1
|
Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
Collapse
Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
| |
Collapse
|
2
|
Bhayani J, Iglesias MJ, Minen RI, Cereijo AE, Ballicora MA, Iglesias AA, Asencion Diez MD. Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools. Front Microbiol 2022; 13:867384. [PMID: 35572620 PMCID: PMC9093745 DOI: 10.3389/fmicb.2022.867384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1-2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties.
Collapse
Affiliation(s)
- Jaina Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Maria Josefina Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Romina I. Minen
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Antonela E. Cereijo
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Matias D. Asencion Diez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| |
Collapse
|
3
|
Classification, characterization and structural analysis of sugar nucleotidylyltransferase family of enzymes. Biochem Biophys Res Commun 2020; 525:780-785. [PMID: 32147095 DOI: 10.1016/j.bbrc.2020.02.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
Sugar Nucleotidyl Transferases (SNTs) constitute a large family of enzymes that play important metabolic roles. Earlier, for one such SNT, termed N-acetylglucosamine-1-phosphate uridyltransferase- GlmU, we had established that two magnesium ions - Mg2+A and Mg2+B - catalyze the sugar-nucleotidyl transfer reaction. Despite a common structural framework that SNTs share, we recognized key differences around the active-site based on the analysis of available structures. Based on these differences, we had classified SNTs into two major groups, Group - I & II; and further, variation in 'Mg2+A-stabilizing motifs' led us to sub-classify them into five distinct sub-groups. Since group specific conservation of 'Mg2+A-stabilizing motifs' was based only for 45 available structures, here we validate this via an exhaustive analysis of 1,42,025 protein sequences. Previously, we had hypothesized that a metal-ion-catalyzed mechanism would be operative in all SNTs. Here, we validate it biochemically and establish that Mg2+ is a strict requirement for nucleotidyl transfer reactions in every group or sub-group and that a common metal ion dependent mechanism operates in SNTs. Further, mutating Mg2+A coordinating residue in each sub-group led to abolished catalysis, indicating an important role for both of these residues and suggest that SNTs employ variations over 'a conserved catalytic mechanism mediated by Mg2+ ion(s)', to bring about functional diversity. This would constitute a comprehensive study to establish the catalytic mechanism across the family of SNTs.
Collapse
|
4
|
Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
Collapse
|
5
|
Hill BL, Mascarenhas R, Patel HP, Asencion Diez MD, Wu R, Iglesias AA, Liu D, Ballicora MA. Structural analysis reveals a pyruvate-binding activator site in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. J Biol Chem 2019; 294:1338-1348. [PMID: 30401744 DOI: 10.1074/jbc.ra118.004246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/21/2018] [Indexed: 11/06/2022] Open
Abstract
The pathways for biosynthesis of glycogen in bacteria and starch in plants are evolutionarily and biochemically related. They are regulated primarily by ADP-glucose pyrophosphorylase, which evolved to satisfy metabolic requirements of a particular organism. Despite the importance of these two pathways, little is known about the mechanism that controls pyrophosphorylase activity or the location of its allosteric sites. Here, we report pyruvate-bound crystal structures of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens, identifying a previously elusive activator site for the enzyme. We found that the tetrameric enzyme binds two molecules of pyruvate in a planar conformation. Each binding site is located in a crevice between the C-terminal domains of two subunits where they stack via a distinct β-helix region. Pyruvate interacts with the side chain of Lys-43 and with the peptide backbone of Ser-328 and Gly-329 from both subunits. These structural insights led to the design of two variants with altered regulatory properties. In one variant (K43A), the allosteric effect was absent, whereas in the other (G329D), the introduced Asp mimicked the presence of pyruvate. The latter generated an enzyme that was preactivated and insensitive to further activation by pyruvate. Our study furnishes a deeper understanding of how glycogen biosynthesis is regulated in bacteria and the mechanism by which transgenic plants increased their starch production. These insights will facilitate rational approaches to enzyme engineering for starch production in crops of agricultural interest and will promote further study of allosteric signal transmission and molecular evolution in this important enzyme family.
