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Wang C, Defoirdt T, Rajkovic A. The Effect of Caco-2 Cells on Sporulation and Enterotoxin Expression by Foodborne Clostridium perfringens. Pathogens 2024; 13:433. [PMID: 38921731 PMCID: PMC11206550 DOI: 10.3390/pathogens13060433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/13/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Clostridium perfringens enterotoxin (Cpe)-producing strains cause gastrointestinal infections in humans and account for the second-largest number of all foodborne outbreaks caused by bacterial toxins. The Cpe toxin is only produced during sporulation; this process might be affected when C. perfringens comes into contact with host cells. The current study determined how the cpe expression levels and spore formation changed over time during co-culture with Caco-2 cells (as a model of intestinal epithelial cells). In co-culture with Caco-2 cells, total C. perfringens cell counts first decreased and then remained more or less stable, whereas spore counts were stable over the whole incubation period. The cpe mRNA level in the co-culture with Caco-2 cells increased more rapidly than in the absence of Caco-2 cells (3.9-fold higher levels in coculture than in the absence of Caco-2 cells after 8 h of incubation). Finally, we found that cpe expression is inhibited by a cue released by Caco-2 cells (8.3-fold lower levels in the presence of supernatants of Caco-2 cells than in the absence of the supernatants after 10 h of incubation); as a consequence, the increased expression in co-culture with Caco-2 cells must be caused by a factor associated with the Caco-2 cells.
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Affiliation(s)
- Chao Wang
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Tom Defoirdt
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
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2
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Yang XT, Wang J, Jiang YH, Zhang L, Du L, Li J, Liu F. Insight into the mechanism of gallstone disease by proteomic and metaproteomic characterization of human bile. Front Microbiol 2023; 14:1276951. [PMID: 38111640 PMCID: PMC10726133 DOI: 10.3389/fmicb.2023.1276951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/16/2023] [Indexed: 12/20/2023] Open
Abstract
Introduction Cholesterol gallstone disease is a prevalent condition that has a significant economic impact. However, the role of the bile microbiome in its development and the host's responses to it remain poorly understood. Methods In this study, we conducted a comprehensive analysis of microbial and human bile proteins in 40 individuals with either gallstone disease or gallbladder polyps. We employed a combined proteomic and metaproteomic approach, as well as meta-taxonomic analysis, functional pathway enrichment, and Western blot analyses. Results Our metaproteomic analysis, utilizing the lowest common ancestor algorithm, identified 158 microbial taxa in the bile samples. We discovered microbial taxa that may contribute to gallstone formation, including β-glucuronidase-producing bacteria such as Streptococcus, Staphylococcus, and Clostridium, as well as those involved in biofilm formation like Helicobacter, Cyanobacteria, Pseudomonas, Escherichia coli, and Clostridium. Furthermore, we identified 2,749 human proteins and 87 microbial proteins with a protein false discovery rate (FDR) of 1% and at least 2 distinct peptides. Among these proteins, we found microbial proteins crucial to biofilm formation, such as QDR3, ompA, ndk, pstS, nanA, pfIB, and dnaK. Notably, QDR3 showed a gradual upregulation from chronic to acute cholesterol gallstone disease when compared to polyp samples. Additionally, we discovered other microbial proteins that enhance bacterial virulence and gallstone formation by counteracting host oxidative stress, including sodB, katG, rbr, htrA, and ahpC. We also identified microbial proteins like lepA, rtxA, pckA, tuf, and tpiA that are linked to bacterial virulence and potential gallstone formation, with lepA being upregulated in gallstone bile compared to polyp bile. Furthermore, our analysis of the host proteome in gallstone bile revealed enhanced inflammatory molecular profiles, including innate immune molecules against microbial infections. Gallstone bile exhibited overrepresented pathways related to blood coagulation, folate metabolism, and the IL-17 pathway. However, we observed suppressed metabolic activities, particularly catabolic metabolism and transport activities, in gallstone bile compared to polyp bile. Notably, acute cholelithiasis bile demonstrated significantly impaired metabolic activities compared to chronic cholelithiasis bile. Conclusion Our study provides a comprehensive metaproteomic analysis of bile samples related to gallstone disease, offering new insights into the microbiome-host interaction and gallstone formation mechanism.
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Affiliation(s)
- Xue-Ting Yang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Jie Wang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Ying-Hua Jiang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
| | - Ling Du
- Key Laboratory of Digestive Cancer Full Cycle Monitoring and Precise Intervention of Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, China
| | - Jun Li
- Department of Surgery, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Liu
- Minhang Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical of Sciences, Fudan University, Shanghai, China
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Brockhurst M, Cavet J, Diggle SP, Grainger D, Mangenelli R, Sychrova H, Martin-Verstraete I, Welch M, Palmer T, Thomas GH. Shaping microbiology for 75 years: highlights of research published in Microbiology. Part 1 - Physiology and growth. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37379229 DOI: 10.1099/mic.0.001356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Affiliation(s)
- Michael Brockhurst
- Division of Evolution, Infection and Genomics, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Jennifer Cavet
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Stephen P Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Hana Sychrova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
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Grenda T, Jarosz A, Sapała M, Grenda A, Patyra E, Kwiatek K. Clostridium perfringens-Opportunistic Foodborne Pathogen, Its Diversity and Epidemiological Significance. Pathogens 2023; 12:768. [PMID: 37375458 DOI: 10.3390/pathogens12060768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The C. perfringens species is associated with various environments, such as soils, sewage, and food. However, it is also a component of the gastrointestinal (GI) microflora (i.e., microbiota) of sick and healthy humans and animals. C. perfringens is linked with different systemic and enteric diseases in livestock and humans, such as gas gangrene, food poisoning, non-foodborne diarrhoea, and enterocolitis. The strains of this opportunistic pathogen are known to secrete over 20 identified toxins that are considered its principal virulence factors. C. perfringens belongs to the anaerobic bacteria community but can also survive in the presence of oxygen. The short time between generations, the multi-production capability of toxins and heat-resistant spores, the location of many virulence genes on mobile genetic elements, and the inhabitance of this opportunistic pathogen in different ecological niches make C. perfringens a very important microorganism for public health protection. The epidemiological evidence for the association of these strains with C. perfringens-meditated food poisoning and some cases of non-foodborne diseases is very clear and well-documented. However, the genetic diversity and physiology of C. perfringens should still be studied in order to confirm the importance of suspected novel virulence traits. A very significant problem is the growing antibiotic resistance of C. perfringens strains. The aim of this review is to show the current basic information about the toxins, epidemiology, and genetic and molecular diversity of this opportunistic pathogen.
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Affiliation(s)
- Tomasz Grenda
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Aleksandra Jarosz
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Magdalena Sapała
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Anna Grenda
- Department of Pneumonology, Oncology and Allergology, Medical University in Lublin, Jaczewskiego 8, 20-950 Lublin, Poland
| | - Ewelina Patyra
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Krzysztof Kwiatek
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
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Description of a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. Syst Appl Microbiol 2023; 46:126376. [PMID: 36375421 DOI: 10.1016/j.syapm.2022.126376] [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: 09/05/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 T, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25-50 °C and pH 5.5-8.0 in the presence of 0-25 g l-1 NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 T was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were iso-C15:0 and C14:0. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to vancomycin (10 mg l-1). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based phylogenetic analysis showed that strain JN-28 T shares ≤ 89.3 % sequence similarity with its closest relatives Sporanaerobacter acetigenes DSM 13106 T and other members in the order Tissierellales. Based on phenotypic and phylogenetic characteristics, Acidilutibacter cellobiosedens gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 T (=CCAM 418 T = JCM 39087 T). Further phylogenetic and phylogenomic analyses suggested strain JN-28 T represents a novel family within the order Tissierellales, for which Acidilutibacteraceae fam. nov. is proposed. In addition, the family Tissierellaceae was reclassified, Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. were formally proposed. Emended description of the family Tissierellaceae is also provided.
