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Organic Acid Profiles of Phosphate Solubilizing Bacterial Strains in the Presence of Different Insoluble Phosphatic Sources Under In vitro Buffered Conditions. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of weak organic acids by microorganisms has been attributed as the prime reason for the solubilization of insoluble phosphates under both in vitro and soil conditions. Literature seems to be heavily biased towards gluconic acid production by microbes and its subsequent release into the environment as the key factor responsible for phosphate solubilization. This has found credibility since gluconic acid being a product of the Kreb’s cycle is often detected in large quantities in the culture media, when assayed under in vitro conditions. In the present work, the organic acid profiles of four elite phosphate solubilising isolates were determined in the presence of different insoluble sources of phosphates, under in vitro buffered culture conditions by HPLC (High-Performance Liquid Chromatography). While most previous studies did not use a buffered culture media for elucidating the organic acid profile of phosphate solubilizing bacterial isolates, we used a buffered media for estimation of the organic acid profiles. The results revealed that apart from gluconic acid, malic acid is produced in significant levels by phosphate solubilizing bacterial isolates, and there seems to be a differential pattern of production of these two organic acids by the isolates in the presence of different insoluble phosphate sources.
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2
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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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3
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Harding CJ, Cadby IT, Moynihan PJ, Lovering AL. A rotary mechanism for allostery in bacterial hybrid malic enzymes. Nat Commun 2021; 12:1228. [PMID: 33623032 PMCID: PMC7902834 DOI: 10.1038/s41467-021-21528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial hybrid malic enzymes (MaeB grouping, multidomain) catalyse the transformation of malate to pyruvate, and are a major contributor to cellular reducing power and carbon flux. Distinct from other malic enzyme subtypes, the hybrid enzymes are regulated by acetyl-CoA, a molecular indicator of the metabolic state of the cell. Here we solve the structure of a MaeB protein, which reveals hybrid enzymes use the appended phosphotransacetylase (PTA) domain to form a hexameric sensor that communicates acetyl-CoA occupancy to the malic enzyme active site, 60 Å away. We demonstrate that allostery is governed by a large-scale rearrangement that rotates the catalytic subunits 70° between the two states, identifying MaeB as a new model enzyme for the study of ligand-induced conformational change. Our work provides the mechanistic basis for metabolic control of hybrid malic enzymes, and identifies inhibition-insensitive variants that may find utility in synthetic biology.
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Affiliation(s)
- Christopher John Harding
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Ian Thomas Cadby
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Patrick Joseph Moynihan
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Andrew Lee Lovering
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
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Burley KH, Cuthbert BJ, Basu P, Newcombe J, Irimpan EM, Quechol R, Foik IP, Mobley DL, Beste DJV, Goulding CW. Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target. ACS Infect Dis 2021; 7:174-188. [PMID: 33356117 DOI: 10.1021/acsinfecdis.0c00735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.
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Affiliation(s)
| | | | - Piyali Basu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Jane Newcombe
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | | | | | | | | | - Dany J. V. Beste
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
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5
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Mendes Ferreira A, Mendes-Faia A. The Role of Yeasts and Lactic Acid Bacteria on the Metabolism of Organic Acids during Winemaking. Foods 2020; 9:E1231. [PMID: 32899297 PMCID: PMC7555314 DOI: 10.3390/foods9091231] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022] Open
Abstract
The main role of acidity and pH is to confer microbial stability to wines. No less relevant, they also preserve the color and sensory properties of wines. Tartaric and malic acids are generally the most prominent acids in wines, while others such as succinic, citric, lactic, and pyruvic can exist in minor concentrations. Multiple reactions occur during winemaking and processing, resulting in changes in the concentration of these acids in wines. Two major groups of microorganisms are involved in such modifications: the wine yeasts, particularly strains of Saccharomyces cerevisiae, which carry out alcoholic fermentation; and lactic acid bacteria, which commonly conduct malolactic fermentation. This review examines various such modifications that occur in the pre-existing acids of grape berries and in others that result from this microbial activity as a means to elucidate the link between microbial diversity and wine composition.
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Affiliation(s)
- Ana Mendes Ferreira
- University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- WM&B—Wine Microbiology & Biotechnology Laboratory, Department of Biology and Environment, UTAD, 5001-801 Vila Real, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Arlete Mendes-Faia
- University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- WM&B—Wine Microbiology & Biotechnology Laboratory, Department of Biology and Environment, UTAD, 5001-801 Vila Real, Portugal
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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The NADP-dependent malic enzyme MaeB is a central metabolic hub controlled by the acetyl-CoA to CoASH ratio. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140462. [PMID: 32485238 DOI: 10.1016/j.bbapap.2020.140462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/20/2022]
Abstract
Malic enzymes participate in key metabolic processes, the MaeB-like malic enzymes carry a catalytic inactive phosphotransacetylase domain whose function remains elusive. Here we show that acetyl-CoA directly binds and inhibits MaeB-like enzymes with a saturable profile under physiological relevant acetyl-CoA concentrations. A MaeB-like enzyme from the nitrogen-fixing bacterium Azospirillum brasilense, namely AbMaeB1, binds both acetyl-CoA and unesterified CoASH in a way that inhibition of AbMaeB1 by acetyl-CoA is relieved by increasing CoASH concentrations. Hence, AbMaeB1 senses the acetyl-CoA/CoASH ratio. We revisited E. coli MaeB regulation to determine the inhibitory constant for acetyl-CoA. Our data support that the phosphotransacetylase domain of MaeB-like enzymes senses acetyl-CoA to dictate the fate of carbon distribution at the phosphoenol-pyruvate / pyruvate / oxaloacetate metabolic node.
