Guevara
- Proteolysis Lab, Molecular Biology Institute of Barcelona, Spanish Research Council (Consejo Superior de Investigaciones Cientificas), Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Barbara Potempa
- Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Anja Pomowski
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - James A Huntington
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jan Potempa
- Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202,; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland, and.
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona, Spanish Research Council (Consejo Superior de Investigaciones Cientificas), Barcelona Science Park, Helix Building, Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain,.
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Abstract
Gingipains, a group of arginine or lysine specific cysteine proteinases (also known as RgpA, RgpB and Kgp), have been recognized as major virulence factors in Porphyromonas gingivalis. This bacterium is one of a handful of pathogens that cause chronic periodontitis. Gingipains are involved in adherence to and colonization of epithelial cells, haemagglutination and haemolysis of erythrocytes, disruption and manipulation of the inflammatory response, and the degradation of host proteins and tissues. RgpA and Kgp are multi-domain proteins composed of catalytic domains and haemagglutinin/adhesin (HA) regions. The structure of the HA regions have previously been defined by a gingipain domain structure hypothesis which is a set of putative domain boundaries derived from the sequences of fragments of these proteins extracted from the cell surface. However, multiple sequence alignments and hidden Markov models predict an alternative domain architecture for the HA regions of gingipains. In this alternate model, two or three repeats of the so-called "cleaved adhesin" domains (and one other undefined domain in some strains) are the modules which constitute the substructure of the HA regions. Recombinant forms of these putative cleaved adhesin domains are indeed stable folded protein modules and recently determined crystal structures support the hypothesis of a modular organisation of the HA region. Based on the observed K2 and K3 structures as well as multiple sequence alignments, it is proposed that all the cleaved adhesin domains in gingipains will share the same β-sandwich jelly roll fold. The new domain model of the structure for gingipains and the haemagglutinin (HagA) proteins of P. gingivalis will guide future functional studies of these virulence factors.
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Affiliation(s)
- N Li
- School of Molecular Bioscience, University of Sydney NSW Australia
| | - C A Collyer
- School of Molecular Bioscience, University of Sydney NSW Australia
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46
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Veith PD, Chen YY, Gorasia DG, Chen D, Glew MD, O’Brien-Simpson NM, Cecil JD, Holden JA, Reynolds EC. Porphyromonas gingivalis Outer Membrane Vesicles Exclusively Contain Outer Membrane and Periplasmic Proteins and Carry a Cargo Enriched with Virulence Factors. J Proteome Res 2014; 13:2420-32. [DOI: 10.1021/pr401227e] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paul D. Veith
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Yu-Yen Chen
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Dhana G. Gorasia
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Dina Chen
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Michelle D. Glew
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Neil M. O’Brien-Simpson
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Jessica D. Cecil
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - James A. Holden
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
| | - Eric C. Reynolds
- Oral Health
CRC, Melbourne
Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston
Street, Victoria, 3010, Australia
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48
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Popovics P, Lu J, Nadia Kamil L, Morgan K, Millar RP, Schmid R, Blindauer CA, Stewart AJ. A Canonical EF-Loop Directs Ca2+-Sensitivity in Phospholipase C-η2. J Cell Biochem 2014; 115:557-65. [DOI: 10.1002/jcb.24690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/08/2013] [Indexed: 01/24/2023]
Affiliation(s)
- Petra Popovics
- School of Medicine; University of St Andrews; St Andrews UK
| | - Jin Lu
- Department of Chemistry; University of Warwick; Coventry UK
| | - L. Nadia Kamil
- School of Medicine; University of St Andrews; St Andrews UK
| | - Kevin Morgan
- MRC Human Reproductive Sciences Unit; Queen's Medical Research Institute; Edinburgh UK
| | - Robert P. Millar
- MRC Human Reproductive Sciences Unit; Queen's Medical Research Institute; Edinburgh UK
- Mammal Research Institute; University of Pretoria; Pretoria South Africa
| | - Ralf Schmid
- Department of Biochemistry; University of Leicester; Leicester UK
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49
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Zhou XY, Gao JL, Hunter N, Potempa J, Nguyen KA. Sequence-independent processing site of the C-terminal domain (CTD) influences maturation of the RgpB protease from Porphyromonas gingivalis. Mol Microbiol 2013; 89:903-17. [PMID: 23869473 DOI: 10.1111/mmi.12319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2013] [Indexed: 11/29/2022]
Abstract
The Gram-negative periodontal pathogen Porphyromonas gingivalis produces a family of outer membrane-anchored proteases, the gingipains, shown to play an essential role in virulence of the organism. The C-terminal domain (CTD) of gingipains and other secreted proteins is known to be the targeting signal for maturation and translocation of the protein through the outer membrane. The CTD is subsequently cleaved during the secretion process. Multiple alignment of various CTDs failed to define a consensus sequence at the putative CTD processing site. Using mutagenesis, we were able to show that cleavage at the site is not dependent on a specific residue and that recognition of the site is independent of local sequence. Interestingly, length of the junction between the CTD and adjacent Ig-like subdomain has a critical influence on post-translational glycan modification of the protein, whereby insertion of additional residues immediately N-terminal to the cleavage site results in failure of glycan modification and release of soluble protease into the culture medium. Various hypotheses are presented to explain these phenomena. Knowledge of the role CTDs play in maturation of gingipains has broader application for understanding maturation of CTD homologues expressed by bacteria of the Bacteriodetes phylum.
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Affiliation(s)
- Xiao-Yan Zhou
- Institute of Dental Research, Westmead Centre for Oral Health and Westmead Millennium Institute, Sydney, NSW, Australia
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Dall E, Brandstetter H. Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation. Proc Natl Acad Sci U S A 2013; 110:10940-5. [PMID: 23776206 DOI: 10.1073/pnas.1300686110] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cysteine protease legumain plays important functions in immunity and cancer at different cellular locations, some of which appeared conflicting with its proteolytic activity and stability. Here, we report crystal structures of legumain in the zymogenic and fully activated form in complex with different substrate analogs. We show that the eponymous asparagine-specific endopeptidase activity is electrostatically generated by pH shift. Completely unexpectedly, the structure points toward a hidden carboxypeptidase activity that develops upon proteolytic activation with the release of an activation peptide. These activation routes reconcile the enigmatic pH stability of legumain, e.g., lysosomal, nuclear, and extracellular activities with relevance in immunology and cancer. Substrate access and turnover is controlled by selective protonation of the S1 pocket (KM) and the catalytic nucleophile (kcat), respectively. The multibranched and context-dependent activation process of legumain illustrates how proteases can act not only as signal transducers but as decision makers.
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