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Kumar R, Sharma P, Chauhan A, Singh N, Prajapati VM, Singh SK. Malate:quinone oxidoreductase knockout makes Mycobacterium tuberculosis susceptible to stress and affects its in vivo survival. Microbes Infect 2024; 26:105215. [PMID: 37689346 DOI: 10.1016/j.micinf.2023.105215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023]
Abstract
Mycobacterium tuberculosis H37Ra (Mtb-Ra) ORF MRA_2875, annotated as malate:quinone oxidoreductase (mqo), is thought to have a role in TCA cycle in converting malate to oxaloacetate. To study its physiological relevance, we developed mqo knockout (KO) in Mtb-Ra. A KO complemented (KOC) strain was also developed by complementing the KO with mqo over-expressing construct. Under normal in vitro conditions, KO does not show any growth defect but showed reduced CFU burden in macrophages and in mice lungs. In vitro studies with KO showed reduced fitness under oxidative and low pH stress, and also increased susceptibility to levofloxacin and D-cycloserine. Transcript analysis of mqo showed increased expression levels under oxidative and low pH stress. This is the first study to show physiological relevance of mqo encoded by MRA_2875 in Mtb-Ra under oxidative and low pH stress. In summary, the present study shows that MRA_2875 encoded malate:quinone oxidoreductase is a functional enzyme which contributes to oxidative stress and low pH tolerance, and survival in macrophages and in mice.
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Affiliation(s)
- Ram Kumar
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Princi Sharma
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anu Chauhan
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nirbhay Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - V M Prajapati
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sudheer Kumar Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Shi HX, Liu SY, Guo JS, Fang F, Chen YP, Yan P. Potential role of AgNPs within wastewater in deteriorating sludge floc structure and settleability during activated sludge process: Filamentous bacteria and quorum sensing. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119536. [PMID: 37972492 DOI: 10.1016/j.jenvman.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/22/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
Excellent sludge floc structure and settleability are essential to maintain the process stability and excellent effluent quality during the activated sludge process. The underlying effect of silver nanoparticles (AgNPs) within wastewater on sludge floc structure and settleability is still unclear. The potential role of AgNPs in promoting filamentous bacterial proliferation and deteriorating sludge floc structure and settleability based on quorum sensing (QS) were investigated in this study. The results indicated that N-acyl homoserine lactose (AHL) concentration sharply increased from 23.56 to 108.41 ng/g VSS in the sequencing batch reactor with 1 mg/L AgNPs. AgNPs strengthened communication between filamentous bacteria, which triggered the filamentous bacterial QS system involving the synthetic gene hdtS and sensing genes traR and lasR. Filamentous bacterial proliferation was promoted by the triggered QS via positively regulating its cell cycle progression including chromosomal replication and divisome formation. In addition, extracellular protein production was obviously increased from 43.56 to 97.91 mg/g VSS through QS by regulating arginine and tyrosine secretion during filamentous bacterial proliferation under 1 mg/L AgNPs condition, which led to an increase in the negative charge and hydrophily at the cell surface. AgNPs resulted in an obvious increase in the surface energy barrier (WT) between bacteria. The change in the physicochemical properties of extracellular polymeric substance (EPS) induced by QS among filamentous bacteria obviously inhibited bacterial aggregation between filamentous bacteria and floc-forming bacteria under AgNPs condition, thus resulting in serious deterioration of the sludge floc structure and settleability. This study provided new insights into the microcosmic mechanism for the effect of AgNPs on sludge floc structure and settleability.
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Affiliation(s)
- Hong-Xin Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Shao-Yang Liu
- Department of Chemistry and Physics, Troy University, Troy, AL, 36082, USA
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
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Matthews CJ, Patrick WM. An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range. Protein Sci 2023; 32:e4743. [PMID: 37515423 PMCID: PMC10451018 DOI: 10.1002/pro.4743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
l-Malate is a key flavor enhancer and acidulant in the food and beverage industry, particularly winemaking. Enzyme-based amperometric biosensors offer convenience for monitoring its concentration. However, only a small number of off-the-shelf malate-oxidizing enzymes have been used in previous devices. These typically have linear ranges poorly suited for the l-malate concentrations found in fruit processing and winemaking, making it necessary to use precisely diluted samples. Here, we describe a pipeline of database-mining, gene synthesis, recombinant expression, and spectrophotometric assays to characterize previously untested enzymes for their suitability in biosensors. The pipeline yielded a bespoke biocatalyst-the Ascaris suum malic enzyme carrying mutation R181Q [AsME(R181Q)]. Our first prototype with AsME(R181Q) had an ultra-wide linear range of 50-200 mM l-malate, corresponding to concentrations found in undiluted fruit juices (including grape). Changing the dication from Mg2+ to Mn2+ increased sensitivity five-fold and adding citrate (100 mM) increased it another six-fold, albeit decreasing the linear range to 1-10 mM. To our knowledge, this is the first time an l-malate biosensor with a tuneable combination of sensitivity and linear range has been described. The sensor response was also tested in the presence of various molecules abundant in juices and wines, with ascorbate shown to be a potent interferent. Interference was mitigated by the addition of ascorbate oxidase, allowing for differential measurements on an undiluted, untreated wine sample that corresponded well with commercial l-malate testing kits. Overall, this work demonstrates the power of an enzyme-centric approach for designing electrochemical biosensors with improved operational parameters and novel functionality.
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Affiliation(s)
- Christopher J. Matthews
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Wayne M. Patrick
- Centre for Biodiscovery, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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4
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Monte AA, Vest A, Reisz JA, Berninzoni D, Hart C, Dylla L, D'Alessandro A, Heard KJ, Wood C, Pattee J. A Multi-Omic Mosaic Model of Acetaminophen Induced Alanine Aminotransferase Elevation. J Med Toxicol 2023; 19:255-261. [PMID: 37231244 PMCID: PMC10212224 DOI: 10.1007/s13181-023-00951-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Acetaminophen (APAP) is the most common cause liver injury following alcohol in US patients. Predicting liver injury and subsequent hepatic regeneration in patients taking therapeutic doses of APAP may be possible using new 'omic methods such as metabolomics and genomics. Multi'omic techniques increase our ability to find new mechanisms of injury and regeneration. METHODS We used metabolomic and genomic data from a randomized controlled trial of patients administered 4 g of APAP per day for 14 days or longer with blood samples obtained at 0 (baseline), 4, 7, 10, 13 and 16 days. We used the highest ALT as the clinical outcome to be predicted in our integrated analysis. We used penalized regression to model the relationship between genetic variants and day 0 metabolite level, and then performed a metabolite-wide colocalization scan to associate the genetically regulated component of metabolite expression with ALT elevation. Genome-wide association study (GWAS) analyses were conducted for ALT elevation and metabolite level using linear regression, with age, sex, and the first five principal components included as covariates. Colocalization was tested via a weighted sum test. RESULTS Out of the 164 metabolites modeled, 120 met the criteria for predictive accuracy and were retained for genetic analyses. After genomic examination, eight metabolites were found to be under genetic control and predictive of ALT elevation due to therapeutic acetaminophen. The metabolites were: 3-oxalomalate, allantoate, diphosphate, L-carnitine, L-proline, maltose, and ornithine. These genes are important in the tricarboxylic acid cycle (TCA), urea breakdown pathway, glutathione production, mitochondrial energy production, and maltose metabolism. CONCLUSIONS This multi'omic approach can be used to integrate metabolomic and genomic data allowing identification of genes that control downstream metabolites. These findings confirm prior work that have identified mitochondrial energy production as critical to APAP induced liver injury and have confirmed our prior work that demonstrate the importance of the urea cycle in therapeutic APAP liver injury.
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Affiliation(s)
- Andrew A Monte
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA.
- Center for Bioinformatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
- Skaggs School of Pharmacy, University of Colorado, Aurora, CO, USA.