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Rozova ON, Mustakhimov II, But SY, Reshetnikov AS, Khmelenina VN. Role of the malic enzyme in metabolism of the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z. PLoS One 2019; 14:e0225054. [PMID: 31738793 PMCID: PMC6860931 DOI: 10.1371/journal.pone.0225054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The bacteria utilizing methane as a growth substrate (methanotrophs) are important constituents of the biosphere. Methanotrophs mitigate the emission of anthropogenic and natural greenhouse gas methane to the environment and are the promising agents for future biotechnologies. Many aspects of CH4 bioconversion by methanotrophs require further clarification. This study was aimed at characterizing the biochemical properties of the malic enzyme (Mae) from the halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z. The His6-tagged Mae was obtained by heterologous expression in Escherichia coli BL21 (DE3) and purified by affinity metal chelating chromatography. As determined by gel filtration and non-denaturating gradient gel electrophoresis, the molecular mass of the native enzyme is 260 kDa. The homotetrameric Mae (65x4 kDa) catalyzed an irreversible NAD+-dependent reaction of L-malate decarboxylation into pyruvate with a specific activity of 32 ± 2 units mg-1 and Km value of 5.5 ± 0.8 mM for malate and 57 ± 5 μM for NAD+. The disruption of the mae gene by insertion mutagenesis resulted in a 20-fold increase in intracellular malate level in the mutant compared to the wild type strain. Based on both enzyme and mutant properties, we conclude that the malic enzyme is involved in the control of intracellular L-malate level in Mtm. alcaliphilum 20Z. Genomic analysis has revealed that Maes present in methanotrophs fall into two different clades in the amino acid-based phylogenetic tree, but no correlation of the division with taxonomic affiliations of the host bacteria was observed.
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Affiliation(s)
- Olga N. Rozova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ildar I. Mustakhimov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergei Y. But
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Aleksandr S. Reshetnikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina N. Khmelenina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Liu A, Contador CA, Fan K, Lam HM. Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes. FRONTIERS IN PLANT SCIENCE 2018; 9:1860. [PMID: 30619423 PMCID: PMC6305480 DOI: 10.3389/fpls.2018.01860] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
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Affiliation(s)
- Ailin Liu
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carolina A. Contador
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kejing Fan
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Hon-Ming Lam,
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Zhang Y, Smallbone LA, diCenzo GC, Morton R, Finan TM. Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti. BMC Microbiol 2016; 16:163. [PMID: 27456220 PMCID: PMC4960864 DOI: 10.1186/s12866-016-0780-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. Despite the wide distribution of these enzymes, their biological roles are unclear in part because the reaction catalyzed by these enzymes can be by-passed by other pathways. The N2-fixing alfalfa symbiont Sinorhizobium meliloti contains both a NAD(P)-malic enzyme (DME) and a separate NADP-malic enzyme (TME) and to help understand the role of these enzymes, we investigated growth, metabolomic, and transcriptional consequences resulting from loss of these enzymes in free-living cells. RESULTS Loss of DME, TME, or both enzymes had no effect on growth with the glycolytic substrate, glucose. In contrast, the dme mutants, but not tme, grew slowly on the gluconeogenic substrate succinate and this slow growth was further reduced upon the addition of glucose. The dme mutant strains incubated with succinate accumulated trehalose and hexose sugar phosphates, secreted malate, and relative to wild-type, these cells had moderately increased transcription of genes involved in gluconeogenesis and pathways that divert metabolites away from the TCA cycle. While tme mutant cells grew at the same rate as wild-type on succinate, they accumulated the compatible solute putrescine. CONCLUSIONS NAD(P)-malic enzyme (DME) of S. meliloti is required for efficient metabolism of succinate via the TCA cycle. In dme mutants utilizing succinate, malate accumulates and is excreted and these cells appear to increase metabolite flow via gluconeogenesis with a resulting increase in the levels of hexose-6-phosphates and trehalose. For cells utilizing succinate, TME activity alone appeared to be insufficient to produce the levels of pyruvate required for efficient TCA cycle metabolism. Putrescine was found to accumulate in tme cells growing with succinate, and whether this is related to altered levels of NADPH requires further investigation.
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Affiliation(s)
- Ye Zhang
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Laura Anne Smallbone
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - George C diCenzo
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - Richard Morton
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON, L8S 4K1, Canada.
