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Patel HP, Martinez‐Ramirez G, Dobrzynski E, Iglesias AA, Liu D, Ballicora MA. A critical inter-subunit interaction for the transmission of the allosteric signal in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2023; 32:e4747. [PMID: 37551561 PMCID: PMC10461462 DOI: 10.1002/pro.4747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
ADP-glucose pyrophosphorylase is a key regulatory enzyme involved in starch and glycogen synthesis in plants and bacteria, respectively. It has been hypothesized that inter-subunit communications are important for the allosteric effect in this enzyme. However, no specific interactions have been identified as part of the regulatory signal. The enzyme from Agrobacterium tumefaciens is a homotetramer allosterically regulated by fructose 6-phosphate and pyruvate. Three pairs of distinct subunit-subunit interfaces are present. Here we focus on an interface that features two symmetrical interactions between Arg11 and Asp141 from one subunit with residues Asp141 and Arg11 of the neighbor subunit, respectively. Previously, scanning mutagenesis showed that a mutation at the Arg11 position disrupted the activation of the enzyme. Considering the distance of these residues from the allosteric and catalytic sites, we hypothesized that the interaction between Arg11 and Asp141 is critical for allosteric signaling rather than effector binding. To prove our hypothesis, we mutated those two sites (D141A, D141E, D141N, D141R, R11D, and R11K) and performed kinetic and binding analysis. Mutations that altered the charge affected the regulation the most. To prove that the interaction per se (rather than the presence of specific residues) is critical, we partially rescued the R11D protein by introducing a second mutation (R11D/D141R). This could not restore the activator effect on kcat , but it did rescue the effect on substrate affinity. Our results indicate the critical functional role of Arg11 and Asp141 to relay the allosteric signal in this subunit interface.
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Affiliation(s)
- Hiral P. Patel
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Emily Dobrzynski
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | | | - Dali Liu
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
| | - Miguel A. Ballicora
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
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2
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Variot C, Capule D, Arolli X, Baumgartner J, Reidl C, Houseman C, Ballicora MA, Becker DP, Kuhn ML. Mapping roles of active site residues in the acceptor site of the PA3944 Gcn5-related N-acetyltransferase (GNAT) enzyme. Protein Sci 2023:e4725. [PMID: 37418656 PMCID: PMC10364583 DOI: 10.1002/pro.4725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
An increased understanding of how the acceptor site in Gcn5-related N-acetyltransferase (GNAT) enzymes recognizes various substrates provides important clues for GNAT functional annotation and their use as chemical tools. In this study, we explored how the PA3944 enzyme from Pseudomonas aeruginosa recognizes three different acceptor substrates, including aspartame, NANMO, and polymyxin B, and identified acceptor residues that are critical for substrate specificity. To achieve this, we performed a series of molecular docking simulations and tested methods to identify acceptor substrate binding modes that are catalytically relevant. We found that traditional selection of best docking poses by lowest S scores did not reveal acceptor substrate binding modes that were generally close enough to the donor for productive acetylation. Instead, sorting poses based on distance between the acceptor amine nitrogen atom and donor carbonyl carbon atom placed these acceptor substrates near residues that contribute to substrate specificity and catalysis. To assess whether these residues are indeed contributors to substrate specificity, we mutated seven amino acid residues to alanine and determined their kinetic parameters. We identified several residues that improved the apparent affinity and catalytic efficiency of PA3944, especially for NANMO and/or polymyxin B. Additionally, one mutant (R106A) exhibited substrate inhibition toward NANMO, and we propose scenarios for the cause of this inhibition based on additional substrate docking studies with R106A. Ultimately, we propose that this residue is a key gatekeeper between the acceptor and donor sites by restricting and orienting the acceptor substrate within the acceptor site. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cillian Variot
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Daniel Capule
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Xhulio Arolli
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Jackson Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Cory Reidl
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Charles Houseman
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
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3
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Alghamdi MA, Hussien RA, Zheng Y, Patel HP, Asencion Diez MD, A Iglesias A, Liu D, Ballicora MA. Site-directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase. Protein Sci 2022; 31:e4376. [PMID: 35762722 PMCID: PMC9234290 DOI: 10.1002/pro.4376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/27/2022] [Accepted: 06/05/2022] [Indexed: 11/10/2022]
Abstract
