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Olczak T, Śmiga M, Antonyuk SV, Smalley JW. Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution. Microbiol Mol Biol Rev 2024; 88:e0013123. [PMID: 38305743 PMCID: PMC10966948 DOI: 10.1128/mmbr.00131-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
SUMMARY Heme (iron protoporphyrin IX, FePPIX) is the main source of iron and PPIX for host-associated pathogenic bacteria, including members of the Bacteroidota (formerly Bacteroidetes) phylum. Porphyromonas gingivalis, a keystone oral pathogen, uses a unique heme uptake (Hmu) system, comprising a hemophore-like protein, designated as the first member of the novel HmuY family. Compared to classical, secreted hemophores utilized by Gram-negative bacteria or near-iron transporter domain-based hemophores utilized by Gram-positive bacteria, the HmuY family comprises structurally similar proteins that have undergone diversification during evolution. The best characterized are P. gingivalis HmuY and its homologs from Tannerella forsythia (Tfo), Prevotella intermedia (PinO and PinA), Bacteroides vulgatus (Bvu), and Bacteroides fragilis (BfrA, BfrB, and BfrC). In contrast to the two histidine residues coordinating heme iron in P. gingivalis HmuY, Tfo, PinO, PinA, Bvu, and BfrA preferentially use two methionine residues. Interestingly, BfrB, despite conserved methionine residue, binds the PPIX ring without iron coordination. BfrC binds neither heme nor PPIX in keeping with the lack of conserved histidine or methionine residues used by other members of the HmuY family. HmuY competes for heme binding and heme sequestration from host hemoproteins with other members of the HmuY family to increase P. gingivalis competitiveness. The participation of HmuY in the host immune response confirms its relevance in relation to the survival of P. gingivalis and its ability to induce dysbiosis not only in the oral microbiome but also in the gut microbiome or other host niches, leading to local injuries and involvement in comorbidities.
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Affiliation(s)
- Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, the University of Liverpool, Liverpool, United Kingdom
| | - John W. Smalley
- Institute of Life Course and Medical Sciences, School of Dentistry, the University of Liverpool, Liverpool, United Kingdom
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Ali Mohammed MM, Pettersen VK, Nerland AH, Wiker HG, Bakken V. Label-free quantitative proteomic analysis of the oral bacteria Fusobacterium nucleatum and Porphyromonas gingivalis to identify protein features relevant in biofilm formation. Anaerobe 2021; 72:102449. [PMID: 34543761 DOI: 10.1016/j.anaerobe.2021.102449] [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: 05/15/2021] [Revised: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The opportunistic pathogens Fusobacterium nucleatum and Porphyromonas gingivalis are Gram-negative bacteria associated with oral biofilm and periodontal disease. This study investigated interactions between F. nucleatum and P. gingivalis proteomes with the objective to identify proteins relevant in biofilm formation. METHODS We applied liquid chromatography-tandem mass spectrometry to determine the expressed proteome of F. nucleatum and P. gingivalis cells grown in biofilm or planktonic culture, and as mono- and dual-species models. The detected proteins were classified into functional categories and their label-free quantitative (LFQ) intensities statistically compared. RESULTS The proteomic analyses detected 1,322 F. nucleatum and 966 P. gingivalis proteins, including abundant virulence factors. Using univariate statistics, we identified significant changes between biofilm and planktonic culture (p-value ≤0.05) in 0,4% F. nucleatum, 7% P. gingivalis, and 14% of all proteins in the dual-species model. For both species, proteins involved in vitamin B2 (riboflavin) metabolism had significantly increased levels in biofilm. In both mono- and dual-species biofilms, P. gingivalis increased the production of proteins for translation, oxidation-reduction, and amino acid metabolism compared to planktonic cultures. However, when we compared LFQ intensities between mono- and dual-species, over 90% of the significantly changed P. gingivalis proteins had their levels reduced in biofilm and planktonic settings of the dual-species model. CONCLUSIONS The findings suggest that P. gingivalis reduces the production of multiple proteins because of the F. nucleatum presence. The results highlight the complex interactions of bacteria contributing to oral biofilms, which need to be considered in the design of prevention strategies.
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Affiliation(s)
| | | | - Audun H Nerland
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Harald G Wiker
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Vidar Bakken
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
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Bostanci N, Grant M, Bao K, Silbereisen A, Hetrodt F, Manoil D, Belibasakis GN. Metaproteome and metabolome of oral microbial communities. Periodontol 2000 2020; 85:46-81. [PMID: 33226703 DOI: 10.1111/prd.12351] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.