- Denver Health and Hospital Authority, Rocky Mountain Poison & Drug Center, Denver, CO, USA.
| | - Alexis Vest
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Julie A Reisz
- Metabolomics Core, Department of Biochemistry and Molecular Genetics, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Danielle Berninzoni
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Claire Hart
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
| | - Layne Dylla
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
- Center for Bioinformatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Angelo D'Alessandro
- Metabolomics Core, Department of Biochemistry and Molecular Genetics, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Kennon J Heard
- Department of Emergency Medicine, University of Colorado School of Medicine, Leprino Building, 7th Floor Campus Box B-215, 12401 E. 17th Avenue, Aurora, CO, 80045, USA
- Denver Health and Hospital Authority, Rocky Mountain Poison & Drug Center, Denver, CO, USA
| | - Cheyret Wood
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Jack Pattee
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado-Denver Anschutz Medical Campus, Aurora, CO, USA
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Frolova AA, Merkel AY, Kevbrin VV, Kopitsyn DS, Slobodkin AI. Sulfurospirillum tamanensis sp. nov., a Facultatively Anaerobic Alkaliphilic Bacterium from a Terrestrial Mud Volcano. Microbiology (Reading) 2023. [DOI: 10.1134/s0026261722602226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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6
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Strachan CR, Yu XA, Neubauer V, Mueller AJ, Wagner M, Zebeli Q, Selberherr E, Polz MF. Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome. Nat Microbiol 2023; 8:309-320. [PMID: 36635570 PMCID: PMC9894753 DOI: 10.1038/s41564-022-01300-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/05/2022] [Indexed: 01/14/2023]
Abstract
The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.
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Affiliation(s)
- Cameron R Strachan
- Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Xiaoqian A Yu
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Viktoria Neubauer
- Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Anna J Mueller
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Qendrim Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Vienna, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Martin F Polz
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent. THE ISME JOURNAL 2023; 17:12-20. [PMID: 36151459 PMCID: PMC9751133 DOI: 10.1038/s41396-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
Abstract
Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.
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8
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Biochemical Studies of Mitochondrial Malate: Quinone Oxidoreductase from Toxoplasma gondii. Int J Mol Sci 2021; 22:ijms22157830. [PMID: 34360597 PMCID: PMC8345934 DOI: 10.3390/ijms22157830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/17/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
Toxoplasma gondii is a protozoan parasite that causes toxoplasmosis and infects almost one-third of the global human population. A lack of effective drugs and vaccines and the emergence of drug resistant parasites highlight the need for the development of new drugs. The mitochondrial electron transport chain (ETC) is an essential pathway for energy metabolism and the survival of T. gondii. In apicomplexan parasites, malate:quinone oxidoreductase (MQO) is a monotopic membrane protein belonging to the ETC and a key member of the tricarboxylic acid cycle, and has recently been suggested to play a role in the fumarate cycle, which is required for the cytosolic purine salvage pathway. In T. gondii, a putative MQO (TgMQO) is expressed in tachyzoite and bradyzoite stages and is considered to be a potential drug target since its orthologue is not conserved in mammalian hosts. As a first step towards the evaluation of TgMQO as a drug target candidate, in this study, we developed a new expression system for TgMQO in FN102(DE3)TAO, a strain deficient in respiratory cytochromes and dependent on an alternative oxidase. This system allowed, for the first time, the expression and purification of a mitochondrial MQO family enzyme, which was used for steady-state kinetics and substrate specificity analyses. Ferulenol, the only known MQO inhibitor, also inhibited TgMQO at IC50 of 0.822 μM, and displayed different inhibition kinetics compared to Plasmodium falciparum MQO. Furthermore, our analysis indicated the presence of a third binding site for ferulenol that is distinct from the ubiquinone and malate sites.
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Steiner TM, Lettl C, Schindele F, Goebel W, Haas R, Fischer W, Eisenreich W. Substrate usage determines carbon flux via the citrate cycle in Helicobacter pylori. Mol Microbiol 2021; 116:841-860. [PMID: 34164854 DOI: 10.1111/mmi.14775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/07/2021] [Accepted: 06/19/2021] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori displays a worldwide infection rate of about 50%. The Gram-negative bacterium is the main reason for gastric cancer and other severe diseases. Despite considerable knowledge about the metabolic inventory of H. pylori, carbon fluxes through the citrate cycle (TCA cycle) remained enigmatic. In this study, different 13 C-labeled substrates were supplied as carbon sources to H. pylori during microaerophilic growth in a complex medium. After growth, 13 C-excess and 13 C-distribution were determined in multiple metabolites using GC-MS analysis. [U-13 C6 ]Glucose was efficiently converted into glyceraldehyde but only less into TCA cycle-related metabolites. In contrast, [U-13 C5 ]glutamate, [U-13 C4 ]succinate, and [U-13 C4 ]aspartate were incorporated at high levels into intermediates of the TCA cycle. The comparative analysis of the 13 C-distributions indicated an adaptive TCA cycle fully operating in the closed oxidative direction with rapid equilibrium fluxes between oxaloacetate-succinate and α-ketoglutarate-citrate. 13 C-Profiles of the four-carbon intermediates in the TCA cycle, especially of malate, together with the observation of an isocitrate lyase activity by in vitro assays, suggested carbon fluxes via a glyoxylate bypass. In conjunction with the lack of enzymes for anaplerotic CO2 fixation, the glyoxylate bypass could be relevant to fill up the TCA cycle with carbon atoms derived from acetyl-CoA.
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Affiliation(s)
- Thomas M Steiner
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Clara Lettl
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Franziska Schindele
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany
| | - Werner Goebel
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany
| | - Rainer Haas
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Wolfgang Fischer
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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11
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Enzyme-based amperometric biosensors for malic acid - A review. Anal Chim Acta 2021; 1156:338218. [PMID: 33781460 DOI: 10.1016/j.aca.2021.338218] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Malic acid is a key flavour component of many fruits and vegetables. There is significant interest in technologies for monitoring its concentration, particularly in winemaking. In this review we systematically and comprehensively chart progress in the development of enzyme-based amperometric biosensors for malic acid. We summarise the components and analytical parameters of malic acid sensors that have been reported over the past four decades, discussing their merits and pitfalls in terms of accuracy, sensitivity, linear range, response time and stability. We discuss how advances in electrode materials, electron mediators and the use of coupled enzymes have improved sensitivity and minimised interference, but also uncover a trade-off between sensitivity and linear range. A particular focus of our review is the three types of malate oxidoreductase enzyme that have been used in malic acid biosensors. We describe their different properties and conclude that identifying and/or engineering superior alternatives will be a key future direction for improving the commercial utility of malic acid biosensors.
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12
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Choi JY, Kim SC, Lee PC. Comparative Genome Analysis of Psychrobacillus Strain PB01, Isolated from an Iceberg. J Microbiol Biotechnol 2020; 30:237-243. [PMID: 31838800 PMCID: PMC9728334 DOI: 10.4014/jmb.1909.09008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mb) and a plasmid (19 Kb). As potential low-temperature adaptation strategies, strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggests that strain PB01 might have evolved to adapt to extreme environments by changing its genome content to gain higher capacity for DNA repair, translation, and membrane transport. Notably, strain PB01 possesses a complete TCA cycle consisting of eight enzymes as well as three additional Helicobacter pylori-type enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes has also been identified in the other five Psychrobacillus strains.
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea,Corresponding author Phone: +82-31-219-2461 Fax: +82-31-219-1610 E-mail:
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13
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Hards K, Adolph C, Harold LK, McNeil MB, Cheung CY, Jinich A, Rhee KY, Cook GM. Two for the price of one: Attacking the energetic-metabolic hub of mycobacteria to produce new chemotherapeutic agents. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:35-44. [PMID: 31733221 DOI: 10.1016/j.pbiomolbio.2019.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Cellular bioenergetics is an area showing promise for the development of new antimicrobials, antimalarials and cancer therapy. Enzymes involved in central carbon metabolism and energy generation are essential mediators of bacterial physiology, persistence and pathogenicity, lending themselves natural interest for drug discovery. In particular, succinate and malate are two major focal points in both the central carbon metabolism and the respiratory chain of Mycobacterium tuberculosis. Both serve as direct links between the citric acid cycle and the respiratory chain due to the quinone-linked reactions of succinate dehydrogenase, fumarate reductase and malate:quinone oxidoreductase. Inhibitors against these enzymes therefore hold the promise of disrupting two distinct, but essential, cellular processes at the same time. In this review, we discuss the roles and unique adaptations of these enzymes and critically evaluate the role that future inhibitors of these complexes could play in the bioenergetics target space.
