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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.
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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
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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.
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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
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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.
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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
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Hill BL, Wong J, May BM, Huerta FB, Manley TE, Sullivan PRF, Olsen KW, Ballicora MA. Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase. Protein Sci 2015; 24:714-28. [PMID: 25620658 DOI: 10.1002/pro.2644] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 11/09/2022]
Abstract
The synthesis of glycogen in bacteria and starch in plants is allosterically controlled by the production of ADP-glucose by ADP-glucose pyrophosphorylase. Using computational studies, site-directed mutagenesis, and kinetic characterization, we found a critical region for transmitting the allosteric signal in the Escherichia coli ADP-glucose pyrophosphorylase. Molecular dynamics simulations and structural comparisons with other ADP-glucose pyrophosphorylases provided information to hypothesize that a Pro103-Arg115 loop is part of an activation path. It had strongly correlated movements with regions of the enzyme associated with regulation and ATP binding, and a network analysis showed that the optimal network pathways linking ATP and the activator binding Lys39 mainly involved residues of this loop. This hypothesis was biochemically tested by mutagenesis. We found that several alanine mutants of the Pro103-Arg115 loop had altered activation profiles for fructose-1,6-bisphosphate. Mutants P103A, Q106A, R107A, W113A, Y114A, and R115A had the most altered kinetic profiles, primarily characterized by a lack of response to fructose-1,6-bisphosphate. This loop is a distinct insertional element present only in allosterically regulated sugar nucleotide pyrophosphorylases that could have been acquired to build a triggering mechanism to link proto-allosteric and catalytic sites.
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Affiliation(s)
- Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Road, Chicago, Illinois
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The UDP-glucose pyrophosphorylase from Giardia lamblia is redox regulated and exhibits promiscuity to use galactose-1-phosphate. Biochim Biophys Acta Gen Subj 2015; 1850:88-96. [DOI: 10.1016/j.bbagen.2014.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 08/26/2014] [Accepted: 10/06/2014] [Indexed: 12/21/2022]
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Asención Diez MD, Demonte AM, Syson K, Arias DG, Gorelik A, Guerrero SA, Bornemann S, Iglesias AA. Allosteric regulation of the partitioning of glucose-1-phosphate between glycogen and trehalose biosynthesis in Mycobacterium tuberculosis. Biochim Biophys Acta Gen Subj 2014; 1850:13-21. [PMID: 25277548 PMCID: PMC4331664 DOI: 10.1016/j.bbagen.2014.09.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 11/16/2022]
Abstract
Background Mycobacterium tuberculosis is a pathogenic prokaryote adapted to survive in hostile environments. In this organism and other Gram-positive actinobacteria, the metabolic pathways of glycogen and trehalose are interconnected. Results In this work we show the production, purification and characterization of recombinant enzymes involved in the partitioning of glucose-1-phosphate between glycogen and trehalose in M. tuberculosis H37Rv, namely: ADP-glucose pyrophosphorylase, glycogen synthase, UDP-glucose pyrophosphorylase and trehalose-6-phosphate synthase. The substrate specificity, kinetic parameters and allosteric regulation of each enzyme were determined. ADP-glucose pyrophosphorylase was highly specific for ADP-glucose while trehalose-6-phosphate synthase used not only ADP-glucose but also UDP-glucose, albeit to a lesser extent. ADP-glucose pyrophosphorylase was allosterically activated primarily by phosphoenolpyruvate and glucose-6-phosphate, while the activity of trehalose-6-phosphate synthase was increased up to 2-fold by fructose-6-phosphate. None of the other two enzymes tested exhibited allosteric regulation. Conclusions Results give information about how the glucose-1-phosphate/ADP-glucose node is controlled after kinetic and regulatory properties of key enzymes for mycobacteria metabolism. General significance This work increases our understanding of oligo and polysaccharides metabolism in M. tuberculosis and reinforces the importance of the interconnection between glycogen and trehalose biosynthesis in this human pathogen. Nucleotide-glucose synthesis in Mycobacterium tuberculosis was analyzed. The characterization of four enzymes involved in glucose-1P partitioning is reported. Mycobacterial ADP-glucose pyrophosphorylase is allosterically regulated. Trehalose-6P synthase exhibits higher catalytic efficiency for ADP-glucose. Trehalose-6P synthase is activated by fructose-6P.
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Affiliation(s)
- Matías D Asención Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Ana M Demonte
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Karl Syson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Diego G Arias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Andrii Gorelik
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sergio A Guerrero
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Stephen Bornemann
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Paraje El Pozo, S3000ZAA Santa Fe, Argentina.
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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.
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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:
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