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Patridge E, Gorakshakar A, Molusky MM, Ogundijo O, Janevski A, Julian C, Hu L, Vuyisich M, Banavar G. Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness. Comput Struct Biotechnol J 2024; 23:834-842. [PMID: 38328005 PMCID: PMC10847690 DOI: 10.1016/j.csbj.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129). Through this validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions.
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Affiliation(s)
- Eric Patridge
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Anmol Gorakshakar
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | | | - Oyetunji Ogundijo
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Angel Janevski
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Cristina Julian
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | - Lan Hu
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
| | | | - Guruduth Banavar
- Viome Research Institute, Viome Life Sciences Inc., New York City, USA
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2
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Ordinola-Zapata R, Costalonga M, Dietz M, Lima BP, Staley C. The root canal microbiome diversity and function. A whole-metagenome shotgun analysis. Int Endod J 2024; 57:872-884. [PMID: 36861850 DOI: 10.1111/iej.13911] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023]
Abstract
AIM To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing. METHODOLOGY Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes. RESULTS Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase. CONCLUSIONS Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.
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Affiliation(s)
- Ronald Ordinola-Zapata
- Division of Endodontics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Massimo Costalonga
- Division of Basic Sciences, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew Dietz
- Division of Basic & Translational Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bruno P Lima
- Division of Basic Sciences, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher Staley
- Division of Basic & Translational Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
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3
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Barbosa CDB, Monici Silva I, Dame-Teixeira N. The action of microbial collagenases in dentinal matrix degradation in root caries and potential strategies for its management: a comprehensive state-of-the-art review. J Appl Oral Sci 2024; 32:e20240013. [PMID: 38775556 PMCID: PMC11182643 DOI: 10.1590/1678-7757-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
Conventional views associate microbial biofilm with demineralization in root caries (RC) onset, while research on their collagenases role in the breakdown of collagen matrix has been sporadically developed, primarily in vitro. Recent discoveries, however, reveal proteolytic bacteria enrichment, specially Porphyromonas and other periodontitis-associated bacteria in subgingivally extended lesions, suggesting a potential role in RC by the catabolism of dentin organic matrix. Moreover, genes encoding proteases and bacterial collagenases, including the U32 family collagenases, were found to be overexpressed in both coronal and root dentinal caries. Despite these advancements, to prove microbial collagenolytic proteases' definitive role in RC remains a significant challenge. A more thorough investigation is warranted to explore the potential of anti-collagenolytic agents in modulating biofilm metabolic processes or inhibiting/reducing the size of RC lesions. Prospective treatments targeting collagenases and promoting biomodification through collagen fibril cross-linking show promise for RC prevention and management. However, these studies are currently in the in vitro phase, necessitating additional research to translate findings into clinical applications. This is a comprehensive state-of-the-art review aimed to explore contributing factors to the formation of RC lesions, particularly focusing on collagen degradation in root tissues by microbial collagenases.
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Affiliation(s)
- Cecília de Brito Barbosa
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, Brasil
| | - Isabela Monici Silva
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, Brasil
| | - Naile Dame-Teixeira
- Universidade de Brasília, Faculdade de Ciências da Saúde, Departamento de Odontologia, Brasília, Brasil
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4
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Streptococcus mutans Proteases Degrade Dentinal Collagen. Dent J (Basel) 2022; 10:dj10120223. [PMID: 36547039 PMCID: PMC9776523 DOI: 10.3390/dj10120223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Here, we explored the role of S. mutans’s whole cell and discrete fractions in the degradation of type I collagen and dentinal collagen. Type I collagen gels and human demineralized dentin slabs (DS) were incubated in media alone or with one of the following: overnight (O/N) or newly inoculated (NEW) cultures of S. mutans UA159; intracellular proteins, supernatant or bacterial membranes of O/N cultures. Media from all groups were analyzed for protease-mediated release of the collagen-specific imino acid hydroxyproline. Images of type I collagen and DS were analyzed, respectively. Type I collagen degradation was highest for the supernatant (p < 0.05) fractions, followed by intracellular components and O/N cultures. Collagen degradation for DS samples was highest for O/N samples, followed by supernatant, and intracellular components (p < 0.05). There was lower detectable degradation for both type I collagen and DS from NEW culture samples (p < 0.05), and there was no type I collagen or DS degradation detected for bacterial membrane samples. Structural changes to type I collagen gel and dentinal collagen were observed, respectively, following incubation with S. mutans cultures (O/N and NEW), intracellular components, and supernatant. This study demonstrates that intracellular and extracellular proteolytic activities from S. mutans enable this cariogenic bacterium to degrade type I and dentinal collagen in a growth-phase dependent manner, potentially contributing to the progression of dental caries.
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5
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Salmonella Typhimurium U32 peptidase, YdcP, promotes bacterial survival by conferring protection against in vitro and in vivo oxidative stress. Microb Pathog 2022; 173:105862. [PMID: 36402347 DOI: 10.1016/j.micpath.2022.105862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022]
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6
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Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche. NPJ Biofilms Microbiomes 2022; 8:8. [PMID: 35190575 PMCID: PMC8861167 DOI: 10.1038/s41522-022-00270-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 12/14/2022] Open
Abstract
Porphyromonas asaccharolytica and Porphyromonas uenonis are common inhabitants of the vaginal microbiome, but their presence has been linked to adverse health outcomes for women, including bacterial vaginosis and preterm birth. However, little is known about the pathogenesis mechanisms of these bacteria. The related oral opportunistic pathogen, Porphyromonas gingivalis, is comparatively well-studied and known to secrete numerous extracellular matrix-targeting proteases. Among these are the gingipain family of cysteine proteases that drive periodontal disease progression and hematogenic transmission to the placenta. In this study, we demonstrate that vaginal Porphyromonas species secrete broad-acting proteases capable of freely diffusing within the cervicovaginal niche. These proteases degrade collagens that are enriched within the cervix (type I) and chorioamniotic membranes (type IV), as well as fibrinogen, which inhibits clot formation. Bioinformatic queries confirmed the absence of gingipain orthologs and identified five serine, cysteine, and metalloprotease candidates in each species. Inhibition assays revealed that each species’ proteolytic activity can be partially attributed to a secreted metalloprotease with broad substrate specificity that is distantly related to the P. gingivalis endopeptidase PepO. This characterization of virulence activities in vaginal Porphyromonas species highlights their potential to alter the homeostasis of reproductive tissues and harm human pregnancy through clotting disruption, fetal membrane weakening, and premature cervical remodeling.
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Candidates for Repurposing as Anti-Virulence Agents Based on the Structural Profile Analysis of Microbial Collagenase Inhibitors. Pharmaceutics 2021; 14:pharmaceutics14010062. [PMID: 35056958 PMCID: PMC8780423 DOI: 10.3390/pharmaceutics14010062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/26/2021] [Indexed: 01/17/2023] Open
Abstract
The pharmacological inhibition of the bacterial collagenases (BC) enzymes is considered a promising strategy to block the virulence of the bacteria without targeting the selection mechanism leading to drug resistance. The chemical structures of the Clostridium perfringens collagenase A (ColA) inhibitors were analyzed using Bemis-Murcko skeletons, Murcko frameworks, the type of plain rings, and docking studies. The inhibitors were classified based on their structural architecture and various scoring methods were implemented to predict the probability of new compounds to inhibit ColA and other BC. The analyses indicated that all compounds contain at least one aromatic ring, which is often a nitrobenzene fragment. 2-Nitrobenzene based compounds are, on average, more potent BC inhibitors compared to those derived from 4-nitrobenzene. The molecular descriptors MDEO-11, AATS0s, ASP-0, and MAXDN were determined as filters to identify new BC inhibitors and highlighted the necessity for a compound to contain at least three primary oxygen atoms. The DrugBank database was virtually screened using the developed methods. A total of 100 compounds were identified as potential BC inhibitors, of which, 10 are human approved drugs. Benzthiazide, entacapone, and lodoxamide were chosen as the best candidates for in vitro testing based on their pharmaco-toxicological profile.