Collapse
Affiliation(s)
- Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Hiral P Patel
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Matías D Asencion Diez
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660; Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral-Consejo Nacional de Investigaciones Científicas y Técnicas (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB) Paraje "El Pozo," Centro Científico Tecnológico (CCT)-Santa Fe, Colectora Ruta Nacional, 168 km 0, 3000 Santa Fe, Argentina
| | - Rui Wu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral-Consejo Nacional de Investigaciones Científicas y Técnicas (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas (FBCB) Paraje "El Pozo," Centro Científico Tecnológico (CCT)-Santa Fe, Colectora Ruta Nacional, 168 km 0, 3000 Santa Fe, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660.
| |
Collapse
|
6
|
Ebrecht AC, Solamen L, Hill BL, Iglesias AA, Olsen KW, Ballicora MA. Allosteric Control of Substrate Specificity of the Escherichia coli ADP-Glucose Pyrophosphorylase. Front Chem 2017; 5:41. [PMID: 28674689 PMCID: PMC5474683 DOI: 10.3389/fchem.2017.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/07/2017] [Indexed: 11/29/2022] Open
Abstract
The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism toward the synthesis of reserve polysaccharides. Here, we show that the allosteric activator fructose-1,6-bisphosphate plays a role in such selection by increasing the catalytic efficiency of the enzyme toward the use of ATP rather than other nucleotides. In the presence of fructose-1,6-bisphosphate, the kcat/S0.5 for ATP was near ~600-fold higher that other nucleotides, whereas in the absence of activator was only ~3-fold higher. We propose that the allosteric regulation of certain enzymes is an evolutionary mechanism of adaptation for the selection of specific substrates.
Collapse
Affiliation(s)
- Ana C Ebrecht
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States.,Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICETSanta Fe, Argentina
| | - Ligin Solamen
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICETSanta Fe, Argentina
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University ChicagoChicago, IL, United States
| |
Collapse
|
7
|
Comino N, Cifuente JO, Marina A, Orrantia A, Eguskiza A, Guerin ME. Mechanistic insights into the allosteric regulation of bacterial ADP-glucose pyrophosphorylases. J Biol Chem 2017; 292:6255-6268. [PMID: 28223362 DOI: 10.1074/jbc.m116.773408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Indexed: 11/06/2022] Open
Abstract
ADP-glucose pyrophosphorylase (AGPase) controls bacterial glycogen and plant starch biosynthetic pathways, the most common carbon storage polysaccharides in nature. AGPase activity is allosterically regulated by a series of metabolites in the energetic flux within the cell. Very recently, we reported the first crystal structures of the paradigmatic AGPase from Escherichia coli (EcAGPase) in complex with its preferred physiological negative and positive allosteric regulators, adenosine 5'-monophosphate (AMP) and fructose 1,6-bisphosphate (FBP), respectively. However, understanding the molecular mechanism by which AMP and FBP allosterically modulates EcAGPase enzymatic activity still remains enigmatic. Here we found that single point mutations of key residues in the AMP-binding site decrease its inhibitory effect but also clearly abolish the overall AMP-mediated stabilization effect in wild-type EcAGPase. Single point mutations of key residues for FBP binding did not revert the AMP-mediated stabilization. Strikingly, an EcAGPase-R130A mutant displayed a dramatic increase in activity when compared with wild-type EcAGPase, and this increase correlated with a significant increment of glycogen content in vivo The crystal structure of EcAGPase-R130A revealed unprecedented conformational changes in structural elements involved in the allosteric signal transmission. Altogether, we propose a model in which the positive and negative energy reporters regulate AGPase catalytic activity via intra- and interprotomer cross-talk, with a "sensory motif" and two loops, RL1 and RL2, flanking the ATP-binding site playing a significant role. The information reported herein provides exciting possibilities for industrial/biotechnological applications.