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Affiliation(s)
- Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Melissa Grant
- Biological Sciences, School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Kai Bao
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Franziska Hetrodt
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Manoil
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Bostanci N, Bao K, Greenwood D, Silbereisen A, Belibasakis GN. Periodontal disease: From the lenses of light microscopy to the specs of proteomics and next-generation sequencing. Adv Clin Chem 2019; 93:263-290. [PMID: 31655732 DOI: 10.1016/bs.acc.2019.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Periodontal disease entails the inflammatory destruction of the tooth supporting (periodontal) tissues as a result of polymicrobial colonization of the tooth surface in the form of biofilms. Extensive data collected over the past decades on this chronic disease demonstrate that its progression is infrequent and episodic, and the susceptibility to it can vary among individuals. Physical assessments of previously occurring damage to periodontal tissues remain the cornerstone of detection and diagnosis, whereas traditionally used diagnostic procedures do neither identify susceptible individuals nor distinguish between disease-active and disease-inactive periodontal sites. Thus, more sensitive and accurate "measurable biological indicators" of periodontal diseases are needed in order to place diagnosis (e.g., the presence or stage) and management of the disease on a more rational less empirical basis. Contemporary "omics" technologies may help unlock the path to this quest. High throughput nucleic acid sequencing technologies have enabled us to examine the taxonomic distribution of microbial communities in oral health and disease, whereas proteomic technologies allowed us to decipher the molecular state of the host in disease, as well as the interactive cross-talk of the host with the microbiome. The newly established field of metaproteomics has enabled the identification of the repertoire of proteins that oral microorganisms use to compete or co-operate with each other. Vast such data is derived from oral biological fluids, including gingival crevicular fluid and saliva, which is progressively completed and catalogued as the analytical technologies and bioinformatics tools progressively advance. This chapter covers the current "omics"-derived knowledge on the microbiome, the host and their "interactome" with regard to periodontal diseases, and addresses challenges and opportunities ahead.
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Affiliation(s)
- Nagihan Bostanci
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Kai Bao
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Greenwood
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Sánchez MC, Romero-Lastra P, Ribeiro-Vidal H, Llama-Palacios A, Figuero E, Herrera D, Sanz M. Comparative gene expression analysis of planktonic Porphyromonas gingivalis ATCC 33277 in the presence of a growing biofilm versus planktonic cells. BMC Microbiol 2019; 19:58. [PMID: 30866810 PMCID: PMC6417203 DOI: 10.1186/s12866-019-1423-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/19/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis, a microorganism residing in the oral cavity within complex multispecies biofilms, is one of the keystone pathogens in the onset and progression of periodontitis. In this in vitro study, using DNA microarray, we investigate the differential gene expression of Porphyromonas gingivalis ATCC 33277 when growing in the presence or in absence of its own monospecies biofilm. RESULTS Approximately 1.5% of genes (28 out of 1909 genes, at 1.5 fold change or more, p-value < 0.05) were differentially expressed by P. gingivalis cells when in the presence of a biofilm. These genes were predominantly related to the metabolism of iron, bacterial adhesion, invasion, virulence and quorum-sensing system. The results from microarrays were consistent with those obtained by RT-qPCR. CONCLUSION This study provides insight on the transcriptional changes of planktonic P. gingivalis cells when growing in the presence of a biofilm. The resulting phenotypes provide information on changes occurring in the gene expression of this pathogen.
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Affiliation(s)
- María C. Sánchez
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | | | - Honorato Ribeiro-Vidal
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Arancha Llama-Palacios
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Elena Figuero
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - David Herrera
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
| | - Mariano Sanz
- Etiology and Therapy of Periodontal Diseases (ETEP) Research Group, University Complutense, Madrid, Spain
- Department of Dental Clinical Specialities (DDCS), Faculty of Odontology, Plaza Ramón y Cajal s/n Ciudad Universitaria, 28040 Madrid, Spain
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Bender P, Egger A, Westermann M, Taudte N, Sculean A, Potempa J, Möller B, Buchholz M, Eick S. Expression of human and Porphyromonas gingivalis glutaminyl cyclases in periodontitis and rheumatoid arthritis-A pilot study. Arch Oral Biol 2018; 97:223-230. [PMID: 30399509 DOI: 10.1016/j.archoralbio.2018.10.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Human glutaminyl cyclases (QC and isoQC) play an important role in maintaining inflammatory conditions. Meanwhile a glutaminyl cyclase synthesized by Porphyromonas gingivalis (PgQC), a key pathogen in developing periodontitis and a potential link of periodontitis with rheumatoid arthritis (RA), was discovered. This study was aimed to determine the expression of QC, isoQC and PgQC in patients with chronic periodontitis (CP) and RA. DESIGN Thirty volunteers were enrolled in a pilot study and divided into 3 groups (healthy, CP and RA individuals). Blood samples, biofilm and gingival crevicular fluid (GCF) were analysed for mRNA expression of QC, isoQC and P. gingivalis QC. Major bacteria being associated with periodontal disease were quantified in subgingival biofilm and protein levels for monocyte chemoattractant protein (MCP)-1, MCP-3 and interleukin (IL)-1β) were determined in the GCF. Expression of PgQC on the mRNA and protein levels was assessed in two P. gingivalis strains. RESULTS PgQC is expressed in P. gingivalis strains and the protein seems to be located mainly in peri-plasmatic space. mRNA expression of QC was significantly increased in the peripheral blood from RA patients vs. healthy subjects and CP patients (p = 0.013 and p = 0.003, respectively). In GCF of RA patients, QC mRNA was detected more frequently than in healthy controls (p = 0.043). In these samples IL-1β levels were also elevated compared to GCF from periodontally healthy individuals (p = 0.003). PgQC was detected in eight out of the 13 P. gingivalis positive biofilm samples. CONCLUSION Activity of QC may play a supportive role in maintaining chronic periodontal inflammation and destruction in RA. PgQC is expressed in vivo but further research is needed to evaluate biological importance of this enzyme and if it constitutes a potential target in periodontal antimicrobial therapy.