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8
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Ning Y, Yang H, Weng P, Wu Z. Zymogram Analysis and Identification of the Extracellular Proteases from Bacillus velezensis SW5. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Maturation process and characterization of a novel thermostable and halotolerant subtilisin-like protease with high collagenolytic but low gelatinolytic activity. Appl Environ Microbiol 2021; 88:e0218421. [DOI: 10.1128/aem.02184-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymatic degradation of collagen is of great industrial and environmental significance; however, little is known about thermophile-derived collagenolytic proteases. Here, we report a novel collagenolytic protease (TSS) from thermophilic
Brevibacillus
sp. WF146. The TSS precursor comprises a signal peptide, an N-terminal propeptide, a subtilisin-like catalytic domain, a β-jelly roll (βJR) domain, and a prepeptidase C-terminal (PPC) domain. The maturation of TSS involves a stepwise autoprocessing of the N-terminal propeptide and the PPC domain, and the βJR rather than the PPC domain is necessary for correct folding of the enzyme. Purified mature TSS displayed optimal activity at 70°C and pH 9.0, a half-life of 1.5 h at 75°C, and an increased thermostability with rising salinity up to 4 M. TSS possesses an increased number of surface acidic residues and ion pairs, as well as four Ca
2+
-binding sites, which contribute to its high thermostability and halotolerance. At high temperatures, TSS exhibited high activity toward insoluble type I collagen and azocoll, but showed a low gelatinolytic activity, with a strong preference for Arg and Gly at the P1 and P1’ positions, respectively. Both the βJR and PPC domains could bind but not swell collagen, and thus facilitate TSS-mediated collagenolysis via improving the accessibility of the enzyme to the substrate. Additionally, TSS has the ability to efficiently degrade fish scale collagen at high temperatures.
IMPORTANCE
Proteolytic degradation of collagen at high temperatures has the advantages of increasing degradation efficiency and minimizing the risk of microbial contamination. Reports on thermostable collagenolytic proteases are limited, and their maturation and catalytic mechanisms remain to be elucidated. Our results demonstrate that the thermophile-derived TSS matures in an autocatalytic manner, and represents one of the most thermostable collagenolytic proteases reported so far. At elevated temperatures, TSS prefers hydrolyzing insoluble heat-denatured collagen rather than gelatin, providing new insight into the mechanism of collagen degradation by thermostable collagenolytic proteases. Moreover, TSS has the potential to be used in recycling collagen-rich wastes such as fish scales.
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10
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Reed CJ, Hutinet G, de Crécy-Lagard V. Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. Biomolecules 2021; 11:1282. [PMID: 34572495 PMCID: PMC8469502 DOI: 10.3390/biom11091282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Members of the DUF34 (domain of unknown function 34) family, also known as the NIF3 protein superfamily, are ubiquitous across superkingdoms. Proteins of this family have been widely annotated as "GTP cyclohydrolase I type 2" through electronic propagation based on one study. Here, the annotation status of this protein family was examined through a comprehensive literature review and integrative bioinformatic analyses that revealed varied pleiotropic associations and phenotypes. This analysis combined with functional complementation studies strongly challenges the current annotation and suggests that DUF34 family members may serve as metal ion insertases, chaperones, or metallocofactor maturases. This general molecular function could explain how DUF34 subgroups participate in highly diversified pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.
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Affiliation(s)
- Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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11
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Kin LX, Butler CA, Slakeski N, Hoffmann B, Dashper SG, Reynolds EC. Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola. J Oral Microbiol 2020; 12:1808750. [PMID: 32944158 PMCID: PMC7482830 DOI: 10.1080/20002297.2020.1808750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Porphyromonas gingivalis and Treponema denticola are proteolytic periodontopathogens that co-localize in polymicrobial subgingival plaque biofilms, display in vitro growth symbiosis and synergistic virulence in animal models of disease. These symbioses are underpinned by a range of metabolic interactions including cooperative hydrolysis of glycine-containing peptides to produce free glycine, which T. denticola uses as a major energy and carbon source. Objective To characterize the P. gingivalis gene products essential for these interactions. Methods: The P. gingivalis transcriptome exposed to cell-free T. denticola conditioned medium was determined using RNA-seq. P. gingivalis proteases potentially involved in hydrolysis of glycine-containing peptides were identified using a bioinformatics approach. Results One hundred and thirty-twogenes displayed differential expression, with the pattern of gene expression consistent with succinate cross-feeding from T. denticola to P. gingivalis and metabolic shifts in the P. gingivalis folate-mediated one carbon superpathway. Interestingly, no P. gingivalis proteases were significantly up-regulated. Three P. gingivalis proteases were identified as candidates and inactivated to determine their role in the release of free glycine. P. gingivalis PG0753 and PG1788 but not PG1605 are involved in the hydrolysis of glycine-containing peptides, making free glycine available for T. denticola utilization. Conclusion Collectively these metabolic interactions help to partition resources and engage synergistic interactions between these two species.
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Affiliation(s)
- Lin Xin Kin
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Catherine A Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Nada Slakeski
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Brigitte Hoffmann
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Stuart G Dashper
- 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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12
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Evolutionary genetic analysis of unassigned peptidase clan-associated microbial virulence and pathogenesis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00529-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Mohanty R, Asopa SJ, Joseph MD, Singh B, Rajguru JP, Saidath K, Sharma U. Red complex: Polymicrobial conglomerate in oral flora: A review. J Family Med Prim Care 2019; 8:3480-3486. [PMID: 31803640 PMCID: PMC6881954 DOI: 10.4103/jfmpc.jfmpc_759_19] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/12/2019] [Accepted: 10/10/2019] [Indexed: 11/10/2022] Open
Abstract
Oral diseases are the complex host responses composed of a broad array of inflammatory cells, and cytokines, chemokines, and mediators derived from the cells resident in the gingival tissues, as well as from the emigrating inflammatory cells. A chronic polymicrobial challenge to the local host tissues triggers this response, which under certain circumstances, and in a subset of the population, leads to the progressing soft and hard tissue destruction that characterizes periodontitis. The red complex has been proposed as a pathogenic consortium, consisting of P. gingivalis, T. denticola, and T. forsythia. This review has attempted to examine the virulence potential and determinants of these commensal opportunists.
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Affiliation(s)
- Rinkee Mohanty
- Department of Periodontics, Institute of Dental Sciences, SOA Deemed to University, Bhubaneswar, Odisha, India
| | - Swati Joshi Asopa
- Department of Prosthodontics, Rajasthan Dental College and Hospital, Jaipur, Rajasthan, India
| | - M Derick Joseph
- Department of Conservative Dentistry and Endodontics, P.S.M Dental College and Research Centre, Akkikavu, Thrissur, Kerala, India
| | - Bhupender Singh
- Department of Oral Medicine and Radiology, Government Dental College Kottyam, Kerala, India
| | - Jagadish Prasad Rajguru
- Department of Oral and Maxillofacial Pathology, Hi-Tech Dental College and Hospital, Bhubaneswar, Odisha, India
| | - K Saidath
- Department of Orthodontics, A.B. Shetty Memorial Institute of Dental Sciences, Deralakatte, Mangalore, Karnataka, India
| | - Uma Sharma
- Department of Periodontics, BRS Dental College and Hospital, Haryana, India
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Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota. J Bacteriol 2019; 201:JB.00272-19. [PMID: 31405919 PMCID: PMC6779451 DOI: 10.1128/jb.00272-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/29/2019] [Indexed: 11/20/2022] Open
Abstract
This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected. The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings. Colonic spirochetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance, and only a few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. Of these individuals, 17 (2.3%) had colonic spirochetosis, which was associated with eosinophilic infiltration and a 3-fold-increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole-genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochetosis we successfully isolated, cultured, and performed whole-genome sequencing of in total 17 isolates, including the Brachyspira aalborgi type strain, 513A. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and nonspirochetosis controls. We found one isolate to be of the species Brachyspira pilosicoli; all remaining isolates were of the species Brachyspira aalborgi. Besides displaying extensive genetic heterogeneity, the isolates harbored several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies failed to detect Brachyspira due to primer incompatibility. IMPORTANCE This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected. The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.
