1
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Soussan D, Salze M, Ledormand P, Sauvageot N, Boukerb A, Lesouhaitier O, Fichant G, Rincé A, Quentin Y, Muller C. The NagY regulator: A member of the BglG/SacY antiterminator family conserved in Enterococcus faecalis and involved in virulence. Front Microbiol 2022; 13:1070116. [PMID: 36875533 PMCID: PMC9981650 DOI: 10.3389/fmicb.2022.1070116] [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: 10/14/2022] [Accepted: 12/21/2022] [Indexed: 02/19/2023] Open
Abstract
Enterococcus faecalis is a commensal bacterium of the gastrointestinal tract but also a major nosocomial pathogen. This bacterium uses regulators like BglG/SacY family of transcriptional antiterminators to adapt its metabolism during host colonization. In this report, we investigated the role of the BglG/SacY family antiterminator NagY in the regulation of the nagY-nagE operon in presence of N-acetylglucosamine, with nagE encoding a transporter of this carbohydrate, as well as the expression of the virulence factor HylA. We showed that this last protein is involved in biofilm formation and glycosaminoglycans degradation that are important features in bacterial infection, confirmed in the Galleria mellonella model. In order to elucidate the evolution of these actors, we performed phylogenomic analyses on E. faecalis and Enterococcaceae genomes, identified orthologous sequences of NagY, NagE, and HylA, and we report their taxonomic distribution. The study of the conservation of the upstream region of nagY and hylA genes showed that the molecular mechanism of NagY regulation involves ribonucleic antiterminator sequence overlapping a rho-independent terminator, suggesting a regulation conforming to the canonical model of BglG/SacY family antiterminators. In the perspective of opportunism understanding, we offer new insights into the mechanism of host sensing thanks to the NagY antiterminator and its targets expression.
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Affiliation(s)
- Diane Soussan
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Marine Salze
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Pierre Ledormand
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Nicolas Sauvageot
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Amine Boukerb
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France.,Plateforme de Génomique, CBSA EA4312, Normandie Université, UNIROUEN, Évreux, France
| | - Olivier Lesouhaitier
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Alain Rincé
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Cécile Muller
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
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2
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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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3
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Enterococcus faecalis Maltodextrin Gene Regulation by Combined Action of Maltose Gene Regulator MalR and Pleiotropic Regulator CcpA. Appl Environ Microbiol 2020; 86:AEM.01147-20. [PMID: 32680872 DOI: 10.1128/aem.01147-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/08/2020] [Indexed: 01/13/2023] Open
Abstract
Enterococci are Gram-positive bacteria present in the healthy human microbiota, but they are also a leading cause of nosocomial infections. Maltodextrin utilization by Enterococcus faecalis has been identified as an important factor for colonization of mammalians hosts. Here, we show that the LacI/GalR transcriptional regulator MalR, the maltose gene regulator, is also the main regulator of the operons encoding an ABC transporter (mdxEFG) and three metabolic enzymes (mmdH-gmdH-mmgT) required for the uptake and catabolism of maltotetraose and longer maltodextrins. The utilization of maltose and maltodextrins is consequently coordinated and induced by the disaccharide maltose, which binds to MalR. Carbon catabolite repression of the mdxEFG and mmdH-gmdH-mmgT operons is mediated by both P-Ser-HPr/MalR and P-Ser-HPr/CcpA. The latter complex exerts only moderate catabolite repression, which became visible when comparing maltodextrin operon expression levels of a malR - mutant (with a mutant allele for the malR gene) and a malR - ΔccpA double mutant grown in the presence of maltose, which is transported via a phosphotransferase system and, thus, favors the formation of P-Ser-HPr. Moreover, maltodextrin transport via MdxEFG slows rapidly when glucose is added, suggesting an additional regulation via inducer exclusion. This complex regulation of metabolic operons likely allows E. faecalis to fine-tune gene expression in response to changing environmental conditions.IMPORTANCE Enterococcus faecalis represents a leading cause of hospital-acquired infections worldwide. Several studies highlighted the importance of carbohydrate metabolism in the infection process of this bacterium. The genes required for maltodextrin metabolism are particularly induced during mouse infection and, therefore, should play an important role for pathogenesis. Since no data were hitherto available concerning the regulation of expression of the maltodextrin operons, we have conducted experiments to study the underlying mechanisms.
