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Tan J, Lamont GJ, Scott DA. Tobacco-enhanced biofilm formation by Porphyromonas gingivalis and other oral microbes. Mol Oral Microbiol 2024; 39:270-290. [PMID: 38229003 PMCID: PMC11250950 DOI: 10.1111/omi.12450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/08/2023] [Accepted: 12/25/2023] [Indexed: 01/18/2024]
Abstract
Microbial biofilms promote pathogenesis by disguising antigens, facilitating immune evasion, providing protection against antibiotics and other antimicrobials and, generally, fostering survival and persistence. Environmental fluxes are known to influence biofilm formation and composition, with recent data suggesting that tobacco and tobacco-derived stimuli are particularly important mediators of biofilm initiation and development in vitro and determinants of polymicrobial communities in vivo. The evidence for tobacco-augmented biofilm formation by oral bacteria, tobacco-induced oral dysbiosis, tobacco-resistance strategies, and bacterial physiology is summarized herein. A general overview is provided alongside specific insights gained through studies of the model and archetypal, anaerobic, Gram-negative oral pathobiont, Porphyromonas gingivalis.
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Affiliation(s)
- Jinlian Tan
- Department of Oral Immunology and Infectious Diseases,
University of Louisville, Louisville, KY, USA
| | - Gwyneth J. Lamont
- Department of Oral Immunology and Infectious Diseases,
University of Louisville, Louisville, KY, USA
| | - David A. Scott
- Department of Oral Immunology and Infectious Diseases,
University of Louisville, Louisville, KY, USA
- Center for Microbiomics, Inflammation and Pathogenicity,
University of Louisville, Louisville, KY, USA
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2
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Stocke K, Lamont G, Tan J, Scott DA. Delineation of global, absolutely essential and conditionally essential pangenomes of Porphyromonas gingivalis. Sci Rep 2024; 14:22247. [PMID: 39333542 PMCID: PMC11436796 DOI: 10.1038/s41598-024-72451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/06/2024] [Indexed: 09/29/2024] Open
Abstract
Porphyromonas gingivalis is a Gram-negative, anaerobic oral pathobiont, an etiological agent of periodontitis and the most commonly studied periodontal bacterium. Multiple low passage clinical isolates were sequenced, and their genomes compared to several laboratory strains. Phylogenetic distances were mapped, a gene absence-presence matrix generated, and core (present in all genomes) and accessory (absent in one or more genomes) genes delineated. Subsequently, a second pangenome delineating the prevalence of inherently essential genes was generated. The prevalence of genes conditionally essential for surviving tobacco exposure, abscess formation and epithelial invasion was also determined, in addition to genes encoding key proteolytic enzymes containing putative signal peptides. While the absolutely essential pangenome was highly conserved, significant differences in the complete and conditionally essential pangenomes were apparent. Thus, genetic plasticity appears to lie primarily in gene sets facilitating adaptation to variant disease-related environments. Those genes that are highly pervasive in the P. gingivalis absolutely essential pangenome or are highly prevalent and essential for fitness in disease-relevant models, may represent particularly attractive therapeutic targets worthy of further investigation. As mutations in absolutely essential genes are expected to be lethal, the data provided herein should also facilitate improved planning for P. gingivalis gene mutation strategies.
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Affiliation(s)
- Kendall Stocke
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 S. Preston St., Louisville, KY, 40292, USA
| | - Gwyneth Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 S. Preston St., Louisville, KY, 40292, USA
| | - Jinlian Tan
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 S. Preston St., Louisville, KY, 40292, USA
| | - David A Scott
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 S. Preston St., Louisville, KY, 40292, USA.
- Center for Microbiomics, Inflammation and Pathogenicity, University of Louisville, Louisville, KY, 40292, USA.
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3
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Dou Y, Mishra A, Fletcher HM. Involvement of PG1037 in the repair of 8-oxo-7,8-dihydroguanine caused by oxidative stress in Porphyromonas gingivalis. Mol Oral Microbiol 2024. [PMID: 39206509 DOI: 10.1111/omi.12482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The PG1037 gene is part of the uvrA-PG1037-pcrA operon in Porphyromonas gingivalis. It encodes for a protein of unknown function upregulated under hydrogen peroxide (H2O2)-induced oxidative stress. Bioinformatic analysis shows that PG1037 has a zinc-finger motif, two peroxidase motifs, and one cytidylate kinase domain. The aim of this study is to characterize further the role of the PG1037 recombinant protein in the unique 8-oxoG repair system in P. gingivalis. MATERIALS AND METHODS PG1037 recombinant proteins with deletions in the zinc-finger or peroxidase motifs were created. Electrophoretic mobility shift assays were used to evaluate the ability of the recombinant proteins to bind 8-oxoG-containing oligonucleotides. Zinc binding, peroxidase, and Fenton reaction assays were used to assess the functional roles of the rPG1037 protein. A bacterial adenylate cyclase two-bride assay was used to identify the partner protein of PG1037 in the repair of 8-oxoG. RESULTS The recombinant PG1037 (rPG1037) protein carrying an N-terminal His-tag demonstrated an ability to recognize and bind 8-oxoG-containing oligonucleotide. In contrast to the wild-type rPG1037 protein, the zinc-finger motif deletion resulted in the loss of zinc and 8-oxoG binding activities. A deletion of the peroxidase motif-1 showed a decrease in peroxidase activity. Using a bacterial adenylate cyclase two-hybrid system, there was no observed protein-protein interaction of PG1037 with UvrA (PG1036), PcrA (PG1038), or mismatch repair system proteins. CONCLUSIONS Taken together, the results show that PG1037 is an important member of a novel mechanism that recognizes and repairs oxidative stress-induced DNA damage in P. gingivalis.
