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Chen Y, Ying Y, Lalsiamthara J, Zhao Y, Imani S, Li X, Liu S, Wang Q. From bacteria to biomedicine: Developing therapies exploiting NAD + metabolism. Bioorg Chem 2024; 142:106974. [PMID: 37984103 DOI: 10.1016/j.bioorg.2023.106974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) serves as a critical cofactor in cellular metabolism and redox reactions. Bacterial pathways rely on NAD+ participation, where its stability and concentration govern essential homeostasis and functions. This review delves into the role and metabolic regulation of NAD+ in bacteria, highlighting its influence on physiology and virulence. Notably, we explore enzymes linked to NAD+ metabolism as antibacterial drug targets and vaccine candidates. Moreover, we scrutinize NAD+'s medical potential, offering insights for its application in biomedicine. This comprehensive assessment informs future research directions in the dynamic realm of NAD+ and its biomedical significance.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Yuanyuan Ying
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Jonathan Lalsiamthara
- Molecular Microbiology & Immunology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Yuheng Zhao
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang 310015, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Xin Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Sijing Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Qingjing Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China.
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2
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Jin Y, Fan Y, Sun H, Zhang Y, Wang H. Transcriptome Analysis Reveals Catabolite Control Protein A Regulatory Mechanisms Underlying Glucose-Excess or -Limited Conditions in a Ruminal Bacterium, Streptococcus bovis. Front Microbiol 2021; 12:767769. [PMID: 34867900 PMCID: PMC8637274 DOI: 10.3389/fmicb.2021.767769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/05/2022] Open
Abstract
Ruminants may suffer from rumen acidosis when fed with high-concentrate diets due to the higher proliferation and overproduction of lactate by Streptococcus bovis. The catabolite control protein A (CcpA) regulates the transcription of lactate dehydrogenase (ldh) and pyruvate formate-lyase (pfl) in S. bovis, but its role in response to different carbon concentrations remains unclear. To characterize the regulatory mechanisms of CcpA in S. bovis S1 at different levels of carbon, herein, we analyzed the transcriptomic and physiological characteristics of S. bovis S1 and its ccpA mutant strain grown in glucose-excess and glucose-limited conditions. A reduced growth rate and a shift in fermentation pattern from homofermentation to heterofermentation were observed under glucose-limited condition as compared to glucose-excess condition, in S. bovis S1. Additionally, the inactivation of ccpA significantly affected the growth and end metabolites in both conditions. For the glycolytic intermediate, fructose 1,6-bisphosphate (FBP), the concentration significantly reduced at lower glucose conditions; its concentration decreased significantly in the ccpA mutant strain. Transcriptomic results showed that about 46% of the total genes were differentially transcribed between the wild-type strain and ccpA mutant strain grown in glucose-excess conditions; while only 12% genes were differentially transcribed in glucose-limited conditions. Different glucose concentrations led to the differential expression of 38% genes in the wild-type strain, while only half of these were differentially expressed in the ccpA-knockout strain. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the substrate glucose concentration significantly affected the gene expression in histidine metabolism, nitrogen metabolism, and some carbohydrate metabolism pathways. The deletion of ccpA affected several genes involved in carbohydrate metabolism, such as glycolysis, pyruvate metabolism, fructose and mannose metabolism, as well as in fatty acid biosynthesis pathways in bacteria grown in glucose-excess conditions; this effect was attenuated under glucose-limited conditions. Overall, these findings provide new information on gene transcription and metabolic mechanisms associated with substrate glucose concentration and validate the important role of CcpA in the regulation of carbon metabolism in S. bovis S1 at differential glucose availability.
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Affiliation(s)
- Yaqian Jin
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yaotian Fan
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hua Sun
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ying Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hongrong Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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3
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Purification and characterization of bacteriocins-like inhibitory substances from food isolated Enterococcus faecalis OS13 with activity against nosocomial enterococci. Sci Rep 2021; 11:3795. [PMID: 33589735 PMCID: PMC7884432 DOI: 10.1038/s41598-021-83357-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
Nosocomial infections caused by enterococci are an ongoing global threat. Thus, finding therapeutic agents for the treatment of such infections are crucial. Some Enterococcus faecalis strains are able to produce antimicrobial peptides called bacteriocins. We analyzed 65 E. faecalis isolates from 43 food samples and 22 clinical samples in Egypt for 17 common bacteriocin-encoding genes of Enterococcus spp. These genes were absent in 11 isolates that showed antimicrobial activity putatively due to bacteriocins (three from food, including isolate OS13, and eight from clinical isolates). The food-isolated E. faecalis OS13 produced bacteriocin-like inhibitory substances (BLIS) named enterocin OS13, which comprised two peptides (enterocin OS13α OS13β) that inhibited the growth of antibiotic-resistant nosocomial E. faecalis and E. faecium isolates. The molecular weights of enterocin OS13α and OS13β were determined as 8079 Da and 7859 Da, respectively, and both were heat-labile. Enterocin OS13α was sensitive to proteinase K, while enterocin OS13β was resistant. Characterization of E. faecalis OS13 isolate revealed that it belonged to sequence type 116. It was non-hemolytic, bile salt hydrolase-negative, gelatinase-positive, and sensitive to ampicillin, penicillin, vancomycin, erythromycin, kanamycin, and gentamicin. In conclusion, BLIS as enterocin OS13α and OS13β represent antimicrobial agents with activities against antibiotic-resistant enterococcal isolates.
