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Mao Q, Jiang J, Wu X, Ma Y, Zhang Y, Zhao Y, Zhang Y, Wang Q. Bifunctional alcohol/aldehyde dehydrogenase AdhE controls phospho-transferase system sugar utilization and virulence gene expression by interacting PtsH in Edwardsiella piscicida. Microbiol Res 2022; 260:127018. [DOI: 10.1016/j.micres.2022.127018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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Shanbhag AP, Ghatak A, Rajagopal S. Industrial light at the end of the Iron-containing (group III) alcohol dehydrogenase tunnel. Biotechnol Appl Biochem 2022; 70:537-552. [PMID: 35751426 DOI: 10.1002/bab.2376] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022]
Abstract
There are three prominent alcohol dehydrogenases superfamilies: Short-chain, Medium-chain, and Iron-containing alcohol dehydrogenases (FeADHs). Many members are valuable catalysts for producing industrially relevant products such as Active pharmaceutical Intermediates, Chiral synthons, Biopolymers, Biofuels and secondary metabolites. However, FeADHs are the least explored enzymes among the superfamilies for commercial tenacities. They portray a conserved structure having a 'tunnel-like' cofactor and substrate binding site with particular functions, despite representing high sequence diversity. Interestingly, phylogenetic analysis demarcates enzymes catalyzing distinct native substrates where closely related clades convert similar molecules. Further, homologs from various mesophilic and thermophilic microbes have been explored for designing a solvent and temperature resistant enzyme for industrial purposes. The review explores different Iron-containing alcohol dehydrogenases potential engineering of the enzymes and substrates helpful in manufacturing commercial products. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India
| | - Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK Campus, Bangalore, 560065
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Improved Hydrogen Peroxide Stress Resistance of Zymomonas mobilis NADH Dehydrogenase (ndh) and Alcohol Dehydrogenase (adhB) Mutants. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Unintended shifts in stress resistance of microbial strains with engineered central metabolism may impact their growth and production performance under oxidative, lignocellulosic, solvent, and other stress conditions, and as such, must be taken into account in bioprocess design. In the present work, we studied oxidative stress resistance in mutant strains of the facultatively anaerobic, ethanologenic bacterium Zymomonas mobilis with modified respiratory (inactivated NADH dehydrogenase Ndh, by disruption of ndh) and ethanologenic (inactivated iron-containing alcohol dehydrogenase isoenzyme ADH II, by disruption of adhB) catabolism, using exogenously added H2O2 in the concentration range of 2–6 mM as the oxidative stressor. Both mutations improved H2O2 resistance and enhanced catalase activity by a factor of 2–5, while the overexpression of Ndh had an opposite effect. Strains with a catalase-negative background were unable to grow already at 1 mM hydrogen peroxide, and their H2O2 resistance did not depend on AdhB or Ndh expression levels. Hence, the improved resistance of the ndh and adhB mutants to H2O2 resulted from their elevated catalase activity. The interrelation between these mutations, the catabolic redox balance, catalase activity, and oxidative stress defense in Z. mobilis is discussed.
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Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation. mSystems 2022; 7:e0126321. [PMID: 35384695 PMCID: PMC9040609 DOI: 10.1128/msystems.01263-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Photoheterotrophy is a widespread mode of microbial metabolism, notably in the oligotrophic surface ocean, where microbes experience chronic nutrient limitation. One especially widespread form of photoheterotrophy is based on proteorhodopsin (PR), which uses light to generate proton motive force that can drive ATP synthesis, flagellar movement, or nutrient uptake. To clarify the physiological benefits conferred by PR under nutrient stress conditions, we quantified protein-level gene expression of Vibrio campbellii CAIM 519 under both carbon and nitrogen limitation and under both light and dark conditions. Using a novel membrane proteomics strategy, we determined that PR expression is higher under C limitation than N limitation but is not light regulated. Despite expression of PR photosystems, V. campbellii does not exhibit any growth or survival advantages in the light and only a few proteins show significant expression differences between light and dark conditions. While protein-level proteorhodopsin expression in V. campbellii is clearly responsive to nutrient limitation, photoheterotrophy does not appear to play a central role in the survival physiology of this organism under these nutrient stress conditions. C limitation and N limitation, however, result in very different survival responses: under N-limited conditions, viability declines, cultivability is lost rapidly, central carbon flux through the Entner-Doudoroff pathway is increased, and ammonium is assimilated via the GS-GOGAT pathway. In contrast, C limitation drives cell dwarfing with maintenance of viability, as well as utilization of the glyoxylate shunt, glutamate dehydrogenase and anaplerotic C fixation, and a stringent response mediated by the Pho regulon. IMPORTANCE Understanding the nutrient stress responses of proteorhodopsin-bearing microbes like Vibrio campbellii yields insights into microbial contributions to nutrient cycling, lifestyles of emerging pathogens in aquatic environments, and protein-level adaptations implemented during times of nutrient limitation. In addition to its broad taxonomic and geographic prevalence, the physiological role of PR is diverse, so we developed a novel proteomics strategy to quantify its expression at the protein level. We found that proteorhodopsin expression levels in this wild-type photoheterotroph under these experimental conditions, while higher under C than under N limitation, do not afford measurable light-driven growth or survival advantages. Additionally, this work links differential protein expression patterns between C- and N-limited cultures to divergent stationary-phase survival phenotypes.
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Adewara OA, Ogunbanwo ST. Acid stress responses of Lactobacillus amylovorus and Candida kefyr isolated from fermented sorghum gruel and their application in food fermentation. Can J Microbiol 2022; 68:269-280. [PMID: 35038286 DOI: 10.1139/cjm-2021-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Exposure of Lactic Acid Bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress, consequently, microbes develop adaptive responses. In this study, the physiological and proteomic responses of LAB and yeast to acid stress, and their application in food fermentation was investigated. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry method, SDS-PAGE and LC-MS/MS respectively. The technique previously reported by Association of Official Analytical Chemists (AOAC) were employed for evaluation of the physiocochemical and organoleptic properties of the sorghum gruel fermented using the LAB and yeast in singly and combination as starter cultures and spontaneous fermentation as control. Growth of L. amylovorus LS07 was optimal at pH 1.0 and C. kefyr YSI2 at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was noted at pH 1 and 4 respectively suggesting increased microbial metabolism thereby reducing stress encountered. Sorghum gruel produced with combined starters had the highest crude protein (10.94 %), Iron content (0.0085 %), organoleptic acceptability (7.29) significantly different from products produced with the single starters and control. The combined starter's (L. amylovorus LS07 and C. kefyr YSI2 as starter) adapted stress yielded foods with improved sensory properties, mineral and reduced anti-nutrient contents.
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Affiliation(s)
- Oluwaseun Adeola Adewara
- University of Ibadan, 58987, Microbiology, Ibadan, Ibadan, Nigeria.,Caleb University, 202110, Biological Sciences and Biotechnology, Lagos, Lagos, Nigeria;
| | - S T Ogunbanwo
- University of Ibadan, Microbiology, P.O. Box 22346, University of Ibadan, Ibadan, Nigeria, Ibadan, Oyo, Nigeria, +234;
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6
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Transcriptional and Metabolic Response of Wine-Related Lactiplantibacillus plantarum to Different Conditions of Aeration and Nitrogen Availability. FERMENTATION 2021. [DOI: 10.3390/fermentation7020068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lactic acid bacteria (LAB) perform the process of malolactic fermentation (MLF) in wine. Availability of oxygen and nitrogen nutrients could influence LAB growth, malolactic activity, and other metabolic pathways, impacting the subsequent wine quality. The impact of these two factors has received limited investigation within LAB, especially on a transcriptome level. The aim of this study was to evaluate metabolic changes in the strain Lactiplantibacillus plantarum IWBT B063, growing in synthetic grape juice medium (GJM) under different oxygen exposure conditions, and with low availability of nitrogen-based nutrients. Next-generation sequencing was used to analyze expression across the transcriptome (RNA-seq), in combination with conventional microbiological and chemical analysis. L. plantarum consumed the malic acid present in all the conditions evaluated, with a slight delay and impaired growth for nitrogen limitation and for anaerobiosis. Comparison of L. plantarum transcriptome during growth in GJM with and without O2 revealed differential expression of 148 functionally annotated genes, which were mostly involved in carbohydrate metabolism, genetic information processing, and signaling and cellular processes. In particular, genes with a protective role against oxidative stress and genes related to amino acid metabolism were differentially expressed. This study confirms the suitability of L. plantarum IWBT B063 to carry out MLF in different environmental conditions due to its potential adaption to the stress conditions tested and provides a better understanding of the genetic background of an industrially relevant strain.