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10
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Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
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Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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11
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Zhang H, Zhang L, Chen H, Chen YQ, Ratledge C, Song Y, Chen W. Regulatory properties of malic enzyme in the oleaginous yeast, Yarrowia lipolytica, and its non-involvement in lipid accumulation. Biotechnol Lett 2013; 35:2091-8. [PMID: 23892983 DOI: 10.1007/s10529-013-1302-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/10/2013] [Indexed: 02/05/2023]
Abstract
Malic enzyme (EC 1.1.1.40) converts L-malate to pyruvate and CO2 providing NADPH for metabolism especially for lipid biosynthesis in oleaginous microorganisms. However, its role in the oleaginous yeast, Yarrowia lipolytica, is unclear. We have cloned the malic enzyme gene (YALI0E18634g) from Y. lipolytica into pET28a, expressed it in Escherichia coli and purified the recombinant protein (YlME). YlME used NAD(+) as the primary cofactor. Km values for NAD(+) and NADP(+) were 0.63 and 3.9 mM, respectively. Citrate, isocitrate and α-ketoglutaric acid (>5 mM) were inhibitory while succinate (5-15 mM) increased NADP(+)- but not NAD(+)-dependent activity. To determine if fatty acid biosynthesis could be increased in Y. lipolytica by providing additional NADPH from an NADP(+)-dependent malic enzyme, the malic enzyme gene (mce2) from an oleaginous fungus, Mortierella alpina, was expressed in Y. lipolytica. No significant changes occurred in lipid content or fatty acid profiles suggesting that malic enzyme is not the main source of NADPH for lipid accumulation in Y. lipolytica.
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Affiliation(s)
- Huaiyuan Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China,
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12
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Dao TV, Nomura M, Hamaguchi R, Kato K, Itakura M, Minamisawa K, Sinsuwongwat S, Le HTP, Kaneko T, Tabata S, Tajima S. NAD-Malic Enzyme Affects Nitrogen Fixing Activity of Bradyrhizobium japonicum USDA 110 Bacteroids in Soybean Nodules. Microbes Environ 2012; 23:215-20. [PMID: 21558711 DOI: 10.1264/jsme2.23.215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The NAD(+)-dependent malic enzyme (DME) has been reported to play a key role supporting nitrogenase activity in bacteroids of Sinorhizobium meliloti. Genetic evidence for a similar role in Bradyrhizobium japonicum USDA110 was obtained by constructing a dme mutant. Soybean plants inoculated with a dme mutant did not show delayed nodulation, but formed small root nodules and exhibited significant nitrogen-deficiency symptoms. Nodule numbers and the acetylene reducting activity per nodule as a dry weight value 14 and 28 days after inoculation with the dme mutant were comparable to those of plants inoculated with wild-type B. japonicum. However, shoot dry weight and acetylene reducting activity per nodule decreased to ca. 30% of the values in plants with wild-type B. japonicum. The sucrose and organic acid (malate, succinate, acetate, α-ketoglutarate and lactate) contents of the nodules were investigated. Amounts of sucrose, malate and a-ketoglutarate increased on inoculation with the dme mutant, suggesting that the decreased DME and nitrogenase activities in the bacteroids resulted in a reduction in the consumption of these respiratory metabolites by the nodules. The data suggest that the DME activity of B. japonicum bacteroids plays a role in nodule metabolism and supports nitrogen fixation.
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Affiliation(s)
- Tan Van Dao
- Centre for Ressources and Environmental Studies, Vietnam National University
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13
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Zhang Y, Aono T, Poole P, Finan TM. NAD(P)+-malic enzyme mutants of Sinorhizobium sp. strain NGR234, but not Azorhizobium caulinodans ORS571, maintain symbiotic N2 fixation capabilities. Appl Environ Microbiol 2012; 78:2803-12. [PMID: 22307295 PMCID: PMC3318798 DOI: 10.1128/aem.06412-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 01/23/2012] [Indexed: 11/20/2022] Open
Abstract
C(4)-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (TCA) cycle in N(2)-fixing bacteria (bacteroids) within legume nodules. In Sinorhizobium meliloti bacteroids from alfalfa, NAD(+)-malic enzyme (DME) is required for N(2) fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. In contrast, in the pea symbiont Rhizobium leguminosarum, pyruvate synthesis occurs via either DME or a pathway catalyzed by phosphoenolpyruvate carboxykinase (PCK) and pyruvate kinase (PYK). Here we report that dme mutants of the broad-host-range Sinorhizobium sp. strain NGR234 formed nodules whose level of N(2) fixation varied from 27 to 83% (plant dry weight) of the wild-type level, depending on the host plant inoculated. NGR234 bacteroids had significant PCK activity, and while single pckA and single dme mutants fixed N(2) at reduced rates, a pckA dme double mutant had no N(2)-fixing activity (Fix(-)). Thus, NGR234 bacteroids appear to synthesize pyruvate from TCA cycle intermediates via DME or PCK pathways. These NGR234 data, together with other reports, suggested that the completely Fix(-) phenotype of S. meliloti dme mutants may be specific to the alfalfa-S. meliloti symbiosis. We therefore examined the ME-like genes azc3656 and azc0119 from Azorhizobium caulinodans, as azc3656 mutants were previously shown to form Fix(-) nodules on the tropical legume Sesbania rostrata. We found that purified AZC3656 protein is an NAD(P)(+)-malic enzyme whose activity is inhibited by acetyl-coenzyme A (acetyl-CoA) and stimulated by succinate and fumarate. Thus, whereas DME is required for symbiotic N(2) fixation in A. caulinodans and S. meliloti, in other rhizobia this activity can be bypassed via another pathway(s).