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15
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Shekhter AB, Balakireva AV, Kuznetsova NV, Vukolova MN, Litvitsky PF, Zamyatnin AA. Collagenolytic Enzymes and their Applications in Biomedicine. Curr Med Chem 2019; 26:487-505. [PMID: 28990520 DOI: 10.2174/0929867324666171006124236] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/24/2017] [Accepted: 09/26/2017] [Indexed: 01/31/2023]
Abstract
Nowadays, enzymatic therapy is a very promising line of treatment for many different diseases. There is a group of disorders and conditions, caused by fibrotic and scar processes and associated with the excessive accumulation of collagen that needs to be catabolized to normalize the connective tissue content. The human body normally synthesizes special extracellular enzymes, matrix metalloproteases (MMPs) by itself. These enzymes can cleave components of extracellular matrix (ECM) and different types of collagen and thus maintain the balance of the connective tissue components. MMPs are multifunctional enzymes and are involved in a variety of organism processes. However, under pathological conditions, the function of MMPs is not sufficient, and these enzymes fail to deal with disease. Thus, medical intervention is required. Enzymatic therapy is a very effective way of treating such collagen-associated conditions. It involves the application of exogenous collagenolytic enzymes that catabolize excessive collagen at the affected site and lead to the successful elimination of disease. Such collagenolytic enzymes are synthesized by many organisms: bacteria, animals (especially marine organisms), plants and fungi. The most studied and commercially available are collagenases from Clostridium histolyticum and from the pancreas of the crab Paralithodes camtschatica, due to their ability to effectively hydrolyse human collagen without affecting other tissues, and their wide pH ranges of collagenolytic activity. In the present review, we summarize not only the data concerning existing collagenase-based medications and their applications in different collagen-related diseases and conditions, but we also propose collagenases from different sources for their potential application in enzymatic therapy.
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Affiliation(s)
- Anatoly B Shekhter
- Sechenov First Moscow State Medical University, Institute for Regenerative Medicine, Trubetskaya Str. 8, Moscow, 119991, Russian Federation
| | - Anastasia V Balakireva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya Str. 8, Moscow, 119991, Russian Federation
| | - Natalia V Kuznetsova
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya Str. 8, Moscow, 119991, Russian Federation
| | - Marina N Vukolova
- Sechenov First Moscow State Medical University, Department of Pathophysiology, Trubetskaya Str. 8, Moscow, 119991, Russian Federation
| | - Petr F Litvitsky
- Sechenov First Moscow State Medical University, Department of Pathophysiology, Trubetskaya Str. 8, Moscow, 119991, Russian Federation
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya Str. 8, Moscow, 119991, Russian Federation.,Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russian Federation
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16
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Sánchez MC, Romero-Lastra P, Ribeiro-Vidal H, Llama-Palacios A, Figuero E, Herrera D, Sanz M. Comparative gene expression analysis of planktonic Porphyromonas gingivalis ATCC 33277 in the presence of a growing biofilm versus planktonic cells. BMC Microbiol 2019; 19:58. [PMID: 30866810 PMCID: PMC6417203 DOI: 10.1186/s12866-019-1423-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/19/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis, a microorganism residing in the oral cavity within complex multispecies biofilms, is one of the keystone pathogens in the onset and progression of periodontitis. In this in vitro study, using DNA microarray, we investigate the differential gene expression of Porphyromonas gingivalis ATCC 33277 when growing in the presence or in absence of its own monospecies biofilm. RESULTS Approximately 1.5% of genes (28 out of 1909 genes, at 1.5 fold change or more, p-value < 0.05) were differentially expressed by P. gingivalis cells when in the presence of a biofilm. These genes were predominantly related to the metabolism of iron, bacterial adhesion, invasion, virulence and quorum-sensing system. The results from microarrays were consistent with those obtained by RT-qPCR. CONCLUSION This study provides insight on the transcriptional changes of planktonic P. gingivalis cells when growing in the presence of a biofilm. The resulting phenotypes provide information on changes occurring in the gene expression of this pathogen.
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Affiliation(s)
- María C. Sánchez
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | | | - Honorato Ribeiro-Vidal
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Arancha Llama-Palacios
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Elena Figuero
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - David Herrera
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Mariano Sanz
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
- Department of Dental Clinical Specialities (DDCS), Faculty of Odontology, Plaza Ramón y Cajal s/n Ciudad Universitaria, 28040 Madrid, Spain
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17
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Bhattacharya S, Bhattacharya S, Gachhui R, Hazra S, Mukherjee J. U32 collagenase from Pseudoalteromonas agarivorans NW4327: Activity, structure, substrate interactions and molecular dynamics simulations. Int J Biol Macromol 2019; 124:635-650. [DOI: 10.1016/j.ijbiomac.2018.11.206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 11/30/2022]
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18
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19
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Bakermans C. Adaptations to marine versus terrestrial low temperature environments as revealed by comparative genomic analyses of the genus Psychrobacter. FEMS Microbiol Ecol 2018; 94:5032373. [DOI: 10.1093/femsec/fiy102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/27/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Corien Bakermans
- Division of Mathematics and Natural Sciences, Penn State Altoona, United States
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20
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Damé-Teixeira N, Parolo CCF, Maltz M, Rup AG, Devine DA, Do T. Gene expression of bacterial collagenolytic proteases in root caries. J Oral Microbiol 2018; 10:1424475. [PMID: 34394852 PMCID: PMC5774410 DOI: 10.1080/20002297.2018.1424475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2018] [Indexed: 01/22/2023] Open
Abstract
Objective: It is unknown whether bacteria play a role in the collagen matrix degradation that occurs during caries progression. Our aim was to characterize the expression level of genes involved in bacterial collagenolytic proteases in root biofilms with and without caries. Method: we collected samples from active cavitated root caries lesions (RC, n = 30) and from sound root surfaces (SRS, n = 10). Total microbial RNA was isolated and cDNA sequenced on the Illumina Hi-Seq2500. Reads were mapped to 162 oral bacterial reference genomes. Genes encoding putative bacterial collagenolytic proteases were identified. Normalization and differential expression analysis was performed on all metatranscriptomes (FDR<10-3). Result: Genes encoding collagenases were identified in 113 bacterial species the majority were peptidase U32. In RC, Streptococcus mutans and Veillonella parvula expressed the most collagenases. Organisms that overexpressed collagenolytic protease genes in RC (Log2FoldChange>8) but none in SRS were Pseudoramibacter alactolyticus [HMPREF0721_RS02020; HMPREF0721_RS04640], Scardovia inopinata [SCIP_RS02440] and Olsenella uli DSM7084 [OLSU_RS02990]. Conclusion: Our findings suggest that the U32 proteases may be related to carious dentine. The contribution of a small number of species to dentine degradation should be further investigated. These proteases may have potential in future biotechnological and medical applications, serving as targets for the development of therapeutic agents.
