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Daller B, Auer DL, Buchalla W, Bartsch S, Gessner A, Jakubovics NS, Al-Ahmad A, Hiergeist A, Cieplik F. Genomic and Transcriptomic Adaptation to Chlorhexidine in Streptococcus spp. J Dent Res 2025:220345251320912. [PMID: 40181292 DOI: 10.1177/00220345251320912] [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: 04/05/2025] Open
Abstract
Antiseptics such as chlorhexidine digluconate (CHX) are widely used in clinical dental practice, but their potential risks, particularly regarding antimicrobial resistance (AMR), are not yet known. This study explores the genomic and transcriptomic mechanisms of CHX adaptation in 3 clinical isolates of Streptococcus spp. and their adapted counterparts. The genomic analysis revealed mutations in genes related to membrane structure, DNA repair, and metabolic processes. Mutations include those in diacylglycerol kinase that occurred in Streptococcus salivarius and the autolysin N-acetylmuramoyl-L-alanine amidase homologues in both Streptococcus mitis and Streptococcus vestibularis, which may contribute to enhanced CHX resistance. Our findings showed stress response genes constantly expressed in all 3 CHX-adapted strains, regardless of acute CHX exposure. Commonly upregulated genes were related to oxidative stress, DNA repair, and metabolic pathway changes, especially amino acid related metabolism. In addition, cell surface restructuring, multiple ABC transporter genes, as well as antimicrobial resistance-associated genes were constitutively expressed. Homologue genes that were significantly upregulated across all 3 species after mutation included recD (DNA repair), potE (amino acid transport), and groEL (stress response). In addition, we saw an increase in a gene associated with the penicillin-binding protein PBP2a in all strains. Beyond these conserved adaptations, we observed species-specific shifts under prolonged CHX exposure. In S. vestibularis, glutathione synthesis genes increased while fatty acid metabolism genes were downregulated. S. salivarius showed elevated expression of genes related to organic anion transport and RNA modification. S. mitis exhibited changes in pyrimidine metabolism, ion homeostasis, and pyruvate dehydrogenase complex genes. Uniquely, S. mitis also showed acute CHX response with upregulation of carbohydrate metabolism and phosphotransferase system genes. These findings highlight the complexity of CHX-induced adaptation, suggesting connections to genetic mutations and emphasizing the need for further research to understand and mitigate AMR risks.
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Affiliation(s)
- B Daller
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - D L Auer
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - W Buchalla
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - S Bartsch
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg, Medical Faculty, University of Freiburg, Freiburg i. Br., Germany
| | - A Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - N S Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - A Al-Ahmad
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg, Medical Faculty, University of Freiburg, Freiburg i. Br., Germany
| | - A Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - F Cieplik
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg, Medical Faculty, University of Freiburg, Freiburg i. Br., Germany
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Neha, Chaudhary S, Tiwari P, Parvez S. Amelioration of Phytanic Acid-Induced Neurotoxicity by Nutraceuticals: Mechanistic Insights. Mol Neurobiol 2024; 61:7303-7318. [PMID: 38374317 DOI: 10.1007/s12035-024-03985-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
Phytanic acid (PA) (3,7,11,15-tetramethylhexadecanoic acid) is a methyl-branched fatty acid that enters the body through food consumption, primarily through red meat, dairy products, and fatty marine foods. The metabolic byproduct of phytol is PA, which is then oxidized by the ruminal microbiota and some marine species. The first methyl group at the 3-position prevents the β-oxidation of branched-chain fatty acid (BCFA). Instead, α-oxidation of PA results in the production of pristanic acid (2,10,14-tetramethylpentadecanoic acid) with CO2. This fatty acid (FA) builds up in individuals with certain peroxisomal disorders and is historically linked to neurological impairment. It also causes oxidative stress in synaptosomes, as demonstrated by an increase in the production of reactive oxygen species (ROS), which is a sign of oxidative stress. This review concludes that the nutraceuticals (melatonin, piperine, quercetin, curcumin, resveratrol, epigallocatechin-3-gallate (EGCG), coenzyme Q10, ω-3 FA) can reduce oxidative stress and enhanced the activity of mitochondria. Furthermore, the use of nutraceuticals completely reversed the neurotoxic effects of PA on NO level and membrane potential. Additionally, the review further emphasizes the urgent need for more research into dairy-derived BCFAs and their impact on human health.
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Affiliation(s)
- Neha
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110 062, India
| | - Shaista Chaudhary
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110 062, India
| | - Prachi Tiwari
- Department of Physiotherapy, School of Nursing Sciences and Allied Health, Jamia Hamdard, New Delhi, 110 062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110 062, India.
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Giles-Gómez M, Morales Huerta X, Pastelin-Palacios R, López-Macías C, Flores Montesinos MS, Astudillo-Melgar F, Escalante A. Analysis of the Probiotic Potential of Lactiplantibacillus plantarum LB1_P46 Isolated from the Mexican Fermented Pulque Beverage: A Functional and Genomic Analysis. Microorganisms 2024; 12:1652. [PMID: 39203494 PMCID: PMC11356911 DOI: 10.3390/microorganisms12081652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The traditional Mexican fermented beverage pulque has been considered a healthy product for treating gastrointestinal disorders. Lactic acid bacteria (LAB) have been identified as one of the most abundant microbial groups during pulque fermentation. As traditional pulque is consumed directly from the fermentation vessel, the naturally associated LABs are ingested, reaching the consumer's small intestine alive, suggesting their potential probiotic capability. In this contribution, we assayed the probiotic potential of the strain of Lactiplantibacillus plantarum LB1_P46 isolated from pulque produced in Huitzilac, Morelos State, Mexico. The characterization included resistance to acid pH (3.5) and exposure to bile salts at 37 °C; the assay of the hemolytic activity and antibiotic resistance profiling; the functional traits of cholesterol reduction and β-galactosidase activity; and several cell surface properties, indicating that this LAB possesses probiotic properties comparable to other LAB. Additionally, this L. plantarum showed significance in in vitro antimicrobial activity against several Gram-negative and Gram-positive bacteria and in vivo preventive anti-infective capability against Salmonella in a BALB/c mouse model. Several functional traits and probiotic activities assayed were correlated with the corresponding enzymes encoded in the complete genome of the strain. The genome mining for bacteriocins led to the identification of several bacteriocins and a ribosomally synthesized and post-translationally modified peptide encoding for the plantaricin EF. Results indicated that L. plantarum LB1_P46 is a promising probiotic LAB for preparing functional non-dairy and dairy beverages.
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Affiliation(s)
- Martha Giles-Gómez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Ximena Morales Huerta
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Rodolfo Pastelin-Palacios
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Cuauhtémoc, Ciudad de México 06720, Mexico
| | - Mayrene Sarai Flores Montesinos
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
| | - Fernando Astudillo-Melgar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
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Tian L, Xu P, Chen J, Chen H, Qin J, Wu X, Liu C, He Z, Liu Y, Guan T. Comprehensive analysis of spatial heterogeneity reveals the important role of the upper-layer fermented grains in the fermentation and flavor formation of Qingxiangxing baijiu. Food Chem X 2024; 22:101508. [PMID: 38883913 PMCID: PMC11176670 DOI: 10.1016/j.fochx.2024.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
Different spatial positions lead to inconsistent fermentation effects and flavors, however, the spatial heterogeneity of Qingxiangxing (QXX) Baijiu remains unknown. We investigated the microbes, flavors, and physicochemical properties of different layers in fermented grains of QXX Baijiu using Illumina HiSeq sequencing, two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) and ultra-high performance liquid chromatography-mass (UHPLC-MS). A total of 79 volatiles, 1596 metabolites, 50 bacterial genera, and 52 fungal genera were identified. The contents distribution followed the order: upper layer > bottom layer > middle layer. Organic acids and derivatives were the main differential metabolites across the three layers. Starch, pH, and reducing sugar levels increased from the upper to bottom layer. Saccharomyces and Lactobacillus were dominant microbes. Pediococcus, the biomarker of upper layer, showed positive correlations with formic acid, ethyl lactate, acetic acid, ethyl linoleate, and ethyl oleate. These findings deepen our understanding of the fermentation and flavor formation mechanisms of QXX Baijiu.
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Affiliation(s)
- Lei Tian
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Pei Xu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Junyu Chen
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Hang Chen
- College of Mechanical Engineering, Xihua University, Chengdu 610039, China
| | - Ji Qin
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Xiaotian Wu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Chengzhe Liu
- Sichuan Tujiu Liquor Co., Ltd, Nanchong 637919, China
| | - Zongjun He
- Sichuan Tujiu Liquor Co., Ltd, Nanchong 637919, China
| | - Ying Liu
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
| | - Tongwei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu 610039, PR China
- Food Microbiology Key Laboratory of Sichuan Province, Chengdu 610039, PR China
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Chen C, Naveed H, Chen K. Research progress on branched-chain amino acid aminotransferases. Front Genet 2023; 14:1233669. [PMID: 38028625 PMCID: PMC10658711 DOI: 10.3389/fgene.2023.1233669] [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: 06/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.
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Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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6
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Lu Y, Lin Y, Li M, He J. Roles of Streptococcus mutans- Candida albicans interaction in early childhood caries: a literature review. Front Cell Infect Microbiol 2023; 13:1151532. [PMID: 37260705 PMCID: PMC10229052 DOI: 10.3389/fcimb.2023.1151532] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
As one of the most common oral diseases in kids, early childhood caries affects the health of children throughout the world. Clinical investigations show the copresence of Candida albicans and Streptococcus mutans in ECC lesions, and mechanistic studies reveal co-existence of C. albicans and S. mutans affects both of their cariogenicity. Clearly a comprehensive understanding of the interkingdom interaction between these two microorganisms has important implications for ECC treatment and prevention. To this end, this review summarizes advances in our understanding of the virulence of both C. albicans and S. mutans. More importantly, the synergistic and antagonistic interactions between these two microbes are discussed.