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Hu WS, Woo DU, Kang YJ, Koo OK. Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress. Antibiotics (Basel) 2021; 10:antibiotics10040396. [PMID: 33917564 PMCID: PMC8067515 DOI: 10.3390/antibiotics10040396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/05/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022] Open
Abstract
Clostridium perfringens is a major human pathogen that causes gastroenteritis via enterotoxin production and has the ability to form spores and biofilms for environmental persistence and disease transmission. This study aimed to compare the disinfectant and environmental resistance properties of C. perfringens vegetative cells and spores in planktonic and sessile conditions, and to examine the nucleotide polymorphisms and transcription under sessile conditions in C. perfringens strains isolated from meat. The sporulation rate of sessile C. perfringens TYJAM-D-66 (cpe+) was approximately 19% at day 5, while those of CMM-C-80 (cpe−) and SDE-B-202 (cpe+) were only 0.26% and 0.67%, respectively, at day 7. When exposed to aerobic conditions for 36 h, TYJAM-D-66, CMM-C-80, and SDE-B-202 vegetative cells showed 1.70 log, 5.36 log, and 5.67 log reductions, respectively. After treatment with sodium hypochlorite, the survival rates of TYJAM-D-66 vegetative cells (53.6%) and spores (82.3%) in biofilms were higher than those of planktonic cells (9.23%). Biofilm- and spore-related genes showed different expression within TYJAM-D-66 (–4.66~113.5), CMM-C-80 (–3.02~2.49), and SDE-B-202 (–5.07~2.73). Our results indicate the resistance of sessile cells and spores of C. perfringens upon exposure to stress conditions after biofilm formation.
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Affiliation(s)
- Wen Si Hu
- Department of Food Science and Engineering, Liaocheng University, Liaocheng 252059, China;
| | - Dong U Woo
- Division of Life Science Department, Gyeongsang National University, Jinju 52828, Korea; (D.U.W.); (Y.J.K.)
- Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea
| | - Yang Jae Kang
- Division of Life Science Department, Gyeongsang National University, Jinju 52828, Korea; (D.U.W.); (Y.J.K.)
- Division of Bio & Medical Big Data Department (BK4 Program), Gyeongsang National University, Jinju 52828, Korea
| | - Ok Kyung Koo
- Department of Food and Nutrition, Gyeongsang National University, Jinju 52828, Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-55-772-1441
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la Mora ZVD, Macías-Rodríguez ME, Arratia-Quijada J, Gonzalez-Torres YS, Nuño K, Villarruel-López A. Clostridium perfringens as Foodborne Pathogen in Broiler Production: Pathophysiology and Potential Strategies for Controlling Necrotic Enteritis. Animals (Basel) 2020; 10:E1718. [PMID: 32972009 PMCID: PMC7552638 DOI: 10.3390/ani10091718] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/29/2022] Open
Abstract
Clostridium perfringens (Cp.) is the cause of human foodborne desease. Meat and poultry products are identified as the main source of infection for humans. Cp. can be found in poultry litter, feces, soil, dust, and healthy birds' intestinal contents. Cp. strains are known to secrete over 20 identified toxins and enzymes that could potentially be the principal virulence factors, capable of degrading mucin, affecting enterocytes, and the small intestine epithelium, involved in necrotic enteritis (NE) pathophysiology, also leading to immunological responses, microbiota modification and anatomical changes. Different environmental and dietary factors can determine the colonization of this microorganism. It has been observed that the incidence of Cp-associated to NE in broilers has increased in countries that have stopped using antibiotic growth promoters. Since the banning of such antibiotic growth promoters, several strategies for Cp. control have been proposed, including dietary modifications, probiotics, prebiotics, synbiotics, phytogenics, organic acids, and vaccines. However, there are aspects of the pathology that still need to be clarified to establish better actions to control and prevention. This paper reviews the current knowledge about Cp. as foodborne pathogen, the pathophysiology of NE, and recent findings on potential strategies for its control.
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Affiliation(s)
- Zuamí Villagrán-de la Mora
- Departamento de Ciencias de la Salud, Centro Universitario de Los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47620, Mexico; (Z.V.-d.l.M.); (Y.S.G.-T.)
| | - María Esther Macías-Rodríguez
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Olímpica 44430, Guadalajara, Mexico;
| | - Jenny Arratia-Quijada
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Nuevo Perif. Ote. 555, Ejido San José, Tateposco 45425, Tonalá, Mexico;
| | - Yesica Sughey Gonzalez-Torres
- Departamento de Ciencias de la Salud, Centro Universitario de Los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47620, Mexico; (Z.V.-d.l.M.); (Y.S.G.-T.)
| | - Karla Nuño
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Nuevo Perif. Ote. 555, Ejido San José, Tateposco 45425, Tonalá, Mexico;
| | - Angélica Villarruel-López
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Olímpica 44430, Guadalajara, Mexico;
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Jia Z, Liu Y, Hwang CA, Huang L. Effect of combination of Oxyrase and sodium thioglycolate on growth of Clostridium perfringens from spores under aerobic incubation. Food Microbiol 2020; 89:103413. [PMID: 32138984 DOI: 10.1016/j.fm.2020.103413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
Clostridium perfringens is a strictly anaerobic pathogen that requires absence of oxygen for its growth in laboratory experiments, which is usually attained by using an anaerobic chamber or anaerobic jars. However, it has been demonstrated that C. perfringens may survive for short periods of times due to its adaptive response to O2. Therefore, the objective of this study was to explore the application of Oxyrase (OX) and sodium thioglycolate (ST) as oxygen scavengers, used alone or in combination, for observation of the growth of C. perfringens under aerobic incubation. The growth of C. perfringens from spores in Schaedler Anaerobe Agar containing different levels and combinations of OX and ST was observed at temperatures between 20 and 50 °C. The kinetic parameters, including lag time, specific growth rate, and maximum cell concentrations in the stationary phase, were determined. The results indicated that ST at concentrations of 0.025 and 0.05% (w/w), although allowing eventual growth of C. perfringens, prolonged its lag times, while OX at 1.5% only allowed growth at a lower growth rate in comparison to anaerobic incubation. OX at 3% enhanced the growth of C. perfringens at temperatures between 30 and 50 °C, while higher levels of OX were needed in the medium to support the growth of C. perfringens during storage at 25 °C (>6% OX) and 20 °C (>9% OX), due to the effect of temperature on enzyme activity. No significant difference was found in the kinetic parameters of C. perfringens incubated aerobically with OX and the control (without OX or ST) in an anaerobic chamber. Therefore, OX at appropriate concentrations may allow the observation of the growth of C. perfringens under aerobic incubation conditions without the need of an anaerobic device.
