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Śmiga M, Roszkiewicz E, Ślęzak P, Tracz M, Olczak T. cAMP-independent Crp homolog adds to the multi-layer regulatory network in Porphyromonas gingivalis. Front Cell Infect Microbiol 2025; 15:1535009. [PMID: 40308968 PMCID: PMC12040651 DOI: 10.3389/fcimb.2025.1535009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 03/21/2025] [Indexed: 05/02/2025] Open
Abstract
Introduction Porphyromonas gingivalis encodes three CRP/FNR superfamily proteins: HcpR, PgRsp, and CrpPg, with CrpPg similar to cAMP-sensing proteins but not classified into known families. This study investigates the role of CrpPg in regulating the expression of factors essential for P. gingivalis virulence in A7436 and ATCC 33277 strains. Methods The role of CrpPg protein in P. gingivalis was determined using the ΔcrpPg mutant strains to characterize their phenotype and to assess the impact of crpPg inactivation on gene expression using RNA-seq and RT-qPCR. Additionally, the CrpPg protein was purified and characterized. Results Key findings in the ΔcrpPg mutant strain include up-regulated mfa1-5 and rgpA genes and down-regulated trxA, soxR, and ustA genes. While crpPg inactivation does not affect growth in liquid culture media, it impairs biofilm formation and enhances adhesion to and invasion of gingival keratinocytes. CrpPg binds directly to its own and mfa promoters without interacting with cyclic nucleotides or di-nucleotides. Its three-dimensional structure, resembling E. coli Crp in complex with cAMP and DNA, suggests that CrpPg functions as a global regulator independently of cAMP binding. The highest crpPg expression in the early exponential growth phase declines as cell density and metabolic conditions change over time, suggesting a regulatory function depending on the CrpPg protein amount. Conclusions By controlling the shift from planktonic to biofilm lifestyle, CrpPg may play a role in pathogenicity. Regulating the expression of virulence factors required for host cell invasion and intracellular replication, CrpPg may help P. gingivalis evade immune responses.
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Affiliation(s)
- Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Ewa Roszkiewicz
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Paulina Ślęzak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Michał Tracz
- Laboratory of Protein Mass Spectrometry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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2
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Yadalam PK, Neelakandan A, Arunraj R, Anegundi RV, Ardila CM. Exploring the interplay between Porphyromonas gingivalis KGP gingipain, herpes virus MicroRNA-6, and Icp4 transcript in periodontitis: Computational and clinical insights. PLoS One 2024; 19:e0312162. [PMID: 39480863 PMCID: PMC11527181 DOI: 10.1371/journal.pone.0312162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/30/2024] [Indexed: 11/02/2024] Open
Abstract
BACKGROUND Porphyromonas gingivalis, a major pathogen in periodontitis, produces KGP (Lys-gingipain), a cysteine protease that enhances bacterial virulence by promoting tissue invasion and immune evasion. Recent studies highlight microRNAs' role in viral latency, potentially affecting lytic replication through host mechanisms. Herpes virus (HSV) establishes latency via interactions between microRNA-6 (miRH-6) and the ICP4 transcription factor in neural ganglia. This suggests a potential link between periodontitis and HSV-induced latency. This study aims to identify and validate the insilico inhibitory interaction of P. gingivalis KGP with ICP4 transcripts and correlate the presence of viral latency-associated transcript micro-RNA-6 with periodontitis. METHODS Computational docking analysis was performed to investigate the potential interaction between ICP4 and KGP gingipain. The binding energy and RMSD ligand values were calculated to determine the interaction's strength. Ten patients with recurrent clinical attachment loss despite conventional therapy were included in the clinical study. Subgingival tissue samples were collected post-phase I therapy, and HSV microRNA-6 presence was detected via polymerase chain reaction and confirmed through gel electrophoresis. RESULTS Computational docking identified the ICP4-KGP gingipain complex with the lowest binding energy (-288.29 kJ mol^1) and an RMSD ligand of 1.5 Angstroms, indicating strong interaction potential. Gel electrophoresis confirmed miRH-6 presence in all samples. CONCLUSION The identification of miRNA-6 in periodontitis patients and the strong interaction potential between P. gingivalis KGP gingipain and ICP4 transcripts indicate a possible link between bacterial virulence factors and viral latency dynamics in periodontal tissues. These results highlight the complex interplay between oral pathogens, viral microRNAs, and host immune responses in periodontitis.
