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Grzechowiak M, Sliwiak J, Link A, Ruszkowski M. Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies. Int J Biol Macromol 2024; 278:134648. [PMID: 39142482 DOI: 10.1016/j.ijbiomac.2024.134648] [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: 02/28/2024] [Revised: 06/28/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024]
Abstract
Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2). We measured MtGDH2 activity in both the Glu → 2-oxoglutarate (2OG) and 2OG → Glu reaction directions and obtained kinetic parameters for Glu, 2OG, NAD+, and NADH. Inhibition assays revealed that compounds possessing di- or tricarboxylates act as inhibitors of plant GDHs. Interestingly, 2,6-pyridinedicarboxylate (PYR) weakly inhibits MtGDH2 compared to Arabidopsis thaliana homologs. Furthermore, we explored tetrazole derivatives to discover 3-(1H-tetrazol-5-yl)benzoic acid (TBA) as an MtGDH2 inhibitor. The kinetic experiments are supported by six crystal structures, solved as: (i) unliganded enzyme, (ii) trapping the reaction intermediate 2-amino-2-hydroxyglutarate and NAD+, and also complexed with NAD+ and inhibitors such as (iii) citrate, (iv) PYR, (v) isophthalate, and (vi) TBA. The complex with TBA revealed a new mode of action that, in contrast to other inhibitors, prevents domain closure. This discovery points to TBA as a starting point for the development of novel GDH inhibitors to study the functions of GDH in plants and potentially boost biomass production.
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Affiliation(s)
- Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Joanna Sliwiak
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
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2
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Grewal SK, Gill RK. Insights into carbon and nitrogen metabolism and antioxidant potential during vegetative phase in quinoa (Chenopodium quinoa Willd.). PROTOPLASMA 2022; 259:1301-1319. [PMID: 35064825 DOI: 10.1007/s00709-022-01736-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The present investigation was carried out to understand the impact of carbon and nitrogen metabolism in quinoa genotypes IC411824, IC411825, EC507747 and EC507742 during pre-anthesis stage. It was observed that activities of acid invertase, sucrose synthase (cleavage) and sucrose phosphate synthase (SPS) increased up to 75 days after sowing (DAS) and this might be responsible for providing reducing sugars for the development of vegetative parts. Enhanced activities of nitrate reductase, glutamate synthase, glutamine synthetase during vegetative growth of leaves and stem at 90 DAS assist the fixation of ammonia on glutamate molecule to synthesize amino acids at early stages. However, the glutamate dehydrogenase and nitrite reductase play a central role in the re-assimilation of amides from the amino group of asparaginase. As a result, these photosynthetic products will be responsible for providing both the energy and the C-skeletons for ammonium assimilation during amino acid biosynthesis. Leaves and stem of IC411824 and IC411825 had higher total phenol and total flavonoid content. DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity was found to be higher in leaves of IC411825 and in stem of IC411824 and IC411825 indicating their capability to act as natural antioxidants.
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Affiliation(s)
- Satvir Kaur Grewal
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
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3
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Ozone reduces the fruit decay of postharvest winter jujube by altering the microbial community structure on fruit surface. Microbiol Res 2022; 262:127110. [DOI: 10.1016/j.micres.2022.127110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/19/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
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Godsora BKJ, Prakash P, Punekar NS, Bhaumik P. Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites. Proteins 2021; 90:810-823. [PMID: 34748226 DOI: 10.1002/prot.26276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Glutamate dehydrogenase (GDH) is a salient metabolic enzyme which catalyzes the NAD+ - or NADP+ -dependent reversible conversion of α-ketoglutarate (AKG) to l-glutamate; and thereby connects the carbon and nitrogen metabolism cycles in all living organisms. The function of GDH is extensively regulated by both metabolites (citrate, succinate, etc.) and non-metabolites (ATP, NADH, etc.) but sufficient molecular evidences are lacking to rationalize the inhibitory effects by the metabolites. We have expressed and purified NADP+ -dependent Aspergillus terreus GDH (AtGDH) in recombinant form. Succinate, malonate, maleate, fumarate, and tartrate independently inhibit the activity of AtGDH to different extents. The crystal structures of AtGDH complexed with the dicarboxylic acid metabolites and the coenzyme NADPH have been determined. Although AtGDH structures are not complexed with substrate; surprisingly, they acquire super closed conformation like previously reported for substrate and coenzyme bound catalytically competent Aspergillus niger GDH (AnGDH). These dicarboxylic acid metabolites partially occupy the same binding pocket as substrate; but interact with varying polar interactions and the coenzyme NADPH binds to the Domain-II of AtGDH. The low inhibition potential of tartrate as compared to other dicarboxylic acid metabolites is due to its weaker interactions of carboxylate groups with AtGDH. Our results suggest that the length of carbon skeleton and positioning of the carboxylate groups of inhibitors between two conserved lysine residues at the GDH active site might be the determinants of their inhibitory potency. Molecular details on the dicarboxylic acid metabolites bound AtGDH active site architecture presented here would be applicable to GDHs in general.
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Affiliation(s)
| | - Prem Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Narayan S Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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5
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Zhao Y, Gao J, Su S, Shan X, Li S, Liu H, Yuan Y, Li H. Regulation of the activity of maize glutamate dehydrogenase by ammonium and potassium. Biosci Biotechnol Biochem 2021; 85:262-271. [PMID: 33604622 DOI: 10.1093/bbb/zbaa020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/18/2020] [Indexed: 11/14/2022]
Abstract
Glutamate dehydrogenase (GDH) is an important enzyme in ammonium metabolism, the activity of which is regulated by multiple factors. In this study, we investigate the effects of ammonium and potassium on the activity of maize GDH. Our results show that both ammonium and potassium play multiple roles in regulating the activity of maize GDH, with the specific roles depending on the concentration of potassium. Together with the structural information of GDH, we propose models for the substrate inhibition of ammonium, and the elimination of substrate inhibition by potassium. These models are supported by the analysis of statistic thermodynamics. We also analyze the binding sites of ammonium and potassium on maize GDH, and the conformational changes of maize GDH. The findings provide insight into the regulation of maize GDH activity by ammonium and potassium and reveal the importance of the dose and ratio of nitrogen and potassium in crop cultivation.