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4
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Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J. Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium. Front Cell Infect Microbiol 2020; 10:600325. [PMID: 33324581 PMCID: PMC7724050 DOI: 10.3389/fcimb.2020.600325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
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Affiliation(s)
- Charlotte Michaux
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Milan Gerovac
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
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5
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Balasubramanian S, Subramanian R. Metabolic perturbation of acrylate pathway in Lactobacillus plantarum. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1606215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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6
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Sharma D, Khan AU. Role of cell division protein divIVA in Enterococcus faecalis pathogenesis, biofilm and drug resistance: A future perspective by in silico approaches. Microb Pathog 2018; 125:361-365. [PMID: 30290265 DOI: 10.1016/j.micpath.2018.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022]
Abstract
Antibiotics resistance is the major problem in clinical settings which leads to the emergence of drug resistant bacteria. Biofilm formation is one of the grounds for the emergence of antibiotics resistant strains of Enterococcus faecalis. Our group previously reported in a comparative proteomic study of biofilm and planktonic state of E. faecalis that cell division protein divIVA was two folds overexpressed in biofilm state as compared to planktonic one and suggested its involvement in biofilm formation and antibiotics resistance. In this in silico study molecular docking showed that DNA bind to the conserved amino acid residues of divIVA domain and suggested that divIVA possibly secretes DNA into extra polymeric substance (EPS) which is the part of biofilm. We also performed the STRING analysis of cell division protein divIVA and predicted their interactive partners {cell division proteins/divisome complex (ftsZ, ftsA, divIV, ftsL, & gpsB), hypothetical proteins (sepF, EF_0261, EF_1000, EF_0998, EF_1006 & EF_1040), isoleucyl-tRNA synthetase (ileS), septation ring formation regulator (ezrA), S4 domain-containing protein (EF_1001), rod shape-determining protein (mreC), UDP-N-acetylmuramoyl-L-alanyl-d-glutamate synthetase (murD), UDP-diphospho-muramoyl-pentapeptide beta-N- acetylglucosaminyltransferase (murG), Lipoprotein signal peptidase (lspA), adenylate kinase (adk) and DNA-binding response regulator (vicR)}. We suggest that cumulatively divIVA and its interactive partners might be directly or indirectly involved in E. faecalis cell division, growth, biofilm formation, virulence and resistance.
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Affiliation(s)
- Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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7
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Zhu H, Wang Y, Ni Y, Zhou J, Han L, Yu Z, Mao A, Wang D, Fan H, He K. The Redox-Sensing Regulator Rex Contributes to the Virulence and Oxidative Stress Response of Streptococcus suis Serotype 2. Front Cell Infect Microbiol 2018; 8:317. [PMID: 30280091 PMCID: PMC6154617 DOI: 10.3389/fcimb.2018.00317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/20/2018] [Indexed: 01/06/2023] Open
Abstract
Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen responsible for septicemia and meningitis. The redox-sensing regulator Rex has been reported to play critical roles in the metabolism regulation, oxidative stress response, and virulence of various pathogens. In this study, we identified and characterized a Rex ortholog in the SS2 virulent strain SS2-1 that is involved in bacterial pathogenicity and stress environment susceptibility. Our data show that the Rex-knockout mutant strain Δrex exhibited impaired growth in medium with hydrogen peroxide or a low pH compared with the wildtype strain SS2-1 and the complementary strain CΔrex. In addition, Δrex showed a decreased level of survival in whole blood and in RAW264.7 macrophages. Further analyses revealed that Rex deficiency significantly attenuated bacterial virulence in an animal model. A comparative proteome analysis found that the expression levels of several proteins involved in virulence and oxidative stress were significantly different in Δrex compared with SS2-1. Electrophoretic mobility shift assays revealed that recombinant Rex specifically bound to the promoters of target genes in a manner that was modulated by NADH and NAD+. Taken together, our data suggest that Rex plays critical roles in the virulence and oxidative stress response of SS2.