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Affiliation(s)
- Yuetan Dou
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Arunima Mishra
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Hansel M Fletcher
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
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Murai H, Kuboniwa M, Kakiuchi M, Matsumura R, Hirata Y, Amano A. Curcumin inhibits growth of Porphyromonas gingivalis by arrest of bacterial dipeptidyl peptidase activity. J Oral Microbiol 2024; 16:2373040. [PMID: 38974504 PMCID: PMC11225630 DOI: 10.1080/20002297.2024.2373040] [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: 10/03/2023] [Accepted: 06/23/2024] [Indexed: 07/09/2024] Open
Abstract
Background Curcumin is a multi-functional polyphenol with anti-bacterial and anti-inflammatory effects and may have potential for treatment of periodontal diseases. The present study was conducted to examine the molecular basis of the anti-bacterial effect of curcumin against Porphyromonas gingivalis using metabolome analysis. Materials and Methods P. gingivalis were incubated with 10 µg/mL curcumin, and then metabolites were analyzed with CE-TOF/MS. Expression levels of sigma factors were also evaluated using RT-PCR assays. The activities of dipeptidyl peptidases (DPPs) were assessed by examining the degradation reactions of MCA-labeled peptides. Results The relative amounts of various glycogenic amino acids were significantly decreased when P. gingivalis was incubated with curcumin. Furthermore, the metabolites on the amino acid degradation pathway, including high-energy compounds such as ATP, various intermediate metabolites of RNA/DNA synthesis, nucleoside sugars and amino sugars were also decreased. Additionally, the expression levels of sigma-54 and sigma-70 were significantly decreased, and the same results as noted following nutrient starvation. Curcumin also significantly suppressed the activities of some DPPs, while the human DPP-4 inhibitors markedly inhibited the growth of P. gingivalis and activities of the DPPs. Conclusions Curcumin suppresses the growth of P. gingivalis by inhibiting DPPs and also interferes with nucleic acid synthesis and central metabolic pathways, beginning with amino acid metabolism.
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Affiliation(s)
- Hiroki Murai
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
- Saraya Research Institute, Saraya Co., Ltd, Osaka, Kashiwara, Japan
| | - Masae Kuboniwa
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
| | - Miho Kakiuchi
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
| | - Reiko Matsumura
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
- Saraya Research Institute, Saraya Co., Ltd, Osaka, Kashiwara, Japan
| | - Yoshihiko Hirata
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
- Saraya Research Institute, Saraya Co., Ltd, Osaka, Kashiwara, Japan
| | - Atsuo Amano
- Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA), Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Suita, Japan
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Guo XP, Yang J, Wu L, Fang C, Gu JM, Li F, Liu HS, Li LY, Wang SY. Periodontitis relates to benign prostatic hyperplasia via the gut microbiota and fecal metabolome. Front Microbiol 2023; 14:1280628. [PMID: 38163068 PMCID: PMC10756679 DOI: 10.3389/fmicb.2023.1280628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Objectives Periodontitis is associated with benign prostatic hyperplasia (BPH), whether it related to gut floramicrobiota and metabonomics is unclear. Methods We established ligature-induced periodontitis (EP), testosterone-induced BPH, and composite rat models. Fecal samples were collected to detect gut microbiota by 16S rDNA sequencing and metabonomics were detected by liquid chromatography tandem mass spectrometry (LC-MS/MS). Results Sequencing results revealed differential gut floramicrobiota composition between EP+BPH group and other three groups. The abundances of Ruminococcus flavefaciens were significantly increased in EP+BPH group compared with other groups. Tenericutes, Mollicutes, RF39 and Ruminococcus gnavus were significantly decreased in EP+BPH group compared with BPH group, while Ruminococcus callidus and Escherichia were significantly decreased compared with EP group. For gut metabonomics, LC-MS/MS showed that fecal metabolites and seven metabolic pathways were changed in EP+BPH group, such as biosynthesis of unsaturated fatty acids, steroid hormone biosynthesis. Correlation analysis showed that the alterations of gut metabolism were significantly correlated with differential gut floramicrobiota, such as Ruminococcus callidus and Ruminococcus flavefaciens. Conclusion Our study highlights the relationship of periodontitis and BPH, the alterations of gut floramicrobiota and metabolites may be involved in two diseases, which provides new idea for prevention and treatment of patients with periodontitis concurrent BPH.
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Affiliation(s)
- Xing-Pei Guo
- Department of General Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jun Yang
- Department of Urology, The First People's Hospital of Tianmen in Hubei Province, The Affiliated Hospital of Hubei University of Science and Technology, Tianmen, China
| | - Lan Wu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Cheng Fang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jia-Min Gu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fei Li
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Han-Song Liu
- Department of General Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Lu-Yao Li
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuang-Ying Wang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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Szczęśniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D. The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins. mBio 2023; 14:e0098023. [PMID: 37750700 PMCID: PMC10653852 DOI: 10.1128/mbio.00980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Exclusively in the Bacteroidetes phylum, most proteins exported across the inner membrane via the Sec system and released into the periplasm by type I signal peptidase have N-terminal glutamine converted to pyroglutamate. The reaction is catalyzed by the periplasmic enzyme glutaminyl cyclase (QC), which is essential for the growth of Porphyromonas gingivalis and other periodontopathogens. Apparently, pyroglutamyl formation stabilizes extracytoplasmic proteins and/or protects them from proteolytic degradation in the periplasm. Given the role of P. gingivalis as the keystone pathogen in periodontitis, P. gingivalis QC is a promising target for the development of drugs to treat and/or prevent this highly prevalent chronic inflammatory disease leading to tooth loss and associated with severe systemic diseases.
