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Guan Y, Cui Y, Qu X, Li B, Zhang L. Post-acidification of fermented milk and its molecular regulatory mechanism. Int J Food Microbiol 2024; 426:110920. [PMID: 39316924 DOI: 10.1016/j.ijfoodmicro.2024.110920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 09/08/2024] [Accepted: 09/15/2024] [Indexed: 09/26/2024]
Abstract
The fermented milk products with lactic acid bacteria (LAB) are widely accepted by consumers. During the chilled-chain transportation and storage, LAB in the product keep producing lactic acid, and this will lead to post-acidification, which can affect the flavor, consumer acceptance and even shelf-life of the product. LAB is the determining factor affecting post-acidification. The acid production pathway in LAB and methods inhibiting post-acidification received widespread attention. This review will focus on the post-acidification from the perspective of fermentation starters, including acid production pathway in LAB, main factors and key enzymes affecting post-acidification. Lactobacillus delbrueckii subsp. bulgaricus is a key bacterial species responsible for post acidification in the fermented milk products. The different species and strains presented various differences in process like acid production, acid resistance and post-acidification. Furthermore, multiple factors, such as milk composition, fermentation temperature, and homogenization, also can influence post-acidification. Lactose transport and utilization pathways, as well as its subsequent products metabolic pathway directly influence the post-acidification. F0F1-ATPase, β-galactosidase, and lactate dehydrogenase are recognized as important enzymes related to post-acidification. The degree of post-acidification is mainly related to the acid production and acid resistance abilities of the fermentation starters, so the key enzymes related to post-acidification are mostly taking part in these two capacities. Recently, some new post-acidification related biomarker genes were found, providing a reference adjusting post-acidification without affecting fermentation rate and bacteria viability. To clarify the post-acidification mechanism at the molecular level will help control post- acidification.
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Affiliation(s)
- Yuxuan Guan
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150090, China
| | - Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010, China
| | - Baolei Li
- National Center of Technology Innovation for Dairy, Hohhot 010000, China
| | - Lanwei Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
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Cheng Q, Han Y, Xiao Y, Li Z, Qin A, Ji S, Kan B, Liang W. The ArgR-Regulated ADI Pathway Facilitates the Survival of Vibrio fluvialis under Acidic Conditions. Int J Mol Sci 2024; 25:5679. [PMID: 38891866 PMCID: PMC11172107 DOI: 10.3390/ijms25115679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Vibrio fluvialis is an emerging foodborne pathogenic bacterium that can cause severe cholera-like diarrhea and various extraintestinal infections, posing challenges to public health and food safety worldwide. The arginine deiminase (ADI) pathway plays an important role in bacterial environmental adaptation and pathogenicity. However, the biological functions and regulatory mechanisms of the pathway in V. fluvialis remain unclear. In this study, we demonstrate that L-arginine upregulates the expression of the ADI gene cluster and promotes the growth of V. fluvialis. The ADI gene cluster, which we proved to be comprised of two operons, arcD and arcACB, significantly enhances the survival of V. fluvialis in acidic environments both in vitro (in culture medium and in macrophage) and in vivo (in mice). The mRNA level and reporter gene fusion analyses revealed that ArgR, a transcriptional factor, is necessary for the activation of both arcD and arcACB transcriptions. Bioinformatic analysis predicted the existence of multiple potential ArgR binding sites at the arcD and arcACB promoter regions that were further confirmed by electrophoretic mobility shift assay, DNase I footprinting, or point mutation analyses. Together, our study provides insights into the important role of the ArgR-ADI pathway in the survival of V. fluvialis under acidic conditions and the detailed molecular mechanism. These findings will deepen our understanding of how environmental changes and gene expression interact to facilitate bacterial adaptations and virulence.
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Affiliation(s)
| | | | | | | | | | | | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Weili Liang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Altamura S, Augello FR, Ortu E, Pietropaoli D, Cinque B, Giannoni M, Lombardi F. Efficacy of the Probiotic L. brevis in Counteracting the Demineralizing Process of the Tooth Enamel Surface: Results from an In Vitro Study. Biomolecules 2024; 14:605. [PMID: 38786012 PMCID: PMC11118116 DOI: 10.3390/biom14050605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Enamel plays an essential role in protecting the underlying layers of the human tooth; therefore, preserving it is vital. This experimental study aimed to evaluate the potential ability of L. brevis to counteract the action of a demineralizing agent on dental enamel morphology and mineral composition in vitro. METHODS The sample consisted of 12 healthy human posterior teeth. The coronal portion of each tooth was subdivided into two equal parts longitudinally. The specimens were randomly divided into four groups: artificial saliva, L. brevis suspension, demineralizing agent (DA), and DA plus L. brevis. Scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) were used to evaluate the surface micromorphology and the mineral content, respectively. The statistical analysis was conducted using a one-way ANOVA, followed by Tukey's post hoc test. RESULTS SEM analysis did not highlight significant changes in the enamel microstructure of L. brevis-treated specimens compared to the control. DA-induced damage to the enamel structure was drastically reduced when the specimens were contextually exposed to the probiotic. The treatment with DA substantially reduced the weight % of crucial enamel minerals, i.e., Ca and P. Notably, the probiotic was able to reverse the demineralization process, bringing Ca and P weight % back to basal levels, including the Ca/P ratio. CONCLUSIONS The findings indicate that L. brevis is able to efficiently protect the dental enamel surface from the damage caused by DA and increase the enamel resistance to demineralization. Overall, L. brevis confirms its efficacy in preventing or counteracting the action of carious lesions through a novel mechanism that protects the tooth surface under a chemical challenge that mimics the caries process.
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Affiliation(s)
- Serena Altamura
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
- Ph.D. School in Medicine and Public Health, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy
- Center of Oral Diseases, Prevention and Translational Research—Dental Clinic, 67100 L’Aquila, Italy
- Oral Diseases and Systemic Interactions Study Group (ODISSY Group), 67100 L’Aquila, Italy
| | - Francesca Rosaria Augello
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
| | - Eleonora Ortu
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
- Center of Oral Diseases, Prevention and Translational Research—Dental Clinic, 67100 L’Aquila, Italy
- Oral Diseases and Systemic Interactions Study Group (ODISSY Group), 67100 L’Aquila, Italy
| | - Davide Pietropaoli
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
- Center of Oral Diseases, Prevention and Translational Research—Dental Clinic, 67100 L’Aquila, Italy
- Oral Diseases and Systemic Interactions Study Group (ODISSY Group), 67100 L’Aquila, Italy
| | - Benedetta Cinque
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
| | - Mario Giannoni
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
- Center of Oral Diseases, Prevention and Translational Research—Dental Clinic, 67100 L’Aquila, Italy
| | - Francesca Lombardi
- Department of Life, Health & Environmental Sciences, University of L’Aquila, Building Rita Levi Montalcini, Coppito, 67100 L’Aquila, Italy; (S.A.); (F.R.A.); (E.O.); (D.P.); (F.L.)
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Liu Y, Cheng YY, Thompson J, Zhou Z, Vivas EI, Warren MF, Rey FE, Anantharaman K, Venturelli OS. Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.10.523442. [PMID: 37986770 PMCID: PMC10659395 DOI: 10.1101/2023.01.10.523442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The arginine dihydrolase pathway (arc operon) present in a subset of diverse human gut species enables arginine catabolism. This specialized metabolic pathway can alter environmental pH and nitrogen availability, which in turn could shape gut microbiota inter-species interactions. By exploiting synthetic control of gene expression, we investigated the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and health-relevant metabolite profiles in vitro and in the murine gut. By stabilizing environmental pH, the arc operon reduced variability in community composition across different initial pH perturbations. The abundance of butyrate producing bacteria were altered in response to arc operon activity and butyrate production was enhanced in a physiologically relevant pH range. While the presence of the arc operon altered community dynamics, it did not impact production of short chain fatty acids. Dynamic computational modeling of pH-mediated interactions reveals the quantitative contribution of this mechanism to community assembly. In sum, our framework to quantify the contribution of molecular pathways and mechanism modalities on microbial community dynamics and functions could be applied more broadly.
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Affiliation(s)
- Yiyi Liu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew F. Warren
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | | | - Ophelia S. Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
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5
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Mann AE, Chakraborty B, O'Connell LM, Nascimento MM, Burne RA, Richards VP. Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species. Microbiol Spectr 2024; 12:e0144523. [PMID: 38411054 PMCID: PMC10986539 DOI: 10.1128/spectrum.01445-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS-competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remain an open question. Here, we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic and in vitro citrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping and de novo assembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low-abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups. IMPORTANCE Tooth decay is the most common preventable chronic disease, affecting more than two billion people globally. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of arginine deiminase system (ADS) activity among oral bacteria in a community context remain an open question. In the current study, we use a multi-omics approach to document the pervasiveness of the expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.
