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Bystrom LT, Wolthers KR. New Electron-Transfer Chain to a Flavodiiron Protein in Fusobacterium nucleatum Couples Butyryl-CoA Oxidation to O 2 Reduction. Biochemistry 2024; 63:2352-2368. [PMID: 39206807 DOI: 10.1021/acs.biochem.4c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Fusobacterium nucleatum, a Gram-negative obligate anaerobe, is common to the oral microbiota, but the species is known to infect other sites of the body where it is associated with a range of pathologies. At present, little is known about the mechanisms by which F. nucleatum mitigates against oxidative and nitrosative stress. Inspection of the F. nucleatum subsp. polymorphum ATCC 10953 genome reveals that it encodes a flavodiiron protein (FDP; FNP2073) that is known in other organisms to reduce NO to N2O and/or O2 to H2O. FNP2073 is dicistronic with a gene encoding a multicomponent enzyme termed BCR for butyryl-CoA reductase. BCR is composed of a butyryl-CoA dehydrogenase domain (BCD), the C-terminal domain of the α-subunit of the electron-transfer flavoprotein (Etfα), and a rubredoxin domain. We show that BCR and the FDP form an α4β4 heterotetramic complex and use butyryl-CoA to selectively reduce O2 to H2O. The FAD associated with the Etfα domain (α-FAD) forms red anionic semiquinone (FAD•-), whereas the FAD present in the BCD domain (δ-FAD) forms the blue-neutral semiquinone (FADH•), indicating that both cofactors participate in one-electron transfers. This was confirmed in stopped-flow studies where the reduction of oxidized BCR with an excess of butyryl-CoA resulted in rapid (<1.6 ms) interflavin electron transfer evidenced by the formation of the FAD•-. Analysis of bacterial genomes revealed that the dicistron is present in obligate anaerobic gut bacteria considered to be beneficial by virtue of their ability to produce butyrate. Thus, BCR-FDP may help to maintain anaerobiosis in the colon.
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Affiliation(s)
- Liam T Bystrom
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1 V 1 V7, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1 V 1 V7, Canada
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Darbyshire AL, Wolthers KR. Characterization of a Structurally Distinct ATP-Dependent Reactivating Factor of Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase. Biochemistry 2024; 63:913-925. [PMID: 38471967 DOI: 10.1021/acs.biochem.3c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Several anaerobic bacterial species, including the Gram-negative oral bacterium Fusobacterium nucleatum, ferment lysine to produce butyrate, acetate, and ammonia. The second step of the metabolic pathway─isomerization of β-l-lysine to erythro-3,5-diaminohexanoate─is catalyzed by the adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme, lysine 5,6-aminomutase (5,6-LAM). Similar to other AdoCbl-dependent enzymes, 5,6-LAM undergoes mechanism-based inactivation due to loss of the AdoCbl 5'-deoxyadenosyl moiety and oxidation of the cob(II)alamin intermediate to hydroxocob(III)alamin. Herein, we identified kamB and kamC, two genes responsible for ATP-dependent reactivation of 5,6-LAM. KamB and KamC, which are encoded upstream of the genes corresponding to α and β subunits of 5,6-LAM (kamD and kamE), co-purified following coexpression of the genes in Escherichia coli. KamBC exhibited a basal level of ATP-hydrolyzing activity that was increased 35% in a reaction mixture that facilitated 5,6-LAM turnover with β-l-lysine or d,l-lysine. Ultraviolet-visible (UV-vis) spectroscopic studies performed under anaerobic conditions revealed that KamBC in the presence of ATP/Mg2+ increased the steady-state concentration of the cob(II)alamin intermediate in the presence of excess β-l-lysine. Using a coupled UV-visible spectroscopic assay, we show that KamBC is able to reactivate 5,6-LAM through exchange of the damaged hydroxocob(III)alamin for AdoCbl. KamBC is also specific for 5,6-LAM as it had no effect on the rate of substrate-induced inactivation of the homologue, ornithine 4,5-aminomutase. Based on sequence homology, KamBC is structurally distinct from previously characterized B12 chaperones and reactivases, and correspondingly adds to the list of proteins that have evolved to maintain the cellular activity of B12 enzymes.
