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Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL. Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiol Spectr 2024; 12:e0401723. [PMID: 38488280 PMCID: PMC10986600 DOI: 10.1128/spectrum.04017-23] [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: 11/23/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility. IMPORTANCE Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
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Affiliation(s)
| | | | - Jonathan Tang
- The Forsyth Institute, Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Eicher C, Coulon J, Favier M, Alexandre H, Reguant C, Grandvalet C. Citrate metabolism in lactic acid bacteria: is there a beneficial effect for Oenococcus oeni in wine? Front Microbiol 2024; 14:1283220. [PMID: 38249489 PMCID: PMC10798043 DOI: 10.3389/fmicb.2023.1283220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Abstract
Lactic acid bacteria (LAB) are Gram positive bacteria frequently used in the food industry for fermentation, mainly transformation of carbohydrates into lactic acid. In addition, these bacteria also have the capacity to metabolize citrate, an organic acid commonly found in food products. Its fermentation leads to the production of 4-carbon compounds such as diacetyl, resulting in a buttery flavor desired in dairy products. Citrate metabolism is known to have several beneficial effects on LAB physiology. Nevertheless, a controversial effect of citrate has been described on the acid tolerance of the wine bacterium Oenococcus oeni. This observation raises questions about the effect of citrate on the capacity of O. oeni to conduct malolactic fermentation in highly acidic wines. This review aims to summarize the current understanding of citrate metabolism in LAB, with a focus on the wine bacterium O. oeni. Metabolism with the related enzymes is detailed, as are the involved genes organized in cit loci. The known systems of cit locus expression regulation are also described. Finally, the beneficial effects of citrate catabolism on LAB physiology are reported and the negative impact observed in O. oeni is discussed.
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Affiliation(s)
- Camille Eicher
- UMR PAM, Université de Bourgogne Franche-Comté, Institut Agro, Université de Bourgogne, INRAE, Dijon, France
| | | | | | - Hervé Alexandre
- UMR PAM, Université de Bourgogne Franche-Comté, Institut Agro, Université de Bourgogne, INRAE, Dijon, France
| | - Cristina Reguant
- Universitat Rovira i Virgili, Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Tarragona, Catalonia, Spain
| | - Cosette Grandvalet
- UMR PAM, Université de Bourgogne Franche-Comté, Institut Agro, Université de Bourgogne, INRAE, Dijon, France
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Silva LF, Sunakozawa TN, Monteiro DA, Casella T, Conti AC, Todorov SD, Barretto Penna AL. Potential of Cheese-Associated Lactic Acid Bacteria to Metabolize Citrate and Produce Organic Acids and Acetoin. Metabolites 2023; 13:1134. [PMID: 37999230 PMCID: PMC10673126 DOI: 10.3390/metabo13111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Lactic acid bacteria (LAB) are pivotal in shaping the technological, sensory, and safety aspects of dairy products. The evaluation of proteolytic activity, citrate utilization, milk pH reduction, and the production of organic compounds, acetoin, and diacetyl by cheese associated LAB strains was carried out, followed by Principal Component Analysis (PCA). Citrate utilization was observed in all Leuconostoc (Le.) mesenteroides, Le. citreum, Lactococcus (Lc.) lactis, Lc. garvieae, and Limosilactobacillus (Lm.) fermentum strains, and in some Lacticaseibacillus (Lact.) casei strains. Most strains exhibited proteolytic activity, reduced pH, and generated organic compounds. Multivariate PCA revealed Le. mesenteroides as a prolific producer of acetic, lactic, formic, and pyruvic acids and acetoin at 30 °C. Enterococcus sp. was distinguished from Lact. casei based on acetic, formic, and pyruvic acid production, while Lact. casei primarily produced lactic acid at 37 °C. At 42 °C, Lactobacillus (L.) helveticus and some L. delbrueckii subsp. bulgaricus strains excelled in acetoin production, whereas L. delbrueckii subsp. bulgaricus and Streptococcus (S.) thermophilus strains primarily produced lactic acid. Lm. fermentum stood out with its production of acetic, formic, and pyruvic acids. Overall, cheese-associated LAB strains exhibited diverse metabolic capabilities which contribute to desirable aroma, flavor, and safety of dairy products.
