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Carrasco-Navarro U, Aguirre J. H 2O 2 Induces Major Phosphorylation Changes in Critical Regulators of Signal Transduction, Gene Expression, Metabolism and Developmental Networks in Aspergillus nidulans. J Fungi (Basel) 2021; 7:624. [PMID: 34436163 PMCID: PMC8399174 DOI: 10.3390/jof7080624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) regulate several aspects of cell physiology in filamentous fungi including the antioxidant response and development. However, little is known about the signaling pathways involved in these processes. Here, we report Aspergillus nidulans global phosphoproteome during mycelial growth and show that under these conditions, H2O2 induces major changes in protein phosphorylation. Among the 1964 phosphoproteins we identified, H2O2 induced the phosphorylation of 131 proteins at one or more sites as well as the dephosphorylation of a larger set of proteins. A detailed analysis of these phosphoproteins shows that H2O2 affected the phosphorylation of critical regulatory nodes of phosphoinositide, MAPK, and TOR signaling as well as the phosphorylation of multiple proteins involved in the regulation of gene expression, primary and secondary metabolism, and development. Our results provide a novel and extensive protein phosphorylation landscape in A. nidulans, indicating that H2O2 induces a shift in general metabolism from anabolic to catabolic, and the activation of multiple stress survival pathways. Our results expand the significance of H2O2 in eukaryotic cell signaling.
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Affiliation(s)
| | - Jesús Aguirre
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, Ciudad de México 04510, Mexico;
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2
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Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans. mSystems 2021; 6:6/1/e01316-20. [PMID: 33500332 PMCID: PMC7842366 DOI: 10.1128/msystems.01316-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes lethal fungal infections in immunocompromised patients. Lysine crotonylation is a newly discovered PTM (posttranslational modification) epigenetic type that may play a critical role in regulating gene expression. In this study, we used an antibody-enrichment approach along with LC-MS/MS to carry out a quantitative crotonylome analysis in C. albicans We found a total of 5,242 crotonylation sites and 1,584 crotonylated proteins among 9,038 proteins in this organism. Of these crotonylated proteins, a few unique crotonylated motifs are noted such as D and E in positions +1, +2, or +3 or K and R in positions +5 or +6, while A, E, F, G, P, W, and Y are in the -1 position or A, K, and R are found in positions -5, -6, -7, or -8. Functional analysis has shown that a majority of the crotonylated proteins are related to biosynthetic events and carbon metabolism. When combined with previously collected data on acetylation and succinylation, PPI (protein-protein interaction network) analysis reveals that proteins with functions in ribosomal biogenesis, oxidative phosphorylation, nucleus activity, and proteasome formation are heavily modified by these three PTM types. To the best of our knowledge, this is the first crotonylome study carried out in C. albicans and is an important step to a better understanding of the biological and pathogenic impact of PTM in C. albicans IMPORTANCE C. albicans is a kind of pathogen of fungal infections that is found worldwide. Lysine crotonylation of proteins as a recently discovered PTM (posttranslational modification) may have a critical role in regulating cells. We first carried out large-scale analysis of crotonylated proteome and multiple PTM analysis (acetylation, succinylation, and crotonylation), then drew a diagram to show multiple PTM sites on histones in C. albicans of our study. This study about crotonylome in human pathogenic fungi is a milestone that first and deeply investigates the functional analysis of crotonylated proteins in C. albicans, which marks an important start for further research.
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Black MH, Osinski A, Park GJ, Gradowski M, Servage KA, Pawłowski K, Tagliabracci VS. A Legionella effector ADP-ribosyltransferase inactivates glutamate dehydrogenase. J Biol Chem 2021; 296:100301. [PMID: 33476647 PMCID: PMC7949102 DOI: 10.1016/j.jbc.2021.100301] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
ADP-ribosyltransferases (ARTs) are a widespread superfamily of enzymes frequently employed in pathogenic strategies of bacteria. Legionella pneumophila, the causative agent of a severe form of pneumonia known as Legionnaire's disease, has acquired over 330 translocated effectors that showcase remarkable biochemical and structural diversity. However, the ART effectors that influence L. pneumophila have not been well defined. Here, we took a bioinformatic approach to search the Legionella effector repertoire for additional divergent members of the ART superfamily and identified an ART domain in Legionella pneumophila gene0181, which we hereafter refer to as Legionella ADP-Ribosyltransferase 1 (Lart1) (Legionella ART 1). We show that L. pneumophila Lart1 targets a specific class of 120-kDa NAD+-dependent glutamate dehydrogenase (GDH) enzymes found in fungi and protists, including many natural hosts of Legionella. Lart1 targets a conserved arginine residue in the NAD+-binding pocket of GDH, thereby blocking oxidative deamination of glutamate. Therefore, Lart1 could be the first example of a Legionella effector which directly targets a host metabolic enzyme during infection.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marcin Gradowski
- Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Howard Hughes Medical Institute, Dallas, Texas, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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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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5
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Mara P, Fragiadakis GS, Gkountromichos F, Alexandraki D. The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:170. [PMID: 30384856 PMCID: PMC6211499 DOI: 10.1186/s12934-018-1018-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
Ammonium assimilation is linked to fundamental cellular processes that include the synthesis of non-essential amino acids like glutamate and glutamine. In Saccharomyces cerevisiae glutamate can be synthesized from α-ketoglutarate and ammonium through the action of NADP-dependent glutamate dehydrogenases Gdh1 and Gdh3. Gdh1 and Gdh3 are evolutionarily adapted isoforms and cover the anabolic role of the GDH-pathway. Here, we review the role and function of the GDH pathway in glutamate metabolism and we discuss the additional contributions of the pathway in chromatin regulation, nitrogen catabolite repression, ROS-mediated apoptosis, iron deficiency and sphingolipid-dependent actin cytoskeleton modulation in S.cerevisiae. The pleiotropic effects of GDH pathway in yeast biology highlight the importance of glutamate homeostasis in vital cellular processes and reveal new features for conserved enzymes that were primarily characterized for their metabolic capacity. These newly described features constitute insights that can be utilized for challenges regarding genetic engineering of glutamate homeostasis and maintenance of redox balances, biosynthesis of important metabolites and production of organic substrates. We also conclude that the discussed pleiotropic features intersect with basic metabolism and set a new background for further glutamate-dependent applied research of biotechnological interest.