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4
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Sharma K, Sultana T, Dahms TES, Dillon JAR. CcpN: a moonlighting protein regulating catabolite repression of gluconeogenic genes in Bacillus subtilis also affects cell length and interacts with DivIVA. Can J Microbiol 2020; 66:723-732. [PMID: 32762636 DOI: 10.1139/cjm-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CcpN is a transcriptional repressor in Bacillus subtilis that binds to the promoter region of gapB and pckA, downregulating their expression in the presence of glucose. CcpN also represses sr1, which encodes a small noncoding regulatory RNA that suppresses the arginine biosynthesis gene cluster. CcpN has homologues in other Gram-positive bacteria, including Enterococcus faecalis. We report the interaction of CcpN with DivIVA of B. subtilis as determined using bacterial two-hybrid and glutathione S-transferase pull-down assays. Insertional inactivation of CcpN leads to cell elongation and formation of straight chains of cells. These findings suggest that CcpN is a moonlighting protein involved in both gluconeogenesis and cell elongation.
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Affiliation(s)
- Kusum Sharma
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada
| | - Taranum Sultana
- Department of Chemistry and Biochemistry, 3737 Wascana Parkway, University of Regina, Regina, SK S4S 0A2, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, 3737 Wascana Parkway, University of Regina, Regina, SK S4S 0A2, Canada
| | - Jo-Anne R Dillon
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N 5E3, Canada
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5
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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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6
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Grand M, Blancato VS, Espariz M, Deutscher J, Pikis A, Hartke A, Magni C, Sauvageot N. Enterococcus faecalisMalR acts as a repressor of the maltose operons and additionally mediates their catabolite repression via direct interaction with seryl‐phosphorylated‐HPr. Mol Microbiol 2019; 113:464-477. [DOI: 10.1111/mmi.14431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | - Victor Sebastián Blancato
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Martín Espariz
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris‐Saclay Jouy‐en‐Josas France
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico‐Chimique Paris France
| | - Andreas Pikis
- Center for Drug Evaluation and Research, Food and Drug Administration Silver Spring Maryland
- Microbial Biochemistry and Genetics Unit, Laboratory of Cell and Developmental Biology NIDCR, National Institutes of Health Bethesda Maryland
| | | | - Christian Magni
- Instituto de Biología Molecular y Celular de Rosario (IBR‐CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas Universidad Nacional de Rosario Rosario Argentina
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Adaptation to Adversity: the Intermingling of Stress Tolerance and Pathogenesis in Enterococci. Microbiol Mol Biol Rev 2019; 83:83/3/e00008-19. [PMID: 31315902 DOI: 10.1128/mmbr.00008-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enterococcus is a diverse and rugged genus colonizing the gastrointestinal tract of humans and numerous hosts across the animal kingdom. Enterococci are also a leading cause of multidrug-resistant hospital-acquired infections. In each of these settings, enterococci must contend with changing biophysical landscapes and innate immune responses in order to successfully colonize and transit between hosts. Therefore, it appears that the intrinsic durability that evolved to make enterococci optimally competitive in the host gastrointestinal tract also ideally positioned them to persist in hospitals, despite disinfection protocols, and acquire new antibiotic resistances from other microbes. Here, we discuss the molecular mechanisms and regulation employed by enterococci to tolerate diverse stressors and highlight the role of stress tolerance in the biology of this medically relevant genus.