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Affiliation(s)
- Amanda L Darbyshire
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
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Hara T, Sakanaka A, Lamont RJ, Amano A, Kuboniwa M. Interspecies metabolite transfer fuels the methionine metabolism of Fusobacterium nucleatum to stimulate volatile methyl mercaptan production. mSystems 2024; 9:e0076423. [PMID: 38289043 PMCID: PMC10878106 DOI: 10.1128/msystems.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
The major oral odor compound methyl mercaptan (CH3SH) is strongly associated with halitosis and periodontitis. CH3SH production stems from the metabolism of polymicrobial communities in periodontal pockets and on the tongue dorsum. However, understanding of CH3SH-producing oral bacteria and their interactions is limited. This study aimed to investigate CH3SH production by major oral bacteria and the impact of interspecies interactions on its generation. Using a newly constructed large-volume anaerobic noncontact coculture system, Fusobacterium nucleatum was found to be a potent producer of CH3SH, with that production stimulated by metabolic interactions with Streptococcus gordonii, an early dental plaque colonizer. Furthermore, analysis of extracellular amino acids using an S. gordonii arginine-ornithine antiporter (ArcD) mutant demonstrated that ornithine excreted from S. gordonii is a key contributor to increased CH3SH production by F. nucleatum. Further study with 13C, 15N-methionine, as well as gene expression analysis, revealed that ornithine secreted by S. gordonii increased the demand for methionine through accelerated polyamine synthesis by F. nucleatum, leading to elevated methionine pathway activity and CH3SH production. Collectively, these findings suggest that interaction between S. gordonii and F. nucleatum plays a key role in CH3SH production, providing a new insight into the mechanism of CH3SH generation in oral microbial communities. A better understanding of the underlying interactions among oral bacteria involved in CH3SH generation can lead to the development of more appropriate prophylactic approaches to treat halitosis and periodontitis. An intervention approach like selectively disrupting this interspecies network could also offer a powerful therapeutic strategy.IMPORTANCEHalitosis can have a significant impact on the social life of affected individuals. Among oral odor compounds, CH3SH has a low olfactory threshold and halitosis is a result of its production. Recently, there has been a growing interest in the collective properties of oral polymicrobial communities, regarded as important for the development of oral diseases, which are shaped by physical and metabolic interactions among community participants. However, it has yet to be investigated whether interspecies interactions have an impact on the production of volatile compounds, leading to the development of halitosis. The present findings provide mechanistic insights indicating that ornithine, a metabolite excreted by Streptococcus gordonii, promotes polyamine synthesis by Fusobacterium nucleatum, resulting in a compensatory increase in demand for methionine, which results in elevated methionine pathway activity and CH3SH production. Elucidation of the mechanisms related to CH3SH production is expected to lead to the development of new strategies for managing halitosis.
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Affiliation(s)
- Takeshi Hara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Advanced Technology Institute, Mandom Corporation, Osaka, Japan
| | - Akito Sakanaka
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Richard J. Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - Atsuo Amano
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Masae Kuboniwa
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
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Britton TA, Wu C, Chen YW, Franklin D, Chen Y, Camacho MI, Luong TT, Das A, Ton-That H. The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum. mBio 2024; 15:e0175123. [PMID: 38059640 PMCID: PMC10790702 DOI: 10.1128/mbio.01751-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE This paper illuminates the significant question of how the oral commensal Fusobacterium nucleatum adapts to the metabolically changing environments of several extra-oral sites such as placenta and colon to promote various diseases as an opportunistic pathogen. We demonstrate here that the highly conserved Rhodobacter nitrogen-fixation complex, commonly known as Rnf complex, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, hydrogen sulfide production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.