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Affiliation(s)
- Haodan Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Yong Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yanxiu Ni
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Junming Zhou
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China.,Key Lab of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Nanjing, China
| | - Lixiao Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhengyu Yu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Aihua Mao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Dandan Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Hongjie Fan
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Kongwang He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China.,Key Lab of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Nanjing, China
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8
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Afzal M, Shafeeq S, Kuipers OP. NADH-Mediated Gene Expression in Streptococcus pneumoniae and Role of Rex as a Transcriptional Repressor of the Rex-Regulon. Front Microbiol 2018; 9:1300. [PMID: 29971050 PMCID: PMC6018154 DOI: 10.3389/fmicb.2018.01300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/28/2018] [Indexed: 11/17/2022] Open
Abstract
Nicotinamide adenine dinucleotides (NAD(H)) play a vital role in various biological processes, including keeping the cellular redox balance. In this study, we investigate the regulatory responses of Streptococcus pneumoniae D39 to NADH and characterize the role of the Rex protein as a transcriptional repressor of the gapN, fba, pncB, adhB2, gap, and adhE genes. Transcriptomic analysis was used to observe the response of S. pneumoniae D39 to NADH. Our microarray studies revealed elevated expression of various genes/operons involved in transport and biosynthesis of niacin (gapN, fba, pncB, adhB2, gap, and adhE). Promoter lacZ-fusion assays and microarray studies with the rex mutant revealed the role of Rex as a transcriptional repressor of gapN, fba, pncB, adhB2, gap, and adhE involved in niacin uptake and biosynthesis, in the presence of NADH. We predict the operator site (5′-TTGTKAWAAWWTTCACAA-3′) of Rex in the regulatory regions of Rex-regulated genes that was subsequently validated by promoter mutational experiments.
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Affiliation(s)
- Muhammad Afzal
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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9
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McLeod A, Mosleth EF, Rud I, Branco dos Santos F, Snipen L, Liland KH, Axelsson L. Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome. PLoS One 2017; 12:e0187542. [PMID: 29099858 PMCID: PMC5669474 DOI: 10.1371/journal.pone.0187542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/20/2017] [Indexed: 01/08/2023] Open
Abstract
Effects of glucose availability were investigated in Lactobacillus sakei strains 23K and LS25 cultivated in anaerobic, glucose-limited chemostats set at high (D = 0.357 h-1) and low (D = 0.045 h-1) dilution rates. We observed for both strains a shift from homolactic towards more mixed acid fermentation when comparing high to low growth rates. However, this change was more pronounced for LS25 than for 23K, where dominating products were lactate>formate>acetate≥ethanol at both conditions. A multivariate approach was used for analyzing proteome and transcriptome data from the bacterial cultures, where the predictive power of the omics data was used for identifying features that can explain the differences in the end-product profiles. We show that the different degree of response to the same energy restriction revealed interesting strain specific regulation. An elevated formate production level during slow growth, more for LS25 than for 23K, was clearly reflected in correlating pyruvate formate lyase expression. With stronger effect for LS25, differential expression of the Rex transcriptional regulator and NADH oxidase, a target of Rex, indicated that maintainance of the cell redox balance, in terms of the NADH/NAD+ ratio, may be a key process during the metabolic change. The results provide a better understanding of different strategies that cells may deploy in response to changes in substrate availability.
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Affiliation(s)
- Anette McLeod
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Ellen F. Mosleth
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Ida Rud
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Kristian Hovde Liland
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Lars Axelsson
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
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10
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Kaur M, Jayaraman G. Hyaluronan production and molecular weight is enhanced in pathway-engineered strains of lactate dehydrogenase-deficient Lactococcus lactis. Metab Eng Commun 2016; 3:15-23. [PMID: 29468110 PMCID: PMC5779726 DOI: 10.1016/j.meteno.2016.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 11/08/2015] [Accepted: 01/19/2016] [Indexed: 12/31/2022] Open
Abstract
The potential advantages of hyaluronic acid (HA) production by metabolically-engineered Lactococcus lactis is constrained by the lower molecular weight and yield of HA obtained in these strains, compared to natural producers. Earlier studies have correlated lower HA yield with excessive lactate production in L. lactis cultures (Chauhan et al., 2014). In the present study, a three-fold increase was observed in the amount as well as molecular weight of HA produced by recombinant ldh-mutant L. lactis strains. The diversion from lactate production in the ldh-mutant strains resulted in excess ethanol and acetoin production and higher NAD+/NADH ratio in these cultures. The initial NAD+/NADH ratio showed a positive correlation with HA molecular weight as well as with the HA-precursor ratio (UDP-GlcUA/UDP-GlcNAc). The influence of NAD+/NADH ratio on regulation of the concerned metabolic pathways was assessed by transcriptional analysis of key genes having putative binding sites of the NADH-binding transcriptional factor, Rex.