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Affiliation(s)
- Yifei Lu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Yifan Lin
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Mingyun Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China
| | - Jinzhi He
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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7
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Li X, Tan G, Chen P, Cai K, Dong W, Peng N, Zhao S. Uncovering acid resistance genes in lactic acid bacteria and impact of non-viable bacteria on bacterial community during Chinese strong-flavor baijiu fermentation. Food Res Int 2023; 167:112741. [PMID: 37087286 DOI: 10.1016/j.foodres.2023.112741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Chinese strong-flavor baijiu (CSFB) brewing is a spontaneously solid-state fermentation process for approximately 60 days. Numerous microorganisms grow, die, and spark a series of metabolic reactions during fermentation. In this study, the microbial community and structure between total and viable bacteria in zaopei from the 5- and 20-year pits of CSFB are revealed by amplicon sequencing. Metagenome sequencing was applied to investigate acid resistance genes in Lactobacillus and predict carbohydrate active enzyme in zaopei. Besides, SourceTracker was conducted to expose bacterial sources. Results revealed that there was no significant difference in the bacterial community and structure between the total and viable bacteria; Lactobacillus was the most dominant bacterium in zaopei of two types of pits. Meanwhile, acid resistance genes argR, aspA, ilvE, gshA, DnaK, and cfa were genes that sustained Lactobacillus survival in the late stages of fermentation with high contents of acid and ethanol, and glycosyltransferases were identified as the predominated enzymes during the CSFB fermentation which catalyzed the process of lactic acid generation via Embden-Meyerhof-Parnas pathway and Hexose Monophosphate Pathway. Moreover, the environment contributed most bacteria to zaopei of the 5- and 20-year pits. These findings will provide a deeper understanding of the microbial community structure of viable and total bacteria and the reason for the dominance of Lactobacillus in the later stages of CSFB fermentation.
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Niacin inhibits post-acidification of yogurt based on the mining of LDB_RS00370 biomarker gene. Food Res Int 2022; 162:111929. [DOI: 10.1016/j.foodres.2022.111929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2022]
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9
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Izumi M, Sonoki K, Akifusa S. Correlation of Salivary Occult Blood with the Plasma Concentration of Branched-Chain Amino Acids: A Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19158930. [PMID: 35897295 PMCID: PMC9332040 DOI: 10.3390/ijerph19158930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 02/05/2023]
Abstract
Background: Plasma branched-chain amino acids (BCAA) levels are predictors of glycometabolic disorders, leading to diabetes. Microbes, including periodontal pathogens, are thought to be associated with elevated plasma BCAA levels. This study aimed to evaluate the relationship between salivary occult blood (SOB) and plasma BCAA levels in middle-aged Japanese individuals. Methods: Sixty-four Japanese individuals aged ≥ 40 years were recruited for this study, which was conducted in Fukuoka Prefecture, Japan, from August to December 2021. Individuals diagnosed with and/or treated for diabetes were excluded from the study. The body mass index (BMI); plasma concentrations of total, high-density, and low-density lipoprotein cholesterol; triglyceride, glucose, and BCAA; and glycosylated hemoglobin ratio were measured. A basic periodontal examination was performed after the SOB test. Results: The median age of participants (men—20; women—44) was 55 (range, 41–78) years. The plasma BCAA concentration in the SOB-positive group (477 [400–658] μmol/L) was higher than that in the SOB-negative group (432 [307–665] μmol/L). Linear regression analysis revealed that SOB remained independently associated with the plasma BCAA level with statistical significance (β = 0.17, p = 0.02) after adjusting for sex, age, and BMI. Conclusions: SOB was positively correlated with plasma BCAA levels in middle-aged Japanese individuals. Thus, SOB may be a predictor of elevated plasma BCAA levels.
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Román-Camacho JJ, Mauricio JC, Santos-Dueñas IM, García-Martínez T, García-García I. Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus. Front Microbiol 2022; 13:840119. [PMID: 35572698 PMCID: PMC9100681 DOI: 10.3389/fmicb.2022.840119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
The industrial production of vinegar is carried out by the activity of a complex microbiota of acetic acid bacteria (AAB) working, mainly, within bioreactors providing a quite specific and hard environment. The “omics” sciences can facilitate the identification and characterization analyses of these microbial communities, most of which are difficult to cultivate by traditional methods, outside their natural medium. In this work, two acetification profiles coming from the same AAB starter culture but using two natural raw materials of different alcoholic origins (fine wine and craft beer), were characterized and compared and the emphasis of this study is the effect of these raw materials. For this purpose, the composition and natural behavior of the microbiota present throughout these profiles were analyzed by metaproteomics focusing, mainly, on the quantitative protein profile of Komagataeibacter europaeus. This species provided a protein fraction significantly higher (73.5%) than the others. A submerged culture system and semi-continuous operating mode were employed for the acetification profiles and liquid chromatography with tandem mass spectrometry (LC-MS/MS) for the protein analyses. The results showed that neither of two raw materials barely modified the microbiota composition of the profiles, however, they had an effect on the protein expression changes in different biological process. A molecular strategy in which K. europaeus would prevail over other species by taking advantage of the different features offered by each raw material has been suggested. First, by assimilating the excess of inner acetic acid through the TCA cycle and supplying biosynthetic precursors to replenish the cellular material losses; second, by a previous assimilation of the excess of available glucose, mainly in the beer medium, through the glycolysis and the pentose phosphate pathway (PPP); and third, by triggering membrane mechanisms dependent on proton motive force to detoxify the cell at the final moments of acetification. This study could complement the current knowledge of these bacteria as well as to expand the use of diverse raw materials and optimize operating conditions to obtain quality vinegars.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
- *Correspondence: Juan C. Mauricio,
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
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Liang S, Hu X, Wang R, Fang M, Yu Y, Xiao X. The combination of thymol and cinnamaldehyde reduces the survival and virulence of Listeria monocytogenes on autoclaved chicken breast. J Appl Microbiol 2022; 132:3937-3950. [PMID: 35178822 DOI: 10.1111/jam.15496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
AIMS To reveal the antibacterial mechanism of the combination of thymol and cinnamaldehyde to Listeria monocytogenes ATCC 19115 on autoclaved chicken breast. METHODS AND RESULTS In this study, Listeria monocytogenes ATCC 19115 on autoclaved chicken breast was exposed to the stress of 125 μg/mL thymol and 125 μg/mL cinnamaldehyde, and transcriptome analysis was used to reveal the crucial antibacterial mechanism. According to the results, 1303 significantly differentially expressed genes (DEGs) were identified. Treated by thymol and cinnamaldehyde in combination, pyrimidine and branched-chain amino acids biosynthesis of L. monocytogenes were thwarted which impairs its nucleic acid biosynthesis and intracellular metabolism. The up-regulated DEGs involved in membrane composition and function contributed to membrane repair. Besides, pyruvate catabolism and TCA cycle were restrained which brought about the disturbance of amino acid metabolism. ABC transporters were also perturbed, for instance, the uptake of cysteine, D-methionine and betaine was activated, while the uptake of vitamin, iron and carnitine was repressed. Thus, L. monocytogenes tended to activate PTS, glycolysis, glycerol catabolism, and pentose phosphate pathways to obtain energy to adapt to the hostile condition. Noticeably, DEGs involved in virulence factors were totally down-regulated, including genes devoted to encoding flagella, chemotaxis, biofilm formation, internalin as well as virulence gene clusters. CONCLUSIONS The combination of thymol and cinnamaldehyde is effective to reduce the survival and potential virulence of L. monocytogenes on autoclaved chicken breast. SIGNIFICANCE AND IMPACT OF STUDY This work contributes to providing theoretical information for the application and optimization of thymol and cinnamaldehyde in ready-to-eat meat products to inhibit L. monocytogenes.
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Affiliation(s)
- Siwei Liang
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
| | - Xinyi Hu
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
| | - Ruifei Wang
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
| | - Meimei Fang
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
| | - Yigang Yu
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
| | - Xinglong Xiao
- Research Center of Food Safety and Detection, School of Food Sciences and Engineering, South China University of Technology, Guangdong Province, Guangzhou City, 510640, China
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12
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Peng MY, Zhang XJ, Huang T, Zhong XZ, Chai LJ, Lu ZM, Shi JS, Xu ZH. Komagataeibacter europaeus improves community stability and function in solid-state cereal vinegar fermentation ecosystem: Non-abundant species plays important role. Food Res Int 2021; 150:110815. [PMID: 34863491 DOI: 10.1016/j.foodres.2021.110815] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/14/2021] [Accepted: 11/13/2021] [Indexed: 01/03/2023]
Abstract
Solid-state fermentation of Chinese traditional cereal vinegar is a complex and retractable ecosystem with multi-species involved, including few abundant and many non-abundant species. However, the roles of non-abundant species in vinegar fermentation remain unknown. Here, we studied the assembly and co-occurrence patterns for abundant and non-abundant bacterial sub-communities using Zhenjiang aromatic vinegar fermentation as a model system. Our results showed that the change of reducing sugar and total titratable acid were the main driving forces for the assembly of abundant and non-abundant sub-communities, respectively. The non-abundant sub-community was more sensitive to the environmental variation of acetic acid fermentation (AAF) process. Integrated co-occurrence network revealed that non-abundant sub-communities occupied most of the nodes in the network, which play fundamental roles in network stability. Importantly, non-abundant species-Komagataeibacter europaeus, showed the highest value of degree in the co-occurrence network, implying its importance for the metabolic function and resilience of the microbial community. Bioaugmentation of K. europaeus JNP1 verified that it can effectively modulate bacterial composition and improve the robustness of co-occurrence network in situ, accompanied by (i) increased acetic acid content (14.78%) and decreased reducing sugar content (40.38%); and (ii) increased the gene numbers of phosphogluconate dehydratase (212.24%) and aldehyde dehydrogenase (192.31%). Overall, the results showed that non-abundant bacteria could be used to regulate the desired metabolic function of the community, and might play an important ecological significance in traditional fermented foods.