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Affiliation(s)
- Timmie A. Britton
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Yi-Wei Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Dana Franklin
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Yimin Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Martha I. Camacho
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Truc T. Luong
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
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Britton TA, Wu C, Chen YW, Franklin D, Chen Y, Camacho MI, Luong TT, Das A, Ton-That H. The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544113. [PMID: 37398403 PMCID: PMC10312631 DOI: 10.1101/2023.06.13.544113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
A prominent oral commensal and opportunistic pathogen, Fusobacterium nucleatum can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by the rnfCDGEAB gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of rnfC (Δ rnfC ) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing Δ rnfC cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (Δ kamAΔ ) that fails to metabolize extracellular lysine. Strikingly, the Δ rnfC mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in Δ rnfC cells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the Δ rnfC mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.
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Mothersole RG, Kolesnikov M, Chan ACK, Oduro E, Murphy MEP, Wolthers KR. Sequence Divergence in the Arginase Domain of Ornithine Decarboxylase/Arginase in Fusobacteriacea Leads to Loss of Function in Oral Associated Species. Biochemistry 2022; 61:1378-1391. [PMID: 35732022 DOI: 10.1021/acs.biochem.2c00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A number of species within the Fusobacteriaceae family of Gram-negative bacteria uniquely encode for an ornithine decarboxylase/arginase (ODA) that ostensibly channels l-ornithine generated by hydrolysis of l-arginine to putrescine formation. However, two aspartate residues required for coordination to a catalytically obligatory manganese cluster of arginases are substituted for a serine and an asparagine. Curiously, these natural substitutions occur only in a clade of Fusobacterium species that inhabit the oral cavity. Herein, we expressed and isolated full-length ODA from the opportunistic oral pathogen Fusobacterium nucleatum along with the individual arginase and ornithine decarboxylase components. The crystal structure of the arginase domain reveals that it adopts the classical α/β arginase-fold, but metal ions are absent in the active site. As expected, the ureohydrolase activity with l-arginine was not detected for wild-type ODA or the isolated arginase domain. However, engineering of the complete metal coordination environment through site-directed mutagenesis restored Mn2+ binding capacity and arginase activity, although the catalytic efficiency for l-arginine was low (60-100 M-1 s-1). Full-length ODA and the isolated ODC component were able to decarboxylate both l-ornithine and l-arginine to form putrescine and agmatine, respectively, but kcat/KM of l-ornithine was ∼20-fold higher compared to l-arginine. We discuss environmental conditions that may have led to the natural selection of an inactive arginase in the oral associated species of Fusobacterium.
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Affiliation(s)
- Robert G Mothersole
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Emmanuella Oduro
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna V1V 1V7, Canada
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Genetic and molecular determinants of polymicrobial interactions in Fusobacterium nucleatum. Proc Natl Acad Sci U S A 2021; 118:2006482118. [PMID: 34074747 DOI: 10.1073/pnas.2006482118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions-termed coaggregation-by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. Here, we employed genome-wide transposon mutagenesis to uncover fusobacterial coaggregation factors, revealing the intertwined function of a two-component signal transduction system (TCS), named CarRS, and a lysine metabolic pathway in regulating the critical coaggregation factor RadD. Transcriptome analysis shows that CarR modulates a large regulon including radD and lysine metabolic genes, such as kamA and kamD, the expression of which are highly up-regulated in the ΔcarR mutant. Significantly, the native culture medium of ΔkamA or ΔkamD mutants builds up abundant amounts of free lysine, which blocks fusobacterial coaggregation with streptococci. Our demonstration that lysine-conjugated beads trap RadD from the membrane lysates suggests that lysine utilizes RadD as its receptor to act as a metabolic inhibitor of coaggregation. Lastly, using a mouse model of preterm birth, we show that fusobacterial virulence is significantly attenuated with the ΔkamA and ΔcarR mutants, in contrast to the enhanced virulence phenotype observed upon diminishing RadD (ΔradD or ΔcarS mutant). Evidently, F. nucleatum employs the TCS CarRS and environmental lysine to modulate RadD-mediated interspecies interaction, virulence, and nutrient acquisition to thrive in the adverse environment of oral biofilms and extraoral sites.