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Affiliation(s)
- Nailê Damé-Teixeira
- Faculty of Health Science, Department of Dentistry, University of Brasilia, Brasilia, Brazil
| | | | - Marisa Maltz
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ariel Goulart Rup
- Faculty of Dentistry, Department of Social and Preventive Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Deirdre Ann Devine
- School of Dentistry, Division of Oral Biology, University of Leeds, Leeds, United Kingdom
| | - Thuy Do
- School of Dentistry, Division of Oral Biology, University of Leeds, Leeds, United Kingdom
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21
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Kimura S, Sakai Y, Ishiguro K, Suzuki T. Biogenesis and iron-dependency of ribosomal RNA hydroxylation. Nucleic Acids Res 2018; 45:12974-12986. [PMID: 29069499 PMCID: PMC5727448 DOI: 10.1093/nar/gkx969] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Post-transcriptional modifications of ribosomal RNAs (rRNAs) are involved in ribosome biogenesis and fine-tuning of translation. 5-Hydroxycytidine (ho5C), a modification of unknown biogenesis and function, is present at position 2501 of Escherichia coli 23S rRNA. We conducted a genome-wide screen in E. coli to identify genes required for ho5C2501 formation, and found a previously-uncharacterized gene, ydcP (renamed rlhA), iron-sulfur cluster (isc) genes, and a series of genes responsible for prephenate biosynthesis, indicating that iron-sulfur clusters and prephenate are required for ho5C2501 formation. RlhA interacted with precursors of the 50S ribosomal subunit, suggesting that this protein is directly involved in formation of ho5C2501. RlhA belongs to a family of enzymes with an uncharacterized peptidase U32 motif and conserved Cys residues in the C-terminal region. These elements were essential for ho5C2501 formation. We also found that the frequency of ho5C2501 is modulated by environmental iron concentration. Together, our results reveal a novel biosynthetic pathway for RNA hydroxylation and its response to iron.
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Affiliation(s)
- Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yusuke Sakai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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22
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do Nascimento Silva A, de Avila ED, Nakano V, Avila-Campos MJ. Pathogenicity and genetic profile of oral Porphyromonas species from canine periodontitis. Arch Oral Biol 2017; 83:20-24. [PMID: 28692827 DOI: 10.1016/j.archoralbio.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVE In this study, the presence of the prtC and fimA genes involved in the pathogenicity of oral Porphyromonas spp. isolated from dogs with periodontitis and healthy, as well as their genetic diversity was investigated. DESIGN Thirty-two Beagle dogs, 24 with periodontitis and 8 healthy were evaluated. Subgingival samples from only one gingival site of both groups were collected. Bacteria grown in anaerobiosis were identified by RAPID ID 32A kits. From each strain the respective DNA was obtained and used to genotyping by conventional PCR and AP-PCR. RESULTS Dogs with periodontitis harbored 28 P. gulae, 2 P. creviocaricanis, 1 P. cangingivalis and 7 P. macacae; and from healthy dogs, 11 P. gulae and 5 P. circumdentaria. In P. gulae isolated from periodontal dogs the gene prtC was observed in 19 (67.85%) and in 7 (63.63%) from healthy dogs. P. gulae strains from periodontal dogs harbored either the gene fimA I or fimA II; while strains from healthy dogs harbored the gene fimA I, fimA II, fimA III or fimA IV, as well as 1 P. circumdentaria the gene fimA II. By AP-PCR strains were grouped in different clusters suggesting heterogeneity of these microorganisms. CONCLUSIONS The results presented herein inform that Porphyromonas spp. isolated from dogs with and without periodontitis harbored the prtC and fimA genes and it could be a role in the establishment of the infectious process.
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Affiliation(s)
- Amanda do Nascimento Silva
- Anaerobe Laboratory, Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo - USP, Sao Paulo, SP, Brazil
| | - Erica Dorigatti de Avila
- Department of Dental Materials and Prosthodontics, School of Dentistry of Araraquara, Univ Estadual Paulista - UNESP, Araraquara, SP, Brazil
| | - Viviane Nakano
- Anaerobe Laboratory, Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo - USP, Sao Paulo, SP, Brazil
| | - Mario J Avila-Campos
- Anaerobe Laboratory, Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo - USP, Sao Paulo, SP, Brazil.
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23
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Rodriguez Herrero E, Boon N, Pauwels M, Bernaerts K, Slomka V, Quirynen M, Teughels W. Necrotrophic growth of periodontopathogens is a novel virulence factor in oral biofilms. Sci Rep 2017; 7:1107. [PMID: 28439126 PMCID: PMC5430626 DOI: 10.1038/s41598-017-01239-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/28/2017] [Indexed: 01/05/2023] Open
Abstract
The oral use of antimicrobial agents embedded in toothpastes and mouth rinses results in an oral microbial massacre with high amounts of dead bacteria in close proximity to few surviving bacteria. It was hypothesized that this provides the surviving pathogenic bacteria a large amount of dead microbial biomass as a nutritional source for growth (necrotrophy). This study demonstrated the necrotrophic growth of periodontal pathogens in the presence of different dead oral species. In addition, the presence of dead bacteria resulted in an outgrowth of several periodontal pathogens in complex multi-species biofilms. Additionally, upon contact with dead oral bacteria, virulence genes of P. intermedia and P. gingivalis were up-regulated (necrovirulence). This resulted in a more pronounced epithelial cytotoxicity (necrotoxicity). These findings indicate that presence of dead bacteria induce necrotrophy, necrovirulence and necrotoxicity in several oral pathogens.
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Affiliation(s)
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure links 653, 9000, Gent, Belgium
| | - Martine Pauwels
- Department of Oral Health Sciences, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety, Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven Chem&Tech, Celestijnenlaan 200F (bus 2424), 3001, Leuven, Belgium
| | - Vera Slomka
- Department of Oral Health Sciences, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium
| | - Marc Quirynen
- Department of Oral Health Sciences, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium.,Dentistry, University Hospitals Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium
| | - Wim Teughels
- Department of Oral Health Sciences, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium. .,Dentistry, University Hospitals Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium.
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24
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Functional study of gene hp0169 in Helicobacter pylori pathogenesis. Microb Pathog 2017; 104:225-231. [PMID: 28131950 DOI: 10.1016/j.micpath.2017.01.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 12/15/2022]
Abstract
Many virulence genes have been reported to play important roles in Helicobacter pylori pathogenesis. However the detailed mechanisms of many of them have not been completely clear. In this study, we found gene hp0169, encoding a putative collagenase (HpPrtC), was involved in pathogenesis of H. pylori. Recombinant HpPrtC shows activities to both native and heat-denatured collagens. This result indicated that HpPrtC may act as a virulence factor to help the bacterium colonize in their host stomach by degrading surrounding collagens. hp0169 was deleted by homologous recombination to study its function in bacterium-host cell interaction. For the pathogenic functions on the host cells, the hp0169 mutant exhibits no significant changes on inducing apoptosis of GES-1 cells. However, the viability and proliferation rate of GES-1 cells infected with mutant strain were higher than the cells infected with wild-type strain. These results indicated that except for its collagenolytic activity, HpPrtC might participate in H. pylori pathogenesis through an additional pathway. Functional studies on hp0169 involved in pathogenesis would shed light on deep understanding of the pathogenic mechanism of H. pylori.
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25
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Chioma O, Aruni AW, Milford TA, Fletcher HM. Filifactor alocis collagenase can modulate apoptosis of normal oral keratinocytes. Mol Oral Microbiol 2016; 32:166-177. [PMID: 27149930 DOI: 10.1111/omi.12163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2016] [Indexed: 12/22/2022]
Abstract
To successfully colonize host cells, pathogenic bacteria must circumvent the host's structural barrier such as the collagen-rich extracellular matrix (ECM), as a preliminary step to invasion and colonization of the periodontal tissue. Filifactor alocis possesses a putative Peptidase U32 family protein (HMPREF0389_00504) with collagenase activity that may play a significant role in colonization of host tissue during periodontitis by breaking down collagen into peptides and disruption of the host cell. Domain architecture of the HMPREF0389_00504 protein predicted the presence of a characteristic PrtC-like collagenase domain, and a peptidase domain. Our study demonstrated that the recombinant F. alocis peptidase U32 protein (designated PrtFAC) can interact with, and degrade, type I collagen, heat-denatured collagen and gelatin in a calcium-dependent manner. PrtFAC decreased viability and induced apoptosis of normal oral keratinocytes (NOKs) in a time and dose-dependent manner. Transcriptome analysis of NOK cells treated with PrtFAC showed an upregulation of the genes encoding human pro-apoptotic proteins: Apoptotic peptidase activating factor 1 (Apaf1) cytochrome C, as well as caspase 3 and caspase 9, suggesting the involvement of the mitochondrial apoptotic pathway. There was a significant increase in caspase 3/7 activity in NOK cells treated with PrtFAC. Taken together, these findings suggest that F. alocis PrtFAC protein may play a role in the virulence and pathogenesis of F. alocis.
