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Chowdhury N, Wellslager B, Lee H, Gilbert JL, Yilmaz Ö. Glutamate is a key nutrient for Porphyromonas gingivalis growth and survival during intracellular autophagic life under nutritionally limited conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602514. [PMID: 39026746 PMCID: PMC11257440 DOI: 10.1101/2024.07.08.602514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Porphyromonas gingivalis survives in special autophagic vacuoles that serve as major replicative habitats in human primary gingival epithelial cells (GECs). As an asaccharolytic strict anaerobe, P. gingivalis is dependent on amino acids and peptides for nutrient sources. However, it is largely unknown as to P. gingivalis' metabolic processing under the nutritionally limited intracellular environments such the vacuoles, especially the preferred amino acids and associated-metabolic machineries. Here we elucidate that a Glutamate (Glu) catabolic enzyme, glutamate dehydrogenase (GdhA) is highly enriched in the isolated P. gingivalis -containing vacuoles. Interestingly, we found that P. gingivalis induces conversion of intracellular glutamine pool to Glu determined by analyses of the P. gingivalis- containing vacuoles and the whole infected-GECs. Critically, exogenous Glu-Glu dipeptide, a simple precursor of Glu, significantly increases the size of isolated intact P. gingivalis containing-vacuoles and live wild-type P. gingivalis numbers in GECs. In contrast, the isogenic GdhA-deficient-strain, Δ gdhA displayed a significant growth defect with collapsed-vacuoles in GECs. Next, we confirmed that P. gingivalis uptakes 14 C-Glu and it preferentially utilizes Glu-Glu-dipeptide using a nutritionally reduced Tryptic-Soy-Broth (TSB) media supplemented with Glu-Glu. Contrary, Δ gdhA -strain showed no detectable growth especially in nutritionally reduced TSB media with Glu-Glu. Using Atomic-Force-Microscopy, we observed that, wild-type P. gingivalis but not Δ gdhA strain notably increased the cell volume upon Glu-Glu supplementation, an indicator of higher metabolism and growth. Utilization of a human gingiva-mimicking organoid-system further validated the importance of Glu as an essential nutrient for the intramucosal colonization of P. gingivalis via the protected replicative vacuoles in GECs. Importance This study reveals that P. gingivalis heavily depends on preferential utilization of Glutamate (Glu) for autophagic vacuolar growth and survival in human GECs. Several novel observations are made to support this: (i) GdhA of P. gingivalis is highly enriched in these vacuoles, (ii) P. gingivalis induces a large conversion of intracellular glutamine to Glu, (iii) size of vacuoles are significantly increased in the presence of Glu-Glu in P. gingivalis wild-type strain infection which is opposite in a Δ gdhA strain, (iv) P. gingivalis uptakes 14 C-Glu and preferentially utilizes Glu-Glu dipeptide, (v) similarly, wild-type strain shows growth increase in a nutritionally reduced bacterial culture media, and (vi) finally, Glu-Glu supplementation increases bacterial cell-volume of P. gingivalis wild-type but not Δ gdhA strain, an indicator of higher metabolism and growth. Taken together, this study highlights the pathophysiological importance of Glu for P. gingivalis growth-rate, biomass induction and survival in nutritionally limited host subcellular environments.
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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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Kaneda T, Watanabe M, Honda H, Yamamoto M, Inagaki T, Hironaka S. Fourier transform infrared spectroscopy and machine learning for Porphyromonas gingivalis detection in oral bacteria. ANAL SCI 2024; 40:691-699. [PMID: 38374487 DOI: 10.1007/s44211-023-00501-7] [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: 10/06/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
Abstract
Porphyromonas gingivalis, a Gram-negative anaerobic bacillus, is the primary pathogen in periodontitis. Herein, we cultivated strains of oral bacteria, including P. gingivalis and the oral commensal bacteria Actinomyces viscosus and Streptococcus mutans, and recorded the infrared absorption spectra of the gases released by the cultured bacteria at a resolution of 0.5 cm-1 within the wavenumber range of 500-7500 cm-1. From these spectra, we identified the infrared wavenumbers associated with characteristic absorptions in the gases released by P. gingivalis using a decision tree-based machine learning algorithm. Finally, we compared the obtained absorbance spectra of ammonia (NH3) and carbon monoxide (CO) using the HITRAN database. We observed peaks at similar positions in the P. gingivalis gases, NH3, and CO spectra. Our results suggest that P. gingivalis releases higher amounts of NH3 and CO than A. viscosus and S. mutans. Thus, combining Fourier transform infrared spectroscopy with machine learning enabled us to extract the specific wavenumber range that differentiates P. gingivalis from a vast dataset of peak intensity ratios. Our method distinguishes the gases from P. gingivalis from those of other oral bacteria and provides an effective strategy for identifying P. gingivalis in oral bacteria. Our proposed methodology could be valuable in clinical settings as a simple, noninvasive pathogen diagnosis technique.
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Affiliation(s)
- Tomomi Kaneda
- Department of Hygiene and Oral Health, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Masahiro Watanabe
- Department of Hygiene and Oral Health, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
| | - Hidehiko Honda
- Faculty of Arts and Sciences, Fujiyoshida, Showa University, 4562, Kami-yoshida, Fuji-yoshida-shi, Yamanashi, 403-0005, Japan
| | - Masato Yamamoto
- Faculty of Arts and Sciences, Fujiyoshida, Showa University, 4562, Kami-yoshida, Fuji-yoshida-shi, Yamanashi, 403-0005, Japan
| | - Takae Inagaki
- Department of Hygiene and Oral Health, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Shouji Hironaka
- Department of Hygiene and Oral Health, Showa University School of Dentistry, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024. [PMID: 38442041 DOI: 10.1021/acs.jproteome.3c00912] [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] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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Sharma G, Garg N, Hasan S, Saffarini D, Shirodkar S. Fumarate and nitrite reduction by Prevotella nigrescens and Prevotella buccae isolated from Chronic Periodontitis patients. Microb Pathog 2023; 176:106022. [PMID: 36739100 DOI: 10.1016/j.micpath.2023.106022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study is an investigation of anaerobic nitrite and fumarate reduction/respiration abilities of two characterised Prevotella species namely Prevotella nigrescens (SS6B) and Prevotella buccae (GS6B) isolated from the periodontal pockets of chronic periodontitis (ChP) patients. METHODS Isolation and identification of the periodontal bacteria from 20 patients showing clinical symptoms of ChP. Characterisation of anaerobic nitrite and fumarate reduction was done in P. nigrescens (SS6B) and P. buccae (GS6B) using reduction assays, inhibition assays with use of specific inhibitors, growth assays and enzyme activity assays. Degenerate PCR was used to detect and amplify nitrite reductase (nrfA) and fumarate reductase (frdA) gene sequences in these Prevotella isolates. In addition, molecular and in silico analysis of the amplified anaerobic reductase gene sequences was performed using NCBI conserved domain analysis, Interpro database and MegaX. RESULTS We provided experimental evidence for presence of active nitrite and fumarate reductase activities through enzyme activity, reduction, inhibitor and growth assays. Moreover, we were able to detect presence of 505 bps nrfA gene fragment and 400 bps frdA gene fragment in these Prevotella spp. These fragments show similarity to multiheme ammonia forming cytochrome c nitrite reductases and fumarate reductases flavoprotein subunit, respectively. CONCLUSION Anaerobic nitrite and fumarate respiration abilities in P. nigrescens and P. buccae isolates appear to be important for detoxification process and growth, respectively.
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Affiliation(s)
- Geetika Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Nancy Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Shamimul Hasan
- Department of Oral Medicine and Radiology, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Daad Saffarini
- Department of Biological Sciences, University of Wisconsin Milwaukee, 3209 N. Maryland Ave Milwaukee, WI, 53211, USA
| | - Sheetal Shirodkar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India.
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Chen WA, Dou Y, Fletcher HM, Boskovic DS. Local and Systemic Effects of Porphyromonas gingivalis Infection. Microorganisms 2023; 11:470. [PMID: 36838435 PMCID: PMC9963840 DOI: 10.3390/microorganisms11020470] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Porphyromonas gingivalis, a gram-negative anaerobe, is a leading etiological agent in periodontitis. This infectious pathogen can induce a dysbiotic, proinflammatory state within the oral cavity by disrupting commensal interactions between the host and oral microbiota. It is advantageous for P. gingivalis to avoid complete host immunosuppression, as inflammation-induced tissue damage provides essential nutrients necessary for robust bacterial proliferation. In this context, P. gingivalis can gain access to the systemic circulation, where it can promote a prothrombotic state. P. gingivalis expresses a number of virulence factors, which aid this pathogen toward infection of a variety of host cells, evasion of detection by the host immune system, subversion of the host immune responses, and activation of several humoral and cellular hemostatic factors.