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Affiliation(s)
- P. Mara
- Department of Chemistry, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Present Address: Woods Hole Oceanographic Institution, Woods Hole, MA 02543 USA
| | - G. S. Fragiadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
| | - F. Gkountromichos
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Faculty of Biology, Biocenter, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - D. Alexandraki
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
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6
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Chen Y, Nielsen J. Flux control through protein phosphorylation in yeast. FEMS Yeast Res 2017; 16:fow096. [PMID: 27797916 DOI: 10.1093/femsyr/fow096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 01/26/2023] Open
Abstract
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
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7
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Multiple Forms of Glutamate Dehydrogenase in Animals: Structural Determinants and Physiological Implications. BIOLOGY 2016; 5:biology5040053. [PMID: 27983623 PMCID: PMC5192433 DOI: 10.3390/biology5040053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/26/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022]
Abstract
Glutamate dehydrogenase (GDH) of animal cells is usually considered to be a mitochondrial enzyme. However, this enzyme has recently been reported to be also present in nucleus, endoplasmic reticulum and lysosomes. These extramitochondrial localizations are associated with moonlighting functions of GDH, which include acting as a serine protease or an ATP-dependent tubulin-binding protein. Here, we review the published data on kinetics and localization of multiple forms of animal GDH taking into account the splice variants, post-translational modifications and GDH isoenzymes, found in humans and apes. The kinetic properties of human GLUD1 and GLUD2 isoenzymes are shown to be similar to those published for GDH1 and GDH2 from bovine brain. Increased functional diversity and specific regulation of GDH isoforms due to alternative splicing and post-translational modifications are also considered. In particular, these structural differences may affect the well-known regulation of GDH by nucleotides which is related to recent identification of thiamine derivatives as novel GDH modulators. The thiamine-dependent regulation of GDH is in good agreement with the fact that the non-coenzyme forms of thiamine, i.e., thiamine triphosphate and its adenylated form are generated in response to amino acid and carbon starvation.
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8
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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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9
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Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2011; 12:104-17. [DOI: 10.1111/j.1567-1364.2011.00765.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ana Paula Oliveira
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
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Abstract
The TOR (target of rapamycin) serine/threonine kinases are fascinating in that they influence many different aspects of eukaryote physiology including processes often dysregulated in disease. Beginning with the initial characterization of rapamycin as an antifungal agent, studies with yeast have contributed greatly to our understanding of the molecular pathways in which TORs operate. Recently, building on advances in quantitative MS, the rapamycin-dependent phosphoproteome in the budding yeast Saccharomyces cerevisiae was elucidated. These studies emphasize the central importance of TOR and highlight its many previously unrecognized functions. One of these, the regulation of intermediary metabolism, is discussed.
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Regulation of liver glutamate dehydrogenase by reversible phosphorylation in a hibernating mammal. Comp Biochem Physiol B Biochem Mol Biol 2010; 157:310-6. [PMID: 20674762 DOI: 10.1016/j.cbpb.2010.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/23/2010] [Accepted: 07/25/2010] [Indexed: 11/20/2022]
Abstract
Glutamate dehydrogenase (GDH) is a key enzyme that links amino acid and carbohydrate metabolism in cells. Regulation is likely most important when organisms are confronted with extreme stresses such as the low environmental temperatures and lack of food associated with winter. Many small mammals, such as Richardson's ground squirrels, Spermophilus richardsonii, cope with these conditions by hibernating. Animals enter long periods of profound torpor where metabolic rate is greatly suppressed, body temperature drops to near-ambient and all metabolic needs must be met from fixed internal body stores of fuels. To investigate how GDH is regulated under these conditions, kinetic properties of GDH were analyzed in liver from euthermic and torpid squirrels, revealing significant differences in V(max), K(m) glutamate, K(a) ADP and inhibition by urea between the two forms of GDH. These data suggested an activation of the glutamate-oxidizing activity of GDH in the hypometabolic state. Subsequent experiments suggested that the molecular basis of the kinetic differences was a change in the protein phosphorylation state of GDH between euthermia and torpor. Specifically, liver GDH appears to be dephosphorylated and activated when animals transition into torpor and this may serve to promote amino acid oxidation to contribute to energy production and gluconeogenesis. This is the first study to show that mammalian liver GDH can be regulated by reversible phosphorylation, providing an important new regulatory mechanism for GDH control.