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Affiliation(s)
- Ming-Ye Peng
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiao-Juan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China.
| | - Ting Huang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xiao-Zhong Zhong
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Li-Juan Chai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China
| | - Jin-Song Shi
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, PR China; Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou 646000, PR China.
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13
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Mayumi S, Kuboniwa M, Sakanaka A, Hashino E, Ishikawa A, Ijima Y, Amano A. Potential of Prebiotic D-Tagatose for Prevention of Oral Disease. Front Cell Infect Microbiol 2021; 11:767944. [PMID: 34804997 PMCID: PMC8604381 DOI: 10.3389/fcimb.2021.767944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/25/2022] Open
Abstract
Recent studies have shown phenotypic and metabolic heterogeneity in related species including Streptococcus oralis, a typical oral commensal bacterium, Streptococcus mutans, a cariogenic bacterium, and Streptococcus gordonii, which functions as an accessory pathogen in periodontopathic biofilm. In this study, metabolites characteristically contained in the saliva of individuals with good oral hygiene were determined, after which the effects of an identified prebiotic candidate, D-tagatose, on phenotype, gene expression, and metabolic profiles of those three key bacterial species were investigated. Examinations of the saliva metabolome of 18 systemically healthy volunteers identified salivary D-tagatose as associated with lower dental biofilm abundance in the oral cavity (Spearman’s correlation coefficient; r = -0.603, p = 0.008), then the effects of D-tagatose on oral streptococci were analyzed in vitro. In chemically defined medium (CDM) containing D-tagatose as the sole carbohydrate source, S. mutans and S. gordonii each showed negligible biofilm formation, whereas significant biofilms were formed in cultures of S. oralis. Furthermore, even in the presence of glucose, S. mutans and S. gordonii showed growth suppression and decreases in the final viable cell count in a D-tagatose concentration-dependent manner. In contrast, no inhibitory effects of D-tagatose on the growth of S. oralis were observed. To investigate species-specific inhibition by D-tagatose, the metabolomic profiles of D-tagatose-treated S. mutans, S. gordonii, and S. oralis cells were examined. The intracellular amounts of pyruvate-derived amino acids in S. mutans and S. gordonii, but not in S. oralis, such as branched-chain amino acids and alanine, tended to decrease in the presence of D-tagatose. This phenomenon indicates that D-tagatose inhibits growth of those bacteria by affecting glycolysis and its downstream metabolism. In conclusion, the present study provides evidence that D-tagatose is abundant in saliva of individuals with good oral health. Additionally, experimental results demonstrated that D-tagatose selectively inhibits growth of the oral pathogens S. mutans and S. gordonii. In contrast, the oral commensal S. oralis seemed to be negligibly affected, thus highlighting the potential of administration of D-tagatose as an oral prebiotic for its ability to manipulate the metabolism of those targeted oral streptococci.
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Affiliation(s)
- Shota Mayumi
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Akito Sakanaka
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Ei Hashino
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Asuka Ishikawa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Yura Ijima
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
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14
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Wongthong S, Taron W, Chanawong A, Tippayawat P, Pongdontri P, Srisrattakarn A, Panpru P, Lulitanond A. Effect of Vancomycin on Cellular Fatty Acid Profiles of Vancomycin-Susceptible and Nonsusceptible Staphylococcus aureus. Microb Drug Resist 2021; 28:267-273. [PMID: 34748415 DOI: 10.1089/mdr.2021.0055] [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: 11/13/2022] Open
Abstract
Vancomycin is widely used for treatment of infection caused by methicillin-resistant Staphylococcus aureus (MRSA) leading to an increasing appearance of low-level vancomycin-resistant isolates called heterogeneous vancomycin-intermediate S. aureus (hVISA). The mechanism of vancomycin tolerance in hVISA is still unclear. This study aimed to investigate the fatty acid compositions of S. aureus isolates under the stress environment with vancomycin. The different responses of hVISA and vancomycin-susceptible S. aureus (VSSA) may lead to more understanding the mechanism. The bacterial lipid profiles were tested three times from three extractions of each isolate cultured on tryptic soy agar (TSA) and TSA with vancomycin. Of the 30 MRSA isolates studied, 13, 12, and 5 isolates were VSSA, hVISA, and VISA, respectively. The analysis of bacterial lipid profiles showed that under vancomycin stress, there was a reduction of straight chain fatty acids (SCFAs) in VSSA isolates but an increase in branched chain fatty acids (BCFAs). In contrast, the hVISA group exhibited an increase only in the BCFAs but not in SCFAs. Of interest, vancomycin had no effect on either BCFAs or SCFAs of the VISA cells. This study provided information of bacterial adaptation during stress with vancomycin that may be helpful to overcome the resistant bacteria.
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Affiliation(s)
- Sujintana Wongthong
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Faculty of Medical Technology, Nakhon Ratchasima College, Nakhon Ratchasima, Thailand
| | - Wichit Taron
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonwadee Chanawong
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Patcharaporn Tippayawat
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Paweena Pongdontri
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Arpasiri Srisrattakarn
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Pimchanok Panpru
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonlug Lulitanond
- Department of Clinical Microbiology and Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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15
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Shen ZJ, Qin YY, Luo MR, Li Z, Ma DN, Wang WH, Zheng HL. Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress. J Proteomics 2021; 248:104349. [PMID: 34411764 DOI: 10.1016/j.jprot.2021.104349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023]
Abstract
Low temperature in winter was the most crucial abiotic stress that limits the mangrove afforestation northward. Previous study demonstrated that Sonneratia apetala initially transplanted to high latitude area exhibited a stronger plasticity of cold tolerance. To clarify the underlying mechanism, the physiological and proteomic responses to chilling stress were investigated in S. apetala leaves. Our results found that cold-acclimated seedlings had lower relative electrolyte leakage and MDA content than non-acclimated seedlings. On the contrary, higher chlorophyll content and photosynthetic capacity were observed in cold-acclimated seedlings. With proteomic analyses, the differentially accumulated proteins (DAPs) involved in ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding were suggested to play important roles in enhancing the cold tolerance of S. apetala. However, the down-regulation DAPs were suggested as a tradeoff between plant growth and chilling response. By the protein-protein interaction analyses, translation elongation factor G, chlorophyll A-B binding protein and ascorbate peroxidase 1 were suggested as the important regulators in cold-acclimated S. apetala seedlings under chilling stress. Based on the above results, a schematic diagram describing the mechanism of cold tolerance of exotic mangrove species S. apetala that was achieved by cold acclimation was presented in this study. SIGNIFICANCE: The major environmental factor limits the mangrove afforestation northward is the low temperature in winter. Previous study reported that Sonneratia apetala grew in high latitude exhibited a higher cold tolerance than that in low latitude, which was suggested as a result of cold acclimation. To further understand "how cold acclimation enhance the cold tolerance in S. apetala", the response of S. apetala subjected to chilling stress with or without cold acclimation was investigated in this study at the physiological and proteomic aspects. Our physiological results showed that S. apetala seedlings treated with cold acclimation exhibited a higher tolerance under chilling stress than that without cold acclimation. By using the comparative proteomic approaches and bioinformatic analyses, various biological processes were suggested to play an important role in enhancing the cold tolerance of S. apetala under chilling stress, such as ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding. Among these differentially accumulated proteins, translation elongation factor G (eEF-G), chlorophyll A-B binding protein (CAB) and ascorbate peroxidase 1 (APX1) were identified as the hub proteins function in coordinated regulating ROS scavenging, photosynthesis and protein biosynthesis in chloroplast and subsequently enhanced the cold tolerance of S. apetala under chilling stress. Our results provided a further understanding of cold acclimation in improving the cold tolerance in exotic mangrove species S. apetala.
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Affiliation(s)
- Zhi-Jun Shen
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Ying-Ying Qin
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China; Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Environment and Resources, Guangxi Normal University, Guilin, Guangxi 541004, PR China
| | - Mei-Rong Luo
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Zan Li
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Dong-Na Ma
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Wen-Hua Wang
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, Fujian 361006, PR China
| | - Hai-Lei Zheng
- Key Laboratory for Subtropical Wetland Ecosystem Research of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361005, PR China.
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16
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Yan Z, He F, Xiao F, He H, Li D, Cong L, Lin L, Zhu H, Wu Y, Yan R, Li X, Shan H. A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis. MICROBIOME 2021; 9:12. [PMID: 33436102 PMCID: PMC7805185 DOI: 10.1186/s40168-020-00967-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn's disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis. RESULTS We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events. CONCLUSIONS This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance. Video abstract.
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Affiliation(s)
- Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
| | - Feixiang He
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Fei Xiao
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Huanhuan He
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Dan Li
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Li Cong
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Lu Lin
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Huijin Zhu
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Yanyan Wu
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
| | - Hong Shan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
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17
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Baker JL, Morton JT, Dinis M, Alvarez R, Tran NC, Knight R, Edlund A. Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules. Genome Res 2020; 31:64-74. [PMID: 33239396 PMCID: PMC7849383 DOI: 10.1101/gr.265645.120] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022]
Abstract
Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.