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Affiliation(s)
- Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and technology sciences, SIMATS, Saveetha University, Chennai, Tamil Nadu, India
| | | | - Rex Arunraj
- Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kanchipuram, Tamil Nadu, India
| | - Raghavendra Vamsi Anegundi
- Department of Periodontics, Saveetha Dental College, Saveetha Institute of Medical and technology sciences, SIMATS, Saveetha University, Chennai, Tamil Nadu, India
| | - Carlos M. Ardila
- Basic Sciences Department, Faculty of Dentistry, Universidad de Antioquia U de A, Medellín, Colombia
- Biomedical Stomatology Research Group, Universidad de Antioquia U de A, Medellín, Colombia
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Kim B, Hwang J, Im S, Do H, Shim YS, Lee JH. First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis. Acta Crystallogr F Struct Biol Commun 2024; 80:252-262. [PMID: 39325582 PMCID: PMC11448926 DOI: 10.1107/s2053230x24008185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/17/2024] [Indexed: 09/28/2024] Open
Abstract
Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9-5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.
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Affiliation(s)
- Bogeun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Sehyeok Im
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Youn Soo Shim
- Department of Dental Hygiene, Sunmoon University, Asan 31460, Republic of Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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Śmiga M, Ślęzak P, Olczak T. Comparative analysis of Porphyromonas gingivalis A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems. Microbiol Spectr 2024; 12:e0286523. [PMID: 38289063 PMCID: PMC10913741 DOI: 10.1128/spectrum.02865-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/15/2023] [Indexed: 03/06/2024] Open
Abstract
Porphyromonas gingivalis strains exhibit different phenotypes in vitro, different virulence potential in animal models, and different associations with human diseases, with strains classified as virulent/more virulent (e.g., A7436 and W83) or as less virulent/avirulent (e.g., ATCC 33277). In this study, we comparatively analyzed the A7436 and ATCC 33277 strains to better understand their variability. Global gene expression analysis in response to heme and iron limitation revealed more pronounced differences in the A7436 than in the ATCC 33277 strain; however, in both strains, the largest changes were observed in genes encoding hypothetical proteins, genes whose products participate in energy metabolism, and in genes encoding proteins engaged in transport and binding proteins. Our results confirmed that variability between P. gingivalis strains is due to differences in the arrangement of their genomes. Analysis of gene expression of heme acquisition systems demonstrated that not only the availability of iron and heme in the external environment but also the ability to store iron intracellularly can influence the P. gingivalis phenotype. Therefore, we assume that differences in virulence potential may also be due to differences in the production of systems involved in iron and heme acquisition, mainly the Hmu system. In addition, our study showed that hemoglobin, in a concentration-dependent manner, differentially influences the virulence potential of P. gingivalis strains. We conclude that iron and heme homeostasis may add to the variability observed between P. gingivalis strains. IMPORTANCE Periodontitis belongs to a group of multifactorial diseases, characterized by inflammation and destruction of tooth-supporting tissues. P. gingivalis is one of the most important microbial factors involved in the initiation and progression of periodontitis. To survive in the host, the bacterium must acquire heme as a source of iron and protoporphyrin IX. P. gingivalis strains respond differently to changing iron and heme concentrations, which may be due to differences in the expression of systems involved in iron and heme acquisition. The ability to accumulate iron intracellularly, being different in more and less virulent P. gingivalis strains, may influence their phenotypes, production of virulence factors (including proteins engaged in heme acquisition), and virulence potential of this bacterium.
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Affiliation(s)
- Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Paulina Ślęzak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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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: 0.8] [Reference Citation Analysis] [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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Tamomh AG, Suliman MA, Yousif SR, Liu H. The Oral Parasitic Microbiome in Hepatitis B Virus Infected Sudanese Patients with Gum Disease. IRANIAN JOURNAL OF PARASITOLOGY 2020; 15:602-607. [PMID: 33884018 PMCID: PMC8039478 DOI: 10.18502/ijpa.v15i4.4874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background We aimed to evaluate a potential link between colonization of gingival crevices by the Entamoeba gingivalis as oral parasite microbiome and Hepatitis B infection among gum disease Sudanese patients. Methods This study was conducted on 448 gum disease patients attending to Dental Clinic of Kosti Teaching Hospital, Kosti, Sudan in 2017-2018. Oral symptoms were registered in 336 patients at different stages of the HBV infection and in 112 HBV seronegative gum disease control. All participants were screened for HBV using ELISA test. Unstimulated whole saliva and gingival scraping were obtained and analyzed for the presence of the amoeba using a parasitological technique. Results Statistically highly significant correlation was found between the detection of the E. gingivalis in Saliva/gingival scraping and gum illness disease with HBV-infected patients than healthy control group (P<0.05). There was high association between the occurrence of the amoeba between the two groups and smoking, snuffing habitats (P<0.05), inversely, no association with the oral personal hygiene. Conclusion The presence of the amoeba was not related to the degree of gum diseases only, but to the HBV infection diagnosis. To our knowledge, this is the first study of E. gingivalis in association with HBV infection among gum disease Sudanese patients; maybe predict the role of oral parasitic microbiome in the status of gum disease in HBV infection.