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Affiliation(s)
| | - Guhan Jayaraman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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11
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Abstract
Pathogenic bacteria must contend with immune systems that actively restrict the availability of nutrients and cofactors, and create a hostile growth environment. To deal with these hostile environments, pathogenic bacteria have evolved or acquired virulence determinants that aid in the acquisition of nutrients. This connection between pathogenesis and nutrition may explain why regulators of metabolism in nonpathogenic bacteria are used by pathogenic bacteria to regulate both metabolism and virulence. Such coordinated regulation is presumably advantageous because it conserves carbon and energy by aligning synthesis of virulence determinants with the nutritional environment. In Gram-positive bacterial pathogens, at least three metabolite-responsive global regulators, CcpA, CodY, and Rex, have been shown to coordinate the expression of metabolism and virulence genes. In this chapter, we discuss how environmental challenges alter metabolism, the regulators that respond to this altered metabolism, and how these regulators influence the host-pathogen interaction.
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12
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Zha M, Yu J, Zhang Y, Wang H, Bai N, Qin Y, Liangliang D, Liu W, Zhang H, Bilige M. Study on Streptococcus thermophilus isolated from Qula and associated characteristic of acetaldehyde and diacetyl in their fermented milk. J GEN APPL MICROBIOL 2016; 61:50-6. [PMID: 26018501 DOI: 10.2323/jgam.61.50] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, the lactic acid bacterial population of Qula cheese from the Gansu and Sichuan provinces of China were isolated and identified. Eight strains of Streptococcus thermophilus were isolated, of which five strains were selected for further characterization based on their fermentation properties. The changes in a number of parameters, including titration acidity, pH, viable counts, PrtS protease activity and the production of acetaldehyde, diacetyl and organic acid, were monitored during fermentation and the storage of fermented milks produced by the respective strain. All of the strains displaying acidifying capacity and all five fermented milks maintained high viable counts of S. thermophilus from fermentation to storage. Our study found that the changes in the monitored parameters were strain-specific and varied considerably among the five tested strains. Fermented milks produced by strain IMAU80809 had the highest concentration of acetaldehyde and were most favorable in the sensory evaluation. This study confirms that Qula cheese is a good source for isolating novel lactic acid bacterial strains with different fermentation properties, which will be very useful for further development and industrialization of traditionally fermented dairy products.
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Affiliation(s)
- Musu Zha
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry Education of China
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13
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Bitoun JP, Wen ZT. Transcription factor Rex in regulation of pathophysiology in oral pathogens. Mol Oral Microbiol 2015; 31:115-24. [PMID: 26172563 DOI: 10.1111/omi.12114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2015] [Indexed: 11/29/2022]
Abstract
The NAD(+) and NADH-sensing transcriptional regulator Rex is widely conserved across gram-positive bacteria. Rex monitors cellular redox poise and controls the expression of genes/operons involved in diverse pathways including alternative fermentation, oxidative stress responses, and biofilm formation. The oral cavity undergoes frequent and drastic fluctuations in nutrient availability, pH, temperature, oxygen tension, saliva, and shear forces. The oral streptococci are major colonizers of oral mucosa and tooth surfaces and include commensals as well as opportunistic pathogens, including the primary etiological agent of dental caries, Streptococcus mutans. Current understanding of the Rex regulon in oral bacteria is mostly based on studies in S. mutans and endodontic pathogen Enterococcus faecalis. Indeed, other oral bacteria encode homologs of the Rex protein and much is to be gleaned from more in-depth studies. Our current understanding has Rex positioned at the interface of oxygen and energy metabolism. In biofilms, heterogeneous oxygen tension influences the ratio of intracellular NADH and NAD(+) , which is finely tuned through glycolysis and fermentation. In S. mutans, Rex regulates the expression of glycolytic enzyme NAD(+) -dependent glyceraldehyde 3-phosphate dehydrogenase, and NADH-dependent fermentation enzymes/complexes lactate dehydrogenase, pyruvate dehydrogenase, alcohol-acetaldehyde dehydrogenase, and fumarate reductase. In addition, Rex controls the expression of NADH oxidase, a major enzyme used to eliminate oxidative stress and regenerate NAD(+) . Here, we summarize recent studies carried out on the Rex regulators in S. mutans and E. faecalis. This research has important implications for understanding how Rex monitors redox balance and optimizes fermentation pathways for survival and subsequent pathogenicity.