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Affiliation(s)
- O Chioma
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - A W Aruni
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - T-A Milford
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - H M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Institute of Oral Biology, Kyung Hee University, Seoul, Korea
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26
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Schönauer E, Brandstetter H. Inhibition and Activity Regulation of Bacterial Collagenases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Bhagwat PK, Jhample SB, Jalkute CB, Dandge PB. Purification, properties and application of a collagenolytic protease produced by Pseudomonas sp. SUK. RSC Adv 2016. [DOI: 10.1039/c6ra08157f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Purified collagenolytic protease produced byPseudomonassp. SUK, its biophysical characterization and applicatory study.
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Affiliation(s)
| | | | | | - Padma B. Dandge
- Department of Biochemistry
- Shivaji University
- Kolhapur 416004
- India
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28
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Schacherl M, Montada AAM, Brunstein E, Baumann U. The first crystal structure of the peptidase domain of the U32 peptidase family. ACTA ACUST UNITED AC 2015; 71:2505-12. [PMID: 26627657 DOI: 10.1107/s1399004715019549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022]
Abstract
The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (βα)8 TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to a Strep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.
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Affiliation(s)
- Magdalena Schacherl
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany
| | - Angelika A M Montada
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany
| | - Elena Brunstein
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany
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29
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Jurczak A, Kościelniak D, Papież M, Vyhouskaya P, Krzyściak W. A study on β-defensin-2 and histatin-5 as a diagnostic marker of early childhood caries progression. Biol Res 2015; 48:61. [PMID: 26520150 PMCID: PMC4628373 DOI: 10.1186/s40659-015-0050-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recently, a continuous growth of interest has been observed in antimicrobial peptides (AMPs) in the light of an alarming increase in resistance of bacteria and fungi against antibiotics. AMPs are used as biomarkers in diagnosis and monitoring of oral cavity pathologies. Therefore, the determination of specific protein profiles in children diagnosed with early childhood caries (ECC) might be a basis for effective screening tests and specialized examinations which may enable progression of disease. Methods The objective of the studies was to determine the role of histatin-5 and β-defensing-2 as a diagnostic marker of early childhood caries progression. In this work, results of concentration determination of two salivary proteins (histatin-5 and β-defensin-2) were presented. In addition, bacterial profiles from dental plaque in various stages of ECC and control were marked. The assessment of alteration in the concentration of these two proteins in a study group of children with various stages of ECC and a control group consisting of children with no symptoms was performed by enzyme-linked immunosorbent assays. Results The statistical analysis showed a significant increase in the concentration of histatin-5 and β-defensin-2 in the study group compared to the control group and correlated with the progression of the disease. Conclusions The confirmation of concentration changes in these proteins during the progression of dental caries may discover valuable disease progression biomarkers.
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Affiliation(s)
- Anna Jurczak
- Department of Pediatric Dentistry, Institute of Dentistry, Jagiellonian University, Medical College, Krakow, Poland.
| | - Dorota Kościelniak
- Department of Pediatric Dentistry, Institute of Dentistry, Jagiellonian University, Medical College, Krakow, Poland.
| | - Monika Papież
- Department of Cytobiology, Pharmacy Faculty, Jagiellonian University, Medical College, Krakow, Poland.
| | - Palina Vyhouskaya
- Department of Medical Diagnostics, Pharmacy Faculty, Jagiellonian University, Medical College, 9 Medyczna St., 30-688, Krakow, Poland.
| | - Wirginia Krzyściak
- Department of Medical Diagnostics, Pharmacy Faculty, Jagiellonian University, Medical College, 9 Medyczna St., 30-688, Krakow, Poland.
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30
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Zhang XX, Li Y, Wang SY, Wang YY, Du KL, Xu JY, Lei LS, Feng X, Liang XY, Ruan HH. Identification of a collagenase produced by Bacillus cereus R75E isolated from human colostrum. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s000368381505018x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases. Appl Environ Microbiol 2015; 81:6098-107. [PMID: 26150451 DOI: 10.1128/aem.00883-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacterial collagenolytic proteases are important because of their essential role in global collagen degradation and because of their virulence in some human bacterial infections. Bacterial collagenolytic proteases include some metalloproteases of the M9 family from Clostridium or Vibrio strains, some serine proteases distributed in the S1, S8, and S53 families, and members of the U32 family. In recent years, there has been remarkable progress in discovering new bacterial collagenolytic proteases and in investigating the collagen-degrading mechanisms of bacterial collagenolytic proteases. This review provides comprehensive insight into bacterial collagenolytic proteases, especially focusing on the structures and collagen-degrading mechanisms of representative bacterial collagenolytic proteases in each family. The roles of bacterial collagenolytic proteases in human diseases and global nitrogen cycling, together with the biotechnological and medical applications for these proteases, are also briefly discussed.
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32
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Navais R, Méndez J, Pérez-Pascual D, Cascales D, Guijarro JA. The yrpAB operon of Yersinia ruckeri encoding two putative U32 peptidases is involved in virulence and induced under microaerobic conditions. Virulence 2014; 5:619-24. [PMID: 24865652 DOI: 10.4161/viru.29363] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In an attempt to dissect the virulence mechanisms of Yersinia ruckeri two adjacent genes, yrpA and yrpB, encoding putative peptidases belonging to the U32 family, were analyzed. Similar genes, with the same genetic organization were identified in genomic analysis of human-pathogenic yersiniae. RT-PCR studies indicated that these genes form an operon in Y. ruckeri. Transcriptional studies using an yrpB::lacZY fusion showed high levels of expression of these genes in the presence of peptone in the culture medium, as well as under oxygen-limited conditions. These two factors had a synergic effect on gene induction when both were present simultaneously during bacterial incubation, which indicates the important role that environmental conditions in the fish gut can play in the regulation of specific genes. LD 50 experiments using an yrpA insertional mutant strain demonstrated the participation of this gene in the virulence of Y. ruckeri.
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Affiliation(s)
- Roberto Navais
- Área de Microbiología; Departamento de Biología Funcional; Facultad de Medicina; IUBA; Universidad de Oviedo; Oviedo, Spain
| | - Jessica Méndez
- Área de Microbiología; Departamento de Biología Funcional; Facultad de Medicina; IUBA; Universidad de Oviedo; Oviedo, Spain
| | - David Pérez-Pascual
- Área de Microbiología; Departamento de Biología Funcional; Facultad de Medicina; IUBA; Universidad de Oviedo; Oviedo, Spain
| | - Desirée Cascales
- Área de Microbiología; Departamento de Biología Funcional; Facultad de Medicina; IUBA; Universidad de Oviedo; Oviedo, Spain
| | - José A Guijarro
- Área de Microbiología; Departamento de Biología Funcional; Facultad de Medicina; IUBA; Universidad de Oviedo; Oviedo, Spain
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33
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Belibasakis G, Thurnheer T, Bostanci N. Porphyromonas gingivalis: a heartful oral pathogen? Virulence 2014; 5:463-4. [PMID: 24759693 PMCID: PMC4063808 DOI: 10.4161/viru.28930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Georgios Belibasakis
- Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich, Switzerland
| | - Thomas Thurnheer
- Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich, Switzerland
| | - Nagihan Bostanci
- Oral Translational Research; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich, Switzerland
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Abstract
Bacterial collagenases are metalloproteinases involved in the degradation of the extracellular matrices of animal cells, due to their ability to digest native collagen. These enzymes are important virulence factors in a variety of pathogenic bacteria. Nonetheless, there is a lack of scientific consensus for a proper and well-defined classification of these enzymes and a vast controversy regarding the correct identification of collagenases. Clostridial collagenases were the first ones to be identified and characterized and are the reference enzymes for comparison of newly discovered collagenolytic enzymes. In this review we present the most recent data regarding bacterial collagenases and overview the functional and structural diversity of bacterial collagenases. An overall picture of the molecular diversity and distribution of these proteins in nature will also be given. Particular aspects of the different proteolytic activities will be contextualized within relevant areas of application, mainly biotechnological processes and therapeutic uses. At last, we will present a new classification guide for bacterial collagenases that will allow the correct and straightforward classification of these enzymes.