Collapse
Affiliation(s)
- Natalia Comino
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Javier O Cifuente
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alberto Marina
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Ane Orrantia
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Ander Eguskiza
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Marcelo E Guerin
- From the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain, .,Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, 48940 Bizkaia, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Leioa, 48940 Bizkaia, Spain, and.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| |
Collapse
|
8
|
Cifuente JO, Comino N, Madariaga-Marcos J, López-Fernández S, García-Alija M, Agirre J, Albesa-Jové D, Guerin ME. Structural Basis of Glycogen Biosynthesis Regulation in Bacteria. Structure 2016; 24:1613-22. [PMID: 27545622 DOI: 10.1016/j.str.2016.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022]
Abstract
ADP-glucose pyrophosphorylase (AGPase) catalyzes the rate-limiting step of bacterial glycogen and plant starch biosynthesis, the most common carbon storage polysaccharides in nature. A major challenge is to understand how AGPase activity is regulated by metabolites in the energetic flux within the cell. Here we report crystal structures of the homotetrameric AGPase from Escherichia coli in complex with its physiological positive and negative allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP, and sucrose in the active site. FBP and AMP bind to partially overlapping sites located in a deep cleft between glycosyltransferase A-like and left-handed β helix domains of neighboring protomers, accounting for the fact that sensitivity to inhibition by AMP is modulated by the concentration of the activator FBP. We propose a model in which the energy reporters regulate EcAGPase catalytic activity by intra-protomer interactions and inter-protomer crosstalk, with a sensory motif and two regulatory loops playing a prominent role.
Collapse
Affiliation(s)
- Javier O Cifuente
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain
| | - Julene Madariaga-Marcos
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain
| | - Sonia López-Fernández
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain
| | - Mikel García-Alija
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD, UK
| | - David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
| |
Collapse
|
9
|
Cereijo AE, Asencion Diez MD, Dávila Costa JS, Alvarez HM, Iglesias AA. On the Kinetic and Allosteric Regulatory Properties of the ADP-Glucose Pyrophosphorylase from Rhodococcus jostii: An Approach to Evaluate Glycogen Metabolism in Oleaginous Bacteria. Front Microbiol 2016; 7:830. [PMID: 27313571 PMCID: PMC4890535 DOI: 10.3389/fmicb.2016.00830] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/17/2016] [Indexed: 01/29/2023] Open
Abstract
Rhodococcus spp. are oleaginous bacteria that accumulate glycogen during exponential growth. Despite the importance of these microorganisms in biotechnology, little is known about the regulation of carbon and energy storage, mainly the relationship between glycogen and triacylglycerols metabolisms. Herein, we report the molecular cloning and heterologous expression of the gene coding for ADP-glucose pyrophosphorylase (EC 2.7.7.27) of Rhodococcus jostii, strain RHA1. The recombinant enzyme was purified to electrophoretic homogeneity to accurately characterize its oligomeric, kinetic, and regulatory properties. The R. jostii ADP-glucose pyrophosphorylase is a homotetramer of 190 kDa exhibiting low basal activity to catalyze synthesis of ADP-glucose, which is markedly influenced by different allosteric effectors. Glucose-6P, mannose-6P, fructose-6P, ribose-5P, and phosphoenolpyruvate were major activators; whereas, NADPH and 6P-gluconate behaved as main inhibitors of the enzyme. The combination of glucose-6P and other effectors (activators or inhibitors) showed a cross-talk effect suggesting that the different metabolites could orchestrate a fine regulation of ADP-glucose pyrophosphorylase in R. jostii. The enzyme exhibited some degree of affinity toward ATP, GTP, CTP, and other sugar-1P substrates. Remarkably, the use of glucosamine-1P was sensitive to allosteric activation. The relevance of the fine regulation of R. jostii ADP-glucose pyrophosphorylase is further analyzed in the framework of proteomic studies already determined for the bacterium. Results support a critical role for glycogen as a temporal reserve that provides a pool of carbon able of be re-routed to produce long-term storage of lipids under certain conditions.