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Affiliation(s)
- Ye Zhang
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Toshihiro Aono
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Phillip Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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14
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Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli. J Microbiol 2011; 49:797-802. [PMID: 22068497 DOI: 10.1007/s12275-011-0487-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 04/25/2011] [Indexed: 10/15/2022]
Abstract
Malic enzymes catalyze the reversible oxidative decarboxylation of L-malate using NAD(P)(+) as a cofactor. NADP-dependent malic enzyme (MaeB) from Escherichia coli MG1655 was expressed and purified as a fusion protein. The molecular weight of MaeB was about 83 kDa, as determined by SDS-PAGE. The recombinant MaeB showed a maximum activity at pH 7.8 and 46°C. MaeB activity was dependent on the presence of Mn(2+) but was strongly inhibited by Zn(2+). In order to understand the physiological roles, recombinant E. coli strains (icd (NADP)/ΔmaeB and icd (NAD)/ΔmaeB) containing NADP-dependent isocitrate dehydrogenase (IDH), or engineered NAD-dependent IDH with the deletion of the maeB gene, were constructed using homologous recombination. During growth on acetate, icd (NAD)/ΔmaeB grew poorly, having a growth rate only 60% that of the wild-type strain (icd (NADP)). Furthermore, icd (NADP)/ΔmaeB exhibited a 2-fold greater adaptability to acetate than icd (NAD)/ΔmaeB, which may be explained by more NADPH production for biosynthesis in icd (NADP)/ΔmaeB due to its NADP-dependent IDH. These results indicated that MaeB was important for NADPH production for bacterial growth on acetate. We also observed that MaeB activity was significantly enhanced (7.83-fold) in icd (NAD), which was about 3-fold higher than that in icd (NADP), when switching from glucose to acetate. The marked increase of MaeB activity was probably induced by the shortage of NADPH in icd (NAD). Evidently, MaeB contributed to the NADPH generation needed for bacterial growth on two carbon compounds.
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15
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Espariz M, Repizo G, Blancato V, Mortera P, Alarcón S, Magni C. Identification of malic and soluble oxaloacetate decarboxylase enzymes in Enterococcus faecalis. FEBS J 2011; 278:2140-51. [PMID: 21518252 DOI: 10.1111/j.1742-4658.2011.08131.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two paralogous genes, maeE and citM, that encode putative malic enzyme family members were identified in the Enterococcus faecalis genome. MaeE (41 kDa) and CitM (42 kDa) share a high degree of homology between them (47% identities and 68% conservative substitutions). However, the genetic context of each gene suggested that maeE is associated with malate utilization whereas citM is linked to the citrate fermentation pathway. In the present work, we focus on the biochemical characterization and physiological contribution of these enzymes in E. faecalis. With this aim, the recombinant versions of the two proteins were expressed in Escherichia coli, affinity purified and finally their kinetic parameters were determined. This approach allowed us to establish that MaeE is a malate oxidative decarboxylating enzyme and CitM is a soluble oxaloacetate decarboxylase. Moreover, our genetic studies in E. faecalis showed that the citrate fermentation phenotype is not affected by citM deletion. On the other hand, maeE gene disruption resulted in a malate fermentation deficient strain indicating that MaeE is responsible for malate metabolism in E. faecalis. Lastly, it was demonstrated that malate fermentation in E. faecalis is associated with cytoplasmic and extracellular alkalinization which clearly contributes to pH homeostasis in neutral or mild acidic conditions.
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Affiliation(s)
- Martín Espariz
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
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16
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Anaplerotic role for cytosolic malic enzyme in engineered Saccharomyces cerevisiae strains. Appl Environ Microbiol 2010; 77:732-8. [PMID: 21131518 DOI: 10.1128/aem.02132-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malic enzyme catalyzes the reversible oxidative decarboxylation of malate to pyruvate and CO(2). The Saccharomyces cerevisiae MAE1 gene encodes a mitochondrial malic enzyme whose proposed physiological roles are related to the oxidative, malate-decarboxylating reaction. Hitherto, the inability of pyruvate carboxylase-negative (Pyc(-)) S. cerevisiae strains to grow on glucose suggested that Mae1p cannot act as a pyruvate-carboxylating, anaplerotic enzyme. In this study, relocation of malic enzyme to the cytosol and creation of thermodynamically favorable conditions for pyruvate carboxylation by metabolic engineering, process design, and adaptive evolution, enabled malic enzyme to act as the sole anaplerotic enzyme in S. cerevisiae. The Escherichia coli NADH-dependent sfcA malic enzyme was expressed in a Pyc(-) S. cerevisiae background. When PDC2, a transcriptional regulator of pyruvate decarboxylase genes, was deleted to increase intracellular pyruvate levels and cells were grown under a CO(2) atmosphere to favor carboxylation, adaptive evolution yielded a strain that grew on glucose (specific growth rate, 0.06 ± 0.01 h(-1)). Growth of the evolved strain was enabled by a single point mutation (Asp336Gly) that switched the cofactor preference of E. coli malic enzyme from NADH to NADPH. Consistently, cytosolic relocalization of the native Mae1p, which can use both NADH and NADPH, in a pyc1,2Δ pdc2Δ strain grown under a CO(2) atmosphere, also enabled slow-growth on glucose. Although growth rates of these strains are still low, the higher ATP efficiency of carboxylation via malic enzyme, compared to the pyruvate carboxylase pathway, may contribute to metabolic engineering of S. cerevisiae for anaerobic, high-yield C(4)-dicarboxylic acid production.