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Affiliation(s)
- Yanjie Zhao
- College of Plant Science, Jilin University, Changchun, China
| | - Jie Gao
- College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, China
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Pathan EK, Kulkarni AM, Prasanna NVL, Ramana CV, Deshpande MV. NADP-dependent glutamate dehydrogenases in a dimorphic zygomycete Benjaminiella poitrasii: Purification, characterization and their evaluation as an antifungal drug target. Biochim Biophys Acta Gen Subj 2020; 1864:129696. [PMID: 32768460 DOI: 10.1016/j.bbagen.2020.129696] [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] [Received: 05/18/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND It has been reported that the genes coding for NADP-dependent glutamate dehydrogenases (NADP-GDHs) showed a cause-effect relationship with Yeast-Hypha (YH) reversible transition in a zygomycete Benjaminiella poitrasii. As YH transition is significant in human pathogenic fungi for their survival and proliferation in the host, the NADP-GDHs can be explored as antifungal drug targets. METHODS The yeast-form specific BpNADPGDH I and hyphal-form specific BpNADPGDH II of B. poitrasii were purified by heterologous expression in E. coli BL-21 cells and characterized. The structural analogs of L-glutamate, dimethyl esters of isophthalic acid (DMIP) and its derivatives were designed, synthesized and screened for inhibition of NADP-GDH activity as well as YH transition in B. poitrasii, and also in human pathogenic Candida albicans strains. RESULTS The BpNADPGDH I and BpNADPGDH II were found to be homo-hexameric proteins with native molecular mass of 282 kDa and 298 kDa, respectively and subunit molecular weights of 47 kDa and 49 kDa, respectively. Besides the distinct kinetic properties, BpNADPGDH I and BpNADPGDH II were found to be regulated by cAMP-dependent- and Calmodulin (CaM) dependent- protein kinases, respectively. The DMIP compounds showed a more pronounced effect on H-form specific BpNADPGDH II and inhibited YH transition as well as growth in B. poitrasii and C. albicans strains. CONCLUSION The present study will be useful to design and develop antifungal drugs against dimorphic human pathogens using glutamate dehydrogenase as a target. SIGNIFICANCE Glutamate dehydrogenases can be explored as a target against human pathogenic fungi.
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Affiliation(s)
- Ejaj K Pathan
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Anand M Kulkarni
- Division of organic chemistry, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Chepuri V Ramana
- Division of organic chemistry, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Mukund V Deshpande
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M. Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. FRONTIERS IN PLANT SCIENCE 2020; 11:754. [PMID: 32655590 PMCID: PMC7326016 DOI: 10.3389/fpls.2020.00754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/12/2020] [Indexed: 05/24/2023]
Abstract
Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)+-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD+-specific, NAD+/NADP+ dual-specific, and NADP+-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD+-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD+ at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD+, it forms D 3-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD+ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD+ hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.
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Affiliation(s)
- Marta Grzechowiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Du CQ, Lin JZ, Dong LA, Liu C, Tang DY, Yan L, Chen MD, Liu S, Liu XM. Overexpression of an NADP(H)-dependent glutamate dehydrogenase gene, TrGDH, from Trichurus improves nitrogen assimilation, growth status and grain weight per plant in rice. BREEDING SCIENCE 2019; 69:429-438. [PMID: 31598075 PMCID: PMC6776155 DOI: 10.1270/jsbbs.19014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/16/2019] [Indexed: 05/03/2023]
Abstract
As glutamate dehydrogenases (GDHs) of microorganisms usually have higher affinity for NH4 + than do those of higher plants, it is expected that ectopic expression of these GDHs can improve nitrogen assimilation in higher plants. Here, a novel NADP(H)-GDH gene (TrGDH) was isolated from the fungus Trichurus and introduced into rice (Oryza sativa L.). Investigation of kinetic properties in vitro showed that, compared with the rice GDH (OsGDH4), TrGDH exhibited higher affinity for NH4 + (K m = 1.48 ± 0.11 mM). Measurements of the NH4 + assimilation rate demonstrated that the NADP(H)-GDH activities of TrGDH transgenic lines were significantly higher than those of the controls. Hydroponic experiments revealed that the fresh weight, dry weight and nitrogen content significantly increased in the TrGDH transgenic lines. Field trials further demonstrated that the number of effective panicles, 1,000-grain weight and grain weight per plant of the transgenic lines were significantly higher than those of the controls, especially under low-nitrogen levels. Moreover, glutelin and prolamine were found to be markedly increased in seeds from the transgenic rice plants. These results sufficiently confirm that overexpression of TrGDH in rice can improve the growth status and grain weight per plant by enhancing nitrogen assimilation. Thus, TrGDH is a promising candidate gene for maintaining yields in crop plants via genetic engineering.