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Affiliation(s)
- Zhen Jia
- School of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, 350001, China
| | - Yanhong Liu
- Eastern Regional Research Center, USDA Agricultural Research Service, Wyndmoor, PA, 19038, USA
| | - Chang-An Hwang
- Eastern Regional Research Center, USDA Agricultural Research Service, Wyndmoor, PA, 19038, USA
| | - Lihan Huang
- Eastern Regional Research Center, USDA Agricultural Research Service, Wyndmoor, PA, 19038, USA.
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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Zhang J, Wang S, Zeng Z, Qin Y, Li P. The complete genome sequence of Bifidobacterium animalis subsp. lactis 01 and its integral components of antioxidant defense system. 3 Biotech 2019; 9:352. [PMID: 31501753 DOI: 10.1007/s13205-019-1890-6] [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: 07/15/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
The strain Bifidobacterium animalis 01, isolated from centenarians, showed promising antioxidant potential in our previous studies. In this study, the genome information on strain 01 and the important antioxidant components are presented. The complete genome comprises a single circular chromosome (1,931,632 bp; 60.49% G + C content) with 1569 coding DNA sequences, 52 tRNA, and 9 rRNA operons. Based on phylogenomic analyses, strain 01 was designated as B. animalis subsp. lactis 01. The genomic analysis reveals that at least eight protein-coding genes are antioxidant-related genes. The conditions for simulating the oxidative stress have been determined. The results of quantitative reverse transcription PCR further demonstrated that the genes encoding the thioredoxin system (ahpC, ahpF, bcp, trxB, trxA, nrdH, and msrAB) and non-enzyme factors of the divalent cation transporter gene (mntH) were upregulated under the H2O2 challenge, indicating that the eight genes were effective components of the antioxidant system. The results of this study could benefit for understanding the antioxidant mechanism of B. animalis 01 and future utilization of it as a potential antioxidant agent.
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Affiliation(s)
- Jinlan Zhang
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, HaiDian District, Beijing, 10083 China
| | - Shibo Wang
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, HaiDian District, Beijing, 10083 China
| | - Zhu Zeng
- 2College of Biotechnology, Southwest University, No. 2 Tiansheng, Beibei District, Chongqing, 400715 China
| | - Yuxuan Qin
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, HaiDian District, Beijing, 10083 China
| | - Pinglan Li
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, HaiDian District, Beijing, 10083 China
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Ślesak I, Kula M, Ślesak H, Miszalski Z, Strzałka K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free Radic Biol Med 2019; 140:61-73. [PMID: 30862543 DOI: 10.1016/j.freeradbiomed.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O2), 2) O2-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O2 in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O2 in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O2 tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O2-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O2/ROS tolerant anaerobes, where the role of the O2/ROS detoxification system is separated from O2-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O2/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O2/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O2/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Monika Kula
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Zbigniew Miszalski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Kazimierz Strzałka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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12
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Modelling the effect of oxygen concentration on bacterial growth rates. Food Microbiol 2019; 77:21-25. [DOI: 10.1016/j.fm.2018.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 07/18/2018] [Accepted: 08/10/2018] [Indexed: 11/24/2022]
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13
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Hamblin MR, Abrahamse H. Can light-based approaches overcome antimicrobial resistance? Drug Dev Res 2019; 80:48-67. [PMID: 30070718 PMCID: PMC6359990 DOI: 10.1002/ddr.21453] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/10/2023]
Abstract
The relentless rise of antibiotic resistance is considered one of the most serious problems facing mankind. This mini-review will cover three cutting-edge approaches that use light-based techniques to kill antibiotic-resistant microbial species, and treat localized infections. First, we will discuss antimicrobial photodynamic inactivation using rationally designed photosensitizes combined with visible light, with the added possibility of strong potentiation by inorganic salts such as potassium iodide. Second, the use of blue and violet light alone that activates endogenous photoactive porphyrins within the microbial cells. Third, it is used for "safe UVC" at wavelengths between 200 nm and 230 nm that can kill microbial cells without damaging host mammalian cells. We have gained evidence that all these approaches can kill multidrug resistant bacteria in vitro, and they do not induce themselves any resistance, and moreover can treat animal models of localized infections caused by resistant species that can be monitored by noninvasive bioluminescence imaging. Light-based antimicrobial approaches are becoming a growing translational part of anti-infective treatments in the current age of resistance.
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Affiliation(s)
- Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, South Africa
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14
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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15
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Majou D, Christieans S. Mechanisms of the bactericidal effects of nitrate and nitrite in cured meats. Meat Sci 2018; 145:273-284. [PMID: 30005374 DOI: 10.1016/j.meatsci.2018.06.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022]
Abstract
For cured meat products, nitrite is recognized for its antimicrobial effects against pathogenic bacteria, even though the specific inhibitory mechanisms are not well known. Nitrite contributes to oxidative stress by being the precursor of peroxynitrite (ONOO-), which is the major strong oxidant. Thus, bacterial stress (highly pH-very low partial pressure of oxygen-dependent) is enhanced by the nitrate-nitrite-peroxynitrite system which is also highly pH- and low partial pressure of oxygen-dependent. Nitrite is a hurdle technology which effectiveness depends on several other hurdle technologies including sodium chloride (accelerating the autoxidation of oxymyoglobin and promote peroxynitrite formation), ascorbate (increasing ONOO- synthesis), and Aw. In this environment, certain species are more resistant than others to acidic, oxidative, and nitrative stresses. The most resistant are gram-negative aerobic/facultative anaerobic bacteria (Escherichia coli, Salmonella), and the most fragile are gram-positive anaerobic bacteria (Clostridium botulinum). This position review highlights the major chemical mechanisms involved, the active molecules and their actions on bacterial metabolisms in the meat ecosystem.
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Affiliation(s)
- Didier Majou
- Association pour la Coordination Technique pour l'Industrie Agro-Alimentaire (ACTIA), 16, rue Claude Bernard, 75005 Paris 05, France
| | - Souad Christieans
- Association pour le Développement de l'Industrie de la Viande (ADIV), 10, rue Jacqueline Auriol, 63039 Clermont-Ferrand, France..
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Chellapandi P, Prisilla A. Clostridium botulinum type A-virulome-gut interactions: A systems biology insight. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.humic.2018.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Gyulev IS, Willson BJ, Hennessy RC, Krabben P, Jenkinson ER, Thomas GH. Part by Part: Synthetic Biology Parts Used in Solventogenic Clostridia. ACS Synth Biol 2018; 7:311-327. [PMID: 29186949 DOI: 10.1021/acssynbio.7b00327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solventogenic Clostridia are of interest to the chemical industry because of their natural ability to produce chemicals such as butanol, acetone and ethanol from diverse feedstocks. Their use as whole cell factories presents multiple metabolic engineering targets that could lead to improved sustainability and profitability of Clostridium industrial processes. However, engineering efforts have been held back by the scarcity of genetic and synthetic biology tools. Over the past decade, genetic tools to enable transformation and chromosomal modifications have been developed, but the lack of a broad palette of synthetic biology parts remains one of the last obstacles to the rapid engineered improvement of these species for bioproduction. We have systematically reviewed existing parts that have been used in the modification of solventogenic Clostridia, revealing a narrow range of empirically chosen and nonengineered parts that are in current use. The analysis uncovers elements, such as promoters, transcriptional terminators and ribosome binding sites where increased fundamental knowledge is needed for their reliable use in different applications. Together, the review provides the most comprehensive list of parts used and also presents areas where an improved toolbox is needed for full exploitation of these industrially important bacteria.