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Affiliation(s)
- William A Chen
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Yuetan Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Hansel M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Danilo S Boskovic
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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Zhao G, Qi M, Wang Q, Hu C, Li X, Chen Y, Yang J, Yu H, Chen H, Guo A. Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment. BMC Genomics 2023; 24:62. [PMID: 36737703 PMCID: PMC9896789 DOI: 10.1186/s12864-023-09142-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies. RESULTS The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals. CONCLUSION Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.
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Affiliation(s)
- Gang Zhao
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Qiankun Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Changmin Hu
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiang Li
- grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jingyuan Yang
- Hubei Key Laboratory of Conservation Biology of Shennongjia Golden Monkey (Shennongjia National Park Administration), Shennongjia Forest Ecosystem Research Station, Shennongjia, 442411 China
| | - Huiliang Yu
- Hubei Key Laboratory of Conservation Biology of Shennongjia Golden Monkey (Shennongjia National Park Administration), Shennongjia Forest Ecosystem Research Station, Shennongjia, 442411 China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Shennongjia Science & Technology Innovation Center, Huazhong Agricultural University, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137National Professional Laboratory for Animal Tuberculosis (Wuhan), Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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Ghods S, Moradali MF, Duryea D, Walker AR, Davey ME. Growth of Porphyromonas gingivalis on human serum albumin triggers programmed cell death. J Oral Microbiol 2022; 15:2161182. [PMID: 36570975 PMCID: PMC9788703 DOI: 10.1080/20002297.2022.2161182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims Gingival crevicular fluid (GCF) constitutes the primary growth substrate for Porphyromonas gingivalis in vivo. The goal of this work was to evaluate the growth of different strains of P. gingivalis on human serum albumin (HSA), a major constituent of GCF. Methods Growth of five different strains of P. gingivalis in the HSA medium was examined and, surprisingly, three of the strains underwent autolysis within 24 h. Comparative transcriptomic analysis was used to identify genes involved in autolysis. Results Two highly related reference strains (W50 and W83) differed dramatically in their survival when grown on HSA. Strain W83 grew fast and lysed within 24 h, while W50 survived for an additional 20 h. Differential gene expression analysis led us to a gene cluster containing enzymes involved in arginine metabolism and a gene predicted to be lytic murein transglycosylase, which are known to play a role in autolysis. Deletion of this gene (PG0139) resulted in a mutant that did not lyse, and complementation restored the HSA lysis phenotype, indicating that this enzyme plays a central role in the autolysis of P. gingivalis. Conclusions P. gingivalis undergoes autolysis when provided with HSA as a substrate for growth.
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Affiliation(s)
| | | | | | | | - Mary E. Davey
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA,CONTACT Mary E. Davey The Forsyth Institute, Cambridge, MA02142, USA
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Saiki K, Urano-Tashiro Y, Yamanaka Y, Takahashi Y. Calcium ions and vitamin B 12 are growth factors for Porphyromonas gingivalis. J Oral Biosci 2022; 64:445-451. [PMID: 36103977 DOI: 10.1016/j.job.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Porphyromonas gingivalis is a causative agent of chronic periodontitis. Standard strains of P. gingivalis, such as W83 and ATCC 33277, proliferate in minimal medium when protein is added as the energy source and hemin and menadione are added as growth factors. Nevertheless, minimal medium containing bovine serum albumin sometimes fails to support growth. HIGHLIGHTS The proliferation of two W83 strains and seven ATCC 33277 strains in various minimal media was investigated. Previously, we determined that calcium chloride (CaCl2) was a growth factor for W83NM, a W83 strain. In this study, we found that vitamin B12 enhanced the proliferation of W83NM in a minimal medium with cultures from the fourth passage but not from the first to the third passage. Therefore, using fourth-passage cultures, we assessed the proliferation of two W83 and seven ATCC 33277 strains in minimal media and the effects of CaCl2 and vitamin B12. Surprisingly, the nine P. gingivalis strains all differed with respect to their proliferation in minimal media, and protein products used as energy sources showed product-to-product and lot-to-lot heterogeneity. Even though strains or protein products were different, we found CaCl2-dependent growth in nine strains and vitamin B12-dependent growth in seven strains. CONCLUSION These results suggest that calcium ions and vitamin B12 are novel growth factors for P. gingivalis.
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Affiliation(s)
- Keitarou Saiki
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yumiko Urano-Tashiro
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yuki Yamanaka
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yukihiro Takahashi
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
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Baldewijns S, Sillen M, Palmans I, Vandecruys P, Van Dijck P, Demuyser L. The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis. Front Microbiol 2021; 12:705779. [PMID: 34276639 PMCID: PMC8282898 DOI: 10.3389/fmicb.2021.705779] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.
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Affiliation(s)
- Silke Baldewijns
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Mart Sillen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ilse Palmans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
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11
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Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7. Sci Rep 2021; 11:7929. [PMID: 33846449 PMCID: PMC8041751 DOI: 10.1038/s41598-021-86965-x] [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: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. While the molecular mechanisms underlining strict specificity at the S1 subsite of S46 peptidases have been well studied, those of relatively broad preference at the S2 subsite of these peptidases are unknown. In this study, we performed structural and biochemical analyses on DPP7 from Stenotrophomonas maltophilia (SmDPP7). SmDPP7 showed preference for the accommodation of hydrophobic amino acids at the S2 subsite in general, but as an exception, also for asparagine, a hydrophilic amino acid. Structural analyses of SmDPP7 revealed that this exceptional preference to asparagine is caused by a hydrogen bonding network at the bottom of the S2 subsite. The residues in the S2 subsite are well conserved among S46 peptidases as compared with those in the S1 subsite. We expect that our findings will contribute toward the development of a universal inhibitor of S46 peptidases.
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12
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Dahlstrand Rudin A, Khamzeh A, Venkatakrishnan V, Persson T, Gabl M, Savolainen O, Forsman H, Dahlgren C, Christenson K, Bylund J. Porphyromonas gingivalis Produce Neutrophil Specific Chemoattractants Including Short Chain Fatty Acids. Front Cell Infect Microbiol 2021; 10:620681. [PMID: 33542906 PMCID: PMC7851090 DOI: 10.3389/fcimb.2020.620681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 01/01/2023] Open
Abstract
Neutrophil migration from blood to tissue-residing microbes is governed by a series of chemoattractant gradients of both endogenous and microbial origin. Periodontal disease is characterized by neutrophil accumulation in the gingival pocket, recruited by the subgingival biofilm consisting mainly of gram-negative, anaerobic and proteolytic species such as Porphyromonas gingivalis. The fact that neutrophils are the dominating cell type in the gingival pocket suggests that neutrophil-specific chemoattractants are released by subgingival bacteria, but characterization of chemoattractants released by subgingival biofilm species remains incomplete. In the present study we characterized small (< 3 kDa) soluble chemoattractants released by growing P. gingivalis, and show that these are selective for neutrophils. Most neutrophil chemoattractant receptors are expressed also by mononuclear phagocytes, the free fatty acid receptor 2 (FFAR2) being an exception. In agreement with the selective neutrophil recruitment, the chemotactic activity found in P. gingivalis supernatants was mediated in part by a mixture of short chain fatty acids (SCFAs) that are recognized by FFAR2, and other leukocytes (including monocytes) did not respond to SCFA stimulation. Although SCFAs, produced by bacterial fermentation of dietary fiber in the gut, has previously been shown to utilize FFAR2, our data demonstrate that the pronounced proteolytic metabolism employed by P. gingivalis (and likely also other subgingival biofilm bacteria associated with periodontal diseases) may result in the generation of SCFAs that attract neutrophils to the gingival pocket. This finding highlights the interaction between SCFAs and FFAR2 in the context of P. gingivalis colonization during periodontal disease, but may also have implications for other inflammatory pathologies involving proteolytic bacteria.