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Van Schaftingen E. Fructose 2,6-bisphosphate. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 59:315-95. [PMID: 3028056 DOI: 10.1002/9780470123058.ch7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Ohshima T, Soda K. Biochemistry and biotechnology of amino acid dehydrogenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 42:187-209. [PMID: 2291437 DOI: 10.1007/bfb0000734] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the last decade, amino acid dehydrogenases such as alanine dehydrogenase (Ala DH), leucine dehydrogenase (Leu DH), and phenylalanine dehydrogenase (Phe DH) have been applied to the enantiomer-specific synthesis and analysis of various amino acids. In perticular, amino acid dehydrogenases from thermophiles have received much attention because of their high stability. Their productivity was enhanced and the purification facilitated by the gene cloning. The advances in biotechnological applications of these enzymes are based on fundamental studies concerning characteristics of the enzymes and reaction mechanism as described in this chapter. Further elucidation of the structure and function of these enzymes based on genetic engineering and protein engineering may enable their properties to be improved for their future uses in biotechnology.
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Affiliation(s)
- T Ohshima
- Department of Chemistry, Kyoto University of Education, Japan
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14
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Vallorani L, Polidori E, Sacconi C, Agostini D, Pierleoni R, Piccoli G, Zeppa S, Stocchi V. Biochemical and molecular characterization of NADP-glutamate dehydrogenase from the ectomycorrhizal fungus Tuber borchii. THE NEW PHYTOLOGIST 2002; 154:779-790. [PMID: 33873467 DOI: 10.1046/j.1469-8137.2002.00409.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• NADP-glutamate dehydrogenase (NADP-GDH) from Tuber borchii was purified and the corresponding gene was cloned in order to elucidate the physiological role of the enzyme in this ectomycorrhizal fungus. • NADP-GDH was purified using an anion-exchange column followed by affinity chromatography. The complete gene was cloned from a 30-d-old-mycelium cDNA library and characterized. • T. borchii NADP-GDH appears to be physically and kinetically similar to those from other fungi and the deduced amino acid sequence of the gdh gene showed a significant similarity to other fungal NADP-dependent GDHs. Biochemical and Northern blotting analyses carried out with mycelia grown on different nitrogen sources clearly showed that the regulation of T. borchii NADP-GDH in response to different nitrogen sources was markedly different from the responses of the NADP-GDHs of other ascomycetes. Northern blotting analyses highlighted that the gdh gene was also expressed in the symbiotic phase. • The biochemical and molecular data suggest that the fungal NADP-GDH contributes to the primary nitrogen metabolism in the ectomycorrhizal tissues.
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Affiliation(s)
- Luciana Vallorani
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Emanuela Polidori
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Cinzia Sacconi
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Deborah Agostini
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Raffaella Pierleoni
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Giovanni Piccoli
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Sabrina Zeppa
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
| | - Vilberto Stocchi
- Istituto di Chimica Biologica 'Giorgio Fornaini', Università degli Studi di Urbino, via Saffi, 2-61029 Urbino (PU), Italy
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15
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Camardella L, Di Fraia R, Antignani A, Ciardiello MA, di Prisco G, Coleman JK, Buchon L, Guespin J, Russell NJ. The Antarctic Psychrobacter sp. TAD1 has two cold-active glutamate dehydrogenases with different cofactor specificities. Characterisation of the NAD+-dependent enzyme. Comp Biochem Physiol A Mol Integr Physiol 2002; 131:559-67. [PMID: 11867281 DOI: 10.1016/s1095-6433(01)00507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Psychrobacter sp. TAD1 is a psychrotolerant bacterium from Antarctic frozen continental water that grows from 2 to 25 degrees C with optimal growth rate at 20 degrees C. The new isolate contains two glutamate dehydrogenases (GDH), differing in their cofactor specificities, subunit sizes and arrangements, and thermal properties. NADP+-dependent GDH is a hexamer of 47 kDa subunits and it is comparable to other hexameric GDHs of family-I from bacteria and lower eukaria. The NAD+-dependent enzyme, described in this communication, has a subunit weight of 160 kDa and belongs to the novel class of GDHs with large size subunits. The enzyme is a dimer; this oligomeric arrangement has not been reported previously for GDH. Both enzymes have an apparent optimum temperature for activity of approximately 20 degrees C, but their cold activities and thermal labilities are different. The NAD+-dependent enzyme is more cold active: at 10 C it retains 50% of its maximal activity, compared with 10% for the NADP+-dependent enzyme. The NADP+-dependent enzyme is more heat stable, losing only 10% activity after heating for 30 min, compared with 95% for the NAD+-dependent enzyme. It is concluded that in Psychrobacter sp. TAD1 not only does NAD+-dependent GDH have a novel subunit molecular weight and arrangement, but that its polypeptide chains are folded differently from those of NADP+-dependent GDH, providing different cold-active properties to the two enzymes.