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Affiliation(s)
- Allison E. Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Brinta Chakraborty
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Lauren M. O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Marcelle M. Nascimento
- Division of Operative Dentistry, Department of Restorative Dental Sciences, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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6
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Song K, Chen L, Suo N, Kong X, Li J, Wang T, Song L, Cheng M, Guo X, Huang Z, Huang Z, Yang Y, Tian X, Choo SW. Whole-transcriptome analysis reveals mechanisms underlying antibacterial activity and biofilm inhibition by a malic acid combination (MAC) in Pseudomonas aeruginosa. PeerJ 2023; 11:e16476. [PMID: 38084141 PMCID: PMC10710775 DOI: 10.7717/peerj.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Background Pseudomonas aeruginosa is a highly prevalent bacterial species known for its ability to cause various infections and its remarkable adaptability and biofilm-forming capabilities. In earlier work, we conducted research involving the screening of 33 metabolites obtained from a commercial source against two prevalent bacterial strains, Escherichia coli and Staphylococcus aureus. Through screening assays, we discovered a novel malic acid combination (MAC) consisting of malic acid, citric acid, glycine, and hippuric acid, which displayed significant inhibitory effects. However, the precise underlying mechanism and the potential impact of the MAC on bacterial biofilm formation remain unknown and warrant further investigation. Methods To determine the antibacterial effectiveness of the MAC against Pseudomonas aeruginosa, we conducted minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques were employed to observe bacterial morphology and biofilm formation. We further performed a biofilm inhibition assay to assess the effect of the MAC on biofilm formation. Whole-transcriptome sequencing and bioinformatics analysis were employed to elucidate the antibacterial mechanism of the MAC. Additionally, the expression levels of differentially expressed genes were validated using the real-time PCR approach. Results Our findings demonstrated the antibacterial activity of the MAC against P. aeruginosa. SEM analysis revealed that the MAC can induce morphological changes in bacterial cells. The biofilm assay showed that the MAC could reduce biofilm formation. Whole-transcriptome analysis revealed 1093 differentially expressed genes consisting of 659 upregulated genes and 434 downregulated genes, in response to the MAC treatment. Mechanistically, the MAC inhibited P. aeruginosa growth by targeting metabolic processes, secretion system, signal transduction, and cell membrane functions, thereby potentially compromising the survival of this human pathogen. This study provides valuable insights into the antibacterial and antibiofilm activities of the MAC, a synergistic and cost-effective malic acid combination, which holds promise as a potential therapeutic drug cocktail for treating human infectious diseases in the future.
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Affiliation(s)
- Kunping Song
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
| | - Li Chen
- Universiti Malaya, Institute of Biological Sciences, Faculty of Science, Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Nanhua Suo
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
| | - Xinyi Kong
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
| | - Juexi Li
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
| | - Tianyu Wang
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
| | - Lanni Song
- Wenzhou-Kean University, Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
| | - Mengwei Cheng
- Wenzhou-Kean University, Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
| | - Xindian Guo
- Wenzhou No.2 Foreign Language School, Wenzhou, Zhejiang, China
| | - Zhenghe Huang
- Wenzhou No.2 Foreign Language School, Wenzhou, Zhejiang, China
| | - Zichen Huang
- Wenzhou No.2 Foreign Language School, Wenzhou, Zhejiang, China
| | - Yixin Yang
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
- Wenzhou-Kean University, Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
- Wenzhou-Kean University, Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
| | - Xuechen Tian
- Wenzhou-Kean University, Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
- Wenzhou-Kean University, Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
| | - Siew Woh Choo
- Wenzhou-Kean University, College of Science, Mathematics and Technology, Wenzhou, Zhejiang, China
- Wenzhou-Kean University, Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang, China
- Wenzhou-Kean University, Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang, China
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Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae. Nat Commun 2023; 14:7305. [PMID: 37951938 PMCID: PMC10640624 DOI: 10.1038/s41467-023-43196-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
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Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
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Kim HJ, Kim HJ, Kim HC, Lee D, Jung HY, Kang T, Jo C. Mathematical modeling for freshness/spoilage of chicken breast using chemometric analysis. Curr Res Food Sci 2023; 7:100590. [PMID: 37727874 PMCID: PMC10506101 DOI: 10.1016/j.crfs.2023.100590] [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: 04/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023] Open
Abstract
Chicken meat spoilage is a significant concern for food safety and quality, and this study aims to predict the spoilage point of chicken breast meat through various attributes and metabolites. Chicken meat was stored in anaerobic packaging at 4 °C for 13 days, and various meat quality attributes (pH, drip loss, color, volatile basic nitrogen [VBN], total aerobic bacteria [TAB], and metabolites) were examined. First, the spoiled point (VBN >20 mg/100 g and/or TAB >7 log CFU/g) of the chicken breast meat was determined. Using univariate and multivariate analyses, twenty-four candidate metabolites were identified. A receiver operating characteristic (ROC) analysis was used to validate the obtained binary logistic regression model using nine metabolites (proline, methionine, glutamate, threonine, acetate, uridine 5'-monophosphate, hypoxanthine, glycine, and glutamine). The results showed a high area under the ROC curve value (0.992). Thus, this study confirmed the predictability of spoilage points in chicken breast meat through these nine metabolites.
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Affiliation(s)
- Hyun-Jun Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye-Jin Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun Cheol Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongheon Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun Young Jung
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taemin Kang
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Green BioScience and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
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9
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Wu JF, Wei XP, Li JY, Sun WX. Recombinant Expression and Characterization of an Arginine Deiminase from Pseudomonas sp. LJY. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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10
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Falkinham JO. Nontuberculous mycobacteria in the environment. Tuberculosis (Edinb) 2022; 137:102267. [PMID: 36191391 DOI: 10.1016/j.tube.2022.102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023]
Abstract
The nontuberculous mycobacteria (NTM) are normal inhabitants of soils and waters and thereby surround humans due to their presence in water that is distributed to homes, apartments, offices, hospitals and long-term care facilities in pipes. The NTM are not contaminants of drinking water, rather they are colonists ideally adapted to growth and persistence in natural waters. Further those adaptations also favor NTM survival, persistence, and growth in drinking water systems. Thereby, NTM surround humans. The NTM love plumbing as it offers a high surface to volume ratio, ideal for surface adherence and biofilm formation. As a consequence, these slow growing bacteria are not flushed out by flowing water. Factors that support NTM growth and persistence in drinking water include: disinfectant-resistance, growth at low organic matter content (oligotrophic), surface attachment and biofilm formation, growth at low oxygen content (stagnant water), and desiccation-tolerance. A major determinant of the ecology of NTM is the lipid-rich outer membrane. The outer membrane provides a hydrophobic barrier that is relatively impermeable. Although the outer membrane reduces influx of nutrients, it also impedes transport of hydrophilic disinfectants (e.g., chlorine) and antibiotics. NTM are quite adaptable: able to grow in fresh or brackish natural waters and able to induce a high-temperature-resistant state.
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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12
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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13
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Romão VC, Fonseca JE. Disease mechanisms in preclinical rheumatoid arthritis: A narrative review. Front Med (Lausanne) 2022; 9:689711. [PMID: 36059838 PMCID: PMC9437632 DOI: 10.3389/fmed.2022.689711] [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: 04/01/2021] [Accepted: 08/04/2022] [Indexed: 11/20/2022] Open
Abstract
In the last decades, the concept of preclinical rheumatoid arthritis (RA) has become established. In fact, the discovery that disease mechanisms start years before the onset of clinical RA has been one of the major recent insights in the understanding of RA pathogenesis. In accordance with the complex nature of the disease, preclinical events extend over several sequential phases. In a genetically predisposed host, environmental factors will further increase susceptibility for incident RA. In the initial steps of preclinical disease, immune disturbance mechanisms take place outside the joint compartment, namely in mucosal surfaces, such as the lung, gums or gut. Herein, the persistent immunologic response to altered antigens will lead to breach of tolerance and trigger autoimmunity. In a second phase, the immune response matures and is amplified at a systemic level, with epitope spreading and widening of the autoantibody repertoire. Finally, the synovial and bone compartment are targeted by specific autoantibodies against modified antigens, initiating a local inflammatory response that will eventually culminate in clinically evident synovitis. In this review, we discuss the elaborate disease mechanisms in place during preclinical RA, providing a broad perspective in the light of current evidence.
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Affiliation(s)
- Vasco C. Romão
- Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon Academic Medical Centre and European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ERN-ReCONNET), Lisbon, Portugal
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - João Eurico Fonseca
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
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14
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Ghazisaeedi F, Meens J, Hansche B, Maurischat S, Schwerk P, Goethe R, Wieler LH, Fulde M, Tedin K. A virulence factor as a therapeutic: the probiotic Enterococcus faecium SF68 arginine deiminase inhibits innate immune signaling pathways. Gut Microbes 2022; 14:2106105. [PMID: 35921516 PMCID: PMC9351580 DOI: 10.1080/19490976.2022.2106105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The probiotic bacterial strain Enterococcus faecium SF68 has been shown to alleviate symptoms of intestinal inflammation in human clinical trials and animal feed supplementation studies. To identify factors involved in immunomodulatory effects on host cells, E. faecium SF68 and other commensal and clinical Enterococcus isolates were screened using intestinal epithelial cell lines harboring reporter fusions for NF-κB and JNK(AP-1) activation to determine the responses of host cell innate immune signaling pathways when challenged with bacterial protein and cell components. Cell-free, whole-cell lysates of E. faecium SF68 showed a reversible, inhibitory effect on both NF-κB and JNK(AP-1) signaling pathway activation in intestinal epithelial cells and abrogated the response to bacterial and other Toll-like receptor (TLR) ligands. The inhibitory effect was species-specific, and was not observed for E. avium, E. gallinarum, or E. casseliflavus. Screening of protein fractions of E. faecium SF68 lysates yielded an active fraction containing a prominent protein identified as arginine deiminase (ADI). The E. faecium SF68 arcA gene encoding arginine deiminase was cloned and introduced into E. avium where it conferred the same NF-κB inhibitory effects on intestinal epithelial cells as seen for E. faecium SF68. Our results indicate that the arginine deiminase of E. faecium SF68 is responsible for inhibition of host cell NF-κB and JNK(AP-1) pathway activation, and is likely to be responsible for the anti-inflammatory and immunomodulatory effects observed in prior clinical human and animal trials. The implications for the use of this probiotic strain for preventive and therapeutic purposes are discussed.
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Affiliation(s)
- Fereshteh Ghazisaeedi
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany
| | - Jochen Meens
- Institute for Microbiology, University of Veterinary Medicine, Hannover, Germany
| | - Bianca Hansche
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany,Sanofi-AventisGmbH, Berlin, Germany
| | - Sven Maurischat
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany,German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Peter Schwerk
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany
| | - Ralph Goethe
- Institute for Microbiology, University of Veterinary Medicine, Hannover, Germany
| | - Lothar H. Wieler
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany,Robert Koch Institute, Berlin, Germany
| | - Marcus Fulde
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany
| | - Karsten Tedin
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Berlin, Germany,CONTACT Karsten Tedin Institute of Microbiology and Epizootics, Centre for Infection Medicine, Free University of Berlin, Robert-von-Ostertag-Strasse7, Berlin14163Germany
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15
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Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Commun 2022; 13:4110. [PMID: 35840579 PMCID: PMC9287336 DOI: 10.1038/s41467-022-31847-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.