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Affiliation(s)
- Ivan S. Gyulev
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Benjamin J. Willson
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Rosanna C. Hennessy
- Department
of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Preben Krabben
- Green Biologics Limited, Milton Park, Abingdon, Oxfordshire OX14 4RU, United Kingdom
| | | | - Gavin H. Thomas
- Department
of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
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18
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Huang L, Vinyard BT. Direct Dynamic Kinetic Analysis and Computer Simulation of Growth ofClostridium perfringensin Cooked Turkey during Cooling. J Food Sci 2016; 81:M692-701. [DOI: 10.1111/1750-3841.13202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/04/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Lihan Huang
- U.S. Dept. of AgricultureAgricultural Research Service, Eastern Regional Research Center 600 E. Mermaid Lane Wyndmoor Pa. 19038 U.S.A
| | - Bryan T. Vinyard
- U.S. Dept. of AgricultureAgricultural Research Service, Northeast Area 10300 Baltimore Avenue Beltsville Md. 20705–2350 U.S.A
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19
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Huang L. Dynamic determination of kinetic parameters, computer simulation, and probabilistic analysis of growth of Clostridium perfringens in cooked beef during cooling. Int J Food Microbiol 2015; 195:20-9. [DOI: 10.1016/j.ijfoodmicro.2014.11.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 10/01/2014] [Accepted: 11/22/2014] [Indexed: 02/07/2023]
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20
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Venkataramanan KP, Min L, Hou S, Jones SW, Ralston MT, Lee KH, Papoutsakis ET. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:81. [PMID: 26269711 PMCID: PMC4533764 DOI: 10.1186/s13068-015-0260-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/30/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. RESULTS The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. CONCLUSIONS The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.
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Affiliation(s)
- Keerthi P. Venkataramanan
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Lie Min
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shuyu Hou
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shawn W. Jones
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Matthew T. Ralston
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />15 Innovation Way, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA
| | - Kelvin H. Lee
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - E. Terry Papoutsakis
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
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21
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The non-enzymatic reduction of azo dyes by flavin and nicotinamide cofactors under varying conditions. Anaerobe 2013; 23:87-96. [DOI: 10.1016/j.anaerobe.2013.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/09/2013] [Accepted: 07/17/2013] [Indexed: 11/20/2022]
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22
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Yin R, Dai T, Avci P, Jorge AES, de Melo WCMA, Vecchio D, Huang YY, Gupta A, Hamblin MR. Light based anti-infectives: ultraviolet C irradiation, photodynamic therapy, blue light, and beyond. Curr Opin Pharmacol 2013; 13:731-62. [PMID: 24060701 DOI: 10.1016/j.coph.2013.08.009] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 12/26/2022]
Abstract
Owing to the worldwide increase in antibiotic resistance, researchers are investigating alternative anti-infective strategies to which it is supposed microorganisms will be unable to develop resistance. Prominent among these strategies, is a group of approaches which rely on light to deliver the killing blow. As is well known, ultraviolet light, particularly UVC (200-280 nm), is germicidal, but it has not been much developed as an anti-infective approach until recently, when it was realized that the possible adverse effects to host tissue were relatively minor compared to its high activity in killing pathogens. Photodynamic therapy is the combination of non-toxic photosensitizing dyes with harmless visible light that together produce abundant destructive reactive oxygen species (ROS). Certain cationic dyes or photosensitizers have good specificity for binding to microbial cells while sparing host mammalian cells and can be used for treating many localized infections, both superficial and even deep-seated by using fiber optic delivered light. Many microbial cells are highly sensitive to killing by blue light (400-470 nm) due to accumulation of naturally occurring photosensitizers such as porphyrins and flavins. Near infrared light has also been shown to have antimicrobial effects against certain species. Clinical applications of these technologies include skin, dental, wound, stomach, nasal, toenail and other infections which are amenable to effective light delivery.
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Affiliation(s)
- Rui Yin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA; Department of Dermatology, Harvard Medical School, Boston, MA, USA; Department of Dermatology, Southwest Hospital, Third Military Medical University, Chongqing, China
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23
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Rothe M, Blaut M. Evolution of the gut microbiota and the influence of diet. Benef Microbes 2013; 4:31-7. [PMID: 23257016 DOI: 10.3920/bm2012.0029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Diet is a major force that shapes the composition and activity of the gut microbiota. This is evident from alterations in gut microbiota composition after weaning or drastic dietary changes. Owing to the complexity of the microbiota, interactions of intestinal bacteria with the host are difficult to study. Gnotobiotic animal models offer the opportunity to reduce the complexity and the interindividual variability of the intestinal microbiota. Germ-free animals were associated with a simplified microbial community consisting of eight bacterial species, that are found in the human gut. These microbes were selected because their genome sequences are available, and they mimic to some extent the metabolic activity of the human gut microbiota. The microbiota responded to dietary modifications by changes in the relative proportions of the community members. This model offers the chance to better define the role of intestinal bacteria in obesity development, but little is known on how diet affects intestinal bacteria at the cellular level. Mice monoassociated with Escherichia coli were used as a simplified model to investigate the influence of dietary factors on bacterial protein expression in the intestine. The mice were fed three different diets: a carbohydrate (lactose)-rich diet, a protein-rich diet and a diet rich in starch. The lactose-rich diet led to an induction of proteins involved in E. coli's oxidative stress response (Fur, AhpF, Dps). The corresponding genes are under control of the OxyR transcriptional regulator which is activated by oxidative stress. Further experiments demonstrated that osmotic stress exerted by various carbohydrates leads to an upregulation of proteins belonging to the oxyR regulon. The data suggest that the upregulated proteins enable intestinal E. coli to better cope with diet-induced osmotic stress. These examples demonstrate that gnotobiotic animal models are a valuable tool for studying diet-induced changes at the community and the cell level.
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Affiliation(s)
- M Rothe
- Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114.116, 14558 Nuthetal, Germany
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24
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Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring. Appl Environ Microbiol 2013; 79:3637-48. [PMID: 23563939 DOI: 10.1128/aem.00153-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (-5°C), hypersalinity (salinity, 24%), and reducing (≈-165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day(-1)). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.
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25
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Bassi D, Cappa F, Cocconcelli PS. Array-based transcriptional analysis of Clostridium sporogenes UC9000 during germination, cell outgrowth and vegetative life. Food Microbiol 2012; 33:11-23. [PMID: 23122496 DOI: 10.1016/j.fm.2012.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/04/2012] [Accepted: 08/05/2012] [Indexed: 01/22/2023]
Abstract
The members of the genus Clostridium, including the spore-forming anaerobic bacteria, have a complex and strictly regulated life cycle, but very little is known about the genetic pathways involved in the different stages of their life cycle. Clostridium sporogenes, a Gram-positive bacterium usually involved in food spoilage and frequently isolated from late blowing cheese, is genetically indistinguishable from the proteolytic Clostridium botulinum. As the non-neurotoxic counterpart, it is often used as an exemplar for the toxic subtypes. In this work, we performed a microscopic study combined with a custom array-based analysis of the C. sporogenes cycle, from dormant spores to the early stationary phase. We identified a total of 211 transcripts in spores, validating the hypothesis that mRNAs are abundant in spores and the pattern of mRNA expression is strikingly different from that present in growing cells. The spore transcripts included genes responsible for different life-sustaining functions, suggesting there was transcript entrapment or basic poly-functional gene activation for future steps. In addition, 3 h after the beginning of the germination process, 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appeared to be more active in terms of gene transcription and protein synthesis than the spore, and genes coding for germination and sporulation factors seemed to be expressed at this point. These results suggest that spores are not silent entities, and a broader knowledge of the genetic pathways involved in the Clostridium life cycle could provide a better understanding of pathogenic clostridia types.