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Affiliation(s)
- Philip Bender
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Andreas Egger
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Martin Westermann
- Center of Electron Microscopy, University Hospital of Jena, Jena, Germany
| | - Nadine Taudte
- Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle/Saale, Germany
| | - Anton Sculean
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Krakow, Poland; Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, USA
| | - Burkhard Möller
- Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Bern, Switzerland
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle/Saale, Germany
| | - Sigrun Eick
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland.
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A proteomic characterization shows differences in the milk fat globule membrane of buffalo and bovine milk. FOOD BIOSCI 2017. [DOI: 10.1016/j.fbio.2017.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Bostanci N, Bao K. Contribution of proteomics to our understanding of periodontal inflammation. Proteomics 2017; 17. [DOI: 10.1002/pmic.201500518] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/15/2016] [Accepted: 12/15/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Nagihan Bostanci
- Department of Dental Medicine; Karolinska Institute; Huddinge Sweden
| | - Kai Bao
- Division of Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
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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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Khemiri A, Jouenne T, Cosette P. Proteomics dedicated to biofilmology: What have we learned from a decade of research? Med Microbiol Immunol 2015; 205:1-19. [PMID: 26068406 DOI: 10.1007/s00430-015-0423-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 06/03/2015] [Indexed: 12/31/2022]
Abstract
Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.
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Affiliation(s)
- Arbia Khemiri
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France.
- University of Normandy, UR, Mont-Saint-Aignan, France.
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France.
| | - Thierry Jouenne
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Laboratory "Polymères, Biopolymères, Surfaces", 76820, Mont-Saint-Aignan, France
- University of Normandy, UR, Mont-Saint-Aignan, France
- PISSARO Proteomic Facility, IRIB, 76820, Mont-Saint-Aignan, France
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Butler CA, Dashper SG, Khan HS, Zhang L, Reynolds EC. The interplay between iron, haem and manganese in Porphyromonas gingivalis. J Oral Biosci 2015. [DOI: 10.1016/j.job.2014.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Karched M, Bhardwaj RG, Inbamani A, Asikainen S. Quantitation of biofilm and planktonic life forms of coexisting periodontal species. Anaerobe 2015; 35:13-20. [PMID: 25926392 DOI: 10.1016/j.anaerobe.2015.04.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Complexity of oral polymicrobial communities has prompted a need for developing in vitro models to study behavior of coexisting bacteria. Little knowledge is available of in vitro co-growth of several periodontitis-associated species without early colonizers of dental plaque. THE AIM was to determine temporal changes in the quantities of six periodontal species in an in vitro biofilm model in comparison with parallel planktonic cultures. MATERIAL AND METHODS Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Parvimonas micra, Campylobacter rectus and Fusobacterium nucleatum were anaerobically grown as multispecies and monospecies biofilms and parallel planktonic cultures using cell culture plates and microfuge tubes, respectively. After incubating 2, 4, 6, 8 days, biofilms and planktonic cultures were harvested, DNA extracted and the target species quantified using qPCR with species-specific 16S rDNA primers. Biofilm growth as monocultures was visualized at day 2 and 8 with confocal microscopy and crystal violet staining. RESULTS The six species were found throughout the test period in all culture conditions, except that P. gingivalis and F. nucleatum were not detected in multispecies planktonic cultures at day 8. In multispecies biofilm, P. gingivalis qPCR counts (cells/ml) increased (P<0.05) from day 2-8 and were then higher (P<0.05) than those of A. actinomycetemcomitans and C. rectus, whereas in monospecies biofilm, P. gingivalis counts were lower (P<0.05) than those of the other species, except A. actinomycetemcomitans. When multi- and monospecies biofilm cultures were compared, P. gingivalis counts were higher (P<0.05) but those of the other species, except P. intermedia, lower (P<0.05) in multispecies biofilm. Comparison between planktonic and biofilm cultures showed that A. actinomycetemcomitans, P. micra and C. rectus had higher (P<0.05) counts in planktonic cultures no matter whether grown in mono- or multispecies environment. CONCLUSIONS Six periodontal species were able to form multispecies biofilm up to 8 days in vitro without pioneer plaque bacteria. P. gingivalis seemed to prefer multispecies biofilm environment whereas P. micra and A. actinomycetemcomitans planktonic culture.
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Affiliation(s)
- Maribasappa Karched
- Oral Microbiology, General Facility Laboratory, Faculty of Dentistry, Kuwait University, Kuwait
| | - Radhika G Bhardwaj
- Oral Microbiology, General Facility Laboratory, Faculty of Dentistry, Kuwait University, Kuwait
| | - Anandavalli Inbamani
- Oral Microbiology, General Facility Laboratory, Faculty of Dentistry, Kuwait University, Kuwait
| | - Sirkka Asikainen
- Oral Microbiology, General Facility Laboratory, Faculty of Dentistry, Kuwait University, Kuwait.