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Bernardi S, Karygianni L, Filippi A, Anderson AC, Zürcher A, Hellwig E, Vach K, Macchiarelli G, Al-Ahmad A. Combining culture and culture-independent methods reveals new microbial composition of halitosis patients' tongue biofilm. Microbiologyopen 2019; 9:e958. [PMID: 31725203 PMCID: PMC7002105 DOI: 10.1002/mbo3.958] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Oral malodor is a very discomforting condition deriving from the presence of volatile sulfur compounds in the expired air. In halitosis of intraoral etiology, the volatile sulfur compounds are metabolic products of the oral microorganisms within the biofilm coating the tongue dorsum as well as other tissues in the oral cavity. The aim of this study was to characterize and compare the microbial composition of tongue biofilm in volunteers suffering from halitosis and healthy volunteers by means of both the culture method and culture‐independent cloning technique. Results A high bacterial variety (more than 80 different species) was detected using the combination of both methods. A distinct bacterial composition was revealed in the halitosis‐associated biofilms compared with the health‐associated biofilms. Actinomyces graevenitzii was shown to be significantly associated with the halitosis condition. The culture method identified 47 species, included Veillonella rogosae, never isolated from the tongue biofilm of halitosis patients so far. In the healthy condition, the culture‐dependent method showed that the most frequent species were Streptococcus parasanguinis among the aerobes and Veillonella spp. among the anaerobes. The culture‐independent cloning method detected more than 50 species. Streptococci, in particular S. mitis/oralis, S. pseudopneumoniae, and S. infantis as well as Prevotella spp., were found most frequently in halitosis patients. Streptococcus salivarius and Rothia mucilaginosa were found more frequently in the healthy condition. Conclusions The combination of the culture‐dependent and culture‐independent cloning techniques allowed for a widespread analysis of the tongue biofilm in halitosis patients. The results can support further pharmacological research for new antimicrobial agents and halitosis therapy strategies.
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Affiliation(s)
- Sara Bernardi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Lamprini Karygianni
- Clinic for Preventive Dentistry, Periodontology and Cariology, University of Zurich, Zurich, Switzerland
| | - Andreas Filippi
- Department of Oral Surgery, Center of Dental Traumatology, University Center for Dental Medicine Basel UZB, Basel, Switzerland
| | - Annette Carola Anderson
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrea Zürcher
- Department of Oral Surgery, Center of Dental Traumatology, University Center for Dental Medicine Basel UZB, Basel, Switzerland
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kirstin Vach
- Institute for Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
| | - Guido Macchiarelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Zepeda Mendoza ML, Roggenbuck M, Manzano Vargas K, Hansen LH, Brunak S, Gilbert MTP, Sicheritz-Pontén T. Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. Acta Vet Scand 2018; 60:61. [PMID: 30309375 PMCID: PMC6182802 DOI: 10.1186/s13028-018-0415-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut. Results We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut. Conclusions Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging. Electronic supplementary material The online version of this article (10.1186/s13028-018-0415-3) contains supplementary material, which is available to authorized users.
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Ramezani M, White RL. Enantioselective catabolism of racemic serine: preparation of d-serine using whole cells of Fusobacterium nucleatum. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.tetasy.2011.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Resmer KL, White RL. Metabolic footprinting of the anaerobic bacterium Fusobacterium varium using 1H NMR spectroscopy. MOLECULAR BIOSYSTEMS 2011; 7:2220-7. [PMID: 21547305 DOI: 10.1039/c1mb05105a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolic footprinting of the anaerobic bacterium Fusobacterium varium demonstrated the accumulation of six carboxylic acids as metabolic end-products and revealed specific growth requirements and utilization capabilities towards amino acids. Guided by (1)H NMR determinations of residual amino acids in spent medium, a modified chemically defined minimal medium (CDMM*) was developed by minimizing the amino acid composition while satisfying nutritional requirements to support abundant growth of F. varium. Quantitative determinations of carboxylate salts and residual substrates were readily performed by (1)H NMR analysis of lyophilized residues from CDMM* cultures without interference from initial medium components. Only small concentrations of alanine, arginine, glycine, isoleucine, leucine, methionine, proline and valine were required to support growth of F. varium, whereas larger quantities of aspartate, asparagine, cysteine, glutamine, glutamate, histidine, lysine, serine and threonine were utilized, most likely as energy sources. Both bacterial growth and the distribution of carboxylate end-products depended on the composition of the chemically defined medium. In cultures provided with glucose as the primary energy source, the accumulation of butyrate and lactate correlated with growth, consistent with the regeneration of reduced coenzyme formed by the oxidative steps of glucose catabolism.