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17
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Bologna FP, Andreo CS, Drincovich MF. Escherichia coli malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure. J Bacteriol 2007; 189:5937-46. [PMID: 17557829 PMCID: PMC1952036 DOI: 10.1128/jb.00428-07] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malic enzymes (MEs) catalyze the oxidative decarboxylation of malate in the presence of a divalent metal ion. In eukaryotes, well-conserved cytoplasmic, mitochondrial, and plastidic MEs have been characterized. On the other hand, distinct groups can be detected among prokaryotic MEs, which are more diverse in structure and less well characterized than their eukaryotic counterparts. In Escherichia coli, two genes with a high degree of homology to ME can be detected: sfcA and maeB. MaeB possesses a multimodular structure: the N-terminal extension shows homology to ME, while the C-terminal extension shows homology to phosphotransacetylases (PTAs). In the present work, a detailed characterization of the products of E. coli sfcA and maeB was performed. The results indicate that the two MEs exhibit relevant kinetic, regulatory, and structural differences. SfcA is a NAD(P) ME, while MaeB is a NADP-specific ME highly regulated by key metabolites. Characterization of truncated versions of MaeB indicated that the PTA domain is not essential for the ME reaction. Nevertheless, truncated MaeB without the PTA domain loses most of its metabolic ME modulation and its native oligomeric state. Thus, the association of the two structural domains in MaeB seems to facilitate metabolic control of the enzyme. Although the PTA domain in MaeB is highly similar to the domains of proteins with PTA activity, MaeB and its PTA domain do not exhibit PTA activity. Determination of the distinct properties of recombinant products of sfcA and maeB performed in the present work will help to clarify the roles of MEs in prokaryotic metabolism.
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Affiliation(s)
- Federico P Bologna
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI)-Facultad Cs Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Argentina
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18
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Mitsch MJ, Cowie A, Finan TM. Malic enzyme cofactor and domain requirements for symbiotic N2 fixation by Sinorhizobium meliloti. J Bacteriol 2006; 189:160-8. [PMID: 17071765 PMCID: PMC1797227 DOI: 10.1128/jb.01425-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The NAD(+)-dependent malic enzyme (DME) and the NADP(+)-dependent malic enzyme (TME) of Sinorhizobium meliloti are representatives of a distinct class of malic enzymes that contain a 440-amino-acid N-terminal region homologous to other malic enzymes and a 330-amino-acid C-terminal region with similarity to phosphotransacetylase enzymes (PTA). We have shown previously that dme mutants of S. meliloti fail to fix N(2) (Fix(-)) in alfalfa root nodules, whereas tme mutants are unimpaired in their N(2)-fixing ability (Fix(+)). Here we report that the amount of DME protein in bacteroids is 10 times greater than that of TME. We therefore investigated whether increased TME activity in nodules would allow TME to function in place of DME. The tme gene was placed under the control of the dme promoter, and despite elevated levels of TME within bacteroids, no symbiotic nitrogen fixation occurred in dme mutant strains. Conversely, expression of dme from the tme promoter resulted in a large reduction in DME activity and symbiotic N(2) fixation. Hence, TME cannot replace the symbiotic requirement for DME. In further experiments we investigated the DME PTA-like domain and showed that it is not required for N(2) fixation. Thus, expression of a DME C-terminal deletion derivative or the Escherichia coli NAD(+)-dependent malic enzyme (sfcA), both of which lack the PTA-like region, restored wild-type N(2) fixation to a dme mutant. Our results have defined the symbiotic requirements for malic enzyme and raise the possibility that a constant high ratio of NADPH + H(+) to NADP in nitrogen-fixing bacteroids prevents TME from functioning in N(2)-fixing bacteroids.