The allosteric regulation of ADP-glucose pyrophosphorylase is critical for the biosynthesis of glycogen in bacteria and starch in plants. The enzyme from Agrobacterium tumefaciens is activated by fructose 6-phosphate (Fru6P) and pyruvate (Pyr). The Pyr site has been recently found, but the site where Fru6P binds has remained unknown. We hypothesize that a sulfate ion previously found in the crystal structure reveals a part of the regulatory site mimicking the presence of the phosphoryl moiety of the activator Fru6P. Ser72 interacts with this sulfate ion and, if the hypothesis is correct, Ser72 would affect the interaction with Fru6P and activation of the enzyme. Here, we report structural, binding, and kinetic analysis of Ser72 mutants of the A. tumefaciens ADP-glucose pyrophosphorylase. By X-ray crystallography, we found that when Ser72 was replaced by Asp or Glu side chain carboxylates protruded into the sulfate-binding pocket. They would present a strong steric and electrostatic hindrance to the phosphoryl moiety of Fru6P, while being remote from the Pyr site. In agreement, we found that Fru6P could not activate or bind to S72E or S72D mutants, whereas Pyr was still an effective activator. These mutants also blocked the binding of the inhibitor AMP. This could potentially have biotechnological importance in obtaining enzyme forms insensitive to inhibition. Other mutations in this position (Ala, Cys, and Trp) confirmed the importance of Ser72 in regulation. We propose that the ADP-glucose pyrophosphorylase from A. tumefaciens have two distinct sites for Fru6P and Pyr working in tandem to regulate glycogen biosynthesis.
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Affiliation(s)
- Mashael A Alghamdi
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Rania A Hussien
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Department of Chemistry, Al Baha University, Al Baha, Saudi Arabia
| | - Yuanzhang Zheng
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Hiral P Patel
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Matías D Asencion Diez
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois.,Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Paraje "El Pozo", CCT-Santa Fe, Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), FBCB Paraje "El Pozo", CCT-Santa Fe, Santa Fe, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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5
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Minen RI, Bhayani JA, Hartman MD, Cereijo AE, Zheng Y, Ballicora MA, Iglesias AA, Liu D, Figueroa CM. Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases. Plant Cell Physiol 2022; 63:658-670. [PMID: 35243499 DOI: 10.1093/pcp/pcac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/07/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Sugar alcohols are major photosynthetic products in plant species from the Apiaceae and Plantaginaceae families. Mannose-6-phosphate reductase (Man6PRase) and aldose-6-phosphate reductase (Ald6PRase) are key enzymes for synthesizing mannitol and glucitol in celery (Apium graveolens) and peach (Prunus persica), respectively. In this work, we report the first crystal structures of dimeric plant aldo/keto reductases (AKRs), celery Man6PRase (solved in the presence of mannonic acid and NADP+) and peach Ald6PRase (obtained in the apo form). Both structures displayed the typical TIM barrel folding commonly observed in proteins from the AKR superfamily. Analysis of the Man6PRase holo form showed that residues putatively involved in the catalytic mechanism are located close to the nicotinamide ring of NADP+, where the hydride transfer to the sugar phosphate should take place. Additionally, we found that Lys48 is important for the binding of the sugar phosphate. Interestingly, the Man6PRase K48A mutant had a lower catalytic efficiency with mannose-6-phosphate but a higher catalytic efficiency with mannose than the wild type. Overall, our work sheds light on the structure-function relationships of important enzymes to synthesize sugar alcohols in plants.
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Affiliation(s)
- Romina I Minen
- UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Jaina A Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Matías D Hartman
- UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Antonela E Cereijo
- UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Yuanzhang Zheng
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Alberto A Iglesias
- UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Carlos M Figueroa
- UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina
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6
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Figueroa CM, Asencion Diez MD, Ballicora MA, Iglesias AA. Structure, function, and evolution of plant ADP-glucose pyrophosphorylase. Plant Mol Biol 2022; 108:307-323. [PMID: 35006475 DOI: 10.1007/s11103-021-01235-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/15/2021] [Indexed: 05/25/2023]
Abstract
This review outlines research performed in the last two decades on the structural, kinetic, regulatory and evolutionary aspects of ADP-glucose pyrophosphorylase, the regulatory enzyme for starch biosynthesis. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the pathway of glycogen and starch synthesis in bacteria and plants, respectively. Plant ADP-Glc PPase is a heterotetramer allosterically regulated by metabolites and post-translational modifications. In this review, we focus on the three-dimensional structure of the plant enzyme, the amino acids that bind the regulatory molecules, and the regions involved in transmitting the allosteric signal to the catalytic site. We provide a model for the evolution of the small and large subunits, which produce heterotetramers with distinct catalytic and regulatory properties. Additionally, we review the various post-translational modifications observed in ADP-Glc PPases from different species and tissues. Finally, we discuss the subcellular localization of the enzyme found in grain endosperm from grasses, such as maize and rice. Overall, this work brings together research performed in the last two decades to better understand the multiple mechanisms involved in the regulation of ADP-Glc PPase. The rational modification of this enzyme could improve the yield and resilience of economically important crops, which is particularly important in the current scenario of climate change and food shortage.