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Affiliation(s)
- Katarzyna Szczęśniak
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kamila Chudzik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Ferenc
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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Liu S, Xie G, Chen M, He Y, Yu W, Chen X, Mao W, Liu N, Zhang Y, Chang Q, Qiao Y, Ma X, Xue J, Jin M, Guo S, Hou Y, Gao Z. Oral microbial dysbiosis in patients with periodontitis and chronic obstructive pulmonary disease. Front Cell Infect Microbiol 2023; 13:1121399. [PMID: 36844402 PMCID: PMC9948037 DOI: 10.3389/fcimb.2023.1121399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Background Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment strategies of individuals, this study compared and investigated the bacterial signatures in periodontitis and chronic obstructive pulmonary disease (COPD). Materials and methods We collected subgingival plaque and gingival crevicular fluid samples from 112 individuals (31 healthy controls, 24 patients with periodontitis, 28 patients with COPD, and 29 patients with both periodontitis and COPD). The oral microbiota was analyzed using 16S rRNA gene sequencing and diversity and functional prediction analysis were performed. Results We observed higher bacterial richness in individuals with periodontitis in both types of oral samples. Using LEfSe and DESeq2 analyses, we found differentially abundant genera that may be potential biomarkers for each group. Mogibacterium is the predominant genus in COPD. Ten genera, including Desulfovibrio, Filifactor, Fretibacterium, Moraxella, Odoribacter, Pseudoramibacter Pyramidobacter, Scardovia, Shuttleworthia and Treponema were predominant in periodontitis. Bergeyella, Lautropia, Rothia, Propionibacterium and Cardiobacterium were the signature of the healthy controls. The significantly different pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) between healthy controls and other groups were concentrated in genetic information processing, translation, replication and repair, and metabolism of cofactors and vitamins. Conclusions We found the significant differences in the bacterial community and functional characterization of oral microbiota in periodontitis, COPD and comorbid diseases. Compared to gingival crevicular fluid, subgingival plaque may be more appropriate for reflecting the difference of subgingival microbiota in periodontitis patients with COPD. These results may provide potentials for predicting, screening, and treatment strategies for individuals with periodontitis and COPD.
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Affiliation(s)
- Siqin Liu
- School of Stomatology, Binzhou Medical University, Yantai, China
| | - Guofang Xie
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Meifeng Chen
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Xiaobo Chen
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Weigang Mao
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Nanxia Liu
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Yuanjie Zhang
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Qin Chang
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Yingying Qiao
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Jianbo Xue
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Mengtong Jin
- Department of Science and Education, Linfen Central Hospital, Linfen, China
| | - Shuming Guo
- Nursing department, Linfen Central Hospital, Linfen, China
| | - Yudong Hou
- School of Stomatology, Binzhou Medical University, Yantai, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
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Moradali MF, Ghods S, Bähre H, Lamont RJ, Scott DA, Seifert R. Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence. NPJ Biofilms Microbiomes 2022; 8:53. [PMID: 35794154 PMCID: PMC9259658 DOI: 10.1038/s41522-022-00316-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
Microbial pathogens employ signaling systems through cyclic (di-) nucleotide monophosphates serving as second messengers to increase fitness during pathogenesis. However, signaling schemes via second messengers in Porphyromonas gingivalis, a key Gram-negative anaerobic oral pathogen, remain unknown. Here, we report that among various ubiquitous second messengers, P. gingivalis strains predominantly synthesize bis-(3',5')-cyclic di-adenosine monophosphate (c-di-AMP), which is essential for their growth and survival. Our findings demonstrate an unusual regulation of c-di-AMP synthesis in P. gingivalis. P. gingivalis c-di-AMP phosphodiesterase (PDE) gene (pdepg) positively regulates c-di-AMP synthesis and impedes a decrease in c-di-AMP concentration despite encoding conserved amino acid motifs for phosphodiesterase activity. Instead, the predicted regulator gene cdaR, unrelated to the c-di-AMP PDE genes, serves as a potent negative regulator of c-di-AMP synthesis in this anaerobe. Further, our findings reveal that pdepg and cdaR are required to regulate the incorporation of ATP into c-di-AMP upon pyruvate utilization, leading to enhanced biofilm formation. We show that shifts in c-di-AMP signaling change the integrity and homeostasis of cell envelope, importantly, the structure and immunoreactivity of the lipopolysaccharide layer. Additionally, microbe-microbe interactions and the virulence potential of P. gingivalis were modulated by c-di-AMP. These studies provide the first glimpse into the scheme of second messenger signaling in P. gingivalis and perhaps other Bacteroidetes. Further, our findings indicate that c-di-AMP signaling promotes the fitness of the residents of the oral cavity and the development of a pathogenic community.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Louisville, KY, USA.
| | - Shirin Ghods
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Louisville, KY, USA
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Louisville, KY, USA
| | - David A Scott
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Louisville, KY, USA
| | - Roland Seifert
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
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9
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Porphyromonas gingivalis Tyrosine Kinase Is a Fitness Determinant in Polymicrobial Infections. Infect Immun 2022; 90:e0017022. [PMID: 35575504 PMCID: PMC9202411 DOI: 10.1128/iai.00170-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many pathogenic microbial ecosystems are polymicrobial, and community function can be shaped by interbacterial interactions. Little is known, however, regarding the genetic determinants required for fitness in heterotypic community environments. In periodontal diseases, Porphyromonas gingivalis is a primary pathogen, but only within polymicrobial communities. Here, we used a transposon sequencing (Tn-Seq) library of P. gingivalis to screen for genes that influence fitness of the organism in a coinfection murine abscess model with the oral partner species Streptococcus gordonii and Fusobacterium nucleatum. Genes impacting fitness with either organism were involved in diverse processes, including metabolism and energy production, along with cell wall and membrane biogenesis. Despite the overall similarity of function, the majority of identified genes were specific to the partner species, indicating that synergistic mechanisms of P. gingivalis vary to a large extent according to community composition. Only two genes were identified as essential for P. gingivalis fitness in abscess development with both S. gordonii and F. nucleatum: ptk1, encoding a tyrosine kinase, and inlJ, encoding an internalin family surface protein. Ptk1, but not InlJ, is required for community development with S. gordonii, and we found that the action of this kinase is similarly required for P. gingivalis to accumulate in a community with F. nucleatum. A limited number of P. gingivalis genes are therefore required for species-independent synergy, and the Ptk1 tyrosine kinase network may integrate and coordinate input from multiple organisms.