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8
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Abstract
The study of the genetics of enterococci has focused heavily on mobile genetic elements present in these organisms, the complex regulatory circuits used to control their mobility, and the antibiotic resistance genes they frequently carry. Recently, more focus has been placed on the regulation of genes involved in the virulence of the opportunistic pathogenic species Enterococcus faecalis and Enterococcus faecium. Little information is available concerning fundamental aspects of DNA replication, partition, and division; this article begins with a brief overview of what little is known about these issues, primarily by comparison with better-studied model organisms. A variety of transcriptional and posttranscriptional mechanisms of regulation of gene expression are then discussed, including a section on the genetics and regulation of vancomycin resistance in enterococci. The article then provides extensive coverage of the pheromone-responsive conjugation plasmids, including sections on regulation of the pheromone response, the conjugative apparatus, and replication and stable inheritance. The article then focuses on conjugative transposons, now referred to as integrated, conjugative elements, or ICEs, and concludes with several smaller sections covering emerging areas of interest concerning the enterococcal mobilome, including nonpheromone plasmids of particular interest, toxin-antitoxin systems, pathogenicity islands, bacteriophages, and genome defense.
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9
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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: 9] [Impact Index Per Article: 1.5] [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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10
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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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11
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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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12
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Großeholz R, Koh CC, Veith N, Fiedler T, Strauss M, Olivier B, Collins BC, Schubert OT, Bergmann F, Kreikemeyer B, Aebersold R, Kummer U. Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis. NPJ Syst Biol Appl 2016; 2:16017. [PMID: 28725473 PMCID: PMC5516852 DOI: 10.1038/npjsba.2016.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/10/2016] [Accepted: 06/17/2016] [Indexed: 01/19/2023] Open
Abstract
Genome-scale metabolic models represent the entirety of metabolic reactions of an organism based on the annotation of the respective genome. These models commonly allow all reactions to proceed concurrently, disregarding the fact that at no point all proteins will be present in a cell. The metabolic reaction space can be constrained to a more physiological state using experimentally obtained information on enzyme abundances. However, high-quality, genome-wide protein measurements have been challenging and typically transcript abundances have been used as a surrogate for protein measurements. With recent developments in mass spectrometry-based proteomics, exemplified by SWATH-MS, the acquisition of highly quantitative proteome-wide data at reasonable throughput has come within reach. Here we present methodology to integrate such proteome-wide data into genome-scale models. We applied this methodology to study cellular changes in Enterococcus faecalis during adaptation to low pH. Our results indicate reduced proton production in the central metabolism and decreased membrane permeability for protons due to different membrane composition. We conclude that proteomic data constrain genome-scale models to a physiological state and, in return, genome-scale models are useful tools to contextualize proteomic data.
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Affiliation(s)
- Ruth Großeholz
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Ching-Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Nadine Veith
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Madlen Strauss
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Brett Olivier
- Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, Amsterdam, Netherlands
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Frank Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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13
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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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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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15
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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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16
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Suárez C, Espariz M, Blancato VS, Magni C. Expression of the agmatine deiminase pathway in Enterococcus faecalis is activated by the AguR regulator and repressed by CcpA and PTS(Man) systems. PLoS One 2013; 8:e76170. [PMID: 24155893 PMCID: PMC3796520 DOI: 10.1371/journal.pone.0076170] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/21/2013] [Indexed: 11/29/2022] Open
Abstract
Although the agmatine deiminase system (AgDI) has been investigated in Enterococcus faecalis, little information is available with respect to its gene regulation. In this study we demonstrate that the presence of exogenous agmatine induces the expression of agu genes in this bacterium. In contrast to the homologous and extensively characterized AgDI system of S. mutants, the aguBDAC operon in E. faecalis is not induced in response to low pH. In spite of this, agmatine catabolism in this bacterium contributes by neutralizing the external medium while enhancing bacterial growth. Our results indicate that carbon catabolic repression (CCR) operates on the AgDI system via a mechanism that involves interaction of CcpA and P-Ser-HPr with a cre site found in an unusual position considering the aguB promoter (55 nt upstream the +1 position). In addition, we found that components of the mannose phosphotransferase (PTSMan) system also contributed to CCR in E. faecalis since a complete relief of the PTS-sugars repressive effect was observed only in a PTSMan and CcpA double defective strain. Our gene context analysis revealed that aguR is present in oral and gastrointestinal microorganisms. Thus, regulation of the aguBDAC operon in E. faecalis seems to have evolved to obtain energy and resist low pH conditions in order to persist and colonize gastrointestinal niches.