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Affiliation(s)
- Abdelhakam G Tamomh
- Department of Microbiology and Clinical Immunology, College of Medical Laboratory, Dalian Medical University, Dalian 116044, China.,Department of Parasitology and Medical Entomology, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti, Sudan
| | - Mohammed A Suliman
- Department of Parasitology and Medical Entomology, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti, Sudan
| | - Sabah R Yousif
- Department of Clinical Laboratory, Kosti Teaching Hospital, Kosti, Sudan
| | - Hui Liu
- Department of Microbiology and Clinical Immunology, College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
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Jia L, Han N, Du J, Guo L, Luo Z, Liu Y. Pathogenesis of Important Virulence Factors of Porphyromonas gingivalis via Toll-Like Receptors. Front Cell Infect Microbiol 2019; 9:262. [PMID: 31380305 PMCID: PMC6657652 DOI: 10.3389/fcimb.2019.00262] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/04/2019] [Indexed: 12/18/2022] Open
Abstract
Periodontitis is a common intraoral infection and is inextricably linked to systemic diseases. Recently, the regulation between host immunologic response and periodontal pathogens has become a hotspot to explain the mechanism of periodontitis and related systemic diseases. Since Porphyromonas gingivalis (P. gingivalis) was proved as critical periodontal pathogen above all, researches focusing on the mechanism of its virulence factors have received extensive attention. Studies have shown that in the development of periodontitis, in addition to the direct release of virulent factors by periodontal pathogens to destroy periodontal tissues, over-low or over-high intrinsic immune and inflammatory response mediated by Toll-like receptors (TLRs) can lead to more lasting destruction of periodontal tissues. It is very necessary to sort out how various cytopathic factors of P. gingivalis mediate inflammation and immune responses between the host through TLRs so as to help precisely prevent, diagnose, and treat periodontitis in clinic. This review summarizes the role of three most widely studied pathogenic factors produced by P. gingivalis (lipopolysaccharide, gingipains, pili) and their interactions with TLRs at the cellular and molecular level in the progress of periodontitis.
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Affiliation(s)
- Lu Jia
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Nannan Han
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Juan Du
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Lijia Guo
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, China
| | - Zhenhua Luo
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Yi Liu
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
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Veillard F, Sztukowska M, Nowakowska Z, Mizgalska D, Thøgersen IB, Enghild JJ, Bogyo M, Potempa B, Nguyen KA, Potempa J. Proteolytic processing and activation of gingipain zymogens secreted by T9SS of Porphyromonas gingivalis. Biochimie 2019; 166:161-172. [PMID: 31212040 DOI: 10.1016/j.biochi.2019.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022]
Abstract
Porphyromonas gingivalis uses a type IX secretion system (T9SS) to deliver more than 30 proteins to the bacterial surface using a conserved C-terminal domain (CTD) as an outer membrane translocation signal. On the surface, the CTD is cleaved and an anionic lipopolysaccharide (A-PLS) is attached by PorU sortase. Among T9SS cargo proteins are cysteine proteases, gingipains, which are secreted as inactive zymogens requiring removal of an inhibiting N-terminal prodomain (PD) for activation. Here, we have shown that the gingipain proRgpB isolated from the periplasm of a T9SS-deficient P. gingivalis strain was stable and did not undergo autocatalytic activation. Addition of purified, active RgpA or RgpB, but not Lys-specific Kgp, efficiently cleaved the PD of proRgpB but catalytic activity remained inhibited because of inhibition of the catalytic domain in trans by the PD. In contrast, active RgpB was generated from the zymogen, although at a slow rate, by gingipain-null P. gingivalis lysate or intact bacterial cell suspension. This activation was dependent on the presence of the PorU sortase. Interestingly, maturation of proRgpB with the catalytic cysteine residues mutated to Ala expressed in the ΔRgpA mutant strain was indistinguishable from that in the parental strain. Cumulatively, this suggests that PorU not only has sortase activity but is also engaged in activation of gingipain zymogens on the bacterial cell surface.