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Affiliation(s)
- Jonathon L Baker
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - James T Morton
- Systems Biology Group, Flatiron Institute, New York, New York 10010, USA
| | - Márcia Dinis
- Section of Pediatric Dentistry, UCLA School of Dentistry, Los Angeles, California 90095-1668, USA
| | - Ruth Alvarez
- Section of Pediatric Dentistry, UCLA School of Dentistry, Los Angeles, California 90095-1668, USA
| | - Nini C Tran
- Section of Pediatric Dentistry, UCLA School of Dentistry, Los Angeles, California 90095-1668, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, California 92161, USA.,Department of Pediatrics, University of California at San Diego, La Jolla, California 92161, USA.,Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA.,Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, USA
| | - Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California 92037, USA.,Department of Pediatrics, University of California at San Diego, La Jolla, California 92161, USA
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18
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Shanmugam K, Sarveswari HB, Udayashankar A, Swamy SS, Pudipeddi A, Shanmugam T, Solomon AP, Neelakantan P. Guardian genes ensuring subsistence of oral Streptococcus mutans. Crit Rev Microbiol 2020; 46:475-491. [PMID: 32720594 DOI: 10.1080/1040841x.2020.1796579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite the substantial research advancements on oral diseases, dental caries remains a major healthcare burden. A disease of microbial dysbiosis, dental caries is characterised by the formation of biofilms that assist demineralisation and destruction of the dental hard tissues. While it is well understood that this is a multi-kingdom biofilm-mediated disease, it has been elucidated that acid producing and acid tolerant bacteria play pioneering roles in the process. Specifically, Streptococcus mutans houses major virulence pathways that enable it to thrive in the oral cavity and cause caries. This pathogen adheres to the tooth substrate, forms biofilms, resists external stress, produces acids, kills closely related species, and survives the acid as well as the host clearance mechanisms. For an organism to be able to confer such virulence, it requires a large and complex gene network which synergise to establish disease. In this review, we have charted how these multi-faceted genes control several caries-related functions of Streptococcus mutans. In a futuristic thinking approach, we also briefly discuss the potential roles of omics and machine learning, to ease the study of non-functional genes that may play a major role and enable the integration of experimental data.
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Affiliation(s)
- Karthi Shanmugam
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Hema Bhagavathi Sarveswari
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Akshaya Udayashankar
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shogan Sugumar Swamy
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Akhila Pudipeddi
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Tamilarasi Shanmugam
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Prasanna Neelakantan
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong
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19
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Ahn SJ, Kim HM, Desai S, Deep K, Rice KC. Regulation of cid and lrg expression by CodY in Streptococcus mutans. Microbiologyopen 2020; 9:e1040. [PMID: 32282137 PMCID: PMC7349109 DOI: 10.1002/mbo3.1040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/21/2020] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
The ability of Streptococcus mutans to persist in a variety of adverse environments and to emerge as a numerically dominant member of stable oral biofilm communities are essential elements for its cariogenicity. The S. mutans Cid/Lrg system has been studied as a key player in the integration of complex environmental signals into regulatory networks that modulate virulence and cell homeostasis. Cid/Lrg has also been shown to be closely associated with metabolic pathways of this organism, due to distinct patterns of cid and lrg expression in response to growth phase and glucose/oxygen levels. In this study, a comparison of cid and lrg promoter regions with conserved CodY (a regulator which responds to starvation stress)-binding motifs revealed the presence of a potential CodY-binding site, which is arranged similarly in both cid and lrg promoters. Electrophoretic mobility shift assays (EMSAs) and promoter reporter assays demonstrated that expression of the cid and lrg operons is directly mediated by the global transcriptional regulator CodY. DNase I footprinting analyses confirmed the predicted binding sequences for CodY in both the cid and the lrg promoter regions. Overexpression of CodY had no obvious effect on lrgAB expression, but deficiency of CodY still affected lrgAB expression in a lytST-overexpressing strain, suggesting that CodY is required for the full regulation of lrgAB by LytST. We also demonstrated that both CodY and CcpA are involved in regulating pyruvate flux and utilization. Collectively, these data show that CodY directly regulates cid and lrg expression, and together with CcpA (previously shown to directly regulate cid and lrg promoters) contributes to coordinating pyruvate uptake and utilization in response to both the external environment and the cellular metabolic status.
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Affiliation(s)
- Sang-Joon Ahn
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hey-Min Kim
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Shailja Desai
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Kamal Deep
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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20
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Ganguly T, Kajfasz JK, Abranches J, Lemos JA. Regulatory circuits controlling Spx levels in Streptococcus mutans. Mol Microbiol 2020; 114:109-126. [PMID: 32189382 DOI: 10.1111/mmi.14499] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 02/01/2023]
Abstract
Spx is a major regulator of stress responses in Firmicutes. In Streptococcus mutans, two Spx homologues, SpxA1 and SpxA2, were identified as mediators of oxidative stress responses but the regulatory circuits controlling their levels and activity are presently unknown. Comparison of SpxA1 and SpxA2 protein sequences revealed differences at the C-terminal end, with SpxA1 containing an unusual number of acidic residues. Here, we showed that a green fluorescence protein (GFP) reporter becomes unstable when fused to the last 10 amino acids of SpxA2 but remained stable when fused to the C-terminal acidic tail of SpxA1. Inactivation of clpP or simultaneous inactivation of clpC and clpE stabilized the GFP::SpxA2tail fusion protein. Addition of acidic amino acids to the GFP::SpxA2tail chimera stabilized GFP, while deletion of the acidic residues destabilized GFP::SpxA1tail . Promoter reporter fusions revealed that spxA1 transcription is co-repressed by the metalloregulators PerR and SloR while spxA2 transcription is largely dependent on the envelope stress regulator LiaFSR. In agreement with spxA2 being part of the LiaR regulon, SpxA2 was found to be critical for the growth of S. mutans under envelope stress conditions. Finally, we showed that redox sensing is essential for SpxA1-dependent activation of oxidative stress responses but dispensable for SpxA2-mediated envelope stress responses.
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Affiliation(s)
- Tridib Ganguly
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Jessica K Kajfasz
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Jacqueline Abranches
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - José A Lemos
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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21
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Disruption of l-Rhamnose Biosynthesis Results in Severe Growth Defects in Streptococcus mutans. J Bacteriol 2020; 202:JB.00728-19. [PMID: 31871035 DOI: 10.1128/jb.00728-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
The rhamnose-glucose cell wall polysaccharide (RGP) of Streptococcus mutans plays a significant role in cell division, virulence, and stress protection. Prior studies examined function of the RGP using strains carrying deletions in the machinery involved in RGP assembly. In this study, we explored loss of the substrate for RGP, l-rhamnose, via deletion of rmlD (encoding the protein responsible for the terminal step in l-rhamnose biosynthesis). We demonstrate that loss of rhamnose biosynthesis causes a phenotype similar to strains with disrupted RGP assembly (ΔrgpG and ΔrgpF strains). Deletion of rmlD not only caused a severe growth defect under nonstress growth conditions but also elevated susceptibility of the strain to acid and oxidative stress, common conditions found in the oral cavity. A genetic complement of the ΔrmlD strain completely restored wild-type levels of growth, whereas addition of exogenous rhamnose did not. The loss of rhamnose production also significantly disrupted biofilm formation, an important aspect of S. mutans growth in the oral cavity. Further, we demonstrate that loss of either rmlD or rgpG results in ablation of rhamnose content in the S. mutans cell wall. Taken together, these results highlight the importance of rhamnose production in both the fitness and the ability of S. mutans to overcome environmental stresses.IMPORTANCE Streptococcus mutans is a pathogenic bacterium that is the primary etiologic agent of dental caries, a disease that affects billions yearly. Rhamnose biosynthesis is conserved not only in streptococcal species but in other Gram-positive, as well as Gram-negative, organisms. This study highlights the importance of rhamnose biosynthesis in RGP production for protection of the organism against acid and oxidative stresses, the two major stressors that the organism encounters in the oral cavity. Loss of RGP also severely impacts biofilm formation, the first step in the onset of dental caries. The high conservation of the rhamnose synthesis enzymes, as well as their importance in S. mutans and other organisms, makes them favorable antibiotic targets for the treatment of disease.
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22
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Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae. CRYSTALS 2019. [DOI: 10.3390/cryst9110551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biosynthesis of branched-chain amino acids (BCAAs), including isoleucine, leucine and valine, is required for survival and virulence of a bacterial pathogen such as Streptococcus pneumoniae. IlvC, a ketol-acid reductoisomerase (E.C. 1.1.1.86) with NADP(H) and Mg2+ as cofactors from the pathogenic Streptococcus pneumoniae (SpIlvC), catalyzes the second step in the BCAA biosynthetic pathway. To elucidate the structural basis for the IlvC-mediated reaction, we determined the crystal structure of SpIlvC at 1.69 Å resolution. The crystal structure of SpIlvC contains an asymmetric dimer in which one subunit is in apo-form and the other in NADP(H) and Mg2+-bound form. Crystallographic analysis combined with an activity assay and small-angle X-ray scattering suggested that SpIlvC retains dimeric arrangement in solution and that D83 in the NADP(H) binding site and E195 in the Mg2+ binding site are the most critical in the catalytic activity of SpIlvC. Crystal structures of SpIlvC mutants (R49E, D83G, D191G and E195S) revealed local conformational changes only in the NADP(H) binding site. Taken together, our results establish the molecular mechanism for understanding functions of SpIlvC in pneumococcal growth and virulence.
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Solinski AE, Scharnow AM, Fraboni AJ, Wuest WM. Synthetic Simplification of Carolacton Enables Chemical Genetic Studies in Streptococcus mutans. ACS Infect Dis 2019; 5:1480-1486. [PMID: 31243986 PMCID: PMC7169375 DOI: 10.1021/acsinfecdis.9b00213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the broader biological impact of carolacton, a macrolactone natural product, has been ongoing for the past decade. Multiple studies have shown connections to regulatory systems, acid tolerance mechanisms, biofilm formation, and recently folate dehydrogenase (FolD). Progress elucidating the cause of biofilm-specific activity in Streptococcus mutans has been limited due to low-throughput analyses of carolacton-treated cells. We disclose the discovery of a simplified carolacton-inspired analog that demonstrates inhibitory activity against S. mutans biofilm cells. This discovery permitted a proof of concept chemical genetic screen of S. mutans mutants identifying the carbon catabolite protein A signaling pathway as a putative target.