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Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond. Appl Environ Microbiol 2020; 86:AEM.01575-20. [PMID: 32978125 DOI: 10.1128/aem.01575-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/14/2020] [Indexed: 01/01/2023] Open
Abstract
Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on one modified-atmosphere-packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and beyond. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive of the sensory quality of the beef: acceptable product (AP), early spoilage (ES), and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced differences than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO, according to the transcribed reads. Leuconostoc species were the most abundant active LAB throughout the study period, whereas the transcription activity of Streptococcaceae (mainly Lactococcus) increased after the product had spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses, which were followed by expression of the genes involved in managing oxidative stress. Glycolysis, the pentose phosphate pathway, and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional transcription activities of the enzymes in these pathways changed over time.IMPORTANCE It is generally known which organisms are the typical SSO in foods, whereas the actively transcribed genes and pathways during microbial succession are poorly understood. This knowledge is important, since better approaches to food quality evaluation and shelf life determination are needed. Therefore, we conducted this study to find longitudinal markers that are connected to quality deterioration in a MAP beef product. This kind of RNA marker could be used to develop novel types of rapid quality analysis tools in the future. New tools are needed, since even though SSO can be detected and their concentrations determined using the current microbiological methods, results from these analyses cannot predict how close in time a spoilage community is to the production of clear sensory defects. The main reason for this is that the species composition of a spoilage community does not change dramatically during late shelf life, whereas the ongoing metabolic activities lead to the development of notable sensory deterioration.
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Cabezas CE, Laulié AM, Briones AC, Pardo-Esté C, Lorca DE, Cofré AA, Morales EH, Mora AY, Krüger GI, Bueno SM, Hidalgo AA, Saavedra CP. Activation of regulator ArcA in the presence of hypochlorite in Salmonella enterica serovar Typhimurium. Biochimie 2020; 180:178-185. [PMID: 33188860 DOI: 10.1016/j.biochi.2020.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/24/2023]
Abstract
Oxidative stress is the main mechanism behind efficient disinfectants, causing damage in bacterial macromolecules. Importantly, bacteria activate resistance mechanisms in response to damage generated by oxidative stress. Strategies allowing pathogens to survive oxidative stress are highly conserved among microorganisms. Many of these strategies entail genomic responses triggered by signals transduced through Two Component Systems (TCS). Recently, we demonstrated that the TCS ArcAB (specifically ArcA) participates in bacterial responses to hypochlorite, regulating the uptake of this toxic compound and being involved in resistance and survival inside neutrophils, where hypochlorous acid abounds. Here, we demonstrated that ArcA is required in the response to oxidative stress generated by hypochlorite, independent of its cognate sensor ArcB or the Asp54 of ArcA, the only phosphorylable residue in ArcA, which is required to function as a gene regulator. Our results suggest that ArcA could have additional functions to respond to oxidative stress, independent of its regulatory activity, which might require interaction with other unknown relevant proteins.
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Affiliation(s)
- Carolina E Cabezas
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Arlette M Laulié
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alan C Briones
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Diego E Lorca
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Agustin A Cofré
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Aracely Y Mora
- Laboratorio de patogénesis molecular y antimicrobianos y Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Gabriel I Krüger
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandr A Hidalgo
- Laboratorio de patogénesis molecular y antimicrobianos y Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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Gu Y, Wang S, Huang L, Sa W, Li J, Huang J, Dai M, Cheng G. Development of Resistance in Escherichia coli ATCC25922 under Exposure of Sub-Inhibitory Concentration of Olaquindox. Antibiotics (Basel) 2020; 9:E791. [PMID: 33182563 PMCID: PMC7696260 DOI: 10.3390/antibiotics9110791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/31/2023] Open
Abstract
Quinoxaline1,4-di-N-oxides (QdNOs) are a class of important antibacterial drugs of veterinary use, of which the drug resistance mechanism has not yet been clearly explained. This study investigated the molecular mechanism of development of resistance in Escherichia coli (E. coli) under the pressure of sub-inhibitory concentration (sub-MIC) of olaquindox (OLA), a representative QdNOs drug. In vitro challenge of E. coli with 1/100× MIC to 1/2× MIC of OLA showed that the bacteria needed a longer time to develop resistance and could only achieve low to moderate levels of resistance as well as form weak biofilms. The transcriptomic and genomic profiles of the resistant E. coli induced by sub-MIC of OLA demonstrated that genes involved in tricarboxylic acid cycle, oxidation-reduction process, biofilm formation, and efflux pumps were up-regulated, while genes involved in DNA repair and outer membrane porin were down-regulated. Mutation rates were significantly increased in the sub-MIC OLA-treated bacteria and the mutated genes were mainly involved in the oxidation-reduction process, DNA repair, and replication. The SNPs were found in degQ, ks71A, vgrG, bigA, cusA, and DR76-4702 genes, which were covered in both transcriptomic and genomic profiles. This study provides new insights into the resistance mechanism of QdNOs and increases the current data pertaining to the development of bacterial resistance under the stress of antibacterials at sub-MIC concentrations.
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Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuge Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Sa
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Jun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Menghong Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
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Gao Y, Liu Y, Ma F, Sun M, Mu G, Tuo Y. Global transcriptomic and proteomics analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. J Proteomics 2020; 226:103903. [PMID: 32682107 DOI: 10.1016/j.jprot.2020.103903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/23/2020] [Accepted: 07/11/2020] [Indexed: 12/22/2022]
Abstract
Our previous study demonstrated that Lactobacillus plantarum Y44 exhibited antioxidant activity. However, the physiological characteristics of L. plantarum Y44 exposure to oxidative stress was not clear. In this research, the differentially expressed proteins and genes in L. plantarum Y44 under 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress at different concentrations were studied by using integrated transcriptomic and proteomic methods. Under 100 mM AAPH stress condition, 1139 differentially expressed genes (DEGs, 546 up-regulated and 593 down-regulated) and 329 differentially expressed proteins (DEPs, 127 up-regulated and 202 down-regulated) were observed. Under 200 mM AAPH stress condition, 1526 DEGs (751 up-regulated and 775 down-regulated) and 382 DEPs (139 up-regulated and 243 down-regulated) were observed. Overall, we found that L. plantarum Y44 fought against AAPH induced oxidative stress by up-regulating antioxidant enzymes and DNA repair proteins, such as ATP-dependent DNA helicase RuvA, adenine DNA glycosylase, single-strand DNA-binding protein SSB, DNA-binding ferritin-like protein DPS, thioredoxin reductase, protein-methionine-S-oxide reductase and glutathione peroxidase. Additionally, cell envelope composition of L. plantarum Y44 was highly remodeled by accelerating peptidoglycan and teichoic-acid (LTA) biosynthesis and modulating the fatty acids (FA) composition to achieve a higher ratio of unsaturated/saturated fatty acids (UFAs/SFAs) against AAPH stress. Moreover, metabolism processes including carbohydrate metabolism, amino acid biosynthesis, and nucleotide metabolism altered to respond to AAPH-induced damage. Altogether, our findings allow us to facilitate a better understanding of L. plantarum Y44 against oxidative stress. SIGNIFICANCE: This study represents an integrated proteomic and transcriptomic analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. Differentially expressed proteins and genes were identified between the proteome and transcriptome of L. plantarum Y44 under different AAPH stress. AAPH-induced response of L. plantarum Y44 appears to be primarily based on ROS scavenging, DNA repair, highly remodeled cell surface and specific metabolic processes. The knowledge about these proteomes and transcriptomes provides significant insights into the oxidative stress response of Lactobacillus plantarum.
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Affiliation(s)
- Yuan Gao
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Yujun Liu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China
| | - Fenglian Ma
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Mengying Sun
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Guangqing Mu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
| | - Yanfeng Tuo
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
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11
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Castro-Severyn J, Pardo-Esté C, Mendez KN, Morales N, Marquez SL, Molina F, Remonsellez F, Castro-Nallar E, Saavedra CP. Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano. Front Microbiol 2020; 11:1632. [PMID: 32760381 PMCID: PMC7374977 DOI: 10.3389/fmicb.2020.01632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Sebastián L Marquez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag CNRS/Alcediag, CNRS UMR 3145, Montpellier, France
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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12
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Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation. Nat Commun 2020; 11:1426. [PMID: 32188856 PMCID: PMC7080775 DOI: 10.1038/s41467-020-15214-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/26/2020] [Indexed: 11/08/2022] Open
Abstract
Acetaldehyde-alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD+ regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. Here, we use cryo-electron microscopy to obtain structures of Escherichia coli spirosomes in different conformational states. We show that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity.
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A novel Xanthomonas citri subsp. citri NADPH quinone reductase involved in salt stress response and virulence. Biochim Biophys Acta Gen Subj 2020; 1864:129514. [PMID: 31911239 DOI: 10.1016/j.bbagen.2020.129514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker is maintained as an epiphyte on citrus leaves until entering the plant tissue. During epiphytic survival, bacteria may encounter low water availability that challenges the infection process. Proteomics analyses of Xcc under saline stress, mimicking the conditions found during epiphytic survival, showed increased abundance of a putative NAD(P)H dehydrogenase encoded by XAC2229. METHODS Expression levels of XAC2229 and a Xcc mutant in XAC2229 were analyzed in salt and oxidative stress and during plant-pathogen interaction. An Escherichia coli expressing XAC2229 was obtained, and the role of this protein in oxidative stress resistance and in reactive oxygen species production was studied. Finally, Xac2229 protein was purified, spectrophotometric and cofactor analyses were done and enzymatic activities determined. RESULTS XAC2229 was expressed under salt stress and during plant-pathogen interaction. ΔXAC2229 mutant showed less number of cankers and impaired epiphytic survival than the wild type strain. ΔXAC2229 survived less in the presence of H2O2 and produced more reactive oxygen species and thiobarbituric acid-reactive substances than the wild type strain. Similar results were observed for E. coli expressing XAC2229. Xac2229 is a FAD containing flavoprotein, displays diaphorase activity with an optimum at pH 6.0 and has quinone reductase activity using NADPH as an electron donor. CONCLUSIONS A FAD containing flavoprotein from Xcc is a new NADPH quinone reductase required for bacterial virulence, particularly in Xcc epiphytic survival on citrus leaves. GENERAL SIGNIFICANCE A novel protein involved in the worldwide disease citrus canker was characterized.