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9
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Agarwal N, Walvekar AS, Punekar NS. 2-Oxoglutarate cooperativity and biphasic ammonium saturation of Aspergillus niger NADP-glutamate dehydrogenase are structurally coupled. Arch Biochem Biophys 2019; 669:50-60. [PMID: 31136734 DOI: 10.1016/j.abb.2019.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/18/2022]
Abstract
NADP-glutamate dehydrogenase from Aspergillus niger (AnGDH) exhibits sigmoidal 2-oxoglutarate saturation. Despite sharing 88% amino acid identity, the homologous enzyme from Aspergillus terreus (AtGDH) shows hyperbolic 2-oxoglutarate saturation. In order to address the structural origins of this phenomenon, six AnGDH-AtGDH chimeras were constructed and characterized. The C-terminal sequence (residues 315-460, named the D-segment) was implicated in the AnGDH cooperativity. The D-segment residues largely contribute to the monomer-monomer interface of each trimer in the native hexamer and are far removed from the enzyme active site. The D-segment appears to be a part of the allosteric network responsible for 2-oxoglutarate homotropic interactions in AnGDH. AnGDH and its C415S mutant, but not AtGDH, also showed atypical, biphasic ammonium saturation, particularly at sub-saturating 2-oxoglutarate concentrations. We found that the sigmoidal 2-oxoglutarate saturation and the biphasic ammonium response are tightly coupled; the analysis of AnGDH-AtGDH chimeras ascribes the two features to the AnGDH D-segment. The two non-Michaelis-Menten substrate saturations of AnGDH were influenced by ionic strength. Increase in ionic strength reduced the nH of 2-oxoglutarate saturation as well as abolished the biphasic response, suggesting that polar/ionic interactions determine the allosteric, inter-subunit communications. The biochemical analysis in the context of available structural data implicates the D-segment of AnGDH in the allosteric feature of this enzyme. The coupling of sigmoidal 2-oxoglutarate saturation and the biphasic ammonium response could possibly confer growth advantage to A. niger experiencing carbon and/or nitrogen limitation.
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Affiliation(s)
- Nupur Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India
| | - Adhish S Walvekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India
| | - Narayan S Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India.
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Saragadam T, Kumar S, Punekar NS. Characterization of 4-guanidinobutyrase from Aspergillus niger. MICROBIOLOGY-SGM 2019; 165:396-410. [PMID: 30806615 DOI: 10.1099/mic.0.000782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Arginase is the only fungal ureohydrolase that is well documented in the literature. More recently, a novel route for agmatine catabolism in Aspergillus niger involving another ureohydrolase, 4-guanidinobutyrase (GBase), was reported. We present here a detailed characterization of A. niger GBase - the first fungal (and eukaryotic) enzyme to be studied in detail. A. niger GBase is a homohexamer with a native molecular weight of 336 kDa and an optimal pH of 7.5. Unlike arginase, the Mn2+ enzyme from the same fungus, purified GBase protein is associated with Zn2+ ions. A sensitive fluorescence assay was used to determine its kinetic parameters. GBase acted 25 times more efficiently on 4-guanidinobutyrate (GB) than 3-guanidinopropionic acid (GP). The Km for GB was 2.7±0.4 mM, whereas for GP it was 53.7±0.8 mM. While GB was an efficient nitrogen source, A. niger grew very poorly on GP. Constitutive expression of GBase favoured fungal growth on GP, indicating that GP catabolism is limited by intracellular GBase levels in A. niger. The absence of a specific GPase and the inability of GP to induce GBase expression confine the fungal growth on GP. That GP is a poor substrate for GBase and a very poor nitrogen source for A. niger offers an opportunity to select GBase specificity mutations. Further, it is now possible to compare two distinct ureohydrolases, namely arginase and GBase, from the same organism.
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Affiliation(s)
- Tejaswani Saragadam
- Metabolism and Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Sunil Kumar
- Metabolism and Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.,†Present address: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Narayan S Punekar
- Metabolism and Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Pirog TP. THE PROPERTIES OF SURFACTANTS SYNTHESIZED BY Acinetobacter calcoaceticus ІMV В-7241 ON REFINED AND WASTE SUNFLOWER OIL. BIOTECHNOLOGIA ACTA 2018. [DOI: 10.15407/biotech11.06.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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12
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Prakash P, Punekar NS, Bhaumik P. Structural basis for the catalytic mechanism and α-ketoglutarate cooperativity of glutamate dehydrogenase. J Biol Chem 2018. [PMID: 29540480 DOI: 10.1074/jbc.ra117.000149] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP+-dependent allosteric enzyme that is forward-inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (α-ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (α-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously reported. The AnGDH hexamers having subunits with different conformations indicated that its α-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp-154 and Gly-153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning α-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.
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Affiliation(s)
- Prem Prakash
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Narayan S Punekar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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Campero‐Basaldua C, Quezada H, Riego‐Ruíz L, Márquez D, Rojas E, González J, El‐Hafidi M, González A. Diversification of the kinetic properties of yeast NADP-glutamate-dehydrogenase isozymes proceeds independently of their evolutionary origin. Microbiologyopen 2017; 6:e00419. [PMID: 27864882 PMCID: PMC5387307 DOI: 10.1002/mbo3.419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 02/02/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, the ScGDH1 and ScGDH3 encoded glutamate dehydrogenases (NADP-GDHs) catalyze the synthesis of glutamate from ammonium and α-ketoglutarate (α-KG). Previous kinetic characterization showed that these enzymes displayed different allosteric properties and respectively high or low rate of α-KG utilization. Accordingly, the coordinated action of ScGdh1 and ScGdh3, regulated balanced α-KG utilization for glutamate biosynthesis under either fermentative or respiratory conditions, safeguarding energy provision. Here, we have addressed the question of whether there is a correlation between the regulation and kinetic properties of the NADP-GDH isozymes present in S. cerevisiae (ScGdh1 and ScGdh3), Kluyveromyces lactis (KlGdh1), and Lachancea kluyveri (LkGdh1) and their evolutionary history. Our results show that the kinetic properties of K. lactis and L. kluyveri single NADP-GDHs are respectively similar to either ScGDH3 or ScGDH1, which arose from the whole genome duplication event of the S. cerevisiae lineage, although, KlGDH1 and LkGDH1 originated from a GDH clade, through an ancient interspecies hybridization event that preceded the divergence between the Saccharomyces clade and the one containing the genera Kluyveromyces, Lachancea, and Eremothecium. Thus, the kinetic properties which determine the NADP-GDHs capacity to utilize α-KG and synthesize glutamate do not correlate with their evolutionary origin.