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Affiliation(s)
- Luana Faria Silva
- Institute of Biosciences, Humanities and Exact Sciences, Food Engineering and Technology Department, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (L.F.S.); (T.N.S.); (D.A.M.); (A.C.C.)
| | - Tássila Nakata Sunakozawa
- Institute of Biosciences, Humanities and Exact Sciences, Food Engineering and Technology Department, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (L.F.S.); (T.N.S.); (D.A.M.); (A.C.C.)
| | - Diego Alves Monteiro
- Institute of Biosciences, Humanities and Exact Sciences, Food Engineering and Technology Department, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (L.F.S.); (T.N.S.); (D.A.M.); (A.C.C.)
| | - Tiago Casella
- Department of Dermatological, Infectious and Parasitic Diseases, FAMERP—São José do Rio Preto Medical School, São José do Rio Preto 15090-000, SP, Brazil;
| | - Ana Carolina Conti
- Institute of Biosciences, Humanities and Exact Sciences, Food Engineering and Technology Department, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (L.F.S.); (T.N.S.); (D.A.M.); (A.C.C.)
| | - Svetoslav Dimitrov Todorov
- ProBacLab, Department of Food Science and Experimental Nutrition, Faculty of Pharmaceutical Sciences, USP—São Paulo University, São Paulo 05508-000, SP, Brazil;
- CISAS—Center for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, 4900-347 Viana do Castelo, Portugal
| | - Ana Lúcia Barretto Penna
- Institute of Biosciences, Humanities and Exact Sciences, Food Engineering and Technology Department, UNESP—São Paulo State University, São José do Rio Preto 15054-000, SP, Brazil; (L.F.S.); (T.N.S.); (D.A.M.); (A.C.C.)
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Yao Q, Chen J, Li X, Yang W, Ning J, Liang Q, Li Q. Site-selective covalent immobilization of PPARγ using a label-free strategy for chromatographic study. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Li H, Ramia NE, Borges F, Revol-Junelles AM, Vogensen FK, Leisner JJ. Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum. Microorganisms 2021; 9:microorganisms9102169. [PMID: 34683489 PMCID: PMC8537297 DOI: 10.3390/microorganisms9102169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed (Cm 3-1 and Cm 5-1) citrate utilization activity. The remaining two strains, Cm 4-1 and Cm 1-2 gave negative results. Additional analysis showed no or very limited utilization of citrate in media containing 1% glucose and 22 or 30 mM citrate and inoculated with Cm 6-1 or ATCC 35586. Two potential pathways of citrate metabolism were identified by bioinformatics analyses in C. maltaromaticum including either oxaloacetate (pathway 1) or tricarboxylic compounds such as isocitrate and α-ketoglutarate (pathway 2) as intermediates. Genes encoding pathway 1 were present in two out of six strains while pathway 2 included genes present in all six strains. The two potential citrate metabolism pathways in C. maltaromaticum may potentially affect the sensory profiles of milk and soft cheeses subjected to growth with this species.
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Affiliation(s)
- Heng Li
- Pasteurien College, Soochow University, Suzhou 215123, China;
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Nancy E. Ramia
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Frédéric Borges
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Anne-Marie Revol-Junelles
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Finn Kvist Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg, Denmark;
| | - Jørgen J. Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
- Correspondence:
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Terán LC, Mortera P, Tubio G, Alarcón SH, Blancato VS, Espariz M, Esteban L, Magni C. Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed. J Appl Microbiol 2021; 132:1152-1165. [PMID: 34487594 DOI: 10.1111/jam.15292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022]
Abstract
AIMS Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed. METHODS AND RESULTS We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates. CONCLUSIONS We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.