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Affiliation(s)
- Agnes Dahlstrand Rudin
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Arsham Khamzeh
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Tishana Persson
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Michael Gabl
- Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Huamei Forsman
- Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Claes Dahlgren
- Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Karin Christenson
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johan Bylund
- Department of Oral Microbiology and Immunology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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13
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Maus I, Tubbesing T, Wibberg D, Heyer R, Hassa J, Tomazetto G, Huang L, Bunk B, Spröer C, Benndorf D, Zverlov V, Pühler A, Klocke M, Sczyrba A, Schlüter A. The Role of Petrimonas mucosa ING2-E5A T in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms 2020; 8:E2024. [PMID: 33348776 PMCID: PMC7768429 DOI: 10.3390/microorganisms8122024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Tom Tubbesing
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Database and Software Engineering Group, Department of Computer Science, Institute for Technical and Business Information Systems, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Geizecler Tomazetto
- Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, 8000 Aarhus, Denmark;
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany;
- Institute of Molecular Genetics, National Research Centre «Kurchatov Institute», Kurchatov Sq. 2, 123128 Moscow, Russia
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects Affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
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14
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Wang Z, Li L, Liu P, Wang C, Lu Q, Liu L, Wang X, Luo Q, Shao H. Role of aspartate ammonia-lyase in Pasteurella multocida. BMC Microbiol 2020; 20:369. [PMID: 33272193 PMCID: PMC7713322 DOI: 10.1186/s12866-020-02049-2] [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: 06/27/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Pasteurella multocida is responsible for a highly infectious and contagious disease in birds, leading to heavy economic losses in the chicken industry. However, the pathogenesis of this disease is poorly understood. We recently identified an aspartate ammonia-lyase (aspA) in P. multocida that was significantly upregulated under iron-restricted conditions, the protein of which could effectively protect chicken flocks against P. multocida. However, the functions of this gene remain unclear. In the present study, we constructed aspA mutant strain △aspA::kan and complementary strain C△aspA::kan to investigate the function of aspA in detail. RESULT Deletion of the aspA gene in P. multocida resulted in a significant reduction in bacterial growth in LB (Luria-Bertani) and MH (Mueller-Hinton) media, which was rescued by supplementation with 20 mM fumarate. The mutant strain △aspA::kan showed significantly growth defects in anaerobic conditions and acid medium, compared with the wild-type strain. Moreover, growth of △aspA::kan was more seriously impaired than that of the wild-type strain under iron-restricted conditions, and this growth recovered after supplementation with iron ions. AspA transcription was negatively regulated by iron conditions, as demonstrated by quantitative reverse transcription-polymerase chain reaction. Although competitive index assay showed the wild-type strain outcompetes the aspA mutant strain and △aspA::kan was significantly more efficient at producing biofilms than the wild-type strain, there was no significant difference in virulence between the mutant and the wild-type strains. CONCLUSION These results demonstrate that aspA is required for bacterial growth in complex medium, and under anaerobic, acid, and iron-limited conditions.
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Affiliation(s)
- Zui Wang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - Li Li
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - Peng Liu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Animal Disease Prevention and Control Center of Yichang, Yichang, 443000, China
| | - Chen Wang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Animal Disease Prevention and Control Center of Yichang, Yichang, 443000, China
| | - Qin Lu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - Lina Liu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - Xiaozhong Wang
- Animal Disease Prevention and Control Center of Yichang, Yichang, 443000, China
| | - Qingping Luo
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China. .,Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.
| | - Huabin Shao
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special one, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China. .,Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.
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15
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Nemoto TK, Ohara Nemoto Y. Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:145-156. [PMID: 33006264 PMCID: PMC8048996 DOI: 10.1111/omi.12317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023]
Abstract
Porphyromonas gingivalis, a pathogen of chronic periodontitis, is an asaccharolytic microorganism that solely utilizes nutritional amino acids as its energy source and cellular constituents. The bacterium is considered to incorporate proteinaceous nutrients mainly as dipeptides, thus exopeptidases that produce dipeptides from polypeptides are critical for survival and proliferation. We present here an overview of dipeptide production by P. gingivalis mediated by dipeptidyl-peptidases (DPPs), e.g., DPP4, DPP5, DPP7, and DPP11, serine exopeptidases localized in periplasm, which release dipeptides from the N-terminus of polypeptides. Additionally, two other exopeptidases, acylpeptidyl-oligopeptidase (AOP) and prolyl tripeptidyl-peptidase A (PTP-A), which liberate N-terminal acylated di-/tri-peptides and tripeptides with Pro at the third position, respectively, provide polypeptides in an acceptable form for DPPs. Hence, a large fraction of dipeptides is produced from nutritional polypeptides by DPPs with differential specificities in combination with AOP and PTP-A. The resultant dipeptides are then incorporated across the inner membrane mainly via a proton-dependent oligopeptide transporter (POT), a member of the major facilitator superfamily. Recent studies also indicate that DPP4 and DPP7 directly link between periodontal and systemic diseases, such as type 2 diabetes mellitus and coagulation abnormality, respectively. Therefore, these dipeptide-producing and incorporation molecules are considered to be potent targets for prevention and treatment of periodontal and related systemic diseases.
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Affiliation(s)
- Takayuki K Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuko Ohara Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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16
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Zeng J, Wu L, Chen Q, Wang L, Qiu W, Zheng X, Yin X, Liu J, Ren Y, Li Y. Comprehensive profiling of protein lysine acetylation and its overlap with lysine succinylation in the Porphyromonas gingivalis fimbriated strain ATCC 33277. Mol Oral Microbiol 2020; 35:240-250. [PMID: 32939976 DOI: 10.1111/omi.12312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Porphyromonas gingivalis is a pathogen closely associated with periodontal and systemic infections. Recently, lysine acetylation (Kac) and lysine succinylation (Ksuc) have been identified in bacterial proteins with diverse biological and pathological functions. The Ksuc of P. gingivalis ATCC 33277 has been characterized in our previous work, and here, we report the systematic analysis of Kac and its crosstalk with Ksuc in this bacterium. A combination of the affinity enrichment by the acetyl-lysine antibody with highly sensitive LC-MS/MS was used to identify the lysine-acetylated proteins and sites in P. gingivalis ATCC 33277. A total of 1,112 lysine-acetylated sites matching 438 proteins were identified. These proteins involved in several cellular processes, especially those proteins related to protein biosynthesis and central metabolism had a high tendency to be lysine acetylated. Moreover, lysine sites flanked by tyrosine, phenylalanine, and histidine in the +1 position, as well as residue lysine in position +4 to +5, were the targets of Kac. Additionally, proteins involved in adhesins, gingipains, black pigmentation, and oxidative stress resistance were identified as substrates of Kac. Collectively, these results suggest Kac may play a critical role in the regulation of physiology and virulence of P. gingivalis. Furthermore, we discovered that, Ksuc and Kac were extensively overlapped in P. gingivalis ATCC 33277, especially in proteins related to ribosomes and metabolism. This study provides a significant beginning for further investigating the role of Kac and Ksuc in the pathogenicity of P. gingivalis.
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Affiliation(s)
- Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Lingyun Wang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Qiu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoming Yin
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jie Liu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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17
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Chuang ST, Ho ST, Tu PW, Li KY, Kuo YL, Shiu JS, Wang SY, Chen MJ. The Rumen Specific Bacteriome in Dry Dairy Cows and Its Possible Relationship with Phenotypes. Animals (Basel) 2020; 10:E1791. [PMID: 33019774 PMCID: PMC7601041 DOI: 10.3390/ani10101791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Most microbiome studies of dairy cows have investigated the compositions and functions of rumen microbial communities in lactating dairy cows. The importance of the relationships among hosts, microbiota, diet composition, and milk production remains unknown in dry dairy cows. Thus, in the present study, the composition of the rumen microbiome in cows from three dairy farms was investigated to identify core bacteria contributing to various physiological roles during rumen fermentation in dry dairy cows. The results indicated that ruminal fluid in dry dairy cows from different regional farms had core rumen microbiota that could be clearly distinguished from that of cows of the other farms. Further identification of key microorganisms associated with each farm revealed that Prevotella, Methanobrevibacter, Pseudobutyrivibrio, Ruminococcus, Bacteroides, and Streptococcus were major contributors. Spearman's correlation indicated that the abundance of genera such as Prevotella and Ruminococcus in dry dairy cows could indicate milk yield in the previous lactating period. Functional pathway analysis of the rumen bacterial communities demonstrated that amino acid metabolism and carbohydrate metabolism were the major pathways. Our findings provide knowledge of the composition and predicted functions of rumen microbiota in dry dairy cows from regional farms, which underscore the importance of the relationships among hosts, microbiota, diet composition, and milk production.
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Affiliation(s)
- Shih-Te Chuang
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan;
| | - Shang-Tse Ho
- Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan; (S.-T.H.); (P.-W.T.); (K.-Y.L.); (S.-Y.W.)
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi 600, Taiwan
| | - Po-Wen Tu
- Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan; (S.-T.H.); (P.-W.T.); (K.-Y.L.); (S.-Y.W.)
| | - Kuan-Yi Li
- Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan; (S.-T.H.); (P.-W.T.); (K.-Y.L.); (S.-Y.W.)
| | - Yu-Lun Kuo
- Biotools Co., Ltd., New Taipei City 221, Taiwan;
| | - Jia-Shian Shiu
- Hengchun Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Pingtung 946, Taiwan;
| | - Sheng-Yao Wang
- Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan; (S.-T.H.); (P.-W.T.); (K.-Y.L.); (S.-Y.W.)
| | - Ming-Ju Chen
- Department of Animal Science and Technology, National Taiwan University, Taipei 106, Taiwan; (S.-T.H.); (P.-W.T.); (K.-Y.L.); (S.-Y.W.)