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Affiliation(s)
- Carlos Campero‐Basaldua
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Héctor Quezada
- Laboratorio de Inmunología y ProteómicaHospital Infantil de México Federico GómezMexico CityMéxico
| | | | - Dariel Márquez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Erendira Rojas
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - James González
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Mohammed El‐Hafidi
- Departamento de Biomedicina CardiovascularInstituto Nacional de Cardiología Ignacio ChávezMexico CityMéxico
| | - Alicia González
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
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Expression of Lactate Dehydrogenase in Aspergillus niger for L-Lactic Acid Production. PLoS One 2015; 10:e0145459. [PMID: 26683313 PMCID: PMC4684279 DOI: 10.1371/journal.pone.0145459] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
Different engineered organisms have been used to produce L-lactate. Poor yields of lactate at low pH and expensive downstream processing remain as bottlenecks. Aspergillus niger is a prolific citrate producer and a remarkably acid tolerant fungus. Neither a functional lactate dehydrogenase (LDH) from nor lactate production by A. niger is reported. Its genome was also investigated for the presence of a functional ldh. The endogenous A. niger citrate synthase promoter relevant to A. niger acidogenic metabolism was employed to drive constitutive expression of mouse lactate dehydrogenase (mldhA). An appraisal of different branches of the A. niger pyruvate node guided the choice of mldhA for heterologous expression. A high copy number transformant C12 strain, displaying highest LDH specific activity, was analyzed under different growth conditions. The C12 strain produced 7.7 g/l of extracellular L-lactate from 60 g/l of glucose, in non-neutralizing minimal media. Significantly, lactate and citrate accumulated under two different growth conditions. Already an established acidogenic platform, A. niger now promises to be a valuable host for lactate production.
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Zhou Y, Zhang C, Lin J, Yang Y, Peng Y, Tang D, Zhao X, Zhu Y, Liu X. Over-expression of a glutamate dehydrogenase gene, MgGDH, from Magnaporthe grisea confers tolerance to dehydration stress in transgenic rice. PLANTA 2015; 241:727-40. [PMID: 25486886 DOI: 10.1007/s00425-014-2214-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/24/2014] [Indexed: 05/03/2023]
Abstract
Heterologous expression of a fungal NADP(H)-GDH gene ( MgGDH ) from Magnaporthe grisea can improve dehydration stress tolerance in rice by preventing toxic accumulation of ammonium. Glutamate dehydrogenase (GDH; EC 1.4.1.2 and EC 1.4.1.4) may act as a stress-responsive enzyme in detoxification of high intracellular ammonia and production of glutamate for proline synthesis under stress conditions. In present study, a fungal NADP(H)-GDH gene (MgGDH) from Magnaporthe grisea was over-expressed in rice (Oryza sativa L. cv. 'kitaake'), and the transgenic plants showed the improvement of tolerance to dehydration stress. The kinetic analysis showed that His-TF-MgGDH preferentially utilizes ammonium to produce L-glutamate. Moreover, the affinity of His-TF-MgGDH for ammonium was dramatically higher than that of His-TF-OsGDH for ammonium. Over-expressing MgGDH transgenic rice plants showed lower water-loss rate and higher completely close stomata than the wild-type plants under dehydration stress conditions. In transgenic plants, the NADP(H)-GDH activities were markedly higher than those in wild-type plants and the amination activity was significantly higher than the deamination activity. Compared with wild-type plants, the transgenic plants accumulated much less NH4 (+) but higher amounts of glutamate, proline and soluble sugar under dehydration stress conditions. These results indicate that heterologous expression of MgGDH can prevent toxic accumulation of ammonium and in return improve dehydration stress tolerance in rice.
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Affiliation(s)
- Yanbiao Zhou
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
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16
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Inhibitors of amino acids biosynthesis as antifungal agents. Amino Acids 2014; 47:227-49. [PMID: 25408465 PMCID: PMC4302243 DOI: 10.1007/s00726-014-1873-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
Fungal microorganisms, including the human pathogenic yeast and filamentous fungi, are able to synthesize all proteinogenic amino acids, including nine that are essential for humans. A number of enzymes catalyzing particular steps of human-essential amino acid biosynthesis are fungi specific. Numerous studies have shown that auxotrophic mutants of human pathogenic fungi impaired in biosynthesis of particular amino acids exhibit growth defect or at least reduced virulence under in vivo conditions. Several chemical compounds inhibiting activity of one of these enzymes exhibit good antifungal in vitro activity in minimal growth media, which is not always confirmed under in vivo conditions. This article provides a comprehensive overview of the present knowledge on pathways of amino acids biosynthesis in fungi, with a special emphasis put on enzymes catalyzing particular steps of these pathways as potential targets for antifungal chemotherapy.
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Prakash P, Walvekar AS, Punekar NS, Bhaumik P. Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase from Aspergillus niger. Acta Crystallogr F Struct Biol Commun 2014; 70:1508-12. [PMID: 25372818 PMCID: PMC4231853 DOI: 10.1107/s2053230x14021499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
Glutamate dehydrogenase (GDH) catalyzes the NAD-dependent or NADP-dependent oxidative deamination of L-glutamate to 2-oxoglutarate and ammonia. This important reversible reaction establishes the link between carbon and nitrogen metabolism. In this study, Aspergillus niger NADP-GDH (AnGDH) has been overexpressed and purified. Purified AnGDH, with a high specific activity of 631.1 units per milligram of protein, was crystallized and the crystal diffracted to 2.9 Å resolution using a home X-ray source. Preliminary analysis of the X-ray diffraction data showed that the crystal belonged to space group R32, with unit-cell parameters a=b=173.8, c=241.5 Å, α=β=90, γ=120°. The crystals exhibited an unusually high solvent content (83.0%) and had only one molecule in the asymmetric unit. Initial phases were obtained by molecular replacement, and model building and structure refinement of AnGDH are in progress.