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Affiliation(s)
- Lucrecia C Terán
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Centro de Referencia para Lactobacilos, CERELA-CONICET, San Miguel de Tucuman, Tucumán, Argentina
| | - Pablo Mortera
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Gisela Tubio
- Instituto de Procesos Biotecnológicos y Químicos Rosario, IPROByQ (CONICET-UNR), Rosario, Argentina
| | - Sergio H Alarcón
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Instituto de Química de Rosario, IQUIR (CONICET-UNR), Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, FBioyF-UNR, Rosario, Argentina
| | - Luis Esteban
- Química Biológica, Facultad de Ciencias Médicas, UNR, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
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7
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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D'Angelo M, Martino GP, Blancato VS, Espariz M, Hartke A, Sauvageot N, Benachour A, Alarcón SH, Magni C. Diversity of volatile organic compound production from leucine and citrate in Enterococcus faecium. Appl Microbiol Biotechnol 2019; 104:1175-1186. [PMID: 31828406 DOI: 10.1007/s00253-019-10277-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/14/2019] [Accepted: 11/23/2019] [Indexed: 01/22/2023]
Abstract
Enterococcus faecium is frequently isolated from fermented food; in particular, they positively contribute to the aroma compound generation in traditional cheese. Citrate fermentation is a desirable property in these bacteria, but this feature is not uniformly distributed among E. faecium strains. In the present study, three selected E. faecium strains, IQ110 (cit-), GM70 (cit+ type I), and Com12 (cit+ type II), were analyzed in their production of aroma compounds in milk. End products and volatile organic compounds (VOCs) were determined by solid-phase micro-extraction combined with gas chromatography mass spectrometry (SPME-GC-MS). Principal component analysis (PCA) of aroma compound profiles revealed a different VOC composition for the three strains. In addition, resting cell experiments of E. faecium performed in the presence of leucine, citrate, or pyruvate as aroma compound precursors allowed us to determine metabolic differences between the studied strains. GM70 (cit+ type I) showed an active citrate metabolism, with increased levels of diacetyl and acetoin generation relative to Com12 or to citrate defective IQ110 strains. In addition, in the experimental conditions tested, a defective citrate-fermenting phenotype for the Com12 strain was found, while its leucine degradation and pyruvate metabolism were conserved. In conclusion, rational selection of E. faecium strains could be performed based on genotypic and phenotypic analyses. This would result in a performing strain, such as GM70, that could positively contribute to flavor, with typical notes of diacetyl, acetoin, 3-methyl butanal, and 3-methyl butanol in an adjuvant culture.
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Affiliation(s)
- Matilde D'Angelo
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Instituto de Química de Rosario (IQUIR), FBioyF, UNR-CONICET, Suipacha 570, Rosario, Argentina
| | - Gabriela P Martino
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Axel Hartke
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | | | | | - Sergio H Alarcón
- Instituto de Química de Rosario (IQUIR), FBioyF, UNR-CONICET, Suipacha 570, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina.
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina.
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France.