Collapse
Affiliation(s)
- Antonela E Cereijo
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral, CONICET, Centro Científico Tecnológico, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral Santa Fe, Argentina
| | - Matías D Asencion Diez
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral, CONICET, Centro Científico Tecnológico, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral Santa Fe, Argentina
| | - José S Dávila Costa
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales Universidad Nacional de la Patagonia San Juan Bosco Comodoro Rivadavia, Argentina
| | - Héctor M Alvarez
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales Universidad Nacional de la Patagonia San Juan Bosco Comodoro Rivadavia, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral, CONICET, Centro Científico Tecnológico, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral Santa Fe, Argentina
| |
Collapse
|
10
|
Abstract
Glycogen accumulation occurs in Escherichia coli and Salmonella enterica serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited because of the lack of a growth nutrient, e.g., a nitrogen source. This review describes the enzymatic reactions involved in glycogen synthesis and the allosteric regulation of the first enzyme, ADP-glucose pyrophosphorylase. The properties of the enzymes involved in glycogen synthesis, ADP-glucose pyrophosphorylase, glycogen synthase, and branching enzyme are also characterized. The data describing the genetic regulation of the glycogen synthesis are also presented. An alternate pathway for glycogen synthesis in mycobacteria is also described.
Collapse
|
11
|
Ebrecht AC, Orlof AM, Sasoni N, Figueroa CM, Iglesias AA, Ballicora MA. On the Ancestral UDP-Glucose Pyrophosphorylase Activity of GalF from Escherichia coli. Front Microbiol 2015; 6:1253. [PMID: 26617591 PMCID: PMC4643126 DOI: 10.3389/fmicb.2015.01253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/28/2015] [Indexed: 11/13/2022] Open
Abstract
In bacteria, UDP-glucose is a central intermediate in carbohydrate metabolism. The enzyme responsible for its synthesis is encoded by the galU gene and its deletion generates cells unable to ferment galactose. In some bacteria, there is a second gene, galF, encoding for a protein with high sequence identity to GalU. However, the role of GalF has been contradictory regarding its catalytic capability and not well understood. In this work we show that GalF derives from a catalytic (UDP-glucose pyrophosphorylase) ancestor, but its activity is very low compared to GalU. We demonstrated that GalF has some residual UDP-glucose pyrophosphorylase activity by in vitro and in vivo experiments in which the phenotype of a galU (-) strain was reverted by the over-expression of GalF and its mutant. To demonstrate its evolutionary path of "enzyme inactivation" we enhanced the catalysis by mutagenesis and showed the importance of the quaternary structure. This study provides important information to understand the structural and functional evolutionary origin of the protein GalF in enteric bacteria.
Collapse
Affiliation(s)
- Ana C Ebrecht
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Científico Tecnológico CONICET Santa Fe Santa Fe, Argentina ; Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago IL, USA
| | - Agnieszka M Orlof
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago IL, USA
| | - Natalia Sasoni
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Científico Tecnológico CONICET Santa Fe Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Científico Tecnológico CONICET Santa Fe Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas - Centro Científico Tecnológico CONICET Santa Fe Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago IL, USA
| |
Collapse
|
12
|
Structural comparison, substrate specificity, and inhibitor binding of AGPase small subunit from monocot and dicot: present insight and future potential. BIOMED RESEARCH INTERNATIONAL 2014; 2014:583606. [PMID: 25276800 PMCID: PMC4167649 DOI: 10.1155/2014/583606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Accepted: 04/21/2014] [Indexed: 11/18/2022]
Abstract
ADP-glucose pyrophosphorylase (AGPase) is the first rate limiting enzyme of starch biosynthesis pathway and has been exploited as the target for greater starch yield in several plants. The structure-function analysis and substrate binding specificity of AGPase have provided enormous potential for understanding the role of specific amino acid or motifs responsible for allosteric regulation and catalytic mechanisms, which facilitate the engineering of AGPases. We report the three-dimensional structure, substrate, and inhibitor binding specificity of AGPase small subunit from different monocot and dicot crop plants. Both monocot and dicot subunits were found to exploit similar interactions with the substrate and inhibitor molecule as in the case of their closest homologue potato tuber AGPase small subunit. Comparative sequence and structural analysis followed by molecular docking and electrostatic surface potential analysis reveal that rearrangements of secondary structure elements, substrate, and inhibitor binding residues are strongly conserved and follow common folding pattern and orientation within monocot and dicot displaying a similar mode of allosteric regulation and catalytic mechanism. The results from this study along with site-directed mutagenesis complemented by molecular dynamics simulation will shed more light on increasing the starch content of crop plants to ensure the food security worldwide.