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Butler CA, Dashper SG, Zhang L, Seers CA, Mitchell HL, Catmull DV, Glew MD, Heath JE, Tan Y, Khan HSG, Reynolds EC. The Porphyromonas gingivalis ferric uptake regulator orthologue binds hemin and regulates hemin-responsive biofilm development. PLoS One 2014; 9:e111168. [PMID: 25375181 PMCID: PMC4222909 DOI: 10.1371/journal.pone.0111168] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/26/2014] [Indexed: 12/27/2022] Open
Abstract
Porphyromonas gingivalis is a Gram-negative pathogen associated with the biofilm-mediated disease chronic periodontitis. P. gingivalis biofilm formation is dependent on environmental heme for which P. gingivalis has an obligate requirement as it is unable to synthesize protoporphyrin IX de novo, hence P. gingivalis transports iron and heme liberated from the human host. Homeostasis of a variety of transition metal ions is often mediated in Gram-negative bacteria at the transcriptional level by members of the Ferric Uptake Regulator (Fur) superfamily. P. gingivalis has a single predicted Fur superfamily orthologue which we have designated Har (heme associated regulator). Recombinant Har formed dimers in the presence of Zn2+ and bound one hemin molecule per monomer with high affinity (Kd of 0.23 µM). The binding of hemin resulted in conformational changes of Zn(II)Har and residue 97Cys was involved in hemin binding as part of a predicted -97C-98P-99L- hemin binding motif. The expression of 35 genes was down-regulated and 9 up-regulated in a Har mutant (ECR455) relative to wild-type. Twenty six of the down-regulated genes were previously found to be up-regulated in P. gingivalis grown as a biofilm and 11 were up-regulated under hemin limitation. A truncated Zn(II)Har bound the promoter region of dnaA (PGN_0001), one of the up-regulated genes in the ECR455 mutant. This binding decreased as hemin concentration increased which was consistent with gene expression being regulated by hemin availability. ECR455 formed significantly less biofilm than the wild-type and unlike wild-type biofilm formation was independent of hemin availability. P. gingivalis possesses a hemin-binding Fur orthologue that regulates hemin-dependent biofilm formation.
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Affiliation(s)
- Catherine A. Butler
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Stuart G. Dashper
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Christine A. Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Helen L. Mitchell
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Deanne V. Catmull
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Michelle D. Glew
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Jacqueline E. Heath
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Yan Tan
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Hasnah S. G. Khan
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
- * E-mail:
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Cross KJ, Huq NL, Park SH, Park JS, Pham P, Quah M, Ranjan M, Reynolds EC. Bioinformatic investigation of the cost management strategies of five oral microbes. Mol Oral Microbiol 2014; 30:87-96. [PMID: 25052707 DOI: 10.1111/omi.12071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2014] [Indexed: 01/08/2023]
Abstract
Some amino acids are more energetically costly to synthesize de novo, therefore many microbes have evolved to regulate the metabolic expenditure of the cell and reduce the energy burden of extracellular unrecyclable proteins. Several oral bacterial species take up amino acids and peptides obtained from proteolysis of host proteins and hence do not rely only on de novo synthesis. The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins. Since the relative de novo amino acid synthesis costs are proportional to the masses of the amino acids, the energy costs of producing proteins were assessed by calculating the mean amino acid mass for each protein. For Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia and Streptococcus sanguinis, the outer membrane/extracellular proteins are made up of a much larger percentage of lower average mass amino acids whereas cytoplasmic proteins are made up of a larger proportion of higher average mass amino acid residues. These results are consistent with the five oral bacterial species employing energy-saving mechanisms in the production of extracellular unrecyclable proteins. Interestingly, the P. gingivalis and S. sanguinis genomes exhibited significantly lower predicted mean amino acid masses compared with those of the genomes of the other three species, suggesting that this may provide them with an energy advantage with respect to protein biosynthetic cost.
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Affiliation(s)
- K J Cross
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Vic., Australia
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15
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Wright CJ, Burns LH, Jack AA, Back CR, Dutton LC, Nobbs AH, Lamont RJ, Jenkinson HF. Microbial interactions in building of communities. Mol Oral Microbiol 2013; 28:83-101. [PMID: 23253299 PMCID: PMC3600090 DOI: 10.1111/omi.12012] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2012] [Indexed: 12/31/2022]
Abstract
Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development.
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Affiliation(s)
- Christopher J. Wright
- Department of Oral Health and Systemic Disease, University of Louisville, 570 South Preston Street, Louisville, Kentucky, 40202, USA
| | - Logan H. Burns
- Department of Oral Health and Systemic Disease, University of Louisville, 570 South Preston Street, Louisville, Kentucky, 40202, USA
| | - Alison A. Jack
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS12LY, UK
| | - Catherine R. Back
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS12LY, UK
| | - Lindsay C. Dutton
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS12LY, UK
| | - Angela H. Nobbs
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS12LY, UK
| | - Richard J. Lamont
- Department of Oral Health and Systemic Disease, University of Louisville, 570 South Preston Street, Louisville, Kentucky, 40202, USA
| | - Howard F. Jenkinson
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS12LY, UK
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16
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Kuboniwa M, Tribble GD, Hendrickson EL, Amano A, Lamont RJ, Hackett M. Insights into the virulence of oral biofilms: discoveries from proteomics. Expert Rev Proteomics 2013; 9:311-23. [PMID: 22809209 DOI: 10.1586/epr.12.16] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review covers developments in the study of polymicrobial communities, biofilms and selected areas of host response relevant to dental plaque and related areas of oral biology. The emphasis is on recent studies in which proteomic methods, particularly those using mass spectrometry as a readout, have played a major role in the investigation. The last 5-10 years have seen a transition of such methods from the periphery of oral biology to the mainstream, as in other areas of biomedical science. For reasons of focus and space, the authors do not discuss biomarker studies relevant to improved diagnostics for oral health, as this literature is rather substantial in its own right and deserves a separate treatment. Here, global gene regulation studies of plaque-component organisms, biofilm formation, multispecies interactions and host-microbe interactions are discussed. Several aspects of proteomics methodology that are relevant to the studies of multispecies systems are commented upon.