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Implications of the expression of Enterococcus faecalis citrate fermentation genes during infection. PLoS One 2018; 13:e0205787. [PMID: 30335810 PMCID: PMC6193673 DOI: 10.1371/journal.pone.0205787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/02/2018] [Indexed: 12/05/2022] Open
Abstract
Citrate is an ubiquitous compound in nature. However, citrate fermentation is present only in a few pathogenic or nonpathogenic microorganisms. The citrate fermentation pathway includes a citrate transporter, a citrate lyase complex, an oxaloacetate decarboxylase and a regulatory system. Enterococcus faecalis is commonly present in the gastro-intestinal microbiota of warm-blooded animals and insect guts. These bacteria can also cause infection and disease in immunocompromised individuals. In the present study, we performed whole genome analysis in Enterococcus strains finding that the complete citrate pathway is present in all of the E. faecalis strains isolated from such diverse habitats as animals, hospitals, water, milk, plants, insects, cheese, etc. These results indicate the importance of this metabolic preservation for persistence and growth of E. faecalis in different niches. We also analyzed the role of citrate metabolism in the E. faecalis pathogenicity. We found that an E. faecalis citrate fermentation-deficient strain was less pathogenic for Galleria mellonella larvae than the wild type. Furthermore, strains with deletions in the oxaloacetate decarboxylase subunits or in the α-acetolactate synthase resulted also less virulent than the wild type strain. We also observed that citrate promoters are induced in blood, urine and also in the hemolymph of G. mellonella. In addition, we showed that citrate fermentation allows E. faecalis to grow better in blood, urine and G. mellonella. The results presented here clearly indicate that citrate fermentation plays an important role in E. faecalis opportunistic pathogenic behavior.
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Lo R, Ho VTT, Bansal N, Turner MS. The genetic basis underlying variation in production of the flavour compound diacetyl by Lactobacillus rhamnosus strains in milk. Int J Food Microbiol 2018; 265:30-39. [DOI: 10.1016/j.ijfoodmicro.2017.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/01/2017] [Accepted: 10/28/2017] [Indexed: 01/16/2023]
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Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, Amador-Noguez D, Tian L, Sauer U, Lynd LR. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng 2016; 39:169-180. [PMID: 27914869 DOI: 10.1016/j.ymben.2016.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme. First we showed that there is no flux through the ODC pathway by enzyme assay. Flux through the remaining two pathways (PPDK and malate shunt) was determined by dynamic 13C labeling. In the wild-type strain, the malate shunt accounts for about 33±2% of the flux to pyruvate, with the remainder via the PPDK pathway. Deletion of the ppdk gene resulted in a redirection of all pyruvate flux through the malate shunt. This provides the first direct evidence of the in-vivo function of the malate shunt.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jingxuan Cui
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jilai Zhou
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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12
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Zuljan FA, Mortera P, Alarcón SH, Blancato VS, Espariz M, Magni C. Lactic acid bacteria decarboxylation reactions in cheese. Int Dairy J 2016. [DOI: 10.1016/j.idairyj.2016.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Soleimani M, Mirmohammad-Sadeghi H, Sadeghi-Aliabadi H, Jahanian-Najafabadi A. Expression and purification of toxic anti-breast cancer p28-NRC chimeric protein. Adv Biomed Res 2016; 5:70. [PMID: 27169101 PMCID: PMC4854029 DOI: 10.4103/2277-9175.180639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/25/2015] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Chimeric proteins consisting of a targeting moiety and a cytotoxic moiety are now under intense research focus for targeted therapy of cancer. Here, we report cloning, expression, and purification of such a targeted chimeric protein made up of p28 peptide as both targeting and anticancer moiety fused to NRC peptide as a cytotoxic moiety. However, since the antimicrobial activity of the NRC peptide would intervene expression of the chimeric protein in Escherichia coli, we evaluated the effects of two fusion tags, that is, thioredoxin (Trx) and 6x-His tags, and various expression conditions, on the expression of p28-NRC chimeric protein. MATERIALS AND METHODS In order to express the chimeric protein with only 6x-His tag, pET28 expression plasmid was used. Cloning in pET32 expression plasmid was performed to add both Trx and 6x-His tags to the chimeric protein. Expression of the chimeric protein with both plasmids was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis following optimization of expression conditions and host strains. RESULTS Expression of the chimeric protein in pET28a was performed. However, expression yield of the chimeric protein was low. Optimization of culture conditions and host strains led to reasonable expression yield of the toxic chimeric protein in pET32a vector. In cases of both plasmids, approximately 10 kDa deviation of the apparent molecular weight from the theoretical one was seen in SDS-PAGE of purified chimeric proteins. CONCLUSIONS The study leads to proper expression and purification yield of p28-NRC chimeric protein with Trx tag following optimizing culture conditions and host strains.