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Affiliation(s)
- Ana Sofia Duarte
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Antonio Correia
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Ana Cristina Esteves
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
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Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep 2013; 3:1843. [PMID: 23673380 PMCID: PMC3654486 DOI: 10.1038/srep01843] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/01/2013] [Indexed: 11/09/2022] Open
Abstract
Although attempts have been made to reveal the relationships between bacteria and human health, little is known about the species and function of the microbial community associated with oral diseases. In this study, we report the sequencing of 16 metagenomic samples collected from dental swabs and plaques representing four periodontal states. Insights into the microbial community structure and the metabolic variation associated with periodontal health and disease were obtained. We observed a strong correlation between community structure and disease status, and described a core disease-associated community. A number of functional genes and metabolic pathways including bacterial chemotaxis and glycan biosynthesis were over-represented in the microbiomes of periodontal disease. A significant amount of novel species and genes were identified in the metagenomic assemblies. Our study enriches the understanding of the oral microbiome and sheds light on the contribution of microorganisms to the formation and succession of dental plaques and oral diseases.
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Affiliation(s)
- Jinfeng Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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36
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Rawlings ND. Identification and prioritization of novel uncharacterized peptidases for biochemical characterization. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat022. [PMID: 23584835 PMCID: PMC3625958 DOI: 10.1093/database/bat022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genome sequencing projects are generating enormous amounts of biological data that require analysis, which in turn identifies genes and proteins that require characterization. Enzymes that act on proteins are especially difficult to characterize because of the time required to distinguish one from another. This is particularly true of peptidases, the enzymes that activate, inactivate and degrade proteins. This article aims to identify clusters of sequences each of which represents the species variants of a single putative peptidase that is widely distributed and is thus merits biochemical characterization. The MEROPS database maintains large collections of sequences, references, substrate cleavage positions and inhibitor interactions of peptidases and their homologues. MEROPS also maintains a hierarchical classification of peptidase homologues, in which sequences are clustered as species variants of a single peptidase; homologous sequences are assembled into a family; and families are clustered into a clan. For each family, an alignment and a phylogenetic tree are generated. By assigning an identifier to a peptidase that has been biochemically characterized from a particular species (called a holotype), the identifier can be automatically extended to sequences from other species that cluster with the holotype. This permits transference of annotation from the holotype to other members of the cluster. By extending this concept to all peptidase homologues (including those of unknown function that have not been characterized) from model organisms representing all the major divisions of cellular life, clusters of sequences representing putative peptidases can also be identified. The 42 most widely distributed of these putative peptidases have been identified and discussed here and are prioritized as ideal candidates for biochemical characterization. Database URL:http://merops.sanger.ac.uk
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Affiliation(s)
- Neil D Rawlings
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Yung PY, Kjelleberg S, Thomas T. A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica. FEMS Microbiol Lett 2011; 321:24-9. [PMID: 21569081 DOI: 10.1111/j.1574-6968.2011.02306.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Collagen is an important, extracellular structural protein for metazoans and provides a rich nutrient source for bacteria that possess collagen-degrading enzymes. In a symbiotic host system, collagen degradation could benefit the bacteria, but would be harmful for the eukaryotic host. Using a polyphasic approach, we investigated the presence of collagenolytic activity in the bacterial community hosted by the marine sponge Cymbastela concentrica. Functional screening for collagenase activity using metagenomic library clones (227 Mbp) and cultured isolates of sponge's bacterial community, as well as bioinformatic analysis of metagenomic shotgun-sequencing data (106,679 predicted genes) were used. The results show that the abundant members of the bacterial community contain very few genes encoding for collagenolytic enzymes, while some low-abundance sponge isolates possess collagenolytic activities. These findings indicate that collagen is not a preferred nutrient source for the majority of the members of the bacterial community associated with healthy C. concentrica, and that some low-abundance bacteria have collagenase activities that have the potential to harm the sponge through tissue degradation.
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Affiliation(s)
- Pui Yi Yung
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Lin FPY, Lan R, Sintchenko V, Gilbert GL, Kong F, Coiera E. Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae. PLoS One 2011; 6:e17964. [PMID: 21483735 PMCID: PMC3070697 DOI: 10.1371/journal.pone.0017964] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 02/21/2011] [Indexed: 12/30/2022] Open
Abstract
The phylogenetic profile of a gene is a reflection of its evolutionary history
and can be defined as the differential presence or absence of a gene in a set of
reference genomes. It has been employed to facilitate the prediction of gene
functions. However, the hypothesis that the application of this concept can also
facilitate the discovery of bacterial virulence factors has not been fully
examined. In this paper, we test this hypothesis and report a computational
pipeline designed to identify previously unknown bacterial virulence genes using
group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS
genes across 467 bacterial reference genomes were determined by
candidate-against-all BLAST searches,which were then used to identify candidate
virulence genes by machine learning models. Evaluation experiments with known
GBS virulence genes suggested good functional and model consistency in
cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively).
Inspection of the top-10 genes in each of the 15 virulence functional groups
revealed at least 15 (of 119) homologous genes implicated in virulence in other
human pathogens but previously unrecognized as potential virulence genes in GBS.
Among these highly-ranked genes, many encode hypothetical proteins with possible
roles in GBS virulence. Thus, our approach has led to the identification of a
set of genes potentially affecting the virulence potential of GBS, which are
potential candidates for further in vitro and in
vivo investigations. This computational pipeline can also be
extended to in silico analysis of virulence determinants of
other bacterial pathogens.
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Affiliation(s)
- Frank Po-Yen Lin
- Centre for Health Informatics, University of New South Wales, Sydney, Australia.
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Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire. ISME JOURNAL 2011; 5:1471-83. [PMID: 21451583 DOI: 10.1038/ismej.2011.19] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vibrio coralliilyticus has been implicated as an important pathogen of coral species worldwide. In this study, the nearly complete genome of Vibrio coralliilyticus strain P1 (LMG23696) was sequenced and proteases implicated in virulence of the strain were specifically investigated. The genome sequence of P1 (5,513,256 bp in size) consisted of 5222 coding sequences and 58 RNA genes (53 tRNAs and at least 5 rRNAs). Seventeen metalloprotease and effector (vgrG, hlyA and hcp) genes were identified in the genome and expressed proteases were also detected in the secretome of P1. As the VcpA zinc-metalloprotease has been considered an important virulence factor of V. coralliilyticus, a vcpA deletion mutant was constructed to evaluate the effect of this gene in animal pathogenesis. Both wild-type and mutant (ΔvcpA) strains exhibited similar virulence characteristics that resulted in high mortality in Artemia and Drosophila pathogenicity bioassays and strong photosystem II inactivation of the coral dinoflagellate endosymbiont (Symbiodinium). In contrast, the ΔvcpA mutant demonstrated higher hemolytic activity and secreted 18 proteins not secreted by the wild type. These proteins included four types of metalloproteases, a chitinase, a hemolysin-related protein RbmC, the Hcp protein and 12 hypothetical proteins. Overall, the results of this study indicate that V. coralliilyticus strain P1 has a diverse virulence repertoire that possibly enables this bacterium to be an efficient animal pathogen.