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Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
| | - Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
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14
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Wang X, Miyazaki Y, Inaoka DK, Hartuti ED, Watanabe YI, Shiba T, Harada S, Saimoto H, Burrows JN, Benito FJG, Nozaki T, Kita K. Identification of Plasmodium falciparum Mitochondrial Malate: Quinone Oxidoreductase Inhibitors from the Pathogen Box. Genes (Basel) 2019; 10:genes10060471. [PMID: 31234346 PMCID: PMC6627850 DOI: 10.3390/genes10060471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022] Open
Abstract
Malaria is one of the three major global health threats. Drug development for malaria, especially for its most dangerous form caused by Plasmodium falciparum, remains an urgent task due to the emerging drug-resistant parasites. Exploration of novel antimalarial drug targets identified a trifunctional enzyme, malate quinone oxidoreductase (MQO), located in the mitochondrial inner membrane of P. falciparum (PfMQO). PfMQO is involved in the pathways of mitochondrial electron transport chain, tricarboxylic acid cycle, and fumarate cycle. Recent studies have shown that MQO is essential for P. falciparum survival in asexual stage and for the development of experiment cerebral malaria in the murine parasite P. berghei, providing genetic validation of MQO as a drug target. However, chemical validation of MQO, as a target, remains unexplored. In this study, we used active recombinant protein rPfMQO overexpressed in bacterial membrane fractions to screen a total of 400 compounds from the Pathogen Box, released by Medicines for Malaria Venture. The screening identified seven hit compounds targeting rPfMQO with an IC50 of under 5 μM. We tested the activity of hit compounds against the growth of 3D7 wildtype strain of P. falciparum, among which four compounds showed an IC50 from low to sub-micromolar concentrations, suggesting that PfMQO is indeed a potential antimalarial drug target.
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Affiliation(s)
- Xinying Wang
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
| | - Yukiko Miyazaki
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
| | - Endah Dwi Hartuti
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Hashikamicho, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Hashikamicho, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8550, Japan.
| | | | | | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
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15
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Taylor AJ, Kelly DJ. The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen. Adv Microb Physiol 2019; 74:239-329. [PMID: 31126532 DOI: 10.1016/bs.ampbs.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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Affiliation(s)
- Aidan J Taylor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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16
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Han B, Zhang Z, Xie Y, Hu X, Wang H, Xia W, Wang Y, Li H, Wang Y, Sun H. Multi-omics and temporal dynamics profiling reveal disruption of central metabolism in Helicobacter pylori on bismuth treatment. Chem Sci 2018; 9:7488-7497. [PMID: 30510674 PMCID: PMC6223348 DOI: 10.1039/c8sc01668b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022] Open
Abstract
Integration of multi-omics enables uncovering cellular responses to stimuli or the mechanism of action of a drug at a system level. Bismuth drugs have long been used for the treatment of Helicobacter pylori infection and their antimicrobial activity was attributed to dysfunction of multiple proteins based on previous proteome-wide studies. Herein, we investigated the response of H. pylori to a bismuth drug at transcriptome and metabolome levels. Our multi-omics data together with bioassays comprehensively reveal the impact of bismuth on a diverse array of intracellular pathways, in particular, disruption of central carbon metabolism is systematically evaluated as a primary bismuth-targeting system in H. pylori. Through temporal dynamics profiling, we demonstrate that bismuth initially perturbs the TCA cycle and then urease activity, followed by the induction of oxidative stress and inhibition of energy production, and in the meantime, induces extensive down-regulation in H. pylori metabolome. The present study thus expands our knowledge on the inhibitory actions of bismuth and provides a novel systematic perspective of H. pylori in response to a clinical drug that sheds light on enhanced therapeutic methodologies.
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Affiliation(s)
- Bingjie Han
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
| | - Zhen Zhang
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
| | - Yanxuan Xie
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
| | - Xuqiao Hu
- Department of Chemistry , The University of Hong Kong , Hong Kong , P. R. China .
| | - Haibo Wang
- Department of Chemistry , The University of Hong Kong , Hong Kong , P. R. China .
| | - Wei Xia
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems , State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan , 430071 , P. R. China
| | - Hongyan Li
- Department of Chemistry , The University of Hong Kong , Hong Kong , P. R. China .
| | - Yuchuan Wang
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
| | - Hongzhe Sun
- School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , P. R. China .
- Department of Chemistry , The University of Hong Kong , Hong Kong , P. R. China .
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17
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Identification of novel therapeutic candidates in Cryptosporidium parvum: an in silico approach. Parasitology 2018; 145:1907-1916. [PMID: 29692282 DOI: 10.1017/s0031182018000677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Unavailability of vaccines and effective drugs are primarily responsible for the growing menace of cryptosporidiosis. This study has incorporated a bioinformatics-based screening approach to explore potential vaccine candidates and novel drug targets in Cryptosporidium parvum proteome. A systematic strategy was defined for comparative genomics, orthology with related Cryptosporidium species, prioritization parameters and MHC class I and II binding promiscuity. The approach reported cytoplasmic protein cgd7_1830, a signal peptide protein, as a novel drug target. SWISS-MODEL online server was used to generate the 3D model of the protein and was validated by PROCHECK. The model has been subjected to in silico docking study with screened potent lead compounds from the ZINC database, PubChem and ChEMBL database using Flare software package of Cresset®. Furthermore, the approach reported protein cgd3_1400, as a vaccine candidate. The predicted B- and T-cell epitopes on the proposed vaccine candidate with highest scores were also subjected to docking study with MHC class I and II alleles using ClusPro web server. Results from this study could facilitate selection of proteins which could serve as drug targets and vaccine candidates to efficiently tackle the growing threat of cryptosporidiosis.
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18
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Hartuti ED, Inaoka DK, Komatsuya K, Miyazaki Y, Miller RJ, Xinying W, Sadikin M, Prabandari EE, Waluyo D, Kuroda M, Amalia E, Matsuo Y, Nugroho NB, Saimoto H, Pramisandi A, Watanabe YI, Mori M, Shiomi K, Balogun EO, Shiba T, Harada S, Nozaki T, Kita K. Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase, a potential drug target. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:191-200. [PMID: 29269266 DOI: 10.1016/j.bbabio.2017.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc1 complex inhibitor.
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Affiliation(s)
- Endah Dwi Hartuti
- Master program of Biomedical Science, Faculty of Medicine, University of Indonesia, Indonesia; Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
| | - Keisuke Komatsuya
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko Miyazaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Russell J Miller
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wang Xinying
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Mohamad Sadikin
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | - Danang Waluyo
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Marie Kuroda
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuichi Matsuo
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Nuki B Nugroho
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Amila Pramisandi
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia; Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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19
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Chong TM, Chen JW, See-Too WS, Yu CY, Ang GY, Lim YL, Yin WF, Grandclément C, Faure D, Dessaux Y, Chan KG. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express 2017; 7:138. [PMID: 28655216 PMCID: PMC5484659 DOI: 10.1186/s13568-017-0437-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 12/30/2022] Open
Abstract
Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
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Affiliation(s)
- Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Geik-Yong Ang
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Yan Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
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20
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Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. Front Microbiol 2017; 8:2082. [PMID: 29163388 PMCID: PMC5671600 DOI: 10.3389/fmicb.2017.02082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated "Novel Archaeal Group 1" (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.
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Affiliation(s)
- Eric D Becraft
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, San Bernardino, CA, United States.,School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - J Ingemar Ohlsson
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
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21
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Convergent evolution of a modified, acetate-driven TCA cycle in bacteria. Nat Microbiol 2017; 2:17067. [PMID: 28452983 PMCID: PMC5482284 DOI: 10.1038/nmicrobiol.2017.67] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/28/2017] [Indexed: 11/08/2022]
Abstract
The tricarboxylic acid (TCA) cycle is central to energy production and biosynthetic precursor synthesis in aerobic organisms. There exist few known variations of a complete TCA cycle, with the common notion being that the enzymes involved have already evolved towards optimal performance. Here, we present evidence that an alternative TCA cycle, in which acetate:succinate CoA-transferase (ASCT) replaces the enzymatic step typically performed by succinyl-CoA synthetase (SCS), has arisen in diverse bacterial groups, including microbial symbionts of animals such as humans and insects.