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Affiliation(s)
- Daniela Bassi
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza/Via Milano 24, 26100 Cremona, Italy.
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Monturiol-Gross L, Flores-Díaz M, Araya-Castillo C, Pineda-Padilla MJ, Clark GC, Titball RW, Alape-Girón A. Reactive oxygen species and the MEK/ERK pathway are involved in the toxicity of clostridium perfringens α-toxin, a prototype bacterial phospholipase C. J Infect Dis 2012; 206:1218-26. [PMID: 22904339 DOI: 10.1093/infdis/jis496] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clostridium perfringens, the most broadly distributed pathogen in nature, produces a prototype phospholipase C, also called α-toxin, which plays a key role in the pathogenesis of gas gangrene. α-Toxin causes plasma membrane disruption at high concentrations, but the role of intracellular mediators in its toxicity at low concentrations is unknown. This work demonstrates that α-toxin causes oxidative stress and activates the MEK/ERK pathway in cultured cells and furthermore provides compelling evidence that O(2)(-.), hydrogen peroxide, and the OH(.) radical are involved in its cytotoxic and myotoxic effects. The data show that antioxidants and MEK1 inhibitors reduce the cytotoxic and myotoxic effects of α-toxin and demonstrate that edaravone, a clinically used hydroxyl radical trap, reduces the myonecrosis and the mortality caused by an experimental infection with C. perfringens in a murine model of gas gangrene. This knowledge provides new insights for the development of novel therapies to reduce tissue damage during clostridial myonecrosis.
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Affiliation(s)
- Laura Monturiol-Gross
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
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27
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Role of the Irr protein in the regulation of iron metabolism in Rhodobacter sphaeroides. PLoS One 2012; 7:e42231. [PMID: 22879920 PMCID: PMC3413700 DOI: 10.1371/journal.pone.0042231] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 07/05/2012] [Indexed: 12/21/2022] Open
Abstract
In Rhizobia the Irr protein is an important regulator for iron-dependent gene expression. We studied the role of the Irr homolog RSP_3179 in the photosynthetic alpha-proteobacterium Rhodobacter sphaeroides. While Irr had little effect on growth under iron-limiting or non-limiting conditions its deletion resulted in increased resistance to hydrogen peroxide and singlet oxygen. This correlates with an elevated expression of katE for catalase in the Irr mutant compared to the wild type under non-stress conditions. Transcriptome studies revealed that Irr affects the expression of genes for iron metabolism, but also has some influence on genes involved in stress response, citric acid cycle, oxidative phosphorylation, transport, and photosynthesis. Most genes showed higher expression levels in the wild type than in the mutant under normal growth conditions indicating an activator function of Irr. Irr was however not required to activate genes of the iron metabolism in response to iron limitation, which showed even stronger induction in the absence of Irr. This was also true for genes mbfA and ccpA, which were verified as direct targets for Irr. Our results suggest that in R. sphaeroides Irr diminishes the strong induction of genes for iron metabolism under iron starvation.
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Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res 2012; 22:1974-84. [PMID: 22665442 PMCID: PMC3460192 DOI: 10.1101/gr.138198.112] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances.
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Affiliation(s)
- Catherine Lozupone
- Department of Chemistry & Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
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Holý O, Chmelař D. Oxygen tolerance in anaerobic pathogenic bacteria. Folia Microbiol (Praha) 2012; 57:443-6. [PMID: 22573259 DOI: 10.1007/s12223-012-0149-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 04/09/2012] [Indexed: 11/25/2022]
Abstract
A prerequisite for successful identification of anaerobic pathogenic bacteria from samples of clinical material is the method of cultivation. Currently, several methods of cultivation in anaerobic environment are used: cultivation in anaerobic box, anaerobic jar, and in nonrecurring cultivation system. Here, we determined the suitability of the above methods of cultivation using the estimation of the growth (diameters of colony size) of commonly isolated anaerobic pathogens (Bacteroides fragilis, Clostridium difficile, and Clostridium perfringens). The tested bacterial strains were exposed to atmospheric oxygen for various time periods and then they were cultivated using different anaerobic cultivation systems. Maximum growth differed, depending on the type of cultivation and the strain used. Thus, largest zone diameters, in the majority of measurements, were achieved in the anaerobic box. However, nonrecurring cultivation system seemed better in several cases; this applied to the cultivation of C. perfringens after 15, 30, and 60 min exposure to atmospheric oxygen as well as the cultivation of B. fragilis after 30 and 60 min of oxygen exposure. The cultivation in anaerobic box was the most convenient method for growth of C. difficile. In almost all cases, higher growth was observed in nonrecurring cultivation system than in the system of anaerobic jar. On the other hand, no significant differences were observed among these anaerobic cultivation systems which confirmed their applicability (taking into account some individual features concerning the optimization of cultivations) for identification of pathogenic anaerobes.
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Affiliation(s)
- Ondřej Holý
- Department of Preventive Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hnětovínská 3, 775 15, Olomouc, Czech Republic.
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Murdoch LE, Maclean M, Endarko E, MacGregor SJ, Anderson JG. Bactericidal effects of 405 nm light exposure demonstrated by inactivation of Escherichia, Salmonella, Shigella, Listeria, and Mycobacterium species in liquid suspensions and on exposed surfaces. ScientificWorldJournal 2012; 2012:137805. [PMID: 22566760 PMCID: PMC3330698 DOI: 10.1100/2012/137805] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 12/08/2011] [Indexed: 12/31/2022] Open
Abstract
The bactericidal effect of 405 nm light was investigated on taxonomically diverse bacterial pathogens from the genera Salmonella, Shigella, Escherichia, Listeria, and Mycobacterium. High-intensity 405 nm light, generated from an array of 405-nm light-emitting diodes (LEDs), was used to inactivate bacteria in liquid suspension and on exposed surfaces. L. monocytogenes was most readily inactivated in suspension, whereas S. enterica was most resistant. In surface exposure tests, L. monocytogenes was more susceptible than Gram-negative enteric bacteria to 405 nm light when exposed on an agar surface but interestingly less susceptible than S. enterica after drying onto PVC and acrylic surfaces. The study findings, that 405 nm light inactivates diverse types of bacteria in liquids and on surfaces, in addition to the safety advantages of this visible (non-UV wavelength) light, indicate the potential of this technology for a range of decontamination applications.
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Affiliation(s)
- Lynne E Murdoch
- The Robertson Trust Laboratory for Electronic Sterilisation Technologies, Department of Electronic and Electrical Engineering, University of Strathclyde-Glasgow, Glasgow G1 1XW, UK.