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Affiliation(s)
- Laura Camardella
- Institute of Protein Biochemistry and Enzymology, C.N.R. Via Marconi 12, I-80125 Naples, Italy
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16
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Lu CD, Abdelal AT. The gdhB gene of Pseudomonas aeruginosa encodes an arginine-inducible NAD(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation. J Bacteriol 2001; 183:490-9. [PMID: 11133942 PMCID: PMC94904 DOI: 10.1128/jb.183.2.490-499.2001] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The NAD(+)-dependent glutamate dehydrogenase (NAD-GDH) from Pseudomonas aeruginosa PAO1 was purified, and its amino-terminal amino acid sequence was determined. This sequence information was used in identifying and cloning the encoding gdhB gene and its flanking regions. The molecular mass predicted from the derived sequence for the encoded NAD-GDH was 182.6 kDa, in close agreement with that determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme (180 kDa). Cross-linking studies established that the native NAD-GDH is a tetramer of equal subunits. Comparison of the derived amino acid sequence of NAD-GDH from P. aeruginosa with the GenBank database showed the highest homology with hypothetical polypeptides from Pseudomonas putida, Mycobacterium tuberculosis, Rickettsia prowazakii, Legionella pneumophila, Vibrio cholerae, Shewanella putrefaciens, Sinorhizobium meliloti, and Caulobacter crescentus. A moderate degree of homology, primarily in the central domain, was observed with the smaller tetrameric NAD-GDH (protomeric mass of 110 kDa) from Saccharomyces cerevisiae or Neurospora crassa. Comparison with the yet smaller hexameric GDH (protomeric mass of 48 to 55 kDa) of other prokaryotes yielded a low degree of homology that was limited to residues important for binding of substrates and for catalytic function. NAD-GDH was induced 27-fold by exogenous arginine and only 3-fold by exogenous glutamate. Primer extension experiments established that transcription of gdhB is initiated from an arginine-inducible promoter and that this induction is dependent on the arginine regulatory protein, ArgR, a member of the AraC/XyIS family of regulatory proteins. NAD-GDH was purified to homogeneity from a recombinant strain of P. aeruginosa and characterized. The glutamate saturation curve was sigmoid, indicating positive cooperativity in the binding of glutamate. NAD-GDH activity was subject to allosteric control by arginine and citrate, which function as positive and negative effectors, respectively. Both effectors act by influencing the affinity of the enzyme for glutamate. NAD-GDH from this organism differs from previously characterized enzymes with respect to structure, protomer mass, and allosteric properties indicate that this enzyme represents a novel class of microbial glutamate dehydrogenases.
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Affiliation(s)
- C D Lu
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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17
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Rijnen L, Courtin P, Gripon JC, Yvon M. Expression of a heterologous glutamate dehydrogenase gene in Lactococcus lactis highly improves the conversion of amino acids to aroma compounds. Appl Environ Microbiol 2000; 66:1354-9. [PMID: 10742211 PMCID: PMC91992 DOI: 10.1128/aem.66.4.1354-1359.2000] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first step of amino acid degradation in lactococci is a transamination, which requires an alpha-keto acid as the amino group acceptor. We have previously shown that the level of available alpha-keto acid in semihard cheese is the first limiting factor for conversion of amino acids to aroma compounds, since aroma formation is greatly enhanced by adding alpha-ketoglutarate to cheese curd. In this study we introduced a heterologous catabolic glutamate dehydrogenase (GDH) gene into Lactococcus lactis so that this organism could produce alpha-ketoglutarate from glutamate, which is present at high levels in cheese. Then we evaluated the impact of GDH activity on amino acid conversion in in vitro tests and in a cheese model by using radiolabeled amino acids as tracers. The GDH-producing lactococcal strain degraded amino acids without added alpha-ketoglutarate to the same extent that the wild-type strain degraded amino acids with added alpha-ketoglutarate. Interestingly, the GDH-producing lactococcal strain produced a higher proportion of carboxylic acids, which are major aroma compounds. Our results demonstrated that a GDH-producing lactococcal strain could be used instead of adding alpha-ketoglutarate to improve aroma development in cheese.
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Affiliation(s)
- L Rijnen
- Unité de Recherches de Biochimie et Structure des Protéines INRA, 78352 Jouy-en-Josas Cedex, France
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18
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Garnier A, Berredjem A, Botton B. Purification and characterization of the NAD-dependent glutamate dehydrogenase in the ectomycorrhizal fungus laccaria bicolor (Maire) orton. Fungal Genet Biol 1997; 22:168-76. [PMID: 9454644 DOI: 10.1006/fgbi.1997.1004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The NAD-dependent glutamate dehydrogenase (GDH) (EC 1.4.1.2) from Laccaria bicolor was purified 410-fold to apparent electrophoretic homogeneity with a 40% recovery through a three-step procedure involving ammonium sulfate precipitation, anion-exchange chromatography on DEAE-Trisacryl, and gel filtration. The molecular weight of the native enzyme determined by gel filtration was 470 kDa, whereas sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave rise to a single band of 116 kDa, suggesting that the enzyme is composed of four identical subunits. The enzyme was specific for NAD(H). The pH optima were 7.4 and 8.8 for the amination and deamination reactions, respectively. The