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22
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Zorzoli A, Grayczyk JP, Alonzo F. Staphylococcus aureus Tissue Infection During Sepsis Is Supported by Differential Use of Bacterial or Host-Derived Lipoic Acid. PLoS Pathog 2016; 12:e1005933. [PMID: 27701474 PMCID: PMC5049849 DOI: 10.1371/journal.ppat.1005933] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/13/2016] [Indexed: 01/31/2023] Open
Abstract
To thrive in diverse environments, bacteria must shift their metabolic output in response to nutrient bioavailability. In many bacterial species, such changes in metabolic flux depend upon lipoic acid, a cofactor required for the activity of enzyme complexes involved in glycolysis, the citric acid cycle, glycine catabolism, and branched chain fatty acid biosynthesis. The requirement of lipoic acid for metabolic enzyme activity necessitates that bacteria synthesize the cofactor and/or scavenge it from environmental sources. Although use of lipoic acid is a conserved phenomenon, the mechanisms behind its biosynthesis and salvage can differ considerably between bacterial species. Furthermore, low levels of circulating free lipoic acid in mammals underscore the importance of lipoic acid acquisition for pathogenic microbes during infection. In this study, we used a genetic approach to characterize the mechanisms of lipoic acid biosynthesis and salvage in the bacterial pathogen Staphylococcus aureus and evaluated the requirements for both pathways during murine sepsis. We determined that S. aureus lipoic acid biosynthesis and salvage genes exist in an arrangement that directly links redox stress response and acetate biosynthesis genes. In addition, we found that lipoic acid salvage is dictated by two ligases that facilitate growth and lipoylation in distinct environmental conditions in vitro, but that are fully compensatory for survival in vivo. Upon infection of mice, we found that de novo biosynthesis or salvage promotes S. aureus survival in a manner that depends upon the infectious site. In addition, when both lipoic acid biosynthesis and salvage are blocked S. aureus is rendered avirulent, implying an inability to induce lipoic acid-independent metabolic programs to promote survival. Together, our results define the major pathways of lipoic acid biosynthesis and salvage in S. aureus and support the notion that bacterial nutrient acquisition schemes are instrumental in dictating pathogen proclivity for an infectious niche. Staphylococcus aureus is a predominant cause of infectious diseases ranging from superficial skin and soft tissue infections to necrotizing pneumonia and sepsis. A remarkable aspect of S. aureus pathobiology lies in the ability of the microorganism to infect a wide variety of host tissues. This infectious promiscuity implies S. aureus exhibits significant adaptability when faced with disparate environments and nutritional deficiencies. In this work, we examine the mechanisms by which S. aureus acquires lipoic acid, a key cofactor involved in maintaining metabolic flux. Our studies determine that S. aureus engages in both de novo biosynthesis and salvage of lipoic acid in a manner that is reminiscent of pathways used by both B. subtilis and L. monocytogenes combined. Further, our work suggests that the complex mechanisms of lipoic acid acquisition dictate the range of tissues S. aureus infects and identifies a lipoic acid salvage enzyme that is dispensable for growth in vitro, but required for S. aureus pathogenesis in vivo. In sum, our results highlight the adaptability of S. aureus in the face of nutrient paucity; the importance of complex nutrient acquisition/biosynthesis pathways in promoting infection; and identify potential novel therapeutic targets that may be effective against S. aureus.
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Affiliation(s)
- Azul Zorzoli
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
| | - James P. Grayczyk
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago—Stritch School of Medicine, Maywood, Illinois, United States of America
- * E-mail:
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Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. mBio 2016; 7:mBio.01173-16. [PMID: 27486197 PMCID: PMC4981724 DOI: 10.1128/mbio.01173-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis is a leading cause of bacterial meningitis and septicemia, affecting infants and adults worldwide. N. meningitidis is also a common inhabitant of the human nasopharynx and, as such, is highly adapted to its niche. During bacteremia, N. meningitidis gains access to the blood compartment, where it adheres to endothelial cells of blood vessels and causes dramatic vascular damage. Colonization of the nasopharyngeal niche and communication with the different human cell types is a major issue of the N. meningitidis life cycle that is poorly understood. Here, highly saturated random transposon insertion libraries of N. meningitidis were engineered, and the fitness of mutations during routine growth and that of colonization of endothelial and epithelial cells in a flow device were assessed in a transposon insertion site sequencing (Tn-seq) analysis. This allowed the identification of genes essential for bacterial growth and genes specifically required for host cell colonization. In addition, after having identified the small noncoding RNAs (sRNAs) located in intergenic regions, the phenotypes associated with mutations in those sRNAs were defined. A total of 383 genes and 8 intergenic regions containing sRNA candidates were identified to be essential for growth, while 288 genes and 33 intergenic regions containing sRNA candidates were found to be specifically required for host cell colonization. Meningococcal meningitis is a common cause of meningitis in infants and adults. Neisseria meningitidis (meningococcus) is also a commensal bacterium of the nasopharynx and is carried by 3 to 30% of healthy humans. Under some unknown circumstances, N. meningitidis is able to invade the bloodstream and cause either meningitis or a fatal septicemia known as purpura fulminans. The onset of symptoms is sudden, and death can follow within hours. Although many meningococcal virulence factors have been identified, the mechanisms that allow the bacterium to switch from the commensal to pathogen state remain unknown. Therefore, we used a Tn-seq strategy coupled to high-throughput DNA sequencing technologies to find genes for proteins used by N. meningitidis to specifically colonize epithelial cells and primary brain endothelial cells. We identified 383 genes and 8 intergenic regions containing sRNAs essential for growth and 288 genes and 33 intergenic regions containing sRNAs required specifically for host cell colonization.
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Unden G, Strecker A, Kleefeld A, Kim OB. C4-Dicarboxylate Utilization in Aerobic and Anaerobic Growth. EcoSal Plus 2016; 7. [PMID: 27415771 DOI: 10.1128/ecosalplus.esp-0021-2015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 06/06/2023]
Abstract
C4-dicarboxylates and the C4-dicarboxylic amino acid l-aspartate support aerobic and anaerobic growth of Escherichia coli and related bacteria. In aerobic growth, succinate, fumarate, D- and L-malate, L-aspartate, and L-tartrate are metabolized by the citric acid cycle and associated reactions. Because of the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of C4-dicarboxylates depends on fumarate reduction to succinate (fumarate respiration). In some related bacteria (e.g., Klebsiella), utilization of C4-dicarboxylates, such as tartrate, is independent of fumarate respiration and uses a Na+-dependent membrane-bound oxaloacetate decarboxylase. Uptake of the C4-dicarboxylates into the bacteria (and anaerobic export of succinate) is achieved under aerobic and anaerobic conditions by different sets of secondary transporters. Expression of the genes for C4-dicarboxylate metabolism is induced in the presence of external C4-dicarboxylates by the membrane-bound DcuS-DcuR two-component system. Noncommon C4-dicarboxylates like l-tartrate or D-malate are perceived by cytoplasmic one-component sensors/transcriptional regulators. This article describes the pathways of aerobic and anaerobic C4-dicarboxylate metabolism and their regulation. The citric acid cycle, fumarate respiration, and fumarate reductase are covered in other articles and discussed here only in the context of C4-dicarboxylate metabolism. Recent aspects of C4-dicarboxylate metabolism like transport, sensing, and regulation will be treated in more detail. This article is an updated version of an article published in 2004 in EcoSal Plus. The update includes new literature, but, in particular, the sections on the metabolism of noncommon C4-dicarboxylates and their regulation, on the DcuS-DcuR regulatory system, and on succinate production by engineered E. coli are largely revised or new.
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Affiliation(s)
- Gottfried Unden
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Alexander Strecker
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Alexandra Kleefeld
- Institute for Microbiology und Wine Research, Johannes Gutenberg-University, 55099 Mainz, Germany
| | - Ok Bin Kim
- Department of Life Sciences, Ewha Womans University, 120-750 Seoul, Korea
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25
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Marreiros BC, Calisto F, Castro PJ, Duarte AM, Sena FV, Silva AF, Sousa FM, Teixeira M, Refojo PN, Pereira MM. Exploring membrane respiratory chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1039-1067. [PMID: 27044012 DOI: 10.1016/j.bbabio.2016.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/20/2023]
Abstract
Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Paulo J Castro
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Afonso M Duarte
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.
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Takahashi-Íñiguez T, Aburto-Rodríguez N, Vilchis-González AL, Flores ME. Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase *. J Zhejiang Univ Sci B 2016; 17:247-261. [PMCID: PMC4829630 DOI: 10.1631/jzus.b1500219] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/14/2015] [Indexed: 09/12/2023]
Abstract
Malate dehydrogenase (MDH) is an enzyme widely distributed among living organisms and is a key protein in the central oxidative pathway. It catalyzes the interconversion between malate and oxaloacetate using NAD+ or NADP+ as a cofactor. Surprisingly, this enzyme has been extensively studied in eukaryotes but there are few reports about this enzyme in prokaryotes. It is necessary to review the relevant information to gain a better understanding of the function of this enzyme. Our review of the data generated from studies in bacteria shows much diversity in their molecular properties, including weight, oligomeric states, cofactor and substrate binding affinities, as well as differences in the direction of the enzymatic reaction. Furthermore, due to the importance of its function, the transcription and activity of this enzyme are rigorously regulated. Crystal structures of MDH from different bacterial sources led to the identification of the regions involved in substrate and cofactor binding and the residues important for the dimer-dimer interface. This structural information allows one to make direct modifications to improve the enzyme catalysis by increasing its activity, cofactor binding capacity, substrate specificity, and thermostability. A comparative analysis of the phylogenetic reconstruction of MDH reveals interesting facts about its evolutionary history, dividing this superfamily of proteins into two principle clades and establishing relationships between MDHs from different cellular compartments from archaea, bacteria, and eukaryotes.