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Affiliation(s)
- J P Bitoun
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Z T Wen
- Department of Comprehensive Dentistry and Biomaterials, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Center of Oral and Craniofacial Biology, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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14
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Innocenti N, Golumbeanu M, Fouquier d'Hérouël A, Lacoux C, Bonnin RA, Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA (NEW YORK, N.Y.) 2015; 21:1018-30. [PMID: 25737579 PMCID: PMC4408782 DOI: 10.1261/rna.048470.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/22/2014] [Indexed: 05/21/2023]
Abstract
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
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Affiliation(s)
- Nicolas Innocenti
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland
| | - Aymeric Fouquier d'Hérouël
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Caroline Lacoux
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Rémy A Bonnin
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Sean P Kennedy
- INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Françoise Wessner
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Pascale Serror
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Philippe Bouloc
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Francis Repoila
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Erik Aurell
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland
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Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl Environ Microbiol 2014; 81:1622-33. [PMID: 25527553 DOI: 10.1128/aem.03279-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Increasing antibiotic resistance in pathogenic bacteria necessitates the development of new medication strategies. Interfering with the metabolic network of the pathogen can provide novel drug targets but simultaneously requires a deeper and more detailed organism-specific understanding of the metabolism, which is often surprisingly sparse. In light of this, we reconstructed a genome-scale metabolic model of the pathogen Enterococcus faecalis V583. The manually curated metabolic network comprises 642 metabolites and 706 reactions. We experimentally determined metabolic profiles of E. faecalis grown in chemically defined medium in an anaerobic chemostat setup at different dilution rates and calculated the net uptake and product fluxes to constrain the model. We computed growth-associated energy and maintenance parameters and studied flux distributions through the metabolic network. Amino acid auxotrophies were identified experimentally for model validation and revealed seven essential amino acids. In addition, the important metabolic hub of glutamine/glutamate was altered by constructing a glutamine synthetase knockout mutant. The metabolic profile showed a slight shift in the fermentation pattern toward ethanol production and increased uptake rates of multiple amino acids, especially l-glutamine and l-glutamate. The model was used to understand the altered flux distributions in the mutant and provided an explanation for the experimentally observed redirection of the metabolic flux. We further highlighted the importance of gene-regulatory effects on the redirection of the metabolic fluxes upon perturbation. The genome-scale metabolic model presented here includes gene-protein-reaction associations, allowing a further use for biotechnological applications, for studying essential genes, proteins, or reactions, and the search for novel drug targets.
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16
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Abstract
We show that Enterococcus faecalis can utilize ascorbate for fermentative growth. In chemically defined media, growth yield was limited by the supply of amino acids, and the cells showed a much higher demand for amino acids than when they were grown on glucose.
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17
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Redox balance via lactate dehydrogenase is important for multiple stress resistance and virulence in Enterococcus faecalis. Infect Immun 2013; 81:2662-8. [PMID: 23649090 DOI: 10.1128/iai.01299-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Enterococcus faecalis is a highly stress resistant opportunistic pathogen. The intrinsic ruggedness of this bacterium is supposed to be the basis of its capacity to colonize the hostile environments of hospitals and to cause several kinds of infections. We show in this work that general resistance to very different environmental stresses depends on the ability of E. faecalis to maintain redox balance via lactate dehydrogenase (LDH). Furthermore, LDH-deficient mutants are less successful than the wild type at colonizing host organs in a murine model of systemic infection. Taken together, our results, as well as those previously published for Staphylococcus aureus (A. R. Richardson, S. J. Libby, and F. C. Fang, Science 319:1672-1676, 2008), identify LDH as an attractive drug target. These drugs may have additional applications, as in the fight against glycopeptide antibiotic-resistant bacteria and even cancer.