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Affiliation(s)
- Michael J Mitsch
- Center for Environmental Genomics, Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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19
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Gao JL, Weissenmayer B, Taylor AM, Thomas-Oates J, López-Lara IM, Geiger O. Identification of a gene required for the formation of lyso-ornithine lipid, an intermediate in the biosynthesis of ornithine-containing lipids. Mol Microbiol 2004; 53:1757-70. [PMID: 15341653 DOI: 10.1111/j.1365-2958.2004.04240.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Under phosphate-limiting conditions, some bacteria replace their membrane phospholipids by lipids not containing any phosphorus. One of these phosphorus-free lipids is an ornithine-containing lipid (OL) that is widespread among eubacteria. In earlier work, we had identified a gene (olsA) required for OL biosynthesis that probably encodes an O-acyltransferase using acyl-acyl carrier protein (acyl-AcpP) as an acyl donor and that converts lyso-ornithine lipid into OL. We now report on a second gene (olsB) required for OL biosynthesis that is needed for the incorporation of radiolabelled ornithine into OL. Overexpression of OlsB in an olsA-deficient mutant of Sinorhizobium (Rhizobium) meliloti leads to the transient accumulation of lyso-ornithine lipid, the biosynthetic intermediate of OL biosynthesis. Overexpression of OlsB in Escherichia coli is sufficient to cause the in vivo formation of lyso-ornithine lipid in this organism and is the cause for a 3-hydroxyacyl-AcpP-dependent acyltransferase activity forming lyso-ornithine lipid from ornithine. These results demonstrate that OlsB is required for the first step of OL biosynthesis, in which ornithine is N-acylated with a 3-hydroxy-fatty acyl residue in order to obtain lyso-ornithine lipid. OL formation in a wild-type S. meliloti is increased upon growth under phosphate-limiting conditions. Expression of OlsB from a broad host range vector leads to the constitutive formation of relatively high amounts of OL (12-14% of total membrane lipids) independently of whether strains are grown in the presence of low or high concentrations of phosphate, suggesting that in S. meliloti the formation of OlsB is usually limiting for the amount of OL formed in this organism. Open reading frames homologous to OlsA and OlsB were identified in many eubacteria and although in S. meliloti the olsB and olsA gene are 14 kb apart, in numerous other bacteria they form an operon.
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Affiliation(s)
- Jun-Lian Gao
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, Mexico
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20
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Sauer U, Eikmanns BJ. The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 2004; 29:765-94. [PMID: 16102602 DOI: 10.1016/j.femsre.2004.11.002] [Citation(s) in RCA: 358] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Revised: 10/27/2004] [Accepted: 11/01/2004] [Indexed: 11/16/2022] Open
Abstract
In many organisms, metabolite interconversion at the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node involves a structurally entangled set of reactions that interconnects the major pathways of carbon metabolism and thus, is responsible for the distribution of the carbon flux among catabolism, anabolism and energy supply of the cell. While sugar catabolism proceeds mainly via oxidative or non-oxidative decarboxylation of pyruvate to acetyl-CoA, anaplerosis and the initial steps of gluconeogenesis are accomplished by C3- (PEP- and/or pyruvate-) carboxylation and C4- (oxaloacetate- and/or malate-) decarboxylation, respectively. In contrast to the relatively uniform central metabolic pathways in bacteria, the set of enzymes at the PEP-pyruvate-oxaloacetate node represents a surprising diversity of reactions. Variable combinations are used in different bacteria and the question of the significance of all these reactions for growth and for biotechnological fermentation processes arises. This review summarizes what is known about the enzymes and the metabolic fluxes at the PEP-pyruvate-oxaloacetate node in bacteria, with a particular focus on the C3-carboxylation and C4-decarboxylation reactions in Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum. We discuss the activities of the enzymes, their regulation and their specific contribution to growth under a given condition or to biotechnological metabolite production. The present knowledge unequivocally reveals the PEP-pyruvate-oxaloacetate nodes of bacteria to be a fascinating target of metabolic engineering in order to achieve optimized metabolite production.
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Affiliation(s)
- Uwe Sauer
- Institute of Biotechnology, ETH Zürich, Switzerland
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21
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Shearer HL, Turpin DH, Dennis DT. Characterization of NADP-dependent malic enzyme from developing castor oil seed endosperm. Arch Biochem Biophys 2004; 429:134-44. [PMID: 15313216 DOI: 10.1016/j.abb.2004.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Revised: 07/01/2004] [Indexed: 10/26/2022]
Abstract
Metabolic pathways sequestered within the leucoplast of developing oilseeds ensure a balanced supply of substrates and cofactors for fatty acid biosynthesis. NADP-dependent malic enzyme (NADP-ME) may be important in supplying both carbon and NADPH for fatty acid biosynthesis in the developing endosperm of the oilseed Ricinus communis. NADP-ME was purified 5160-fold to a specific activity of 18.2 U/mg protein. NADP-ME is a homotetramer with a native mass of 254 kDa and a subunit size of approximately 63 kDa. Effectors of castor NADP-ME are typical of the NADP-malic enzymes, with the exception of acetyl-CoA and its derivatives, which were found to act as activators. This is consistent with a regulatory role for these molecules during fatty acid biosynthesis in vivo. NADP-ME was found to have maximal activity at stage 7 of endosperm development, coincident with maximal lipid accumulation.
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Affiliation(s)
- Heather L Shearer
- Department of Biology, Queen's University, Kingston, Ont., Canada K7L 3N6.
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22
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Claudel-Renard C, Chevalet C, Faraut T, Kahn D. Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res 2004; 31:6633-9. [PMID: 14602924 PMCID: PMC275543 DOI: 10.1093/nar/gkg847] [Citation(s) in RCA: 281] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes.