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14
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Zhou J, Lu X, Tian B, Wang C, Shi H, Luo C, Zhu X, Yuan X, Li X. Knockout of acetoacetate degradation pathway gene atoDA enhances the toxicity tolerance of Escherichia coli to isopropanol and acetone. 3 Biotech 2019; 9:343. [PMID: 31497461 DOI: 10.1007/s13205-019-1867-5] [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: 05/30/2019] [Accepted: 08/12/2019] [Indexed: 01/13/2023] Open
Abstract
Isopropanol and acetone are important chemical products and potential high-quality new fuels. Both of them are metabolites of isopropanol synthesis pathway, but they are toxic to most bacteria. In this study, toxicity tolerance of Escherichia coli strains was evaluated by detecting their growth rates under different concentrations of isopropanol and acetone. It was showed that isopropanol was more toxic to E. coli than acetone, and the native strain MG1655 had better tolerance over DH5α to either acetone or isopropanol of 300 mM. Key genes of ethanol synthesis pathway, acetic acid metabolism pathway, and acetoacetic acid degradation pathway, including adhE, ackA-pta, and atoDA, were knocked out in MG1655 to form mutants MGΔadhE, MGΔackA-pta, and MGΔatoDA. The tolerance performances of the mutants to isopropanol and acetone were determined under various concentrations including 300 mM, 500 mM, and 700 mM, respectively. The mutant MGΔatoDA exhibited excellent tolerance to both acetone and isopropanol of 500 mM, and MGΔackA-pta could tolerate acetone at 500 mM rather than isopropanol, while the deletion of adhE in MGΔadhE resulted in a severe cell growth defection. Although isopropanol and acetone at 700 mM caused severe growth inhibition on each strain, cell growth could be restored to varying degrees with the prolongation of culture time. This phenomenon was suggested to be related to the volatilization of isopropanol and acetone based on volatilization tests. It was envisioned that MG1655 was a suitable host strain for isopropanol metabolic engineering research, and the acetoacetic acid degradation pathway gene atoDA, was probably the key optimizing point for isopropanol production.
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Affiliation(s)
- Jia Zhou
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoqing Lu
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Baoxia Tian
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Chonglong Wang
- 3School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123 People's Republic of China
| | - Hao Shi
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Chuping Luo
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoyan Zhu
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoqing Yuan
- Suzhou Xuhui Analysis Co., Ltd, 168 Yuan Feng Road, Kunshan High Tech Zone, Suzhou, 215300 People's Republic of China
| | - Xiangqian Li
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
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15
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Doi Y. Lactic acid fermentation is the main aerobic metabolic pathway in Enterococcus faecalis metabolizing a high concentration of glycerol. Appl Microbiol Biotechnol 2018; 102:10183-10192. [DOI: 10.1007/s00253-018-9351-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/18/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
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16
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Pardo-Esté C, Hidalgo AA, Aguirre C, Briones AC, Cabezas CE, Castro-Severyn J, Fuentes JA, Opazo CM, Riedel CA, Otero C, Pacheco R, Valvano MA, Saavedra CP. The ArcAB two-component regulatory system promotes resistance to reactive oxygen species and systemic infection by Salmonella Typhimurium. PLoS One 2018; 13:e0203497. [PMID: 30180204 PMCID: PMC6122832 DOI: 10.1371/journal.pone.0203497] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica Serovar Typhimurium (S. Typhimurium) is an intracellular bacterium that overcomes host immune system barriers for successful infection. The bacterium colonizes the proximal small intestine, penetrates the epithelial layer, and is engulfed by macrophages and neutrophils. Intracellularly, S. Typhimurium encounters highly toxic reactive oxygen species including hydrogen peroxide and hypochlorous acid. The molecular mechanisms of Salmonella resistance to intracellular oxidative stress is not completely understood. The ArcAB two-component system is a global regulatory system that responds to oxygen. In this work, we show that the ArcA response regulator participates in Salmonella adaptation to changing oxygen levels and is also involved in promoting intracellular survival in macrophages and neutrophils, enabling S. Typhimurium to successfully establish a systemic infection.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alejandro A. Hidalgo
- Laboratorio de Patogenesis Bacteriana, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Camila Aguirre
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Alan C. Briones
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina E. Cabezas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Cecilia M. Opazo
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de la Vida y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Claudia A. Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de la Vida y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Carolina Otero
- Center for Integrative Medicine and Innovative Science (CIMIS), Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Pacheco
- Laboratorio de Neuroinmunología, Fundación Ciencia & Vida, Santiago, Chile
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Miguel A. Valvano
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de la Vida y Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
- * E-mail:
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17
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Cabezas CE, Briones AC, Aguirre C, Pardo-Esté C, Castro-Severyn J, Salinas CR, Baquedano MS, Hidalgo AA, Fuentes JA, Morales EH, Meneses CA, Castro-Nallar E, Saavedra CP. The transcription factor SlyA from Salmonella Typhimurium regulates genes in response to hydrogen peroxide and sodium hypochlorite. Res Microbiol 2018; 169:263-278. [DOI: 10.1016/j.resmic.2018.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 03/29/2018] [Accepted: 04/21/2018] [Indexed: 11/15/2022]
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18
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Reactive oxygen species-independent apoptotic pathway by gold nanoparticles in Candida albicans. Microbiol Res 2018; 207:33-40. [DOI: 10.1016/j.micres.2017.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/28/2017] [Accepted: 11/04/2017] [Indexed: 11/23/2022]
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19
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Pineda E, Perdomo D. Entamoeba histolytica under Oxidative Stress: What Countermeasure Mechanisms Are in Place? Cells 2017; 6:cells6040044. [PMID: 29160807 PMCID: PMC5755502 DOI: 10.3390/cells6040044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 02/06/2023] Open
Abstract
Entamoeba histolytica is the causative agent of human amoebiasis; it affects 50 million people worldwide and causes approximately 100,000 deaths per year. Entamoeba histolytica is an anaerobic parasite that is primarily found in the colon; however, for unknown reasons, it can become invasive, breaching the gut barrier and migrating toward the liver causing amoebic liver abscesses. During the invasive process, it must maintain intracellular hypoxia within the oxygenated human tissues and cellular homeostasis during the host immune defense attack when it is confronted with nitric oxide and reactive oxygen species. But how? This review will address the described and potential mechanisms available to counter the oxidative stress generated during invasion and the possible role that E. histolytica’s continuous endoplasmic reticulum (Eh-ER) plays during these events.
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Affiliation(s)
- Erika Pineda
- Laboratory of Fundamental Microbiology and Pathogenicity (MFP), University of Bordeaux, CNRS UMR-5234, 33000 Bordeaux, France.
| | - Doranda Perdomo
- Laboratory of Fundamental Microbiology and Pathogenicity (MFP), University of Bordeaux, CNRS UMR-5234, 33000 Bordeaux, France.
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20
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Nabu S, Lawung R, Isarankura-Na-Ayudhya P, Roytrakul S, Dolprasit S, Sengyee S, Isarankura-Na-Ayudhya C, Prachayasittikul V. Comparative proteomics analysis of Neisseria gonorrhoeae strains in response to extended-spectrum cephalosporins. EXCLI JOURNAL 2017; 16:1207-1229. [PMID: 29285017 PMCID: PMC5736987 DOI: 10.17179/excli2017-832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/18/2017] [Indexed: 01/02/2023]
Abstract
Neisseria gonorrhoeae strains displaying reduced susceptibility and resistance to extended-spectrum cephalosporins (ESCs) are major public health concerns. Although resistance mechanisms of ESCs have extensively been studied, the proteome-wide investigation on the biological response to the antibiotic stress is still limited. Herein, a proteomics approach based on two-dimensional gel electrophoresis and MALDI-TOF/TOF-MS analysis was applied to investigate the global protein expression under ESC stresses of ESC-susceptible and ESC-reduced susceptible N. gonorrhoeae strains. Upon exposure to ceftriaxone, 14 and 21 proteins of ESC-susceptible and ESC-reduced susceptible strains, respectively, were shown to be differentially expressed. In the meanwhile, differential expressions of 13 and 17 proteins were detected under cefixime stress for ESC-susceptible and ESC-reduced susceptible strains, respectively. ESC antibiotics have been proven to trigger the expression of several proteins implicated in a variety of biological functions including transport system, energy metabolism, stress response and pathogenic virulence factors. Interestingly, macrophage infectivity potentiators (Ng-MIP) showed increased expression for ESC-reduced susceptible strain under ESC stress. The altered expression of Ng-MIP was found to be a unique response to ESC stresses. Our finding proposes a broad view on proteomic changes in N. gonorrhoeae in response to ESC antibiotics that provides further insights into the gonococcal antimicrobial resistance and physiological adaptation mechanism.