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Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
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16
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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease. Clin Microbiol Rev 2022; 35:e0014021. [PMID: 35658516 DOI: 10.1128/cmr.00140-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
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17
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Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment. Proc Natl Acad Sci U S A 2022; 119:2114909119. [PMID: 34992141 PMCID: PMC8764695 DOI: 10.1073/pnas.2114909119] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 01/10/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) is a large monophyletic lineage with poorly understood biology. Saccharibacteria are ultrasmall parasitic CPR bacteria with highly reduced genomes that have made the transition from an environmental origin to mammals. We tested the function and impact of the arginine deiminase system (ADS), an arginine catabolism pathway likely acquired by mammal-associated Saccharibacteria during their environment-to-mammal niche transition. We showed that the acquired ADS not only helped facilitate Saccharibacterial adaptation to mammals but also contributed to the establishment of cooperative episymbiotic interaction with their bacterial hosts within mammalian microbiomes. Our study provides experimental evidence demonstrating the importance of function acquired by Saccharibacteria during niche transition in facilitating their adaptation from the environment to a mammalian niche. Saccharibacteria are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to the Candidate Phyla Radiation. Comparative genomic analyses suggest convergent evolution of key functions enabling the adaptation of environmental Saccharibacteria to mammalian microbiomes. Currently, our understanding of this environment-to-mammal niche transition within Saccharibacteria and their obligate episymbiotic association with host bacteria is limited. Here, we identified a complete arginine deiminase system (ADS), found in further genome streamlined mammal-associated Saccharibacteria but missing in their environmental counterparts, suggesting acquisition during environment-to-mammal niche transition. Using TM7x, the first cultured Saccharibacteria strain from the human oral microbiome and its host bacterium Actinomyces odontolyticus, we experimentally tested the function and impact of the ADS. We demonstrated that by catabolizing arginine and generating adenosine triphosphate, the ADS allows metabolically restrained TM7x to maintain higher viability and infectivity when disassociated from the host bacterium. Furthermore, the ADS protects TM7x and its host bacterium from acid stress, a condition frequently encountered within the human oral cavity due to bacterial metabolism of dietary carbohydrates. Intriguingly, with a restricted host range, TM7x forms obligate associations with Actinomyces spp. lacking the ADS but not those carrying the ADS, suggesting the acquired ADS may also contribute to partner selection for cooperative episymbiosis within a mammalian microbiome. These data present experimental characterization of a mutualistic interaction between TM7x and their host bacteria, and illustrate the benefits of acquiring a novel pathway in the transition of Saccharibacteria to mammalian microbiomes.
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18
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Isaac RD, Sanjeev K, Subbulakshmi CL, Amirtharaj LV, Sekar M. Identification of a novel bacterium Scardovia wiggsiae in high caries risk adolescence: A metagenomic and melt curve analysis. J Conserv Dent 2022; 25:297-305. [PMID: 35836558 PMCID: PMC9274687 DOI: 10.4103/jcd.jcd_79_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Mutans streptococci which comprise only 2% have long been presumed to be the specific pathogen responsible for caries. A novel caries associated bacterium namely Scardovia wiggsiae is recognized to be ecologically competitive in active caries lesions. The actual pathogen needs to be identified, so as to specifically target and reduce the prevalence of caries in a given community. AIM The aim of the study is to evaluate the presence of S. wiggsiae in combination with other bacteria in caries risk adolescence. METHODS Sixty adolescent subjects were screened. Phase I-to determine the prevalence of S. wiggsiae in saliva, plaque and dentinal caries samples of low and high caries risk individuals (n = 30 each) using polymerase chain reaction (PCR); Phase-II-to identify its presence by 16SrRNA metagenomic analysis and quantitatively evaluate the cariogenic pathogen using high-resolution melt curve analysis and real-time PCR. RESULTS Highest prevalence of S. wiggsiae was observed in dentinal caries followed by plaque and saliva samples of high caries risk individuals under PCR analysis. Metagenomic analysis showed two-fold statistically increased presence of Lactobacilli and Bifidobacteriaceae (S. wiggsiae) in dentinal samples compared to plaque samples (P = 0.05). Mutans streptococcus recorded the minimum. CONCLUSION Scardovia wiggsiae is identified as one of the predominant microorganism.
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Affiliation(s)
- Roger Derick Isaac
- Department of Conservative Dentistry and Endodontics, Best Dental Science College, Madurai, Tamil Nadu, India
| | - Kavitha Sanjeev
- Department of Conservative Dentistry and Endodontics, SRM Dental College, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India,Address for correspondence: Dr. Kavitha Sanjeev, Department of Conservative Dentistry and Endodontics, SRM Dental College, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India. E-mail:
| | - C. L. Subbulakshmi
- Department of Conservative Dentistry and Endodontics, Karpaga Vinayaga Dental College, Chennai, Tamil Nadu, India
| | - L. Vijay Amirtharaj
- Department of Conservative Dentistry and Endodontics, SRM Dental College, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Mahalaxmi Sekar
- Department of Conservative Dentistry and Endodontics, SRM Dental College, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
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19
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Park T, Im J, Kim AR, Lee D, Jeong S, Yun CH, Han SH. Short-chain fatty acids inhibit the biofilm formation of Streptococcus gordonii through negative regulation of competence-stimulating peptide signaling pathway. J Microbiol 2021; 59:1142-1149. [PMID: 34865199 DOI: 10.1007/s12275-021-1576-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022]
Abstract
Streptococcus gordonii, a Gram-positive commensal bacterium, is an opportunistic pathogen closely related to initiation and progression of various oral diseases, such as periodontitis and dental caries. Its biofilm formation is linked with the development of such diseases by enhanced resistance against antimicrobial treatment or host immunity. In the present study, we investigated the effect of short-chain fatty acids (SCFAs) on the biofilm formation of S. gordonii. SCFAs, including sodium acetate (NaA), sodium propionate (NaP), and sodium butyrate (NaB), showed an effective inhibitory activity on the biofilm formation of S. gordonii without reduction in bacterial growth. SCFAs suppressed S. gordonii biofilm formation at early time points whereas SCFAs did not affect its preformed biofilm. A quorum-sensing system mediated by competence-stimulating peptide (CSP) is known to regulate biofilm formation of streptococci. Interestingly, SCFAs substantially decreased mRNA expression of comD and comE, which are CSP-sensor and its response regulator responsible for CSP pathway, respectively. Although S. gordonii biofilm formation was enhanced by exogenous synthetic CSP treatment, such effect was not observed in the presence of SCFAs. Collectively, these results suggest that SCFAs have an anti-biofilm activity on S. gordonii through inhibiting comD and comE expression which results in negative regulation of CSP quorum-sensing system. SCFAs could be an effective anti-biofilm agent against S. gordonii for the prevention of oral diseases.
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Affiliation(s)
- Taehwan Park
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jintaek Im
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - A Reum Kim
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongwook Lee
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungho Jeong
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea.
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20
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Li B, Liang J, Hanfrey CC, Phillips MA, Michael AJ. Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis. J Biol Chem 2021; 297:101219. [PMID: 34560100 PMCID: PMC8503589 DOI: 10.1016/j.jbc.2021.101219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 11/15/2022] Open
Abstract
Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5'-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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21
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Wu Q, Zhang C, Wa Y, Qu H, Gu R, Chen D, Song Z, Chen X. Correlation between exopolysaccharide biosynthesis and gastrointestinal tolerance of Lactiplantibacillus plantarum. J Appl Microbiol 2021; 132:584-591. [PMID: 34261198 DOI: 10.1111/jam.15213] [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: 05/10/2021] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
AIM This study aimed to investigate the correlation between the level of exopolysaccharide (EPS) biosynthesis and gastrointestinal tolerance of 12 Lactiplantibacillus plantarum strains. METHODS AND RESULTS In this study, the EPS production and survival rate of 12 strains of L. plantarum under gastrointestinal stress were determined. Results showed that the EPS biosynthesis level of L. plantarum in semi-defined medium ranged from 9.84 to 26.05 mg/L. The survival rates of all strains in simulated gastric juice at pH 3.0 ranged from 43.52% to 112.73%. Among them, eight strains were higher than 90%, while only one strain was lower than 50%. The survival rates of all strains in simulated intestinal juice ranged from 50.36% to 125.39%, among which eight strains were higher than 80%. The survival rates of all strains under 0.1% bile salt stress ranged from 3.39% to 109.34%, among which four strains were higher than 80% and three strains were lower than 60%. Besides, the survival rates of all strains under 0.5% bile salt stress ranged from 0.42% to 95.34%. The results indicated that the 12 L. plantarum strains had good tolerance to simulated gastric juice at pH 3.0, simulated intestinal juice and 0.1% bile salt. Notably, it was observed that the survival rates of L. plantarum strains under simulated gastric juice at pH 3.0 and simulated intestinal juice were significantly positively correlated with EPS biosynthesis (p < 0.01). CONCLUSION The yield of EPS of L. plantarum was related to simulated gastric juice and simulated intestinal juice environment. SIGNIFICANCE AND IMPACT OF STUDY It was speculated that the production of EPS may be one of the strategies for L. plantarum to adapt to the part of gastrointestinal environment. In the future, we could analyse the protection mechanism of EPS from the gene level.