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Affiliation(s)
- Prem Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Adhish S. Walvekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Narayan S. Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Rahmad N, Al-Obaidi JR, Rashid NMN, Zean NB, Yusoff MHYM, Shaharuddin NS, Jamil NAM, Saleh NM. Comparative proteomic analysis of different developmental stages of the edible mushroom Termitomyces heimii. Biol Res 2014; 47:30. [PMID: 25053143 PMCID: PMC4105490 DOI: 10.1186/0717-6287-47-30] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/25/2014] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Termitomyces heimii is a basidiomycete fungus that has a symbiotic relationship with termites, and it is an edible mushroom with a unique flavour and texture. T. heimii is also one of the most difficult mushrooms to cultivate throughout the world. Little is known about the growth and development of these mushrooms, and the available information is insufficient or poor. The purpose of this study was to provide a base of knowledge regarding the biological processes involved in the development of T. heimii. The proteomic method of 2 dimensional difference gel electrophoresis 2D-DIGE was used to determine and examine the protein profiles of each developmental stage (mycelium, primordium and fruiting body). Total proteins were extracted by TCA-acetone precipitation. RESULTS A total of 271 protein spots were detected by electrophoresis covering pH 3-10 and 10-250 kDa. Selected protein spots were subjected to mass spectrometric analyses with matrix-assisted laser desorption/ionisation (MALDI TOF/TOF). Nineteen protein spots were identified based on peptide mass fingerprinting by matching peptide fragments to the NCBI non-redundant database using MASCOT software. The 19 protein spots were categorised into four major groups through KEGG pathway analysis, as follows: carbohydrate metabolism, energy metabolism, amino acid metabolism and response to environmental stress. CONCLUSIONS The results from our study show that there is a clear correlation between the changes in protein expression that occur during different developmental stages. Enzymes related to cell wall synthesis were most highly expressed during fruiting body formation compared to the mycelium and primordial stages. Moreover, enzymes involved in cell wall component degradation were up-regulated in the earlier stages of mushroom development.
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Affiliation(s)
- Norasfaliza Rahmad
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Jameel R Al-Obaidi
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Noraswati Mohd Nor Rashid
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Ng Boon Zean
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | | | - Nur Syahidah Shaharuddin
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Nor Azreen Mohd Jamil
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
| | - Norihan Mohd Saleh
- Agro-biotechnology Institute Malaysia (ABI), c/o MARDI Headquarters, Serdang, Selangor 43400 Malaysia
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Walvekar AS, Choudhury R, Punekar NS. Mixed disulfide formation at Cys141 leads to apparent unidirectional attenuation of Aspergillus niger NADP-glutamate dehydrogenase activity. PLoS One 2014; 9:e101662. [PMID: 24987966 PMCID: PMC4079599 DOI: 10.1371/journal.pone.0101662] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
NADP-Glutamate dehydrogenase from Aspergillus niger (AnGDH) exhibits sigmoid 2-oxoglutarate saturation. Incubation with 2-hydroxyethyl disulfide (2-HED, the disulfide of 2-mercaptoethanol) resulted in preferential attenuation of AnGDH reductive amination (forward) activity but with a negligible effect on oxidative deamination (reverse) activity, when monitored in the described standard assay. Such a disulfide modified AnGDH displaying less than 1.0% forward reaction rate could be isolated after 2-HED treatment. This unique forward inhibited GDH form (FIGDH), resembling a hypothetical 'one-way' active enzyme, was characterized. Kinetics of 2-HED mediated inhibition and protein thiol titrations suggested that a single thiol group is modified in FIGDH. Two site-directed cysteine mutants, C141S and C415S, were constructed to identify the relevant thiol in FIGDH. The forward activity of C141S alone was insensitive to 2-HED, implicating Cys141 in FIGDH formation. It was observed that FIGDH displayed maximal reaction rate only after a pre-incubation with 2-oxoglutarate and NADPH. In addition, compared to the native enzyme, FIGDH showed a four fold increase in K0.5 for 2-oxoglutarate and a two fold increase in the Michaelis constants for ammonium and NADPH. With no change in the GDH reaction equilibrium constant, the FIGDH catalyzed rate of approach to equilibrium from reductive amination side was sluggish. Altered kinetic properties of FIGDH at least partly account for the observed apparent loss of forward activity when monitored under defined assay conditions. In sum, although Cys141 is catalytically not essential, its covalent modification provides a striking example of converting the biosynthetic AnGDH into a catabolic enzyme.
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Affiliation(s)
- Adhish S. Walvekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Rajarshi Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Narayan S. Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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20
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Du C, Lin J, Yang Y, Liu H, Li C, Zhou Y, Li Y, Tang D, Zhao X, Zhu Y, Liu X. Molecular cloning, characterization and function analysis of a GDH gene from Sclerotinia sclerotiorum in rice. Mol Biol Rep 2014; 41:3683-93. [DOI: 10.1007/s11033-014-3233-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/04/2014] [Indexed: 11/29/2022]
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21
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Joshi CV, Pathan EK, Punekar NS, Tupe SG, Kapadnis BP, Deshpande MV. A biochemical correlate of dimorphism in a zygomycete Benjaminiella poitrasii: characterization of purified NAD-dependent glutamate dehydrogenase, a target for antifungal agents. Antonie van Leeuwenhoek 2013; 104:25-36. [PMID: 23588417 DOI: 10.1007/s10482-013-9921-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/05/2013] [Indexed: 10/27/2022]
Abstract
The fungal organisms, especially pathogens, change their vegetative (Y, unicellular yeast and H, hypha) morphology reversibly for survival and proliferation in the host environment. NAD-dependent glutamate dehydrogenase (NAD-GDH, EC 1.4.1.2) from a non-pathogenic dimorphic zygomycete Benjaminiella poitrasii was previously reported to be an important biochemical correlate of the transition process. The enzyme was purified to homogeneity and characterized. It is a 371 kDa native molecular weight protein made up of four identical subunits. Kinetic studies showed that unlike other NAD-GDHs, it may act as an anabolic enzyme and has more affinity towards 2-oxoglutarate than L-glutamate. Chemical modifications revealed the involvement of single histidine and lysine residues in the catalytic activity of the enzyme. The phosphorylation and dephosphorylation study showed that the NAD-GDH is present in active phosphorylated form in hyphal cells of B. poitrasii. Two of the 1,2,3 triazole linked β-lactam-bile acid conjugates synthesized in the laboratory (B18, B20) were found to be potent inhibitors of purified NAD-GDH which also significantly affected Y-H transition in B. poitrasii. Furthermore, the compound B20 inhibited germ tube formation during Y-H transition in Candida albicans strains and Yarrowia lipolytica. The possible use of NAD-GDH as a target for antifungal agents is discussed.