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27
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Babnigg G, Jedrzejczak R, Nocek B, Stein A, Eschenfeldt W, Stols L, Marshall N, Weger A, Wu R, Donnelly M, Joachimiak A. Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. ACTA ACUST UNITED AC 2015; 16:113-28. [PMID: 26671275 DOI: 10.1007/s10969-015-9200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Two approaches are presented and compared which resulted in co-expression of paired genes from a single expression vector. Native operons encoding predicted interacting proteins were selected from a repertoire of genomes, and cloned directly to expression vector. In an alternative approach, Helicobacter pylori proteins predicted to interact strongly were cloned, each associated with translational control elements, then linked into an artificial operon. Proteins were then expressed and purified by standard HTP protocols, resulting to date in the structure determination of two H. pylori complexes.
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Affiliation(s)
- György Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Adam Stein
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - William Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Norman Marshall
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Alicia Weger
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Ruiying Wu
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Mark Donnelly
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
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Abstract
C4-dicarboxylates, like succinate, fumarate, L- and D-malate, tartrate, and the C4-dicarboxylic amino acid aspartate, support aerobic and anaerobic growth of Escherichia coli and related bacteria and can serve as carbon and energy sources. In aerobic growth, the C4-dicarboxylates are oxidized in the citric acid cycle. Due to the interruption of the citric acid cycle under anaerobic conditions, anaerobic metabolism of the C4-dicarboxylates depends on fumarate reduction to succinate. In some related bacteria (e.g., Klebsiella), degradation of C4-dicarboxylates, like tartrate, uses a different mechanism and pathway. It requires the functioning of an Na+-dependent and membrane-associated oxaloacetate decarboxylase. Due to the incomplete function of the citric acid cycle in anaerobic growth, succinate supports only aerobic growth of E. coli. This chapter describes the pathways of and differences in aerobic and anaerobic C4-dicarboxylate metabolism and the physiological consequences. The citric acid cycle, fumarate respiration, and fumarate reductase are discussed here only in the context of aerobic and anaerobic C4-dicarboxylate metabolism. Some recent aspects of C4-dicarboxylate metabolism, such as transport and sensing of C4-dicarboxylates, and their relationships are treated in more detail.
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Sawada K, Wada M, Hagiwara T, Zen-In S, Imai K, Yokota A. Effect of pyruvate kinase gene deletion on the physiology of Corynebacterium glutamicum ATCC13032 under biotin-sufficient non-glutamate-producing conditions: Enhanced biomass production. Metab Eng Commun 2015; 2:67-75. [PMID: 34150510 PMCID: PMC8193254 DOI: 10.1016/j.meteno.2015.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 04/21/2015] [Accepted: 07/02/2015] [Indexed: 11/17/2022] Open
Abstract
The effect of pyruvate kinase gene (pyk) deletion on the physiology of Corynebacterium glutamicum ATCC13032 was investigated under biotin-sufficient, non-glutamate-producing conditions. In a complex medium containing 100 g/L glucose, a defined pyk deletion mutant, strain D1, exhibited 35% enhancement in glucose consumption rate, 37% increased growth and a 57% reduction in respiration rate compared to the wild-type parent. Significant upregulation of phosphoenolpyruvate (PEP) carboxylase and downregulation of PEP carboxykinase activities were observed in the D1 mutant, which may have prevented over-accumulation of PEP caused by the pyk deletion. Moreover, we found a dramatic 63% reduction in the activity of malate:quinone oxidoreductase (MQO) in the D1 mutant. MQO, a TCA cycle enzyme that converts malate to oxaloacetate (OAA), constitutes a major primary gate to the respiratory chain in C. glutamicum, thus explaining the reduced respiration rate in the mutant. Additionally, pyruvate carboxylase gene expression was downregulated in the mutant. These changes seemed to prevent OAA over-accumulation caused by the activity changes of PEP carboxylase/PEP carboxykinase. Intrinsically the same alterations were observed in the cultures conducted in a minimal medium containing 20 g/L glucose. Despite these responses in the mutant, metabolic distortion caused by pyk deletion under non-glutamate-producing conditions required amelioration by increased biomass production, as metabolome analysis revealed increased intracellular concentrations of several precursor metabolites for building block formation associated with pyk deletion. These fermentation profiles and metabolic alterations observed in the mutant reverted completely to the wild-type phenotypes in the pyk-complemented strain, suggesting the observed metabolic changes were caused by the pyk deletion. These results demonstrated multilateral strategies to overcome metabolic disturbance caused by pyk deletion in this bacterium. The effect of pyk-deletion was investigated under non-glutamate-producing conditions. Pyk-deletion induced enhanced growth, glucose consumption, and reduced respiration. Metabolic changes that suppressed PEP/OAA over-accumulation led to enhanced growth. MQO was proposed as a key controller regulating OAA formation and respiration.
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Affiliation(s)
- Kazunori Sawada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Masaru Wada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Takuya Hagiwara
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Susumu Zen-In
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Keita Imai
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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Rokitta SD, Von Dassow P, Rost B, John U. Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis. BMC Genomics 2014; 15:1051. [PMID: 25467008 PMCID: PMC4301891 DOI: 10.1186/1471-2164-15-1051] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 11/18/2014] [Indexed: 02/03/2023] Open
Abstract
Background Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient utilization on the subcellular basis, we assessed the transcriptomic responses of the life-cycle stages of the biogeochemically important microalgae Emiliania huxleyi to nitrogen-limitation. Cells grown in batch cultures were harvested at ‘early’ and ‘full’ nitrogen-limitation and were compared with non-limited cells. We applied microarray-based transcriptome profilings, covering ~10.000 known E. huxleyi gene models, and screened for expression patterns that indicate the subcellular responses. Results The diploid life-cycle stage scavenges nitrogen from external organic sources and -like diatoms- uses the ornithine-urea cycle to rapidly turn over cellular nitrogen. The haploid stage reacts similarly, although nitrogen scavenging is less pronounced and lipid oxidation is more prominent. Generally, polyamines and proline appear to constitute major organic pools that back up cellular nitrogen. Both stages induce a malate:quinone-oxidoreductase that efficiently feeds electrons into the respiratory chain and drives ATP generation with reduced respiratory carbon throughput. Conclusions The use of the ornithine-urea cycle to budget the cellular nitrogen in situations of limitation resembles the responses observed earlier in diatoms. This suggests that underlying biochemical mechanisms are conserved among distant clades of marine phototrophic protists. The ornithine-urea cycle and proline oxidation appear to constitute a sensory-regulatory system that monitors and controls cellular nitrogen budgets under limitation. The similarity between the responses of the life-cycle stages, despite the usage of different genes, also indicates a strong functional consistency in the responses to nitrogen-limitation that appears to be owed to biochemical requirements. The malate:quinone-oxidoreductase is a genomic feature that appears to be absent from diatom genomes, and it is likely to strongly contribute to the uniquely high endurance of E. huxleyi under nutrient limitation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1051) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian D Rokitta
- Alfred Wegener Institute - Helmholtz-Centre for Polar- and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
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Goris T, Schubert T, Gadkari J, Wubet T, Tarkka M, Buscot F, Adrian L, Diekert G. Insights into organohalide respiration and the versatile catabolism ofSulfurospirillum multivoransgained from comparative genomics and physiological studies. Environ Microbiol 2014; 16:3562-80. [DOI: 10.1111/1462-2920.12589] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 07/31/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Goris
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena 07743 Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena 07743 Germany
| | - Jennifer Gadkari
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena 07743 Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; Helmholtz Centre for Environmental Research - UFZ; Halle 06120 Germany
| | - Mika Tarkka
- Department of Soil Ecology; Helmholtz Centre for Environmental Research - UFZ; Halle 06120 Germany
| | - Francois Buscot
- Department of Soil Ecology; Helmholtz Centre for Environmental Research - UFZ; Halle 06120 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena - Leipzig; Leipzig 04103 Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig 04318 Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena 07743 Germany
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Arifin Y, Archer C, Lim S, Quek LE, Sugiarto H, Marcellin E, Vickers CE, Krömer JO, Nielsen LK. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Appl Microbiol Biotechnol 2014; 98:9033-44. [DOI: 10.1007/s00253-014-5956-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
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Wisecaver JH, Brosnahan ML, Hackett JD. Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates. Genome Biol Evol 2014; 5:2368-81. [PMID: 24259313 PMCID: PMC3879968 DOI: 10.1093/gbe/evt179] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
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Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glöckner FO, Golyshina OV, Golyshin PN, Teeling H. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader. Environ Microbiol 2014; 16:2525-37. [PMID: 24428220 PMCID: PMC4257568 DOI: 10.1111/1462-2920.12393] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 01/05/2014] [Indexed: 11/28/2022]
Abstract
Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.