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Affiliation(s)
- Qingqing Wu
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Chenchen Zhang
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Yunchao Wa
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Hengxian Qu
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Ruixia Gu
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Dawei Chen
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Zhixin Song
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
| | - Xia Chen
- College of Food Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, China
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22
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Pols T, Singh S, Deelman‐Driessen C, Gaastra BF, Poolman B. Enzymology of the pathway for ATP production by arginine breakdown. FEBS J 2021; 288:293-309. [PMID: 32306469 PMCID: PMC7818446 DOI: 10.1111/febs.15337] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/02/2023]
Abstract
In cells, the breakdown of arginine to ornithine and ammonium ion plus carbon dioxide is coupled to the generation of metabolic energy in the form of ATP. The arginine breakdown pathway is minimally composed of arginine deiminase, ornithine transcarbamoylase, carbamate kinase, and an arginine/ornithine antiporter; ammonia and carbon dioxide most likely diffuse passively across the membrane. The genes for the enzymes and transporter have been cloned and expressed, and the proteins have been purified from Lactococcus lactis IL1403 and incorporated into lipid vesicles for sustained production of ATP. Here, we study the kinetic parameters and biochemical properties of the individual enzymes and the antiporter, and we determine how the physicochemical conditions, effector composition, and effector concentration affect the enzymes. We report the KM and VMAX values for catalysis and the native oligomeric state of all proteins, and we measured the effect of pathway intermediates, pH, temperature, freeze-thaw cycles, and salts on the activity of the cytosolic enzymes. We also present data on the protein-to-lipid ratio and lipid composition dependence of the antiporter.
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Affiliation(s)
- Tjeerd Pols
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Shubham Singh
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Cecile Deelman‐Driessen
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Bauke F. Gaastra
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
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23
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Qiao W, Qiao Y, Liu F, Zhang Y, Li R, Wu Z, Xu H, Saris PEJ, Qiao M. Engineering Lactococcus lactis as a multi-stress tolerant biosynthetic chassis by deleting the prophage-related fragment. Microb Cell Fact 2020; 19:225. [PMID: 33298073 PMCID: PMC7727215 DOI: 10.1186/s12934-020-01487-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/28/2020] [Indexed: 01/02/2023] Open
Abstract
Background In bioengineering, growth of microorganisms is limited because of environmental and industrial stresses during fermentation. This study aimed to construct a nisin-producing chassis Lactococcus lactis strain with genome-streamlined, low metabolic burden, and multi-stress tolerance characteristics. Results The Cre-loxP recombination system was applied to reduce the genome and obtain the target chassis strain. A prophage-related fragment (PRF; 19,739 bp) in the L. lactis N8 genome was deleted, and the mutant strain L. lactis N8-1 was chosen for multi-stress tolerance studies. Nisin immunity of L. lactis N8-1 was increased to 6500 IU/mL, which was 44.44% higher than that of the wild-type L. lactis N8 (4500 IU/mL). The survival rates of L. lactis N8-1 treated with lysozyme for 2 h and lactic acid for 1 h were 1000- and 10,000-fold higher than that of the wild-type strain, respectively. At 39 ℃, the L. lactis N8-1 could still maintain its growth, whereas the growth of the wild-type strain dramatically dropped. Scanning electron microscopy showed that the cell wall integrity of L. lactis N8-1 was well maintained after lysozyme treatment. Tandem mass tags labeled quantitative proteomics revealed that 33 and 9 proteins were significantly upregulated and downregulated, respectively, in L. lactis N8-1. These differential proteins were involved in carbohydrate and energy transport/metabolism, biosynthesis of cell wall and cell surface proteins. Conclusions PRF deletion was proven to be an efficient strategy to achieve multi-stress tolerance and nisin immunity in L. lactis, thereby providing a new perspective for industrially obtaining engineered strains with multi-stress tolerance and expanding the application of lactic acid bacteria in biotechnology and synthetic biology. Besides, the importance of PRF, which can confer vital phenotypes to bacteria, was established.
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Affiliation(s)
- Wanjin Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Yu Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Fulu Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Yating Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Ran Li
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Zhenzhou Wu
- State Key Laboratory of Medicinal Chemical Biology & Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin, China
| | - Haijin Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mingqiang Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
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24
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Park S, Nam EW, Kim Y, Lee S, Kim SI, Yoon H. Transcriptomic Approach for Understanding the Adaptation of Salmonella enterica to Contaminated Produce. J Microbiol Biotechnol 2020; 30:1729-1738. [PMID: 32830190 PMCID: PMC9728351 DOI: 10.4014/jmb.2007.07036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Abstract
Salmonellosis is a form of gastroenteritis caused by Salmonella infection. The main transmission route of salmonellosis has been identified as poorly cooked meat and poultry products contaminated with Salmonella. However, in recent years, the number of outbreaks attributed to contaminated raw produce has increased dramatically. To understand how Salmonella adapts to produce, transcriptomic analysis was conducted on Salmonella enterica serovar Virchow exposed to fresh-cut radish greens. Considering the different Salmonella lifestyles in contact with fresh produce, such as motile and sessile lifestyles, total RNA was extracted from planktonic and epiphytic cells separately. Transcriptomic analysis of S. Virchow cells revealed different transcription profiles between lifestyles. During bacterial adaptation to fresh-cut radish greens, planktonic cells were likely to shift toward anaerobic metabolism, exploiting nitrate as an electron acceptor of anaerobic respiration, and utilizing cobalamin as a cofactor for coupled metabolic pathways. Meanwhile, Salmonella cells adhering to plant surfaces showed coordinated upregulation in genes associated with translation and ribosomal biogenesis, indicating dramatic cellular reprogramming in response to environmental changes. In accordance with the extensive translational response, epiphytic cells showed an increase in the transcription of genes that are important for bacterial motility, nucleotide transporter/metabolism, cell envelope biogenesis, and defense mechanisms. Intriguingly, Salmonella pathogenicity island (SPI)-1 and SPI-2 displayed up- and downregulation, respectively, regardless of lifestyles in contact with the radish greens, suggesting altered Salmonella virulence during adaptation to plant environments. This study provides molecular insights into Salmonella adaptation to plants as an alternative environmental reservoir.
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Affiliation(s)
- Sojung Park
- Department of Molecular Science and Technology, Ajou University, Suwon6499, Republic of Korea
| | - Eun woo Nam
- Department of Molecular Science and Technology, Ajou University, Suwon6499, Republic of Korea
| | - Yeeun Kim
- Department of Molecular Science and Technology, Ajou University, Suwon6499, Republic of Korea
| | - Seohyeon Lee
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon16499 Republic of Korea
| | - Seul I Kim
- Department of Molecular Science and Technology, Ajou University, Suwon6499, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon6499, Republic of Korea,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon16499 Republic of Korea,Corresponding author Phone: +82-31-219-2450 Fax: +82-31-219-1610 E-mail:
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25
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Freiberg JA, Le Breton Y, Harro JM, Allison DL, McIver KS, Shirtliff ME. The Arginine Deiminase Pathway Impacts Antibiotic Tolerance during Biofilm-Mediated Streptococcus pyogenes Infections. mBio 2020; 11:e00919-20. [PMID: 32636245 PMCID: PMC7343988 DOI: 10.1128/mbio.00919-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial biofilms are responsible for a variety of serious human infections and are notoriously difficult to treat due to their recalcitrance to antibiotics. Further work is necessary to elicit a full understanding of the mechanism of this antibiotic tolerance. The arginine deiminase (ADI) pathway is responsible for bacterial pH maintenance and is highly expressed during biofilm growth in multiple bacterial species. Using the group A Streptococcus (GAS) as a model human pathogen, the ADI pathway was demonstrated to contribute to biofilm growth. The inability of antibiotics to reduce GAS populations when in a biofilm was demonstrated by in vitro studies and a novel animal model of nasopharyngeal infection. However, disruption of the ADI pathway returned GAS biofilms to planktonic levels of antibiotic sensitivity, suggesting the ADI pathway is influential in biofilm-related antibiotic treatment failure and provides a new strategic target for the treatment of biofilm infections in GAS and potentially numerous other bacterial species.IMPORTANCE Biofilm-mediated bacterial infections are a major threat to human health because of their recalcitrance to antibiotic treatment. Through the study of Streptococcus pyogenes, a significant human pathogen that is known to form antibiotic-tolerant biofilms, we demonstrated the role that a bacterial pathway known for responding to acid stress plays in biofilm growth and antibiotic tolerance. This not only provides some insight into antibiotic treatment failure in S. pyogenes infections but also, given the widespread nature of this pathway, provides a potentially broad target for antibiofilm therapies. This discovery has the potential to impact the treatment of many different types of recalcitrant biofilm infections.
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Affiliation(s)
- Jeffrey A Freiberg
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Janette M Harro
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Devon L Allison
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Kevin S McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Mark E Shirtliff
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Baltimore, Maryland, USA
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26
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Flores-Tinoco CE, Tschan F, Fuhrer T, Margot C, Sauer U, Christen M, Christen B. Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation. Mol Syst Biol 2020; 16:e9419. [PMID: 32490601 PMCID: PMC7268258 DOI: 10.15252/msb.20199419] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant-provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism-two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCH-N cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.
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Affiliation(s)
| | - Flavia Tschan
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Céline Margot
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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27
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Rakhimuzzaman M, Noda M, Danshiitsoodol N, Sugiyama M. Development of a System of High Ornithine and Citrulline Production by a Plant-Derived Lactic Acid Bacterium, Weissella confusa K-28. Biol Pharm Bull 2019; 42:1581-1589. [PMID: 31474718 DOI: 10.1248/bpb.b19-00410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As a bacterium used in industry for production of several amino acids, an endotoxin-free Corynebacterium (C.) glutamicum is well known. However, it is also true that the endotoxin-producing other Corynebacterium species is present. An aim of this study is to obtain a lactic acid bacterium (LAB) that produces ornithine and citrulline at high levels. We successfully isolated a strain, designated K-28, and identified it as Weissella (W.) confusa. The production of ornithine and citrulline by K-28 was 18 ± 1 and 10 ± 2 g/L, respectively, with a 100 ± 9% conversion rate when arginine was continuously fed into a jar fermenter. Although the ornithine high production using C. glutamicum is industrially present, the strains have been genetically modified. In that connection, the wild-type of C. glutamicum produces only 0.5 g/L ornithine, indicating that W. confusa K-28 is superior to C. glutamicum to use a probiotic microorganism. We confirmed that W. confusa K-28 harbors an arginine deiminase (ADI) gene cluster, wkaABDCR. The production of ornithine and the expression of these genes significantly decreased under the aerobic condition rather than anaerobic one. The expression level of the five genes did not differ with or without arginine, suggesting that the production of amino acids in the K-28 strain was not induced by exogenous arginine.