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Affiliation(s)
- Cristian Suárez
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET), Rosario, Santa Fe, Argentina
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET), Rosario, Santa Fe, Argentina
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Víctor S. Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET), Rosario, Santa Fe, Argentina
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET), Rosario, Santa Fe, Argentina
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- * E-mail:
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Basal levels of (p)ppGpp in Enterococcus faecalis: the magic beyond the stringent response. mBio 2013; 4:e00646-13. [PMID: 24065631 PMCID: PMC3781836 DOI: 10.1128/mbio.00646-13] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The stringent response (SR), mediated by the alarmone (p)ppGpp, is a conserved bacterial adaptation system controlling broad metabolic alterations necessary for survival under adverse conditions. In Enterococcus faecalis, production of (p)ppGpp is controlled by the bifunctional protein RSH (for "Rel SpoT homologue"; also known as RelA) and by the monofunctional synthetase RelQ. Previous characterization of E. faecalis strains lacking rsh, relQ, or both revealed that RSH is responsible for activation of the SR and that alterations in (p)ppGpp production negatively impact bacterial stress survival and virulence. Despite its well-characterized role as the effector of the SR, the significance of (p)ppGpp during balanced growth remains poorly understood. Microarrays of E. faecalis strains producing different basal amounts of (p)ppGpp identified several genes and pathways regulated by modest changes in (p)ppGpp. Notably, expression of numerous genes involved in energy generation were induced in the rsh relQ [(p)ppGpp(0)] strain, suggesting that a lack of basal (p)ppGpp places the cell in a "transcriptionally relaxed" state. Alterations in the fermentation profile and increased production of H2O2 in the (p)ppGpp(0) strain substantiate the observed transcriptional changes. We confirm that, similar to what is seen in Bacillus subtilis, (p)ppGpp directly inhibits the activity of enzymes involved in GTP biosynthesis, and complete loss of (p)ppGpp leads to dysregulation of GTP homeostasis. Finally, we show that the association of (p)ppGpp with antibiotic survival does not relate to the SR but rather relates to basal (p)ppGpp pools. Collectively, this study highlights the critical but still underappreciated role of basal (p)ppGpp pools under balanced growth conditions. IMPORTANCE Drug-resistant bacterial infections continue to pose a significant public health threat by limiting therapeutic options available to care providers. The stringent response (SR), mediated by the accumulation of two modified guanine nucleotides collectively known as (p)ppGpp, is a highly conserved stress response that broadly remodels bacterial physiology to a survival state. Given the strong correlation of the SR with the ability of bacteria to survive antibiotic treatment and the direct association of (p)ppGpp production with bacterial infectivity, understanding how bacteria produce and utilize (p)ppGpp may reveal potential targets for the development of new antimicrobial therapies. Using the multidrug-resistant pathogen Enterococcus faecalis as a model, we show that small alterations to (p)ppGpp levels, well below concentrations needed to trigger the SR, severely affected bacterial metabolism and antibiotic survival. Our findings highlight the often-underappreciated contribution of basal (p)ppGpp levels to metabolic balance and stress tolerance in bacteria.
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Library screen identifies Enterococcus faecalis CcpA, the catabolite control protein A, as an effector of Ace, a collagen adhesion protein linked to virulence. J Bacteriol 2013; 195:4761-8. [PMID: 23974022 DOI: 10.1128/jb.00706-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Enterococcus faecalis cell wall-anchored protein Ace is an important virulence factor involved in cell adhesion and infection. Expression of Ace on the cell surface is affected by many factors, including stage of growth, culture temperature, and environmental components, such as serum, urine, and collagen. However, the mechanisms that regulate or modulate Ace display are not well understood. With interest in identifying genes associated with Ace expression, we utilized a whole-cell enzyme-linked immunosorbent assay (ELISA)-based screening method to identify mutants from a transposon insertion mutant library which exhibited distinct Ace surface expression profiles. We identified a ccpA insertion mutant which showed significantly decreased levels of Ace surface expression at early growth phase versus those of wild-type OG1RF. Confirmation of the observation was achieved through flow cytometry and complementation analysis. Compared to the wild type, the E. faecalis ccpA mutant had an impaired ability to adhere to collagen when grown to early exponential phase, consistent with the lack of Ace expression in the early growth phase. As a key component of carbon catabolite regulation, CcpA has been previously reported to play a critical role in regulating expression of proteins involved in E. faecalis carbohydrate uptake and utilization. Our discovery is the first to associate CcpA with the production of a major E. faecalis virulence factor, providing new insights into the regulation of E. faecalis pathogenesis.