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18
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Saiki K, Urano-Tashiro Y, Takahashi Y. Reassessment of minimal media reveals differences in growth among Porphyromonas gingivalis standard strains. J Oral Biosci 2020; 62:315-321. [PMID: 32937181 DOI: 10.1016/j.job.2020.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Porphyromonas gingivalis is one of the etiologic agents of chronic periodontitis. Our previous study showed that the use of minimal media for P. gingivalis allowed to isolate novel inhibitors of P. gingivalis growth. However, growth of P. gingivalis in minimal media was not always reproducible. METHODS To explain this phenomenon, we analyzed the growth of seven wild-type ATCC 33277 strains and two wild-type W83 strains in 10 minimal media and three complex media. RESULTS All nine strains grew in LF (Lactalbumin-Ferric chloride), GC (bovine γ-immunoglobulin G-Calcium chloride), and newly developed mC (milk-Casein) minimal media. Therefore, LF, GC, and mC could be used as minimal media for P. gingivalis. In contrast, other six minimal media containing bovine serum albumin (BSA) supported the growth of several less strains; among these, two media also showed lack of reproducibility in growth among ATCC 33277 strains. On the other hand, four ATCC 33277 strains grew similarly in all 13 media, but two W83 and other three ATCC 33277 strains grew differently in at least one medium. CONCLUSIONS These results suggest that the lack of reproducibility of P. gingivalis growth on minimal media is caused by the presence of BSA, and by differences among the standard strains of P. gingivalis.
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Affiliation(s)
- Keitarou Saiki
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yumiko Urano-Tashiro
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
| | - Yukihiro Takahashi
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo, Japan.
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19
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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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20
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Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG, Seneviratne CJ. Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis. JDR Clin Trans Res 2020; 6:343-351. [PMID: 32777190 DOI: 10.1177/2380084420948779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Previous studies have largely explored the microbial composition and pathogenesis of pregnancy gingivitis. However, the patterns of microbial colonization during pregnancy in the absence of pregnancy gingivitis have rarely been studied. Characterization of the oral microbiome in pregnant women with healthy gingiva is an important initial step in understanding the role of the microbiome in progression to pregnancy gingivitis. OBJECTIVES In this study, we compared the oral microbiome of pregnant women without gingivitis (healthy pregnancy) with pregnant women having gingivitis and nonpregnant healthy women to understand how pregnancy modifies the oral microbiome and induces progression to pregnancy gingivitis. METHODS Subgingival plaque samples were collected from Chinese pregnant women with gingivitis (n = 10), healthy pregnant women (n = 10), and nonpregnant healthy women (n = 10). The Illumina MiSeq platform was used to perform 16S rRNA gene sequencing targeting the V4 region. RESULTS The alpha and beta diversity was significantly different between pregnant and nonpregnant women, but minimal differences were observed between pregnant women with and without gingivitis. Interestingly, the oral bacterial community showed higher abundance of pathogenic taxa during healthy pregnancy as compared with nonpregnant women despite similar gingival and plaque index scores. However, when compared with overt pregnancy gingivitis, pathogenic taxa were less abundant during healthy pregnancy. PICRUSt analysis (phylogenetic investigation of communities by reconstruction of unobserved states) also suggested no difference in the functional capabilities of the microbiome during pregnancy, irrespective of gingival disease status. However, metabolic pathways related to amino acid metabolism were significantly increased in healthy pregnant women as compared with nonpregnant women. CONCLUSION The presence of pathogenic taxa in healthy pregnancy and pregnancy gingivitis suggests that bacteria may be necessary for initiating disease development but progression to gingivitis may be influenced by the host environmental factors. More efforts are required to plan interventions aimed at sustaining health before the appearance of overt gingivitis. KNOWLEDGE TRANSFER STATEMENT The results of this study draw attention to the importance of oral health maintenance during pregnancy, as women without any prenatal oral conditions are predisposed to the risk of developing pregnancy gingivitis. Hence, it is important to incorporate comprehensive assessment of oral health in the prenatal health care schedules. Pregnant woman should be screened for oral risks, counseled on proper oral hygiene and expected oral changes, and referred for dental treatment, when necessary.
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Affiliation(s)
- P Balan
- Singapore Oral Microbiomics Inititative, National Dental Research Institute Singapore, SingHealth, Singapore.,Oral Health ACP, Duke NUS Medical School, Singapore
| | - B W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry, Amsterdam, the Netherlands
| | - Y S Chong
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Hospital, Singapore
| | - W Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry, Amsterdam, the Netherlands
| | - M L Wong
- Discipline of Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore
| | - V Lopez
- School of Nursing, Hubei University of Medicine, Shiyan City, China
| | - H G He
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - C J Seneviratne
- Singapore Oral Microbiomics Inititative, National Dental Research Institute Singapore, SingHealth, Singapore.,Oral Health ACP, Duke NUS Medical School, Singapore
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21
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Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase. Sci Rep 2019; 9:13587. [PMID: 31537874 PMCID: PMC6753110 DOI: 10.1038/s41598-019-49984-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/30/2019] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.
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22
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Saiki K, Urano-Tashiro Y, Konishi K, Takahashi Y. A screening system using minimal media identifies a flavin-competing inhibitor of Porphyromonas gingivalis growth. FEMS Microbiol Lett 2019; 366:5580286. [PMID: 31578552 DOI: 10.1093/femsle/fnz204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/29/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic periodontitis is caused by dysbiosis of human oral commensals and especially by increase in Porphyromonas gingivalis. Inhibitors of P. gingivalis growth are expected to serve as effective drugs for the periodontal therapy. In the present study, we isolated new growth inhibitors of P. gingivalis using minimal media for P. gingivalis. The minimal media included the previously reported Globulin-Albumin (GA) and the newly developed Lactalbumin-Ferric chloride (LF) and Globulin-Calcium chloride (GC); all supported growth of the wild-type strain of P. gingivalis but did not support the growth of a mutant defective for a type IX secretion system. GC contains CaCl2, indicating that P. gingivalis requires a calcium ion for growth. Using LF and GA, we screened about 100 000 compounds and identified 73 that strongly inhibited the growth of P. gingivalis. More than half of these candidates would not have been obtained if these minimal media had not been used in our screen. One of our candidate inhibitors was diphenyleneiodonium chloride (DPIC), which showed strong bactericidal activity against P. gingivalis. Excess amounts of flavin adenine dinucleotide or flavin mononucleotide suppressed the inhibitory activity of DPIC, suggesting that DPIC would be a novel potent growth inhibitor.
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Affiliation(s)
- Keitarou Saiki
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, 1-9-20 Fujimi, Chiyoda-ku, Tokyo 102-8159, Japan
| | - Yumiko Urano-Tashiro
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, 1-9-20 Fujimi, Chiyoda-ku, Tokyo 102-8159, Japan
| | - Kiyoshi Konishi
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, 1-9-20 Fujimi, Chiyoda-ku, Tokyo 102-8159, Japan
| | - Yukihiro Takahashi
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, 1-9-20 Fujimi, Chiyoda-ku, Tokyo 102-8159, Japan
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23
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Gaál Kovalčíková A, Pančíková A, Konečná B, Klamárová T, Novák B, Kovaľová E, Podracká Ľ, Celec P, Tóthová Ľ. Urea and creatinine levels in saliva of patients with and without periodontitis. Eur J Oral Sci 2019; 127:417-424. [PMID: 31247131 DOI: 10.1111/eos.12642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite the fact that saliva contains measurable concentrations of urea and creatinine, it is not widely used in clinical nephrology. One of the reasons is the high inter- and intra-individual variability in the salivary markers of kidney function. We hypothesized that gingival bleeding in patients with periodontitis could contribute to this variability by increasing the concentration of salivary urea or creatinine. Samples were collected from 25 patients with periodontitis and 29 healthy controls. In addition, saliva samples from five healthy volunteers were artificially contaminated with blood. The concentration of urea, but not that of creatinine, was more than twice as high in patients with periodontitis than in controls. Artificial contamination of saliva with blood did not affect the salivary concentration of creatinine. Salivary urea increased only with very high levels of contamination (≥2.5% blood in saliva), but that did not occur in patients. In conclusion, periodontitis increases the concentration of salivary urea, but this is not likely to be a result of contamination with blood. Future studies should investigate the composition of the oral microbiome, specifically regarding how it affects the concentration of salivary urea. Salivary creatinine seems to be a more robust non-invasive marker of renal functions than salivary urea.