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Affiliation(s)
- Meysam Soleimani
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
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Blancato VS, Pagliai FA, Magni C, Gonzalez CF, Lorca GL. Functional Analysis of the Citrate Activator CitO from Enterococcus faecalis Implicates a Divalent Metal in Ligand Binding. Front Microbiol 2016; 7:101. [PMID: 26903980 PMCID: PMC4746285 DOI: 10.3389/fmicb.2016.00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/19/2016] [Indexed: 02/04/2023] Open
Abstract
The regulator of citrate metabolism, CitO, from Enterococcus faecalis belongs to the FCD family within the GntR superfamily. In the presence of citrate, CitO binds to cis-acting sequences located upstream of the cit promoters inducing the expression of genes involved in citrate utilization. The quantification of the molecular binding affinities, performed by isothermal titration calorimetry (ITC), indicated that CitO has a high affinity for citrate (KD = 1.2 ± 0.2 μM), while it did not recognize other metabolic intermediates. Based on a structural model of CitO where a putative small molecule and a metal binding site were identified, it was hypothesized that the metal ion is required for citrate binding. In agreement with this model, citrate binding to CitO sharply decreased when the protein was incubated with EDTA. This effect was reverted by the addition of Ni2+, and Zn2+ to a lesser extent. Structure-based site-directed mutagenesis was conducted and it was found that changes to alanine in residues Arg97 and His191 resulted in decreased binding affinities for citrate, as determined by EMSA and ITC. Further assays using lacZ fusions confirmed that these residues in CitO are involved in sensing citrate in vivo. These results indicate that the molecular modifications induced by a ligand and a metal binding in the C-terminal domain of CitO are required for optimal DNA binding activity, and consequently, transcriptional activation.
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Affiliation(s)
- Víctor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y TécnicasRosario, Argentina; Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of FloridaGainesville, FL, USA
| | - Fernando A Pagliai
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of Florida Gainesville, FL, USA
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15
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Aroma compounds generation in citrate metabolism of Enterococcus faecium: Genetic characterization of type I citrate gene cluster. Int J Food Microbiol 2016; 218:27-37. [DOI: 10.1016/j.ijfoodmicro.2015.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/24/2015] [Accepted: 11/11/2015] [Indexed: 01/02/2023]
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16
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Ruiz-Cruz S, Espinosa M, Goldmann O, Bravo A. Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis. Front Microbiol 2016; 6:1521. [PMID: 26793169 PMCID: PMC4707282 DOI: 10.3389/fmicb.2015.01521] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/17/2015] [Indexed: 12/27/2022] Open
Abstract
Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. However, as an opportunistic pathogen, it is able to colonize other host niches and cause life-threatening infections. Its adaptation to new environments involves global changes in gene expression. The EF3013 gene (here named mafR) of E. faecalis strain V583 encodes a protein (MafR, 482 residues) that has sequence similarity to global response regulators of the Mga/AtxA family. The enterococcal OG1RF genome also encodes the MafR protein (gene OG1RF_12293). In this work, we have identified the promoter of the mafR gene using several in vivo approaches. Moreover, we show that MafR influences positively the transcription of many genes on a genome-wide scale. The most significant target genes encode components of PTS-type membrane transporters, components of ABC-type membrane transporters, and proteins involved in the metabolism of carbon sources. Some of these genes were previously reported to be up-regulated during the growth of E. faecalis in blood and/or in human urine. Furthermore, we show that a mafR deletion mutant strain induces a significant lower degree of inflammation in the peritoneal cavity of mice, suggesting that enterococcal cells deficient in MafR are less virulent. Our work indicates that MafR is a global transcriptional regulator. It might facilitate the adaptation of E. faecalis to particular host niches and, therefore, contribute to its potential virulence.
