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Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
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Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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2
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Schumacher MA, Salinas R, Travis BA, Singh RR, Lent N. M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation. Nat Commun 2023; 14:7375. [PMID: 37968329 PMCID: PMC10651883 DOI: 10.1038/s41467-023-43243-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei (Mm) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Brady A Travis
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Rajiv Ranjan Singh
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nicholas Lent
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
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3
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Travis BA, Peck JV, Salinas R, Dopkins B, Lent N, Nguyen VD, Borgnia MJ, Brennan RG, Schumacher MA. Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria. Nat Commun 2022; 13:3793. [PMID: 35778410 PMCID: PMC9249791 DOI: 10.1038/s41467-022-31573-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.
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Affiliation(s)
- Brady A Travis
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jared V Peck
- Cryo-EM core, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Brandon Dopkins
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nicholas Lent
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Viet D Nguyen
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Richard G Brennan
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.
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4
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Huang P, Chen S, Chiang W, Ho M, Wu K. Structural basis for the helical filament formation of
Escherichia coli
glutamine synthetase. Protein Sci 2022; 31:e4304. [PMID: 35481643 PMCID: PMC8996467 DOI: 10.1002/pro.4304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023]
Abstract
Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer visible under transmission electron microscopy. Filamentous EcGS is induced by environmental metal ions. We used cryo-electron microscopy (cryo-EM) to decipher the structure of metal ion (nickel)-induced EcGS helical filament at a sub-3Å resolution. EcGS filament formation involves stacking of native dodecamers by chelating nickel ions to residues His5 and His13 in the first N-terminal helix (H1). His5 and His13 from paired parallel H1 helices provide salt bridges and hydrogen bonds to tightly stack two dodecamers. One subunit of the EcGS filament hosts two nickel ions, whereas the dodecameric interface and the ATP/Mg-binding site both host a nickel ion each. We reveal that upon adding glutamate or ATP for catalytic reactions, nickel-induced EcGS filament reverts to individual dodecamers. Such tunable filament formation is often associated with stress responses. Our results provide detailed structural information on the mechanism underlying reversible and tunable EcGS filament formation.
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Affiliation(s)
- Pei‐Chi Huang
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan Normal University Taipei Taiwan
| | - Shao‐Kang Chen
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Wei‐Hung Chiang
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Meng‐Ru Ho
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Kuen‐Phon Wu
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Institute of Biochemical Science College of Life Science, National Taiwan University Taipei Taiwan
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5
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Fernandes GDC, Turchetto‐Zolet AC, Passaglia LMP. Glutamine synthetase evolutionary history revisited: tracing back beyond the Last Universal Common Ancestor. Evolution 2022; 76:605-622. [DOI: 10.1111/evo.14434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriela de Carvalho Fernandes
- Departamento de Genética and Programa de Pós‐graduação em Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul (UFRGS) Av. Bento Gonçalves, 9500, Prédio 43312, Mailbox 15053 Porto Alegre RS 91‐501‐970 Brazil
| | - Andreia Carina Turchetto‐Zolet
- Departamento de Genética and Programa de Pós‐graduação em Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul (UFRGS) Av. Bento Gonçalves, 9500, Prédio 43312, Mailbox 15053 Porto Alegre RS 91‐501‐970 Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós‐graduação em Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul (UFRGS) Av. Bento Gonçalves, 9500, Prédio 43312, Mailbox 15053 Porto Alegre RS 91‐501‐970 Brazil
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6
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Structural Insight into the Contributions of the N-Terminus and Key Active-Site Residues to the Catalytic Efficiency of Glutamine Synthetase 2. Biomolecules 2020; 10:biom10121671. [PMID: 33327463 PMCID: PMC7764910 DOI: 10.3390/biom10121671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
Glutamine synthetase (GS) catalyzes the condensation of ammonia and glutamate, along with ATP, to form glutamine. Despite extensive studies on GSs from eukaryotes and prokaryotes, the roles of the N-terminus and other structural features in catalysis remain unclear. Here we report the decameric structure of Drosophila melanogaster GS 2 (DmGS2). The N-terminal short helices, α1 and α2, constitute a meander region, and form hydrogen bonds with residues 3–5 in the N-terminal loop, which are not present in the GSs of other species. Deletion of α1 or α1-α2 inactivates DmGS2. Notably, the Arg4 in each monomer of one pentamer forms hydrogen bonds with Glu7, and Asp8 in the adjacent monomer of the other pentamer. Replacement of Arg4 with Asp (R4D) abolishes activity. Analytical ultracentrifugation revealed that Arg4 is crucial for oligomerization. Circular dichroism spectra revealed that R4D may alter the secondary structure. We mutated key residues to identify the substrate-binding site. As Glu140 binds glutamate and Glu311 binds ammonia, mutants E140A and E311A have little activity. Conversely, mutant P214A (P contributes to ATP binding) has higher activity than wild-type DmGS2. These findings expand the understanding of the structural and functional features of the N-terminal meander region of DmGS2 and the residues important for catalytic efficiency.