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Affiliation(s)
- C V Joshi
- Biochemical Sciences Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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22
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Eastwood DC, Herman B, Noble R, Dobrovin-Pennington A, Sreenivasaprasad S, Burton KS. Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO₂. Fungal Genet Biol 2013; 55:54-66. [PMID: 23354075 DOI: 10.1016/j.fgb.2013.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/03/2012] [Accepted: 01/01/2013] [Indexed: 11/25/2022]
Abstract
Reproductive phase change from vegetative mycelium to the initiation of fruiting in Agaricus bisporus is regulated in large part by the sensing of environmental conditions. A model is proposed in which three separate environmental factors exert control at different stages of the reproductive developmental process change. The eight carbon volatile 1-octen-3-ol controls the early differentiation from vegetative hyphae to multicellular knots; temperature reduction is essential for the later differentiation of primodia; and carbon dioxide level exerts quantitative control on the number of fruiting bodies developed. Analysis of transcriptomic changes during the reproductive phase change was carried out with initiation-specific microarrays, and the newly published A. bisporus genome was used to analyse the promoter regions of differentially regulated genes. Our studies have shown there to be both early and late initiation responses relating to sensing of eight carbon volatiles and temperature respectively. A subset of 45 genes was transcriptionally regulated during the reproductive phase change which exhibited a range of functions including cell structure, nitrogen and carbon metabolism, and sensing and signalling. Three gene clusters linking increased transcription with developmental stage were identified. Analysis of promoter regions revealed cluster-specific conserved motifs indicative of co-ordinated regulation of transcription.
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Affiliation(s)
- Daniel C Eastwood
- Department of Bioscience, University of Swansea, Singleton Park, Swansea SA2 8PP, United Kingdom.
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23
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Dave K, Ahuja M, Jayashri T, Sirola RB, Punekar NS. A novel selectable marker based on Aspergillus niger arginase expression. Enzyme Microb Technol 2012; 51:53-8. [DOI: 10.1016/j.enzmictec.2012.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/05/2012] [Accepted: 04/05/2012] [Indexed: 11/27/2022]
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Tomita T, Kuzuyama T, Nishiyama M. Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase. J Biol Chem 2011; 286:37406-13. [PMID: 21900230 PMCID: PMC3199488 DOI: 10.1074/jbc.m111.260265] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/26/2011] [Indexed: 11/06/2022] Open
Abstract
Glutamate dehydrogenase (GDH) catalyzes reversible conversion between glutamate and 2-oxoglutarate using NAD(P)(H) as a coenzyme. Although mammalian GDH is regulated by GTP through the antenna domain, little is known about the mechanism of allosteric activation by leucine. An extremely thermophilic bacterium, Thermus thermophilus, possesses GDH with a unique subunit configuration composed of two different subunits, GdhA (regulatory subunit) and GdhB (catalytic subunit). T. thermophilus GDH is unique in that the enzyme is subject to allosteric activation by leucine. To elucidate the structural basis for leucine-induced allosteric activation of GDH, we determined the crystal structures of the GdhB-Glu and GdhA-GdhB-Leu complexes at 2.1 and 2.6 Å resolution, respectively. The GdhB-Glu complex is a hexamer that binds 12 glutamate molecules: six molecules are bound at the substrate-binding sites, and the remaining six are bound at subunit interfaces, each composed of three subunits. The GdhA-GdhB-Leu complex is crystallized as a heterohexamer composed of four GdhA subunits and two GdhB subunits. In this complex, six leucine molecules are bound at subunit interfaces identified as glutamate-binding sites in the GdhB-Glu complex. Consistent with the structure, replacement of the amino acid residues of T. thermophilus GDH responsible for leucine binding made T. thermophilus GDH insensitive to leucine. Equivalent amino acid replacement caused a similar loss of sensitivity to leucine in human GDH2, suggesting that human GDH2 also uses the same allosteric site for regulation by leucine.
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Affiliation(s)
- Takeo Tomita
- From the Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 and
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 and
| | - Makoto Nishiyama
- From the Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 and
- the RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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25
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Dave K, Punekar NS. Utility of Aspergillus niger citrate synthase promoter for heterologous expression. J Biotechnol 2011; 155:173-7. [PMID: 21723343 DOI: 10.1016/j.jbiotec.2011.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/02/2011] [Accepted: 06/17/2011] [Indexed: 02/02/2023]
Abstract
Citrate synthase is a central player in the acidogenic metabolism of Aspergillus niger. The 5' upstream sequence (0.9kb DNA) of citrate synthase gene (citA) from A. niger NCIM 565 was analyzed and its promoter function demonstrated through the heterologous expression of two proteins. The cloned citrate synthase promoter (PcitA) sequence was able to express bar coding sequence thereby conferring phosphinothricin resistance. This sequence was further analyzed by systematic deletions to define an effective but compact functional promoter. The PcitA driven egfp expression showed that PcitA was active in all differentiation cell-stages of A. niger. EGFP expression was highest on non-repressible carbon sources like acetate and glycerol. Mycelial EGFP levels increased during acidogenic growth suggesting that PcitA is functional throughout this cultivation. A. niger PcitA is the first Krebs cycle gene promoter used to express heterologous proteins in filamentous fungi.