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Affiliation(s)
- Amy E. Solinski
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Amber M. Scharnow
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Americo J. Fraboni
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- Emory Antibiotic Resistance Center, Emory University School of Medicine, 201 Dowman Drive, Atlanta, Georgia 30322, United States
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Chen X, Liu C, Peng X, He Y, Liu H, Song Y, Xiong K, Zou L. Sortase A‐mediated modification of the
Streptococcus mutans
transcriptome and virulence traits. Mol Oral Microbiol 2019; 34:219-233. [PMID: 31342653 DOI: 10.1111/omi.12266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Xuan Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
- Department of Periodontics West China Hospital of Stomatology, Sichuan University Chengdu China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
| | - Yuanli He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
| | - Haixia Liu
- Stomatological Hospital of Chongqing Medical University Chongqing China
| | - Ying Song
- Stomatological Hospital of Chongqing Medical University Chongqing China
| | - Kaixin Xiong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
| | - Ling Zou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases Sichuan University Chengdu China
- Department of Conservation Dentistry and Endodontics West China Hospital of Stomatology, Sichuan University Chengdu China
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Duan G, Wu B, Qin H, Wang W, Tan Q, Dai Y, Qin Y, Tan F, Hu G, He M. Replacing water and nutrients for ethanol production by ARTP derived biogas slurry tolerant Zymomonas mobilis strain. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:124. [PMID: 31139254 PMCID: PMC6528197 DOI: 10.1186/s13068-019-1463-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Reducing fresh water consumption and nutrient addition will be an effective way to reduce the whole cost of bioethanol production. On the other hand, treatment of biogas slurry derived from anaerobic digestion (AD), in which a great amount of nutrients is still left, costs too much to remove these pollutants. It would be beneficial for both digestate valorization and ethanol production if biogas slurry is used for producing bioethanol. However, both hyperosmosis and potential biotoxic components of the biogas slurry can severely inhibit fermentation. RESULTS In this study, two rounds of atmospheric and room temperature plasma (ARTP) mutagenesis combined with adaptive laboratory evolution (ALE) were applied to improve the adaptability and genetic stability of Zymomonas mobilis in biogas slurry. Mutants D95 and S912 were identified. Growth of the mutants was remarkably improved in biogas slurry. The highest ethanol productivity reached 0.63 g/L/h which was 61.7% higher than ZM4 (0.39 g/L/h). Genomic re-sequencing results also revealed that single nucleic variations (SNVs) and Indels occurred in the mutants, which are likely related to inhibitor in biogas slurry and low pH tolerance. CONCLUSIONS Our study demonstrated that these mutant strains have great potential to produce ethanol using biogas slurry to replace fresh water and nutrients.
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Affiliation(s)
- Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Qiong Tan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Yonghua Dai
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Yao Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610041 People’s Republic of China
| | - Furong Tan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs) Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
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26
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Wu B, Qin H, Yang Y, Duan G, Yang S, Xin F, Zhao C, Shao H, Wang Y, Zhu Q, Tan F, Hu G, He M. Engineered Zymomonas mobilis tolerant to acetic acid and low pH via multiplex atmospheric and room temperature plasma mutagenesis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:10. [PMID: 30627218 PMCID: PMC6321654 DOI: 10.1186/s13068-018-1348-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/24/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cellulosic biofuels are sustainable compared to fossil fuels. However, inhibitors, such as acetic acid generated during lignocellulose pretreatment and hydrolysis, would significantly inhibit microbial fermentation efficiency. Microbial mutants able to tolerate high concentration of acetic acid are needed urgently to alleviate this inhibition. RESULTS Zymomonas mobilis mutants AQ8-1 and AC8-9 with enhanced tolerance against acetic acid were generated via a multiplex atmospheric and room temperature plasma (mARTP) mutagenesis. The growth and ethanol productivity of AQ8-1 and AC8-9 were both improved in the presence of 5.0-8.0 g/L acetic acid. Ethanol yield reached 84% of theoretical value in the presence of 8.0 g/L acetic acid (~ pH 4.0). Furthermore, a mutant tolerant to pH 3.5, named PH1-29, was generated via the third round of ARTP mutagenesis. PH1-29 showed enhanced growth and ethanol production under both sterilized/unsterilized conditions at pH 4.0 or 3.5. Intracellular NAD levels revealed that mARTP mutants could modulate NADH/NAD+ ratio to respond to acetic acid and low pH stresses. Moreover, genomic re-sequencing revealed that eleven single nucleic variations (SNVs) were likely related to acetic acid and low pH tolerance. Most SNVs were targeted in regions between genes ZMO0952 and ZMO0956, ZMO0152 and ZMO0153, and ZMO0373 and ZMO0374. CONCLUSIONS The multiplex mutagenesis strategy mARTP was efficient for enhancing the tolerance in Z. mobilis. The ARTP mutants generated in this study could serve as potential cellulosic ethanol producers.
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Affiliation(s)
- Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Yiwei Yang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Rd, Pukou District, Nanjing, 211816 China
| | - Chunyan Zhao
- College of Life Science, Sichuan Normal University, Section 2-1819, Chenglong Avenue, Chengdu, 610101 China
| | - Huanhuan Shao
- College of Life Science, Sichuan Normal University, Section 2-1819, Chenglong Avenue, Chengdu, 610101 China
| | - Yanwei Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Qili Zhu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Furong Tan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
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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: 1.4] [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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Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius. BMC Genomics 2018; 19:386. [PMID: 29792173 PMCID: PMC5966866 DOI: 10.1186/s12864-018-4781-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/10/2018] [Indexed: 11/10/2022] Open
Abstract
Background Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5.5, with limited and excessive glucose supply were determined. Results The transcriptomic analysis revealed that CodY was most active at pH 7 under conditions of glucose limitation. Based on whether a CodY binding consensus could be located in the 5′ flanking region of the identified target, the transcriptomic analysis also found that CodY shaped the transcriptome via both direct and indirect regulation. Inactivation of codY reduced the glycolytic capacity and the viability of S. salivarius at pH 5.5 or in the presence of H2O2. Studies using the Galleria mellonella larva model showed that CodY was essential for the toxicity generated from S. salivarius infection, suggesting that CodY regulation was critical for immune evasion and systemic infections. Furthermore, the CodY-null mutant strain exhibited a clumping phenotype and reduced attachment in biofilm assays, suggesting that CodY also modulates cell wall metabolism. Finally, the expression of genes belonging to the CovR regulon was affected by codY inactivation, but CodY and CovR regulated these genes in opposite directions. Conclusions Metabolic adaptation in response to nutrient availability and growth pH is tightly linked to stress responses and virulence expression in S. salivarius. The regulation of metabolism by CodY allows for the maximal utilization of available nutrients and ATP production. The counteractive regulation of the CovR regulon could fine tune the transcriptomes in response to environmental changes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4781-z) contains supplementary material, which is available to authorized users.
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李 转, 许 晓, 陈 璇, 吴 昕, 赵 望. [Role of SMU.2055 gene in regulating acid resistance of Streptococcus mutans UA159]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:198-204. [PMID: 29502060 PMCID: PMC6743886 DOI: 10.3969/j.issn.1673-4254.2018.02.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To evaluate the effect of SMU.2055 gene on acid resistance of Streptococcus mutans. METHODS A SMU.2055-dificient mutant strain of S. mutans was constructed using homologous recombination technique. The growth of the wild-type and mutant strains was monitored in both normal and acidic conditions. The lethal pH level, glycolysis, proton permeability, cell permeability and biofilm formation of the two strains were compared. RESULTS PCR and sequence analyses verified the successful construction of the SMU.2055-dificient mutant strain. The growth and biofilm formation capacity of the mutant strain were obviously lowered in both normal and acidic conditions. The mutant strain also showed increased lethal pH level, proton permeability, and cell permeability with impaired H+-ATPase activity in acidic conditions, but its minimum glycolytic pH remained unaffected. CONCLUSION The SMU.2055-deficient S. mutans mutant exhibits a lowered acid resistance, which affects the growth, lethal pH, proton permeability, H+-ATPase activity, cell permeability and biofilm formation but not the minimum glycolytic pH of the mutant strain.
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Affiliation(s)
- 转玲 李
- 南方医科大学南方医院口腔科,广东 广州 510515Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 晓虎 许
- 深圳市龙华新区中心医院口腔科,广东 深圳 518110Department of Stomatology, Longhua New District Central Hospital, Shenzhen 518110, China
| | - 璇 陈
- 南方医科大学口腔医院,广东 广州 510280Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - 昕彧 吴
- 南方医科大学口腔医院,广东 广州 510280Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - 望泓 赵
- 南方医科大学南方医院口腔科,广东 广州 510515Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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李 转, 许 晓, 陈 璇, 吴 昕, 赵 望. [Role of SMU.2055 gene in regulating acid resistance of Streptococcus mutans UA159]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:198-204. [PMID: 29502060 PMCID: PMC6743886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 10/15/2023]
Abstract
OBJECTIVE To evaluate the effect of SMU.2055 gene on acid resistance of Streptococcus mutans. METHODS A SMU.2055-dificient mutant strain of S. mutans was constructed using homologous recombination technique. The growth of the wild-type and mutant strains was monitored in both normal and acidic conditions. The lethal pH level, glycolysis, proton permeability, cell permeability and biofilm formation of the two strains were compared. RESULTS PCR and sequence analyses verified the successful construction of the SMU.2055-dificient mutant strain. The growth and biofilm formation capacity of the mutant strain were obviously lowered in both normal and acidic conditions. The mutant strain also showed increased lethal pH level, proton permeability, and cell permeability with impaired H+-ATPase activity in acidic conditions, but its minimum glycolytic pH remained unaffected. CONCLUSION The SMU.2055-deficient S. mutans mutant exhibits a lowered acid resistance, which affects the growth, lethal pH, proton permeability, H+-ATPase activity, cell permeability and biofilm formation but not the minimum glycolytic pH of the mutant strain.