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Affiliation(s)
- Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
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17
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Zainal-Abidin Z, Veith PD, Dashper SG, Zhu Y, Catmull DV, Chen YY, Heryanto DC, Chen D, Pyke JS, Tan K, Mitchell HL, Reynolds EC. Differential proteomic analysis of a polymicrobial biofilm. J Proteome Res 2012; 11:4449-64. [PMID: 22808953 DOI: 10.1021/pr300201c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia exist in a polymicrobial biofilm associated with chronic periodontitis. The aim of this study was to culture these three species as a polymicrobial biofilm and to determine proteins important for bacterial interactions. In a flow cell all three species attached and grew as a biofilm; however, after 90 h of culture P. gingivalis and T. denticola were closely associated and dominated the polymicrobial biofilm. For comparison, planktonic cultures of P. gingivalis and T. denticola were grown separately in continuous culture. Whole cell lysates were subjected to SDS-PAGE, followed by in-gel proteolytic H₂¹⁶O/H₂¹⁸O labeling. From two replicates, 135 and 174 P. gingivalis proteins and 134 and 194 T. denticola proteins were quantified by LC-MALDI TOF/TOF MS. The results suggest a change of strategy in iron acquisition by P. gingivalis due to large increases in the abundance of HusA and HusB in the polymicrobial biofilm while HmuY and other iron/haem transport systems decreased. Significant changes in the abundance of peptidases and enzymes involved in glutamate and glycine catabolism suggest syntrophy. These data indicate an intimate association between P. gingivalis and T. denticola in a biofilm that may play a role in disease pathogenesis.
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Affiliation(s)
- Zamirah Zainal-Abidin
- Oral Health CRC, Melbourne Dental School and the Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
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18
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Porphyromonas gingivalis antigens differently participate in the proliferation and cell death of human PBMC. Arch Oral Biol 2012; 57:314-20. [DOI: 10.1016/j.archoralbio.2011.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 09/05/2011] [Indexed: 11/20/2022]
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19
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Seneviratne CJ, Wang Y, Jin L, Wong SSW, Herath TDK, Samaranayake LP. Unraveling the resistance of microbial biofilms: Has proteomics been helpful? Proteomics 2012; 12:651-65. [DOI: 10.1002/pmic.201100356] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/07/2011] [Accepted: 10/11/2011] [Indexed: 01/03/2023]
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20
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Ang CS, Binos S, Knight MI, Moate PJ, Cocks BG, McDonagh MB. Global Survey of the Bovine Salivary Proteome: Integrating Multidimensional Prefractionation, Targeted, and Glycocapture Strategies. J Proteome Res 2011; 10:5059-69. [DOI: 10.1021/pr200516d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ching-Seng Ang
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Steve Binos
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Matthew I Knight
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Peter J Moate
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
| | - Matthew B McDonagh
- Biosciences Research Division, ‡Dairy Futures Cooperative Research Centre, and §Future Farming Research Division, Department of Primary Industries, 1 Park Drive, Bundoora, Victoria, Australia
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Li MY, Peng F, Zuo JH, Yi H, Tang CE, Li C, Zhang PF, Chen ZC, Xiao ZQ. Enhancing the stability of 18O-labeled peptides through removal of immobilized trypsin by ZipTips. Anal Biochem 2011; 408:37-45. [DOI: 10.1016/j.ab.2010.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 07/30/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
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22
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van Alen T, Claus H, Zahedi RP, Groh J, Blazyca H, Lappann M, Sickmann A, Vogel U. Comparative proteomic analysis of biofilm and planktonic cells of Neisseria meningitidis. Proteomics 2010; 10:4512-21. [PMID: 21136603 DOI: 10.1002/pmic.201000267] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neisseria meningitidis is a commensal of the human nasopharynx occasionally causing invasive disease. In vitro biofilms have been employed to model meningococcal carriage. A proteomic analysis of meningococcal biofilms was conducted and metabolic changes related to oxygen and nutrient limitation and upregulation of proteins involved in ROS defense were observed. The upregulated MntC which protects against ROS was shown to be required for meningococcal biofilm formation, but not for planktonic growth. ROS-induced proteomic changes might train the biofilm to cope with immune effectors.
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Affiliation(s)
- Tessa van Alen
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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23
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Liu N, Wu H, Liu H, Chen G, Cai Z. Microwave-Assisted 18O-Labeling of Proteins Catalyzed by Formic Acid. Anal Chem 2010; 82:9122-6. [PMID: 20939519 DOI: 10.1021/ac101888f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ning Liu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Hanzhi Wu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Hongxia Liu
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Guonan Chen
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
| | - Zongwei Cai
- Central Laboratory, The Second Hospital of Jilin University, Changchun, China, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China, The Key Laboratory of Chemical Biology, Guangdong Province, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China, Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou 350002, Fujian, China
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24
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Dashper SG, Seers CA, Tan KH, Reynolds EC. Virulence factors of the oral spirochete Treponema denticola. J Dent Res 2010; 90:691-703. [PMID: 20940357 DOI: 10.1177/0022034510385242] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There is compelling evidence that treponemes are involved in the etiology of several chronic diseases, including chronic periodontitis as well as other forms of periodontal disease. There are interesting parallels with other chronic diseases caused by treponemes that may indicate similar virulence characteristics. Chronic periodontitis is a polymicrobial disease, and recent animal studies indicate that co-infection of Treponema denticola with other periodontal pathogens can enhance alveolar bone resorption. The bacterium has a suite of molecular determinants that could enable it to cause tissue damage and subvert the host immune response. In addition to this, it has several non-classic virulence determinants that enable it to interact with other pathogenic bacteria and the host in ways that are likely to promote disease progression. Recent advances, especially in molecular-based methodologies, have greatly improved our knowledge of this bacterium and its role in disease.