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Affiliation(s)
- Johannes Werner
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany
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Noor E, Bar-Even A, Flamholz A, Reznik E, Liebermeister W, Milo R. Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput Biol 2014; 10:e1003483. [PMID: 24586134 PMCID: PMC3930492 DOI: 10.1371/journal.pcbi.1003483] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 01/08/2014] [Indexed: 12/05/2022] Open
Abstract
In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating the thermodynamic and kinetic quality of different pathway chemistries that produce the same molecules. Given data about enzyme kinetics and reaction thermodynamics, traditional metabolic control analysis (MCA) can pinpoint the enzymes whose expression will have the largest effect on steady-state flux through the pathway. These analyses can aid experimentalists in tuning enzyme expression levels along a metabolic pathway. In this work, we offer a framework that is complementary to MCA. Rather than focusing on the relationship between enzyme levels and pathway flux, we examine a pathway's stoichiometry and thermodynamics and ask whether it is likely to support high flux in cellular conditions. Our framework calculates a single thermodynamically-derived metric (the MDF) for each pathway, which is convenient for selecting the promising pathways from a large collection. This approach has several advantages. First, enzyme kinetic properties are laborious to measure and differ between organisms and isozymes, but no kinetic data is required to calculate the MDF. Second, as our framework accounts for pH, ionic strength and allowed concentration ranges, it is simple to model the effect of these parameters on the MDF. Finally, as it can be difficult to control the exact expression level of enzymes within cells, the MDF helps identify alternative pathways that are less sensitive to the levels of their constituent enzymes.
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Affiliation(s)
- Elad Noor
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Avi Flamholz
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular and Cellular Biology, University of California, Berkely, Berkely, California, United States of America
| | - Ed Reznik
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | | | - Ron Milo
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Tsugawa H. [Study of infection strategies of Helicobacter pylori and host cell response against CagA oncoprotein]. Nihon Saikingaku Zasshi 2014; 69:565-575. [PMID: 25447982 DOI: 10.3412/jsb.69.565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chronic infection with Helicobacter pylori is involved in a variety of clinical outcomes including gastric cancer. In the present study, we focused on the infection strategies of H. pylori associated with establishment of chronic infection. As a result, the following four findings revealed. 1) alpha-ketoglutarate oxidoreductase (KOR) is an essential survival enzyme for energy metabolism in the coccoid form of H. pylori, and inactivation of the KOR activity exerted a potent bactericidal action against H. pylori by preventing induction of the coccoid form. 2) SodB expression is derepressed by amino acids mutation of ferric uptake regulator (Fur), which is associated with the development of Metronidazole resistance. 3) FecA1 is an important determinant of the host-colonization ability through Fe(2+) supply to SodB, suggesting that FecA1 may be a possible target for the development of a novel bactericidal drug. 4) Intracellular CagA oncoprotein is degraded by autophagy and therefore short lived. However, in the CD44v9-expressing gastric cells, CagA specifically accumulated through the repression of autophagy induction.
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Affiliation(s)
- Hitoshi Tsugawa
- Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University
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Kabashima Y, Sone N, Kusumoto T, Sakamoto J. Purification and characterization of malate:quinone oxidoreductase from thermophilic Bacillus sp. PS3. J Bioenerg Biomembr 2012; 45:131-6. [PMID: 23143325 DOI: 10.1007/s10863-012-9485-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/14/2012] [Indexed: 02/03/2023]
Abstract
Several bacteria possess membrane-bound dehydrogenases other than cytosolic dehydrogenases in their respiratory chains. In many cases, the membrane-bound malate:quinone oxidoreductases (MQOs) are essential for growth. However, these MQOs are absent in mammalian mitochondria, and therefore may be a potential drug target for pathogenic bacteria. To characterize the kinetic properties of MQOs, we purified MQO from Bacillus sp. PS3, which is a gram-positive and thermophilic bacterium, and cloned the gene encoding MQO based on the obtained partial N-terminus sequence. Purified MQOs showed a molecular mass of ~90 kDa, which was estimated using gel filtration, and it consists of two subunits with a molecular mass of ~50 kDa. Phylogenetic analysis showed a high similarity to the MQO of the Geobacillus group rather than the Bacillus group. Additionally, the purified enzyme was thermostable and it retained menaquinol reduction activity at high temperatures. Although it is difficult to conduct experiments using menaquinol because of its instability, we were able to measure the oxidase activity of cytochrome bd-type quinol oxidase by using menaquinol-1 by coupling this molecule with the menaquinol reduction reaction using purified MQOs.
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Affiliation(s)
- Yoshiki Kabashima
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka-ken 820-8502, Japan
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The Gluconeogenic Pathway in a Soil Mycobacterium Isolate with Bioremediation Ability. Curr Microbiol 2012; 66:122-31. [DOI: 10.1007/s00284-012-0248-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 09/23/2012] [Indexed: 11/26/2022]
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Danne JC, Gornik SG, Macrae JI, McConville MJ, Waller RF. Alveolate mitochondrial metabolic evolution: dinoflagellates force reassessment of the role of parasitism as a driver of change in apicomplexans. Mol Biol Evol 2012; 30:123-39. [PMID: 22923466 DOI: 10.1093/molbev/mss205] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial metabolism is central to the supply of ATP and numerous essential metabolites in most eukaryotic cells. Across eukaryotic diversity, however, there is evidence of much adaptation of the function of this organelle according to specific metabolic requirements and/or demands imposed by different environmental niches. This includes substantial loss or retailoring of mitochondrial function in many parasitic groups that occupy potentially nutrient-rich environments in their metazoan hosts. Infrakingdom Alveolata comprises a well-supported alliance of three disparate eukaryotic phyla-dinoflagellates, apicomplexans, and ciliates. These major taxa represent diverse lifestyles of free-living phototrophs, parasites, and predators and offer fertile territory for exploring character evolution in mitochondria. The mitochondria of apicomplexan parasites provide much evidence of loss or change of function from analysis of mitochondrial protein genes. Much less, however, is known of mitochondrial function in their closest relatives, the dinoflagellate algae. In this study, we have developed new models of mitochondrial metabolism in dinoflagellates based on gene predictions and stable isotope labeling experiments. These data show that many changes in mitochondrial gene content previously only known from apicomplexans are found in dinoflagellates also. For example, loss of the pyruvate dehydrogenase complex and changes in tricarboxylic acid (TCA) cycle enzyme complement are shared by both groups and, therefore, represent ancestral character states. Significantly, we show that these changes do not result in loss of typical TCA cycle activity fueled by pyruvate. Thus, dinoflagellate data show that many changes in alveolate mitochondrial metabolism are independent of the major lifestyle changes seen in these lineages and provide a revised view of mitochondria character evolution during evolution of parasitism in apicomplexans.