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Affiliation(s)
- Florian Veillard
- Université de Strasbourg, CNRS, Insect Models of Innate Immunity (M3I; UPR9022), 67084, Strasbourg, France; Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA.
| | - Maryta Sztukowska
- Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA; University of Information Technology and Management, Rzeszow, Poland
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ida B Thøgersen
- Interdisciplinary Nanoscience Center (iNANO), and the Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK-8000, Denmark
| | - Jan J Enghild
- Interdisciplinary Nanoscience Center (iNANO), and the Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK-8000, Denmark
| | - Matthew Bogyo
- Department of Pathology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Barbara Potempa
- Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA
| | - Ky-Anh Nguyen
- Discipline of Life Sciences, School of Dentistry, University of Sydney, Sydney, NSW, 2006, Australia; Institute of Dental Research, Westmead Centre for Oral Health, Sydney, NSW, 2145, Australia
| | - Jan Potempa
- Department of Oral Immunity and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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9
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Guevara T, Rodríguez-Banqueri A, Lasica AM, Ksiazek M, Potempa BA, Potempa J, Gomis-Rüth FX. Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor. Sci Rep 2019; 9:4935. [PMID: 30894633 PMCID: PMC6426963 DOI: 10.1038/s41598-019-41354-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/07/2019] [Indexed: 01/24/2023] Open
Abstract
Porphyromonas gingivalis is a member of the dysbiotic oral microbiome and a "keystone pathogen" that causes severe periodontal disease, which is among the most prevalent infectious diseases. Part of the virulence factors secreted by P. gingivalis are the essential cysteine peptidases gingipain K (Kgp) and R (RgpA and RgpB), which account for 85% of the extracellular proteolytic activity of the pathogen and are thus prime targets for inhibition. We report the high-resolution (1.20 Å) complex structure of Kgp with KYT-36, a peptide-derived, potent, bioavailable and highly selective inhibitor, which is widely used for studies in vitro, in cells and in vivo. Sub-nanomolar inhibition of Kgp is achieved by tight binding to the active-site cleft, which is covered for its sub-sites S3 through S1' under establishment of nine hydrophobic interactions, 14 hydrogen bonds and one salt bridge. In addition, an inhibitor carbonyl carbon that mimics the scissile carbonyl of substrates is pyramidalized and just 2.02 Å away from the catalytic nucleophile of Kgp, C477Sγ. Thus, the crystal structure emulates a reaction intermediate of the first nucleophilic attack during catalysis of cysteine peptidases. The present study sets the pace for the development of tailored next-generation drugs to tackle P. gingivalis.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, Helix Building, c/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain
| | - Arturo Rodríguez-Banqueri
- Proteolysis Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, Helix Building, c/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain
| | - Anna M Lasica
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warszawa, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY, 40202, USA
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY, 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Barbara A Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY, 40202, USA.
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, Helix Building, c/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain.
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10
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Usón I, Sheldrick GM. An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features. Acta Crystallogr D Struct Biol 2018; 74:106-116. [PMID: 29533236 PMCID: PMC5947774 DOI: 10.1107/s2059798317015121] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/17/2017] [Indexed: 11/10/2022] Open
Abstract
For the purpose of this article, experimental phasing is understood to mean the determination of macromolecular structures by exploiting small intensity differences of Friedel opposites and possibly of reflections measured at different wavelengths or for heavy-atom derivatives, without the use of specific structural models. The SHELX programs provide a robust and efficient route for routine structure solution by the SAD, MAD and related methods, but involve a number of simplifying assumptions that may limit their applicability in borderline cases. The substructure atoms (i.e. those with significant anomalous scattering) are first located by direct methods, and the experimental data are then used to estimate phase shifts that are added to the substructure phases to obtain starting phases for the native reflections. These are then improved by density modification and, if the resolution of the data and the type of structure permit, polyalanine tracing. A number of extensions to the tracing algorithm are discussed; these are designed to improve its performance at low resolution. Given native data to 2.5 Å resolution or better, a correlation coefficient greater than 25% between the structure factors calculated from such a trace and the native data is usually a good indication that the structure has been solved.