Collapse
|
13
|
Asención Diez MD, Aleanzi MC, Iglesias AA, Ballicora MA. A novel dual allosteric activation mechanism of Escherichia coli ADP-glucose pyrophosphorylase: the role of pyruvate. PLoS One 2014; 9:e103888. [PMID: 25102309 PMCID: PMC4125136 DOI: 10.1371/journal.pone.0103888] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 07/07/2014] [Indexed: 11/23/2022] Open
Abstract
Fructose-1,6-bisphosphate activates ADP-glucose pyrophosphorylase and the synthesis of glycogen in Escherichia coli. Here, we show that although pyruvate is a weak activator by itself, it synergically enhances the fructose-1,6-bisphosphate activation. They increase the enzyme affinity for each other, and the combination increases Vmax, substrate apparent affinity, and decreases AMP inhibition. Our results indicate that there are two distinct interacting allosteric sites for activation. Hence, pyruvate modulates E. coli glycogen metabolism by orchestrating a functional network of allosteric regulators. We postulate that this novel dual activator mechanism increases the evolvability of ADP-glucose pyrophosphorylase and its related metabolic control.
Collapse
Affiliation(s)
- Matías D. Asención Diez
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois, United States of America
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Ciudad Universitaria, Santa Fe, Argentina
| | - Mabel C. Aleanzi
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Ciudad Universitaria, Santa Fe, Argentina
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Ciudad Universitaria, Santa Fe, Argentina
| | - Miguel A. Ballicora
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
14
|
Asención Diez MD, Demonte AM, Guerrero SA, Ballicora MA, Iglesias AA. The ADP-glucose pyrophosphorylase from Streptococcus mutans provides evidence for the regulation of polysaccharide biosynthesis in Firmicutes. Mol Microbiol 2013; 90:1011-27. [PMID: 24112771 DOI: 10.1111/mmi.12413] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2013] [Indexed: 11/28/2022]
Abstract
Streptococcus mutans is the leading cause of dental caries worldwide. The bacterium accumulates a glycogen-like internal polysaccharide, which mainly contributes to its carionegic capacity. S.mutans has two genes (glgC and glgD) respectively encoding putative ADP-glucose pyrophosphorylases (ADP-Glc PPase), a key enzyme for glycogen synthesis in most bacteria. Herein, we report the molecular cloning and recombinant expression of both genes (separately or together) followed by the characterization of the respective enzymes. When expressed individually GlgC had ADP-Glc PPase activity, whereas GlgD was inactive. Interestingly, the coexpressed GlgC/GlgD protein was one order of magnitude more active than GlgC alone. Kinetic characterization of GlgC and GlgC/GlgD pointed out remarkable differences between them. Fructose-1,6-bis-phosphate activated GlgC by twofold, but had no effect on GlgC/GlgD. Conversely, phospho-enol-pyruvate and inorganic salts inhibited GlgC/GlgD without affecting GlgC. However, in the presence of fructose-1,6-bis-phosphate GlgC acquired a GlgC/GlgD-like behaviour, becoming sensitive to the stated inhibitors. Results indicate that S. mutans ADP-Glc PPase is an allosteric regulatory enzyme exhibiting sensitivity to modulation by key intermediates of carbohydrates metabolism in the cell. The particular regulatory properties of the S.mutans enzyme agree with phylogenetic analysis, where GlgC and GlgD proteins found in other Firmicutes arrange in distinctive clusters.