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Affiliation(s)
- Kelly L Resmer
- Department of Chemistry, Dalhousie University, Halifax, Canada
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12
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Abstract
Fusobacterium nucleatum is a gram-negative oral bacterial species associated with periodontal disease progression. This species is perhaps best known for its ability to adhere to a vast array of other bacteria and eukaryotic cells. Numerous studies of F. nucleatum have examined various coaggregation partners and inhibitors, but it is largely unknown whether these interactions induce a particular genetic response. We tested coaggregation between F. nucleatum ATCC strain 25586 and various species of Streptococcus in the presence of a semidefined growth medium containing saliva. We found that this condition could support efficient coaggregation but, surprisingly, also stimulated a similar degree of autoaggregation. We further characterized the autoaggregation response, since few reports have examined this in F. nucleatum. After screening several common coaggregation inhibitors, we identified l-lysine as a competitive inhibitor of autoaggregation. We performed a microarray analysis of the planktonic versus autoaggregated cells and found nearly 100 genes that were affected after only about 60 min of aggregation. We tested a subset of these genes via real-time reverse transcription-PCR and confirmed the validity of the microarray results. Some of these genes were also found to be inducible in cell pellets created by centrifugation. Based upon these data, it appears that autoaggregation activates a genetic program that may be utilized for growth in a high cell density environment, such as the oral biofilm.
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Potrykus J, Mahaney B, White RL, Bearne SL. Proteomic investigation of glucose metabolism in the butyrate-producing gut anaerobeFusobacterium varium. Proteomics 2007; 7:1839-53. [PMID: 17464938 DOI: 10.1002/pmic.200600464] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A proteome survey and MS analysis were conducted to investigate glucose metabolism in Fusobacterium varium, a butyrate-producing constituent of the indigenous human gut microflora. The bacterium was capable of catabolizing glucose as the main energy source via the Embden-Meyerhof-Parnas pathway. 2-DE analyses revealed that the apparent concentrations of the six identified glycolytic enzymes (pyruvate kinase, enolase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase) were specifically increased in response to the presence of glucose in the chemically defined minimal growth medium, and did not diminish when the medium was additionally supplemented with L-glutamate, an amino acid readily fermented by members of the Fusobacterium genus. A substrate pool depletion study revealed that the sugar, and not the amino acid, is the more efficient growth substrate. Both proteomics and substrate pool depletion studies revealed that F. varium can simultaneously utilize both glucose and L-glutamate as energy sources. Enzymes involved in L-glutamate metabolism were also identified, including an NAD-dependent glutamate dehydrogenase and two enzymes of the methylaspartate pathway of L-glutamate catabolism (glutamate mutase and methylaspartate ammonia-lyase). Their apparent intracellular concentrations were elevated when the bacterium was cultured in media supplemented with excess L-glutamate. Our observation that the apparent concentrations of specific proteins were elevated in response to a particular growth substrate supplied as an energy source provides the first evidence for the presence of a nutrient-responsive mechanism governing intracellular protein concentration in F. varium.
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Affiliation(s)
- Joanna Potrykus
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Bachrach G, Rosen G, Bellalou M, Naor R, Sela MN. Identification of a Fusobacterium nucleatum 65 kDa serine protease. ACTA ACUST UNITED AC 2004; 19:155-9. [PMID: 15107066 DOI: 10.1111/j.0902-0055.2004.00132.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A 65 kDa protease was partially purified from extracellular vesicles of Fusobacterium nucleatum cultures by preparative SDS-PAGE followed by electroelution. The pH optimum of the protease is 7.5-8.0 and its activity could be inhibited by serine protease inhibitors. The protease was found to degrade the extracellular matrix proteins fibrinogen and fibronectin as well as collagen I and collagen IV which were degraded at 37 degrees C but not at 28 degrees C, indicating the presence of a gelatinase activity in these bacteria. The 65 kDa protease was also able to digest the alpha-chains of immunoglobulin A but not immunoglobulin G. The 65 kDa F. nucleatum protease, capable of degrading native proteins, may play an important role in both the nutrition and pathogenicity of these periodontal microorganisms. The degradation of extracellular matrix proteins by bacterial enzymes may contribute to the damage of periodontal tissues, and degradation of IgA may help the evasion of the immune system of the host by the bacteria.