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Affiliation(s)
- Md Rakhimuzzaman
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Masafumi Noda
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Narandalai Danshiitsoodol
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Masanori Sugiyama
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
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28
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Billard-Pomares T, Clermont O, Castellanos M, Magdoud F, Royer G, Condamine B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Pognard D, Glodt J, Dion S, Rigal O, Picard B, Denamur E, Branger C. The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli. Antimicrob Agents Chemother 2019; 63:e00635-19. [PMID: 31138573 PMCID: PMC6658758 DOI: 10.1128/aac.00635-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023] Open
Abstract
We previously identified an operon involved in an arginine deiminase (ADI) pathway (arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-β-lactamase (ESBL)-producing E. coli strains. We studied two collections of human E. coli isolated in France (n = 493) and England (n = 1,509) and show that the prevalence of the arc operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.5%), (ii) is higher in CTX-M-producing strains (16%) than in other ESBL producers (3.5%), and (iii) increased over time in ESBL-producing strains from 0% before 2000 to 43.3% in 2011 to 2012. The arc operon, found in strains from various phylogenetic backgrounds, is carried by IncF plasmids (85%) or chromosomes (15%) in regions framed by numerous insertion sequences, indicating multiple arrivals. Competition experiments showed that the arc operon enhances fitness of the strain in vitro in lysogeny broth with arginine. In vivo competition experiments showed that the arc operon is advantageous for the strain in a mouse model of urinary tract infection (UTI), whereas it is a burden in a mouse model of intestinal colonization. In summary, we have identified a trait linked to CTX-M-producing strains that is responsible for a trade-off between two main E. coli lifestyles, UTI and gut commensalism. This trait alone cannot explain the wide spread of ESBLs in E. coli but merits epidemiological surveillance.
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Affiliation(s)
- Typhaine Billard-Pomares
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Olivier Clermont
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Miguel Castellanos
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Fatma Magdoud
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Guilhem Royer
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Bénédicte Condamine
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Stéphane Cruveiller
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Claudine Médigue
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Dominique Pognard
- APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France
| | - Jeremy Glodt
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France
| | - Sara Dion
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Odile Rigal
- Service de Biochimie-Hormonologie, Hôpital Robert Debré, Paris, France
| | - Bertrand Picard
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Erick Denamur
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Catherine Branger
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
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Adaptation to Adversity: the Intermingling of Stress Tolerance and Pathogenesis in Enterococci. Microbiol Mol Biol Rev 2019; 83:83/3/e00008-19. [PMID: 31315902 DOI: 10.1128/mmbr.00008-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enterococcus is a diverse and rugged genus colonizing the gastrointestinal tract of humans and numerous hosts across the animal kingdom. Enterococci are also a leading cause of multidrug-resistant hospital-acquired infections. In each of these settings, enterococci must contend with changing biophysical landscapes and innate immune responses in order to successfully colonize and transit between hosts. Therefore, it appears that the intrinsic durability that evolved to make enterococci optimally competitive in the host gastrointestinal tract also ideally positioned them to persist in hospitals, despite disinfection protocols, and acquire new antibiotic resistances from other microbes. Here, we discuss the molecular mechanisms and regulation employed by enterococci to tolerate diverse stressors and highlight the role of stress tolerance in the biology of this medically relevant genus.
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30
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Hilgarth M, Lehner E, Behr J, Vogel R. Diversity and anaerobic growth ofPseudomonasspp. isolated from modified atmosphere packaged minced beef. J Appl Microbiol 2019; 127:159-174. [DOI: 10.1111/jam.14249] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/29/2022]
Affiliation(s)
- M. Hilgarth
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - E.M. Lehner
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - J. Behr
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - R.F. Vogel
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
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31
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Marques Da Silva W, Oliveira LC, Soares SC, Sousa CS, Tavares GC, Resende CP, Pereira FL, Ghosh P, Figueiredo H, Azevedo V. Quantitative Proteomic Analysis of the Response of Probiotic Putative Lactococcus lactis NCDO 2118 Strain to Different Oxygen Availability Under Temperature Variation. Front Microbiol 2019; 10:759. [PMID: 31031733 PMCID: PMC6470185 DOI: 10.3389/fmicb.2019.00759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
Lactococcus lactis is a gram positive facultative anaerobe widely used in the dairy industry and human health. L. lactis subsp. lactis NCDO 2118 is a strain that exhibits anti-inflammatory and immunomodulatory properties. In this study, we applied a label-free shotgun proteomic approach to characterize and quantify the NCDO 2118 proteome in response to variations of temperature and oxygen bioavailability, which constitute the environmental conditions found by this bacterium during its passage through the host gastro-intestinal tract and in other industrial processes. From this proteomic analysis, a total of 1,284 non-redundant proteins of NCDO 2118 were characterized, which correspond to approximately 54% of its predicted proteome. Comparative proteomic analysis identified 149 and 136 proteins in anaerobic (30°C and 37°C) and non-aerated (30°C and 37°C) conditions, respectively. Our label-free proteomic analysis quantified a total of 1,239 proteins amongst which 161 proteins were statistically differentially expressed. Main differences were observed in cellular metabolism, stress response, transcription and proteins associated to cell wall. In addition, we identified six strain-specific proteins of NCDO 2118. Altogether, the results obtained in our study will help to improve the understanding about the factors related to both physiology and adaptive processes of L. lactis NCDO 2118 under changing environmental conditions.
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Affiliation(s)
- Wanderson Marques Da Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leticia Castro Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | - Siomar Castro Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | - Cassiana Severiano Sousa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Felipe Luis Pereira
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Henrique Figueiredo
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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32
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Girardeau A, Puentes C, Keravec S, Peteuil P, Trelea IC, Fonseca F. Influence of culture conditions on the technological properties of Carnobacterium maltaromaticum CNCM I-3298 starters. J Appl Microbiol 2019; 126:1468-1479. [PMID: 30762266 DOI: 10.1111/jam.14223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 11/29/2022]
Abstract
AIM The aim of this study is to investigate the effect of a broad spectrum of culture conditions on the acidification activity and viability of Carnobacterium maltaromaticum CNCM I-3298, the main technological properties that determine the shelf-life of biological time-temperature integrator (TTI) labels. METHODS AND RESULTS Cells were cultivated at different temperatures (20-37°C) and pH (6-9·5) according to a modified central composite design and harvested at increasing times up to 10 h of stationary phase. Acidification activity and viability of freeze-thawed concentrates were assessed in medium mimicking the biological label. Acidification activity was influenced by all three culture conditions, but pH and harvest time were the most influential. Viability was not significantly affected by the tested range of culture conditions. CONCLUSIONS Carnobacterium maltaromaticum CNCM I-3298 must be cultivated at 20°C, pH 6 and harvested at the beginning of stationary phase to exhibit fastest acidification activities. However, if slower acidification activities are pursued, the recommended culture conditions are 30°C, pH 9·5 and a harvest time between 4-6 h of stationary phase. SIGNIFICANCE AND IMPACT OF THE STUDY Quantifying the impact of fermentation temperature, pH and harvest time has led to a predictive model for the production of biological TTI covering a broad range of shelf-lives.
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Affiliation(s)
- A Girardeau
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France.,CRYOLOG, R&D Department, Nantes, France
| | - C Puentes
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - S Keravec
- CRYOLOG, R&D Department, Nantes, France
| | - P Peteuil
- CRYOLOG, R&D Department, Nantes, France
| | - I C Trelea
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - F Fonseca
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
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Starikova EA, Golovin AS, Vasilyev KA, Karaseva AB, Serebriakova MK, Sokolov AV, Kudryavtsev IV, Burova LA, Voynova IV, Suvorov AN, Vasilyev VB, Freidlin IS. Role of arginine deiminase in thymic atrophy during experimental Streptococcus pyogenes infection. Scand J Immunol 2019; 89:e12734. [PMID: 30471128 DOI: 10.1111/sji.12734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/11/2018] [Accepted: 11/18/2018] [Indexed: 01/08/2023]
Abstract
Expression of gene of arginine deiminase (AD) allows adaptation of Streptococcus pyogenes to adverse environmental conditions. AD activity can lead to L-arginine deficiency in the host cells' microenvironment. Bioavailability of L-arginine is an important factor regulating the functions of the immune cells in mammals. By introducing a mutation into S pyogenes M46-16, we obtained a strain with inactivated arcA/sagp gene (M49-16 delArcA), deficient in AD. This allowed elucidating the function of AD in pathogenesis of streptococcal infection. The virulence of the parental and mutant strains was examined in a murine model of subcutaneous streptococcal infection. L-arginine concentration in the plasma of mice infected with S pyogenes M49-16 delArcA remained unchanged in course of the entire experiment. At the same time mice infected with S pyogenes M49-16 demonstrated gradual diminution of L-arginine concentration in the blood plasma, which might be due to the activity of streptococcal AD. Mice infected with S pyogenes M49-16 delArcA demonstrated less intensive bacterial growth in the primary foci and less pronounced bacterial dissemination as compared with animals infected with the parental strain S pyogenes M46-16. Similarly, thymus involution, alterations in apoptosis, thymocyte subsets and Treg cells differentiation were less pronounced in mice infected with S pyogenes M49-16 delArcA than in those infected with the parental strain. The results obtained showed that S pyogenes M49-16 delArcA, unable to produce AD, had reduced virulence in comparison with the parental S pyogenes M49-16 strain. AD is an important factor for the realization of the pathogenic potential of streptococci.