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10
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Veith PD, Glew MD, Gorasia DG, Cascales E, Reynolds EC. The Type IX Secretion System and Its Role in Bacterial Function and Pathogenesis. J Dent Res 2021; 101:374-383. [PMID: 34889148 DOI: 10.1177/00220345211051599] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Porphyromonas, Tannerella, and Prevotella species found in severe periodontitis use the Type IX Secretion System (T9SS) to load their outer membrane surface with an array of virulence factors. These virulence factors are then released on outer membrane vesicles (OMVs), which penetrate the host to dysregulate the immune response to establish a positive feedback loop of chronic, inflammatory destruction of the tooth's supporting tissues. In this review, we present the latest information on the molecular architecture of the T9SS and provide mechanistic insight into its role in secretion and attachment of cargo proteins to produce a virulence coat on cells and OMVs. The recent molecular structures of the T9SS motor comprising PorL and PorM as well as the secretion pore Sov, together with advances in the overall interactome, have provided insight into the possible mechanisms of secretion. We propose the presence of PorL/M motors arranged in a circle at the inner membrane with bent periplasmic rotors interacting with the PorN protein. At the outer membrane, we envisage a slide carousel model where the PorN protein is driven around a circular track composed of PorK. Cargo proteins are transported by PorN to PorW and the Sov translocon just as slides are rotated to the projection window. Secreted proteins are proposed to then be shuttled along highways consisting of the PorV shuttle protein to an array of attachment complexes distributed around the cell. The cell surface attachment of cargo is a hallmark of the T9SS, and in Porphyromonas gingivalis and Tannerella forsythia, this attachment is achieved via covalent bonding to a linking sugar synthesized by the Wbp/Vim pathway. The cell-surface attached cargo are enriched on OMVs, which are then released from the cell.
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Affiliation(s)
- P D Veith
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - M D Glew
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - D G Gorasia
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - E Cascales
- Laboratoire d'Ingénierie des Syst èmes Macromol éculaires (LISM), Institut de Microbiologie, Bioénergies and Biotechnologie (IM2B), Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), UMR7255, Marseille Cedex, France
| | - E C Reynolds
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
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11
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Tetrahydroimidazo[4,5- c]pyridine-Based Inhibitors of Porphyromonas gingivalis Glutaminyl Cyclase. Pharmaceuticals (Basel) 2021; 14:ph14121206. [PMID: 34959608 PMCID: PMC8709289 DOI: 10.3390/ph14121206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 01/05/2023] Open
Abstract
Periodontitis is a severe yet underestimated oral disease. Since it is linked to several systemic diseases, such as diabetes, artheriosclerosis, and even Alzheimer’s disease, growing interest in treating periodontitis has emerged recently. The major cause of periodontitis is a shift in the oral microbiome. A keystone pathogen that is associated with this shift is Porphyromonas gingivalis. Hence, targeting P. gingivalis came into focus of drug discovery for the development of novel antiinfective compounds. Among others, glutaminyl cyclases (QCs) of oral pathogens might be promising drug targets. Here, we report the discovery and structure–activity relationship of a novel class of P. gingivalis QC inhibitors according to a tetrahydroimidazo[4,5-c]pyridine scaffold. Some compounds exhibited activity in the lower nanomolar range and thus were further characterized with regard to their selectivity and toxicity.
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12
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Perpich JD, Yakoumatos L, Johns P, Stocke KS, Fitzsimonds ZR, Wilkey DW, Merchant ML, Miller DP, Lamont RJ. Identification and characterization of a UbK family kinase in Porphyromonas gingivalis that phosphorylates the RprY response regulator. Mol Oral Microbiol 2021; 36:258-266. [PMID: 34241965 DOI: 10.1111/omi.12347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/03/2023]
Abstract
Phosphorylation of proteins is a key component of bacterial signaling systems that can control important functions such as community development and virulence. We report here the identification of a Ubiquitous bacterial Kinase (UbK) family member, designated UbK1, in the anaerobic periodontal pathogen, Porphyromonas gingivalis. UbK1 contains conserved SPT/S, Hanks-type HxDxYR, EW, and Walker A motifs, and a mutation analysis established the Walker A domain and the Hanks-type domain as required for both autophosphorylation and transphosphorylation. UbK1 autophosphorylates on the proximal serine in the SPT/S domain as well as the tyrosine residue within the HxDxYR domain and the tyrosine residue immediately proximal, indicating both serine/threonine and tyrosine specificity. The orphan two-component system response regulator (RR) RprY was phosphorylated on Y41 in the receiver domain by UbK1. The ubk1 gene is essential in P. gingivalis; however, overexpression of UbK1 showed that UbK1-mediated phosphorylation of RprY functions predominantly to augment its properties as a transcriptional enhancer. These results establish that P. gingivalis possesses an active UbK kinase in addition to a previously described Bacterial Tyrosine family kinase. The RR RprY is identified as the first transcriptional regulator controlled by a UbK enzyme.