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Affiliation(s)
- Kashyap Dave
- Biotechnology Group, Department of Bioscience and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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26
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Tomita T, Miyazaki T, Miyazaki J, Kuzuyama T, Nishiyama M. Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus. MICROBIOLOGY-SGM 2010; 156:3801-3813. [PMID: 20829287 DOI: 10.1099/mic.0.042721-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An extremely thermophilic bacterium, Thermus thermophilus, possesses two glutamate dehydrogenase (GDH) genes, gdhA and gdhB, putatively forming an operon on the genome. To elucidate the functions of these genes, the gene products were purified and characterized. GdhA showed no GDH activity, while GdhB showed GDH activity for reductive amination 1.3-fold higher than that for oxidative deamination. When GdhA was co-expressed with His-tag-fused GdhB, GdhA was co-purified with His-tagged GdhB. Compared with GdhB alone, co-purified GdhA-GdhB had decreased reductive amination activity and increased oxidative deamination activity, resulting in a 3.1-fold preference for oxidative deamination over reductive amination. Addition of hydrophobic amino acids affected the GDH activity of the co-purified GdhA-GdhB hetero-complex. Among the amino acids, leucine had the largest effect on activity: addition of 1 mM leucine elevated the GDH activity of the co-purified GdhA-GdhB by 974 and 245 % for reductive amination and oxidative deamination, respectively, while GdhB alone did not show such marked activation by leucine. Kinetic analysis revealed that the elevation of GDH activity by leucine is attributable to the enhanced turnover number of GDH. In this hetero-oligomeric GDH system, GdhA and GdhB act as regulatory and catalytic subunits, respectively, and GdhA can modulate the activity of GdhB through hetero-complex formation, depending on the availability of hydrophobic amino acids. This study provides the first finding, to our knowledge, of a hetero-oligomeric GDH that can be regulated allosterically.
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Affiliation(s)
- Takeo Tomita
- Biotechnology Research Center, Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Miyazaki
- Biotechnology Research Center, Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Junichi Miyazaki
- Biotechnology Research Center, Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan.,Biotechnology Research Center, Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan
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27
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Abiko T, Wakayama M, Kawakami A, Obara M, Kisaka H, Miwa T, Aoki N, Ohsugi R. Changes in nitrogen assimilation, metabolism, and growth in transgenic rice plants expressing a fungal NADP(H)-dependent glutamate dehydrogenase (gdhA). PLANTA 2010; 232:299-311. [PMID: 20443025 DOI: 10.1007/s00425-010-1172-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 04/11/2010] [Indexed: 05/23/2023]
Abstract
In plants, glutamine synthetase (GS) is the enzyme that is mainly responsible for the assimilation of ammonium. Conversely, in microorganisms such as bacteria and Ascomycota, NADP(H)-dependent glutamate dehydrogenase (GDH) and GS both have important roles in ammonium assimilation. Here, we report the changes in nitrogen assimilation, metabolism, growth, and grain yield of rice plants caused by an ectopic expression of NADP(H)-GDH (gdhA) from the fungus Aspergillus niger in the cytoplasm. An investigation of the kinetic properties of purified recombinant protein showed that the fungal gdhA had 5.4-10.2 times higher V(max) value and 15.9-43.1 times higher K(m) value for NH(4)(+), compared with corresponding values for rice cytosolic GS as reported in the literature. These results suggested that the introduction of fungal GDH into rice could modify its ammonium assimilation pathway. We therefore expressed gdhA in the cytoplasm of rice plants. NADP(H)-GDH activities in the gdhA-transgenic lines were markedly higher than those in a control line. Tracer experiments by feeding with (15)NH(4)(+) showed that the introduced gdhA, together with the endogenous GS, directly assimilated NH(4)(+) absorbed from the roots. Furthermore, in comparison with the control line, the transgenic lines showed an increase in dry weight and nitrogen content when sufficient nitrogen was present, but did not do so under low-nitrogen conditions. Under field condition, the transgenic line examined showed a significant increase in grain yield in comparison with the control line. These results suggest that the introduction of fungal gdhA into rice plants could lead to better growth and higher grain yield by enhancing the assimilation of ammonium.
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Affiliation(s)
- Tomomi Abiko
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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28
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Aspergillus terreus NADP-glutamate dehydrogenase is kinetically distinct from the allosteric enzyme of other Aspergilli. ACTA ACUST UNITED AC 2009; 113:1121-6. [DOI: 10.1016/j.mycres.2009.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 07/14/2009] [Indexed: 11/18/2022]
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29
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Kumar S, Dalvi DB, Moorthy M, Korde SS, Fondekar KP, Sahasrabudhe SD, Schacht HT, Ekkundi VS, Halik C, Choudhury R, Kumar A, Punekar NS. Discriminatory protein binding by a library of 96 new affinity resins: a novel dye-affinity chromatography tool-kit. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:3610-8. [PMID: 19766065 DOI: 10.1016/j.jchromb.2009.08.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 08/13/2009] [Accepted: 08/28/2009] [Indexed: 10/20/2022]
Abstract
Initial acceptance of Cibacron Blue 3G-A based matrices has made dye-ligand affinity chromatography an attractive proposition. This prompted the synthesis and search for new dye structures. A systematic library of 96 affinity resins was generated using novel analogs of Cibacron Blue 3G-A and also by varying spacer lengths for immobilization. The library was tested in a batch binding and elution mode using seven different proteins--four Aspergillus enzymes namely, NADP-glutamate dehydrogenase, laccase, glutamine synthetase and arginase, bovine pancreatic trypsin and the two serum proteins human serum albumin and immunoglobulin G. Unique binding patterns were observed for each of them indicating that the library displayed discriminatory interactions. The significance of spacer length in the interaction with proteins was discernable. Trypsin interacted best with affinity resins that had no spacer. It was possible to resolve IgG and HSA from a mixture using a combination of resins. There was a good spread of HSA binding capacity in the 96 affinity resins. While some showed better HSA binding capacity than the commercial CB3GA-based matrix, a few with lower capacity were also observed. Subsequent to an initial screen, one affinity resin (CR-017) could be used to enrich Aspergillus terreus NADP-GDH from crude cell extracts. The efficacy of this dye-affinity resin was rationalized by characterizing NADP-GDH inhibition kinetics with the corresponding free dye ligand. In the sum, the library provides a set of dye-ligand affinity matrices with a potential for use in high throughput screening for protein purification.