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18
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A Rex family transcriptional repressor influences H2O2 accumulation by Enterococcus faecalis. J Bacteriol 2013; 195:1815-24. [PMID: 23417491 DOI: 10.1128/jb.02135-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Rex factors are bacterial transcription factors thought to respond to the cellular NAD(+)/NADH ratio in order to modulate gene expression by differentially binding DNA. To date, Rex factors have been implicated in regulating genes of central metabolism, oxidative stress response, and biofilm formation. The genome of Enterococcus faecalis, a low-GC Gram-positive opportunistic pathogen, encodes EF2638, a putative Rex factor. To study the role of E. faecalis Rex, we purified EF2638 and evaluated its DNA binding activity in vitro. EF2638 was able to bind putative promoter segments of several E. faecalis genes in an NADH-responsive manner, indicating that it represents an authentic Rex factor. Transcriptome analysis of a ΔEF2638 mutant revealed that genes likely to be involved in anaerobic metabolism were upregulated during aerobic growth, and the mutant exhibited an altered NAD(+)/NADH ratio. The ΔEF2638 mutant also exhibited a growth defect when grown with aeration on several carbon sources, suggesting an impaired ability to cope with oxidative stress. Inclusion of catalase in the medium alleviated the growth defect. H(2)O(2) measurements revealed that the mutant accumulates significantly more H(2)O(2) than wild-type E. faecalis. In summary, EF2638 represents an authentic Rex factor in E. faecalis that influences the production or detoxification of H(2)O(2) in addition to its more familiar role as a regulator of anaerobic gene expression.
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19
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Yin Y, Yu G, Chen Y, Jiang S, Wang M, Jin Y, Lan X, Liang Y, Sun H. Genome-wide transcriptome and proteome analysis on different developmental stages of Cordyceps militaris. PLoS One 2012; 7:e51853. [PMID: 23251642 PMCID: PMC3522581 DOI: 10.1371/journal.pone.0051853] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/13/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cordyceps militaris, an ascomycete caterpillar fungus, has been used as a traditional Chinese medicine for many years owing to its anticancer and immunomodulatory activities. Currently, artificial culturing of this beneficial fungus has been widely used and can meet the market, but systematic molecular studies on the developmental stages of cultured C. militaris at transcriptional and translational levels have not been determined. METHODOLOGY/PRINCIPAL FINDINGS We utilized high-throughput Illumina sequencing to obtain the transcriptomes of C. militaris mycelium and fruiting body. All clean reads were mapped to C. militaris genome and most of the reads showed perfect coverage. Alternative splicing and novel transcripts were predicted to enrich the database. Gene expression analysis revealed that 2,113 genes were up-regulated in mycelium and 599 in fruiting body. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to analyze the genes with expression differences. Moreover, the putative cordycepin metabolism difference between different developmental stages was studied. In addition, the proteome data of mycelium and fruiting body were obtained by one-dimensional gel electrophoresis (1-DGE) coupled with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC-MS/MS). 359 and 214 proteins were detected from mycelium and fruiting body respectively. GO, KEGG and Cluster of Orthologous Groups (COG) analysis were further conducted to better understand their difference. We analyzed the amounts of some noteworthy proteins in these two samples including lectin, superoxide dismutase, glycoside hydrolase and proteins involved in cordycepin metabolism, providing important information for further protein studies. CONCLUSIONS/SIGNIFICANCE The results reveal the difference in gene expression between the mycelium and fruiting body of artificially cultivated C. militaris by transcriptome and proteome analysis. Our study provides an effective resource for the further developmental and medicinal research of this promising fungus.
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Affiliation(s)
- Yalin Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Guojun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Yijie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Shuai Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Man Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Yanxia Jin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Xianqing Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
- Department of Clinical Immunology, Guangdong Medical College, Dongguan, People’s Republic of China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei Province, People’s Republic of China
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, People’s Republic of China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan, People’s Republic of China
- * E-mail:
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20
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Characterization of recombinant FAD-independent catabolic acetolactate synthase from Enterococcus faecalis V583. Enzyme Microb Technol 2012. [PMID: 23199739 DOI: 10.1016/j.enzmictec.2012.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catabolic acetolactate synthase (cALS) of Enterococcus faecalis V583 was cloned, expressed in Escherichia coli, and purified to homogeneity. The purified protein had a molecular weight of 60 kDa. The cALS of E. faecalis is highly homologous with other cALSs, while sharing low homology with its anabolic counterparts. The cALS of E. faecalis exhibits optimum activity at a temperature of 37°C and pH 6.8. Based on the enzyme characterization, the apparent K(m) for pyruvate was calculated to be 1.37 mM, while the K(c) for thiamin diphosphate (ThDP) and Mg(2+) were found to be 0.031 μM and 1.27 mM, respectively. Negligible absorbance at 450 nm and lack of activity enhancement upon addition of flavin adenine dinucleotide (FAD) to the assay buffer suggest that the cALS of E. faecalis is not FAD-dependent. The enzyme showed extreme stability against the organic solvent dimethyl sulfoxide (DMSO), whereas the activity decreased to less than 50% in the presence of acetone and ethanol.