Collapse
Affiliation(s)
- Matías D Asención Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje 'El Pozo' CC 242, S3000ZAA, Santa Fe, Argentina; Department of Chemistry and Biochemistry, Loyola University Chicago, 1068, W Sheridan Rd., Chicago, IL, 60660, USA
| | | | | | | | | |
Collapse
|
15
|
Figueroa CM, Kuhn ML, Falaschetti CA, Solamen L, Olsen KW, Ballicora MA, Iglesias AA. Unraveling the activation mechanism of the potato tuber ADP-glucose pyrophosphorylase. PLoS One 2013; 8:e66824. [PMID: 23826149 PMCID: PMC3691274 DOI: 10.1371/journal.pone.0066824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/10/2013] [Indexed: 11/20/2022] Open
Abstract
ADP-glucose pyrophosphorylase regulates the synthesis of glycogen in bacteria and of starch in plants. The enzyme from plants is mainly activated by 3-phosphoglycerate and is a heterotetramer comprising two small and two large subunits. Here, we found that two highly conserved residues are critical for triggering the activation of the potato tuber ADP-glucose pyrophosphorylase, as shown by site-directed mutagenesis. Mutations in the small subunit, which bears the catalytic function in this potato tuber form, had a more dramatic effect on disrupting the allosteric activation than those introduced in the large subunit, which is mainly modulatory. Our results strongly agree with a model where the modified residues are located in loops responsible for triggering the allosteric activation signal for this enzyme, and the sensitivity to this activation correlates with the dynamics of these loops. In addition, previous biochemical data indicates that the triggering mechanism is widespread in the enzyme family, even though the activator and the quaternary structure are not conserved.
Collapse
Affiliation(s)
- Carlos M. Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral and Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Santa Fe, Argentina
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Christine A. Falaschetti
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Ligin Solamen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Alberto A. Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral and Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Santa Fe, Argentina
- * E-mail:
| |
Collapse
|
16
|
Understanding the allosteric trigger for the fructose-1,6-bisphosphate regulation of the ADP-glucose pyrophosphorylase from Escherichia coli. Biochimie 2011; 93:1816-23. [DOI: 10.1016/j.biochi.2011.06.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 06/24/2011] [Indexed: 11/19/2022]
|
17
|
Corbi J, Debieu M, Rousselet A, Montalent P, Le Guilloux M, Manicacci D, Tenaillon MI. Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:705-22. [PMID: 21060986 DOI: 10.1007/s00122-010-1480-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 10/22/2010] [Indexed: 05/08/2023]
Abstract
Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU(leaf) through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU(end), LSU(emb)) or breeding (LSU(leaf)), two exhibit patterns consistent with diversifying (SSU(leaf)) and balancing selection (SSU(emb)) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.
Collapse
Affiliation(s)
- J Corbi
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
| | | | | | | | | | | | | |
Collapse
|
18
|
Yang J, Xu H, Zhang Y, Bai L, Deng Z, Mahmud T. Nucleotidylation of unsaturated carbasugar in validamycin biosynthesis. Org Biomol Chem 2010; 9:438-49. [PMID: 20981366 DOI: 10.1039/c0ob00475h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Validamycin A is a member of microbial-derived C(7)N-aminocyclitol family of natural products that is widely used as crop protectant and the precursor of the antidiabetic drug voglibose. Its biosynthetic gene clusters have been identified in several Streptomyces hygroscopicus strains, and a number of genes within the clusters have been functionally analyzed. Of these genes, valB, which encodes a sugar nucleotidyltransferase, was found through inactivation study to be essential for validamycin biosynthesis, but its role was unclear. To characterize the role of ValB in validamycin biosynthesis, four carbasugar phosphate analogues were synthesized and tested as substrate for ValB. The results showed that ValB efficiently catalyzes the conversion of valienol 1-phosphate to its nucleotidyl diphosphate derivatives, whereas other unsaturated carbasugar phosphates were found to be not the preferred substrate. ValB requires Mg(2+), Mn(2+), or Co(2+) for its optimal activity and uses the purine-based nucleotidyltriphosphates (ATP and GTP) more efficiently than the pyrimidine-based NTPs (CTP, dTTP, and UTP) as nucleotidyl donor. ValB represents the first member of unsaturated carbasugar nucleotidyltransferases involved in natural products biosynthesis. Its characterization not only expands our understanding of aminocyclitol-derived natural products biosynthesis, but may also facilitate the development of new tools for chemoenzymatic synthesis of carbohydrate mimetics.