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Affiliation(s)
- Alexandra Gaál Kovalčíková
- Department of Paediatrics, National Institute of Children's Diseases and Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | | | - Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Tatiana Klamárová
- Department of Dental Hygiene, Faculty of Health Care, Prešov University, Prešov, Slovakia
| | - Bohuslav Novák
- Department of Stomatology and Maxillofacial Surgery, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Eva Kovaľová
- Department of Dental Hygiene, Faculty of Health Care, Prešov University, Prešov, Slovakia
| | - Ľudmila Podracká
- Department of Paediatrics, National Institute of Children's Diseases and Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Ľubomíra Tóthová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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24
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Moradali MF, Ghods S, Angelini TE, Davey ME. Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis. THE ISME JOURNAL 2019; 13:1560-1574. [PMID: 30783212 PMCID: PMC6775972 DOI: 10.1038/s41396-019-0360-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
Our understanding of how oral microbiota adapt in response to changes in their surroundings remains limited. This is particularly true of the slow-growing anaerobes that persist below the gum line. Here, we report that the oral anaerobe Porphyromonas gingivalis strain 381 can surface translocate when sandwiched between two surfaces. We show that during movement, this bacterium alters its metabolism, specifically side products of arginine utilization including citrulline and ornithine accumulated in the translocating cells; while arginine, N-acetyl-arginine, and the polyamine putrescine, which is produced from arginine were consumed. In addition, our results indicate that movement requires modification of the surrounding environment via proteolysis, cell dispersion, cell-on-cell rolling, and sub-diffusive cell-driven motility. We also show that production of fimbriae and fimbriae-associated proteins; as well as the regulation of contact-dependent growth inhibition genes, which are known to be involved in self-nonself discrimination, and the type IX secretion system are central to surface translocation. These studies provide a first glimpse into P. gingivalis motility and its relationship to ecological variables.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Shirin Ghods
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Thomas E Angelini
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL, 32610, USA
| | - Mary Ellen Davey
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA.
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25
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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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26
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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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27
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Martins CHG, Abrão F, Moraes TS, Oliveira PF, Tavares DC, Magalhães LG, Galvão FC, Veneziani RCS, Ambrósio SR. Kaurenoic acid and its sodium salt derivative: antibacterial activity against Porphyromonas gingivalis and their mechanism of action. Future Microbiol 2018; 13:1585-1601. [DOI: 10.2217/fmb-2018-0140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To evaluate the antibacterial activity of 12 kaurane-type diterpenes against a panel of bacteria that cause endodontic infection. Methods & materials: We conducted tests against bacteria in the planktonic or in the sessile mode, cytotoxic assays for the most promising compounds against human normal lung fibroblast cells, and Porphyromonas gingivalis (ATCC 33277) proteomic analysis. Results & conclusion: Kaurenoic acid and its salt exhibited satisfactory antibacterial action against the evaluated bacteria. Proteomic analysis suggested that these compounds might interfere in bacterial metabolism and virulence factor expression. Kaurane-type diterpenes are an important class of natural products and should be considered in the search for new irrigating solutions to treat endodontic infections.
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Affiliation(s)
- Carlos HG Martins
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Fariza Abrão
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Thaís S Moraes
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Pollyanna F Oliveira
- Laboratory of Mutagenesis, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Denise C Tavares
- Laboratory of Mutagenesis, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Lizandra G Magalhães
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
| | - Fábio C Galvão
- Department of Biological Sciences, São Paulo State University - UNESP, Araraquara, 14800-901, São Paulo, Brazil
| | - Rodrigo CS Veneziani
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
| | - Sérgio R Ambrósio
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
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28
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Degradation of Incretins and Modulation of Blood Glucose Levels by Periodontopathic Bacterial Dipeptidyl Peptidase 4. Infect Immun 2017. [PMID: 28630069 DOI: 10.1128/iai.00277-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Severe periodontitis is known to aggravate diabetes mellitus, though molecular events related to that link have not been fully elucidated. Porphyromonas gingivalis, a major pathogen of periodontitis, expresses dipeptidyl peptidase 4 (DPP4), which is involved in regulation of blood glucose levels by cleaving incretins in humans. We examined the enzymatic characteristics of DPP4 from P. gingivalis as well as two other periodontopathic bacteria, Tannerella forsythia and Prevotella intermedia, and determined whether it is capable of regulating blood glucose levels. Cell-associated DPP4 activity was found in those microorganisms, which was effectively suppressed by inhibitors of human DPP4, and molecules sized 73 kDa in P. gingivalis, and 71 kDa in T. forsythia and P. intermedia were immunologically detected. The kcat/Km values of recombinant DPP4s ranged from 721 ± 55 to 1,283 ± 23 μM-1s-1 toward Gly-Pro-4-methylcoumaryl-7-amide (MCA), while those were much lower for His-Ala-MCA. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis showed His/Tyr-Ala dipeptide release from the N termini of incretins, glucagon-like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide, respectively, with the action of microbial DPP4. Moreover, intravenous injection of DPP4 into mice decreased plasma active GLP-1 and insulin levels, accompanied by a substantial elevation in blood glucose over the control after oral glucose administration. These results are the first to show that periodontopathic bacterial DPP4 is capable of modulating blood glucose levels the same as mammalian DPP4; thus, the incidence of periodontopathic bacteremia may exacerbate diabetes mellitus via molecular events of bacterial DPP4 activities.
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29
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Ebersole JL, Dawson D, Emecen-Huja P, Nagarajan R, Howard K, Grady ME, Thompson K, Peyyala R, Al-Attar A, Lethbridge K, Kirakodu S, Gonzalez OA. The periodontal war: microbes and immunity. Periodontol 2000 2017; 75:52-115. [DOI: 10.1111/prd.12222] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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30
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Bacterial protease uses distinct thermodynamic signatures for substrate recognition. Sci Rep 2017; 7:2848. [PMID: 28588213 PMCID: PMC5460201 DOI: 10.1038/s41598-017-03220-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 12/30/2022] Open
Abstract
Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme (“entropy reservoirs”). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.
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31
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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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32
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Washio J, Ogawa T, Suzuki K, Tsukiboshi Y, Watanabe M, Takahashi N. Amino acid composition and amino acid-metabolic network in supragingival plaque. Biomed Res 2017; 37:251-7. [PMID: 27545001 DOI: 10.2220/biomedres.37.251] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dental plaque metabolizes both carbohydrates and amino acids. The former can be degraded to acids mainly, while the latter can be degraded to various metabolites, including ammonia, acids and amines, and associated with acid-neutralization, oral malodor and tissue inflammation. However, amino acid metabolism in dental plaque is still unclear. This study aimed to elucidate what kinds of amino acids are available as metabolic substrates and how the amino acids are metabolized in supragingival plaque, by a metabolome analysis. Amino acids and the related metabolites in supragingival plaque were extracted and quantified comprehensively by CE-TOFMS. Plaque samples were also incubated with amino acids, and the amounts of ammonia and amino acid-related metabolites were measured. The concentration of glutamate was the highest in supragingival plaque, while the ammonia-production was the highest from glutamine. The obtained metabolome profile revealed that amino acids are degraded through various metabolic pathways, including deamination, decarboxylation and transamination and that these metabolic systems may link each other, as well as with carbohydrate metabolic pathways in dental plaque ecosystem. Moreover, glutamine and glutamate might be the main source of ammonia production, as well as arginine, and contribute to pH-homeostasis and counteraction to acid-induced demineralization in supragingival plaque.
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Ben Hania W, Joseph M, Bunk B, Spröer C, Klenk HP, Fardeau ML, Spring S. Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria. Environ Microbiol 2017; 19:1134-1148. [PMID: 27943642 DOI: 10.1111/1462-2920.13639] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 01/26/2023]
Abstract
The anaerobic, mesophilic and moderately halophilic strain L21-Spi-D4T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein-rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR-022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21-Spi-D4T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co-occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR-022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21-Spi-D4T , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR-022 clade.
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Manon Joseph
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Levine M, Lohinai Z, Teles RP. Low Biofilm Lysine Content in Refractory Chronic Periodontitis. J Periodontol 2016; 88:181-189. [PMID: 27620654 DOI: 10.1902/jop.2016.160302] [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] [Indexed: 01/22/2023]
Abstract
BACKGROUND Chronic periodontitis is controlled without antibiotics by scaling and root planing (SRP) to remove dental biofilm. It has been previously reported that the epithelial barrier to bacterial proinflammatory products is impaired when biofilm lysine falls below the minimal content of normal blood plasma. Aims were to examine whether being refractory and requiring antibiotics to supplement SRP were associated with low biofilm lysine contents. METHODS Sixteen patients with periodontitis and six periodontally healthy volunteers (HVs) (respective mean ages: 57 ± 6 and 36 ± 8 years) were examined. Patients with periodontitis received SRP and surgery, and HVs received prophylaxis. At quarterly maintenance or prophylaxis visits during the subsequent year, therapeutic response was good (GR, n = 9) or poor (PR, n = 7; including five cigarette smokers). Biofilm cadaverine, lysine, and other amino acid (AA) contents were determined by liquid chromatography. Cadaverine mole fraction of lysine plus cadaverine (CF) indicated biofilm lysine decarboxylase activity. RESULTS Biofilm lysine was 0.19 ± 0.10 and 0.20 ± 0.09 μmol/mg in GRs and HVs, but 0.07 ± 0.03 μmol/mg in PRs (Kruskal-Wallis: P <0.01). All AAs were depleted in biofilm from smokers, but only lysine was depleted in biofilm from non-smokers. CF was inversely associated with clinical attachment level (CAL) at baseline before therapy in all patients (R2 = 0.28, P <0.01) and with CAL change after therapy in GR (R2 = 0.49, P <0.05). Lysine and cadaverine contents discriminated PRs from GRs and HVs (Wilks' λ = 0.499, P <0.012). CONCLUSIONS Refractory responses requiring antibiotic therapy result from smoking and/or microbial infections that starve the biofilm and epithelial attachment of lysine. Biofilm CF is associated with periodontitis severity pretherapy and extent of therapeutic response post-therapy.