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21
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Bitoun JP, Liao S, Yao X, Xie GG, Wen ZT. The redox-sensing regulator Rex modulates central carbon metabolism, stress tolerance response and biofilm formation by Streptococcus mutans. PLoS One 2012; 7:e44766. [PMID: 23028612 PMCID: PMC3441419 DOI: 10.1371/journal.pone.0044766] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/06/2012] [Indexed: 01/15/2023] Open
Abstract
The Rex repressor has been implicated in regulation of central carbon and energy metabolism in gram-positive bacteria. We have previously shown that Streptococcus mutans, the primary causative agent of dental caries, alters its transcriptome upon Rex-deficiency and renders S. mutans to have increased susceptibility to oxidative stress, aberrations in glucan production, and poor biofilm formation. In this study, we showed that rex in S. mutans is co-transcribed as an operon with downstream guaA, encoding a putative glutamine amidotransferase. Electrophoretic mobility shift assays showed that recombinant Rex bound promoters of target genes avidly and specifically, including those down-regulated in response to Rex-deficiency, and that the ability of recombinant Rex to bind to selected promoters was modulated by NADH and NAD(+). Results suggest that Rex in S. mutans can function as an activator in response to intracellular NADH/NAD(+) level, although the exact binding site for activator Rex remains unclear. Consistent with a role in oxidative stress tolerance, hydrogen peroxide challenge assays showed that the Rex-deficient mutant, TW239, and the Rex/GuaA double mutant, JB314, were more susceptible to hydrogen peroxide killing than the wildtype, UA159. Relative to UA159, JB314 displayed major defects in biofilm formation, with a decrease of more than 50-fold in biomass after 48-hours. Collectively, these results further suggest that Rex in S. mutans regulates fermentation pathways, oxidative stress tolerance, and biofilm formation in response to intracellular NADH/NAD(+) level. Current effort is being directed to further investigation of the role of GuaA in S. mutans cellular physiology.
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Affiliation(s)
- Jacob P. Bitoun
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Sumei Liao
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Xin Yao
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Gary G. Xie
- Biology and Bioinformatics, Los Alamos National Laboratory, New Mexico, United States of America
| | - Zezhang T. Wen
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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22
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Shao C, Shang W, Yang Z, Sun Z, Li Y, Guo J, Wang X, Zou D, Wang S, Lei H, Cui Q, Yin Z, Li X, Wei X, Liu W, He X, Jiang Z, Du S, Liao X, Huang L, Wang Y, Yuan J. LuxS-Dependent AI-2 Regulates Versatile Functions in Enterococcus faecalis V583. J Proteome Res 2012; 11:4465-75. [DOI: 10.1021/pr3002244] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Changlin Shao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
- The Key Laboratory of Industrial
Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 214122 Wuxi, China
| | - Wei Shang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
- The Key Laboratory of Industrial
Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 214122 Wuxi, China
| | - Zhan Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Zhongke Sun
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Yunmei Li
- College of Food Science and Engineering, Northwest A & F University, 712100 Yangling, China
| | - Jing Guo
- College of Food Science and Engineering, Northwest A & F University, 712100 Yangling, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - DaYang Zou
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Simiao Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Hong Lei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Qian Cui
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Zhitao Yin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Xuelian Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Xiao Wei
- The Key Laboratory of Industrial
Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 214122 Wuxi, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Xiang He
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Zheng Jiang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Shuangkui Du
- College of Food Science and Engineering, Northwest A & F University, 712100 Yangling, China
| | - Xiangru Liao
- The Key Laboratory of Industrial
Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 214122 Wuxi, China
| | - Liuyu Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Yufei Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071 Beijing, China
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23
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Characterization of a Leuconostoc bacteriophage infecting flavor producers of cheese starter cultures. Appl Environ Microbiol 2012; 78:6769-72. [PMID: 22798359 DOI: 10.1128/aem.00562-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dairy siphovirus φLmd1, which infects starter culture isolate Leuconostoc mesenteroides subsp. dextranicum A1, showed resistance to pasteurization and was able to grow on 3 of the 4 commercial starter cultures tested. Its 26,201-bp genome was similar to that of Leuconostoc phage of vegetable origin but not to those of dairy phages infecting Lactococcus.