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Affiliation(s)
- G Bachrach
- Institute of Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
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Duncan MJ. Genomics of oral bacteria. CRITICAL REVIEWS IN ORAL BIOLOGY AND MEDICINE : AN OFFICIAL PUBLICATION OF THE AMERICAN ASSOCIATION OF ORAL BIOLOGISTS 2003; 14:175-87. [PMID: 12799321 DOI: 10.1177/154411130301400303] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.
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Affiliation(s)
- Margaret J Duncan
- Department of Molecular Genetics, The Forsyth Institute, 140 Fenway, Boston, MA 02115, USA.
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Ramezani M, MacIntosh SE, White RL. Utilization of D-amino acids by Fusobacterium nucleatum and Fusobacterium varium. Amino Acids 1999; 17:185-93. [PMID: 10524276 DOI: 10.1007/bf01361881] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The utilization of D- and L-amino acids with acidic, basic or polar side chains was demonstrated by HPLC. Two species of the anaerobe Fusobacterium utilized D-lysine and the L isomers of glutamate, glutamine, histidine, lysine and serine. Only F. varium used L-arginine, D-glutamate and D-serine as substrates, whereas F. nucleatum specifically utilized D-histidine and D-glutamine. D-Glutamate accumulated in F. nucleatum cultures supplemented with D-glutamine, and ornithine was detected when either DL- or L-arginine was included in F. varium cultures. Based on literature precedents, D-glutamate and D-histidine are isomerized to their L isomers prior to degradation, but separate catabolic pathways are possible for each enantiomer of lysine and serine.
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Affiliation(s)
- M Ramezani
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Bouma CL, Reizer J, Reizer A, Robrish SA, Thompson J. 6-phospho-alpha-D-glucosidase from Fusobacterium mortiferum: cloning, expression, and assignment to family 4 of the glycosylhydrolases. J Bacteriol 1997; 179:4129-37. [PMID: 9209025 PMCID: PMC179231 DOI: 10.1128/jb.179.13.4129-4137.1997] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Fusobacterium mortiferum malH gene, encoding 6-phospho-alpha-glucosidase (maltose 6-phosphate hydrolase; EC 3.2.1.122), has been isolated, characterized, and expressed in Escherichia coli. The relative molecular weight of the polypeptide encoded by malH (441 residues; Mr of 49,718) was in agreement with the estimated value (approximately 49,000) obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the enzyme purified from F. mortiferum. The N-terminal sequence of the MalH protein obtained by Edman degradation corresponded to the first 32 amino acids deduced from the malH sequence. The enzyme produced by the strain carrying the cloned malH gene cleaved [U-14C]maltose 6-phosphate to glucose 6-phosphate (Glc6P) and glucose. The substrate analogs p-nitrophenyl-alpha-D-glucopyranoside 6-phosphate (pNP alphaGlc6P) and 4-methylumbelliferyl-alpha-D-glucopyranoside 6-phosphate (4MU alphaGlc6P) were hydrolyzed to yield Glc6P and the yellow p-nitrophenolate and fluorescent 4-methylumbelliferyl aglycons, respectively. The 6-phospho-alpha-glucosidase expressed in E. coli (like the enzyme purified from F. mortiferum) required Fe2+, Mn2+, Co2+, or Ni2+ for activity and was inhibited in air. Synthesis of maltose 6-phosphate hydrolase from the cloned malH gene in E. coli was modulated by addition of various sugars to the growth medium. Computer-based analyses of MalH and its homologs revealed that the phospho-alpha-glucosidase from F. mortiferum belongs to the seven-member family 4 of the glycosylhydrolase superfamily. The cloned 2.2-kb Sau3AI DNA fragment from F. mortiferum contained a second partial open reading frame of 83 residues (designated malB) that was located immediately upstream of malH. The high degree of sequence identity of MalB with IIB(Glc)-like proteins of the phosphoenol pyruvate dependent:sugar phosphotransferase system suggests participation of MalB in translocation of maltose and related alpha-glucosides in F. mortiferum.