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Affiliation(s)
- Jillian C Danne
- School of Botany, University of Melbourne, Victoria, Australia
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Schott T, Kondadi PK, Hänninen ML, Rossi M. Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. BMC Genomics 2011; 12:534. [PMID: 22039924 PMCID: PMC3234257 DOI: 10.1186/1471-2164-12-534] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/31/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The canine Gram-negative Helicobacter bizzozeronii is one of seven species in Helicobacter heilmannii sensu lato that are detected in 0.17-2.3% of the gastric biopsies of human patients with gastric symptoms. At the present, H. bizzozeronii is the only non-pylori gastric Helicobacter sp. cultivated from human patients and is therefore a good alternative model of human gastric Helicobacter disease. We recently sequenced the genome of the H. bizzozeronii human strain CIII-1, isolated in 2008 from a 47-year old Finnish woman suffering from severe dyspeptic symptoms. In this study, we performed a detailed comparative genome analysis with H. pylori, providing new insights into non-pylori Helicobacter infections and the mechanisms of transmission between the primary animal host and humans. RESULTS H. bizzozeronii possesses all the genes necessary for its specialised life in the stomach. However, H. bizzozeronii differs from H. pylori by having a wider metabolic flexibility in terms of its energy sources and electron transport chain. Moreover, H. bizzozeronii harbours a higher number of methyl-accepting chemotaxis proteins, allowing it to respond to a wider spectrum of environmental signals. In this study, H. bizzozeronii has been shown to have high level of genome plasticity. We were able to identify a total of 43 contingency genes, 5 insertion sequences (ISs), 22 mini-IS elements, 1 genomic island and a putative prophage. Although H. bizzozeronii lacks homologues of some of the major H. pylori virulence genes, other candidate virulence factors are present. In particular, we identified a polysaccharide lyase (HBZC1_15820) as a potential new virulence factor of H. bizzozeronii. CONCLUSIONS The comparative genome analysis performed in this study increased the knowledge of the biology of gastric Helicobacter species. In particular, we propose the hypothesis that the high metabolic versatility and the ability to react to a range of environmental signals, factors which differentiate H. bizzozeronii as well as H. felis and H. suis from H. pylori, are the molecular basis of the of the zoonotic nature of H. heilmannii sensu lato infection in humans.
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Affiliation(s)
- Thomas Schott
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Pradeep K Kondadi
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
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Bulusu V, Jayaraman V, Balaram H. Metabolic fate of fumarate, a side product of the purine salvage pathway in the intraerythrocytic stages of Plasmodium falciparum. J Biol Chem 2011; 286:9236-45. [PMID: 21209090 PMCID: PMC3059058 DOI: 10.1074/jbc.m110.173328] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 12/17/2010] [Indexed: 11/06/2022] Open
Abstract
In aerobic respiration, the tricarboxylic acid cycle is pivotal to the complete oxidation of carbohydrates, proteins, and lipids to carbon dioxide and water. Plasmodium falciparum, the causative agent of human malaria, lacks a conventional tricarboxylic acid cycle and depends exclusively on glycolysis for ATP production. However, all of the constituent enzymes of the tricarboxylic acid cycle are annotated in the genome of P. falciparum, which implies that the pathway might have important, yet unidentified biosynthetic functions. Here we show that fumarate, a side product of the purine salvage pathway and a metabolic intermediate of the tricarboxylic acid cycle, is not a metabolic waste but is converted to aspartate through malate and oxaloacetate. P. falciparum-infected erythrocytes and free parasites incorporated [2,3-(14)C]fumarate into the nucleic acid and protein fractions. (13)C NMR of parasites incubated with [2,3-(13)C]fumarate showed the formation of malate, pyruvate, lactate, and aspartate but not citrate or succinate. Further, treatment of free parasites with atovaquone inhibited the conversion of fumarate to aspartate, thereby indicating this pathway as an electron transport chain-dependent process. This study, therefore, provides a biosynthetic function for fumarate hydratase, malate quinone oxidoreductase, and aspartate aminotransferase of P. falciparum.
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Affiliation(s)
- Vinay Bulusu
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, Karnataka, India
| | - Vijay Jayaraman
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, Karnataka, India
| | - Hemalatha Balaram
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, Karnataka, India
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Luque-Almagro VM, Merchán F, Blasco R, Igeño MI, Martínez-Luque M, Moreno-Vivián C, Castillo F, Roldán MD. Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate:quinone oxidoreductase and an associated cyanide-insensitive electron transfer chain. MICROBIOLOGY-SGM 2010; 157:739-746. [PMID: 21178163 DOI: 10.1099/mic.0.045286-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to grow with cyanide as the sole nitrogen source. Membrane fractions from cells grown under cyanotrophic conditions catalysed the production of oxaloacetate from L-malate. Several enzymic activities of the tricarboxylic acid and glyoxylate cycles in association with the cyanide-insensitive respiratory pathway seem to be responsible for the oxaloacetate formation in vivo. Thus, in cyanide-grown cells, citrate synthase and isocitrate lyase activities were significantly higher than those observed with other nitrogen sources. Malate dehydrogenase activity was undetectable, but a malate:quinone oxidoreductase activity coupled to the cyanide-insensitive alternative oxidase was found in membrane fractions from cyanide-grown cells. Therefore, oxaloacetate production was linked to the cyanide-insensitive respiration in P. pseudoalcaligenes CECT5344. Cyanide and oxaloacetate reacted chemically inside the cells to produce a cyanohydrin (2-hydroxynitrile), which was further converted to ammonium. In addition to cyanide, strain CECT5344 was able to grow with several cyano derivatives, such as 2- and 3-hydroxynitriles. The specific system required for uptake and metabolization of cyanohydrins was induced by cyanide and by 2-hydroxynitriles, such as the cyanohydrins of oxaloacetate and 2-oxoglutarate.
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Affiliation(s)
- Victor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Faustino Merchán
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Rafael Blasco
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - M Isabel Igeño
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Manuel Martínez-Luque
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - Francisco Castillo
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
| | - M Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Edificio Severo Ochoa, 1a Planta, Universidad de Córdoba, Córdoba, Spain
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Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L. Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 2010; 6:364. [PMID: 20461071 PMCID: PMC2890322 DOI: 10.1038/msb.2010.18] [Citation(s) in RCA: 327] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 03/05/2010] [Indexed: 12/14/2022] Open
Abstract
GC-MS-based analysis of the metabolic response of Escherichia coli exposed to four different stress conditions reveals reduction of energy expensive pathways. Time-resolved response of E. coli to changing environmental conditions is more specific on the metabolite as compared with the transcript level. Cease of growth during stress response as compared with stationary phase response invokes similar transcript but dissimilar metabolite responses. Condition-dependent associations between metabolites and transcripts are revealed applying co-clustering and canonical correlation analysis.
The response of biological systems to environmental perturbations is characterized by a fast and appropriate adjusting of physiology on every level of the cellular and molecular network. Stress response is usually represented by a combination of both specific responses, aimed at minimizing deleterious effects or repairing damage (e.g. protein chaperones under temperature stress) and general responses which, in part, comprise the downregulation of genes related to translation and ribosome biogenesis. This in turn is reflected by growth cessation or reduction observed under essentially all stress conditions and is an important strategy to adjust cellular physiology to the new condition. E. coli has been intensively investigated in relation to stress responses. Thus far, however, the majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. To better understand system response to perturbation, we designed a time-resolved experiment to compare and integrate metabolic and transcript changes of E. coli using four stress conditions including non-lethal temperature shifts, oxidative stress, and carbon starvation relative to cultures grown under optimal conditions covering both states before and directly after stress application, resumption of growth after stress-induced lag phase, and finally the stationary phase. Metabolic changes occurring after stress application were characterized by a reduction in metabolites of central metabolism (TCA cycle and glycolysis) as well as an increase in free amino acids. Whereas the latter is probably due to protein degradation and stalling of translation, the former supports and extends conclusions based on transcriptome data demonstrating a major decrease in energy-consuming processes as a general stress response. Further comparative analysis of the response on the metabolome and transcriptome, however, revealed in addition to these similarities major differences. Thus, the response on the metabolome displayed a significantly higher specificity towards the specific stress as compared with the transcriptome. Further, when comparing the metabolome of cells ceasing growth due to stress application with cells ceasing growth due to reaching stationary phase the metabolome response differed to a significant extent between both growth arrest phases, whereas the transcriptome response showed significant overlap again, suggesting that the response of E. coli on the metabolome level displays a higher level of significance as compared with the transcriptome level. Subsequently, both data sets were jointly analyzed using co-clustering and canonical correlation approaches to identify coordinated changes on the transcriptome and the metabolite level indicative metabolite–transcript associations. A first outcome of this study was that no association was preserved during all conditions analyzed but rather condition-specific associations were observed. One set of associations found was between metabolites from the oxidative pentose phosphate pathway such as glc-6-P, 6-P-gluconic acid, ribose-5-P, and E-4-P and metabolites from the glycolytic pathway (3PGA and PEP in addition to glc-6-P with two genes encoding pathway enzymes, that is rpe encoding ribulose phosphate 3-epimerase and pps encoding PEP synthase. A second example comprises metabolites of the TCA cycle such as pyruvic acid, 2-ketoglutaric acid, fumaric acid, malic acid, and succinic acid and the mqo gene encoding malate-quinone oxidoreductase (MQO). MQO catalyses the irreversible oxidation of malate to oxaloacetate that in turn regulates the activity of citrate synthase, which is a major rate determining enzyme of the TCA cycle. The strong association between mqo gene expression and multiple members of the TCA cycle as well as pyruvate suggest mqo expression to have a major function for the regulation of the TCA cycle, which need to be experimentally validated. Multiple further associations identified show on the one hand the power of integrative systems oriented approaches for developing new hypothesis, on the other hand their condition-dependent behavior shows the extreme flexibility of the biological systems studied thus requesting a much more intense effort toward parallel analysis of biological systems under several environmental conditions. Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here, we incorporate the metabolite composition together with gene expression data to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared with the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with downregulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition-dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.