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Affiliation(s)
- S G Dashper
- Cooperative Research Centre for Oral Health, Melbourne Dental School and Bio21 Institute, The University of Melbourne, 720 Swanston Street, Victoria 3010, Australia
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25
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ZHAO Y, LU Z, JIA W, YING WT, QIAN XH. Peptide Labeling with Improved <SUP>18</SUP>O Incorporation Method. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.3724/sp.j.1096.2010.00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Bull AT. The renaissance of continuous culture in the post-genomics age. J Ind Microbiol Biotechnol 2010; 37:993-1021. [PMID: 20835748 DOI: 10.1007/s10295-010-0816-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/11/2010] [Indexed: 01/08/2023]
Abstract
The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent CT27NJ, UK.
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27
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Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
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28
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Olczak T, Wójtowicz H, Ciuraszkiewicz J, Olczak M. Species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of Porphyromonas gingivalis HmuY. BMC Microbiol 2010; 10:134. [PMID: 20438645 PMCID: PMC2873494 DOI: 10.1186/1471-2180-10-134] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 05/04/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis is a major etiological agent of chronic periodontitis. The aim of this study was to examine the species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of the P. gingivalis heme-binding protein HmuY. RESULTS HmuY is a unique protein of P. gingivalis since only low amino-acid sequence homology has been found to proteins encoded in other species. It is exposed on the cell surface and highly abundant in the outer membrane of the cell, in outer-membrane vesicles, and is released into culture medium in a soluble form. The protein is produced constitutively at low levels in bacteria grown under high-iron/heme conditions and at higher levels in bacteria growing under the low-iron/heme conditions typical of dental plaque. HmuY is immunogenic and elicits high IgG antibody titers in rabbits. It is also engaged in homotypic biofilm formation by P. gingivalis. Anti-HmuY antibodies exhibit inhibitory activity against P. gingivalis growth and biofilm formation. CONCLUSIONS Here it is demonstrated that HmuY may play a significant role not only in heme acquisition, but also in biofilm accumulation on abiotic surfaces. The data also suggest that HmuY, as a surface-exposed protein, would be available for recognition by the immune response during chronic periodontitis and the production of anti-HmuY antibodies may inhibit biofilm formation.
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Affiliation(s)
- Teresa Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Halina Wójtowicz
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Justyna Ciuraszkiewicz
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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30
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FimR and FimS: biofilm formation and gene expression in Porphyromonas gingivalis. J Bacteriol 2010; 192:1332-43. [PMID: 20061484 DOI: 10.1128/jb.01211-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Porphyromonas gingivalis is a late-colonizing bacterium of the subgingival dental plaque biofilm associated with periodontitis. Two P. gingivalis genes, fimR and fimS, are predicted to encode a two-component signal transduction system comprising a response regulator (FimR) and a sensor histidine kinase (FimS). In this study, we show that fimS and fimR, although contiguous on the genome, are not part of an operon. We inactivated fimR and fimS in both the afimbriated strain W50 and the fimbriated strain ATCC 33277 and demonstrated that both mutants formed significantly less biofilm than their respective wild-type strains. Quantitative reverse transcription-real-time PCR showed that expression of fimbriation genes was reduced in both the fimS and fimR mutants of strain ATCC 33277. The mutations had no effect, in either strain, on the P. gingivalis growth rate or on the response to hydrogen peroxide or growth at pH 9, at 41 degrees C, or at low hemin availability. Transcriptome analysis using DNA microarrays revealed that inactivation of fimS resulted in the differential expression of 10% of the P. gingivalis genome (>1.5-fold; P < 0.05). Notably genes encoding seven different transcriptional regulators, including the fimR gene and three extracytoplasmic sigma factor genes, were differentially expressed in the fimS mutant.
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31
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ZHAO Y, LU Z, JIA W, YING WT, QIAN XH. Peptide Labeling with Improved 18O Incorporation Method. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60017-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Hendrickson EL, Xia Q, Wang T, Lamont RJ, Hackett M. Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database. BMC Microbiol 2009; 9:185. [PMID: 19723305 PMCID: PMC2753363 DOI: 10.1186/1471-2180-9-185] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 09/01/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins. RESULTS Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription. CONCLUSION Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular P. gingivalis may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.
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Affiliation(s)
- Erik L Hendrickson
- Department of Chemical Engineering, Box 355014 University of Washington, Seattle, WA 98195, USA.