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Affiliation(s)
- 转玲 李
- 南方医科大学南方医院口腔科,广东 广州 510515Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - 晓虎 许
- 深圳市龙华新区中心医院口腔科,广东 深圳 518110Department of Stomatology, Longhua New District Central Hospital, Shenzhen 518110, China
| | - 璇 陈
- 南方医科大学口腔医院,广东 广州 510280Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - 昕彧 吴
- 南方医科大学口腔医院,广东 广州 510280Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - 望泓 赵
- 南方医科大学南方医院口腔科,广东 广州 510515Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Arimoto T, Yambe R, Morisaki H, Umezawa H, Kataoka H, Matsui S, Kuwata H. Influence of excess branched-chain amino acid uptake by Streptococcus mutans in human host cells. FEMS Microbiol Lett 2018; 365:4733272. [PMID: 29240953 DOI: 10.1093/femsle/fnx273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/11/2017] [Indexed: 11/12/2022] Open
Abstract
Oral streptococci, including cariogenic bacterium Streptococcus mutans, comprise a large percentage of human supragingival plaque, which contacts both tooth surfaces and gingiva. Eukaryotic cells are able to take up macromolecules and particles, including bacteria, by endocytosis. Increasing evidence indicates endocytosis may be used as an entry process by bacteria. We hypothesized that some endocytosed bacteria might survive and obtain nutrients, such as amino acids, until they are killed. To verify this hypothesis, we focused on bacterial utilization of branched-chain amino acids (BCAAs; isoleucine, leucine and valine) in host cells. A branched-chain aminotransferase, IlvE (EC 2.6.1.42), has been suggested to play an important role in internal synthesis of BCAAs in S. mutans UA159. Therefore, we constructed an ilvE-deficient S. mutans 109c strain and confirmed that it had similar growth behavior as reported previously. 14C radioactive leucine uptake assays showed that ilvE-deficient S. mutans took up more leucine both inside and outside of host cells. We further clarified that a relative decrease of BCAAs in host cells caused enhanced endocytic and autophagic activity. In conclusion, S. mutans is endocytosed by host cells and may survive and obtain nutrients, such as BCAAs, inside the cells, which might affect cellular functions of host cells.
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Affiliation(s)
- Takafumi Arimoto
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Rei Yambe
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Hirobumi Morisaki
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Haruka Umezawa
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Hideo Kataoka
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Shohei Matsui
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan.,Division of Community-Based Comprehensive Dentistry, Department of Special Needs Dentistry, Showa University School of Dentisty, Tokyo 142-8555, Japan
| | - Hirotaka Kuwata
- Department of Oral Microbilogy and Immunology, Showa University School of Dentisty, Tokyo 142-8555, Japan
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Li KH, Yu YH, Dong HJ, Zhang WB, Ma JC, Wang HH. Biological Functions of ilvC in Branched-Chain Fatty Acid Synthesis and Diffusible Signal Factor Family Production in Xanthomonas campestris. Front Microbiol 2017; 8:2486. [PMID: 29312195 PMCID: PMC5733099 DOI: 10.3389/fmicb.2017.02486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
In bacteria, the metabolism of branched-chain amino acids (BCAAs) is tightly associated with branched-chain fatty acids (BCFAs) synthetic pathways. Although previous studies have reported on BCFAs biosynthesis, more detailed associations between BCAAs metabolism and BCFAs biosynthesis remain to be addressed. In this study, we deleted the ilvC gene, which encodes ketol-acid reductoisomerase in the BCAAs synthetic pathway, from the Xanthomonas campestris pv. campestris (Xcc) genome. We characterized gene functions in BCFAs biosynthesis and production of the diffusible signal factor (DSF) family signals. Disruption of ilvC caused Xcc to become auxotrophic for valine and isoleucine, and lose the ability to synthesize BCFAs via carbohydrate metabolism. Furthermore, ilvC mutant reduced the ability to produce DSF-family signals, especially branched-chain DSF-family signals, which might be the main reason for Xcc reduction of pathogenesis toward host plants. In this report, we confirmed that BCFAs do not have major functions in acclimatizing Xcc cells to low temperatures.
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Affiliation(s)
- Kai-Huai Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yong-Hong Yu
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Hui-Juan Dong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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CcpA and CodY Coordinate Acetate Metabolism in Streptococcus mutans. Appl Environ Microbiol 2017; 83:AEM.03274-16. [PMID: 28130304 DOI: 10.1128/aem.03274-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 11/20/2022] Open
Abstract
In the dental caries pathogen Streptococcus mutans, phosphotransacetylase (Pta) and acetate kinase (Ack) convert pyruvate into acetate with the concomitant generation of ATP. The genes for this pathway are tightly regulated by multiple environmental and intracellular inputs, but the basis for differential expression of the genes for Pta and Ack in S. mutans had not been investigated. Here, we show that inactivation in S. mutans of ccpA or codY reduced the activity of the ackA promoter, whereas a ccpA mutant displayed elevated pta promoter activity. The interactions of CcpA with the promoter regions of both genes were observed using electrophoretic mobility shift and DNase protection assays. CodY bound to the ackA promoter region but only in the presence of branched-chain amino acids (BCAAs). DNase footprinting revealed that the upstream region of both genes contains two catabolite-responsive elements (cre1 and cre2) that can be bound by CcpA. Notably, the cre2 site of ackA overlaps with a CodY-binding site. The CcpA- and CodY-binding sites in the promoter region of both genes were further defined by site-directed mutagenesis. Some differences between the reported consensus CodY binding site and the region protected by S. mutans CodY were noted. Transcription of the pta and ackA genes in the ccpA mutant strain was markedly different at low pH relative to transcription at neutral pH. Thus, CcpA and CodY are direct regulators of transcription of ackA and pta in S. mutans that optimize acetate metabolism in response to carbohydrate, amino acid availability, and environmental pH.IMPORTANCE The human dental caries pathogen Streptococcus mutans is remarkably adept at coping with extended periods of carbohydrate limitation during fasting periods. The phosphotransacetylase-acetate kinase (Pta-Ack) pathway in S. mutans modulates carbohydrate flux and fine-tunes the ability of the organisms to cope with stressors that are commonly encountered in the oral cavity. Here, we show that CcpA controls transcription of the pta and ackA genes via direct interaction with the promoter regions of both genes and that branched-chain amino acids (BCAAs), particularly isoleucine, enhance the ability of CodY to bind to the promoter region of the ackA gene. A working model is proposed to explain how regulation of pta and ackA genes by these allosterically controlled regulatory proteins facilitates proper carbon flow and energy production, which are essential functions during infection and pathogenesis as carbohydrate and amino acid availability continually fluctuate.
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Wu C, Huang J, Zhou R. Genomics of lactic acid bacteria: Current status and potential applications. Crit Rev Microbiol 2017; 43:393-404. [PMID: 28502225 DOI: 10.1080/1040841x.2016.1179623] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis. Moreover, strategies to engineer metabolic capacity and stress tolerance of LAB with improved industrial performance are also discussed.
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Affiliation(s)
- Chongde Wu
- a College of Light Industry, Textile & Food Engineering, Sichuan University , Chengdu , China.,b Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University , Chengdu , China
| | - Jun Huang
- a College of Light Industry, Textile & Food Engineering, Sichuan University , Chengdu , China.,b Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University , Chengdu , China
| | - Rongqing Zhou
- a College of Light Industry, Textile & Food Engineering, Sichuan University , Chengdu , China.,b Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University , Chengdu , China
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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Fozo EM, Rucks EA. The Making and Taking of Lipids: The Role of Bacterial Lipid Synthesis and the Harnessing of Host Lipids in Bacterial Pathogenesis. Adv Microb Physiol 2016; 69:51-155. [PMID: 27720012 DOI: 10.1016/bs.ampbs.2016.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In order to survive environmental stressors, including those induced by growth in the human host, bacterial pathogens will adjust their membrane physiology accordingly. These physiological changes also include the use of host-derived lipids to alter their own membranes and feed central metabolic pathways. Within the host, the pathogen is exposed to many stressful stimuli. A resulting adaptation is for pathogens to scavenge the host environment for readily available lipid sources. The pathogen takes advantage of these host-derived lipids to increase or decrease the rigidity of their own membranes, to provide themselves with valuable precursors to feed central metabolic pathways, or to impact host signalling and processes. Within, we review the diverse mechanisms that both extracellular and intracellular pathogens employ to alter their own membranes as well as their use of host-derived lipids in membrane synthesis and modification, in order to increase survival and perpetuate disease within the human host. Furthermore, we discuss how pathogen employed mechanistic utilization of host-derived lipids allows for their persistence, survival and potentiation of disease. A more thorough understanding of all of these mechanisms will have direct consequences for the development of new therapeutics, and specifically, therapeutics that target pathogens, while preserving normal flora.
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Affiliation(s)
- E M Fozo
- University of Tennessee, Knoxville, TN, United States.
| | - E A Rucks
- Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States.