enzyme was found to be highly unstable, with virtually no activity after 20 days at -75 degrees C, 4 days at 4 degrees C, and 1 h at 50 degrees C. The addition of ammonium sulfate improved greatly the stability of the enzyme and full activity was still observed after several months at -75 degrees C. NAD-GDH activity was stimulated by Ca2+ and Mg2+ but strongly inhibited by Cu2+ and slightly by the nucleotides AMP, ADP, and ATP. The Michaelis constants for NAD, NADH, 2-oxoglutarate, and ammonium were 282 &mgr;M, 89 &mgr;M, 1.35 mM, and 37 mM, respectively. The enzyme had a negative cooperativity for glutamate (Hill number of 0.3), and its Km value increased from 0.24 to 3.6 mM when the glutamate concentration exceeded 1 mM. These affinity constants of the substrates, compared with those of the NADP-GDH of the fungus, suggest that the NAD-GDH is mainly involved in the catabolism of glutamate, while the NADP-GDH is involved in the catalysis of this amino acid. Copyright 1997 Academic Press. Copyright 1997 Academic Press
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Affiliation(s)
- A Garnier
- Laboratoire de Biologie Forestiere associe INRA, Universite Henri Poincare Nancy I, Vandoeuvre-Les-Nancy Cedex, 54506, France
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19
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Hudson RC, Daniel RM. L-glutamate dehydrogenases: distribution, properties and mechanism. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1993; 106:767-92. [PMID: 8299344 DOI: 10.1016/0305-0491(93)90031-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R C Hudson
- Microbial Biochemistry and Biotechnology Unit, School of Science and Technology, University of Waikato, Hamilton, New Zealand
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20
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Khale-Kumar A, Deshpande MV. Possible involvement of cyclic adenosine 3',5'-monophosphate in the regulation of NADP-/NAD-glutamate dehydrogenase ratio and in yeast-mycelium transition of Benjaminiella poitrasii. J Bacteriol 1993; 175:6052-5. [PMID: 8397189 PMCID: PMC206690 DOI: 10.1128/jb.175.18.6052-6055.1993] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The effect of different adenine-containing compounds on the NADP-/NAD-glutamate dehydrogenase (GDH) ratio was studied as a function of yeast-mycelium transition in Benjaminiella poitrasii. Under in vivo conditions, at a 5.0 mM concentration, cyclic AMP (cAMP) and dibutyryl cAMP maintained the cells in the yeast form for up to 7 and 5 h, respectively, and this was reflected in the patterns of GDH ratios observed. In vitro studies of phosphorylation and dephosphorylation have also been carried out, and the results suggest a possible correlation between cAMP, the GDH ratio, and cell form in B. poitrasii.
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Affiliation(s)
- A Khale-Kumar
- Biochemical Sciences Division, National Chemical Laboratory, Pune, India
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21
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Morishita T, Matsuura A, Uno I. Characterization of the cyr1-2 UGA mutation in Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1993; 237:463-6. [PMID: 8483461 DOI: 10.1007/bf00279452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
cyr1-2 is a temperature-sensitive mutation of the yeast adenylate cyclase structural gene, CYR1. The cyr1-2 mutation has been suggested to be a UGA mutation since a UGA suppressor SUP201 has been isolated as a suppressor of the cyr1-2 mutation. Construction of chimeric genes restricted the region containing the cyr1-2 mutation, and the cyr1-2 UGA mutation was identified at codon 1282, which lies upstream of the region coding for the catalytic domain of adenylate cyclase. Alterations in the region upstream of the cyr1-2 mutation site result in null mutations. The complete open reading frame of the cyr1-2 gene expressed under the control of the GAL1 promoter complemented cyr1-d1 in a galactose-dependent manner. These results suggest that at the permissive temperature weak readthrough occurs at the cyr1-2 mutation site to produce low levels of active adenylate cyclase. An endogenous suppressor in yeast cells is assumed to be responsible for this readthrough.
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Affiliation(s)
- T Morishita
- Institute of Applied Microbiology, University of Tokyo, Japan
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22
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Britton KL, Baker PJ, Rice DW, Stillman TJ. Structural relationship between the hexameric and tetrameric family of glutamate dehydrogenases. ACTA ACUST UNITED AC 1992; 209:851-9. [PMID: 1358610 DOI: 10.1111/j.1432-1033.1992.tb17357.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The family of glutamate dehydrogenases include a group of hexameric oligomers with a subunit M(r) of around 50,000, which are closely related in amino acid sequence and a smaller group of tetrameric oligomers based on a much larger subunit with M(r) 115,000. Sequence comparisons have indicated a low level of similarity between the C-terminal portion of the tetrameric enzymes and a substantial region of the polypeptide chain for the more widespread hexameric glutamate dehydrogenases. In the light of the solution of the three-dimensional structure of the hexameric NAD(+)-linked glutamate dehydrogenase from Clostridium symbiosum, we have undertaken a detailed examination of the alignment of the sequence for the C-terminal domain of the tetrameric Neurospora crassa glutamate dehydrogenase against the sequence and the molecular structure of that from C. symbiosum. This analysis reveals that the residues conserved between these two families are clustered in the three-dimensional structure and points to a remarkably similar layout of the glutamate-binding site and the active-site pocket, though with some differences in the mode of recognition of the nucleotide cofactor.