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Kawase N, Kishi JI, Nakamura H, Hayakawa T. Collagenolytic activity in sonic extracts of Tannerella forsythia. Arch Oral Biol 2010; 55:545-9. [PMID: 20619781 DOI: 10.1016/j.archoralbio.2010.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 05/22/2010] [Accepted: 05/24/2010] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The purpose of the present study was to characterize the collagenolytic activity in a sonicated extract of Tannerella forsythia and to investigate the activation of proMMMP-2 and -9 by the T. forsythia extract. METHODS The T. forsythia extract was incubated with type I collagen. The cleaved products were then analyzed by SDS-PAGE using the method of Laemmli. We studied the effects of cysteine, DTT, CaCl(2), and various proteinase inhibitors on collagenolytic activity. A HT1080 cell culture supernatant containing proMMP-2 and -9 was incubated with the T. forsythia extract and analyzed for the activation of proMMP-2 and -9 by gelatin zymography. RESULTS The T. forsythia extract degraded type I collagen. Cysteine increased the collagenolytic activity of the extract, and 5mM CaCl(2) was required for this activity. The collagenolytic activity of T. forsythia was inhibited by N-ethylmaleimide, iodoacetamide, iodoacetic acid, EDTA, and leupeptin, but not by PMSF, E-64, TLCK, or TPCK. When proMMP-2 and -9 were incubated with the T. forsythia extract, gelatinases with the relative molecular masses of MMP-2 and -9 were produced. CONCLUSION The present study suggests that T. forsythia extract is able to degrade type I collagen and activate proMMP-2 and -9.
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Affiliation(s)
- Norio Kawase
- Department of Endodontics, Aichi-Gakuin University, Suemori-dori, Chikusa-ku, Nagoya, Japan
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41
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Anti-Porphyromonas gingivalis and anti-inflammatory activities of A-type cranberry proanthocyanidins. Antimicrob Agents Chemother 2010; 54:1778-84. [PMID: 20176905 DOI: 10.1128/aac.01432-09] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A-type cranberry proanthocyanidins (AC-PACs) have recently been reported to be beneficial for human health, especially urinary tract health. The effect of these proanthocyanidins on periodontitis, a destructive disease of tooth-supporting tissues, needs to be investigated. The purpose of this study was to investigate the effects of AC-PACs on various virulence determinants of Porphyromonas gingivalis as well as on the inflammatory response of oral epithelial cells stimulated by this periodontopathogen. We examined the effects of AC-PACs on P. gingivalis growth and biofilm formation, adherence to human oral epithelial cells and protein-coated surfaces, collagenase activity, and invasiveness. We also tested the ability of AC-PACs to modulate the P. gingivalis-induced inflammatory response by human oral epithelial cells. Our results showed that while AC-PACs neutralized all the virulence properties of P. gingivalis in a dose-dependent fashion, they did not interfere with growth. They also inhibited the secretion of interleukin-8 (IL-8) and chemokine (C-C motif) ligand 5 (CCL5) but did not affect the secretion of IL-6 by epithelial cells stimulated with P. gingivalis. This anti-inflammatory effect was associated with reduced activation of the nuclear factor-kappaB (NF-kappaB) p65 pathway. AC-PACs may be potentially valuable bioactive molecules for the development of new strategies to treat and prevent P. gingivalis-associated periodontal diseases.
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42
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Pathirana RD, O'Brien-Simpson NM, Reynolds EC. Host immune responses to Porphyromonas gingivalis antigens. Periodontol 2000 2010; 52:218-37. [DOI: 10.1111/j.1600-0757.2009.00330.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Jie Bao G, Kari K, Tervahartiala T, Sorsa T, Meurman JH. Proteolytic Activities of Oral Bacteria on ProMMP-9 and the Effect of Synthetic Proteinase Inhibitors. Open Dent J 2008; 2:96-102. [PMID: 19088890 PMCID: PMC2581524 DOI: 10.2174/1874210600802010096] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 12/14/2022] Open
Abstract
Tissue reactions to bacteria lead to proinflammatory reactions involving matrix metalloproteinases (MMPs). Synthetic protease inhibitors may offer new possibilities to regulate bacterial proteases. We investigated proteolytic activities of certain periodontal bacteria, their effects on the latent proMMP-9, and the effects of synthetic MMP inhibitors and a serine protease inhibitor Pefabloc. The strains studied were Porphyromonas gingivalis, Prevotella intermedia, Peptostreptoccus micros, Prevotella nigrescens, Fusobacterium nucleatum, and 5 Aggregatibacter actinomycetemcomitans serotypes. Their gelatinolytic activities and the effects of certain synthetic MMP inhibitors and Pefabloc were analyzed by zymography. Bacterial effects on proMMP-9 conversion were investigated by Western immunoblot. All investigated periodontal bacteria produced gelatinolytic cell-bound and extracellular proteinases which could fragment latent proMMP-9, suggesting co-operative processing cascades in oral tissue remodeling. A. actinomycetemcomitans produced the weakest gelatinolytic activity. Synthetic proteinase inhibitors exhibited slight but clear reductive effects on the bacterial proteolytic activities. We conclude that targeted anti-proteolytic treatment modalities against bacterial-host proteolytic cascades can be developed.
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Affiliation(s)
- Guang Jie Bao
- Stomatology School of North-West University for Nationalities, China
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Han HJ, Taki T, Kondo H, Hirono I, Aoki T. Pathogenic potential of a collagenase gene from Aeromonas veronii. Can J Microbiol 2008; 54:1-10. [PMID: 18388966 DOI: 10.1139/w07-109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of collagenase as a mechanism of bacterial pathogenicity in some pathogenic bacteria has been reported. The information on the role of collagenase in Aeromonas spp. pathogenesis is scant. In the present study, a mutant Aeromonas veronii RY001 that is deficient in the putative collagenase gene acg was constructed and compared with the wild-type strain for virulence factors. Bacterial cells and cell-free extracellular products of the mutant had significantly less collagenolytic activity, but there were not significant differences in caseinolytic, gelatinolytic, and elastolytic activities. Adhesion and invasion abilities of the mutant strain on epithelioma papillosum of carp cells was only 56% of that of the wild-type strain, and the cytotoxicity of the mutant strain to epithelioma papillosum of carp cells was only 42% of that of the wild-type strain. The LD50 values of the wild-type strain were determined as 1.6 x 10(6) and 3.5 x 10(5) cfu in goldfish and mice, respectively, whereas the mutant RY001 strain showed slightly higher values (i.e., 2.8 x 10(6) and 1.4 x 10(6) cfu in goldfish and mice, respectively). These results indicated the involvement of the collagenase gene in the pathogenesis of A. veronii.
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Affiliation(s)
- Hyun-Ja Han
- Laboratory of Genome Science, Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, 4-5-7, Minato, Tokyo 1088477, Japan
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Wu YM, Chen LL, Yan J, Zhuang CY, Gu ZY. Effect of Porphyromonas gingivalis PrtC on cytokine expression in ECV304 endothelial cells and its level in subgingival plaques from patients with chronic periodontitis. Acta Pharmacol Sin 2007; 28:1015-23. [PMID: 17588338 DOI: 10.1111/j.1745-7254.2007.00599.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
AIM To investigate the effect of the collagenase gene (prtC) product of Porphyromonas gingivalis on inducing host cells to secrete inflammatory cytokines, and to discuss the correlation between the PrtC level in subgingival plaque samples and clinical parameters. METHODS A prokaryotic expression system pET32a-prtC-Escheria coli BL21DE3 was constructed. Antigenicity and immunoreactivity of the recombinant PrtC protein (rPrtC) was identified by Western blotting. ELISA was applied to detect interleukin (IL)-1alpha, IL-8, and TNF-alpha levels in supernatants from rPrtC-induced human umbilical vein endothelial cells (HUVEC) originated ECV304 cells. Clinical parameters recorded at baseline and after treatment included bleeding on probing (BOP), probing depth (PD), and attachment loss (AL). ELISA was established to measure the PrtC level in 196 subgingival plaque samples from 49 patients with chronic periodontitis. RESULTS After coincubation with 1 microg/mL rPrtC for 24 h and with 5 or 10 microg/mL rPrtC for 12 h, the levels of IL-1 alpha, IL-8, and TNF-alpha secreted by the ECV304 cells increased significantly (P<0.05). The PrtC level in the BOP-positive or the > or =5 mm AL or > or = 6 mm PD sites was higher than that in the BOP-negative or the < or =2 mm AL or < or =6 mm PD sites (P<0.05), respectively. Compared with baseline, the PrtC levels in different AL sites or in the < or =6 mm PD pockets decreased remarkably after treatment (P<0.01), but in the BOP-positive or in the > 6 mm PD sites, the PrtC levels changed insignificantly (P>0.05). CONCLUSION rPrtC is able to directly induce host cells to synthesize and secrete IL-1 alpha, IL-8, and TNF-alpha. The PrtC level in subgingival samples is correlated with BOP, AL, and PD.