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Affiliation(s)
- Sunanta Nabu
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratana Lawung
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.,Center of Medical Laboratory Services, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Supamas Dolprasit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Sineenart Sengyee
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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21
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Morandi GD, Wiseman SB, Guan M, Zhang XW, Martin JW, Giesy JP. Elucidating mechanisms of toxic action of dissolved organic chemicals in oil sands process-affected water (OSPW). CHEMOSPHERE 2017; 186:893-900. [PMID: 28830063 DOI: 10.1016/j.chemosphere.2017.08.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/13/2017] [Accepted: 08/06/2017] [Indexed: 06/07/2023]
Abstract
Oil sands process-affected water (OSPW) is generated during extraction of bitumen in the surface-mining oil sands industry in Alberta, Canada, and is acutely and chronically toxic to aquatic organisms. It is known that dissolved organic compounds in OSPW are responsible for most toxic effects, but knowledge of the specific mechanism(s) of toxicity, is limited. Using bioassay-based effects-directed analysis, the dissolved organic fraction of OSPW has previously been fractionated, ultimately producing refined samples of dissolved organic chemicals in OSPW, each with distinct chemical profiles. Using the Escherichia coli K-12 strain MG1655 gene reporter live cell array, the present study investigated relationships between toxic potencies of each fraction, expression of genes and characterization of chemicals in each of five acutely toxic and one non-toxic extract of OSPW derived by use of effects-directed analysis. Effects on expressions of genes related to response to oxidative stress, protein stress and DNA damage were indicative of exposure to acutely toxic extracts of OSPW. Additionally, six genes were uniquely responsive to acutely toxic extracts of OSPW. Evidence presented supports a role for sulphur- and nitrogen-containing chemical classes in the toxicity of extracts of OSPW.
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Affiliation(s)
- Garrett D Morandi
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Steve B Wiseman
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Biological Sciences and Water Institute for Sustainable Environments (WISE), University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Miao Guan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaowei W Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Jonathan W Martin
- Division of Analytical and Environmental Toxicology, University of Alberta, Edmonton, AB T6G 2G3, Canada; Department of Environmental Sciences and Analytical Chemistry, Stockholm University, Stockholm, 114 18, Sweden
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Zoology Department, Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA; School of Biological Sciences, University of Hong Kong, 999077, Hong Kong Special Administrative Region.
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22
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González L, García-Huertas P, Triana-Chávez O, García GA, Murta SMF, Mejía-Jaramillo AM. Aldo-keto reductase and alcohol dehydrogenase contribute to benznidazole natural resistance in Trypanosoma cruzi. Mol Microbiol 2017; 106:704-718. [PMID: 28884498 DOI: 10.1111/mmi.13830] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2017] [Indexed: 12/16/2022]
Abstract
The improvement of Chagas disease treatment is focused not only on the development of new drugs but also in understanding mechanisms of action and resistance to drugs conventionally used. Thus, some strategies aim to detect specific changes in proteins between sensitive and resistant parasites and to evaluate the role played in these processes by functional genomics. In this work, we used a natural Trypanosoma cruzi population resistant to benznidazole, which has clones with different susceptibilities to this drug without alterations in the NTR I gene. Using 2DE-gel electrophoresis, the aldo-keto reductase and the alcohol dehydrogenase proteins were found up regulated in the natural resistant clone and therefore their possible role in the resistance to benznidazole and glyoxal was investigated. Both genes were overexpressed in a drug sensitive T. cruzi clone and the biological changes in response to these compounds were evaluated. The results showed that the overexpression of these proteins enhances resistance to benznidazole and glyoxal in T. cruzi. Moreover, a decrease in mitochondrial and cell membrane damage was observed, accompanied by a drop in the intracellular concentration of reactive oxygen species after treatment. Our results suggest that these proteins are involved in the mechanism of action of benznidazole.
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Affiliation(s)
- Laura González
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI, Universidad de Antioquia, UdeA, Medellín, Colombia
| | - Paola García-Huertas
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI, Universidad de Antioquia, UdeA, Medellín, Colombia
| | - Omar Triana-Chávez
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI, Universidad de Antioquia, UdeA, Medellín, Colombia
| | - Gabriela Andrea García
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"- ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Ana M Mejía-Jaramillo
- Grupo Biología y Control de Enfermedades Infecciosas-BCEI, Universidad de Antioquia, UdeA, Medellín, Colombia
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23
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Li P, Xu Z, Sun X, Yin Y, Fan Y, Zhao J, Mao X, Huang J, Yang F, Zhu L. Transcript profiling of the immunological interactions between Actinobacillus pleuropneumoniae serotype 7 and the host by dual RNA-seq. BMC Microbiol 2017; 17:193. [PMID: 28899359 PMCID: PMC5596872 DOI: 10.1186/s12866-017-1105-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/05/2017] [Indexed: 02/08/2023] Open
Abstract
Background The complexity of the pathogenic mechanism underlying the host immune response to Actinobacillus pleuropneumonia (App) makes the use of preventive measures difficult, and a more global view of the host-pathogen interactions and new insights into this process are urgently needed to reveal the pathogenic and immune mechanisms underlying App infection. Here, we infected specific pathogen-free Mus musculus with App serotype 7 by intranasal inoculation to construct an acute hemorrhagic pneumonia infection model and isolated the infected lungs for analysis of the interactions by dual RNA-seq. Results Four cDNA libraries were constructed, and 2428 differentially expressed genes (DEGs) of the host and 333 DEGs of App were detected. The host DEGs were mainly enriched in inflammatory signaling pathways, such as the TLR, NLR, RLR, BCR and TCR signaling pathways, resulting in large-scale cytokine up-regulation and thereby yielding a cytokine cascade for anti-infection and lung damage. The majority of the up-regulated cytokines are involved in the IL-23/IL-17 cytokine-regulated network, which is crucial for host defense against bacterial infection. The DEGs of App were mainly related to the transport and metabolism of energy and materials. Most of these genes are metabolic genes involved in anaerobic metabolism and important for challenging the host and adapting to the anaerobic stress conditions observed in acute hemorrhagic pneumonia. Some of these genes, such as adhE, dmsA, and aspA, might be potential virulence genes. In addition, the up-regulation of genes associated with peptidoglycan and urease synthesis and the restriction of major virulence genes might be immune evasion strategies of App. The regulation of metabolic genes and major virulence genes indicate that the dominant antigens might differ during the infection process and that vaccines based on these antigens might allow establishment of a precise and targeted immune response during the early phase of infection. Conclusion Through an analysis of transcriptional data by dual RNA-seq, our study presents a novel global view of the interactions of App with its host and provides a basis for further study. Electronic supplementary material The online version of this article (10.1186/s12866-017-1105-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping Li
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Zhiwen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Xiangang Sun
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China
| | - Yue Yin
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Yi Fan
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Jun Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Xiyu Mao
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Jianbo Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Fan Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Huimin Road 211, Weenjiang District, Chengdu, Sichuan, China. .,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, Sichuan, China.
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Shabayek S, Spellerberg B. Acid Stress Response Mechanisms of Group B Streptococci. Front Cell Infect Microbiol 2017; 7:395. [PMID: 28936424 PMCID: PMC5594096 DOI: 10.3389/fcimb.2017.00395] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/23/2017] [Indexed: 12/20/2022] Open
Abstract
Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple different host niches. The pathophysiology of this bacterium reveals an outstanding ability to withstand varying pH fluctuations of the surrounding environments inside the human host. GBS host pathogen interations include colonization of the acidic vaginal mucosa, invasion of the neutral human blood or amniotic fluid, breaching of the blood brain barrier as well as survival within the acidic phagolysosomal compartment of macrophages. However, investigations on GBS responses to acid stress are limited. Technologies, such as whole genome sequencing, genome-wide transcription and proteome mapping facilitate large scale identification of genes and proteins. Mechanisms enabling GBS to cope with acid stress have mainly been studied through these techniques and are summarized in the current review
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Affiliation(s)
- Sarah Shabayek
- Institute of Medical Microbiology and Hygiene, University of UlmUlm, Germany.,Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal UniversityIsmailia, Egypt
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, University of UlmUlm, Germany
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Silver Nanoparticles Against Salmonella enterica Serotype Typhimurium: Role of Inner Membrane Dysfunction. Curr Microbiol 2017; 74:661-670. [PMID: 28321528 DOI: 10.1007/s00284-017-1235-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
The evolution of antibiotics-resistant bacteria is considered a major concern. To explore promising antibacterial materials and clarify their unknown mechanisms, the mode of action of silver nanoparticles (AgNPs) against Salmonella enterica serotype typhimurium was investigated. We investigated the effect of AgNPs on the bacterial membrane. The N-phenyl-1-naphthylamine assay showed that the permeability of the outer membrane was not changed by treatment with AgNPs. The O-nitrophenyl-β-D-galactopyranoside assay showed that the inner membrane permeability increased as AgNPs concentration increased. Our results showed that AgNPs affected the inner membrane without outer membrane damage. Generally, antibiotic-induced reactive oxygen species (ROS) and changes in the Ca2+ gradient are known to contribute to bacterial cell death. Likewise, we detected that AgNPs induced the accumulation of ROS and intracellular Ca2+ depending on its concentration, using 2',7'-dichlorodihydrofluorescein and Fura-2AM, respectively. At higher concentrations, no relationship between oxidative stress and bactericidal effects of AgNPs was confirmed through a cell viability assay and intracellular Ca2+ assay with antioxidant N-acetylcysteine. In this study, the inner membrane disruption followed by membrane dysfunction played a key role in the antibacterial activity of AgNPs against S. typhimurium. Contrary to the expected results, ROS do not influence growth inhibition of AgNPs.