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Affiliation(s)
- C L Bouma
- School of Pharmacy, Texas Tech University, Amarillo 79106, USA
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18
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Abstract
The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered.
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Bolstad AI, Jensen HB, Bakken V. Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. Clin Microbiol Rev 1996; 9:55-71. [PMID: 8665477 PMCID: PMC172882 DOI: 10.1128/cmr.9.1.55] [Citation(s) in RCA: 266] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered.
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Affiliation(s)
- A I Bolstad
- Department of Periodontology, University of Bergen, Norway
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20
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Rogers AH, Gully NJ, Pfennig AL, Zilm PS. The breakdown and utilization of peptides by strains of Fusobacterium nucleatum. ORAL MICROBIOLOGY AND IMMUNOLOGY 1992; 7:299-303. [PMID: 1494454 DOI: 10.1111/j.1399-302x.1992.tb00592.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It has been claimed that most strains of Fusobacterium nucleatum require peptides rather than free amino acids for growth. In contrast, we have shown that, under continuous culture conditions, all strains tested grow in a chemically defined medium (CDM). The purposes of this study were to determine whether resting cells of F. nucleatum could attack unsubstituted peptides and whether growing cells could utilize a peptide fraction prepared from a commercial peptone. Resting cells cleaved all 19 peptides, containing 3-6 residues, and the 4 key energy-yielding amino acids--Glu, His, Ser and Lys--were rapidly taken up. A hydrophilic Casitone fraction, rich in Glu, promoted growth and peptides < 1 kDa were rapidly utilized. The cleaved residues metabolized were those previously shown to limit growth in CDM: Glu, Ser, His and Lys. The endopeptidase activities of Porphyromonas gingivalis would provide the necessary peptides for the growth of F. nucleatum, which may partly explain why these two organisms frequently coexist in periodontally diseased sites.
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Affiliation(s)
- A H Rogers
- Department of Dentistry, University of Adelaide, South Australia
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Thompson J, Nguyen NY, Robrish SA. Sucrose fermentation by Fusobacterium mortiferum ATCC 25557: transport, catabolism, and products. J Bacteriol 1992; 174:3227-35. [PMID: 1533618 PMCID: PMC205990 DOI: 10.1128/jb.174.10.3227-3235.1992] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Studies of sucrose utilization by Fusobacterium mortiferum ATCC 25557 have provided the first definitive evidence for phosphoenolpyruvate-dependent sugar:phosphotransferase activity in the family Bacteroidaceae. The phosphoenolpyruvate-dependent sucrose:phosphotransferase system and the two enzymes required for the dissimilation of sucrose 6-phosphate are induced specifically by growth of F. mortiferum on the disaccharide. Monomeric sucrose 6-phosphate hydrolase (M(r), 52,000) and a dimeric ATP-dependent fructokinase (subunit M(r), 32,000) have been purified to electrophoretic homogeneity. The physicochemical and catalytic properties of these enzymes have been examined, and the N-terminal amino acid sequences for both proteins are reported. The characteristics of sucrose 6-phosphate hydrolase and fructokinase from F. mortiferum are compared with the same enzymes from both gram-positive and gram-negative species. Butyric, acetic, and D-lactic acids are the end products of sucrose fermentation by F. mortiferum. A pathway is proposed for the translocation, phosphorylation, and metabolism of sucrose by this anaerobic pathogen.