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Affiliation(s)
| | | | | | - Alena Borisovna Karaseva
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia
| | | | - Alexey Victorovich Sokolov
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Igor Vladimirovich Kudryavtsev
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Far Eastern Federal University Vladivostok, Russia
| | | | - Irina Vitalyevna Voynova
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia
| | - Alexander Nikolaevich Suvorov
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Vadim Borisovich Vasilyev
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Irina Solomonovna Freidlin
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia.,Pavlov First Saint-Petersburg State Medical University, St. Petersburg, Russia
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Zarei M, Rahbar MR, Morowvat MH, Nezafat N, Negahdaripour M, Berenjian A, Ghasemi Y. Arginine Deiminase: Current Understanding and Applications. Recent Pat Biotechnol 2019; 13:124-136. [PMID: 30569861 DOI: 10.2174/1872208313666181220121400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/07/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Arginine deiminase (ADI), an arginine catabolizing enzyme, is considered as an anti-tumor agent for the treatment of arginine auxotrophic cancers. However, some obstacles limit its clinical applications. OBJECTIVE This review will summarize the clinical applications of ADI, from a brief history to its limitations, and will discuss the different ways to deal with the clinical limitations. METHOD The structure analysis, cloning, expression, protein engineering and applications of arginine deiminase enzyme have been explained in this review. CONCLUSION Recent patents on ADI are related to ADI engineering to increase its efficacy for clinical application. The intracellular delivery of ADI and combination therapy seem to be the future strategies in the treatment of arginine auxotrophic cancers. Applying ADIs with optimum features from different sources and or ADI engineering, are promising strategies to improve the clinical application of ADI.
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Affiliation(s)
- Mahboubeh Zarei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aydin Berenjian
- School of Engineering, Faculty of Science & Engineering, The University of Waikato, Hamilton, New Zealand
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Corrêa MG, Pires PR, Ribeiro FV, Pimentel SP, Cirano FR, Napimoga MH, Casati MZ, Casarin RCV. Systemic treatment with resveratrol reduces the progression of experimental periodontitis and arthritis in rats. PLoS One 2018; 13:e0204414. [PMID: 30281626 PMCID: PMC6169914 DOI: 10.1371/journal.pone.0204414] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/07/2018] [Indexed: 11/18/2022] Open
Abstract
Rheumatoid arthritis and periodontitis are chronic inflammatory diseases which has been closely associated due to the nature of immune-inflammatory imbalance response. Resveratrol is a naturall product with biological proprieties that may promote immunomodulatory effects on host response. This study investigated resveratrol continuous administration effect on experimental periodontitis and arthritis progression in rats. Thirty-five rats were assigned to the following groups: 1-experimental arthritis + experimental periodontitis + placebo (RA+EP +PL) (n = 12); 2 -RA+EP+ ibuprofen (RA+PE+IB) (n = 11); 3-RA+EP+ resveratrol (RA+PE+RSV) (n = 11). After euthanasia, the specimens were processed for morphometric analysis of bone loss, and the gingival tissue surrounding the first molar was collected for quantification of inflammatory markers using a Luminex/MAGpix assay and anti-citrullinated protein antibody (ACCPA) levels were measured by ELISA assay. Serum level of rheumatoid factor (RF) was measured by ELISA assay. Paw edema was analyzed using a plethysmometer. Higher bone loss was observed in PL group, when compared to IB and RSV groups. RSV group presented higher IL-4 concentration than PL and IB groups. Resveratrol reduced RF serum levels and both IB and RSV decreased ACCPA gingival levels. Besides, paw swelling level was significantly lower in IB and RSV groups in the 21th day and only in RSV group in the 28th day. Histological analyzes showed smooth articular surface and higher width of the subchondral cortical in RSV group. Resveratrol showed modulatory effect and seems to reduce the inflammatory signs of arthritis and articular damage throughout the time.
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Affiliation(s)
- Mônica G. Corrêa
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Paula Rodrigues Pires
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Fernanda Vieira Ribeiro
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Suzana Peres Pimentel
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Fabiano Ribeiro Cirano
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Marcelo Henrique Napimoga
- Laboratory of Immunology and Molecular Biology, São Leopoldo Mandic Institute and Research Center, Campinas, SP, Brazil
| | - Marcio Z. Casati
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
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Hill D, Sugrue I, Tobin C, Hill C, Stanton C, Ross RP. The Lactobacillus casei Group: History and Health Related Applications. Front Microbiol 2018; 9:2107. [PMID: 30298055 PMCID: PMC6160870 DOI: 10.3389/fmicb.2018.02107] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/20/2018] [Indexed: 01/16/2023] Open
Abstract
The Lactobacillus casei group (LCG), composed of the closely related Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are some of the most widely researched and applied probiotic species of lactobacilli. The three species have been extensively studied, classified and reclassified due to their health promoting properties. Differentiation is often difficult by conventional phenotypic and genotypic methods and therefore new methods are being continually developed to distinguish the three closely related species. The group remain of interest as probiotics, and their use is widespread in industry. Much research has focused in recent years on their application for health promotion in treatment or prevention of a number of diseases and disorders. The LCG have the potential to be used prophylactically or therapeutically in diseases associated with a disturbance to the gut microbiota. The group have been extensively researched with regard to stress responses, which are crucial for their survival and therefore application as probiotics.
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Affiliation(s)
- Daragh Hill
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.,Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Ivan Sugrue
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Tobin
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc, Moorepark, Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
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Wu H, Zhao Y, Du Y, Miao S, Liu J, Li Y, Caiyin Q, Qiao J. Quantitative proteomics of Lactococcus lactis F44 under cross-stress of low pH and lactate. J Dairy Sci 2018; 101:6872-6884. [DOI: 10.3168/jds.2018-14594] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
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Redanz S, Cheng X, Giacaman RA, Pfeifer CS, Merritt J, Kreth J. Live and let die: Hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome. Mol Oral Microbiol 2018; 33:337-352. [PMID: 29897662 DOI: 10.1111/omi.12231] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2018] [Indexed: 02/05/2023]
Abstract
The majority of commensal oral streptococci are able to generate hydrogen peroxide (H2 O2 ) during aerobic growth, which can diffuse through the cell membrane and inhibit competing species in close proximity. Competing H2 O2 production is mainly dependent upon the pyruvate oxidase SpxB, and to a lesser extent the lactate oxidase LctO, both of which are important for energy generation in aerobic environments. Several studies point to a broad impact of H2 O2 production in the oral environment, including a potential role in biofilm homeostasis, signaling, and interspecies interactions. Here, we summarize the current research regarding oral streptococcal H2 O2 generation, resistance mechanisms, and the ecological impact of H2 O2 production. We also discuss the potential therapeutic utility of H2 O2 for the prevention/treatment of dysbiotic diseases as well as its potential role as a biomarker of oral health.
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Affiliation(s)
- Sylvio Redanz
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Xingqun Cheng
- The State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,The Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rodrigo A Giacaman
- Cariology Unit, Department of Oral Rehabilitation and Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), University of Talca, Talca, Chile
| | - Carmen S Pfeifer
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, Oregon
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Majsnerowska M, Noens EEE, Lolkema JS. Arginine and Citrulline Catabolic Pathways Encoded by the arc Gene Cluster of Lactobacillus brevis ATCC 367. J Bacteriol 2018; 200:e00182-18. [PMID: 29712874 PMCID: PMC6018368 DOI: 10.1128/jb.00182-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/23/2018] [Indexed: 01/25/2023] Open
Abstract
High concentrations of l-arginine or l-citrulline in the growth medium provided the wine bacterium Lactobacillus brevis with a significant growth advantage. The arginine deiminase pathway (ADI) arc gene cluster of Lactobacillus brevis contains three genes-arcD, arcE1, and arcE2-encoding putative l-arginine/l-ornithine exchangers. Uptake experiments with Lactococcus lactis cells expressing the genes showed that all three transported l-ornithine with affinities in the micromolar range. Similarly, ArcD and ArcE2 transported l-arginine, while ArcE1 transported l-citrulline, an intermediate of the ADI pathway. Chase experiments showed very efficient exchange of l-arginine and l-ornithine by ArcD and ArcE2 and of l-citrulline and l-ornithine by ArcE1. Low affinities (millimolar range) combined with low translocation rates were found for ArcD and ArcE2 with l-citrulline and for ArcE1 with l-arginine. Resting cells of Lactobacillus brevis grown in the presence of l-arginine and l-citrulline rapidly consumed l-arginine and l-citrulline, respectively, while producing ammonia and l-ornithine. About 10% of l-arginine degraded was excreted by the cells as l-citrulline. Degradation of l-arginine and l-citrulline was not subject to carbon catabolite repression by glucose in the medium. At a high medium pH, l-citrulline in the medium was required for induction of the l-citrulline degradation pathway. Pathways are proposed for the catabolic breakdown of l-arginine and l-citrulline that merge at the level of ornithine transcarbamylase in the ADI pathway. l-Arginine uptake is catalyzed by ArcD and/or ArcE2, l-citrulline by ArcE1. l-Citrulline excretion during l-arginine breakdown is proposed to be catalyzed by ArcD and/or ArcE2 through l-arginine/l-citrulline exchange.IMPORTANCELactobacillus brevis, a bacterium isolated from wine, as well as other food environments, expresses a catabolic pathway for the breakdown of l-citrulline in the medium that consists of the l-citrulline/l-ornithine exchanger ArcE1 and part of the catabolic arginine deiminase (ADI) pathway enzymes. The proposed pathways for l-arginine and l-citrulline breakdown provide a mechanism for l-citrulline accumulation in fermented food products that is the precursor of the carcinogen ethyl carbamate.