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Andreevskaya M, Johansson P, Jääskeläinen E, Rämö T, Ritari J, Paulin L, Björkroth J, Auvinen P. Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase. BMC Genomics 2016; 17:539. [PMID: 27487841 PMCID: PMC4972977 DOI: 10.1186/s12864-016-2840-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose. RESULTS The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site. CONCLUSIONS This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth with different carbohydrates differ significantly from those of facultative heterofermentative lactobacilli. The mechanism of CcpA regulation, putatively contributing to the observed similarities between glucose- and xylose-induced transcriptome responses and the absence of stringent carbon catabolite control, requires further studies. Finally, the cell redox balance maintenance, in terms of the NAD(P)+/NAD(P)H ratio, was predicted to be regulated by the Rex transcriptional regulator, supporting the previously made inference of Rex-regulons for members of the Lactobacillaceae family.
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Affiliation(s)
| | - Per Johansson
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Elina Jääskeläinen
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Tanja Rämö
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Present Address: The National Bureau of Investigation, Vantaa, Finland
| | - Jarmo Ritari
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Present Address: Finnish Red Cross Blood Service, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Knudsen GM, Fromberg A, Ng Y, Gram L. Sublethal Concentrations of Antibiotics Cause Shift to Anaerobic Metabolism in Listeria monocytogenes and Induce Phenotypes Linked to Antibiotic Tolerance. Front Microbiol 2016; 7:1091. [PMID: 27462313 PMCID: PMC4940397 DOI: 10.3389/fmicb.2016.01091] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 06/30/2016] [Indexed: 02/05/2023] Open
Abstract
The human pathogenic bacterium Listeria monocytogenes is exposed to antibiotics both during clinical treatment and in its saprophytic lifestyle. As one of the keys to successful treatment is continued antibiotic sensitivity, the purpose of this study was to determine if exposure to sublethal antibiotic concentrations would affect the bacterial physiology and induce antibiotic tolerance. Transcriptomic analyses demonstrated that each of the four antibiotics tested caused an antibiotic-specific gene expression pattern related to mode-of-action of the particular antibiotic. All four antibiotics caused the same changes in expression of several metabolic genes indicating a shift from aerobic to anaerobic metabolism and higher ethanol production. A mutant in the bifunctional acetaldehyde-CoA/alcohol dehydrogenase encoded by lmo1634 did not have altered antibiotic tolerance. However, a mutant in lmo1179 (eutE) encoding an aldehyde oxidoreductase where rerouting caused increased ethanol production was tolerant to three of four antibiotics tested. This shift in metabolism could be a survival strategy in response to antibiotics to avoid generation of ROS production from respiration by oxidation of NADH through ethanol production. The monocin locus encoding a cryptic prophage was induced by co-trimoxazole and repressed by ampicillin and gentamicin, and this correlated with an observed antibiotic-dependent biofilm formation. A monocin mutant (ΔlmaDCBA) had increased biofilm formation when exposed to increasing concentration of co-trimoxazole similar to the wild type, but was more tolerant to killing by co-trimoxazole and ampicillin. Thus, sublethal concentrations of antibiotics caused metabolic and physiological changes indicating that the organism is preparing to withstand lethal antibiotic concentrations.
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Affiliation(s)
- Gitte M Knudsen
- Department of Bioengineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Arvid Fromberg
- National Food Institute, Technical University of Denmark Søborg, Denmark
| | - Yin Ng
- Department of Bioengineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Lone Gram
- Department of Bioengineering, Technical University of Denmark Kongens Lyngby, Denmark
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Antibacterial activity of curcumin via apoptosis-like response in Escherichia coli. Appl Microbiol Biotechnol 2016; 100:5505-14. [PMID: 26960318 DOI: 10.1007/s00253-016-7415-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/21/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Curcumin, a naturally occurring phenolic compound, has been shown to exhibit antimicrobial activity against Candida albicans, Escherichia coli, Pseudomonas aeruginosa, etc., but the mechanism remains unclear. The present study was designed to investigate the novel antibacterial mechanism of curcumin that shows an apoptosis-like response in E. coli. We found that curcumin induces membrane damage at relatively high concentrations, but there was no effect at the minimum inhibitory concentration (MIC). At the MIC, curcumin-treated cells displayed various apoptotic markers such as reactive oxygen species (ROS) accumulation, membrane depolarization, and Ca(2+) influx. Expression of RecA protein, which mediates a bacterial apoptosis-like response, was also increased by curcumin. In order to evaluate the influence of RecA on the appearance of other apoptotic markers, phosphatidylserine (PS) exposure and DNA fragmentation were examined and compared with a RecA deletion strain (ΔRecA). These markers were detected in E. coli wild-type cells, but not in ΔRecA cells. In conclusion, our data demonstrate that curcumin induces an apoptosis-like response in E. coli that involves RecA.
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Branco R, Morais PV. Two superoxide dismutases from TnOtchr are involved in detoxification of reactive oxygen species induced by chromate. BMC Microbiol 2016; 16:27. [PMID: 26944876 PMCID: PMC4779226 DOI: 10.1186/s12866-016-0648-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background Superoxide dismutases (SOD) have been reported as the most relevant bacterial enzymes involved in cells protection from reactive oxygen species (ROS). These toxic species are often the product of heavy metal stress. Results Two genes, chrC and chrF, from TnOtchr genetic determinant of strain Ochrobactrum tritici 5bvl1 were cloned in Escherichia coli in order to overexpress the respective proteins. Both proteins were purified and characterized as superoxide dismutases. ChrC was confirmed as being a Fe-SOD, and the enzymatic activity of the ChrF, not inhibited by hydrogen peroxide or potassium cyanide, suggested its inclusion in the Mn-SOD family. This identification was supported by chemical quantification of total metal content in purified enzyme. Both enzymes showed a maximum activity between pH 7.2-7.5. ChrF retained nearly full activity over a broader range of pH and was slightly more thermostable than ChrC. The genes encoding these enzymes in strain O. tritici 5bvl1 were inactivated, developing single and double mutants, to understand the contribution of these enzymes in detoxification mechanism of reactive oxygen species induced by chromate. During chromate stress, assays using fluorescent dyes indicated an increase of these toxic compounds in chrC, chrF and chrC/chrF mutant cells. Conclusions In spite of the multiple genes coding for putative superoxide dismutase enzymes detected in the genome of O. tritici 5bvl1, the ChrC and ChrF might help the strain to decrease the levels of reactive oxygen species in cells.
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Affiliation(s)
- Rita Branco
- CEMUC-Department of Mechanical Engineering, University of Coimbra, 3030-788, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, 3001-401, Coimbra, Portugal.
| | - Paula V Morais
- CEMUC-Department of Mechanical Engineering, University of Coimbra, 3030-788, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, 3001-401, Coimbra, Portugal.
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Kumar D, Rampuria S, Singh NK, Kirti PB. A novel zinc-binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco. FEBS Open Bio 2016; 6:200-10. [PMID: 27047748 PMCID: PMC4794784 DOI: 10.1002/2211-5463.12040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/11/2015] [Accepted: 01/08/2016] [Indexed: 12/26/2022] Open
Abstract
A novel zinc-binding alcohol dehydrogenase 2 (AdZADH2) was significantly upregulated in a wild peanut, Arachis diogoi treated with conidia of late leaf spot (LLS) pathogen, Phaeoisariopsis personata. This upregulation was not observed in a comparative analysis of cultivated peanut, which is highly susceptible to LLS. This zinc-binding alcohol dehydrogenase possessed a Rossmann fold containing NADB domain in addition to the MDR domain present in all previously characterized plant ADH genes/proteins. Transient over-expression of AdZADH2 under an estradiol inducible promoter (XVE) resulted in hypersensitive response (HR)-like cell death in tobacco leaf. However, the same level of cell death was not observed when the domains were transiently expressed individually. Cell death observed in tobacco was associated with overexpression of cell death related proteins, antioxidative enzymes such as SOD, CAT and APX and pathogenesis-related (PR) proteins. In A. diogoi, AdZADH2 expression was significantly upregulated in response to the plant signaling hormones salicylic acid, methyl jasmonate, and sodium nitroprusside.