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Affiliation(s)
- Martin Levine
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Zsolt Lohinai
- Department of Conservative Dentistry, Semmelweis University, Budapest, Hungary
| | - Ricardo P Teles
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Takahashi N, Nyvad B. Ecological Hypothesis of Dentin and Root Caries. Caries Res 2016; 50:422-31. [PMID: 27458979 DOI: 10.1159/000447309] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/31/2016] [Indexed: 11/19/2022] Open
Abstract
Recent advances regarding the caries process indicate that ecological phenomena induced by bacterial acid production tilt the de- and remineralization balance of the dental hard tissues towards demineralization through bacterial acid-induced adaptation and selection within the microbiota - from the dynamic stability stage to the aciduric stage via the acidogenic stage [Takahashi and Nyvad, 2008]. Dentin and root caries can also be partly explained by this hypothesis; however, the fact that these tissues contain a considerable amount of organic material suggests that protein degradation is involved in caries formation. In this review, we compiled relevant histological, biochemical, and microbiological information about dentin/root caries and refined the hypothesis by adding degradation of the organic matrix (the proteolytic stage) to the abovementioned stages. Bacterial acidification not only induces demineralization and exposure of the organic matrix in dentin/root surfaces but also activation of dentin-embedded and salivary matrix metalloproteinases and cathepsins. These phenomena initiate degradation of the demineralized organic matrix in dentin/root surfaces. While a bacterial involvement has never been confirmed in the initial degradation of organic material, the detection of proteolytic/amino acid-degrading bacteria and bacterial metabolites in dentin and root caries suggests a bacterial digestion and metabolism of partly degraded matrix. Moreover, bacterial metabolites might induce pulpitis as an inflammatory/immunomodulatory factor. Root and dentin surfaces are always at risk of becoming demineralized in the oral cavity, and exposed organic materials can be degraded by host-derived proteases contained in saliva and dentin itself. New approaches to the prevention and treatment of root/dentin caries are required.
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Affiliation(s)
- Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
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Sato M, Yoshida Y, Nagano K, Hasegawa Y, Takebe J, Yoshimura F. Three CoA Transferases Involved in the Production of Short Chain Fatty Acids in Porphyromonas gingivalis. Front Microbiol 2016; 7:1146. [PMID: 27486457 PMCID: PMC4949257 DOI: 10.3389/fmicb.2016.01146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/08/2016] [Indexed: 12/11/2022] Open
Abstract
Butyryl-CoA:acetate CoA transferase, which produces butyrate and acetyl-CoA from butyryl-CoA and acetate, is responsible for the final step of butyrate production in bacteria. This study demonstrates that in the periodontopathogenic bacterium Porphyromonas gingivalis this reaction is not catalyzed by PGN_1171, previously annotated as butyryl-CoA:acetate CoA transferase, but by three distinct CoA transferases, PGN_0725, PGN_1341, and PGN_1888. Gas chromatography/mass spectrometry (GC-MS) and spectrophotometric analyses were performed using crude enzyme extracts from deletion mutant strains and purified recombinant proteins. The experiments revealed that, in the presence of acetate, PGN_0725 preferentially utilized butyryl-CoA rather than propionyl-CoA. By contrast, this preference was reversed in PGN_1888. The only butyryl-CoA:acetate CoA transferase activity was observed in PGN_1341. Double reciprocal plots revealed that all the reactions catalyzed by these enzymes follow a ternary-complex mechanism, in contrast to previously characterized CoA transferases. GC-MS analysis to determine the concentrations of short chain fatty acids (SCFAs) in culture supernatants of P. gingivalis wild type and mutant strains revealed that PGN_0725 and PGN_1888 play a major role in the production of butyrate and propionate, respectively. Interestingly, a triple deletion mutant lacking PGN_0725, PGN_1341, and PGN_1888 produced low levels of SCFAs, suggesting that the microorganism contains CoA transferase(s) in addition to these three enzymes. Growth rates of the mutant strains were mostly slower than that of the wild type, indicating that many carbon compounds produced in the SCFA synthesis appear to be important for the biological activity of this microorganism.
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Affiliation(s)
- Mitsunari Sato
- Department of Microbiology, School of Dentistry, Aichi Gakuin UniversityNagoya, Japan; Department of Removable Prosthodontics, School of Dentistry, Aichi Gakuin UniversityNagoya, Japan
| | - Yasuo Yoshida
- Department of Microbiology, School of Dentistry, Aichi Gakuin University Nagoya, Japan
| | - Keiji Nagano
- Department of Microbiology, School of Dentistry, Aichi Gakuin University Nagoya, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University Nagoya, Japan
| | - Jun Takebe
- Department of Removable Prosthodontics, School of Dentistry, Aichi Gakuin University Nagoya, Japan
| | - Fuminobu Yoshimura
- Department of Microbiology, School of Dentistry, Aichi Gakuin University Nagoya, Japan
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Washio J, Takahashi N. Metabolomic Studies of Oral Biofilm, Oral Cancer, and Beyond. Int J Mol Sci 2016; 17:ijms17060870. [PMID: 27271597 PMCID: PMC4926404 DOI: 10.3390/ijms17060870] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/25/2016] [Accepted: 05/25/2016] [Indexed: 12/19/2022] Open
Abstract
Oral diseases are known to be closely associated with oral biofilm metabolism, while cancer tissue is reported to possess specific metabolism such as the ‘Warburg effect’. Metabolomics might be a useful method for clarifying the whole metabolic systems that operate in oral biofilm and oral cancer, however, technical limitations have hampered such research. Fortunately, metabolomics techniques have developed rapidly in the past decade, which has helped to solve these difficulties. In vivo metabolomic analyses of the oral biofilm have produced various findings. Some of these findings agreed with the in vitro results obtained in conventional metabolic studies using representative oral bacteria, while others differed markedly from them. Metabolomic analyses of oral cancer tissue not only revealed differences between metabolomic profiles of cancer and normal tissue, but have also suggested a specific metabolic system operates in oral cancer tissue. Saliva contains a variety of metabolites, some of which might be associated with oral or systemic disease; therefore, metabolomics analysis of saliva could be useful for identifying disease-specific biomarkers. Metabolomic analyses of the oral biofilm, oral cancer, and saliva could contribute to the development of accurate diagnostic, techniques, safe and effective treatments, and preventive strategies for oral and systemic diseases.
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Affiliation(s)
- Jumpei Washio
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics. Appl Environ Microbiol 2016; 82:3165-73. [PMID: 26994078 DOI: 10.1128/aem.00473-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/12/2016] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Deep Lake in the Vestfold Hills is hypersaline and the coldest system in Antarctica known to support microbial growth (temperatures as low as -20°C). It represents a strong experimental model because the lake supports a low-complexity community of haloarchaea, with the three most abundant species totaling ∼72%. Moreover, the dominant haloarchaea are cultivatable, and their genomes are sequenced. Here we use metaproteomics linked to metagenome data and the genome sequences of the isolates to characterize the main pathways, trophic strategies, and interactions associated with resource utilization. The dominance of the most abundant member, Halohasta litchfieldiae, appears to be predicated on competitive utilization of substrates (e.g., starch, glycerol, and dihydroxyacetone) produced by Dunaliella, the lake's primary producer, while also possessing diverse mechanisms for acquiring nitrogen and phosphorus. The second most abundant member, strain DL31, is proficient in degrading complex proteinaceous matter. Hht. litchfieldiae and DL31 are inferred to release labile substrates that are utilized by Halorubrum lacusprofundi, the third most abundant haloarchaeon in Deep Lake. The study also linked genome variation to specific protein variants or distinct genetic capacities, thereby identifying strain-level variation indicative of specialization. Overall, metaproteomics revealed that rather than functional differences occurring at different lake depths or through size partitioning, the main lake genera possess major trophic distinctions, and phylotypes (e.g., strains of Hht. litchfieldiae) exhibit a more subtle level of specialization. This study highlights the extent to which the lake supports a relatively uniform distribution of taxa that collectively possess the genetic capacity to effectively exploit available nutrients throughout the lake. IMPORTANCE Life on Earth has evolved to colonize a broad range of temperatures, but most of the biosphere (∼85%) exists at low temperatures (≤5°C). By performing unique roles in biogeochemical cycles, environmental microorganisms perform functions that are critical for the rest of life on Earth to survive. Cold environments therefore make a particularly important contribution to maintaining healthy, stable ecosystems. Here we describe the main physiological traits of the dominant microorganisms that inhabit Deep Lake in Antarctica, the coldest aquatic environment known to support life. The hypersaline system enables the growth of halophilic members of the Archaea: haloarchaea. By analyzing proteins of samples collected from the water column, we determined the functions that the haloarchaea were likely to perform. This study showed that the dominant haloarchaea possessed distinct lifestyles yet formed a uniform community throughout the lake that was collectively adept at using available light energy and diverse organic substrates for growth.
