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Pentjuss A, Stalidzans E, Liepins J, Kokina A, Martynova J, Zikmanis P, Mozga I, Scherbaka R, Hartman H, Poolman MG, Fell DA, Vigants A. Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. J Ind Microbiol Biotechnol 2017; 44:1177-1190. [PMID: 28444480 DOI: 10.1007/s10295-017-1946-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/16/2017] [Indexed: 12/11/2022]
Abstract
The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism's potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.
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Affiliation(s)
- A Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - E Stalidzans
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia.
| | - J Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - A Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - J Martynova
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - P Zikmanis
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - I Mozga
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - R Scherbaka
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
| | - H Hartman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - M G Poolman
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - D A Fell
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington, OX, OX3 0BP, UK
| | - A Vigants
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas str. 1, Riga, 1004, Latvia
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Khouja H, Daghino S, Abbà S, Boutaraa F, Chalot M, Blaudez D, Martino E, Perotto S. OmGOGAT-disruption in the ericoid mycorrhizal fungus Oidiodendron maius induces reorganization of the N pathway and reduces tolerance to heavy-metals. Fungal Genet Biol 2014; 71:1-8. [DOI: 10.1016/j.fgb.2014.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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de Barros Pita W, Silva DC, Simões DA, Passoth V, de Morais MA. Physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability. Antonie van Leeuwenhoek 2013; 104:855-68. [DOI: 10.1007/s10482-013-9998-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/07/2013] [Indexed: 12/01/2022]
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Choudhury R, Noor S, Varadarajalu LP, Punekar NS. Delineation of an in vivo inhibitor for Aspergillus glutamate dehydrogenase. Enzyme Microb Technol 2007; 42:151-9. [PMID: 22578865 DOI: 10.1016/j.enzmictec.2007.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/29/2007] [Accepted: 08/30/2007] [Indexed: 11/18/2022]
Abstract
NADP-glutamate dehydrogenase (NADP-GDH) along with glutamine synthetase plays a pivotal role in ammonium assimilation. Specific inhibitors were valuable in defining the importance of glutamine synthetase in nitrogen metabolism. Selective in vivo inhibition of NADP-GDH has so far been an elusive desideratum. Isophthalate, a potent in vitro inhibitor of Aspergillus niger NADP-GDH [Noor S, Punekar NS. Allosteric NADP-glutamate dehydrogenase from aspergilli: purification, characterization and implications for metabolic regulation at the carbon-nitrogen interface. Microbiology 2005;151:1409-19], was evaluated for its efficacy in vivo. Dimethyl ester of isophthalate (DMIP), but not isophthalate, inhibited A. niger growth on agar as well as in liquid culture. This was ascribed to the inability of isophthalate to enter fungal mycelia. Subsequent to DMIP addition however, intracellular isophthalate could be demonstrated. Apart from NAD-GDH, no other enzyme including NAD-glutamate synthase was inhibited by isophthalate. A cross-over at NADP-GDH step of metabolism was observed as a direct consequence of isophthalate (formed in vivo from DMIP) inhibiting this enzyme. Addition of ammonium to DMIP-treated A. niger mycelia resulted in intensive vacuolation, retraction of cytoplasm and autolysis. Taken together, these results implicate glutamate dehydrogenase and NADP-GDH in particular, as a key target of in vivo isophthalate inhibition during ammonium assimilation.
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Affiliation(s)
- Rajarshi Choudhury
- Biotechnology Group, School of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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Choudhury R, Punekar NS. Competitive inhibition of glutamate dehydrogenase reaction. FEBS Lett 2007; 581:2733-6. [PMID: 17531979 DOI: 10.1016/j.febslet.2007.05.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022]
Abstract
Irrespective of their pyridine nucleotide specificity, all glutamate dehydrogenases share a common chemical mechanism that involves an enzyme bound 'iminoglutarate' intermediate. Three compounds, structurally related to this intermediate, were tested for the inhibition of purified NADP-glutamate dehydrogenases from two Aspergilli, as also the bovine liver NAD(P)-glutamate dehydrogenase. 2-Methyleneglutarate, closely resembling iminoglutarate, was a potent competitive inhibitor of the glutamate dehydrogenase reaction. This is the first report of a non-aromatic structure with a better glutamate dehydrogenase inhibitory potency than aryl carboxylic acids such as isophthalate. A suitably located 2-methylene group to mimic the iminium ion could be exploited to design inhibitors of other amino acid dehydrogenases.