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Affiliation(s)
- Dilip Kumar
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Sakshi Rampuria
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Naveen Kumar Singh
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
| | - Pulugurtha B Kirti
- Department of Plant Sciences School of Life Sciences University of Hyderabad India
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Metabolic engineering of Klebsiella pneumoniae and in silico investigation for enhanced 2,3-butanediol production. Biotechnol Lett 2016; 38:975-82. [DOI: 10.1007/s10529-016-2062-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/02/2016] [Indexed: 11/26/2022]
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McCarthy S, Johnson T, Pavlik BJ, Payne S, Schackwitz W, Martin J, Lipzen A, Keffeler E, Blum P. Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution. Appl Environ Microbiol 2016; 82:857-67. [PMID: 26590281 PMCID: PMC4725277 DOI: 10.1128/aem.03225-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. The pH extremes of these habitats, however, often exceed the acid tolerance of type species and strains. Here, adaptive laboratory evolution was used over a 3-year period to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high-temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains were named super-acid-resistant Crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance, while genome resequencing and transcriptome resequencing were conducted for insight into mechanisms responsible for the evolved trait. Among the mutations that were detected, a set of eight nonsynonymous changes may explain the heritability of increased acid resistance despite an unexpected lack of transposition. Four multigene components of the SARC transcriptome implicated oxidative stress as a primary challenge accompanying growth at acid extremes. These components included accelerated membrane biogenesis, induction of the mer operon, and an increased capacity for the generation of energy and reductant.
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Affiliation(s)
- Samuel McCarthy
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tyler Johnson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Benjamin J Pavlik
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sophie Payne
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Erica Keffeler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Shasmal M, Dey S, Shaikh TR, Bhakta S, Sengupta J. E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed. Sci Rep 2016; 6:19936. [PMID: 26822933 PMCID: PMC4731797 DOI: 10.1038/srep19936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 11/24/2022] Open
Abstract
It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosome.
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Affiliation(s)
- Manidip Shasmal
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Sandip Dey
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Tanvir R Shaikh
- Structural Biology Programme, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sayan Bhakta
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Jayati Sengupta
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
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Abstract
Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.
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The production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in Escherichia coli. Appl Microbiol Biotechnol 2015; 99:6667-76. [DOI: 10.1007/s00253-015-6630-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/09/2015] [Accepted: 04/15/2015] [Indexed: 11/25/2022]
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A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions. J Bacteriol 2015; 197:1839-52. [PMID: 25777678 DOI: 10.1128/jb.02475-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/09/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs, trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1-4) for conserved CCUCCUCCC motif stress-induced RNAs 1 to 4. Increased CcsR1-4 expression decreases the expression of genes involved in C1 metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1-4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress. IMPORTANCE Phototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a cluster of four homologous sRNAs in the anoxygenic phototrophic bacterium Rhodobacter sphaeroides. We reveal a function of these regulatory RNAs in the fine-tuning of C1 metabolism. A model that relates oxidative stress defense to C1 metabolism is presented.
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Monrás JP, Collao B, Molina-Quiroz RC, Pradenas GA, Saona LA, Durán-Toro V, Ordenes-Aenishanslins N, Venegas FA, Loyola DE, Bravo D, Calderón PF, Calderón IL, Vásquez CC, Chasteen TG, Lopez DA, Pérez-Donoso JM. Microarray analysis of the Escherichia coli response to CdTe-GSH Quantum Dots: understanding the bacterial toxicity of semiconductor nanoparticles. BMC Genomics 2014; 15:1099. [PMID: 25496196 PMCID: PMC4300170 DOI: 10.1186/1471-2164-15-1099] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/26/2014] [Indexed: 02/06/2023] Open
Abstract
Background Most semiconductor nanoparticles used in biomedical applications are made of heavy metals and involve synthetic methods that require organic solvents and high temperatures. This issue makes the development of water-soluble nanoparticles with lower toxicity a major topic of interest. In a previous work our group described a biomimetic method for the aqueous synthesis of CdTe-GSH Quantum Dots (QDs) using biomolecules present in cells as reducing and stabilizing agents. This protocol produces nanoparticles with good fluorescent properties and less toxicity than those synthesized by regular chemical methods. Nevertheless, biomimetic CdTe-GSH nanoparticles still display some toxicity, so it is important to know in detail the effects of these semiconductor nanoparticles on cells, their levels of toxicity and the strategies that cells develop to overcome it. Results In this work, the response of E. coli exposed to different sized-CdTe-GSH QDs synthesized by a biomimetic protocol was evaluated through transcriptomic, biochemical, microbiological and genetic approaches. It was determined that: i) red QDs (5 nm) display higher toxicity than green (3 nm), ii) QDs mainly induce expression of genes involved with Cd+2 stress (zntA and znuA) and tellurium does not contribute significantly to QDs-mediated toxicity since cells incorporate low levels of Te, iii) red QDs also induce genes related to oxidative stress response and membrane proteins, iv) Cd2+ release is higher in red QDs, and v) QDs render the cells more sensitive to polymyxin B. Conclusion Based on the results obtained in this work, a general model of CdTe-GSH QDs toxicity in E. coli is proposed. Results indicate that bacterial toxicity of QDs is mainly associated with cadmium release, oxidative stress and loss of membrane integrity. The higher toxicity of red QDs is most probably due to higher cadmium content and release from the nanoparticle as compared to green QDs. Moreover, QDs-treated cells become more sensitive to polymyxin B making these biomimetic QDs candidates for adjuvant therapies against bacterial infections. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1099) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - José M Pérez-Donoso
- Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Universidad Andres Bello, Santiago, Chile.
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Ipinza F, Collao B, Monsalva D, Bustamante VH, Luraschi R, Alegría-Arcos M, Almonacid DE, Aguayo D, Calderón IL, Gil F, Santiviago CA, Morales EH, Calva E, Saavedra CP. Participation of the Salmonella OmpD porin in the infection of RAW264.7 macrophages and BALB/c mice. PLoS One 2014; 9:e111062. [PMID: 25360745 PMCID: PMC4215857 DOI: 10.1371/journal.pone.0111062] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/21/2014] [Indexed: 11/18/2022] Open
Abstract
Salmonella Typhimurium is the etiological agent of gastroenteritis in humans and enteric fever in mice. Inside these hosts, Salmonella must overcome hostile conditions to develop a successful infection, a process in which the levels of porins may be critical. Herein, the role of the Salmonella Typhimurium porin OmpD in the infection process was assessed for adherence, invasion and proliferation in RAW264.7 mouse macrophages and in BALB/c mice. In cultured macrophages, a ΔompD strain exhibited increased invasion and proliferation phenotypes as compared to its parental strain. In contrast, overexpression of ompD caused a reduction in bacterial proliferation but did not affect adherence or invasion. In the murine model, the ΔompD strain showed increased ability to survive and replicate in target organs of infection. The ompD transcript levels showed a down-regulation when Salmonella resided within cultured macrophages and when it colonized target organs in infected mice. Additionally, cultured macrophages infected with the ΔompD strain produced lower levels of reactive oxygen species, suggesting that down-regulation of ompD could favor replication of Salmonella inside macrophages and the subsequent systemic dissemination, by limiting the reactive oxygen species response of the host.
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Affiliation(s)
- Francisco Ipinza
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Bernardo Collao
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Debbie Monsalva
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Victor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Roberto Luraschi
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Melissa Alegría-Arcos
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel E. Almonacid
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Iván L. Calderón
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Fernando Gil
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Eduardo H. Morales
- Great Lakes Bioenergy Research Center and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Edmundo Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- * E-mail:
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Improvement of 2,3-butanediol yield in Klebsiella pneumoniae by deletion of the pyruvate formate-lyase gene. Appl Environ Microbiol 2014; 80:6195-203. [PMID: 25085487 DOI: 10.1128/aem.02069-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae is considered a good host strain for the production of 2,3-butanediol, which is a promising platform chemical with various industrial applications. In this study, three genes, including those encoding glucosyltransferase (wabG), lactate dehydrogenase (ldhA), and pyruvate formate-lyase (pflB), were disrupted in K. pneumoniae to reduce both its pathogenic characteristics and the production of several by-products. In flask cultivation with minimal medium, the yield of 2,3-butanediol from rationally engineered K. pneumoniae (ΔwabG ΔldhA ΔpflB) reached 0.461 g/g glucose, which was 92.2% of the theoretical maximum, with a significant reduction in by-product formation. However, the growth rate of the pflB mutant was slightly reduced compared to that of its parental strain. Comparison with similar mutants of Escherichia coli suggested that the growth defect of pflB-deficient K. pneumoniae was caused by redox imbalance rather than reduced level of intracellular acetyl coenzyme A (acetyl-CoA). From an analysis of the transcriptome, it was confirmed that the removal of pflB from K. pneumoniae significantly repressed the expression of genes involved in the formate hydrogen lyase (FHL) system.