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37
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Chen YYM, Chen YY, Hung JL, Chen PM, Chia JS. The GlnR Regulon in Streptococcus mutans Is Differentially Regulated by GlnR and PmrA. PLoS One 2016; 11:e0159599. [PMID: 27454482 PMCID: PMC4959772 DOI: 10.1371/journal.pone.0159599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022] Open
Abstract
GlnR-mediated repression of the GlnR regulon at acidic pH is required for optimal acid tolerance in Streptococcus mutans, the etiologic agent for dental caries. Unlike most streptococci, the GlnR regulon is also regulated by newly identified PmrA (SMUGS5_RS05810) at the transcriptional level in S. mutans GS5. Results from gel mobility shift assays confirmed that both GlnR and PmrA recognized the putative GlnR box in the promoter regions of the GlnR regulon genes. By using a chemostat culture system, we found that PmrA activated the expression of the GlnR regulon at pH 7, and that this activation was enhanced by excess glucose. Deletion of pmrA (strain ΔPmrA) reduced the survival rate of S. mutans GS5 at pH 3 moderately, whereas the GlnR mutant (strain ΔGlnR) exhibited an acid-sensitive phenotype in the acid killing experiments. Elevated biofilm formation in both ΔGlnR and ΔPmrA mutant strains is likely a result of indirect regulation of the GlnR regulon since GlnR and PmrA regulate the regulon differently. Taken together, it is suggested that activation of the GlnR regulon by PmrA at pH 7 ensures adequate biosynthesis of amino acid precursor, whereas repression by GlnR at acidic pH allows greater ATP generation for acid tolerance. The tight regulation of the GlnR regulon in response to pH provides an advantage for S. mutans to better survive in its primary niche, the oral cavity.
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Affiliation(s)
- Yi-Ywan M. Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- * E-mail:
| | - Yueh-Ying Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jui-Lung Hung
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Pei-Min Chen
- Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jean-San Chia
- Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
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38
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Baker JL, Faustoferri RC, Quivey RG. Acid-adaptive mechanisms of Streptococcus mutans-the more we know, the more we don't. Mol Oral Microbiol 2016; 32:107-117. [PMID: 27115703 DOI: 10.1111/omi.12162] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- J L Baker
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - R C Faustoferri
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - R G Quivey
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Andrés-Barrao C, Saad MM, Cabello Ferrete E, Bravo D, Chappuis ML, Ortega Pérez R, Junier P, Perret X, Barja F. Metaproteomics and ultrastructure characterization of Komagataeibacter spp. involved in high-acid spirit vinegar production. Food Microbiol 2016; 55:112-22. [DOI: 10.1016/j.fm.2015.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/15/2015] [Accepted: 10/18/2015] [Indexed: 02/06/2023]
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Cross B, Garcia A, Faustoferri R, Quivey RG. PlsX deletion impacts fatty acid synthesis and acid adaptation in Streptococcus mutans. MICROBIOLOGY-SGM 2016; 162:662-671. [PMID: 26850107 DOI: 10.1099/mic.0.000252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Streptococcus mutans, one of the primary causative agents of dental caries in humans, ferments dietary sugars in the mouth to produce organic acids. These acids lower local pH values, resulting in demineralization of the tooth enamel, leading to caries. To survive acidic environments, Strep. mutans employs several adaptive mechanisms, including a shift from saturated to unsaturated fatty acids in membrane phospholipids. PlsX is an acyl-ACP : phosphate transacylase that links the fatty acid synthase II (FASII) pathway to the phospholipid synthesis pathway, and is therefore central to the movement of unsaturated fatty acids into the membrane. Recently, we discovered that plsX is not essential in Strep. mutans. A plsX deletion mutant was not a fatty acid or phospholipid auxotroph. Gas chromatography of fatty acid methyl esters indicated that membrane fatty acid chain length in the plsX deletion strain differed from those detected in the parent strain, UA159. The deletion strain displayed a fatty acid shift similar to WT, but had a higher percentage of unsaturated fatty acids at low pH. The deletion strain survived significantly longer than the parent strain when cultures were subjected to an acid challenge of pH 2.5.The ΔplsX strain also exhibited elevated F-ATPase activity at pH 5.2, compared with the parent. These results indicate that the loss of plsX affects both the fatty acid synthesis pathway and the acid-adaptive response of Strep. mutans.
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Affiliation(s)
- Benjamin Cross
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Ariana Garcia
- Center for Oral Biology in the Eastman Institute for Oral Health, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Roberta Faustoferri
- Center for Oral Biology in the Eastman Institute for Oral Health, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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A Highly Arginolytic Streptococcus Species That Potently Antagonizes Streptococcus mutans. Appl Environ Microbiol 2016; 82:2187-201. [PMID: 26826230 DOI: 10.1128/aem.03887-15] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
The ability of certain oral biofilm bacteria to moderate pH through arginine metabolism by the arginine deiminase system (ADS) is a deterrent to the development of dental caries. Here, we characterize a novel Streptococcus strain, designated strain A12, isolated from supragingival dental plaque of a caries-free individual. A12 not only expressed the ADS pathway at high levels under a variety of conditions but also effectively inhibited growth and two intercellular signaling pathways of the dental caries pathogen Streptococcus mutans. A12 produced copious amounts of H2O2 via the pyruvate oxidase enzyme that were sufficient to arrest the growth of S. mutans. A12 also produced a protease similar to challisin (Sgc) of Streptococcus gordonii that was able to block the competence-stimulating peptide (CSP)-ComDE signaling system, which is essential for bacteriocin production by S. mutans. Wild-type A12, but not an sgc mutant derivative, could protect the sensitive indicator strain Streptococcus sanguinis SK150 from killing by the bacteriocins of S. mutans. A12, but not S. gordonii, could also block the XIP (comX-inducing peptide) signaling pathway, which is the proximal regulator of genetic competence in S. mutans, but Sgc was not required for this activity. The complete genome sequence of A12 was determined, and phylogenomic analyses compared A12 to streptococcal reference genomes. A12 was most similar to Streptococcus australis and Streptococcus parasanguinis but sufficiently different that it may represent a new species. A12-like organisms may play crucial roles in the promotion of stable, health-associated oral biofilm communities by moderating plaque pH and interfering with the growth and virulence of caries pathogens.
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Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ. Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. MICROBIOME 2015; 3:69. [PMID: 26684897 PMCID: PMC4684605 DOI: 10.1186/s40168-015-0136-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/25/2015] [Indexed: 05/30/2023]
Abstract
BACKGROUND The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. RESULTS In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. CONCLUSIONS Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions.
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Affiliation(s)
- Joel D Rudney
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware St. SE, Minneapolis, MN, 55455, USA.
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
- Center for Mass Spectrometry and Proteomics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
| | - Cavan S Reilly
- Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware St. SE, Minneapolis, MN, 55455, USA.
| | - Ruoqiong Chen
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware St. SE, Minneapolis, MN, 55455, USA.
| | - Todd W Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
- Center for Mass Spectrometry and Proteomics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
- Center for Mass Spectrometry and Proteomics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
| | - James E Johnson
- University of Minnesota Supercomputing Institute, 117 Pleasant St. SE, Minneapolis, MN, 55455, USA.
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
- Center for Mass Spectrometry and Proteomics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
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Mazzeo MF, Lippolis R, Sorrentino A, Liberti S, Fragnito F, Siciliano RA. Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics. PLoS One 2015; 10:e0142376. [PMID: 26544973 PMCID: PMC4636146 DOI: 10.1371/journal.pone.0142376] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/21/2015] [Indexed: 11/24/2022] Open
Abstract
Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes.This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.
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Affiliation(s)
| | - Rosa Lippolis
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
| | - Alida Sorrentino
- Institute of Food Sciences, National Research Council, Avellino, Italy
| | - Sarah Liberti
- Institute of Food Sciences, National Research Council, Avellino, Italy
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Federica Fragnito
- Institute of Food Sciences, National Research Council, Avellino, Italy
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44
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Palmer SR, Burne RA. Post-transcriptional regulation by distal Shine-Dalgarno sequences in the grpE-dnaK intergenic region of Streptococcus mutans. Mol Microbiol 2015; 98:302-17. [PMID: 26172310 DOI: 10.1111/mmi.13122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 12/24/2022]
Abstract
A unique 373 bp region (igr66) between grpE and dnaK of Streptococcus mutans lacks a promoter but is required for optimal production of DnaK. Northern blotting using probes specific to hrcA, igr66 or dnaK revealed multiple transcripts produced from the dnaK operon and 5'-RACE mapped 5' termini of multiple dnaK transcripts within igr66. One product mapped to a predicted 5'-SL (stem-loop) and two others mapped just 5' to Shine-Dalgarno (SD)-like sequences located immediately upstream to dnaK and to a predicted SL 120 bp upstream of the dnaK start codon (3'-SL). A collection of cat reporter-gene strains containing mutant derivatives of igr66 were engineered. Chloramphenicol acetyltransferase (CAT) activity varied greatly between strains, but there were no correlative changes in cat mRNA levels. Interestingly, mutations introduced into the SD-like sequences 5' to the 3'-SL resulted in an 83-98% decrease in CAT activity. Markerless point mutations introduced upstream of dnaK in the SD-like sequences impaired growth at elevated temperatures and resulted in up to a 40% decrease in DnaK protein after heat shock. Collectively, these results indicate processing within igr66 enhances translation in a temperature dependent manner via non-canonical ribosome binding sites positioned >120 bp upstream of dnaK.