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Affiliation(s)
- Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA.
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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7
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Bhayani JA, Ballicora MA. Determination of dissociation constants of protein ligands by thermal shift assay. Biochem Biophys Res Commun 2021; 590:1-6. [PMID: 34959191 DOI: 10.1016/j.bbrc.2021.12.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
The thermal shift assay (TSA) is a powerful tool used to detect molecular interactions between proteins and ligands. Using temperature as a physical denaturant and an extrinsic fluorescent dye, the TSA tracks protein unfolding. This method precisely determines the midpoint of the unfolding transition (Tm), which can shift upon the addition of a ligand. Though experimental protocols have been well developed, the thermal shift assay data traditionally yielded qualitative results. Quantitative methods for Kd determination relied either on empirical and inaccurate usage of Tm or on isothermal approaches, which do not take full advantage of the melting point precision provided by the TSA. We present a new analysis method based on a model that relies on the equilibrium system between the native and molten globule state of the protein using the van't Hoff equation. We propose the Kd can be determined by plotting Tm values versus the logarithm of ligand concentrations and fitting the data to an equation we derived. After testing this procedure with the monomeric maltose-binding protein and an allosterically regulated homotetrameric enzyme (ADP-glucose pyrophosphorylase), we observed that binding results correlated very well with previously established parameters. We demonstrate how this method could potentially offer a broad applicability to a wide range of protein classes and the ability to detect both active and allosteric site binding compounds.
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Affiliation(s)
- Jaina A Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, IL, 60660, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, IL, 60660, USA.
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Ferretti MV, Hussien RA, Ballicora MA, Iglesias AA, Figueroa CM, Asencion Diez MD. The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources. Biochimie 2021; 192:30-37. [PMID: 34560201 DOI: 10.1016/j.biochi.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022]
Abstract
Until recently, the cyanobacterial phylum only included oxygenic photosynthesizer members. The discovery of Melainabacteria as a group of supposed non-photosynthetic cyanobacteria asked to revisit such scenario. From metagenomic data, we were able to identify sequences encoding putative ADP-glucose pyrophosphorylases (ADP-GlcPPase) from free-living and intestinal Melainabacteria. The respective genes were de novo synthesized and over-expressed in Escherichia coli. The purified recombinant proteins from both Melainabacteria species were active as ADP-GlcPPases, exhibiting Vmax values of 2.3 (free-living) and 7.1 U/mg (intestinal). The enzymes showed similar S0.5 values (∼0.3 mM) for ATP, while the one from the intestinal source exhibited a 6-fold higher affinity toward glucose-1P. Both recombinant ADP-GlcPPases were sensitive to glucose-6P activation (A0.5 ∼0.3 mM) and Pi and ADP inhibition (I0.5 between 0.2 and 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. As far as we know, this is the first biochemical characterization of an active enzyme from Melainabacteria. This work contributes to a better understanding of the evolution of allosteric regulation in the ADP-GlcPPase family, which is critical for synthesizing the main reserve polysaccharide in prokaryotes (glycogen) and plants (starch). In addition, our results offer further information to discussions regarding the phylogenetic position of Melainabacteria.
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Affiliation(s)
- María V Ferretti
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Rania A Hussien
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA; Department of Chemistry, Al Baha University, Al Baha, Saudi Arabia
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina.