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7
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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Alexandrov AI, Grosfeld EV, Dergalev AA, Kushnirov VV, Chuprov-Netochin RN, Tyurin-Kuzmin PA, Kireev II, Ter-Avanesyan MD, Leonov SV, Agaphonov MO. Analysis of novel hyperosmotic shock response suggests 'beads in liquid' cytosol structure. Biol Open 2019; 8:bio044529. [PMID: 31285266 PMCID: PMC6679407 DOI: 10.1242/bio.044529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022] Open
Abstract
Proteins can aggregate in response to stresses, including hyperosmotic shock. Formation and disassembly of aggregates is a relatively slow process. We describe a novel instant response of the cell to hyperosmosis, during which chaperones and other proteins form numerous foci with properties uncharacteristic of classical aggregates. These foci appeared/disappeared seconds after shock onset/removal, in close correlation with cell volume changes. Genome-wide and targeted testing revealed chaperones, metabolic enzymes, P-body components and amyloidogenic proteins in the foci. Most of these proteins can form large assemblies and for some, the assembled state was pre-requisite for participation in foci. A genome-wide screen failed to identify genes whose absence prevented foci participation by Hsp70. Shapes of and interconnections between foci, revealed by super-resolution microscopy, indicated that the foci were compressed between other entities. Based on our findings, we suggest a new model of cytosol architecture as a collection of numerous gel-like regions suspended in a liquid network. This network is reduced in volume in response to hyperosmosis and forms small pockets between the gel-like regions.
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Affiliation(s)
- Alexander I Alexandrov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
| | - Erika V Grosfeld
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
- Chair of Molecular and Cell Biology, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Alexander A Dergalev
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Vitaly V Kushnirov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Pyotr A Tyurin-Kuzmin
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, M.V. Lomonosov Moscow State University, Lomonosovskiy pr., 27 bldg 1, Moscow 119192, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Leninskie gori 1, bldg 40, Moscow 119234, Russia
- V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, Moscow 117198, Russia
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Michael D Ter-Avanesyan
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141701, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya str., 3, Moscow Region, 142290 Puschino, Russia
| | - Michael O Agaphonov
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky Ave. 33, bld. 2, Moscow 119071, Russia
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9
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Prouteau M, Loewith R. Regulation of Cellular Metabolism through Phase Separation of Enzymes. Biomolecules 2018; 8:biom8040160. [PMID: 30513998 PMCID: PMC6316564 DOI: 10.3390/biom8040160] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023] Open
Abstract
Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or epigenetic changes, metabolic homeostasis is no longer achievable and diseases such as metabolic syndrome or cancer, aging, and, ultimately, death ensue. Metabolic reactions are catalyzed by proteins, and the in vitro kinetic properties of these enzymes have been studied by biochemists for many decades. These efforts led to the appreciation that enzyme activities can be acutely regulated and that this regulation is critical to metabolic homeostasis. Regulation can be mediated through allosteric interactions with metabolites themselves or via post-translational modifications triggered by intracellular signal transduction pathways. More recently, enzyme regulation has attracted the attention of cell biologists who noticed that change in growth conditions often triggers the condensation of diffusely localized enzymes into one or more discrete foci, easily visible by light microscopy. This reorganization from a soluble to a condensed state is best described as a phase separation. As summarized in this review, stimulus-induced phase separation has now been observed for dozens of enzymes suggesting that this could represent a widespread mode of activity regulation, rather than, or in addition to, a storage form of temporarily superfluous enzymes. Building on our recent structure determination of TOROIDs (TORc1 Organized in Inhibited Domain), the condensate formed by the protein kinase Target Of Rapamycin Complex 1 (TORC1), we will highlight that the molecular organization of enzyme condensates can vary dramatically and that future work aimed at the structural characterization of enzyme condensates will be critical to understand how phase separation regulates enzyme activity and consequently metabolic homeostasis. This information may ultimately facilitate the design of strategies to target the assembly or disassembly of specific enzymes condensates as a therapeutic approach to restore metabolic homeostasis in certain diseases.