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Affiliation(s)
- John D Perpich
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA.,Department of Pharmaceutical Sciences, Sullivan University College of Pharmacy and Health Sciences, Louisville, Kentucky, USA
| | - Lan Yakoumatos
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Parker Johns
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Kendall S Stocke
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Zackary R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Michael L Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
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13
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Potempa J, Madej M, Scott DA. The RagA and RagB proteins of Porphyromonas gingivalis. Mol Oral Microbiol 2021; 36:225-232. [PMID: 34032024 DOI: 10.1111/omi.12345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 11/27/2022]
Abstract
RagA and RagB proteins are major components of the outer membrane of the oral pathogen Porphyromonas gingivalis and, while recently suggested to represent a novel peptide uptake system, their full function is still under investigation. Herein, we (a) discuss the evidence that the rag locus contributes to P. gingivalis virulence; (b) provide insight to Rag protein potential biological function in macromolecular transport and other aspects of bacterial physiology; (c) address the host response to Rag proteins which are immunodominant and immunomodulatory; and (d) review the potential of Rag-focused therapeutic strategies for the control of periodontal diseases.
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Affiliation(s)
- Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA.,Faculty of Biochemistry, Biophysics and Biotechnology, Department of Microbiology, Jagiellonian University, Kraków, Poland
| | - Mariusz Madej
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Microbiology, Jagiellonian University, Kraków, Poland
| | - David A Scott
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky, USA
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14
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Luo H, Lin Y, Liu T, Lai FL, Zhang CT, Gao F, Zhang R. DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. Nucleic Acids Res 2021; 49:D677-D686. [PMID: 33095861 PMCID: PMC7779065 DOI: 10.1093/nar/gkaa917] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/30/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Tao Liu
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Chun-Ting Zhang
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ren Zhang
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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15
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Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT. Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J Biol Chem 2021; 296:100263. [PMID: 33837744 PMCID: PMC7948796 DOI: 10.1016/j.jbc.2021.100263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
The development of a targeted therapy would significantly improve the treatment of periodontitis and its associated diseases including Alzheimer’s disease, rheumatoid arthritis, and cardiovascular diseases. Glutaminyl cyclases (QCs) from the oral pathogens Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia represent attractive target enzymes for small-molecule inhibitor development, as their action is likely to stabilize essential periplasmic and outer membrane proteins by N-terminal pyroglutamination. In contrast to other microbial QCs that utilize the so-called type I enzymes, these oral pathogens possess sequences corresponding to type II QCs, observed hitherto only in animals. However, whether differences between these bacteroidal QCs and animal QCs are sufficient to enable development of selective inhibitors is not clear. To learn more, we recombinantly expressed all three QCs. They exhibit comparable catalytic efficiencies and are inhibited by metal chelators. Crystal structures of the enzymes from P. gingivalis (PgQC) and T. forsythia (TfQC) reveal a tertiary structure composed of an eight-stranded β-sheet surrounded by seven α-helices, typical of animal type II QCs. In each case, an active site Zn ion is tetrahedrally coordinated by conserved residues. Nevertheless, significant differences to mammalian enzymes are found around the active site of the bacteroidal enzymes. Application of a PgQC-selective inhibitor described here for the first time results in growth inhibition of two P. gingivalis clinical isolates in a dose-dependent manner. The insights gained by these studies will assist in the development of highly specific small-molecule bacteroidal QC inhibitors, paving the way for alternative therapies against periodontitis and associated diseases.
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Affiliation(s)
- Nadine Taudte
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany
| | - Miriam Linnert
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Jens-Ulrich Rahfeld
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.
| | - Anke Piechotta
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Mirko Buchholz
- Periotrap Pharmaceuticals GmbH, Halle (Saale), Germany; Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Petr Kolenko
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - John A Houston
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - Florian Veillard
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sigrun Eick
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stephan Schilling
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany; Angewandte Biowissenschaften und Prozesstechnik, Hochschule Anhalt, Köthen, Germany
| | - Hans-Ulrich Demuth
- Department of Molecular Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Milton T Stubbs
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany; ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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16
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Miller DP, Scott DA. Inherently and Conditionally Essential Protein Catabolism Genes of Porphyromonas gingivalis. Trends Microbiol 2020; 29:54-64. [PMID: 33071035 DOI: 10.1016/j.tim.2020.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/01/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023]
Abstract
Proteases are critical virulence determinants of Porphyromonas gingivalis, an emerging Alzheimer's disease, cancer, and arthritis pathogen and established agent of periodontitis. Transposon sequencing has been employed to define the core essential genome of this bacterium and genes conditionally essential in multiple environments - abscess formation; epithelial colonization; and cigarette smoke toxin exposure; as well as to elucidate genes required for iron acquisition and a functional type 9 secretion system. Validated and predicted protein catabolism genes identified include a combination of established virulence factors and a larger set of seemingly more mundane proteolytic genes. The functions and relevance of genes that share essentiality in multiple disease-relevant conditions are examined. These common stress-related genes may represent particularly attractive therapeutic targets for the control of P. gingivalis infections.
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Affiliation(s)
- Daniel P Miller
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - David A Scott
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA.