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Affiliation(s)
- Szymon Jozefczuk
- Molecular Plant Physiology, Max-Planck-Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
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Abstract
Lipoic acid [(R)-5-(1,2-dithiolan-3-yl)pentanoic acid] is an enzyme cofactor required for intermediate metabolism in free-living cells. Lipoic acid was discovered nearly 60 years ago and was shown to be covalently attached to proteins in several multicomponent dehydrogenases. Cells can acquire lipoate (the deprotonated charge form of lipoic acid that dominates at physiological pH) through either scavenging or de novo synthesis. Microbial pathogens implement these basic lipoylation strategies with a surprising variety of adaptations which can affect pathogenesis and virulence. Similarly, lipoylated proteins are responsible for effects beyond their classical roles in catalysis. These include roles in oxidative defense, bacterial sporulation, and gene expression. This review surveys the role of lipoate metabolism in bacterial, fungal, and protozoan pathogens and how these organisms have employed this metabolism to adapt to niche environments.
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Mogi T, Kita K. Diversity in mitochondrial metabolic pathways in parasitic protists Plasmodium and Cryptosporidium. Parasitol Int 2010; 59:305-12. [PMID: 20433942 DOI: 10.1016/j.parint.2010.04.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 09/24/2009] [Accepted: 09/25/2009] [Indexed: 01/29/2023]
Abstract
Apicomplexans are obligate intracellular parasites and occupy diverse niches. They have remodeled mitochondrial carbon and energy metabolism through reductive evolution. Plasmodium lacks mitochondrial pyruvate dehydrogenase and H(+)-translocating NADH dehydrogenase (Complex I, NDH1). The mitochondorion contains a minimal mtDNA ( approximately 6kb) and carries out oxidative phosphorylation in the insect vector stages, by using 2-oxoglutarate as an alternative means of entry into the TCA cycle and a single-subunit flavoprotein as an alternative NADH dehydrogenase (NDH2). In the blood stages of mammalian hosts, mitochondrial enzymes are down-regulated and parasite energy metabolism relies mainly on glycolysis. Mitosomes of Cryptosporidium parvum and Cryptosporidium hominis (human intestine parasites) lack mtDNA, pyruvate dehydrogenase, TCA cycle enzymes except malate-quinone oxidoreductase (MQO), and ATP synthase subunits except alpha and beta. In contrast, mitosomes of Cryptosporidium muris (a rodent gastric parasite) retain all TCA cycle enzymes and functional ATP synthase and carry out oxidative phosphorylation with pyruvate-NADP(+) oxidoreductase (PNO) and a simple and unique respiratory chain consisting of NDH2 and alternative oxidase (AOX). Cryptosporidium and Perkinsus are early branching groups of chromoalveolates (apicomplexa and dinoflagellates, respectively), and both Cryptosporidium mitosome and Perkinsus mitochondrion use PNO, MQO, and AOX. All apicomplexan parasites and dinoflagellates share MQO, which has been acquired from epsilon-proteobacteria via lateral gene transfer. By genome data mining on Plasmodium, Cryptosporidium and Perkinsus, here we summarized their mitochondrial metabolic pathways, which are varied largely from those of mammalian hosts. We hope that our findings will help in understanding the apicomplexan metabolism and development of new chemotherapeutics with novel targets.
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Affiliation(s)
- Tatsushi Mogi
- Department of Biomedical Chemistry, Graduate School of Medicine, the University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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Duckworth MJ, Okoli AS, Mendz GL. Novel Helicobacter pylori therapeutic targets: the unusual suspects. Expert Rev Anti Infect Ther 2009; 7:835-67. [PMID: 19735225 DOI: 10.1586/eri.09.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the current status of the discovery and development of anti-Helicobacter therapies requires an overview of the searches for therapeutic targets performed to date. A summary is given of the very substantial body of work conducted in the quest to find Helicobacter pylori genes that could be suitable candidates for therapeutic intervention. The products of most of these genes perform metabolic functions, and others have roles in growth, cell motility and colonization. The genes identified as potential targets have been organized into three categories according to their degree of characterization. A short description and evaluation is provided of the main candidates in each category. Investigations of potential therapeutic targets have generated a wealth of information about the physiology and genetics of H. pylori, and its interactions with the host, but have yielded little by way of new therapies.
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Affiliation(s)
- Megan J Duckworth
- School of Medicine, Sydney, The University of Notre Dame Australia, 160 Oxford Street, Darlinghurst, NSW 2010, Australia.
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Kihara K, Mori K, Suzuki S, Ono N, Furusawa C, Yomo T. Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum. Biosystems 2009; 96:141-64. [DOI: 10.1016/j.biosystems.2009.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 01/09/2009] [Accepted: 01/12/2009] [Indexed: 01/05/2023]
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Henne KL, Turse JE, Nicora CD, Lipton MS, Tollaksen SL, Lindberg C, Babnigg G, Giometti CS, Nakatsu CH, Thompson DK, Konopka AE. Global Proteomic Analysis of the Chromate Response in Arthrobacter sp. Strain FB24. J Proteome Res 2009; 8:1704-16. [DOI: 10.1021/pr800705f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kristene L. Henne
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Joshua E. Turse
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carrie D. Nicora
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Mary S. Lipton
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Sandra L. Tollaksen
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carl Lindberg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Gyorgy Babnigg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carol S. Giometti
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Cindy H. Nakatsu
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Dorothea K. Thompson
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Allan E. Konopka
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
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Tsugawa H, Suzuki H, Nakagawa I, Nishizawa T, Saito Y, Suematsu M, Hibi T. Alpha-ketoglutarate oxidoreductase, an essential salvage enzyme of energy metabolism, in coccoid form of Helicobacter pylori. Biochem Biophys Res Commun 2008; 376:46-51. [DOI: 10.1016/j.bbrc.2008.08.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 08/17/2008] [Indexed: 10/21/2022]
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Buettner FFR, Bendallah IM, Bosse JT, Dreckmann K, Nash JHE, Langford PR, Gerlach GF. Analysis of the Actinobacillus pleuropneumoniae ArcA regulon identifies fumarate reductase as a determinant of virulence. Infect Immun 2008; 76:2284-95. [PMID: 18378638 PMCID: PMC2423083 DOI: 10.1128/iai.01540-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/10/2008] [Accepted: 03/23/2008] [Indexed: 11/20/2022] Open
Abstract
The ability of the bacterial pathogen Actinobacillus pleuropneumoniae to grow anaerobically allows the bacterium to persist in the lung. The ArcAB two-component system is crucial for metabolic adaptation in response to anaerobic conditions, and we recently showed that an A. pleuropneumoniae arcA mutant had reduced virulence compared to the wild type (F. F. Buettner, A. Maas, and G.-F. Gerlach, Vet. Microbiol. 127:106-115, 2008). In order to understand the attenuated phenotype, we investigated the ArcA regulon of A. pleuropneumoniae by using a combination of transcriptome (microarray) and proteome (two-dimensional difference gel electrophoresis and subsequent mass spectrometry) analyses. We show that ArcA negatively regulates the expression of many genes, including those encoding enzymes which consume intermediates during fumarate synthesis. Simultaneously, the expression of glycerol-3-phosphate dehydrogenase, a component of the respiratory chain serving as a direct reduction equivalent for fumarate reductase, was upregulated. This result, together with the in silico analysis finding that A. pleuropneumoniae has no oxidative branch of the citric acid cycle, led to the hypothesis that fumarate reductase might be crucial for virulence by providing (i) energy via fumarate respiration and (ii) succinate and other essential metabolic intermediates via the reductive branch of the citric acid cycle. To test this hypothesis, an isogenic A. pleuropneumoniae fumarate reductase deletion mutant was constructed and studied by using a pig aerosol infection model. The mutant was shown to be significantly attenuated, thereby strongly supporting a crucial role for fumarate reductase in the pathogenesis of A. pleuropneumoniae infection.
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Affiliation(s)
- Falk F R Buettner
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
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