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Affiliation(s)
- K L Britton
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, England
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23
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Uno I. Role of signal transduction systems in cell proliferation in yeast. INTERNATIONAL REVIEW OF CYTOLOGY 1992; 139:309-32. [PMID: 1330967 DOI: 10.1016/s0074-7696(08)61415-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- I Uno
- Life Science Research Center, Nippon Steel Corporation, Kawasaki, Japan
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25
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Baker PJ, Britton KL, Engel PC, Farrants GW, Lilley KS, Rice DW, Stillman TJ. Subunit assembly and active site location in the structure of glutamate dehydrogenase. Proteins 1992; 12:75-86. [PMID: 1553382 DOI: 10.1002/prot.340120109] [Citation(s) in RCA: 186] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The three-dimensional crystal structure of the NAD(+)-linked glutamate dehydrogenase from Clostridium symbiosum has been solved to 1.96 A resolution by a combination of isomorphous replacement and molecular averaging and refined to a conventional crystallographic R factor of 0.227. Each subunit in this multimeric enzyme is organised into two domains separated by a deep cleft. One domain directs the self-assembly of the molecule into a hexameric oligomer with 32 symmetry. The other domain is structurally similar to the classical dinucleotide binding fold but with the direction of one of the strands reversed. Difference Fourier analysis on the binary complex of the enzyme with NAD+ shows that the dinucleotide is bound in an extended conformation with the nicotinamide moiety deep in the cleft between the two domains. Hydrogen bonds between the carboxyamide group of the nicotinamide ring and the side chains of T209 and N240, residues conserved in all hexameric GDH sequences, provide a positive selection for the syn conformer of this ring. This results in a molecular arrangement in which the A face of the nicotinamide ring is buried against the enzyme surface and the B face is exposed, adjacent to a striking cluster of conserved residues including K89, K113, and K125. Modeling studies, correlated with chemical modification data, have implicated this region as the glutamate/2-oxoglutarate binding site and provide an explanation at the molecular level for the B type stereospecificity of the hydride transfer of GDH during the catalytic cycle.
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Affiliation(s)
- P J Baker
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, United Kingdom
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26
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Lilley KS, Baker PJ, Britton KL, Stillman TJ, Brown PE, Moir AJ, Engel PC, Rice DW, Bell JE, Bell E. The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1080:191-7. [PMID: 1954226 DOI: 10.1016/0167-4838(91)90001-g] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The amino acid sequence is reported for CNBr and tryptic peptide fragments of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum. Together with the N-terminal sequence, these make up about 75% of the total sequence. The sequence shows extensive similarity with that of the NADP(+)-dependent glutamate dehydrogenase of Escherichia coli (52% identical residues out of the 332 compared) allowing confident placing of the peptide fragments within the overall sequence. This demonstrated sequence similarity with the E. coli enzyme, despite different coenzyme specificity, is much greater than the similarity (31% identities) between the GDH's of C. symbiosum and Peptostreptococcus asaccharolyticus, both NAD(+)-linked. The evolutionary implications are discussed. In the 'fingerprint' region of the nucleotide binding fold the sequence Gly X Gly X X Ala is found, rather than Gly X Gly X X Gly. The sequence found here has previously been associated with NADP+ specificity and its finding in a strictly NAD(+)-dependent enzyme requires closer examination of the function of this structural motif.
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Affiliation(s)
- K S Lilley
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
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27
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Consalvi V, Chiaraluce R, Politi L, Gambacorta A, De Rosa M, Scandurra R. Glutamate dehydrogenase from the thermoacidophilic archaebacterium Sulfolobus solfataricus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 196:459-67. [PMID: 1901040 DOI: 10.1111/j.1432-1033.1991.tb15837.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An NAD(P)-dependent glutamate dehydrogenase was purified to homogeneity from the thermoacidophilic archaebacterium Sulfolobus solfataricus. The enzyme is a hexamer (subunit mass 45 kDa) which dissociates into lower states of association when submitted to gel filtration. Isoelectric focusing analysis of the purified enzyme showed a pI of 5.7 and occasionally revealed microheterogeneity. The enzyme is strictly specific for the natural substrates 2-oxoglutarate and L-glutamate, but is active with both NADH and NADPH. S. solfataricus glutamate dehydrogenase revealed a high degree of thermal stability (at 80 C the half-life was 15 h) which was strictly dependent on the protein concentration. Very high levels of glutamate dehydrogenase were found in this archaebacterium which suggests that the conversion of 2-oxoglutarate and ammonia to glutamate is of central importance to the nitrogen metabolism in this bacterium.
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Affiliation(s)
- V Consalvi
- Dipartimento di Scienze Biochimiche, Università La Sapienza, Roma, Italy
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28
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Role of NAD-linked glutamate dehydrogenase in nitrogen metabolism in Saccharomyces cerevisiae. J Bacteriol 1990; 172:4927-35. [PMID: 1975578 PMCID: PMC213147 DOI: 10.1128/jb.172.9.4927-4935.1990] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We cloned GDH2, the gene that encodes the NAD-linked glutamate dehydrogenase in the yeast Saccharomyces cerevisiae, by purifying the enzyme, making polyclonal antibodies to it, and using the antibodies to screen a lambda gt11 yeast genomic library. A yeast strain with a deletion-disruption allele of GDH2 which replaced the wild-type gene grew very poorly with glutamate as a nitrogen source, but growth improved significantly when the strain was also provided with adenine or other nitrogenous compounds whose biosynthesis requires glutamine. Our results indicate that the NAD-linked glutamate dehydrogenase catalyzes the major, but not sole, pathway for generation of ammonia from glutamate. We also isolated yeast mutants that lacked glutamate synthase activity and present evidence which shows that normally NAD-linked glutamate dehydrogenase is not involved in glutamate biosynthesis, but that if the enzyme is overexpressed, it may function reversibly in intact cells.