Collapse
Affiliation(s)
- Jongtae Yang
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | | | | | | | | | | |
Collapse
|
19
|
Zhou T, Li Q, Zhang J, Yang H, Zhao G. Identification of four low molecular and water-soluble proteins from grape (Vitis vinifera L.) seeds. Int J Food Sci Technol 2010. [DOI: 10.1111/j.1365-2621.2010.02264.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
20
|
Kuhn ML, Falaschetti CA, Ballicora MA. Ostreococcus tauri ADP-glucose pyrophosphorylase reveals alternative paths for the evolution of subunit roles. J Biol Chem 2009; 284:34092-102. [PMID: 19737928 DOI: 10.1074/jbc.m109.037614] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ADP-glucose pyrophosphorylase controls starch synthesis in plants and is an interesting case to study the evolution and differentiation of roles in heteromeric enzymes. It includes two homologous subunits, small (S) and large (L), that originated from a common photosynthetic eukaryotic ancestor. In present day organisms, these subunits became complementary after loss of certain roles in a process described as subfunctionalization. For instance, the potato tuber enzyme has a noncatalytic L subunit that complements an S subunit with suboptimal allosteric properties. To understand the evolution of catalysis and regulation in this family, we artificially synthesized both subunit genes from the unicellular alga Ostreococcus tauri. This is among the most ancient species in the green lineage that diverged from the ancestor of all green plants and algae. After heterologous gene expression, we purified and characterized the proteins. The O. tauri enzyme was not redox-regulated, suggesting that redox regulation of ADP-glucose pyrophosphorylases appeared later in evolution. The S subunit had a typical low apparent affinity for the activator 3-phosphoglycerate, but it was atypically defective in the catalytic efficiency (V(max)/K(m)) for the substrate Glc-1-P. The L subunit needed the S subunit for soluble expression. In the presence of a mutated S subunit (to avoid interference), the L subunit had a high apparent affinity for 3-phosphoglycerate and substrates suggesting a leading role in catalysis. Therefore, the subfunctionalization of the O. tauri enzyme was different from previously described cases. To the best of our knowledge, this is the first biochemical description of a system with alternative subfunctionalization paths.
Collapse
Affiliation(s)
- Misty L Kuhn
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
| | | | | |
Collapse
|
21
|
Georgelis N, Shaw JR, Hannah LC. Phylogenetic analysis of ADP-glucose pyrophosphorylase subunits reveals a role of subunit interfaces in the allosteric properties of the enzyme. PLANT PHYSIOLOGY 2009; 151:67-77. [PMID: 19625637 PMCID: PMC2735977 DOI: 10.1104/pp.109.138933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
ADP-glucose pyrophosphorylase (AGPase) catalyzes a rate-limiting step in glycogen and starch synthesis in bacteria and plants, respectively. Plant AGPase consists of two large and two small subunits that were derived by gene duplication. AGPase large subunits have functionally diverged, leading to different kinetic and allosteric properties. Amino acid changes that could account for these differences were identified previously by evolutionary analysis. In this study, these large subunit residues were mapped onto a modeled structure of the maize (Zea mays) endosperm enzyme. Surprisingly, of 29 amino acids identified via evolutionary considerations, 17 were located at subunit interfaces. Fourteen of the 29 amino acids were mutagenized in the maize endosperm large subunit (SHRUNKEN-2 [SH2]), and resulting variants were expressed in Escherichia coli with the maize endosperm small subunit (BT2). Comparisons of the amount of glycogen produced in E. coli, and the kinetic and allosteric properties of the variants with wild-type SH2/BT2, indicate that 11 variants differ from the wild type in enzyme properties or in vivo glycogen level. More interestingly, six of nine residues located at subunit interfaces exhibit altered allosteric properties. These results indicate that the interfaces between the large and small subunits are important for the allosteric properties of AGPase, and changes at these interfaces contribute to AGPase functional specialization. Our results also demonstrate that evolutionary analysis can greatly facilitate enzyme structure-function analyses.