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Baumgartner JT, Habeeb Mohammad TS, Czub MP, Majorek KA, Arolli X, Variot C, Anonick M, Minor W, Ballicora MA, Becker DP, Kuhn ML. Gcn5-Related N-Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too. Front Mol Biosci 2021; 8:646046. [PMID: 33912589 PMCID: PMC8072286 DOI: 10.3389/fmolb.2021.646046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead of a general acid/base mechanism. To simplify this enzyme's kinetic characterization, we synthesized a polymyxin B substrate analog and performed molecular docking experiments. We performed site-directed mutagenesis of key active site residues (S148 and E102) and determined the structure of the E102A mutant. We found that the serine residue is essential for catalysis toward the synthetic substrate analog and polymyxin B, but the glutamate residue is more likely important for substrate recognition or stabilization. Our results challenge the current paradigm of GNAT mechanisms and show that this common enzyme scaffold utilizes different active site residues to accomplish a diversity of catalytic reactions.
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Affiliation(s)
- Jackson T. Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | | | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Xhulio Arolli
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Cillian Variot
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Madison Anonick
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, United States
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, United States
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
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Cereijo AE, Kuhn ML, Hernández MA, Ballicora MA, Iglesias AA, Alvarez HM, Asencion Diez MD. Study of duplicated galU genes in Rhodococcus jostii and a putative new metabolic node for glucosamine-1P in rhodococci. Biochim Biophys Acta Gen Subj 2020; 1865:129727. [PMID: 32890704 DOI: 10.1016/j.bbagen.2020.129727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/11/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGOUND Studying enzymes that determine glucose-1P fate in carbohydrate metabolism is important to better understand microorganisms as biotechnological tools. One example ripe for discovery is the UDP-glucose pyrophosphorylase enzyme from Rhodococcus spp. In the R. jostii genome, this gene is duplicated, whereas R. fascians contains only one copy. METHODS We report the molecular cloning of galU genes from R. jostii and R. fascians to produce recombinant proteins RjoGalU1, RjoGalU2, and RfaGalU. Substrate saturation curves were conducted, kinetic parameters were obtained and the catalytic efficiency (kcat/Km) was used to analyze enzyme promiscuity. We also investigated the response of R. jostii GlmU pyrophosphorylase activity with different sugar-1Ps, which may compete for substrates with RjoGalU2. RESULTS All enzymes were active as pyrophosphorylases and exhibited substrate promiscuity toward sugar-1Ps. Remarkably, RjoGalU2 exhibited one order of magnitude higher activity with glucosamine-1P than glucose-1P, the canonical substrate. Glucosamine-1P activity was also significant in RfaGalU. The efficient use of the phospho-amino-sugar suggests the feasibility of the reaction to occur in vivo. Also, RjoGalU2 and RfaGalU represent enzymatic tools for the production of (amino)glucosyl precursors for the putative synthesis of novel molecules. CONCLUSIONS Results support the hypothesis that partitioning of glucosamine-1P includes an uncharacterized metabolic node in Rhodococcus spp., which could be important for producing diverse alternatives for carbohydrate metabolism in biotechnological applications. GENERAL SIGNIFICANCE Results presented here provide a model to study evolutionary enzyme promiscuity, which could be used as a tool to expand an organism's metabolic repertoire by incorporating non-canonical substrates into novel metabolic pathways.
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Affiliation(s)
- A E Cereijo
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA, United States
| | - M A Hernández
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - M A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL 60660, United States
| | - A A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - H M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
| | - M D Asencion Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina.
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11
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Asencion Diez MD, Figueroa CM, Esper MC, Mascarenhas R, Aleanzi MC, Liu D, Ballicora MA, Iglesias AA. On the simultaneous activation of Agrobacterium tumefaciens ADP-glucose pyrophosphorylase by pyruvate and fructose 6-phosphate. Biochimie 2020; 171-172:23-30. [PMID: 32014504 DOI: 10.1016/j.biochi.2020.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/28/2020] [Indexed: 11/19/2022]
Abstract
Bacterial ADP-glucose pyrophosphorylases are allosterically regulated by metabolites that are key intermediates of central pathways in the respective microorganism. Pyruvate (Pyr) and fructose 6-phosphate (Fru6P) activate the enzyme from Agrobacterium tumefaciens by increasing Vmax about 10- and 20-fold, respectively. Here, we studied the combined effect of both metabolites on the enzyme activation. Our results support a model in which there is a synergistic binding of these two activators to two distinct sites and that each activator leads the enzyme to distinct active forms with different properties. In presence of both activators, Pyr had a catalytically dominant effect over Fru6P determining the active conformational state. By mutagenesis we obtained enzyme variants still sensitive to Pyr activation, but in which the allosteric signal by Fru6P was disrupted. This indicated that the activation mechanism for each effector was not the same. The ability for this enzyme to have more than one allosteric activator site, active forms, and allosteric signaling mechanisms is critical to expand the evolvability of its regulation. These synergistic interactions between allosteric activators may represent a feature in other allosteric enzymes.