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Kim K, Kim JJ, Masui R, Kuramitsu S, Sung MH. A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii. BMC Res Notes 2011; 4:437. [PMID: 22023733 PMCID: PMC3208422 DOI: 10.1186/1756-0500-4-437] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Accepted: 10/24/2011] [Indexed: 11/10/2022] Open
Abstract
Background Symbiobacterium toebii is a commensal symbiotic thermophile that absolutely requires its partner bacterium Geobacillus toebii for growth. Despite development of an independent cultivation method using cell-free extracts, the growth of Symbiobacterium remains unknown due to our poor understanding of the symbiotic relationship with its partner bacterium. Here, we investigated the interrelationship between these two bacteria for growth of S. toebii using different cell-free extracts of G. toebii. Results Symbiobacterium toebii growth-supporting factors were constitutively produced through almost all growth phases and under different oxygen tensions in G. toebii, indicating that the factor may be essential components for growth of G. toebii as well as S. toebii. The growing conditions of G. toebii under different oxygen tension dramatically affected to the initial growth of S. toebii and the retarded lag phase was completely shortened by reducing agent, L-cysteine indicating an evidence of commensal interaction of microaerobic and anaerobic bacterium S. toebii with a facultative aerobic bacterium G. toebii. In addition, the growth curve of S. toebii showed a dependency on the protein concentration of cell-free extracts of G. toebii, demonstrating that the G. toebii-derived factors have nutrient-like characters but not quorum-sensing characters. Conclusions Not only the consistent existence of the factor in G. toebii during all growth stages and under different oxygen tensions but also the concentration dependency of the factor for proliferation and optimal growth of S. toebii, suggests that an important biosynthetic machinery lacks in S. toebii during evolution. The commensal symbiotic bacterium, S. toebii uptakes certain ubiquitous and essential compound for its growth from environment or neighboring bacteria that shares the equivalent compounds. Moreover, G. toebii grown under aerobic condition shortened the lag phase of S. toebii under anaerobic and microaerobic conditions, suggests a possible commensal interaction that G. toebii scavengers ROS/RNS species and helps the initial growth of S. toebii.
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Affiliation(s)
- Kwang Kim
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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Voidarou C, Bezirtzoglou E, Alexopoulos A, Plessas S, Stefanis C, Papadopoulos I, Vavias S, Stavropoulou E, Fotou K, Tzora A, Skoufos I. Occurrence of Clostridium perfringens from different cultivated soils. Anaerobe 2011; 17:320-4. [PMID: 21621626 DOI: 10.1016/j.anaerobe.2011.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 05/12/2011] [Indexed: 11/25/2022]
Abstract
The occurrence of Clostridium perfringens was estimated in 750 samples originated from a variety of soils bearing various bulb crops: Brawnica oderacea (vegetable), Olea europaea, Daucus carota (carote), Solanum tuberosum (potato), Phaseolus vulgaris (green haricot), Beta vulgaris var. rapaceum (beetroot), Cucurbita pepo (squash), Allium cepa (onion), Cucumis sativus (cucumber) and Capsicum annum (pepper). All isolated strains were tested for their antimicrobial activities to amoxicillin, penicillin G, kanamycin, tetracycline, streptomycin, erythromycin, chloramphenicol and metronidazole. When considering the type of the bulb production, it was observed increased number of C. perfringens spore densities in the most undersurface bulb soils. Moreover, C. perfringens spore are likely to occur in particularly large numbers in soil contaminated by fecal matter. Additionally, there is a close relationship between the spore amount and nature of organic content. Presence of C. perfringens was associated with acidic soil. Most of our strains showed resistance to the studied antibiotics applied usually for human and veterinary care. A systematic monitoring of the cultivated soil ecosystems must include bacteriological parameters together with chemical indices of organic pollution in order to obtain information adequate for assessing their overall quality.
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Affiliation(s)
- C Voidarou
- Technological Educational Institute of Epirus, Arta GR47100, Greece
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Expression, purification and characterization of two Clostridium acetobutylicum flavodoxins: Potential electron transfer partners for CYP152A2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:257-64. [DOI: 10.1016/j.bbapap.2010.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/10/2010] [Accepted: 06/17/2010] [Indexed: 11/18/2022]
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André G, Haudecoeur E, Monot M, Ohtani K, Shimizu T, Dupuy B, Martin-Verstraete I. Global regulation of gene expression in response to cysteine availability in Clostridium perfringens. BMC Microbiol 2010; 10:234. [PMID: 20822510 PMCID: PMC2940859 DOI: 10.1186/1471-2180-10-234] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 09/07/2010] [Indexed: 11/24/2022] Open
Abstract
Background Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the expression of the ubiG operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the C. perfringens virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail. Results We first performed a tentative reconstruction of sulfur metabolism in C. perfringens and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, C. perfringens can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (cysK-cysE, cysP1 and cysP2) or an S-box riboswitch (metK and metT). We also showed that the ubiG operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA. In addition, we found that expression of pfoA (theta-toxin), nagL (one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the ldh gene encoding the lactate dehydrogenase was induced during cysteine limitation. Conclusion Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.
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Affiliation(s)
- Gaelle André
- Institut Pasteur, Unité de Génétique des Génomes Bactériens and Unité des Bactéries Anaérobies et Toxines, 28 rue du Docteur Roux, 75015 Paris, France
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Strand KR, Sun C, Li T, Jenney FE, Schut GJ, Adams MWW. Oxidative stress protection and the repair response to hydrogen peroxide in the hyperthermophilic archaeon Pyrococcus furiosus and in related species. Arch Microbiol 2010; 192:447-59. [PMID: 20379702 DOI: 10.1007/s00203-010-0570-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 03/23/2010] [Accepted: 03/25/2010] [Indexed: 11/26/2022]
Abstract
Pyrococcus furiosus is a shallow marine, anaerobic archaeon that grows optimally at 100 degrees C. Addition of H(2)O(2) (0.5 mM) to a growing culture resulted in the cessation of growth with a 2-h lag before normal growth resumed. Whole genome transcriptional profiling revealed that the main response occurs within 30 min of peroxide addition, with the up-regulation of 62 open reading frames (ORFs), 36 of which are part of 10 potential operons. More than half of the up-regulated ORFs are of unknown function, while some others encode proteins that are involved potentially in sequestering iron and sulfide, in DNA repair and in generating NADPH. This response is thought to involve primarily damage repair rather than protection, since cultures exposed to sub-toxic levels of H(2)O(2) were not more resistant to the subsequent addition of H(2)O(2) (0.5-5.0 mM). Consequently, there is little if any induced protective response to peroxide. The organism maintains a constitutive protective mechanism involving high levels of oxidoreductase-type enzymes such as superoxide reductase, rubrerythrin, and alkyl hydroperoxide reductase. Related hyperthermophiles contain homologs of the proteins involved in the constitutive protective mechanism but these organisms were more sensitive to peroxide than P. furiosus and lack several of its peroxide-responsive ORFs.