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Affiliation(s)
- Rajarshi Choudhury
- Biotechnology Group, SBB, Indian Institute of Technology, Powai, Mumbai, India
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Morel M, Buée M, Chalot M, Brun A. NADP-dependent glutamate dehydrogenase: a dispensable function in ectomycorrhizal fungi. THE NEW PHYTOLOGIST 2006; 169:179-89. [PMID: 16390429 DOI: 10.1111/j.1469-8137.2005.01556.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
There is much controversy on the contribution of NADP-dependent glutamate dehydrogenase (NADP-GDH) in NH4+ assimilation in ectomycorrhizal (ECM) fungi and ectomycorrhizas. Experiments reported here provide information on the dispensability of NADP-GDH in various ectomycorrhizal isolates. Glutamate dehydrogenase and glutamine synthetase (GS) enzyme activities were measured on mycelia grown under various nitrogen (N) conditions. The contribution of GDH in ammonium assimilation was further estimated by following 15N incorporation from (15NH4)2SO4 into glutamate, when GS was inhibited by phosphinothricin. Finally, gene amplification on cDNA and genomic DNA was performed using degenerated primers. Two groups of fungi could be distinguished. The GDH+ fungi include Hebeloma cylindrosporum-like fungi, which possess a functional NADP-GDH. The GDH- fungi include Paxillus involutus-like fungi for which the NADP-GDH activity, as well as the GDHA transcripts, were not detected, whatever the growth condition. All the results are consistent with the dispensability of the NADP-GDH function in ECM fungi, suggesting a minor role in ammonium assimilation in ectomycorrhizal fungi. We hypothesize that the lack of a functional NADP-GDH could be an evolutive adaptation in relation to the ecological niche of ECM fungi, rather than a transitional regulation in response to changes in N contents of the extracellular medium.
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Affiliation(s)
- Mélanie Morel
- IFR 110, UMR INRA/UHP 1136 Interactions Arbres Micro-organismes, Université Henri Poincaré- Nancy I, Faculté des Sciences et Techniques BP239, F-54506 Vandoeuvre-les-Nancy Cedex, France
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Suzuki A, Knaff DB. Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism. PHOTOSYNTHESIS RESEARCH 2005; 83:191-217. [PMID: 16143852 DOI: 10.1007/s11120-004-3478-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 09/20/2004] [Indexed: 05/03/2023]
Abstract
Ammonium ion assimilation constitutes a central metabolic pathway in many organisms, and glutamate synthase, in concert with glutamine synthetase (GS, EC 6.3.1.2), plays the primary role of ammonium ion incorporation into glutamine and glutamate. Glutamate synthase occurs in three forms that can be distinguished based on whether they use NADPH (NADPH-GOGAT, EC 1.4.1.13), NADH (NADH-GOGAT, EC 1.4.1.14) or reduced ferredoxin (Fd-GOGAT, EC 1.4.7.1) as the electron donor for the (two-electron) conversion of L-glutamine plus 2-oxoglutarate to L-glutamate. The distribution of these three forms of glutamate synthase in different tissues is quite specific to the organism in question. Gene structures have been determined for Fd-, NADH- and NADPH-dependent glutamate synthases from different organisms, as shown by searches in nucleic acid sequence data banks. Fd-glutamate synthase contains two electron-carrying prosthetic groups, the redox properties of which are discussed. A description of the ferredoxin binding by Fd-glutamate synthase is also presented. In plants, including nitrogen-fixing legumes, Fd-glutamate synthase and NADH-glutamate synthase supply glutamate during the nitrogen assimilation and translocation. The biological functions of Fd-glutamate synthase and NADH-glutamate synthase, which show a highly tissue-specific distribution pattern, are tightly related to the regulation by the light and metabolite sensing systems. Analysis of mutants and transgenic studies have provided insights into the primary individual functions of Fd-glutamate synthase and NADH-glutamate synthase. These studies also provided evidence that glutamate dehydrogenase (NADH-GDH, EC 1.4.1.2) does not represent a significant alternate route for glutamate formation in plants. Taken together, biochemical analysis and genetic and molecular data imply that Fd-glutamate synthase incorporates photorespiratory and non-photorespiratory ammonium and provides nitrogen for transport to maintain nitrogen status in plants. Fd-glutamate synthase also plays a role that is redundant, in several important aspects, to that played by NADH-glutamate synthase in ammonium assimilation and nitrogen transport.