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Affiliation(s)
- Manoël Prouteau
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
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Moreira C, Ramos MJ, Fernandes PA. Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets. Molecules 2016; 21:E1028. [PMID: 27509490 PMCID: PMC6274088 DOI: 10.3390/molecules21081028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Glutamine synthetase (GS) is a crucial enzyme to the nitrogen cycle with great commercial and pharmaceutical value. Current inhibitors target the active site, affecting GS activity indiscriminately in all organisms. As the active site is located at the interface between two monomers, the protein-protein interface (PPI) of GSs gains a new role, by providing new targets for enzyme inhibition. Exploring GSs PPI could allow for the development of inhibitors selective for specific organisms. Here we map the PPI of three GSs-human (hsGS), maize (zmGS) and Mycobacterium tuberculosis (mtGS)-and unravel new drugable pockets. METHODS The PPI binding free energy coming from key residues on three GSs from different organisms were mapped by computational alanine scan mutagenesis, applying a multiple dielectric constant MM-PBSA methodology. The most relevant residues for binding are referred as hot-spots. Drugable pockets on GS were detected with the Fpocket software. RESULTS AND CONCLUSIONS A total of 23, 19 and 30 hot-spots were identified on hsGS, zmGS and mtGS PPI. Even possessing differences in the hot-spots, hsGS and zmGS PPI are overall very similar. On the other hand, mtGS PPI differs greatly from hsGS and zmGS PPI. A novel drugable pocket was detected on the mtGS PPI. It seems particularly promising for the development of selective anti-tuberculosis drugs given its location on a PPI region that is highly populated with hot-spots and is completely different from the hsGS and zmGS PPIs. Drugs targeting this pockets should be inactive on eukaryotic GS II enzymes.
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Affiliation(s)
- Cátia Moreira
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
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11
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Jeitner TM, Battaile K, Cooper AJL. Critical Evaluation of the Changes in Glutamine Synthetase Activity in Models of Cerebral Stroke. Neurochem Res 2015; 40:2544-56. [DOI: 10.1007/s11064-015-1667-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/14/2015] [Accepted: 05/20/2015] [Indexed: 01/04/2023]
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12
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Angelucci F, Bellelli A, Ardini M, Ippoliti R, Saccoccia F, Morea V. One ring (or two) to hold them all – on the structure and function of protein nanotubes. FEBS J 2015; 282:2827-45. [PMID: 26059483 DOI: 10.1111/febs.13336] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 01/07/2023]
Abstract
Understanding the structural determinants relevant to the formation of supramolecular assemblies of homo-oligomeric proteins is a traditional and central scope of structural biology. The knowledge thus gained is crucial both to infer their physiological function and to exploit their architecture for bionanomaterials design. Protein nanotubes made by one-dimensional arrays of homo-oligomers can be generated by either a commutative mechanism, yielding an 'open' structure (e.g. actin), or a noncommutative mechanism, whereby the final structure is formed by hierarchical self-assembly of intermediate 'closed' structures. Examples of the latter process are poorly described and the rules by which they assemble have not been unequivocally defined. We have collected and investigated examples of homo-oligomeric circular arrangements that form one-dimensional filaments of stacked rings by the noncommutative mechanism in vivo and in vitro. Based on their quaternary structure, circular arrangements of protein subunits can be subdivided into two groups that we term Rings of Dimers (e.g. peroxiredoxin and stable protein 1) and Dimers of Rings (e.g. thermosome/rosettasome), depending on the sub-structures that can be identified within the assembly (and, in some cases, populated in solution under selected experimental conditions). Structural analysis allowed us to identify the determinants by which ring-like molecular chaperones form filamentous-like assemblies and to formulate a novel hypothesis by which nanotube assembly, molecular chaperone activity and macromolecular crowding may be interconnected.