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Affiliation(s)
- Kari R Strand
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg., Athens, GA 30602-7229, USA
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Seneviratne CJ, Wang Y, Jin L, Abiko Y, Samaranayake LP. Proteomics of drug resistance in Candida glabrata
biofilms. Proteomics 2010; 10:1444-54. [DOI: 10.1002/pmic.200900611] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Orsburn BC, Melville SB, Popham DL. EtfA catalyses the formation of dipicolinic acid inClostridium perfringens. Mol Microbiol 2010; 75:178-86. [DOI: 10.1111/j.1365-2958.2009.06975.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Semi-continuous propagation and synchronous differentiation of hyper-solventogenic cells of Clostridium thermosaccharolyticum in a xylan medium at 56°C. J Taiwan Inst Chem Eng 2009. [DOI: 10.1016/j.jtice.2008.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Reductive dioxygen scavenging by flavo-diiron proteins of Clostridium acetobutylicum. FEBS Lett 2008; 583:241-5. [PMID: 19084524 DOI: 10.1016/j.febslet.2008.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 12/01/2008] [Accepted: 12/02/2008] [Indexed: 11/22/2022]
Abstract
Two flavo-diiron proteins (FDPs), FprA1 and FprA2, are up-regulated when the strictly anaerobic solvent producer, Clostridium acetobutylicum, is exposed to dioxygen. These two FDPs were purified following heterologous overexpression in Escherichia coli as N-terminal Strep-tag fusion proteins. The recombinant FprA1 and FprA2 were found to be homodimeric and homotetrameric, respectively, and both FDPs functioned as terminal components of NADH oxidases (NADH:O(2) oxidoreductases) when using C. acetobutylicum NADH:rubredoxin oxidoreductase (NROR) and rubredoxin (Rd) as electron transport intermediaries. Both FDPs catalyzed the four-electron reduction of molecular oxygen to water with similar specific activities. The results are consistent with these FDPs functioning as efficient scavengers of intracellular dioxygen under aerobic or microoxic growth conditions.
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Miki Y, Miyamoto K, Kaneko-Hirano I, Fujiuchi K, Akimoto S. Prevalence and characterization of enterotoxin gene-carrying Clostridium perfringens isolates from retail meat products in Japan. Appl Environ Microbiol 2008; 74:5366-72. [PMID: 18606797 PMCID: PMC2546627 DOI: 10.1128/aem.00783-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2008] [Accepted: 06/25/2008] [Indexed: 11/20/2022] Open
Abstract
Clostridium perfringens is an important anaerobic pathogen causing food-borne gastrointestinal (GI) diseases in humans and animals. It is thought that C. perfringens food poisoning isolates typically carry the enterotoxin gene (cpe) on their chromosome, while isolates from other GI diseases, such as antibiotic-associated diarrhea, carry cpe on a transferable plasmid. However, food-borne GI disease outbreaks associated with C. perfringens isolates carrying plasmid-borne cpe (plasmid cpe isolates) were recently reported in Japan and Europe. To investigate whether retail food can be a reservoir for food poisoning generally, we evaluated Japanese retail meat products for the presence of two genotypes of enterotoxigenic C. perfringens. Our results demonstrated that approximately 70% of the Japanese retail raw meat samples tested were contaminated with low numbers of C. perfringens bacteria and 4% were contaminated with cpe-positive C. perfringens. Most of the cpe-positive C. perfringens isolates obtained from Japanese retail meat carried cpe on a plasmid. The plasmid cpe isolates exhibited lower spore heat resistance than did chromosomal cpe isolates. Collectively, these plasmid cpe isolates might be causative agents of food poisoning when foods are contaminated with these isolates from equipment and/or the environment after cooking, or they may survive in food that has not been cooked at a high enough temperature.
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Affiliation(s)
- Yasuhiro Miki
- Department of Microbiology, School of Medicine, Wakayama Medical University, 811-1 Kimiidera, Wakayama 641-0012, Japan
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Gibson DL, Vallance BA. Intestinal microbiota are transiently altered during Salmonella-induced gastroenteritis. Expert Rev Gastroenterol Hepatol 2008; 2:525-9. [PMID: 19072400 DOI: 10.1586/17474124.2.4.525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mammalian GI tract contains a large and diverse ecosystem of microorganisms that play a profound role in our development and physiology. Interestingly, the microbial make-up within the intestine has been found to be altered in many clinically important diseases, including inflammatory bowel disease, irritable bowel syndrome, Types 1 and 2 diabetes, and obesity. Barman et al. used a Salmonella-induced murine model of gastroenteritis to show that the intestinal microbiota are transiently altered during the host inflammatory response to infection. These findings are of interest as understanding how the microbiota are altered during disease states may offer insight into which microbial populations are important in maintaining intestinal homeostasis. Recently, probiotics have been shown to modulate the mucosal immune system and improve intestinal barrier function, validating their potential as therapeutics for gastrointestinal-associated diseases. As we begin to understand the benefits conferred to the intestine by microbiota, the use of probiotics to modify its composition is an attractive option to improve human health.
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Affiliation(s)
- Deanna L Gibson
- Child and Family Research Institute, Room 201-950 West 28th Avenue, Vancouver, British Columbia, V5Z 4H4, Canada.
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Seneviratne CJ, Wang Y, Jin L, Abiko Y, Samaranayake LP. Candida albicans biofilm formation is associated with increased anti-oxidative capacities. Proteomics 2008; 8:2936-47. [DOI: 10.1002/pmic.200701097] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Brioukhanov AL, Netrusov AI. Aerotolerance of strictly anaerobic microorganisms and factors of defense against oxidative stress: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060014] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Girhard M, Schuster S, Dietrich M, Dürre P, Urlacher VB. Cytochrome P450 monooxygenase from Clostridium acetobutylicum: A new α-fatty acid hydroxylase. Biochem Biophys Res Commun 2007; 362:114-119. [PMID: 17706598 DOI: 10.1016/j.bbrc.2007.07.155] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 07/28/2007] [Indexed: 10/23/2022]
Abstract
Cytochrome P450 monooxygenase from the anaerobic microorganism Clostridium acetobutylicum (CYP152A2) has been produced in Escherichia coli. CYP152A2 was shown to bind a broad range of saturated and unsaturated fatty acids and corresponding methyl esters and demonstrated a high peroxygenase activity of up to 200min(-1) with myristic acid. Although a high concentration of hydrogen peroxide of 200microM was necessary for high activities of the enzyme, it led to a fast enzyme inactivation within 2-4min. This might reflect the natural function of CYP152A2 as a rapid hydrogen peroxide scavenging enzyme. In two different reconstituted systems with NADPH, CYP152A2 was able to convert 10 times more substrate, if provided with flavodoxin and flavodoxin reductase from E. coli and even 30-40 times more substrate with the CYP102A1-reductase from Bacillus megaterium. According to the clear preference for hydroxylation at alpha-position, CYP152A2 can be referred to as fatty acid alpha-hydroxylase.
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Affiliation(s)
- Marco Girhard
- Institute of Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Schuster
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Matthias Dietrich
- Institute of Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Vlada B Urlacher
- Institute of Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada S, Fox GE, Haake SK, Weinstock GM, Highlander SK. Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One 2007; 2:e659. [PMID: 17668047 PMCID: PMC1924603 DOI: 10.1371/journal.pone.0000659] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 06/26/2007] [Indexed: 11/19/2022] Open
Abstract
Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.