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24
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Rana NF, Gente S, Rincé A, Auffray Y, Laplace JM. Genetic modifications and introduction of heterologous pdc genes in Enterococcus faecalis for its use in production of bioethanol. Biotechnol Lett 2012; 34:1651-7. [PMID: 22628022 DOI: 10.1007/s10529-012-0964-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/09/2012] [Indexed: 12/01/2022]
Abstract
Genetically-modified Enterococcus faecalis has a potential of survival and can be used in ethanolic fermentations. Fermentation profiles of E. faecalis JH2-2 were assessed using glucose and lactose as carbon sources. Deletion of lactate dehydrogenase (ldh) genes increased the ethanol production from 0.25 to 0.82 g/l, which was further increased to 0.96 g/l by the insertion of a pyruvate decarboxylase (pdc) gene (from Sarcina ventriculi or Clostridium acetobutylicum) in place ldh1. When grown on lactose, the pdcSv and pdcCa showed 13.6 and 17.6 U mg(-1) of pdc specific activity, respectively. Highest activity (47 U mg(-1)) and ethanol concentration (2.3 g/l) were obtained with pdcCa using an expression plasmid. Formate and acetate were also produced in high quantities. Transcriptional analysis showed that aldehyde alcohol dehydrogenase gene was upregulated up to 16-fold. Further optimizations are required for higher ethanol production.
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Affiliation(s)
- N F Rana
- Unité de Recherche Risques Microbiens (U2RM), Université de Caen Basse-Normandie Esplanade de la Paix, 14032 Caen, France
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25
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Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase. Appl Environ Microbiol 2011; 78:170-6. [PMID: 22038603 DOI: 10.1128/aem.06604-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different growth rates (0.05, 0.15, and 0.4 h⁻¹). The fermentation pattern changed with growth rate, from a mostly homolactic profile at a high growth rate to a fermentation dominated by formate, acetate, and ethanol production at a low growth rate. A number of amino acids were consumed at the lower growth rates but not by fast-growing cells. The change in metabolic profile was caused mainly by decreased flux through lactate dehydrogenase. The transcription of ldh-1, encoding the principal lactate dehydrogenase, showed very strong growth rate dependence and differed by three orders of magnitude between the highest and the lowest growth rates. Despite the increase in ldh-1 transcript, the content of the Ldh-1 protein was the same under all conditions. Using microarrays and quantitative PCR, the levels of 227 gene transcripts were found to be affected by the growth rate, and 56 differentially expressed proteins were found by proteomic analyses. Few genes or proteins showed a growth rate-dependent increase or decrease in expression across the whole range of conditions, and many showed a maximum or minimum at the middle growth rate (i.e., 0.15 h⁻¹). For many gene products, a discrepancy between transcriptomic and proteomic data were seen, indicating posttranscriptional regulation of expression.
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26
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Suárez CA, Blancato VS, Poncet S, Deutscher J, Magni C. CcpA represses the expression of the divergent cit operons of Enterococcus faecalis through multiple cre sites. BMC Microbiol 2011; 11:227. [PMID: 21989394 PMCID: PMC3198936 DOI: 10.1186/1471-2180-11-227] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Enterococcus faecalis the genes encoding the enzymes involved in citrate metabolism are organized in two divergent operons, citHO and oadHDB-citCDEFX-oadA-citMG (citCL locus). Expression of both operons is specifically activated by adding citrate to the medium. This activation is mediated by binding of the GntR-like transcriptional regulator (CitO) to the cis-acting sequences located in the cit intergenic region. Early studies indicated that citrate and glucose could not be co-metabolized suggesting some form of catabolite repression, however the molecular mechanism remained unknown. RESULTS In this study, we observed that the citHO promoter is repressed in the presence of sugars transported by the Phosphoenolpyruvate:carbohydrate Phosphotranserase System (PTS sugars). This result strongly suggested that Carbon Catabolic Repression (CCR) impedes the expression of the activator CitO and the subsequent induction of the cit pathway. In fact, we demonstrate that CCR is acting on both promoters. It is partially relieved in a ccpA-deficient E. faecalis strain indicating that a CcpA-independent mechanism is also involved in regulation of the two operons. Furthermore, sequence analysis of the citH/oadH intergenic region revealed the presence of three putative catabolite responsive elements (cre). We found that they are all active and able to bind the CcpA/P-Ser-HPr complex, which downregulates the expression of the cit operons. Systematic mutation of the CcpA/P-Ser-HPr binding sites revealed that cre1 and cre2 contribute to citHO repression, while cre3 is involved in CCR of citCL. CONCLUSION In conclusion, our study establishes that expression of the cit operons in E. faecalis is controlled by CCR via CcpA-dependent and -independent mechanisms.
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Affiliation(s)
- Cristian A Suárez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
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