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Affiliation(s)
- Matías D Asencion Diez
- Instituto de Agrobiotecnología Del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 Km 0, 3000, Santa Fe, Argentina; Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL, 60660, USA
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología Del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 Km 0, 3000, Santa Fe, Argentina
| | - María C Esper
- Instituto de Agrobiotecnología Del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 Km 0, 3000, Santa Fe, Argentina
| | - Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL, 60660, USA
| | - Mabel C Aleanzi
- Instituto de Agrobiotecnología Del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 Km 0, 3000, Santa Fe, Argentina
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL, 60660, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL, 60660, USA.
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología Del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 Km 0, 3000, Santa Fe, Argentina.
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12
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Ferrero DML, Piattoni CV, Asencion Diez MD, Rojas BE, Hartman MD, Ballicora MA, Iglesias AA. Phosphorylation of ADP-Glucose Pyrophosphorylase During Wheat Seeds Development. Front Plant Sci 2020; 11:1058. [PMID: 32754189 PMCID: PMC7366821 DOI: 10.3389/fpls.2020.01058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/26/2020] [Indexed: 05/23/2023]
Abstract
Starch is the dominant reserve polysaccharide accumulated in the seed of grasses (like wheat). It is the most common carbohydrate in the human diet and a material applied to the bioplastics and biofuels industry. Hence, the complete understanding of starch metabolism is critical to design rational strategies to improve its allocation in plant reserve tissues. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the key (regulated) step in the synthetic starch pathway. The enzyme comprises a small (S) and a large (L) subunit forming an S2L2 heterotetramer, which is allosterically regulated by orthophosphate, fructose-6P, and 3P-glycerate. ADP-Glc PPase was found in a phosphorylated state in extracts from wheat seeds. The amount of the phosphorylated protein increased along with the development of the seed and correlated with relative increases of the enzyme activity and starch content. Conversely, this post-translational modification was absent in seeds from Ricinus communis. In vitro, the recombinant ADP-Glc PPase from wheat endosperm was phosphorylated by wheat seed extracts as well as by recombinant Ca2+-dependent plant protein kinases. Further analysis showed that the preferential phosphorylation takes place on the L subunit. Results suggest that the ADP-Glc PPase is a phosphorylation target in seeds from grasses but not from oleaginous plants. Accompanying seed maturation and starch accumulation, a combined regulation of ADP-Glc PPase by metabolites and phosphorylation may provide an enzyme with stable levels of activity. Such concerted modulation would drive carbon skeletons to the synthesis of starch for its long-term storage, which later support seed germination.