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Beckham KSH, Connolly JPR, Ritchie JM, Wang D, Gawthorne JA, Tahoun A, Gally DL, Burgess K, Burchmore RJ, Smith BO, Beatson SA, Byron O, Wolfe AJ, Douce GR, Roe AJ. The metabolic enzyme AdhE controls the virulence of Escherichia coli O157:H7. Mol Microbiol 2014; 93:199-211. [PMID: 24846743 PMCID: PMC4249723 DOI: 10.1111/mmi.12651] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2014] [Indexed: 12/02/2022]
Abstract
Classical studies have focused on the role that individual regulators play in controlling virulence gene expression. An emerging theme, however, is that bacterial metabolism also plays a key role in this process. Our previous work identified a series of proteins that were implicated in the regulation of virulence. One of these proteins was AdhE, a bi-functional acetaldehyde-CoA dehydrogenase and alcohol dehydrogenase. Deletion of its gene (adhE) resulted in elevated levels of extracellular acetate and a stark pleiotropic phenotype: strong suppression of the Type Three Secretion System (T3SS) and overexpression of non-functional flagella. Correspondingly, the adhE mutant bound poorly to host cells and was unable to swim. Furthermore, the mutant was significantly less virulent than its parent when tested in vivo, which supports the hypothesis that attachment and motility are central to the colonization process. The molecular basis by which AdhE affects virulence gene regulation was found to be multifactorial, involving acetate-stimulated transcription of flagella expression and post-transcriptional regulation of the T3SS through Hfq. Our study reveals fascinating insights into the links between bacterial physiology, the expression of virulence genes, and the underlying molecular mechanism mechanisms by which these processes are regulated.
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Affiliation(s)
- Katherine S H Beckham
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - James P R Connolly
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Jennifer M Ritchie
- Faculty of Health and Medical Sciences, University of SurreyGuildford, GU2 7XH, UK
| | - Dai Wang
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
- † Present address: School of Public Health, Xiamen University South Xiangan Rd., Xiamen, Fujian Province, China
| | - Jayde A Gawthorne
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Amin Tahoun
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
- Faculty of Health and Medical Sciences, University of SurreyGuildford, GU2 7XH, UK
| | - David L Gally
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Karl Burgess
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Richard J Burchmore
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Brian O Smith
- Immunity and Infection Division, The Roslin Institute and R(D)SVS, The University of EdinburghEaster Bush, Midlothian, EH25 9RG, UK
| | - Scott A Beatson
- Faculty of Veterinary Medicine, Kafrelsheikh University33516, Kafr el-Sheikh, Egypt
| | - Olwyn Byron
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of QueenslandSt. Lucia, Qld, 4072, Australia
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine2160 S. First Ave., Bldg. 105, Maywood, IL, 60153, USA
| | - Gillian R Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, G12 8TA, UK
- *For correspondence. E-mail ; Tel. (+44) 141 3302980; Fax (+44) 141 330 2981
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Triclosan-induced aminoglycoside-tolerant Listeria monocytogenes isolates can appear as small-colony variants. Antimicrob Agents Chemother 2014; 58:3124-32. [PMID: 24637686 DOI: 10.1128/aac.02266-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Exposure of the human food-borne pathogen Listeria monocytogenes to sublethal concentrations of triclosan can cause resistance to several aminoglycosides. Aminoglycoside-resistant isolates exhibit two colony morphologies: normal-size and pinpoint colonies. The purposes of the present study were to characterize the small colonies of L. monocytogenes and to determine if specific genetic changes could explain the triclosan-induced aminoglycoside resistance in both pinpoint and normal-size isolates. Isolates from the pinpoint colonies grew poorly under aerated conditions, but growth was restored by addition of antibiotics. Pinpoint isolates had decreased hemolytic activity under stagnant conditions and a changed spectrum of carbohydrate utilization compared to the wild type and isolates from normal-size colonies. Genome sequence comparison revealed that all seven pinpoint isolates had a mutation in a heme gene, and addition of heme caused the pinpoint isolates to revert to normal colony size. Triclosan-induced gentamicin-resistant isolates had mutations in several different genes, and it cannot be directly concluded how the different mutations caused gentamicin resistance. However, since many of the mutations affected proteins involved in respiration, it seems likely that the mutations affected the active transport of the antibiotic and thereby caused resistance by decreasing the amount of aminoglycoside that enters the bacterial cell. Our study emphasizes that triclosan likely has more targets than just fabI and that exposure to triclosan can cause resistance to antibiotics that enters the cell via active transport. Further studies are needed to elucidate if L. monocytogenes pinpoint isolates could have any clinical impact, e.g., in persistent infections.
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The Entamoeba histolytica Dnmt2 homolog (Ehmeth) confers resistance to nitrosative stress. EUKARYOTIC CELL 2014; 13:494-503. [PMID: 24562908 DOI: 10.1128/ec.00031-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nitric oxide (NO) has antimicrobial properties against many pathogens due to its reactivity as an S-nitrosylating agent. It inhibits many of the key enzymes that are involved in the metabolism and virulence of the parasite Entamoeba histolytica through S-nitrosylation of essential cysteine residues. Very little information is available on the mechanism of resistance to NO by pathogens in general and by this parasite in particular. Here, we report that exposure of the parasites to S-nitrosoglutathione (GSNO), an NO donor molecule, strongly reduces their viability and protein synthesis. However, the deleterious effects of NO were significantly reduced in trophozoites overexpressing Ehmeth, the cytosine-5 methyltransferase of the Dnmt2 family. Since these trophozoites also exhibited high levels of tRNA(Asp) methylation, the high levels suggested that Ehmeth-mediated tRNA(Asp) methylation is part of the resistance mechanism to NO. We previously reported that enolase, another glycolytic enzyme, binds to Ehmeth and inhibits its activity. We observed that the amount of Ehmeth-enolase complex was significantly reduced in GSNO-treated E. histolytica, which explains the aforementioned increase of tRNA methylation. Specifically, we demonstrated via site-directed mutagenesis that cysteine residues 228 and 229 of Ehmeth are susceptible to S-nitrosylation and are crucial for Ehmeth binding to enolase and for Ehmeth-mediated resistance to NO. These results indicate that Ehmeth has a central role in the response of the parasite to NO, and they contribute to the growing evidence that NO is a regulator of epigenetic mechanisms.
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Cabiscol E, Tamarit J, Ros J. Protein carbonylation: proteomics, specificity and relevance to aging. MASS SPECTROMETRY REVIEWS 2014; 33:21-48. [PMID: 24114980 DOI: 10.1002/mas.21375] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 06/02/2023]
Abstract
Detection and quantification of protein carbonyls present in biological samples has become a popular, albeit indirect, method to determine the existence of oxidative stress. Moreover, the rise of proteomics has allowed the identification of the specific proteins targeted by protein carbonylation. This review discusses these methodologies and proteomic strategies and then focuses on the relationship between protein carbonylation and aging and the parameters that may explain the increased sensitivity of certain proteins to protein carbonylation.
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Affiliation(s)
- Elisa Cabiscol
- Departament de Ciències Mèdiques Bàsiques, IRB Lleida, Universitat de Lleida, Av. Rovira Roure, 80, 25198, Lleida, Catalonia, Spain
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Honsa ES, Johnson MDL, Rosch JW. The roles of transition metals in the physiology and pathogenesis of Streptococcus pneumoniae. Front Cell Infect Microbiol 2013; 3:92. [PMID: 24364001 PMCID: PMC3849628 DOI: 10.3389/fcimb.2013.00092] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/19/2013] [Indexed: 01/01/2023] Open
Abstract
For bacterial pathogens whose sole environmental reservoir is the human host, the acquisition of essential nutrients, particularly transition metals, is a critical aspect of survival due to tight sequestration and limitation strategies deployed to curtail pathogen outgrowth. As such, these bacteria have developed diverse, specialized acquisition mechanisms to obtain these metals from the niches of the body in which they reside. To oppose the spread of infection, the human host has evolved multiple mechanisms to counter bacterial invasion, including sequestering essential metals away from bacteria and exposing bacteria to lethal concentrations of metals. Hence, to maintain homeostasis within the host, pathogens must be able to acquire necessary metals from host proteins and to export such metals when concentrations become detrimental. Furthermore, this acquisition and efflux equilibrium must occur in a tissue-specific manner because the concentration of metals varies greatly within the various microenvironments of the human body. In this review, we examine the functional roles of the metal import and export systems of the Gram-positive pathogen Streptococcus pneumoniae in both signaling and pathogenesis.
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Affiliation(s)
- Erin S Honsa
- Department of Infectious Diseases, St. Jude Children's Research Hospital Memphis, TN, USA
| | - Michael D L Johnson
- Department of Infectious Diseases, St. Jude Children's Research Hospital Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital Memphis, TN, USA
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Calderón IL, Morales EH, Collao B, Calderón PF, Chahuán CA, Acuña LG, Gil F, Saavedra CP. Role of Salmonella Typhimurium small RNAs RyhB-1 and RyhB-2 in the oxidative stress response. Res Microbiol 2013; 165:30-40. [PMID: 24239962 DOI: 10.1016/j.resmic.2013.10.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/04/2013] [Indexed: 11/26/2022]
Abstract
As part of the response to specific stress conditions, bacteria express small molecules of non-coding RNA which maintain cellular homeostasis by regulating gene expression, commonly at the post-transcriptional level. Among these, in Salmonella enterica sv. Typhimurium, the paralog small non-coding RNAs RyhB-1 and RyhB-2 play an important role in iron homeostasis. In addition, in the present work, we show that RyhB-1 and RyhB-2 also participate in the response to hydrogen peroxide (H2O2). Deletion of RyhB-1 and/or RyhB-2 resulted in increased levels of intracellular reactive oxygen species, protein carbonylation and an altered NADH/NAD(+) ratio. Analyses of the transcriptional profiles of ryhB-1 and ryhB-2 by northern blot and qRT-PCR showed that they are induced in response to H2O2 in an OxyR-dependent manner. By using lacZ-fusions and electrophoretic mobility shift assays, we confirmed the requirement of OxyR for inducing expression of both ryhB-1 and ryhB-2. Taken together, our results support a model in which, in response to peroxide treatment, ryhB-1 and ryhB-2 are upregulated by OxyR through direct interaction with their promoter region.