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17
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Shoji M, Shibata S, Sueyoshi T, Naito M, Nakayama K. Biogenesis of Type V pili. Microbiol Immunol 2020; 64:643-656. [DOI: 10.1111/1348-0421.12838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Mikio Shoji
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Satoshi Shibata
- Molecular Cryo‐Electron Microscopy Unit Okinawa Institute of Science and Technology Graduate University Onna Okinawa Japan
| | - Takayuki Sueyoshi
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences Nagasaki University Nagasaki Nagasaki Japan
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18
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Hutcherson JA, Gogenini H, Lamont GJ, Miller DP, Nowakowska Z, Lasica AM, Liu C, Potempa J, Lamont RJ, Yoder-Himes D, Scott DA. Porphyromonas gingivalis genes conferring fitness in a tobacco-rich environment. Mol Oral Microbiol 2020; 35:10-18. [PMID: 31742917 PMCID: PMC8202090 DOI: 10.1111/omi.12273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 02/05/2023]
Abstract
Smokers are more likely than non-smokers to harbour Porphyromonas gingivalis, they are more susceptible to destructive periodontal disease and smokers may, ultimately, benefit from tobacco-specific preventive and treatment strategies. A Mariner transposon insertion library for P. gingivalis ATCC 33277 was exploited to define 256 genes as essential for P. gingivalis survival in a tobacco-rich environment. Genes whose products play roles in protein transport and catabolism, nicotinamide processing, protection against oxidative stress, drug resistance, and transcriptional regulation have all been identified as essential for CSE survival. Many of these tobacco-essential genes are also requisite for epithelial colonization and abscess formation, suggestive of a core stress-related P. gingivalis genome. Single-gene deletions in several of the TnSeq-implicated genes led to significantly reduced P. gingivalis fitness upon competition with the parent strain, under conditions of cigarette smoke extract-induced stress (1,000 ng/ml nicotine equivalents). This study identifies, for the first time, a subset of P. gingivalis genes required for surviving the plethora of insults present in cigarette smoke. Such conditionally essential genes may delineate bacterial persistence strategies and represent novel therapeutic foci for the prevention of P. gingivalis infection and related diseases in smokers and in general.
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Affiliation(s)
| | | | | | - Daniel P. Miller
- Oral Immunology and Infectious Diseases, University of Louisville
| | - Zuzanna Nowakowska
- Oral Immunology and Infectious Diseases, University of Louisville
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Poland
| | - Anna M. Lasica
- Oral Immunology and Infectious Diseases, University of Louisville
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Chengcheng Liu
- Oral Immunology and Infectious Diseases, University of Louisville
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jan Potempa
- Oral Immunology and Infectious Diseases, University of Louisville
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Poland
| | | | | | - David A. Scott
- Oral Immunology and Infectious Diseases, University of Louisville
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19
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Yoshida Y, Sato M, Nonaka T, Hasegawa Y, Kezuka Y. Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production in Porphyromonas gingivalis. J Oral Microbiol 2019; 11:1588086. [PMID: 31007866 PMCID: PMC6461089 DOI: 10.1080/20002297.2019.1588086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
Acetyl phosphate (AcP) is generally produced from acetyl coenzyme A by phosphotransacetylase (Pta), and subsequent reaction with ADP, catalyzed by acetate kinase (Ack), produces ATP. The mechanism of ATP production in Porphyromonas gingivalis is poorly understood. The aim of this study was to explore the molecular basis of the Pta-Ack pathway in this microorganism. Pta and Ack from P. gingivalis ATCC 33277 were enzymatically and structurally characterized. Structural and mutational analyses suggest that Pta is a dimer with two substrate-binding sites in each subunit. Ack is also dimeric, with a catalytic cleft in each subunit, and structural analysis indicates a dramatic domain motion that opens and closes the cleft during catalysis. ATP formation by Ack proceeds via a sequential mechanism. Reverse transcription-PCR analysis demonstrated that the pta (PGN_1179) and ack (PGN_1178) genes, tandemly located in the genome, are cotranscribed as an operon. Inactivation of pta or ack in P. gingivalis by homologous recombination was successful only when the inactivated gene was expressed in trans. Therefore, both pta and ack genes are essential for this microorganism. Insights into the Pta-Ack pathway reported herein would be helpful to understand the energy acquisition in P. gingivalis.
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Affiliation(s)
- Yasuo Yoshida
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Mitsunari Sato
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Takamasa Nonaka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yuichiro Kezuka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan
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20
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Shields RC, Jensen PA. The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing. Mol Oral Microbiol 2019; 34:39-50. [PMID: 30739386 DOI: 10.1111/omi.12256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
Querying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn-seq) technologies (related Tn-seq strategies are known as TraDIS, INSeq, RB-TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next-generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn-seq methodologies and discuss how Tn-seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn-seq has also contributed to our understanding of well-studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn-seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn-seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.
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Affiliation(s)
- Robert C Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida
| | - Paul A Jensen
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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21
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Wu L, Gong T, Zhou X, Zeng J, Huang R, Wu Y, Li Y. Global analysis of lysine succinylome in the periodontal pathogen Porphyromonas gingivalis. Mol Oral Microbiol 2019; 34:74-83. [PMID: 30672658 DOI: 10.1111/omi.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/22/2018] [Accepted: 01/21/2019] [Indexed: 02/05/2023]
Abstract
The gram-negative anaerobe Porphyromonas gingivalis is not only a keystone periodontal pathogen but also an emerging systemic pathogen. Although the newly discovered protein post-translational modification (PTM), lysine succinylation (Ksuc), appears to play an important role in modulating metabolic processes in bacteria, this PTM has not been investigated in P gingivalis. In this study, we used a highly sensitive proteomics approach combining affinity enrichment with high-resolution liquid chromatography coupled with tandem mass spectrometry to examine Ksuc in P gingivalis. In total, 345 Ksuc sites in 233 proteins were identified and determined to be involved in a variety of cellular processes. In the region surrounding Ksuc sites, lysine residues were drastically overrepresented and sequence motifs with succinyl-lysine flanked by a lysine at the +3 or +6 positions appear to be unique to this pathogen. Additionally, our results suggest a crosstalk between Ksuc and glycosylation, but the overlap between Ksuc and acetylation in P gingivalis is quite different from that observed in other organisms. Notably, Ksuc was observed in proteins associated with established virulence factors, including gingipains, fimbriae, RagB, and PorR. Moreover, products of the factors necessary for P gingivalis in vitro survival (18.5%) were found to be succinylated at lysine sites and the same was observed in products of fitness factors for P gingivalis survival in both abscess and epithelial cell colonization environments (12%). Collectively, these results suggest that Ksuc may be a new mechanism in modulating the virulence, adaptation, and fitness of P gingivalis.