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29
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Ward OP, Young CS. Reductive biotransformations of organic compounds by cells or enzymes of yeast. Enzyme Microb Technol 1990; 12:482-93. [PMID: 1366632 DOI: 10.1016/0141-0229(90)90063-v] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Saccharomyces cerevisiae catalyses the asymmetric reductive biotransformation of a variety of compounds containing a carbonyl group or carbon-carbon double bond. Oxidoreductases participating in these reactions which have commercial potential in biotransformation processes are likely to have relatively broad substrate specificity. Important carbonyl reductases falling into this category include YADH- and yeast NADP-dependent beta-ketoester reductases. The enoyl reductase component of the FAS complex may have a role in asymmetric yeast reduction of carbon-carbon double bonds of unnatural substrates. Other nicotinamide-requiring oxidoreductases of yeast are also surveyed to rationalize observed biotransformations of whole yeast cells in terms of specific enzymes. Genetic and protein engineering may enable enzymes to be tailored to accept new substrates. A greater understanding of the enzymes and reactions involved will facilitate further optimization and exploitation of these catalytic systems in industrial processes.
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Affiliation(s)
- O P Ward
- Department of Biology, University of Waterloo, Ontario, Canada
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30
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Affiliation(s)
- J R Broach
- Department of Biology, Princeton University, New Jersey 08544
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31
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Garrett S, Broach J. Loss of Ras activity in Saccharomyces cerevisiae is suppressed by disruptions of a new kinase gene, YAKI, whose product may act downstream of the cAMP-dependent protein kinase. Genes Dev 1989; 3:1336-48. [PMID: 2558053 DOI: 10.1101/gad.3.9.1336] [Citation(s) in RCA: 178] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The yeast Saccharomyces cerevisiae contains two functionally redundant genes RAS1 and RAS2, which are homologous to the mammalian ras gene family and are required for vegetative growth. We isolated and characterized five temperature-sensitive alleles of RAS2. In a ras1 strain, these alleles cause growth arrest at the G1 stage of the cell cycle. Revertants capable of growth at the nonpermissive temperature define four recessive, extragenic complementation groups. Suppressors in one complementation group (designated yak1) are particularly intriguing because they appear to alleviate only the growth defect of the temperature-sensitive ras mutants and do not show any of the phenotypes, such as heat shock sensitivity or starvation sensitivity, associated with increased production of cAMP. The YAK1 gene has been cloned, and disruptions generated in vitro reveal that it is not essential for growth and that its loss confers growth to a strain deleted for tpk1, tpk2, and tpk3, the structural genes for the catalytic subunit of the cAMP-dependent protein kinase. These results place Yak1 downstream from, or on a parallel pathway to, the kinase step in the Ras/cAMP pathway. Finally, the coding region predicts a protein with significant homology to the family of protein kinases, suggesting that loss of cAMP-dependent protein kinase function can be suppressed by the loss of a second protein kinase.
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Affiliation(s)
- S Garrett
- Department of Biology, Princeton University, New Jersey 08544
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32
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Stevens L, Duncan D, Robertson P. Purification and characterisation of NAD-glutamate dehydrogenase from Aspergillus nidulans. FEMS Microbiol Lett 1989; 48:173-7. [PMID: 2524418 DOI: 10.1111/j.1574-6968.1989.tb03294.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
NAD-Glutamate dehydrogenase has been purified from mycelia of A. nidulans. The enzyme comprises subunits of 110 kDa. It is located in the cytosol. It is completely denatured by 1.0 M guanidine hydrochloride, and is not renatured by subsequent dilution. Isophthalate is a strong competitive inhibitor and the enzyme is also inhibited by thiol reagents. The properties of the enzyme were compared to those from other fungi in terms of size, sensitivity to inhibitors, intracellular distribution and mode of regulation, and were found to resemble most closely those of Neurospora crassa.
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Affiliation(s)
- L Stevens
- Department of Biological Science, University of Stirling, Scotland, U.K
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33
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Abstract
Heterokaryons (hets), but not monokaryons of Candida albicans die when grown anaerobically on minimal medium. Their rates of inactivation increase with decreases in growth temperatures from 37 degrees C to 25 degrees C. At 10 degrees C, however, anaerobiosis is not lethal and suppresses the inactivation which normally occurs among hets cultured aerobically at that temperature. Killing of hets by anaerobiosis can be altered significantly by certain exogenously provided amino acids or intermediates of oxidative respiration. Aspartic acid alone promotes inactivation whereas alanine, glutamic acid or lysine individually have no effects. However, glutamate and lysine combined afford slight protection against inactivation while aspartate and glutamate combined, with or without lysine, are highly protective: the activity of the aspartate-glutamate combination is completely negated by the addition of alanine. Other common amino acids have no effects on het responses to anaerobiosis other than the ability, when combined, to relieve the antagonism of alanine for the aspartate-glutamate combination. Anaerobic survivals are also enhanced by oxalacetic acid or alpha-ketoglutaric acid, and even more so by a combination of these two intermediates. The resistances to inactivation elicited by the oxalacetate alpha-ketoglutarate or aspartate-glutamate combinations are not additive. These relationships are interpreted to signify that inactivation of hets by anaerobic growth is largely, if not exclusively, due to depletion of their oxalacetic acid and alpha-ketoglutaric acid contents for amino acid biosyntheses, and the unique inability of het cells to replenish those keto acids upon subsequent return to aerobic conditions. The observations are consistent with previous indications that mitochondria formed by hets are functionally abnormal.