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33
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Veith PD, O’Brien-Simpson NM, Tan Y, Djatmiko DC, Dashper SG, Reynolds EC. Outer Membrane Proteome and Antigens of Tannerella forsythia. J Proteome Res 2009; 8:4279-92. [DOI: 10.1021/pr900372c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul D. Veith
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
| | - Neil M. O’Brien-Simpson
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
| | - Yan Tan
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
| | - Deasy C. Djatmiko
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
| | - Stuart G. Dashper
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
| | - Eric C. Reynolds
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School, Bio21 Institute, The University of Melbourne, 720 Swanston Street, Melbourne, Victoria, 3010, Australia
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34
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Veith PD, Dashper SG, O'Brien-Simpson NM, Paolini RA, Orth R, Walsh KA, Reynolds EC. Major proteins and antigens of Treponema denticola. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1421-32. [PMID: 19501677 DOI: 10.1016/j.bbapap.2009.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 05/20/2009] [Accepted: 06/01/2009] [Indexed: 11/15/2022]
Abstract
Treponema denticola is a Gram-negative, motile, asaccharolytic, anaerobic spirochaete which along with Porphyromonas gingivalis and Tannerella forsythia has been shown to form a bacterial consortium called the Red Complex that is strongly associated with the clinical progression of chronic periodontitis. T. denticola was grown in continuous culture in a complex medium with a mean generation time of 15.75 h. Samples from two different membrane-enriched preparations and a cytoplasm-enriched preparation were separated by two-dimensional gel electrophoresis and the proteins identified by MALDI-TOF/TOF mass spectrometry. In total, 219 non-redundant proteins were identified including numerous virulence factors, lipoproteins, ABC transporter proteins and enzymes involved in the metabolism of nine different amino acids of which glycine seems to be of particular importance. Novel findings include the identification of several abundant peptide uptake systems, and the identification of three flagellar filament outer layer proteins. Two-dimensional Western blot analysis using sera from mice immunized with formalin-killed T. denticola cells suggested that Msp, PrcA, OppA, OppA10, MglB, TmpC and several flagellar filament proteins are antigenic.
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Affiliation(s)
- Paul D Veith
- Melbourne Dental School, Bio21 Molecular Science and Biotechnology Institute, the University of Melbourne, Victoria, 3010, Australia
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35
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Fang F, Liu P, Wang H, Zhang L, Zhang J, Gao Y, Zeng L, Guo Y. Studies of keratins in tongue coating samples of hepatitis B patients by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1703-1709. [PMID: 19412920 DOI: 10.1002/rcm.4060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Pooled tongue coating samples from 64 hepatitis B patients and 24 healthy adults were studied and a major band of differential proteins was found by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The differential proteins in this band were identified and proved to be keratins by liquid chromatography/tandem mass spectrometry (LC/MS/MS) and Western blot analysis. Furthermore, relative quantification of the identified keratins was performed via using stable isotopic labeling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), showing the higher expression level of these keratins in tongue coating samples of hepatitis B patients than healthy adults. These results provided additional information to understand the medical diagnosis depending on the tongue coating.
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Affiliation(s)
- Fang Fang
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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36
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Kuboniwa M, Hendrickson EL, Xia Q, Wang T, Xie H, Hackett M, Lamont RJ. Proteomics of Porphyromonas gingivalis within a model oral microbial community. BMC Microbiol 2009; 9:98. [PMID: 19454014 PMCID: PMC2689231 DOI: 10.1186/1471-2180-9-98] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 05/19/2009] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community. RESULTS 1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms. CONCLUSION Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.
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Affiliation(s)
- Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan.
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Wójtowicz H, Guevara T, Tallant C, Olczak M, Sroka A, Potempa J, Solà M, Olczak T, Gomis-Rüth FX. Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis. PLoS Pathog 2009; 5:e1000419. [PMID: 19424422 PMCID: PMC2671838 DOI: 10.1371/journal.ppat.1000419] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 04/07/2009] [Indexed: 11/18/2022] Open
Abstract
Infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. Among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. Porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. It recruits heme through HmuY, which sequesters heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. Here we report that heme binding does not significantly affect the secondary structure of HmuY. The crystal structure of heme-bound HmuY reveals a new all-β fold mimicking a right hand. The thumb and fingers pinch heme iron through two apical histidine residues, giving rise to highly symmetric octahedral iron co-ordination. The tetrameric quaternary arrangement of the protein found in the crystal structure is consistent with experiments in solution. It shows that thumbs and fingertips, and, by extension, the bound heme groups, are shielded from competing heme-binding proteins from the host. This may also facilitate heme transport to HmuR for internalization. HmuY, both in its apo- and in its heme-bound forms, is resistant to proteolytic digestion by trypsin and the major secreted proteases of P. gingivalis, gingipains K and R. It is also stable against thermal and chemical denaturation. In conclusion, these studies reveal novel molecular properties of HmuY that are consistent with its role as a putative virulence factor during bacterial infection. Pathogenic bacteria cause infection in humans as found in periodontitis, which is a chronic inflammation of the gums caused by Porphyromonas gingivalis. As part of the infective process, bacteria must acquire nutrients to survive and multiply at the infection site, and among such nutrients is heme. This is an iron-dependent co-factor of several indispensable enzymes and proteins. P. gingivalis liberates heme from host heme-binding proteins through the action of proteases and arranges its transport to the bacterial cell through two proteins, HmuY and HmuR. They grab free heme and transport it across the bacterial membrane into the cell, respectively. This function poses stringent conditions on these proteins regarding stability and resistance toward the host immune system. We report here that HmuY is very stable and that it displays a novel protein fold, which consists only of β-strands. It reminds us of a right hand, whose fingers trap heme. Once heme is bound, HmuY forms tetramers, which have the four heme-binding sites buried and thus protected from competing host heme-binding proteins. This feature also facilitates heme transport to HmuR and into the bacterial cell. All these data may help to develop new antibacterial agents at times in which resistance toward antibiotics, both at intensive healthcare stations and in the community, poses serious challenges to human health.