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Affiliation(s)
- Francesco Angelucci
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Matteo Ardini
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Fulvio Saccoccia
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Veronica Morea
- CNR - National Research Council of Italy, Institute of Molecular Biology and Pathology, Rome, Italy
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Seabra AR, Carvalho HG. Glutamine synthetase in Medicago truncatula, unveiling new secrets of a very old enzyme. FRONTIERS IN PLANT SCIENCE 2015; 6:578. [PMID: 26284094 PMCID: PMC4515544 DOI: 10.3389/fpls.2015.00578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/13/2015] [Indexed: 05/03/2023]
Abstract
Glutamine synthetase (GS) catalyzes the first step at which nitrogen is brought into cellular metabolism and is also involved in the reassimilation of ammonium released by a number of metabolic pathways. Due to its unique position in plant nitrogen metabolism, GS plays essential roles in all aspects of plant development, from germination to senescence, and is a key component of nitrogen use efficiency (NUE) and plant yield. Understanding the mechanisms regulating GS activity is therefore of utmost importance and a great effort has been dedicated to understand how GS is regulated in different plant species. The present review summarizes exciting recent developments concerning the structure and regulation of GS isoenzymes, using the model legume Medicago truncatula. These include the understanding of the structural determinants of both the cytosolic and plastid located isoenzymes, the existence of a seed-specific GS gene unique to M. truncatula and closely related species and the discovery that GS isoenzymes are regulated by nitric oxide at the post-translational level. The data is discussed and integrated with the potential roles of the distinct GS isoenzymes within the whole plant context.
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Affiliation(s)
| | - Helena G. Carvalho
- *Correspondence: Helena G. Carvalho, Laboratory of Molecular Biology of Nitrogen Assimilation, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal,
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Petrovska I, Nüske E, Munder MC, Kulasegaran G, Malinovska L, Kroschwald S, Richter D, Fahmy K, Gibson K, Verbavatz JM, Alberti S. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation. eLife 2014; 3:eLife.02409. [PMID: 24771766 PMCID: PMC4011332 DOI: 10.7554/elife.02409] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/10/2014] [Indexed: 01/20/2023] Open
Abstract
One of the key questions in biology is how the metabolism of a cell responds to changes in the environment. In budding yeast, starvation causes a drop in intracellular pH, but the functional role of this pH change is not well understood. Here, we show that the enzyme glutamine synthetase (Gln1) forms filaments at low pH and that filament formation leads to enzymatic inactivation. Filament formation by Gln1 is a highly cooperative process, strongly dependent on macromolecular crowding, and involves back-to-back stacking of cylindrical homo-decamers into filaments that associate laterally to form higher order fibrils. Other metabolic enzymes also assemble into filaments at low pH. Hence, we propose that filament formation is a general mechanism to inactivate and store key metabolic enzymes during a state of advanced cellular starvation. These findings have broad implications for understanding the interplay between nutritional stress, the metabolism and the physical organization of a cell.
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Affiliation(s)
- Ivana Petrovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Matthias C Munder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz Institute Dresden-Rossendorf, Dresden, Germany
| | - Kimberley Gibson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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15
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Torreira E, Seabra AR, Marriott H, Zhou M, Llorca Ó, Robinson CV, Carvalho HG, Fernández-Tornero C, Pereira PJB. The structures of cytosolic and plastid-located glutamine synthetases from Medicago truncatula reveal a common and dynamic architecture. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:981-93. [PMID: 24699643 PMCID: PMC3975887 DOI: 10.1107/s1399004713034718] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/27/2013] [Indexed: 11/21/2022]
Abstract
The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legume Medicago truncatula is reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure of M. truncatula GSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.