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Affiliation(s)
- Iván L Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Eduardo H Morales
- Great Lakes Bioenergy Research Center and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bernardo Collao
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Paulina F Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Catalina A Chahuán
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Lillian G Acuña
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia & Vida, Santiago, Chile.
| | - Fernando Gil
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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Morales EH, Collao B, Desai PT, Calderón IL, Gil F, Luraschi R, Porwollik S, McClelland M, Saavedra CP. Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium. BMC Genomics 2013; 14:626. [PMID: 24044554 PMCID: PMC3848847 DOI: 10.1186/1471-2164-14-626] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hydrogen peroxide (H₂O₂) is a reactive oxygen species (ROS), which is part of the oxidative burst encountered upon internalization of Salmonella enterica serovar Typhimurium (S. Typhimurium) by phagocytic cells. It has previously been established that, the ArcAB two-component system plays a critical role in ROS resistance, but the genes regulated by the system remained undetermined to date. We therefore investigated the ArcA regulon in aerobically growing S. Typhimurium before and after exposure to H₂O₂ by querying gene expression and other physiological changes in wild type and ΔarcA strains. RESULTS In the ΔarcA strain, expression of 292 genes showed direct or indirect regulation by ArcA in response to H₂O₂, of which 141were also regulated in aerobiosis, but in the opposite direction. Gene set enrichment analysis (GSEA) of the expression data from WT and ΔarcA strains, revealed that, in response to H₂O₂ challenge in aerobically grown cells, ArcA down regulated multiple PEP-PTS and ABC transporters, while up regulating genes involved in glutathione and glycerolipid metabolism and nucleotide transport. Further biochemical analysis guided by GSEA results showed that deletion of arcA during aerobic growth lead to increased reactive oxygen species (ROS) production which was concomitant with an increased NADH/NAD+ ratio. In absence of ArcA under aerobic conditions, H₂O₂ exposure resulted in lower levels of glutathione reductase activity, leading to a decreased GSH (reduced glutathione)/GSSG (oxidized glutathione) ratio. CONCLUSION The ArcA regulon was defined in 2 conditions, aerobic growth and the combination of peroxide treatment and aerobic growth in S. Typhimurium. ArcA coordinates a response that involves multiple aspects of the carbon flux through central metabolism, which ultimately modulates the reducing potential of the cell.
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Affiliation(s)
- Eduardo H Morales
- Laboratorio de Microbiología Molecular, Facultad Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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Monounsaturated fatty acids are substrates for aldehyde generation in tellurite-exposed Escherichia coli. BIOMED RESEARCH INTERNATIONAL 2013; 2013:563756. [PMID: 23991420 PMCID: PMC3749545 DOI: 10.1155/2013/563756] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/09/2013] [Indexed: 11/17/2022]
Abstract
Reactive oxygen species (ROS) damage macromolecules and cellular components in nearly all kinds of cells and often generate toxic intracellular byproducts. In this work, aldehyde generation derived from the Escherichia coli membrane oxidation as well as membrane fatty acid profiles, protein oxidation, and bacterial resistance to oxidative stress elicitors was evaluated. Studies included wild-type cells as well as cells exhibiting a modulated monounsaturated fatty acid (MUFA) ratio. The hydroxyaldehyde 4-hydroxy 2-nonenal was found to be most likely produced by E. coli, whose levels are dependent upon exposure to oxidative stress elicitors. Aldehyde amounts and markers of oxidative damage decreased upon exposure to E. coli containing low MUFA ratios, which was paralleled by a concomitant increase in resistance to ROS-generating compounds. MUFAs ratio, lipid peroxidation, and aldehyde generation were found to be directly related; that is, the lower the MUFAs ratio, the lower the peroxide and aldehyde generation levels. These results provide additional evidence about MUFAs being targets for membrane lipid oxidation and their relevance in aldehyde generation.
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Kim DK, Rathnasingh C, Song H, Lee HJ, Seung D, Chang YK. Metabolic engineering of a novel Klebsiella oxytoca strain for enhanced 2,3-butanediol production. J Biosci Bioeng 2013; 116:186-92. [DOI: 10.1016/j.jbiosc.2013.02.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 01/29/2013] [Accepted: 02/20/2013] [Indexed: 11/16/2022]
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Lery LMS, Goulart CL, Figueiredo FR, Verdoorn KS, Einicker-Lamas M, Gomes FM, Machado EA, Bisch PM, von Kruger WMA. A comparative proteomic analysis of Vibrio cholerae O1 wild-type cells versus a phoB mutant showed that the PhoB/PhoR system is required for full growth and rpoS expression under inorganic phosphate abundance. J Proteomics 2013; 86:1-15. [PMID: 23665147 DOI: 10.1016/j.jprot.2013.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/09/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
Abstract
UNLABELLED PhoB/PhoR is a two-component system originally described as involved in inorganic phosphate (Pi) transport and metabolism under Pi limitation. In order to disclose other roles of this system, a proteomic analysis of Vibrio cholerae 569BSR and its phoB/phoR mutant under high Pi levels was performed. Most of the proteins downregulated by the mutant have roles in energy production and conversion and in amino acid transport and metabolism. In contrast, the phoB/phoR mutant upregulated genes mainly involved in adaptation to atypical conditions, indicating that the absence of a functional PhoB/PhoR caused increased expression of a number of genes from distinct stress response pathways. This might be a strategy to overcome the lack of RpoS, whose expression in the stationary phase cells of V. cholerae seems to be controlled by PhoB/PhoR. Moreover, compared to the wild-type strain the phoB/phoR mutant presented a reduced cell density at stationary phase of culture in Pi abundance, lower resistance to acid shock, but higher tolerance to thermal and osmotic stresses. Together our findings show, for the first time, the requirement of PhoB/PhoR for full growth under high Pi level and for the accumulation of RpoS, indicating that PhoB/PhoR is a fundamental system for the biology of V. cholerae. BIOLOGICAL SIGNIFICANCE Certain V. cholerae strains are pathogenic to humans, causing cholera, an acute dehydrating diarrhoeal disease endemic in Southern Asia, parts of Africa and Latin America, where it has been responsible for significant mortality and economical damage. Its ability to grow within distinct niches is dependent on gene expression regulation. PhoB/PhoR is a two-component system originally described as involved in inorganic phosphate (Pi) transport and metabolism under Pi limitation. However, Pho regulon genes also play roles in virulence, motility and biofilm formation, among others. In this paper we report that the absence of a functional PhoB/PhoR caused increased expression of a number of genes from distinct stress response pathways, in Pi abundance. Moreover, we showed, for the first time, that the interrelationship between PhoB-RpoS-(p)ppGpp-poly(P) in V. cholerae, is somewhat diverse from the model of inter-regulation between those systems, described in Escherichia coli. The V. cholerae dependence on PhoB/PhoR for the RpoS mediated stress response and cellular growth under Pi abundance, suggests that this system's roles are broader than previously thought.
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Affiliation(s)
- Letícia M S Lery
- Unidade Multidisciplinar de Genômica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil.
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Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress. Infect Immun 2013; 81:2242-57. [PMID: 23569115 DOI: 10.1128/iai.01273-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis causes Johne's disease, an enteric infection in cattle and other ruminants, greatly afflicting the dairy industry worldwide. Once inside the cell, M. avium subsp. paratuberculosis is known to survive harsh microenvironments, especially those inside activated macrophages. To improve our understanding of M. avium subsp. paratuberculosis pathogenesis, we examined phagosome maturation associated with transcriptional responses of M. avium subsp. paratuberculosis during macrophage infection. Monitoring cellular markers, only live M. avium subsp. paratuberculosis bacilli were able to prevent phagosome maturation and reduce its acidification. On the transcriptional level, over 300 M. avium subsp. paratuberculosis genes were significantly and differentially regulated in both naive and IFN-γ-activated macrophages. These genes include the sigma factor H (sigH) that was shown to be important for M. avium subsp. paratuberculosis survival inside gamma interferon (IFN-γ)-activated bovine macrophages. Interestingly, an sigH-knockout mutant showed increased sensitivity to a sustained level of thiol-specific oxidative stress. Large-scale RNA sequence analysis revealed that a large number of genes belong to the sigH regulon, especially following diamide stress. Genes involved in oxidative stress and virulence were among the induced genes in the sigH regulon with a putative consensus sequence for SigH binding that was recognized in a subset of these genes (n = 30), suggesting direct regulation by SigH. Finally, mice infections showed a significant attenuation of the ΔsigH mutant compared to its parental strain, suggesting a role for sigH in M. avium subsp. paratuberculosis virulence. Such analysis could identify potential targets for further testing as vaccine candidates against Johne's disease.
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