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Affiliation(s)
- Clotilde Claudel-Renard
- Laboratoire de Génétique Cellulaire, INRA, INRA/CNRS, BP27, 31326 Castanet-Tolosan Cedex, France
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23
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Hagedorn PH, Flyvbjerg H, Møller IM. Modelling NADH turnover in plant mitochondria. PHYSIOLOGIA PLANTARUM 2004; 120:370-385. [PMID: 15032834 DOI: 10.1111/j.0031-9317.2003.00252.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
NADH is central to the functioning of mitochondrial respiration. It is produced by enzymes in, or associated with, the tricarboxylic acid cycle in the matrix, and it is oxidized by two respiratory chain enzymes in the inner membrane, the rotenone-sensitive complex I and the rotenone-insensitive internal NADH dehydrogenase (ND(in)). A simplified kinetic model for NADH turnover in the matrix of plant mitochondria is presented. Only the two main NADH-producing enzymes, NAD-malate dehydrogenase [EC 1.1.1.37] (MDH) and NAD-malic enzyme [EC 1.1.1.39] (ME), are considered. This model reproduces the complex behaviour of malate oxidation by isolated mitochondria in response to additions of ADP (state 3/state 4), NAD(+) and/or rotenone, as well as to changes in pH. It is found that MDH always operates at or close to equilibrium. Changes in the activity of complex I, ND(in), or ME are predicted to cause clear changes in the pattern of malate oxidation. In general, the model predicts high sensitivity to changes in the ME activity. In contrast, MDH activity can be reduced 100-fold without detectable changes in malate oxidation. It is demonstrated that it is not the high activity, but the equilibrium properties of MDH that are important for the redox-buffering function of MDH in the mitochondrial matrix. Binding of NAD(+) and NADH in the matrix reduces the concentrations of free NAD(+) and NADH, depending on the concentration of binding sites and the binding strength. On the basis of the modelling results it is estimated that a significant proportion of the mitochondrial NAD is bound.
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Affiliation(s)
- Peter H. Hagedorn
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark
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24
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Doan T, Servant P, Tojo S, Yamaguchi H, Lerondel G, Yoshida KI, Fujita Y, Aymerich S. The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2331-2343. [PMID: 12949160 DOI: 10.1099/mic.0.26256-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A transcriptome comparison of a wild-type Bacillus subtilis strain growing under glycolytic or gluconeogenic conditions was performed. In particular, it revealed that the ywkA gene, one of the four paralogues putatively encoding a malic enzyme, was more transcribed during gluconeogenesis. Using a lacZ reporter fusion to the ywkA promoter, it was shown that ywkA was specifically induced by external malate and not subject to glucose catabolite repression. Northern analysis confirmed this expression pattern and demonstrated that ywkA is cotranscribed with the downstream ywkB gene. The ywkA gene product was purified and biochemical studies demonstrated its malic enzyme activity, which was 10-fold higher with NAD than with NADP (kcat/Km 102 and 10 s(-1) mM(-1), respectively). However, physiological tests with single and multiple mutant strains affected in ywkA and/or in ywkA paralogues showed that ywkA does not contribute to efficient utilization of malate for growth. Transposon mutagenesis allowed the identification of the uncharacterized YufL/YufM two-component system as being responsible for the control of ywkA expression. Genetic analysis and in vitro studies with purified YufM protein showed that YufM binds just upstream of ywkA promoter and activates ywkA transcription in response to the presence of malate in the extracellular medium, transmitted by YufL. ywkA and yufL/yufM could thus be renamed maeA for malic enzyme and malK/malR for malate kinase sensor/malate response regulator, respectively.
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Affiliation(s)
- Thierry Doan
- Génétique Moléculaire et Cellulaire, INRA (UMR216) CNRS (URA1925) and INAP-G, F-78850 Thiverval-Grignon, France
| | - Pascale Servant
- Génétique Moléculaire et Cellulaire, INRA (UMR216) CNRS (URA1925) and INAP-G, F-78850 Thiverval-Grignon, France
| | - Shigeo Tojo
- Department of Biotechnology, Fukuyama University, 985 Sanzo, Higashimura, Fukuyama, Japan
| | - Hirotake Yamaguchi
- Department of Biotechnology, Fukuyama University, 985 Sanzo, Higashimura, Fukuyama, Japan
| | - Guillaume Lerondel
- Génétique Moléculaire et Cellulaire, INRA (UMR216) CNRS (URA1925) and INAP-G, F-78850 Thiverval-Grignon, France
| | - Ken-Ichi Yoshida
- Department of Biotechnology, Fukuyama University, 985 Sanzo, Higashimura, Fukuyama, Japan
| | - Yasutaro Fujita
- Department of Biotechnology, Fukuyama University, 985 Sanzo, Higashimura, Fukuyama, Japan
| | - Stéphane Aymerich
- Génétique Moléculaire et Cellulaire, INRA (UMR216) CNRS (URA1925) and INAP-G, F-78850 Thiverval-Grignon, France
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25
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Volschenk H, van Vuuren HJJ, Viljoen-Bloom M. Malo-ethanolic fermentation in Saccharomyces and Schizosaccharomyces. Curr Genet 2003; 43:379-91. [PMID: 12802505 DOI: 10.1007/s00294-003-0411-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Revised: 05/12/2003] [Accepted: 05/13/2003] [Indexed: 11/28/2022]
Abstract
Yeast species are divided into the K(+) or K(-) groups, based on their ability or inability to metabolise tricarboxylic acid (TCA) cycle intermediates as sole carbon or energy source. The K(-) group of yeasts includes strains of Saccharomyces, Schizosaccharomyces pombe and Zygosaccharomyces bailii, which is capable of utilising TCA cycle intermediates only in the presence of glucose or other assimilable carbon sources. Although grouped together, these yeasts have significant differences in their abilities to degrade malic acid. Typically, strains of Saccharomyces are regarded as inefficient metabolisers of extracellular malic acid, whereas strains of Sch. pombe and Z. bailii can effectively degrade high concentrations of malic acid. The ability of a yeast strain to degrade extracellular malic acid is dependent on both the efficient transport of the dicarboxylic acid and the efficacy of the intracellular malic enzyme. The malic enzyme converts malic acid into pyruvic acid, which is further metabolised to ethanol and carbon dioxide under fermentative conditions via the so-called malo-ethanolic (ME) pathway. This review focuses on the enzymes involved in the ME pathway in Sch. pombe and Saccharomyces species, with specific emphasis on the malate transporter and the intracellular malic enzyme.