Collapse
Affiliation(s)
- Nikolaos Georgelis
- Program in Plant Molecular and Cellular Biology and Horticultural Sciences, University of Florida, Gainesville, Florida 32610-0245, USA
| | | | | |
Collapse
|
22
|
Abstract
The accumulation of glycogen occurs in Escherichia coli and Salmonella enterica serovar Typhimurium as well as in many other bacteria. Glycogen will be formed when there is an excess of carbon under conditions in which growth is limited due to the lack of a growth nutrient, e.g., a nitrogen source. The structural genes of the glycogen biosynthetic enzymes of E. coli and S. serovar Typhimurium have been cloned previously, and that has provided insights in the genetic regulation of glycogen synthesis. An important aspect of the regulation of glycogen synthesis is the allosteric regulation of the ADP-Glc PPase. The current information, views, and concepts regarding the regulation of enzyme activity and the expression of the glycogen biosynthetic enzymes are presented in this review. The recent information on the amino acid residues critical for the activity of both glycogen synthase and branching enzyme (BE) is also presented. The residue involved in catalysis in the E. coli ADP-Glc PPase was determined by comparing a predicted structure of the enzyme with the known three-dimensional structures of sugar-nucleotide PPase domains. The molecular cloning of the E. coliglg K-12 structural genes greatly facilitated the subsequent study of the genetic regulation of bacterial glycogen biosynthesis. Results from studies of glycogen excess E. coli B mutants SG3 and AC70R1, which exhibit enhanced levels of the enzymes in the glycogen synthesis pathway (i.e., they are derepressed mutants), suggested that glycogen synthesis is under negative genetic regulation.
Collapse
|
23
|
Cupp-Vickery JR, Igarashi RY, Perez M, Poland M, Meyer CR. Structural analysis of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens. Biochemistry 2008; 47:4439-51. [PMID: 18355040 DOI: 10.1021/bi701933q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ADP-glucose pyrophosphorylase (ADPGlc PPase) catalyzes the conversion of glucose 1-phosphate and ATP to ADP-glucose and pyrophosphate. As a key step in glucan synthesis, the ADPGlc PPases are highly regulated by allosteric activators and inhibitors in accord with the carbon metabolism pathways of the organism. Crystals of Agrobacterium tumefaciens ADPGlc PPase were obtained using lithium sulfate as a precipitant. A complete anomalous selenomethionyl derivative X-ray diffraction data set was collected with unit cell dimensions a = 85.38 A, b = 93.79 A, and c = 140.29 A (alpha = beta = gamma = 90 degrees ) and space group I 222. The A. tumefaciens ADPGlc PPase model was refined to 2.1 A with an R factor = 22% and R free = 26.6%. The model consists of two domains: an N-terminal alphabetaalpha sandwich and a C-terminal parallel beta-helix. ATP and glucose 1-phosphate were successfully modeled in the proposed active site, and site-directed mutagenesis of conserved glycines in this region (G20, G21, and G23) resulted in substantial loss of activity. The interface between the N- and the C-terminal domains harbors a strong sulfate-binding site, and kinetic studies revealed that sulfate is a competitive inhibitor for the allosteric activator fructose 6-phosphate. These results suggest that the interface between the N- and C-terminal domains binds the allosteric regulator, and fructose 6-phosphate was modeled into this region. The A. tumefaciens ADPGlc PPase/fructose 6-phosphate structural model along with sequence alignment analysis was used to design mutagenesis experiments to expand the activator specificity to include fructose 1,6-bisphosphate. The H379R and H379K enzymes were found to be activated by fructose 1,6-bisphosphate.
Collapse
Affiliation(s)
- Jill R Cupp-Vickery
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
| | | | | | | | | |
Collapse
|
24
|
Tyagi NK, Kumar A, Goyal P, Pandey D, Siess W, Kinne RKH. d-Glucose-Recognition and Phlorizin-Binding Sites in Human Sodium/d-Glucose Cotransporter 1 (hSGLT1): A Tryptophan Scanning Study. Biochemistry 2007; 46:13616-28. [DOI: 10.1021/bi701193x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Navneet K. Tyagi
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| | - Azad Kumar
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| | - Pankaj Goyal
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| | - Dharmendra Pandey
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| | - Wolfgang Siess
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| | - Rolf K. H. Kinne
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany, and the Institute for Prevention of Cardiovascular Disease, Ludwig Maximilian University, Pettenkoferstrasse 9, Munich, 80336, Germany
| |
Collapse
|