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Affiliation(s)
- Eva Torreira
- Chemical and Physical Biology, Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Rita Seabra
- Molecular Biology of Nitrogen Assimilation, IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Hazel Marriott
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, England
| | - Min Zhou
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, England
| | - Óscar Llorca
- Chemical and Physical Biology, Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carol V. Robinson
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, England
| | - Helena G. Carvalho
- Molecular Biology of Nitrogen Assimilation, IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Carlos Fernández-Tornero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas – CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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A sensing role of the glutamine synthetase in the nitrogen regulation network in Fusarium fujikuroi. PLoS One 2013; 8:e80740. [PMID: 24260467 PMCID: PMC3829961 DOI: 10.1371/journal.pone.0080740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/05/2013] [Indexed: 11/29/2022] Open
Abstract
In the plant pathogenic ascomycete Fusarium fujikuroi the synthesis of several economically important secondary metabolites (SM) depends on the nitrogen status of the cells. Of these SMs, gibberellin and bikaverin synthesis is subject to nitrogen catabolite repression (NCR) and is therefore only executed under nitrogen starvation conditions. How the signal of available nitrogen quantity and quality is sensed and transmitted to transcription factors is largely unknown. Earlier work revealed an essential regulatory role of the glutamine synthetase (GS) in the nitrogen regulation network and secondary metabolism as its deletion resulted in total loss of SM gene expression. Here we present extensive gene regulation studies of the wild type, the Δgln1 mutant and complementation strains of the gln1 deletion mutant expressing heterologous GS-encoding genes of prokaryotic and eukaryotic origin or 14 different F. fujikuroi gln1 copies with site-directed mutations. All strains were grown under different nitrogen conditions and characterized regarding growth, expression of NCR-responsive genes and biosynthesis of SM. We provide evidence for distinct roles of the GS in sensing and transducing the signals to NCR-responsive genes. Three site directed mutations partially restored secondary metabolism and GS-dependent gene expression, but not glutamine formation, demonstrating for the first time that the catalytic and regulatory roles of GS can be separated. The distinct mutant phenotypes show that the GS (1) participates in NH4+-sensing and transducing the signal towards NCR-responsive transcription factors and their subsequent target genes; (2) affects carbon catabolism and (3) activates the expression of a distinct set of non-NCR GS-dependent genes. These novel insights into the regulatory role of the GS provide fascinating perspectives for elucidating regulatory roles of GS proteins of different organism in general.
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Betti M, García-Calderón M, Pérez-Delgado CM, Credali A, Estivill G, Galván F, Vega JM, Márquez AJ. Glutamine synthetase in legumes: recent advances in enzyme structure and functional genomics. Int J Mol Sci 2012; 13:7994-8024. [PMID: 22942686 PMCID: PMC3430217 DOI: 10.3390/ijms13077994] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 01/12/2023] Open
Abstract
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N(2) fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism.
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Affiliation(s)
- Marco Betti
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-95-4556917; Fax: +34-95-4626853
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18
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Crystal Structure of Type III Glutamine Synthetase: Surprising Reversal of the Inter-Ring Interface. Structure 2011; 19:471-83. [DOI: 10.1016/j.str.2011.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/31/2011] [Accepted: 02/07/2011] [Indexed: 11/19/2022]
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McDonagh B, Padilla CA, Pedrajas JR, Bárcena JA. Biosynthetic and iron metabolism is regulated by thiol proteome changes dependent on glutaredoxin-2 and mitochondrial peroxiredoxin-1 in Saccharomyces cerevisiae. J Biol Chem 2011; 286:15565-76. [PMID: 21385868 DOI: 10.1074/jbc.m110.193102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Redoxins are involved in maintenance of thiol redox homeostasis, but their exact sites of action are only partly known. We have applied a combined redox proteomics and transcriptomics experimental strategy to discover specific functions of two interacting redoxins: dually localized glutaredoxin 2 (Grx2p) and mitochondrial peroxiredoxin 1 (Prx1p). We have identified 139 proteins showing differential postranslational thiol redox modifications when the cells do not express Grx2p, Prx1p, or both and have mapped the precise cysteines involved in each case. Some of these modifications constitute functional switches that affect metabolic and signaling pathways as the primary effect, leading to gene transcription remodeling as the secondary adaptive effect as demonstrated by a parallel high throughput gene expression analysis. The results suggest that in the absence of Grx2p, the metabolic flow toward nucleotide and aromatic amino acid biosynthesis is slowed down by redox modification of the key enzymes Rpe1p (D-ribulose-5-phosphate 3-epimerase), Tkl1p (transketolase) and Aro4p (3-deoxy-D-arabino-heptulosonate-7-phosphate synthase). The glycolytic mainstream is then diverted toward carbohydrate storage by induction of trehalose and glycogen biosynthesis genes. Porphyrin biosynthesis may also be compromised by inactivation of the redox-sensitive cytosolic enzymes Hem12p (uroporphyrinogen decarboxylase) and Sam1p (S-adenosyl methionine synthetase) and a battery of respiratory genes sensitive to low heme levels are induced. Genes of the Aft1p-dependent iron regulon were induced specifically in the absence of Prx1p despite optimal mitochondrial Fe-S biogenesis, suggesting dysfunction of the mitochondria to the cytosol signaling pathway. Strikingly, requirement of Grx2p for these events places dithiolic Grx2 in the framework of iron metabolism.