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Affiliation(s)
- H Volschenk
- Department of Microbiology, Stellenbosch University, Private Bag X1, 7602 Matieland, South Africa
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26
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Kretzschmar U, Rückert A, Jeoung JH, Görisch H. Malate:quinone oxidoreductase is essential for growth on ethanol or acetate in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3839-3847. [PMID: 12480887 DOI: 10.1099/00221287-148-12-3839] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa ATCC 17933 growing aerobically on ethanol uses a pyrroloquinoline quinone-dependent ethanol oxidation system. A mutant with an interrupted putative mqo gene, in which malate:quinone oxidoreductase (MQO), an enzyme involved in the citric acid cycle/glyoxylate cycle, was defective, showed a severe growth defect on ethanol and was unable to grow on acetate. Glucose, lactate, succinate or malate supported growth of the mutant. However, an NAD-dependent malate dehydrogenase activity could not be detected. Complementation of the mutant by the wild-type allele of the mqo gene restored wild-type behaviour. The wild-type expressed the dye-dependent MQO and NAD(P)-dependent malic enzymes (MEs). Pyruvate carboxylase (PC) was found upon growth of the wild-type and the mutant on all substrates studied. PC activity in the wild-type was induced on glucose and lactate and was always higher on all substrates in the mqo mutant. In P. aeruginosa ATCC 17933, an active MQO is required for growth on ethanol or acetate, while with glucose, lactate, succinate or malate an apparent bypass route operates, with MEs using malate for generating pyruvate, which is carboxylated to oxaloacetate by PC. To the authors' knowledge, this is the first time that a specific mutant MQO phenotype has been observed, caused by the inactivation of a gene encoding MQO activity. mqo of P. aeruginosa ATCC 17933 corresponds to mqoB (PA4640) of the P. aeruginosa PAO1 genome project.
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Affiliation(s)
- Utta Kretzschmar
- Fachgebiet Technische Biochemie, Institut für Biotechnologie der Technischen Universität Berlin, Seestraße 13, D-13353 Berlin, Germany1
| | - Andreas Rückert
- Fachgebiet Technische Biochemie, Institut für Biotechnologie der Technischen Universität Berlin, Seestraße 13, D-13353 Berlin, Germany1
| | - Jae-Hun Jeoung
- Fachgebiet Technische Biochemie, Institut für Biotechnologie der Technischen Universität Berlin, Seestraße 13, D-13353 Berlin, Germany1
| | - Helmut Görisch
- Fachgebiet Technische Biochemie, Institut für Biotechnologie der Technischen Universität Berlin, Seestraße 13, D-13353 Berlin, Germany1
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27
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Coleman DE, Rao GSJ, Goldsmith EJ, Cook PF, Harris BG. Crystal structure of the malic enzyme from Ascaris suum complexed with nicotinamide adenine dinucleotide at 2.3 A resolution. Biochemistry 2002; 41:6928-38. [PMID: 12033925 DOI: 10.1021/bi0255120] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of the Ascaris suum mitochondrial NAD-malic enzyme in binary complex with NAD has been solved to a resolution of 2.3 A by X-ray crystallography. The structure resembles that of the human mitochondrial enzyme determined in complex with NAD [Xu, Y., Bhargava, G., Wu, H., Loeber, G., and Tong, L. (1999) Structure 7, 877-889]. The enzyme is a tetramer comprised of subunits possessing four domains organized in an "open" structure typical of the NAD-bound form. The subunit organization, as in the human enzyme, is a dimer of dimers. The Ascaris enzyme contains 30 additional residues at its amino terminus relative to the human enzyme. These residues significantly increase the interactions that promote tetramer formation and give rise to different subunit-subunit interactions. Unlike the mammalian enzyme, the Ascaris malic enzyme is not regulated by ATP, and no ATP binding site is observed in this structure. Although the active sites of the two enzymes are similar, residues interacting with NAD differ between the two. The structure is discussed in terms of the mechanism and particularly with respect to previously obtained kinetic and site-directed mutagenesis experiments.
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Affiliation(s)
- David E Coleman
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
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