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Affiliation(s)
- Sunil Kumar
- Biotechnology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Vamsee-Krishna C, Phale PS. Carbon source-dependent modulation of NADP-glutamate dehydrogenases in isophthalate-degrading Pseudomonas aeruginosa strain PP4, Pseudomonas strain PPD and Acinetobacter lwoffii strain ISP4. MICROBIOLOGY-SGM 2008; 154:3329-3337. [PMID: 18957586 DOI: 10.1099/mic.0.2008/022087-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acinetobacter lwoffii strain ISP4 metabolizes isophthalate rapidly compared with Pseudomonas aeruginosa strain PP4 and Pseudomonas strain PPD. Isophthalate has been reported to be a potent competitive inhibitor of glutamate dehydrogenase (GDH). Exogenous supplementation of isophthalate with glutamate or alpha-ketoglutarate at 1 mM concentration caused strains PP4 and PPD to grow faster than in the presence of isophthalate alone; however, no such effect was observed in strain ISP4. When grown on isophthalate, all strains showed activity of NADP-dependent GDH (NADP-GDH), while cells grown on glucose, 2x yeast extract-tryptone broth (2YT) or glutamate showed activities of both NAD-dependent GDH (NAD-GDH) and NADP-GDH. Activity staining, inhibition and thermal stability studies indicated the carbon source-dependent presence of two (GDH(I) and GDH(II)), three (GDH(A), GDH(B) and GDH(C)) and one (GDH(P)) forms of NADP-GDH in strains PP4, PPD and ISP4, respectively. The results demonstrate the carbon source-dependent modulation of different forms of NADP-GDH in these bacterial strains. This modulation may help the efficient utilization of isophthalate as a carbon source by overcoming the inhibitory effect on GDH.
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Affiliation(s)
- C Vamsee-Krishna
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
| | - Prashant S Phale
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
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Hamza MA, Engel PC. Homotropic allosteric control in clostridial glutamate dehydrogenase: different mechanisms for glutamate and NAD+? FEBS Lett 2008; 582:1816-20. [PMID: 18472008 DOI: 10.1016/j.febslet.2008.04.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/18/2008] [Accepted: 04/24/2008] [Indexed: 11/16/2022]
Abstract
Clostridial glutamate dehydrogenase mutants with the 5 Trp residues in turn replaced by Phe showed the importance of Trp 64 and 449 in cooperativity with glutamate at pH 9. These mutants are examined here for their behaviour with NAD+ at pH 7.0 and 9.0. The wild-type enzyme displays negative NAD+ cooperativity at both pH values. At pH 7.0 W243F gives Michaelis-Menten kinetics, and the same behaviour is shown by W243F and also W310F at pH 9.0, but not by W64F or W449F. W243 and W310 are apparently much more important than W64 and W449 for the coenzyme negative cooperativity, implying that different conformational transitions are involved in cooperativity with the coenzyme and with glutamate.
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Affiliation(s)
- Muaawia A Hamza
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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32
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Ahuja M, Punekar NS. Phosphinothricin resistance in Aspergillus niger and its utility as a selectable transformation marker. Fungal Genet Biol 2008; 45:1103-10. [PMID: 18479949 DOI: 10.1016/j.fgb.2008.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 03/28/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
Abstract
Aspergillus niger is moderately susceptible to inhibition by phosphinothricin (PPT)-a potent inhibitor of glutamine synthetase. This growth inhibition was relieved by L-glutamine. PPT inhibited A. niger glutamine synthetase in vitro (K(I), 54 microM) and the inhibition was competitive with L-glutamate. The bar gene, imparting resistance to PPT, was successfully exploited as a dominant marker to transform this fungus. Very high PPT concentrations were required in the overlay for selection. Apart from bar transformants, colonies spontaneously resistant to PPT were frequently encountered on selection media. Reasons for such spontaneous resistance, albeit of moderate growth phenotype, were sought using one such isolate (SRPPT). The SRPPT isolate showed a 2-3-fold decrease in its glutamate uptake rate. Elevated external glutamate levels further suppressed the PPT-induced growth inhibition. Cellular entry of PPT could be through the L-glutamate uptake system thereby accounting for the observed spontaneous resistant phenotype. These results were useful in the fine-tuning of bar-selection in A. niger.
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Affiliation(s)
- Manmeet Ahuja
- Biotechnology Group, School of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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Impact of ammonium permeases mepA, mepB, and mepC on nitrogen-regulated secondary metabolism in Fusarium fujikuroi. EUKARYOTIC CELL 2007; 7:187-201. [PMID: 18083831 DOI: 10.1128/ec.00351-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Fusarium fujikuroi, the production of gibberellins and bikaverin is repressed by nitrogen sources such as glutamine or ammonium. Sensing and uptake of ammonium by specific permeases play key roles in nitrogen metabolism. Here, we describe the cloning of three ammonium permease genes, mepA, mepB, and mepC, and their participation in ammonium uptake and signal transduction in F. fujikuroi. The expression of all three genes is strictly regulated by the nitrogen regulator AreA. Severe growth defects of DeltamepB mutants on low-ammonium medium and methylamine uptake studies suggest that MepB functions as the main ammonium permease in F. fujikuroi. In DeltamepB mutants, nitrogen-regulated genes such as the gibberellin and bikaverin biosynthetic genes are derepressed in spite of high extracellular ammonium concentrations. mepA mepB and mepC mepB double mutants show a similar phenotype as DeltamepB mutants. All three F. fujikuroi mep genes fully complemented the Saccharomyces cerevisiae mep1 mep2 mep3 triple mutant to restore growth on low-ammonium medium, whereas only MepA and MepC restored pseudohyphal growth in the mep2/mep2 mutant. Overexpression of mepC in the DeltamepB mutants partially suppressed the growth defect but did not prevent derepression of AreA-regulated genes. These studies provide evidence that MepB functions as a regulatory element in a nitrogen sensing system in F. fujikuroi yet does not provide the sensor activity of Mep2 in yeast, indicating differences in the mechanisms by which nitrogen is sensed in S. cerevisiae and F. fujikuroi.
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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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