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35
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Boy-Marcotte E, Garreau H, Jacquet M. Cyclic AMP controls the switch between division cycle and resting state programs in response to ammonium availability in Saccharomyces cerevisiae. Yeast 1987; 3:85-93. [PMID: 2849258 DOI: 10.1002/yea.320030205] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have identified a mutation called rcal (for rescue by cAMP) which allows adenylate cyclase-deficient mutants to divide in the presence of cAMP. We took advantage of this rcal mutation to study the effect of externally added cAMP on the onset of the resting state when cells are starved for ammonium. We measured the resistance of the cells to zymolyase treatment as a parameter of the resting state. We observed that the onset of the resting state is reversibly blocked by cAMP. This inhibitory effect of cAMP is discussed together with the cAMP control of the start. This leads us to propose a model in which the cAMP level, controlled by the availability of nutrients, should trigger the choice between the entry of the cell into the resting state and the initiation of a new division cycle.
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Affiliation(s)
- E Boy-Marcotte
- Laboratoire d'Information Génétique et Développement, Université de Paris-Sud, Orsay, France
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36
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14 Protein Phosphorylation in Prokaryotes and Single-Celled Eukaryotes. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/s1874-6047(08)60265-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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37
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Dellamora-Ortiz GM, Ortiz CH, Maia JC, Panek AD. Partial purification and characterization of the interconvertible forms of trehalase from Saccharomyces cerevisiae. Arch Biochem Biophys 1986; 251:205-14. [PMID: 3024571 DOI: 10.1016/0003-9861(86)90067-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cryptic trehalase from Saccharomyces cerevisiae was purified about 3000-fold. The recovery of 970% of the original "activity" indicated the removal of an inhibitor of the enzyme. Active trehalase, obtained through phosphorylation of cryptic trehalase by cAMP-dependent protein kinase, was isolated by chromatography on DEAE-cellulose. A major phosphorylated protein, with an apparent Mr of 86,000, was detected after SDS-polyacrylamide gel electrophoresis. This protein band correlated exactly with the elution profile of trehalase activity and 32Pi incorporation into the enzyme on DEAE-cellulose chromatography. Partially purified active trehalase showed absolute specificity towards trehalose with an apparent Km of 4.79 X 10(-3) M. Both forms of the enzyme showed an apparent molecular weight of 160,000, by gel filtration. Centrifugation on a glycerol density gradient indicated multiple forms of trehalase-c, with Mr of 320,000, 160,000, and 80,000. After activation of each of these forms by protein kinase, a single form of trehalase-a was observed, with a Mr of 160,000. Trehalase-c appears to be a totally inactive form of the enzyme. The only mechanism of activation seems to be phosphorylation by cAMP-dependent protein kinase. When the protein kinase concentration was varied, at a fixed trehalase-c concentration, a sigmoidal activation plot was obtained. This result suggests the occurrence of multiple forms of cryptic trehalase.
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38
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Affiliation(s)
- K Matsumoto
- Department of Industrial Chemistry, Tottori University, Japan
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39
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Matsumoto K, Uno I, Kato K, Ishikawa T. Isolation and characterization of a phosphoprotein phosphatase-deficient mutant in yeast. Yeast 1985; 1:25-38. [PMID: 2851899 DOI: 10.1002/yea.320010104] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The ppd1 mutant of yeast, Saccharomyces cerevisiae, was isolated as a suppressor of the cyr2 mutation which caused alteration of the catalytic subunit of cAMP-dependent protein kinase. Three peaks of phosphoprotein phosphatase activity (peak I, II and III) were identified by DEAE-Sephacel chromatography of crude extracts of the wild-type strain. The ppd1 mutant was deficient in peak III phosphoprotein phosphatase activity. The peak III enzyme efficiently utilized the phosphorylated forms of NAD-dependent glutamate dehydrogenase and trehalase as substrate. The ppd1 mutation did not suppress the cyr1, CYR3 or ras1 ras2 mutations. The ppd1 locus was located on chromosome II and had identical characteristics with glc1. The ppd1 mutation suppressed the G1 arrest caused by nutritional limitation, but maintained sensitivity to mating pheromone. In diploids homozygous for the ppd1 mutation, no premeiotic DNA replication and commitment to intragenic recombination occurred and no spores were formed, suggesting that the accumulation of phosphorylated proteins in the absence of one of the phosphoprotein phosphatases is required for mitosis but not for the initiation of meiosis.
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Affiliation(s)
- K Matsumoto
- Department of Industrial Chemistry, Tottori University, Japan
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40
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Moye WS, Amuro N, Rao JK, Zalkin H. Nucleotide sequence of yeast GDH1 encoding nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39500-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Rice DW, Hornby DP, Engel PC. Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum. J Mol Biol 1985; 181:147-9. [PMID: 3981633 DOI: 10.1016/0022-2836(85)90334-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Crystals of a bacterial NAD+-dependent glutamate dehydrogenase (GDHase) have been grown over a wide range of pH values by using the hanging drop method of vapour diffusion with ammonium sulphate as the precipitant. Sodium dodecyl sulphate/polyacrylamide gel electrophoresis of this enzyme together with high pressure liquid chromatography/gel filtration, shows that this GDHase is hexameric like the GDHases of vertebrates. X-ray photographs of the crystals show that they diffract to at least 2.0 A, and an analysis of the diffraction pattern demonstrates that the hexamer is arranged in at least pseudo 32 symmetry.
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42
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Uno I, Matsumoto K, Adachi K, Ishikawa T. Characterization of cyclic AMP-requiring yeast mutants altered in the catalytic subunit of protein kinase. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90776-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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