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Affiliation(s)
- Halina Wójtowicz
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Tibisay Guevara
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Cynthia Tallant
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Mariusz Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Aneta Sroka
- Laboratory of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Laboratory of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Periodontics, University of Louisville School of Dentistry, Louisville, Kentucky, United States of America
| | - Maria Solà
- Structural MitoLab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Teresa Olczak
- Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
- * E-mail: (TO); (FXG-R)
| | - F. Xavier Gomis-Rüth
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
- * E-mail: (TO); (FXG-R)
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Comparative proteomic analysis of tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to furfural, a lignocellulosic inhibitory compound. Appl Environ Microbiol 2009; 75:3765-76. [PMID: 19363068 DOI: 10.1128/aem.02594-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular mechanism involved in tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to inhibitors (such as furfural, acetic acid, and phenol) represented in lignocellulosic hydrolysate is still unclear. Here, (18)O-labeling-aided shotgun comparative proteome analysis was applied to study the global protein expression profiles of S. cerevisiae under conditions of treatment of furfural compared with furfural-free fermentation profiles. Proteins involved in glucose fermentation and/or the tricarboxylic acid cycle were upregulated in cells treated with furfural compared with the control cells, while proteins involved in glycerol biosynthesis were downregulated. Differential levels of expression of alcohol dehydrogenases were observed. On the other hand, the levels of NADH, NAD(+), and NADH/NAD(+) were reduced whereas the levels of ATP and ADP were increased. These observations indicate that central carbon metabolism, levels of alcohol dehydrogenases, and the redox balance may be related to tolerance of ethanologenic yeast for and adaptation to furfural. Furthermore, proteins involved in stress response, including the unfolded protein response, oxidative stress, osmotic and salt stress, DNA damage and nutrient starvation, were differentially expressed, a finding that was validated by quantitative real-time reverse transcription-PCR to further confirm that the general stress responses are essential for cellular defense against furfural. These insights into the response of yeast to the presence of furfural will benefit the design and development of inhibitor-tolerant ethanologenic yeast by metabolic engineering or synthetic biology.
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Wójtowicz H, Wojaczyński J, Olczak M, Króliczewski J, Latos-Grazyński L, Olczak T. Heme environment in HmuY, the heme-binding protein of Porphyromonas gingivalis. Biochem Biophys Res Commun 2009; 383:178-82. [PMID: 19345198 DOI: 10.1016/j.bbrc.2009.03.148] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 03/30/2009] [Indexed: 11/25/2022]
Abstract
Porphyromonas gingivalis, a Gram-negative anaerobic bacterium implicated in the development and progression of chronic periodontitis, acquires heme for growth by a novel mechanism composed of HmuY and HmuR proteins. The aim of this study was to characterize the nature of heme binding to HmuY. The protein was expressed, purified and detailed investigations using UV-vis absorption, CD, MCD, and (1)H NMR spectroscopy were carried out. Ferric heme bound to HmuY may be reduced by sodium dithionite and re-oxidized by potassium ferricyanide. Heme complexed to HmuY, with a midpoint potential of 136mV, is in a low-spin Fe(III) hexa-coordinate environment. Analysis of heme binding to several single and double HmuY mutants with the methionine, histidine, cysteine, or tyrosine residues replaced by an alanine residue identified histidines 134 and 166 as potential heme ligands.
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Affiliation(s)
- Halina Wójtowicz
- Faculty of Biotechnology, Laboratory of Biochemistry, University of Wrocław, Wrocław, Poland
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40
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Fenselau C, Yao X. 18O2-Labeling in Quantitative Proteomic Strategies: A Status Report. J Proteome Res 2009; 8:2140-3. [DOI: 10.1021/pr8009879] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Catherine Fenselau
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Xudong Yao
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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Lo AW, Seers CA, Boyce JD, Dashper SG, Slakeski N, Lissel JP, Reynolds EC. Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells. BMC Microbiol 2009; 9:18. [PMID: 19175941 PMCID: PMC2637884 DOI: 10.1186/1471-2180-9-18] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 01/29/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porphyromonas gingivalis in subgingival dental plaque, as part of a mature biofilm, has been strongly implicated in the onset and progression of chronic periodontitis. In this study using DNA microarray we compared the global gene expression of a P. gingivalis biofilm with that of its planktonic counterpart grown in the same continuous culture. RESULTS Approximately 18% (377 genes, at 1.5 fold or more, P-value < 0.01) of the P. gingivalis genome was differentially expressed when the bacterium was grown as a biofilm. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in cell envelope biogenesis, DNA replication, energy production and biosynthesis of cofactors, prosthetic groups and carriers. A number of genes encoding transport and binding proteins were up-regulated in P. gingivalis biofilm cells. Several genes predicted to encode proteins involved in signal transduction and transcriptional regulation were differentially regulated and may be important in the regulation of biofilm growth. CONCLUSION This study analyzing global gene expression provides insight into the adaptive response of P. gingivalis to biofilm growth, in particular showing a down regulation of genes involved in growth and metabolic activity.
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Affiliation(s)
- Alvin W Lo
- Cooperative Research Centre for Oral Health Science, Melbourne Dental School and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.
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