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Affiliation(s)
- Maria Majsnerowska
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Elke E E Noens
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Juke S Lolkema
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Free lactic acid production under acidic conditions by lactic acid bacteria strains: challenges and future prospects. Appl Microbiol Biotechnol 2018; 102:5911-5924. [DOI: 10.1007/s00253-018-9092-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 11/27/2022]
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Dulebohn DP, Richards CL, Su H, Lawrence KA, Gherardini FC. Weak Organic Acids Decrease Borrelia burgdorferi Cytoplasmic pH, Eliciting an Acid Stress Response and Impacting RpoN- and RpoS-Dependent Gene Expression. Front Microbiol 2017; 8:1734. [PMID: 29033900 PMCID: PMC5626856 DOI: 10.3389/fmicb.2017.01734] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/25/2017] [Indexed: 11/23/2022] Open
Abstract
The spirochete Borrelia burgdorferi survives in its tick vector, Ixodes scapularis, or within various hosts. To transition between and survive in these distinct niches, B. burgdorferi changes its gene expression in response to environmental cues, both biochemical and physiological. Exposure of B. burgdorferi to weak monocarboxylic organic acids, including those detected in the blood meal of fed ticks, decreased the cytoplasmic pH of B. burgdorferi in vitro. A decrease in the cytoplasmic pH induced the expression of genes encoding enzymes that have been shown to restore pH homeostasis in other bacteria. These include putative coupled proton/cation exchangers, a putative Na+/H+ antiporter, a neutralizing buffer transporter, an amino acid deaminase and a proton exporting vacuolar-type VoV1 ATPase. Data presented in this report suggested that the acid stress response triggered the expression of RpoN- and RpoS-dependent genes including important virulence factors such as outer surface protein C (OspC), BBA66, and some BosR (Borreliaoxidative stress regulator)-dependent genes. Because the expression of virulence factors, like OspC, are so tightly connected by RpoS to general cellular stress responses and cell physiology, it is difficult to separate transmission-promoting conditions in what is clearly a multifactorial and complex regulatory web.
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Affiliation(s)
- Daniel P Dulebohn
- Laboratory of Zoonotic Pathogens, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Crystal L Richards
- Laboratory of Zoonotic Pathogens, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Hua Su
- Laboratory of Zoonotic Pathogens, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kevin A Lawrence
- Laboratory of Zoonotic Pathogens, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Frank C Gherardini
- Laboratory of Zoonotic Pathogens, Gene Regulation Section, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
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42
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Arginine Exposure Decreases Acidogenesis in Long-Term Oral Biofilm Microcosms. mSphere 2017; 2:mSphere00295-17. [PMID: 28861520 PMCID: PMC5566835 DOI: 10.1128/msphere.00295-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
Arginine is used in dental health formulations to help prevent dental cavities. This study assessed the effects of the long-term dosing of laboratory dental plaques with an arginine dentifrice. Data indicate that the addition of arginine dentifrice during sucrose challenge significantly increased plaque pH, thus potentially mitigating cariogenesis. Several functional groups of bacteria associated with tooth decay were significantly decreased in the laboratory plaques during exposure to the arginine dentifrice. Arginine is an important pH-elevating agent in the oral cavity. It has been incorporated in oral hygiene formulations to mitigate sensitivity and to prevent caries. In this investigation, the effects of sustained arginine dosing of dental plaque microcosms on bacteriological composition and pH were evaluated under controlled conditions. Plaque microcosms were established in constant-depth film fermentors (CDFFs) using salivary inocula and fed continuously with artificial saliva. To simulate resting and cariogenic states, the CDFFs were supplemented with sterile water or 5% sucrose, respectively. Plaques were then dosed twice daily with a dentifrice with 1.5% arginine arginine added (DA) or without arginine (DN). This regimen continued for over 3 weeks, after which fermentors were maintained without dosing. Microcosms were analyzed by differential viable counting, with a pH microelectrode, and by eubacterial DNA profiling. Sucrose dosing was associated with significantly (P < 0.001) decreased pH, significantly (P < 0.05) increased counts of total aerobes, Gram-negative anaerobes, aciduric species, acidogenic species, arginine utilizing species, bifidobacteria, lactobacilli and streptococci, and significant (P < 0.05) changes in DNA profiles. Plaques dosed with DA had a significantly (P < 0.001) higher pH than those dosed with DN, with or without sucrose supplementation. Dosing with DA but not DN significantly (P < 0.05) decreased counts of all functional bacterial groups apart from the total anaerobes in cariogenic plaques, and in resting plaques, dosing with DA significantly (P < 0.05) decreased counts of streptococci, lactobacilli, bifidobacteria, and acidogenic bacteria. In summary, sustained exposure of oral microcosms to arginine in formulation significantly increased plaque pH and significantly reduced the viability of cariogenic bacterial species. IMPORTANCE Arginine is used in dental health formulations to help prevent dental cavities. This study assessed the effects of the long-term dosing of laboratory dental plaques with an arginine dentifrice. Data indicate that the addition of arginine dentifrice during sucrose challenge significantly increased plaque pH, thus potentially mitigating cariogenesis. Counts of several functional groups of bacteria associated with tooth decay were significantly decreased in the laboratory plaques during exposure to the arginine dentifrice.
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Geraldeli S, Soares EF, Alvarez AJ, Farivar T, Shields RC, Sinhoreti MAC, Nascimento MM. A new arginine-based dental adhesive system: formulation, mechanical and anti-caries properties. J Dent 2017; 63:72-80. [PMID: 28587978 DOI: 10.1016/j.jdent.2017.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/27/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022] Open
Abstract
Secondary caries at the margins of composite restorations has been attributed to adhesive failure and consequent accumulation of cariogenic biofilms. OBJECTIVES To develop and evaluate an etch-and-rinse adhesive system containing arginine for sustainable release and recharge without affecting its mechanical properties. Arginine metabolism by oral bacteria generates ammonia, which neutralizes glycolytic acids and creates a neutral environmental pH that is less favorable to the growth of caries pathogens, thus reducing the caries risk at the tooth-composite interface. METHODS Experimental adhesives were formulated with methacrylate monomers and arginine at 5%, 7%, and 10% or no arginine (control). Adhesives were tested for: (i) mechanical properties of true stress (FS and UTS), modulus of elasticity (E), degree of conversion (DC), Knoop hardness number (KHN) and dentin microtensile bond strength (μ-TBS), (ii) arginine release and recharge, and (iii) antibacterial activities. Data was analyzed by t-test, one-way ANOVA and Tukey's tests. RESULTS FS and UTS results showed no statistically significant differences between the 7% arginine-adhesive and control, while the results for E, DC, KHN and μ-TBS showed no difference among all groups. The 7% arginine-adhesive showed a high release rate of arginine (75.0μmol/cm2) at 2h, and a more sustainable, controlled release rate (up to 0.2μmol/cm2) at 30days. CONCLUSIONS Incorporation of 7% arginine did not affect the physical and mechanical properties of the adhesive. Arginine was released from the adhesive at a rate and concentration that exhibited antibacterial effects, regardless of shifts in biofilm conditions such as sugar availability and pH. CLINICAL SIGNIFICANCE Secondary caries is recognized as the main reason for failure of dental restorations. The development of an arginine-based adhesive system has the potential to dramatically reduce the incidence and severity of secondary caries in adhesive restorations in a very economical fashion.
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Affiliation(s)
- Saulo Geraldeli
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Eveline F Soares
- Department of Restorative Dentistry, Dental Materials Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Andres J Alvarez
- College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Tanaz Farivar
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Robert C Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Mario A C Sinhoreti
- Department of Restorative Dentistry, Dental Materials Division, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Marcelle M Nascimento
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, Gainesville, FL, USA.
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Nascimento MM, Zaura E, Mira A, Takahashi N, Ten Cate JM. Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment. J Dent Res 2017; 96:733-740. [PMID: 28384412 DOI: 10.1177/0022034517701902] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries. For example, the determination of complete bacterial microbiomes of oral samples rather than selected species, together with oral metatranscriptome and metabolome analyses, supports the viewpoint of dysbiosis of the supragingival biofilms. In addition, metabolome studies have been instrumental in disclosing the contributions of major pathways for central carbon and amino acid metabolisms to biofilm pH homeostasis. New, often noncultured, oral streptococci have been identified, and their phenotypic characterization has revealed candidates for probiotic therapy. Although findings from OMICS research have been greatly informative, problems related to study design, data quality, integration, and reproducibility still need to be addressed. Also, the emergence and continuous updates of these computationally demanding technologies require expertise in advanced bioinformatics for reliable interpretation of data. Despite the obstacles cited above, OMICS research is expected to encourage the discovery of novel caries biomarkers and the development of next-generation diagnostics and therapies for caries control. These observations apply equally to the study of other oral diseases.