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Affiliation(s)
- Isabel Usón
- Structural Biology, IBMB–CSIC, Baldiri Reixach 13-15, 08028 Barcelona, Spain
- ICREA, Baldiri Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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Lasica AM, Ksiazek M, Madej M, Potempa J. The Type IX Secretion System (T9SS): Highlights and Recent Insights into Its Structure and Function. Front Cell Infect Microbiol 2017. [PMID: 28603700 DOI: 10.3389/fcimb.2017.00215.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein secretion systems are vital for prokaryotic life, as they enable bacteria to acquire nutrients, communicate with other species, defend against biological and chemical agents, and facilitate disease through the delivery of virulence factors. In this review, we will focus on the recently discovered type IX secretion system (T9SS), a complex translocon found only in some species of the Bacteroidetes phylum. T9SS plays two roles, depending on the lifestyle of the bacteria. It provides either a means of movement (called gliding motility) for peace-loving environmental bacteria or a weapon for pathogens. The best-studied members of these two groups are Flavobacterium johnsoniae, a commensal microorganism often found in water and soil, and Porphyromonas gingivalis, a human oral pathogen that is a major causative agent of periodontitis. In P. gingivalis and some other periodontopathogens, T9SS translocates proteins, especially virulence factors, across the outer membrane (OM). Proteins destined for secretion bear a conserved C-terminal domain (CTD) that directs the cargo to the OM translocon. At least 18 proteins are involved in this still enigmatic process, with some engaged in the post-translational modification of T9SS cargo proteins. Upon translocation across the OM, the CTD is removed by a protease with sortase-like activity and an anionic LPS is attached to the newly formed C-terminus. As a result, a cargo protein could be secreted into the extracellular milieu or covalently attached to the bacterial surface. T9SS is regulated by a two-component system; however, the precise environmental signal that triggers it has not been identified. Exploring unknown systems contributing to bacterial virulence is exciting, as it may eventually lead to new therapeutic strategies. During the past decade, the major components of T9SS were identified, as well as hints suggesting the possible mechanism of action. In addition, the list of characterized cargo proteins is constantly growing. The actual structure of the translocon, situated in the OM of bacteria, remains the least explored area; however, new technical approaches and increasing scientific attention have resulted in a growing body of data. Therefore, we present a compact up-to-date review of this topic.
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Affiliation(s)
- Anna M Lasica
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of WarsawWarsaw, Poland
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
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Lasica AM, Ksiazek M, Madej M, Potempa J. The Type IX Secretion System (T9SS): Highlights and Recent Insights into Its Structure and Function. Front Cell Infect Microbiol 2017; 7:215. [PMID: 28603700 PMCID: PMC5445135 DOI: 10.3389/fcimb.2017.00215] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022] Open
Abstract
Protein secretion systems are vital for prokaryotic life, as they enable bacteria to acquire nutrients, communicate with other species, defend against biological and chemical agents, and facilitate disease through the delivery of virulence factors. In this review, we will focus on the recently discovered type IX secretion system (T9SS), a complex translocon found only in some species of the Bacteroidetes phylum. T9SS plays two roles, depending on the lifestyle of the bacteria. It provides either a means of movement (called gliding motility) for peace-loving environmental bacteria or a weapon for pathogens. The best-studied members of these two groups are Flavobacterium johnsoniae, a commensal microorganism often found in water and soil, and Porphyromonas gingivalis, a human oral pathogen that is a major causative agent of periodontitis. In P. gingivalis and some other periodontopathogens, T9SS translocates proteins, especially virulence factors, across the outer membrane (OM). Proteins destined for secretion bear a conserved C-terminal domain (CTD) that directs the cargo to the OM translocon. At least 18 proteins are involved in this still enigmatic process, with some engaged in the post-translational modification of T9SS cargo proteins. Upon translocation across the OM, the CTD is removed by a protease with sortase-like activity and an anionic LPS is attached to the newly formed C-terminus. As a result, a cargo protein could be secreted into the extracellular milieu or covalently attached to the bacterial surface. T9SS is regulated by a two-component system; however, the precise environmental signal that triggers it has not been identified. Exploring unknown systems contributing to bacterial virulence is exciting, as it may eventually lead to new therapeutic strategies. During the past decade, the major components of T9SS were identified, as well as hints suggesting the possible mechanism of action. In addition, the list of characterized cargo proteins is constantly growing. The actual structure of the translocon, situated in the OM of bacteria, remains the least explored area; however, new technical approaches and increasing scientific attention have resulted in a growing body of data. Therefore, we present a compact up-to-date review of this topic.
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Affiliation(s)
- Anna M Lasica
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of WarsawWarsaw, Poland
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of DentistryLouisville, KY, United States.,Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian UniversityKrakow, Poland
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