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Affiliation(s)
- Sandor E. Karpathy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jason Gioia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Susan Kinder Haake
- Associated Clinical Specialties, University of California at Los Angeles School of Dentistry, Los Angeles, California, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz M, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res 2006; 16:1031-40. [PMID: 16825665 PMCID: PMC1524862 DOI: 10.1101/gr.5238106] [Citation(s) in RCA: 240] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
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Affiliation(s)
- Garry S.A. Myers
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - David A. Rasko
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Jackie K. Cheung
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Rekha Seshadri
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Robert T. DeBoy
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - John Varga
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24601, USA
| | - Milena M. Awad
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | | | | | - Daniel H. Haft
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Robert J. Dodson
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - M.J. Rosovitz
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Kisha L. Watkins
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | | | - Jonathan Benton
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Derek J. Fisher
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Helen S. Atkins
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom
| | - Tom Hiscox
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - B. Helen Jost
- Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA
| | | | - J. Glenn Songer
- Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA
| | - Bruce A. McClane
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Richard W. Titball
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, United Kingdom
| | - Julian I. Rood
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Stephen B. Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24601, USA
| | - Ian T. Paulsen
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Corresponding author.E-mail ; fax (301) 838-0208
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Brioukhanov AL, Netrusov AI, Eggen RIL. The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology (Reading) 2006; 152:1671-1677. [PMID: 16735730 DOI: 10.1099/mic.0.28542-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanosarcina barkeriis a strictly anaerobic methanogenic archaeon, which can survive oxidative stress. The oxidative stress agent paraquat (PQ) suppressed growth ofM. barkeriat concentrations of 50–200 μM. Hydrogen peroxide (H2O2) inhibited growth at concentrations of 0.4–1.6 mM. Catalase activity in cell-free extracts ofM. barkeriincreased about threefold during H2O2stress (1.3 mM H2O2, 2–4 h exposure) and nearly twofold during superoxide stress (160 μM PQ, 2 h exposure). PQ (160 μM, 2–4 h exposure) and H2O2(1.3 mM, 2 h exposure) also influenced superoxide dismutase activity in cell-free extracts ofM. barkeri. Dot-blot analysis was performed on total RNA isolated from H2O2- and PQ-exposed cultures, using labelled internal DNA fragments of thesodandkatgenes. It was shown that H2O2but not PQ strongly induced up-regulation of thekatgene. PQ and to a lesser degree H2O2induced the expression of superoxide dismutase. The results indicate the regulation of the adaptive response ofM. barkerito different oxidative stresses.
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Affiliation(s)
- Andrei L Brioukhanov
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Alexander I Netrusov
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Rik I L Eggen
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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48
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Rudolph G, Semini G, Hauser F, Lindemann A, Friberg M, Hennecke H, Fischer HM. The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein. J Bacteriol 2006; 188:733-44. [PMID: 16385063 PMCID: PMC1347296 DOI: 10.1128/jb.188.2.733-744.2006] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene cluster hmuVUT-hmuR-exbBD-tonB. Transcription of the divergently oriented hmuT and hmuR genes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ICE). Here, we show by deletion analysis that the full-length ICE is needed for this type of positive control. Additional genes associated with ICE-like motifs were identified in the B. japonicum genome, of which bll6680 and blr7895 code for bacterioferritin and rubrerythrin homologs, respectively. Transcription start site mapping revealed that their ICEs directly overlap with either the -10 promoter region or the transcription initiation site, suggesting an involvement of the ICE in negative control of both genes. Consistent with this inference was the observed down-regulation of both genes under iron limitation, which in the case of bll6680 was shown to require an intact ICE motif. Using a yeast one-hybrid system, we demonstrated in vivo interaction of the iron response regulator (Irr) with all three ICEs. Moreover, specific in vitro binding of purified Irr protein to the ICE motifs of bll6680 and blr7895 was shown in electrophoretic mobility shift experiments. A genome-wide survey for iron-regulated genes with a custom-made Affymetrix gene chip revealed 17 genes to be induced and 68 to be repressed under iron-replete conditions. Remarkably, ICE-like motifs are associated with a large subset of those B. japonicum genes. We propose the ICE as an important cis-acting element in B. japonicum which represents the DNA-binding site for the Irr protein and, depending on its location within promoter regions, is involved in positive or negative control of the associated iron-regulated genes.
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Affiliation(s)
- Gesine Rudolph
- Institute of Microbiology, Eidgenössische Technische Hochschule, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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Kawasaki S, Watamura Y, Ono M, Watanabe T, Takeda K, Niimura Y. Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum. Appl Environ Microbiol 2006; 71:8442-50. [PMID: 16332833 PMCID: PMC1317462 DOI: 10.1128/aem.71.12.8442-8450.2005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum and Clostridium aminovalericum, both obligatory anaerobes, grow normally after growth conditions are changed from anoxic to microoxic, where the cells consume oxygen proficiently. In C. aminovalericum, a gene encoding a previously characterized H2O-forming NADH oxidase, designated noxA, was cloned and sequenced. The expression of noxA was strongly upregulated within 10 min after the growth conditions were altered to a microoxic state, indicating that C. aminovalericum NoxA is involved in oxygen metabolism. In C. acetobutylicum, genes suggested to be involved in oxygen metabolism and genes for reactive oxygen species (ROS) scavenging were chosen from the genome database. Although no clear orthologue of C. aminovalericum NoxA was found, Northern blot analysis identified many O2-responsive genes (e.g., a gene cluster [CAC2448 to CAC2452] encoding an NADH rubredoxin oxidoreductase-A-type flavoprotein-desulfoferrodoxin homologue-MerR family-like protein-flavodoxin, an operon [CAC1547 to CAC1549] encoding a thioredoxin-thioredoxin reductase-glutathione peroxidase-like protein, an operon [CAC1570 and CAC1571] encoding two glutathione peroxidase-like proteins, and genes encoding thiol peroxidase, bacterioferritin comigratory proteins, and superoxide dismutase) whose expression was quickly and synchronously upregulated within 10 min after flushing with 5% O2. The corresponding enzyme activities, such as NAD(P)H-dependent peroxide (H2O2 and alkyl hydroperoxides) reductase, were highly induced, indicating that microoxic growth of C. acetobutylicum is associated with the expression of a number of genes for oxygen metabolism and ROS scavenging.
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Affiliation(s)
- Shinji Kawasaki
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Setagaya-ku, Tokyo 156-8502, Japan.
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50
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Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A. Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochimie 2006; 88:85-94. [PMID: 16040186 DOI: 10.1016/j.biochi.2005.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
The method of two-dimensional protein gel electrophoresis was used to evaluate the changes at the proteins level following oxygen exposure of the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Fifty-seven proteins showed significant differential expression. The cellular concentration of 35 proteins decreased while that of nineteen increased as a specific consequence of oxidative conditions. The proteins that were less abundant belonged to various functional categories such as nucleic acid and protein biosynthesis, detoxification mechanisms, or cell division. Interestingly, quantitative real-time PCR revealed that the genes encoding detoxification enzymes (rubrerythrins, superoxide reductase) are down regulated. The loss of viability of D. vulgaris Hildenborough under these oxidative conditions (Fournier et al., J. Biol. Chem. 279 (2004) 1785) can be directly related to the decrease in the cellular concentrations of these proteins, thereby specifying the toxicity of oxygen for the cells. Among the proteins that were more abundant under oxygen exposure, several thiol-specific peroxidases (thiol-peroxidase, BCP-like protein, and putative glutaredoxin) were identified. Using RT-PCR, the up-regulation of the genes encoding the thiol-peroxidase and the BCP was demonstrated. That is the first time that these proteins have been shown to be involved in the defense of D. vulgaris toward an oxidative stress. Several hypothetical proteins were also shown to be differentially expressed. A function in the defense mechanism against an oxidative stress is proposed for these uncharacterized proteins.
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Affiliation(s)
- Marjorie Fournier
- Laboratoire de bioénergétique et ingénierie des protéines, IBSM-CNRS, BIP, 31, chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
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