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Affiliation(s)
- Sofía Ruiz-Cruz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Oliver Goldmann
- Infection Immunology Research Group, Helmholtz Centre for Infection Research Braunschweig, Germany
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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17
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Repizo GD, Espariz M, Blancato VS, Suárez CA, Esteban L, Magni C. Genomic comparative analysis of the environmental Enterococcus mundtii against enterococcal representative species. BMC Genomics 2014; 15:489. [PMID: 24942651 PMCID: PMC4076982 DOI: 10.1186/1471-2164-15-489] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 06/02/2014] [Indexed: 11/30/2022] Open
Abstract
Background Enterococcus mundtii is a yellow-pigmented microorganism rarely found in human infections. The draft genome sequence of E. mundtii was recently announced. Its genome encodes at least 2,589 genes and 57 RNAs, and 4 putative genomic islands have been detected. The objective of this study was to compare the genetic content of E. mundtii with respect to other enterococcal species and, more specifically, to identify genes coding for putative virulence traits present in enterococcal opportunistic pathogens. Results An in-depth mining of the annotated genome was performed in order to uncover the unique properties of this microorganism, which allowed us to detect a gene encoding the antimicrobial peptide mundticin among other relevant features. Moreover, in this study a comparative genomic analysis against commensal and pathogenic enterococcal species, for which genomic sequences have been released, was conducted for the first time. Furthermore, our study reveals significant similarities in gene content between this environmental isolate and the selected enterococci strains (sharing an “enterococcal gene core” of 805 CDS), which contributes to understand the persistence of this genus in different niches and also improves our knowledge about the genetics of this diverse group of microorganisms that includes environmental, commensal and opportunistic pathogens. Conclusion Although E. mundtii CRL1656 is phylogenetically closer to E. faecium, frequently responsible of nosocomial infections, this strain does not encode the most relevant relevant virulence factors found in the enterococcal clinical isolates and bioinformatic predictions indicate that it possesses the lowest number of putative pathogenic genes among the most representative enterococcal species. Accordingly, infection assays using the Galleria mellonella model confirmed its low virulence. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-489) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario S2002LRK, Argentina.
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Ca2+-citrate uptake and metabolism in Lactobacillus casei ATCC 334. Appl Environ Microbiol 2013; 79:4603-12. [PMID: 23709502 DOI: 10.1128/aem.00925-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The putative citrate metabolic pathway in Lactobacillus casei ATCC 334 consists of the transporter CitH, a proton symporter of the citrate-divalent metal ion family of transporters CitMHS, citrate lyase, and the membrane-bound oxaloacetate decarboxylase complex OAD-ABDH. Resting cells of Lactobacillus casei ATCC 334 metabolized citrate in complex with Ca(2+) and not as free citrate or the Mg(2+)-citrate complex, thereby identifying Ca(2+)-citrate as the substrate of the transporter CitH. The pathway was induced in the presence of Ca(2+) and citrate during growth and repressed by the presence of glucose and of galactose, most likely by a carbon catabolite repression mechanism. The end products of Ca(2+)-citrate metabolism by resting cells of Lb. casei were pyruvate, acetate, and acetoin, demonstrating the activity of the membrane-bound oxaloacetate decarboxylase complex OAD-ABDH. Following pyruvate, the pathway splits into two branches. One branch is the classical citrate fermentation pathway producing acetoin by α-acetolactate synthase and α-acetolactate decarboxylase. The other branch yields acetate, for which the route is still obscure. Ca(2+)-citrate metabolism in a modified MRS medium lacking a carbohydrate did not significantly affect the growth characteristics, and generation of metabolic energy in the form of proton motive force (PMF) was not observed in resting cells. In contrast, carbohydrate/Ca(2+)-citrate cometabolism resulted in a higher biomass yield in batch culture. However, also with these cells, no generation of PMF was associated with Ca(2+)-citrate metabolism. It is concluded that citrate metabolism in Lb. casei is beneficial when it counteracts acidification by carbohydrate metabolism in later growth stages.
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