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Affiliation(s)
- Yan-min Wu
- Department of Stomatology, the Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, China.
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46
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Bodet C, Chandad F, Grenier D. Potentiel pathogénique de Porphyromonas gingivalis, Treponema denticola et Tannerella forsythia, le complexe bactérien rouge associé à la parodontite. ACTA ACUST UNITED AC 2007; 55:154-62. [PMID: 17049750 DOI: 10.1016/j.patbio.2006.07.045] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 07/28/2006] [Indexed: 11/30/2022]
Abstract
Periodontitis are mixed bacterial infections leading to destruction of tooth-supporting tissues, including periodontal ligament and alveolar bone. Among over 500 bacterial species living in the oral cavity, a bacterial complex named "red complex" and made of Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia has been strongly related to advanced periodontal lesions. While periodontopathogenic bacteria are the primary etiologic factor of periodontitis, tissue destruction essentially results from the host immune response to the bacterial challenge. Members of the red complex are Gram negative anaerobic bacteria expressing numerous virulence factors allowing bacteria to colonize the subgingival sites, to disturb the host defense system, to invade and destroy periodontal tissue as well as to promote the immunodestructive host response. This article reviews current knowledge of the pathogenic mechanisms of bacteria of the red complex leading to tissue and alveolar bone destruction observed during periodontitis.
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Affiliation(s)
- C Bodet
- Groupe de recherche en écologie buccale, faculté de médecine dentaire, université Laval, G1K 7P4 Québec, Québec, Canada
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Wu YM, Yan J, Chen LL, Gu ZY. Association between infection of different strains of Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans in subgingival plaque and clinical parameters in chronic periodontitis. J Zhejiang Univ Sci B 2007; 8:121-31. [PMID: 17266188 PMCID: PMC1791058 DOI: 10.1631/jzus.2007.b0121] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE The aim of this study was to investigate subgingival infection frequencies of Porphyromonas gingivalis and Actinobacillus actinomycetemcomitans strains with genetic variation in Chinese chronic periodontitis (CP) patients and to evaluate its correlation with clinical parameters. METHODS Two multiplex polymerase chain reaction (PCR) assays were developed to detect the 16SrDNA, collagenase (prtC) and fimbria (fimA) genes of P. gingivalis and the 16SrDNA, leukotoxin (lktA) and fimbria-associated protein (fap) genes of A. actinomycetemcomitans in 60 sulcus samples from 30 periodontal healthy subjects and in 122 subgingival plaque samples from 61 patients with CP. The PCR products were further T-A cloned and sent for nucleotide sequence analysis. RESULTS The 16SrDNA, prtC and fimA genes of P. gingivalis were detected in 92.6%, 85.2% and 80.3% of the subgingival plaque samples respectively, while the 16SrDNA, lktA and fap genes of A. actinomycetemcomitans were in 84.4%, 75.4% and 50.0% respectively. Nucleotide sequence analysis showed 98.62%~100% homology of the PCR products in these genes with the reported sequences. P. gingivalis strains with prtC+/fimA+ and A. actinomycetemcomitans with lktA+ were predominant in deep pockets (>6 mm) or in sites with attachment loss > or =5 mm than in shallow pockets (3~4 mm) or in sites with attachment loss < or =2 mm (P<0.05). P. gingivalis strains with prtC+/fimA+ also showed higher frequency in gingival index (GI)=3 than in GI=1 group (P<0.05). CONCLUSION Infection of P. gingivalis with prtC+/fimA+ and A. actinomycetemcomitans with lktA+ correlates with periodontal destruction of CP in Chinese. Nonetheless P. gingivalis fimA, prtC genes and A. actinomycetemcomitans lktA gene are closely associated with periodontal destruction, while A. actinomycetemcomitans fap gene is not.
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Affiliation(s)
- Yan-min Wu
- Department of Stomatology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Li-li Chen
- Department of Stomatology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- †E-mail:
| | - Zhi-yuan Gu
- Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Stomatology, School of Medicine, Zhejiang University, Hangzhou 310003, China
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Bodet C, Piché M, Chandad F, Grenier D. Inhibition of periodontopathogen-derived proteolytic enzymes by a high-molecular-weight fraction isolated from cranberry. J Antimicrob Chemother 2006; 57:685-90. [PMID: 16473919 DOI: 10.1093/jac/dkl031] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola are three major aetiological agents of chronic periodontitis. The strong proteolytic activities of these bacteria are critical to their survival since their energy source is obtained from peptides and amino acids derived from proteins. In addition, proteases are important factors contributing to periodontal tissue destruction by a variety of mechanisms, including direct tissue degradation and modulation of host inflammatory responses. OBJECTIVES The aim of this study was to investigate the effect of non-dialysable material (NDM) prepared from cranberry juice concentrate on the proteolytic activities of P. gingivalis, T. forsythia and T. denticola. METHODS The effect of NDM on gingipain and dipeptidyl peptidase IV (DPP IV) activities of P. gingivalis, trypsin-like activity of T. forsythia and chymotrypsin-like activity of T. denticola was evaluated using synthetic chromogenic peptides. In addition, the capacity of P. gingivalis to degrade fluorescein-labelled type I collagen and fluorescein-labelled transferrin in the presence of NDM was evaluated by fluorometry. RESULTS NDM dose-dependently inhibited the proteinases of P. gingivalis, T. forsythia and T. denticola as well as type I collagen and transferrin degradation by P. gingivalis. CONCLUSIONS These results suggest that NDM has the potential to reduce either the proliferation of P. gingivalis, T. forsythia and T. denticola in periodontal pockets or their proteinase-mediated destructive process occurring in periodontitis.
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Affiliation(s)
- Charles Bodet
- Groupe de Recherche en Ecologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, Canada
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49
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Holt SC, Ebersole JL. Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia: the "red complex", a prototype polybacterial pathogenic consortium in periodontitis. Periodontol 2000 2005; 38:72-122. [PMID: 15853938 DOI: 10.1111/j.1600-0757.2005.00113.x] [Citation(s) in RCA: 629] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Stanley C Holt
- Department of Periodontology, The Forsyth Institute, Boston, MA, USA
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50
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Petruzzelli R, Clementi ME, Marini S, Coletta M, Di Stasio E, Giardina B, Misiti F. Respiratory inhibition of isolated mammalian mitochondria by salivary antifungal peptide histatin-5. Biochem Biophys Res Commun 2003; 311:1034-40. [PMID: 14623286 DOI: 10.1016/j.bbrc.2003.10.104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Histatin-5 is a peptide secreted in the human saliva, which possesses powerful antifungal activity. Previous studies have shown that this peptide exerts its candidacidal activity, through the inhibition of both mitochondrial respiration and the formation of reactive oxygen species. The purpose of the present study was to investigate the biological consequences of histatin-5 action on mammalian mitochondria to verify if the toxic mechanism exerted on mitochondria from Candida albicans is an exclusive for fungal cells. Moreover, hypothesising that the damage exerted on mitochondria may induce programmed cellular death pathways, we evaluated two main markers of apoptosis: the mitochondrial membrane potential (DeltaPsi) and the release of cytochrome c. The results obtained show that exposure of isolated mammalian mitochondria to histatin-5 determines: (i) a large inhibition of the respiratory chain at the level of complex I, (ii) a slight decrease in the mitochondrial membrane potential, and (iii) no release of cytochrome c.
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Affiliation(s)
- R Petruzzelli
- Department of Biomedical Sciences, University G. D'Annunzio Via dei Vestini, 31, 66100, Chieti Scalo (CH), Italy.
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