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Affiliation(s)
- Akira Suzuki
- Unité de Nutrition Azotée des Plantes, Institut National de la Recherche Agronomique, Route de Saint-Cyr, 78026 Versailles cedex, France.
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DeLuna A, Avendano A, Riego L, Gonzalez A. NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles. J Biol Chem 2001; 276:43775-83. [PMID: 11562373 DOI: 10.1074/jbc.m107986200] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, two NADP(+)-dependent glutamate dehydrogenases (NADP-GDHs) encoded by GDH1 and GDH3 catalyze the synthesis of glutamate from ammonium and alpha-ketoglutarate. The GDH2-encoded NAD(+)-dependent glutamate dehydrogenase degrades glutamate producing ammonium and alpha-ketoglutarate. Until very recently, it was considered that only one biosynthetic NADP-GDH was present in S. cerevisiae. This fact hindered understanding the physiological role of each isoenzyme and the mechanisms involved in alpha-ketoglutarate channeling for glutamate biosynthesis. In this study, we purified and characterized the GDH1- and GDH3-encoded NADP-GDHs; they showed different allosteric properties and rates of alpha-ketoglutarate utilization. Analysis of the relative levels of these proteins revealed that the expression of GDH1 and GDH3 is differentially regulated and depends on the nature of the carbon source. Moreover, the physiological study of mutants lacking or overexpressing GDH1 or GDH3 suggested that these genes play nonredundant physiological roles. Our results indicate that the coordinated regulation of GDH1-, GDH3-, and GDH2-encoded enzymes results in glutamate biosynthesis and balanced utilization of alpha-ketoglutarate under fermentative and respiratory conditions. The possible relevance of the duplicated NADP-GDH pathway in the adaptation to facultative metabolism is discussed.
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Affiliation(s)
- A DeLuna
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, México
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Valenzuela L, Aranda C, González A. TOR modulates GCN4-dependent expression of genes turned on by nitrogen limitation. J Bacteriol 2001; 183:2331-4. [PMID: 11244074 PMCID: PMC95141 DOI: 10.1128/jb.183.7.2331-2334.2001] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, the rapamycin-sensitive TOR signaling pathway plays an essential role in up-regulating translation initiation and cell cycle progression in response to nutrient availability. One of the mechanisms by which TOR regulates cell proliferation is by excluding the GLN3 transcriptional activator from the nucleus and, in consequence, preventing its transcriptional activation therein. We examined the possibility that the TOR cascade could also control the transcriptional activity of Gcn4p, which is known to respond to amino acid availability. The results presented in this paper indicate that GCN4 plays a role in the rapamycin-sensitive signaling pathway, regulating the expression of genes involved in the utilization of poor nitrogen sources, a previously unrecognized role for Gcn4p, and that the TOR pathway controls GCN4 activity by regulating the translation of GCN4 mRNA. This constitutes an additional TOR-dependent mechanism which modulates the action of transcriptional activators.
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Affiliation(s)
- L Valenzuela
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
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