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Yoshida Y, Sato M, Kezuka Y, Hasegawa Y, Nagano K, Takebe J, Yoshimura F. Acyl-CoA reductase PGN_0723 utilizes succinyl-CoA to generate succinate semialdehyde in a butyrate-producing pathway of Porphyromonas gingivalis. Arch Biochem Biophys 2016; 596:138-48. [PMID: 27013206 DOI: 10.1016/j.abb.2016.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/22/2023]
Abstract
The molecular basis of butyrate production in Porphyromonas gingivalis has not been fully elucidated, even though butyrate, a short chain fatty acid (SCFA), can exert both beneficial and harmful effects on a mammalian host. A database search showed that the amino acid sequence of PGN_0723 protein was 50.6% identical with CoA-dependent succinate semialdehyde dehydrogenase (SSADH) in Clostridium kluyveri. By contrast, the protein has limited identity (19.1%) with CoA-independent SSADH in Escherichia coli. Compared with the wild type, growth speed, and final turbidity were lower in the PGN_0723 deletion strain that was constructed by replacing the PGN_0723 gene with an erythromycin resistance cassette. Gas chromatography mass spectrometry revealed the supernatant concentrations of the SCFAs butyrate, isobutyrate, and isovalerate, but not propionate, in the PGN_0723 deletion strain were also lower than those in the wild type. The wild-type phenotype was restored in a complemented strain. We cloned the PGN_0723 gene, purified the recombinant protein, and computationally constructed its three-dimensional model. A colorimetric assay and liquid chromatography-tandem mass spectrometry analysis demonstrated that the recombinant PGN_0723 produces succinate semialdehyde, which is an intermediate in the P. gingivalis butyrate synthesis pathway, not from succinate but from succinyl-CoA in the presence of NAD(P)H via a ping-pong bi-bi mechanism. Asn110Ala and Cys239Ala mutations resulted in a significant loss of the CoA-dependent PGN_0723 enzymatic activity. The study provides new insights into butyrate production, which constitutes a virulence factor 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; Department of Removable Prosthodontics, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yuichiro Kezuka
- Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Keiji Nagano
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Jun Takebe
- Department of Removable Prosthodontics, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Fuminobu Yoshimura
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
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Nemoto TK, Ohara-Nemoto Y, Bezerra GA, Shimoyama Y, Kimura S. A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides. J Biol Chem 2016; 291:5913-5925. [PMID: 26733202 PMCID: PMC4786725 DOI: 10.1074/jbc.m115.687566] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 12/06/2015] [Indexed: 01/01/2023] Open
Abstract
Exopeptidases, including dipeptidyl- and tripeptidylpeptidase, are crucial for the growth of Porphyromonas gingivalis, a periodontopathic asaccharolytic bacterium that incorporates amino acids mainly as di- and tripeptides. In this study, we identified a novel exopeptidase, designated acylpeptidyl oligopeptidase (AOP), composed of 759 amino acid residues with active Ser(615) and encoded by PGN_1349 in P. gingivalis ATCC 33277. AOP is currently listed as an unassigned S9 family peptidase or prolyl oligopeptidase. Recombinant AOP did not hydrolyze a Pro-Xaa bond. In addition, although sequence similarities to human and archaea-type acylaminoacyl peptidase sequences were observed, its enzymatic properties were apparently distinct from those, because AOP scarcely released an N-acyl-amino acid as compared with di- and tripeptides, especially with N-terminal modification. The kcat/Km value against benzyloxycarbonyl-Val-Lys-Met-4-methycoumaryl-7-amide, the most potent substrate, was 123.3 ± 17.3 μm(-1) s(-1), optimal pH was 7-8.5, and the activity was decreased with increased NaCl concentrations. AOP existed predominantly in the periplasmic fraction as a monomer, whereas equilibrium between monomers and oligomers was observed with a recombinant molecule, suggesting a tendency of oligomerization mediated by the N-terminal region (Met(16)-Glu(101)). Three-dimensional modeling revealed the three domain structures (residues Met(16)-Ala(126), which has no similar homologue with known structure; residues Leu(127)-Met(495) (β-propeller domain); and residues Ala(496)-Phe(736) (α/β-hydrolase domain)) and further indicated the hydrophobic S1 site of AOP in accord with its hydrophobic P1 preference. AOP orthologues are widely distributed in bacteria, archaea, and eukaryotes, suggesting its importance for processing of nutritional and/or bioactive oligopeptides.
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Affiliation(s)
- Takayuki K Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Yuko Ohara-Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Gustavo Arruda Bezerra
- the Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria, and.
| | - Yu Shimoyama
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan
| | - Shigenobu Kimura
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan
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Chen W, Roslund K, Fogarty CL, Pussinen PJ, Halonen L, Groop PH, Metsälä M, Lehto M. Detection of hydrogen cyanide from oral anaerobes by cavity ring down spectroscopy. Sci Rep 2016; 6:22577. [PMID: 26940198 PMCID: PMC4778072 DOI: 10.1038/srep22577] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/17/2016] [Indexed: 02/07/2023] Open
Abstract
Hydrogen cyanide (HCN) has been recognized as a potential biomarker for non-invasive diagnosis of Pseudomonas aeruginosa infection in the lung. However, the oral cavity is a dominant production site for exhaled HCN and this contribution can mask the HCN generated in the lung. It is thus important to understand the sources of HCN production in the oral cavity. By screening of oral anaerobes for HCN production, we observed that the genus of Porphyromonas, Prevotella and Fusobacterium generated low levels of HCN in vitro. This is the first study to show that oral anaerobes are capable of producing HCN in vitro. Further investigations were conducted on the species of P. gingivalis and we successfully detected HCN production (0.9-10.9 ppb) in the headspace of three P. gingivalis reference strains (ATCC 33277, W50 and OMG 434) and one clinical isolate. From P. gingivalis ATCC 33277 and W50, a strong correlation between HCN and CO2 concentrations (rs = 0.89, p < 0.001) was observed, indicating that the HCN production of P. gingivalis might be connected with the bacterial metabolic activity. These results indicate that our setup could be widely applied to the screening of in vitro HCN production by both aerobic and anaerobic bacteria.
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Affiliation(s)
- Wen Chen
- Department of Chemistry, University of Helsinki, Finland
| | - Kajsa Roslund
- Department of Chemistry, University of Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Christopher L Fogarty
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Pirkko J Pussinen
- Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Finland
| | - Lauri Halonen
- Department of Chemistry, University of Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Markus Metsälä
- Department of Chemistry, University of Helsinki, Finland
| | - Markku Lehto
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
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Nemoto TK, Ohara-Nemoto Y. Exopeptidases and gingipains in Porphyromonas gingivalis as prerequisites for its amino acid metabolism. JAPANESE DENTAL SCIENCE REVIEW 2016; 52:22-29. [PMID: 28408952 PMCID: PMC5382784 DOI: 10.1016/j.jdsr.2015.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/20/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
Porphyromonas gingivalis, an asaccharolytic bacterium, utilizes amino acids as energy and carbon sources. Since amino acids are incorporated into the bacterial cells mainly as di- and tri-peptides, exopeptidases including dipeptidyl-peptidase (DPP) and tripeptidyl-peptidase are considered to be prerequisite components for their metabolism. We recently discovered DPP11, DPP5, and acylpeptidyl oligopeptidase in addition to previously reported DPP4, DPP7, and prolyl tripeptidyl peptidase A. DPP11 is a novel enzyme specific for acidic P1 residues (Asp and Glu) and distributed ubiquitously in eubacteria, while DPP5 is preferential for the hydrophobic P1 residue and the first entity identified in prokaryotes. Recently, acylpeptidyl oligopeptidase with a preference for hydrophobic P1 residues was found to release N-terminally blocked di- and tri-peptides. Furthermore, we also demonstrated that gingipains R and K contribute to P1-basic dipeptide production. These observations implicate that most, if not all, combinations of di- and tri-peptides are produced from extracellular oligopeptides even with an N-terminal modification. Here, we review P. gingivalis exopeptidases mainly in regard to their enzymatic characteristics. These exopeptidases with various substrate specificities benefit P. gingivalis for obtaining energy and carbon sources from the nutritionally limited subgingival environment.