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Affiliation(s)
- Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jumei Zeng
- Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ruijie Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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22
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Liu J, Xiao Y, Wang X, Huang L, Chen Y, Bao C. Glucose-sensitive delivery of metronidazole by using a photo-crosslinked chitosan hydrogel film to inhibit Porphyromonas gingivalis proliferation. Int J Biol Macromol 2018; 122:19-28. [PMID: 30287380 DOI: 10.1016/j.ijbiomac.2018.09.202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/29/2018] [Accepted: 09/28/2018] [Indexed: 02/05/2023]
Abstract
A novel glucose-sensitive drug delivery system with controlled release of metronidazole was synthesized by using biocompatible photo-crosslinked chitosan hydrogel film. Specifically, methacrylic anhydride, as photosensitive substance, was firstly grafted on chitosan molecular chains and then UV irradiation was applied as the crosslinking method. Glucose sensitivity was endowed by immobilizing glucose oxidase on the surface of chitosan film. The physicochemical characteristics including chemical composition, crosslinking degree, mechanical strength and related enzyme properties were investigated successively. Cytotoxicity test, drug release and anti-bacterial test were carried out, respectively. The results show that this photo-crosslinked hydrogel film has good mechanical properties; meanwhile, the immobilized enzyme's bonding capacity and activity can maintain a relatively high level after surface activation. In addition, this material possesses better biocompatibility than chemical crosslinked samples. What's more, it can sense the ambient glucose stimulus, rapidly and correspondingly adjust its inner pore structure to control the loaded metronidazole release, lead to an improved antimicrobial activity against Porphyromonas gingivalis under high glucose concentration. This glucose sensitive hydrogel film may provide a promising method for diabetic's periodontitis therapy in clinic.
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Affiliation(s)
- Junyu Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China; Shanxi Medical University School and Hospital of Stomatology, No.63, Xin Jian Nan Rd., Taiyuan 030001, China
| | - Yu Xiao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China
| | - Xiangyu Wang
- Shanxi Medical University School and Hospital of Stomatology, No.63, Xin Jian Nan Rd., Taiyuan 030001, China
| | - Lixun Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China
| | - Yu Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China; Department of Oral Pathology, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China.
| | - Chongyun Bao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Section 3, Ren Min Nan Rd., Chengdu 610041, Sichuan, China.
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23
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Roux D, Schaefers M, Clark BS, Weatherholt M, Renaud D, Scott D, LiPuma JJ, Priebe G, Gerard C, Yoder-Himes DR. A putative lateral flagella of the cystic fibrosis pathogen Burkholderia dolosa regulates swimming motility and host cytokine production. PLoS One 2018; 13:e0189810. [PMID: 29346379 PMCID: PMC5773237 DOI: 10.1371/journal.pone.0189810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023] Open
Abstract
Burkholderia dolosa caused an outbreak in the cystic fibrosis clinic at Boston Children's Hospital and was associated with high mortality in these patients. This species is part of a larger complex of opportunistic pathogens known as the Burkholderia cepacia complex (Bcc). Compared to other species in the Bcc, B. dolosa is highly transmissible; thus understanding its virulence mechanisms is important for preventing future outbreaks. The genome of one of the outbreak strains, AU0158, revealed a homolog of the lafA gene encoding a putative lateral flagellin, which, in other non-Bcc species, is used for movement on solid surfaces, attachment to host cells, or movement inside host cells. Here, we analyzed the conservation of the lafA gene and protein sequences, which are distinct from those of the polar flagella, and found lafA homologs to be present in numerous β-proteobacteria but notably absent from most other Bcc species. A lafA deletion mutant in B. dolosa showed a greater swimming motility than wild-type due to an increase in the number of polar flagella, but did not appear to contribute to biofilm formation, host cell invasion, or murine lung colonization or persistence over time. However, the lafA gene was important for cytokine production in human peripheral blood mononuclear cells, suggesting it may have a role in recognition by the human immune response.
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Affiliation(s)
- Damien Roux
- INSERM, IAME, UMR 1137, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
- AP-HP, Louis Mourier Hospital, Intensive Care Unit, Colombes, France
| | - Matthew Schaefers
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bradley S. Clark
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Molly Weatherholt
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Diane Renaud
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - David Scott
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - John J. LiPuma
- Division of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregory Priebe
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig Gerard
- Division of Respiratory Diseases, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Deborah R. Yoder-Himes
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail:
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24
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Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018; 19:54. [PMID: 29338683 PMCID: PMC5771137 DOI: 10.1186/s12864-017-4429-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.
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Affiliation(s)
- Luis Acuña-Amador
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.,Laboratorio de Investigación en Bacteriología Anaerobia, Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Aline Primot
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Alain Roulet
- GenoToul Genome & Transcriptome (GeT-PlaGe), INRA, US1426, Castanet-Tolosan, France
| | - Frédérique Barloy-Hubler
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.