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The putrescine biosynthesis pathway in Lactococcus lactis is transcriptionally regulated by carbon catabolic repression, mediated by CcpA. Int J Food Microbiol 2013; 165:43-50. [DOI: 10.1016/j.ijfoodmicro.2013.04.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 11/19/2022]
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Antunes A, Camiade E, Monot M, Courtois E, Barbut F, Sernova NV, Rodionov DA, Martin-Verstraete I, Dupuy B. Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile. Nucleic Acids Res 2012; 40:10701-18. [PMID: 22989714 PMCID: PMC3510511 DOI: 10.1093/nar/gks864] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The catabolite control protein CcpA is a pleiotropic regulator that mediates the global transcriptional response to rapidly catabolizable carbohydrates, like glucose in Gram-positive bacteria. By whole transcriptome analyses, we characterized glucose-dependent and CcpA-dependent gene regulation in Clostridium difficile. About 18% of all C. difficile genes are regulated by glucose, for which 50% depend on CcpA for regulation. The CcpA regulon comprises genes involved in sugar uptake, fermentation and amino acids metabolism, confirming the role of CcpA as a link between carbon and nitrogen pathways. Using combination of chromatin immunoprecipitation and genome sequence analysis, we detected 55 CcpA binding sites corresponding to ∼140 genes directly controlled by CcpA. We defined the C. difficile CcpA consensus binding site (creCD motif), that is, ‘RRGAAAANGTTTTCWW’. Binding of purified CcpA protein to 19 target creCD sites was demonstrated by electrophoretic mobility shift assay. CcpA also directly represses key factors in early steps of sporulation (Spo0A and SigF). Furthermore, the C. difficile toxin genes (tcdA and tcdB) and their regulators (tcdR and tcdC) are direct CcpA targets. Finally, CcpA controls a complex and extended regulatory network through the modulation of a large set of regulators.
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Affiliation(s)
- Ana Antunes
- Laboratoire Pathogenèse des Bactéries Anaérobies, Département de Microbiologie Institut Pasteur, Paris 75015, France
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Fine-tuned transcriptional regulation of malate operons in Enterococcus faecalis. Appl Environ Microbiol 2012; 78:1936-45. [PMID: 22247139 DOI: 10.1128/aem.07280-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Enterococcus faecalis, the mae locus is constituted by two putative divergent operons, maePE and maeKR. The first operon encodes a putative H(+)/malate symporter (MaeP) and a malic enzyme (MaeE) previously shown to be essential for malate utilization in this bacterium. The maeKR operon encodes two putative proteins with significant similarity to two-component systems involved in sensing malate and activating its assimilation in bacteria. Our transcriptional and genetic assays showed that maePE and maeKR are induced in response to malate by the response regulator MaeR. In addition, we observed that both operons were partially repressed in the presence of glucose. Accordingly, the cometabolism of this sugar and malate was detected. The binding of the complex formed by CcpA and its corepressor P-Ser-HPr to a cre site located in the mae region was demonstrated in vitro and explains the carbon catabolite repression (CCR) observed for the maePE operon. However, our results also provide evidence for a CcpA-independent CCR mechanism regulating the expression of both operons. Finally, a biomass increment of 40 or 75% was observed compared to the biomass of cells grown only on glucose or malate, respectively. Cells cometabolizing both carbon sources exhibit a higher rate of glucose consumption and a lower rate of malate utilization. The growth improvement achieved by E. faecalis during glucose-malate cometabolism might explain why this microorganism employs different regulatory systems to tightly control the assimilation of both carbon sources.
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