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Affiliation(s)
- J Thompson
- Laboratory of Microbial Ecology, National Institute of Dental Research, Bethesda, Maryland
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Robrish SA, Oliver C, Thompson J. Sugar metabolism by fusobacteria: regulation of transport, phosphorylation, and polymer formation by Fusobacterium mortiferum ATCC 25557. Infect Immun 1991; 59:4547-54. [PMID: 1937813 PMCID: PMC259076 DOI: 10.1128/iai.59.12.4547-4554.1991] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Strains of eight Fusobacterium species differed in the ability to use sugars as energy sources for growth. For Fusobacterium russii ATCC 25533, F. gonidiaformans ATCC 25563, and F. nucleatum ATCC 10953 (except for fructose), growth was marginal to poor on all of the sugars tested. Other species displayed reasonable growth on glucose, fructose, mannose, and galactose, and two strains of F. mortiferum (ATCC 25557 and ATCC 9817) grew well on six of the sugars tested, including sucrose and maltose. Glucose transport by resting cells of most of the species was dependent upon (or markedly stimulated by) the presence of a fermentable amino acid. By contrast, F. mortiferum cells rapidly accumulated glucose and other sugars in the absence of amino acids. Although these cells were constitutive for glucose uptake, accumulation of other sugars was specifically induced by growth of F. mortiferum on the appropriate sugar. Spectrophotometric analyses and in situ staining of anionic polyacrylamide gels showed that glucose and fructose (mannose) are phosphorylated by separate ATP-dependent kinases. Fructokinase was stable in air at 4 degrees C, but under these conditions, greater than 70% of the glucokinase activity was lost. After overnight dialysis of the extract, no glucokinase activity was detectable; however, 65% of the initial enzyme activity was retained by inclusion of 1 mM dithiothreitol in the dialysis buffer. Thin-section electron microscopy showed that cells of F. mortiferum produced various amounts of intracellular glycogen during growth on the following sugars (in decreasing order of formation): galactose greater than sucrose greater than glucose greater than mannose greater than fructose. Mechanisms for sugar transport regulation, phosphorylation, and polymer synthesis by F. mortiferum cells are proposed.
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Affiliation(s)
- S A Robrish
- Laboratory of Microbial Ecology, National Institute of Dental Research, Bethesda, Maryland 20892
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Gharbia SE, Shah HN. Comparison of the amino acid uptake profile of reference and clinical isolates of Fusobacterium nucleatum subspecies. ORAL MICROBIOLOGY AND IMMUNOLOGY 1991; 6:264-9. [PMID: 1820562 DOI: 10.1111/j.1399-302x.1991.tb00489.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human isolates of Fusobacterium nucleatum subspecies appear to colonize different niches in the oral cavity, which may be reflected in their nutritional properties. Consequently the utilization of nitrogenous substrates, their sources of energy (supplied here as amino acids) were compared between the 3 subspecies using the reference strain and fresh clinical isolates of each subspecies. All strains incorporated mainly acidic and basic amino acids but significant differences occurred between subspecies. Both reference and clinical isolates of F. nucleatum subspecies polymorphum utilized all amino acids in the medium but the levels of glutamate, arginine and cysteine were noticeably higher in the reference strain. By contrast, F. nucleatum subspecies fusiforme used a very restricted range of amino acids, of which only glutamate, arginine, histidine and cysteine were taken up at greater than 0.5 mM. F. nucleatum subspecies nucleatum utilized fewer amino acids than F. nucleatum subspecies polymorphum but higher concentrations were taken up by the former. Clinical isolates of F. nucleatum subspecies nucleatum incorporated polar and nonpolar neutral amino acids poorly but their levels increased steadily as a clinical isolate was subcultured over a period of 4 months, and was eventually similar to the reference strain. The effect of adding the key catabolic substrate, glutamate (10 mM), on the amino acid uptake profile of F. nucleatum subspecies nucleatum resulted in the complete suppression of the dibasic amino acids arginine, ornithine and histidine. Strains of this subspecies could grow on glutamate as a major source of carbon and energy but, morphologically, the cells appeared somewhat distended and had a tendency to clump.
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Affiliation(s)
- S E Gharbia
- London Hospital Medical College, United Kingdom
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