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Affiliation(s)
- Brian McDonagh
- Department of Biochemistry and Molecular Biology and Córdoba Maimónides Institute for Biomedical Research (IMIBIC), University of Córdoba, 14071 Córdoba, Spain
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van Rooyen J, Abratt V, Belrhali H, Sewell B. Crystallization of recombinant Bacteroides fragilis glutamine synthetase (GlnN) isolated using a novel and rapid purification protocol. Protein Expr Purif 2010; 74:211-6. [DOI: 10.1016/j.pep.2010.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/04/2010] [Accepted: 06/17/2010] [Indexed: 11/15/2022]
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Estivill G, Guardado P, Buser R, Betti M, Márquez AJ. Identification of an essential cysteinyl residue for the structure of glutamine synthetase alpha from Phaseolus vulgaris. PLANTA 2010; 231:1101-1111. [PMID: 20237895 DOI: 10.1007/s00425-010-1115-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 02/01/2010] [Indexed: 05/28/2023]
Abstract
We have studied the possible role, in a plant glutamine synthetase (GS), of the different cysteinyl residues present in this enzyme. For this purpose we carried out the site-directed mutagenesis of the cDNA for alpha-GS polypeptide from Phaseolus vulgaris in the positions corresponding to Cys-92, Cys-159, and Cys-179, followed by heterologous expression in E. coli and enzymatic characterisation of WT and mutant proteins. The results show that neither Cys-92 nor Cys-179 residues were essential for enzyme activity, but the replacement of Cys-159 by alanine or serine strongly affects the quaternary structure and function of the GS enzyme molecule, resulting in a complete loss of enzymatic activity. Other studies using sulfhydryl specific reagents such as pHMB (p-hydroxymercuribenzoate) or DTNB (5,5'-dithiobis-2-nitrobenzoate) confirmed that the profound inhibition produced is associated with an important alteration of the quaternary structure of GS, and suggest that Cys-159 might be the residue responsible for the enzyme inhibition. All these results suggest that the Cys-159 residue is essential for the enzyme structure. The results are also consistent with previous reports based on classical biochemistry studies indicating the presence of essential cysteinyl residues for the enzyme activity of higher plant GS.
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Affiliation(s)
- Guillermo Estivill
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad Sevilla, Seville, Spain
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Seabra AR, Carvalho H, Pereira PJB. Crystallization and preliminary crystallographic characterization of glutamine synthetase from Medicago truncatula. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1309-12. [PMID: 20054137 PMCID: PMC2802889 DOI: 10.1107/s1744309109047381] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 11/09/2009] [Indexed: 11/11/2022]
Abstract
The condensation of ammonium and glutamate into glutamine catalyzed by glutamine synthetase (GS) is a fundamental step in nitrogen metabolism in all kingdoms of life. In plants, this is preceded by the reduction of inorganic nitrogen to an ammonium ion and therefore effectively articulates nitrogen fixation and metabolism. Although the three-dimensional structure of the dodecameric bacterial GS was determined quite some time ago, the quaternary architecture of the plant enzyme has long been assumed to be octameric, mostly on the basis of low-resolution electron-microscopy studies. Recently, the crystallographic structure of a monocotyledonous plant GS was reported that revealed a homodecameric organization. In order to unambiguously establish the quaternary architecture of GS from dicotyledonous plants, GS1a from the model legume Medicago truncatula was overexpressed, purified and crystallized. The collection of synchrotron diffraction data to 2.35 A resolution allowed the determination of the three-dimensional structure of this enzyme by molecular replacement.
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Affiliation(s)
- Ana Rita Seabra
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Helena Carvalho
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
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