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Affiliation(s)
- Sara R Palmer
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Robert A Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
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45
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Baker JL, Abranches J, Faustoferri RC, Hubbard CJ, Lemos JA, Courtney MA, Quivey R. Transcriptional profile of glucose-shocked and acid-adapted strains of Streptococcus mutans. Mol Oral Microbiol 2015; 30:496-517. [PMID: 26042838 DOI: 10.1111/omi.12110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 01/10/2023]
Abstract
The aciduricity of Streptococcus mutans is an important virulence factor of the organism, required to both out-compete commensal oral microorganisms and cause dental caries. In this study, we monitored transcriptional changes that occurred as a continuous culture of either an acid-tolerant strain (UA159) or an acid-sensitive strain (fabM::Erm) moved from steady-state growth at neutral pH, experienced glucose-shock and acidification of the culture, and transitioned to steady-state growth at low pH. Hence, the timing of elements of the acid tolerance response (ATR) could be observed and categorized as acute vs. adaptive ATR mechanisms. Modulation of branched chain amino acid biosynthesis, DNA/protein repair mechanisms, reactive oxygen species metabolizers and phosphoenolpyruvate:phosphotransferase systems occurred in the initial acute phase, immediately following glucose-shock, while upregulation of F1 F0 -ATPase did not occur until the adaptive phase, after steady-state growth had been re-established. In addition to the archetypal ATR pathways mentioned above, glucose-shock led to differential expression of genes suggesting a re-routing of resources away from the synthesis of fatty acids and proteins, and towards synthesis of purines, pyrimidines and amino acids. These adjustments were largely transient, as upon establishment of steady-state growth at acidic pH, transcripts returned to basal expression levels. During growth at steady-state pH 7, fabM::Erm had a transcriptional profile analogous to that of UA159 during glucose-shock, indicating that even during growth in rich media at neutral pH, the cells were stressed. These results, coupled with a recently established collection of deletion strains, provide a starting point for elucidation of the acid tolerance response in S. mutans.
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Affiliation(s)
- J L Baker
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - J Abranches
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - R C Faustoferri
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - C J Hubbard
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - J A Lemos
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - M A Courtney
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - R Quivey
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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46
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Quivey RG, Grayhack EJ, Faustoferri RC, Hubbard CJ, Baldeck JD, Wolf AS, MacGilvray ME, Rosalen PL, Scott-Anne K, Santiago B, Gopal S, Payne J, Marquis RE. Functional profiling in Streptococcus mutans: construction and examination of a genomic collection of gene deletion mutants. Mol Oral Microbiol 2015; 30:474-95. [PMID: 25973955 DOI: 10.1111/omi.12107] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2015] [Indexed: 12/17/2022]
Abstract
A collection of tagged deletion mutant strains was created in Streptococcus mutans UA159 to facilitate investigation of the aciduric capability of this oral pathogen. Gene-specific barcoded deletions were attempted in 1432 open reading frames (representing 73% of the genome), and resulted in the isolation of 1112 strains (56% coverage) carrying deletions in distinct non-essential genes. As S. mutans virulence is predicated upon the ability of the organism to survive an acidic pH environment, form biofilms on tooth surfaces, and out-compete other oral microflora, we assayed individual mutant strains for the relative fitness of the deletion strain, compared with the parent strain, under acidic and oxidative stress conditions, as well as for their ability to form biofilms in glucose- or sucrose-containing medium. Our studies revealed a total of 51 deletion strains with defects in both aciduricity and biofilm formation. We have also identified 49 strains whose gene deletion confers sensitivity to oxidative damage and deficiencies in biofilm formation. We demonstrate the ability to examine competitive fitness of mutant organisms using the barcode tags incorporated into each deletion strain to examine the representation of a particular strain in a population. Co-cultures of deletion strains were grown either in vitro in a chemostat to steady-state values of pH 7 and pH 5 or in vivo in an animal model for oral infection. Taken together, these data represent a mechanism for assessing the virulence capacity of this pathogenic microorganism and a resource for identifying future targets for drug intervention to promote healthy oral microflora.
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Affiliation(s)
- R G Quivey
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA.,Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - E J Grayhack
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
| | - R C Faustoferri
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - C J Hubbard
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - J D Baldeck
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | - A S Wolf
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
| | - M E MacGilvray
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - P L Rosalen
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - K Scott-Anne
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - B Santiago
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
| | - S Gopal
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - J Payne
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
| | - R E Marquis
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
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47
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Terai T, Okumura T, Imai S, Nakao M, Yamaji K, Ito M, Nagata T, Kaneko K, Miyazaki K, Okada A, Nomura Y, Hanada N. Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease. PLoS One 2015; 10:e0128657. [PMID: 26053410 PMCID: PMC4459870 DOI: 10.1371/journal.pone.0128657] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/29/2015] [Indexed: 11/18/2022] Open
Abstract
The oral cavity in healthy subjects has a well-balanced microbiota that consists of more than 700 species. However, a disturbance of this balance, with an increase of harmful microbes and a decrease of beneficial microbes, causes oral disorders such as periodontal disease or dental caries. Nowadays, probiotics are expected to confer oral health benefits by modulating the oral microbiota. This study screened new probiotic candidates with potential oral health benefits and no harmful effects on the oral cavity. We screened 14 lactobacillus strains and 36 streptococcus strains out of 896 oral isolates derived from healthy subjects. These bacteria did not produce volatile sulfur compounds or water-insoluble glucan, had higher antibacterial activity against periodontal bacteria, and had higher adherence activity to oral epithelial cells or salivary-coated hydroxyapatite in vitro. We then evaluated the risk of primary cariogenicity and infective endocarditis of the selected oral isolates. As a result, Lactobacillus crispatus YIT 12319, Lactobacillus fermentum YIT 12320, Lactobacillus gasseri YIT 12321, and Streptococcus mitis YIT 12322 were selected because they showed no cariogenic potential in an artificial mouth system and a lower risk of experimental infective endocarditis in a rat model. These candidates are expected as new probiotics with potential oral health benefits and no adverse effects on general health.
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Affiliation(s)
- Tomohiko Terai
- Yakult Central Institute, Kunitachi, Tokyo, Japan
- * E-mail:
| | | | - Susumu Imai
- Department of Translational Research, Tsurumi University School of Dental Medicine, Yokohama, Kanagawa, Japan
| | - Masumi Nakao
- Yakult Central Institute, Kunitachi, Tokyo, Japan
| | | | - Masahiko Ito
- Yakult Central Institute, Kunitachi, Tokyo, Japan
| | | | | | | | - Ayako Okada
- Department of Translational Research, Tsurumi University School of Dental Medicine, Yokohama, Kanagawa, Japan
| | - Yoshiaki Nomura
- Department of Translational Research, Tsurumi University School of Dental Medicine, Yokohama, Kanagawa, Japan
| | - Nobuhiro Hanada
- Department of Translational Research, Tsurumi University School of Dental Medicine, Yokohama, Kanagawa, Japan
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48
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Liu Y, Tang H, Lin Z, Xu P. Mechanisms of acid tolerance in bacteria and prospects in biotechnology and bioremediation. Biotechnol Adv 2015; 33:1484-92. [PMID: 26057689 DOI: 10.1016/j.biotechadv.2015.06.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 06/02/2015] [Accepted: 06/02/2015] [Indexed: 02/05/2023]
Abstract
Acidogenic and aciduric bacteria have developed several survival systems in various acidic environments to prevent cell damage due to acid stress such as that on the human gastric surface and in the fermentation medium used for industrial production of acidic products. Common mechanisms for acid resistance in bacteria are proton pumping by F1-F0-ATPase, the glutamate decarboxylase system, formation of a protective cloud of ammonia, high cytoplasmic urease activity, repair or protection of macromolecules, and biofilm formation. The field of synthetic biology has rapidly advanced and generated an ever-increasing assortment of genetic devices and biological modules for applications in biofuel and novel biomaterial productions. Better understanding of aspects such as overproduction of general shock proteins, molecular mechanisms, and responses to cell density adopted by microorganisms for survival in low pH conditions will prove useful in synthetic biology for potential industrial and environmental applications.
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Affiliation(s)
- Yuping Liu
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, One Tsinghua Garden Road, Beijing 100084, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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49
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Abstract
Oral colonising bacteria are highly adapted to the various environmental niches harboured within the mouth, whether that means while contributing to one of the major oral diseases of caries, pulp infections, or gingival/periodontal disease or as part of a commensal lifestyle. Key to these infections is the ability to adhere to surfaces via a range of specialised adhesins targeted at both salivary and epithelial proteins, their glycans and to form biofilm. They must also resist the various physical stressors they are subjected to, including pH and oxidative stress. Possibly most strikingly, they have developed the ability to harvest both nutrient sources provided by the diet and those derived from the host, such as protein and surface glycans. We have attempted to review recent developments that have revealed much about the molecular mechanisms at work in shaping the physiology of oral bacteria and how we might use this information to design and implement new treatment strategies.
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50
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Faustoferri RC, Hubbard CJ, Santiago B, Buckley AA, Seifert TB, Quivey RG. Regulation of fatty acid biosynthesis by the global regulator CcpA and the local regulator FabT in Streptococcus mutans. Mol Oral Microbiol 2014; 30:128-46. [PMID: 25131436 DOI: 10.1111/omi.12076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
SMU.1745c, encoding a putative transcriptional regulator of the MarR family, maps to a location proximal to the fab gene cluster in Streptococcus mutans. Deletion of the SMU.1745c (fabTS m ) coding region resulted in a membrane fatty acid composition comprised of longer-chained, unsaturated fatty acids (UFA), compared with the parent strain. Previous reports have indicated a role for FabT in regulation of genes in the fab gene cluster in other organisms, through binding to a palindromic DNA sequence. Consensus FabT motif sequences were identified in S. mutans in the intergenic regions preceding fabM, fabTSm and fabK in the fab gene cluster. Chloramphenicol acetyltransferase (cat) reporter fusions, using the fabM promoter, revealed elevated transcription in a ∆fabTS m background. Transcription of fabTS m was dramatically elevated in cells grown at pH values of 5 and 7 in the ∆ fabTS m background. Transcription of fabTS m was also elevated in a strain carrying a deletion for the carbon catabolite repressor CcpA. Purified FabTS m and CcpA bound to the promoter regions of fabTS m and fabM. Hence, the data indicate that FabTS m acts as a repressor of fabM and fabTS m itself and the global regulator CcpA acts as a repressor for fabTS m .
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Affiliation(s)
- R C Faustoferri
- Center for Oral Biology, University of Rochester, Rochester, NY, USA
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