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Affiliation(s)
- Takayuki K. Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Japan
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Liu JH, Zhang ML, Zhang RY, Zhu WY, Mao SY. Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows. Microb Biotechnol 2016; 9:257-68. [PMID: 26833450 PMCID: PMC4767291 DOI: 10.1111/1751-7915.12345] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 01/19/2023] Open
Abstract
The objective of this research was to compare the composition of bacterial microbiota associated with the ruminal content (RC), ruminal epithelium (RE) and faeces of Holstein dairy cows. The RC, RE and faecal samples were collected from six Holstein dairy cows when the animals were slaughtered. Community compositions of bacterial 16S rRNA genes from RC, RE and faeces were determined using a MiSeq sequencing platform with bacterial‐targeting universal primers 338F and 806R. UniFrac analysis revealed that the bacterial communities of RC, RE and faeces were clearly separated from each other. Statistically significant dissimilarities were observed between RC and faeces (P = 0.002), between RC and RE (P = 0.003), and between RE and faeces (P = 0.001). A assignment of sequences to taxa showed that the abundance of the predominant phyla Bacteroidetes was lower in RE than in RC, while a significant higher (P < 0.01) abundance of Proteobacteria was present in RE than in RC. When compared with the RC, the abundance of Firmicutes and Verrucomicrobia was higher in faeces, and RC contained a greater abundance of Bacteroidetes and Tenericutes. A higher proportions of Butyrivibrio and Campylobacter dominated RE as compared to RC. The faecal microbiota was less diverse than RC and dominated by genera Turicibacter and Clostridium. In general, these findings clearly demonstrated the striking compositional differences among RC, RE and faeces, indicating that bacterial communities are specific and adapted to the harbouring environment.
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Affiliation(s)
- Jun-hua Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Meng-ling Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Rui-yang Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Wei-yun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Sheng-yong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
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44
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Yoshida Y, Sato M, Nagano K, Hasegawa Y, Okamoto T, Yoshimura F. Production of 4-hydroxybutyrate from succinate semialdehyde in butyrate biosynthesis in Porphyromonas gingivalis. Biochim Biophys Acta Gen Subj 2015; 1850:2582-91. [DOI: 10.1016/j.bbagen.2015.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/04/2015] [Accepted: 09/24/2015] [Indexed: 01/14/2023]
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45
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Tanda N, Hoshikawa Y, Ishida N, Sato T, Takahashi N, Hosokawa R, Koseki T. Oral malodorous gases and oral microbiota: From halitosis to carcinogenesis. J Oral Biosci 2015. [DOI: 10.1016/j.job.2015.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Abstract
Recent advances in molecular biology have facilitated analyses of the oral microbiome ("Who are they?"); however, its functions (e.g., metabolic activities) are poorly understood ("What are they doing?"). This review aims to summarize our current understanding of the metabolism of the oral microbiome. Saccharolytic bacteria-including Streptococcus, Actinomyces, and Lactobacillus species-degrade carbohydrates into organic acids via the Embden-Meyerhof-Parnas pathway and several of its branch pathways, resulting in dental caries, while alkalization and acid neutralization via the arginine deiminase system, urease, and so on, counteract acidification. Proteolytic/amino acid-degrading bacteria, including Prevotella and Porphyromonas species, break down proteins and peptides into amino acids and degrade them further via specific pathways to produce short-chain fatty acids, ammonia, sulfur compounds, and indole/skatole, which act as virulent and modifying factors in periodontitis and oral malodor. Furthermore, it is suggested that ethanol-derived acetaldehyde can cause oral cancer, while nitrate-derived nitrite can aid caries prevention and systemic health. Microbial metabolic activity is influenced by the oral environment; however, it can also modify the oral environment, enhance the pathogenicity of bacteria, and induce microbial selection to create more pathogenic microbiome. Taking a metabolomic approach to analyzing the oral microbiome is crucial to improving our understanding of the functions of the oral microbiome.
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Affiliation(s)
- N Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
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47
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Lysine acetylation is a common post-translational modification of key metabolic pathway enzymes of the anaerobe Porphyromonas gingivalis. J Proteomics 2015; 128:352-64. [PMID: 26341301 DOI: 10.1016/j.jprot.2015.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/21/2015] [Accepted: 08/21/2015] [Indexed: 01/12/2023]
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobe considered to be a keystone pathogen in the development of the bacterial-associated inflammatory oral disease chronic periodontitis. Although post-translational modifications (PTMs) of proteins are commonly found to modify protein function in eukaryotes and prokaryotes, PTMs such as lysine acetylation have not been examined in P. gingivalis. Lysine acetylation is the addition of an acetyl group to a lysine which removes this amino acid's positive charge and can induce changes in a protein's secondary structure and reactivity. A proteomics based approach combining immune-affinity enrichment with high sensitivity Orbitrap mass spectrometry identified 130 lysine acetylated peptides from 92 P. gingivalis proteins. The majority of these peptides (71) were attributed to 45 proteins with predicted metabolic activity; these proteins could be mapped to several P. gingivalis metabolic pathways where enzymes catalysing sequential reactions within the same pathway were often found acetylated. In particular, the catabolic pathways of complex anaerobic fermentation of amino acids to produce energy had 12 enzymes lysine acetylated. The results suggest that lysine acetylation may be an important mechanism in metabolic regulation in P. gingivalis, which is vital for P. gingivalis survival and adaptation of its metabolism throughout infection. Statement of significance. Porphyromonas gingivalis is a keystone pathogen in the development of chronic periodontitis, an inflammatory disease of the supporting tissues of the teeth. The ability of the pathogen to induce dysbiosis and disease is related to an array of specific virulence factors and metabolic regulation that enables the bacterium to proliferate in an inflamed periodontal pocket. The mechanisms P. gingivalis uses to adapt to a changing and hostile environment are poorly understood and here we show, for the first time, that enzymes of critical metabolic pathways for energy production in this bacterium were acetylated on certain lysine residues. These enzymes were often found catalysing sequential reactions within the same catabolic pathway. The results suggest that lysine acetylation is an important mechanism of metabolic regulation in P. gingivalis vital for its adaptation and proliferation to produce disease.
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48
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Moir JWB. Meningitis in adolescents: the role of commensal microbiota. Trends Microbiol 2015; 23:181-2. [PMID: 25818619 DOI: 10.1016/j.tim.2015.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/02/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
The pathogen Neisseria meningitidis causes disease amongst infants and adolescents/young adults. Here we argue that disease amongst adolescents is due largely to interaction between N. meningitidis and other members of the upper respiratory tract microbiota, through a metabolic interaction involving exchange of propionic acid.
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Affiliation(s)
- James W B Moir
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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49
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Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sci Rep 2015; 5:11151. [PMID: 26057589 PMCID: PMC4460893 DOI: 10.1038/srep11151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/15/2015] [Indexed: 11/25/2022] Open
Abstract
The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.
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Affiliation(s)
- Yasumitsu Sakamoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Yoshiyuki Suzuki
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Ippei Iizuka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Chika Tateoka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Saori Roppongi
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Mayu Fujimoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Hiroaki Tanaka
- Confocal Science Inc., 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Mitsugu Yamada
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Kazunori Ohta
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Hiroaki Gouda
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takamasa Nonaka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Nobutada Tanaka
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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50
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Real-time monitoring of the metabolic activity of periodontopathic bacteria. J Microbiol Methods 2015; 115:22-6. [PMID: 25986950 DOI: 10.1016/j.mimet.2015.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/14/2015] [Accepted: 05/14/2015] [Indexed: 11/20/2022]
Abstract
Bacterial metabolic activity is associated with the onset and progression mechanisms of oral biofilm-mediated disease; however, at present no method to monitor bacterial metabolism exists, especially for periodontopathic bacteria. Therefore, we aimed to establish a novel method for monitoring the metabolic activity of periodontopathic bacteria, Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi) and Fusobacterium nucleatum (Fn), as well as Streptococcus mutans (Sm) for comparison. The method is based on the dye resazurin, which is converted to the fluorescent molecule resorufin by reducing molecules derived from bacterial metabolism. Additionally, the effects of antimicrobial substances on bacterial metabolic activity were evaluated using this method. When bacterial suspensions were incubated with tryptone, glutamate, aspartate or glucose in the presence of resazurin, the fluorescence intensity increased over time by these bacterial metabolic reactions, indicating that this method can be used to monitor the metabolic activity of periodontopathic bacteria. Chlorhexidine showed the 50% inhibitory concentration (IC50) of 15-49 μg/ml for tryptone metabolism by Pg, Pi, and Fn, and 7.1-18 μg/ml for glucose metabolism by Pi and Sm. The IC50s for cetylpyridinium chloride and sodium dodecyl sulfate were 0.8-2.1 and 28-44 μg/ml, respectively for all bacteria examined. Fluoride had no effect except the IC50 of 640 μg/ml for Sm, while minocycline hydrochloride had no effect on any of the bacteria. The present study established the method for real-time monitoring of the metabolic activity of periodontopathic bacteria, and the method might be useful for evaluating the effects of antimicrobial substances on the bacterial metabolic activity.
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