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25
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Shoji M, Sato K, Yukitake H, Kamaguchi A, Sasaki Y, Naito M, Nakayama K. Identification of genes encoding glycosyltransferases involved in lipopolysaccharide synthesis inPorphyromonas gingivalis. Mol Oral Microbiol 2017; 33:68-80. [DOI: 10.1111/omi.12200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/16/2022]
Affiliation(s)
- M. Shoji
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - K. Sato
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - H. Yukitake
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - A. Kamaguchi
- Department of Oral Microbiology; School of Dentistry; Health Sciences University of Hokkaido; Hokkaido Japan
| | - Y. Sasaki
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - M. Naito
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - K. Nakayama
- Department of Microbiology and Oral Infection; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
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26
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Miller DP, Hutcherson JA, Wang Y, Nowakowska ZM, Potempa J, Yoder-Himes DR, Scott DA, Whiteley M, Lamont RJ. Genes Contributing to Porphyromonas gingivalis Fitness in Abscess and Epithelial Cell Colonization Environments. Front Cell Infect Microbiol 2017; 7:378. [PMID: 28900609 PMCID: PMC5581868 DOI: 10.3389/fcimb.2017.00378] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022] Open
Abstract
Porphyromonas gingivalis is an important cause of serious periodontal diseases, and is emerging as a pathogen in several systemic conditions including some forms of cancer. Initial colonization by P. gingivalis involves interaction with gingival epithelial cells, and the organism can also access host tissues and spread haematogenously. To better understand the mechanisms underlying these properties, we utilized a highly saturated transposon insertion library of P. gingivalis, and assessed the fitness of mutants during epithelial cell colonization and survival in a murine abscess model by high-throughput sequencing (Tn-Seq). Transposon insertions in many genes previously suspected as contributing to virulence showed significant fitness defects in both screening assays. In addition, a number of genes not previously associated with P. gingivalis virulence were identified as important for fitness. We further examined fitness defects of four such genes by generating defined mutations. Genes encoding a carbamoyl phosphate synthetase, a replication-associated recombination protein, a nitrosative stress responsive HcpR transcription regulator, and RNase Z, a zinc phosphodiesterase, showed a fitness phenotype in epithelial cell colonization and in a competitive abscess infection. This study verifies the importance of several well-characterized putative virulence factors of P. gingivalis and identifies novel fitness determinants of the organism.
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Affiliation(s)
- Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States
| | - Justin A Hutcherson
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States
| | - Yan Wang
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States
| | - Zuzanna M Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland
| | | | - David A Scott
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States
| | - Marvin Whiteley
- Department of Molecular Biosciences, University of Texas at AustinAustin, TX, United States
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of LouisvilleLouisville, KY, United States
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27
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Abstract
Even though the oral microbiome is one of the most complex sites on the body it is an excellent model for narrow‐spectrum antimicrobial therapy. Current research indicates that disruption of the microbiome leads to a dysbiotic environment allowing for the overgrowth of pathogenic species and the onset of oral diseases. The gram‐negative colonizer, Porphyromonas gingivalis has long been considered a key player in the initiation of periodontitis and Streptococcus mutans has been linked to dental caries. With antibiotic research still on the decline, new strategies are greatly needed to combat infectious diseases. By targeting key pathogens, it may be possible to treat oral infections while allowing for the recolonization of the beneficial, healthy flora. In this review, we examine unique strategies to specifically target periodontal pathogens and address what is needed for the success of these approaches in the microbiome era.
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Affiliation(s)
- V N Stone
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA
| | - P Xu
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for the Study of Biological Complexity of Virginia Commonwealth University, Richmond, VA, USA
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28
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Hendrickson EL, Beck DAC, Miller DP, Wang Q, Whiteley M, Lamont RJ, Hackett M. Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq. Front Microbiol 2017; 8:261. [PMID: 28293219 PMCID: PMC5329018 DOI: 10.3389/fmicb.2017.00261] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/07/2017] [Indexed: 01/31/2023] Open
Abstract
Many bacterial infections involve polymicrobial communities in which constituent organisms are synergistically pathogenic. Periodontitis, a commonly occurring chronic inflammatory disorder, is induced by multispecies bacterial communities. The periodontal keystone pathogen Porphyromonas gingivalis and the accessory pathogen Streptococcus gordonii exhibit polymicrobial synergy in animal models of disease. Mechanisms of co-adhesion and community formation by P. gingivalis and S. gordonii are well-established; however, little is known regarding the basis for increased pathogenicity. In this study we used time-coursed RNA-Seq to comprehensively and quantitatively examine the dynamic transcriptional landscape of P. gingivalis in a model consortium with S. gordonii. Genes encoding a number of potential virulence determinants had higher relative mRNA levels in the context of dual species model communities than P. gingivalis alone, including adhesins, the Type IX secretion apparatus, and tetratricopeptide repeat (TPR) motif proteins. In contrast, genes encoding conjugation systems and many of the stress responses showed lower levels of expression in P. gingivalis. A notable exception to reduced abundance of stress response transcripts was the genes encoding components of the oxidative stress-related OxyR regulon, indicating an adaptation of P. gingivalis to detoxify peroxide produced by the streptococcus. Collectively, the results are consistent with evolutionary adaptation of P. gingivalis to a polymicrobial oral environment, one outcome of which is increased pathogenic potential.
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Affiliation(s)
- Erik L Hendrickson
- Center for Microbial Proteomics and Chemical Engineering, University of Washington Seattle, WA, USA
| | - David A C Beck
- Center for Microbial Proteomics and Chemical Engineering, University of WashingtonSeattle, WA, USA; eScience Institute, University of WashingtonSeattle, WA, USA
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville, KY, USA
| | - Qian Wang
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville, KY, USA
| | - Marvin Whiteley
- Department of Molecular Biosciences, University of Texas at Austin Austin, TX, USA
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville, KY, USA
| | - Murray Hackett
- Center for Microbial Proteomics and Chemical Engineering, University of Washington Seattle, WA, USA
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29
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A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis. Sci Rep 2017; 7:41923. [PMID: 28165493 PMCID: PMC5292949 DOI: 10.1038/srep41923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/30/2016] [Indexed: 01/14/2023] Open
Abstract
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
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