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Affiliation(s)
- M M Nascimento
- 1 Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - E Zaura
- 2 Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - A Mira
- 3 Department of Health & Genomics, Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain
| | - N Takahashi
- 4 Department of Oral Biology, Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - J M Ten Cate
- 5 Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, the Netherlands
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45
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Corrêa MG, Sacchetti SB, Ribeiro FV, Pimentel SP, Casarin RCV, Cirano FR, Casati MZ. Periodontitis increases rheumatic factor serum levels and citrullinated proteins in gingival tissues and alter cytokine balance in arthritic rats. PLoS One 2017; 12:e0174442. [PMID: 28358812 PMCID: PMC5373534 DOI: 10.1371/journal.pone.0174442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 03/09/2017] [Indexed: 01/10/2023] Open
Abstract
This study investigated some immunological features by experimental periodontitis (EP) and rheumatoid arthritis (RA) disease interact in destructive processes in arthritic rats. Rats were assigned to the following groups: EP +RA; RA; EP; and Negative Control. RA was induced by immunizations with type-II collagen and a local immunization with Complete Freund's adjuvant in the paw. Periodontitis was induced by ligating the right first molars. The serum level of rheumatoid factor (RF) and anti-citrullinated protein antibody (ACCPA) were measured before the induction of EP (T1) and at 28 days after (T2) by ELISA assay. ACCPA levels were also measured in the gingival tissue at T2. The specimens were processed for morphometric analysis of bone loss, and the gingival tissue surrounding the first molar was collected for the quantification of interleukin IL-1β, IL-4, IL-6, IL-17 and TNF-α using a Luminex/MAGpix assay. Paw edema was analyzed using a plethysmometer. Periodontitis increased the RF and ACCPA levels in the serum and in the gingival tissue, respectively. Besides, the level of paw swelling was increased by EP and remained in progress until the end of the experiment, when EP was associated with RA. Greater values of IL-17 were observed only when RA was present, in spite of PE. It can be concluded that periodontitis increases rheumatic factor serum levels and citrullinated proteins level in gingival tissues and alter cytokine balance in arthritic rats; at the same time, arthritis increases periodontal destruction, confirming the bidirectional interaction between diseases.
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Affiliation(s)
- Mônica G. Corrêa
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Silvana B. Sacchetti
- Pediatric Rheumatology Unit, Pediatric Rheumatology Unit, Santa Casa de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Vieira Ribeiro
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Suzana Peres Pimentel
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | | | - Fabiano Ribeiro Cirano
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
| | - Marcio Z. Casati
- Dental Research Division, School of Dentistry, Paulista University, São Paulo, São Paulo, Brazil
- * E-mail:
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46
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Noens EEE, Lolkema JS. Convergent evolution of the arginine deiminase pathway: the ArcD and ArcE arginine/ornithine exchangers. Microbiologyopen 2017; 6:e00412. [PMID: 27804281 PMCID: PMC5300872 DOI: 10.1002/mbo3.412] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 11/10/2022] Open
Abstract
The arginine deiminase (ADI) pathway converts L-arginine into L-ornithine and yields 1 mol of ATP per mol of L-arginine consumed. The L-arginine/L-ornithine exchanger in the pathway takes up L-arginine and excretes L-ornithine from the cytoplasm. Analysis of the genomes of 1281 bacterial species revealed the presence of 124 arc gene clusters encoding the pathway. About half of the clusters contained the gene encoding the well-studied L-arginine/L-ornithine exchanger ArcD, while the other half contained a gene, termed here arcE, encoding a membrane protein that is not a homolog of ArcD. The arcE gene product of Streptococcus pneumoniae was shown to take up L-arginine and L-ornithine with affinities of 0.6 and 1 μmol/L, respectively, and to catalyze metabolic energy-independent, electroneutral exchange. ArcE of S. pneumoniae could replace ArcD in the ADI pathway of Lactococcus lactis and provided the cells with a growth advantage. In contrast to ArcD, ArcE catalyzed translocation of the pathway intermediate L-citrulline with high efficiency. A short version of the ADI pathway is proposed for L-citrulline catabolism and the presence of the evolutionary unrelated arcD and arcE genes in different organisms is discussed in the context of the evolution of the ADI pathway.
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Affiliation(s)
- Elke E. E. Noens
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Juke S. Lolkema
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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47
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Cheng C, Dong Z, Han X, Sun J, Wang H, Jiang L, Yang Y, Ma T, Chen Z, Yu J, Fang W, Song H. Listeria monocytogenes 10403S Arginine Repressor ArgR Finely Tunes Arginine Metabolism Regulation under Acidic Conditions. Front Microbiol 2017; 8:145. [PMID: 28217122 PMCID: PMC5291005 DOI: 10.3389/fmicb.2017.00145] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/19/2017] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is able to colonize human and animal intestinal tracts and to subsequently cross the intestinal barrier, causing systemic infection. For successful establishment of infection, L. monocytogenes must survive the low pH environment of the stomach. L. monocytogenes encodes a functional ArgR, a transcriptional regulator belonging to the ArgR/AhrC arginine repressor family. We aimed at clarifying the specific functions of ArgR in arginine metabolism regulation, and more importantly, in acid tolerance of L. monocytogenes. We showed that ArgR in the presence of 10 mM arginine represses transcription and expression of the argGH and argCJBDF operons, indicating that L. monocytogenes ArgR plays the classical role of ArgR/AhrC family proteins in feedback inhibition of the arginine biosynthetic pathway. Notably, transcription and expression of arcA (encoding arginine deiminase) and sigB (encoding an alternative sigma factor B) were also markedly repressed by ArgR when bacteria were exposed to pH 5.5 in the absence of arginine. However, addition of arginine enabled ArgR to derepress the transcription and expression of these two genes. Electrophoretic mobility shift assays showed that ArgR binds to the putative ARG boxes in the promoter regions of argC, argG, arcA, and sigB. Reporter gene analysis with gfp under control of the argG promoter demonstrated that ArgR was able to activate the argG promoter. Unexpectedly, deletion of argR significantly increased bacterial survival in BHI medium adjusted to pH 3.5 with lactic acid. We conclude that this phenomenon is due to activation of arcA and sigB. Collectively, our results show that L. monocytogenes ArgR finely tunes arginine metabolism through negative transcriptional regulation of the arginine biosynthetic operons and of the catabolic arcA gene in an arginine-independent manner during lactic acid-induced acid stress. ArgR also appears to activate catabolism as well as sigB transcription by anti-repression in an arginine-dependent way.
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Affiliation(s)
- Changyong Cheng
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Zhimei Dong
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Xiao Han
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Jing Sun
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Hang Wang
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Li Jiang
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Yongchun Yang
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Tiantian Ma
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Zhongwei Chen
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Jing Yu
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
| | - Weihuan Fang
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F UniversityLin'an, China; Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang UniversityHangzhou, China
| | - Houhui Song
- College of Animal Science and Technology, China-Australia Joint-Laboratory for Animal Health Big Data Analytics, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang A&F University Lin'an, China
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Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016; 16:197. [PMID: 27716026 PMCID: PMC5052871 DOI: 10.1186/s12862-016-0771-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
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Affiliation(s)
- Lukáš Novák
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Anna Karnkowska
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Courtney W. Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | | | | | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ivan Čepička
- Department of Zoology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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49
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Koopman JE, Hoogenkamp MA, Buijs MJ, Brandt BW, Keijser BJF, Crielaard W, Ten Cate JM, Zaura E. Changes in the oral ecosystem induced by the use of 8% arginine toothpaste. Arch Oral Biol 2016; 73:79-87. [PMID: 27697693 DOI: 10.1016/j.archoralbio.2016.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 09/02/2016] [Accepted: 09/24/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Bacterial metabolism of arginine in the oral cavity has a pH-raising and thus, potential anti-caries effect. However, the influence of arginine on the oral microbial ecosystem remains largely unresolved. DESIGN In this pilot study, nine healthy individuals used toothpaste containing 8% arginine for eight weeks. Saliva was collected to determine arginolytic potential and sucrose metabolic activity at the Baseline, Week 4, Week 8 and after a two weeks Wash-out period. To follow the effects on microbial ecology, 16S rDNA sequencing on saliva and plaque samples at Baseline and Week 8 and metagenome sequencing on selected saliva samples of the same time-points was performed. RESULTS During the study period, the arginolytic potential of saliva increased, while the sucrose metabolism in saliva decreased. These effects were reversed during the Wash-out period. Although a few operational taxonomic units (OTUs) in plaque changed in abundance during the study period, there was no real shift in the plaque microbiome. In the saliva microbiome there was a significant compositional shift, specifically the genus Veillonella had increased significantly in abundance at Week 8. CONCLUSION Indeed, the presence of arginine in toothpaste affects the arginolytic capacity of saliva and reduces its sucrose metabolic activity. Additionally, it leads to a shift in the salivary microbiome composition towards a healthy ecology from a caries point of view. Therefore, arginine can be regarded as a genuine oral prebiotic.
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Affiliation(s)
- Jessica E Koopman
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Michel A Hoogenkamp
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Mark J Buijs
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Bart J F Keijser
- Research Group Microbiology and Systems Biology, TNO Earth, Life and Social Sciences, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Jacob M Ten Cate
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands.
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50
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Großeholz R, Koh CC, Veith N, Fiedler T, Strauss M, Olivier B, Collins BC, Schubert OT, Bergmann F, Kreikemeyer B, Aebersold R, Kummer U. Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis. NPJ Syst Biol Appl 2016; 2:16017. [PMID: 28725473 PMCID: PMC5516852 DOI: 10.1038/npjsba.2016.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/10/2016] [Accepted: 06/17/2016] [Indexed: 01/19/2023] Open
Abstract
Genome-scale metabolic models represent the entirety of metabolic reactions of an organism based on the annotation of the respective genome. These models commonly allow all reactions to proceed concurrently, disregarding the fact that at no point all proteins will be present in a cell. The metabolic reaction space can be constrained to a more physiological state using experimentally obtained information on enzyme abundances. However, high-quality, genome-wide protein measurements have been challenging and typically transcript abundances have been used as a surrogate for protein measurements. With recent developments in mass spectrometry-based proteomics, exemplified by SWATH-MS, the acquisition of highly quantitative proteome-wide data at reasonable throughput has come within reach. Here we present methodology to integrate such proteome-wide data into genome-scale models. We applied this methodology to study cellular changes in Enterococcus faecalis during adaptation to low pH. Our results indicate reduced proton production in the central metabolism and decreased membrane permeability for protons due to different membrane composition. We conclude that proteomic data constrain genome-scale models to a physiological state and, in return, genome-scale models are useful tools to contextualize proteomic data.
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Affiliation(s)
- Ruth Großeholz
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Ching-Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Nadine Veith
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Madlen Strauss
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Brett Olivier
- Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, Amsterdam, Netherlands
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Frank Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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