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Affiliation(s)
- Danisa M. L. Ferrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
| | - Claudia V. Piattoni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
| | - Matías D. Asencion Diez
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
| | - Bruno E. Rojas
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
| | - Matías D. Hartman
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, Argentina
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13
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Filippova EV, Kuhn ML, Osipiuk J, Kiryukhina O, Joachimiak A, Ballicora MA, Anderson WF. Corrigendum to "A Novel Polyamine Allosteric Site of SpeG from Vibrio Cholerae is Revealed by its Dodecameric Structure" [J. Mol. Biol. 427 (6 Part B) (2015) 1316-1334]. J Mol Biol 2019; 431:4527. [PMID: 31653437 DOI: 10.1016/j.jmb.2019.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60626, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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14
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Bhayani JA, Hill BL, Sharma A, Iglesias AA, Olsen KW, Ballicora MA. Mapping of a Regulatory Site of the Escherichia coli ADP-Glucose Pyrophosphorylase. Front Mol Biosci 2019; 6:89. [PMID: 31608288 PMCID: PMC6773804 DOI: 10.3389/fmolb.2019.00089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/06/2019] [Indexed: 11/13/2022] Open
Abstract
The enzyme ADP-glucose pyrophosphorylase (ADP-Glc PPase) controls the biosynthesis of glycogen in bacteria and starch in plants. It is regulated by various activators in different organisms according to their metabolic characteristics. In Escherichia coli, the major allosteric activator is fructose 1,6-bisphosphate (FBP). Other potent activator analogs include 1,6-hexanediol bisphosphate (HBP) and pyridoxal 5'-phosphate (PLP). Recently, a crystal structure with FBP bound was reported (PDB ID: 5L6S). However, it is possible that the FBP site found is not directly responsible for the activation of the enzyme. We hypothesized FBP activates by binding one of its phosphate groups to another site ("P1") in which a sulfate molecule was observed. In the E. coli enzyme, Arg40, Arg52, and Arg386 are part of this "P1" pocket and tightly complex this sulfate, which is also present in the crystal structures of ADP-Glc PPases from Agrobacterium tumefaciens and Solanum tuberosum. To test this hypothesis, we modeled alternative binding conformations of FBP, HBP, and PLP into "P1." In addition, we performed a scanning mutagenesis of Arg residues near potential phosphate binding sites ("P1," "P2," "P3"). We found that Arg40 and Arg52 are essential for FBP and PLP binding and activation. In addition, mutation of Arg386 to Ala decreased the apparent affinity for the activators more than 35-fold. We propose that the activator binds at this "P1" pocket, as well as "P2." Arg40 and Arg52 are highly conserved residues and they may be a common feature to complex the phosphate moiety of different sugar phosphate activators in the ADP-Glc PPase family.
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Affiliation(s)
- Jaina A. Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Benjamin L. Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Anisha Sharma
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET), CCT CONICET, Santa Fe, Argentina
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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16
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Figueroa CM, Kuhn ML, Hill BL, Iglesias AA, Ballicora MA. Resurrecting the Regulatory Properties of the Ostreococcus tauri ADP-Glucose Pyrophosphorylase Large Subunit. Front Plant Sci 2018; 9:1564. [PMID: 30425723 PMCID: PMC6218581 DOI: 10.3389/fpls.2018.01564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/05/2018] [Indexed: 05/09/2023]
Abstract
ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step for the synthesis of glycogen in cyanobacteria and starch in green algae and plants. The enzyme from cyanobacteria is homotetrameric (α4), while that from green algae and plants is heterotetrameric (α2β2). These ADP-Glc PPases are allosterically regulated by 3-phosphoglycerate (3PGA, activator) and inorganic orthophosphate (Pi, inhibitor). Previous studies on the cyanobacterial and plant enzymes showed that 3PGA binds to two highly conserved Lys residues located in the C-terminal domain. We observed that both Lys residues are present in the small (α) subunit of the Ostreococcus tauri enzyme; however, one of these Lys residues is replaced by Arg in the large (β) subunit. In this work, we obtained the K443R and R466K mutants of the O. tauri small and large subunits, respectively, and co-expressed them together or with their corresponding wild type counterparts. Our results show that restoring the Lys residue in the large subunit enhanced 3PGA affinity, whereas introduction of an Arg residue in the small subunit reduced 3PGA affinity of the heterotetramers. Inhibition kinetics also showed that heterotetramers containing the K443R small subunit mutant were less sensitive to Pi inhibition, but only minor changes were observed for those containing the R466K large subunit mutant, suggesting a leading role of the small subunit for Pi inhibition of the heterotetramer. We conclude that, during evolution, the ADP-Glc PPase large subunit from green algae and plants acquired mutations in its regulatory site. The rationale for this could have been to accommodate sensitivity to particular metabolic needs of the cell or tissue.
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Affiliation(s)
- Carlos M. Figueroa
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Benjamin L. Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A. Iglesias
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
- *Correspondence: Alberto A. Iglesias, Miguel A. Ballicora,
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
- *Correspondence: Alberto A. Iglesias, Miguel A. Ballicora,
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17
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Ferrero DML, Asencion Diez MD, Kuhn ML, Falaschetti CA, Piattoni CV, Iglesias AA, Ballicora MA. On the Roles of Wheat Endosperm ADP-Glucose Pyrophosphorylase Subunits. Front Plant Sci 2018; 9:1498. [PMID: 30459778 PMCID: PMC6232684 DOI: 10.3389/fpls.2018.01498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/25/2018] [Indexed: 05/09/2023]
Abstract
The ADP-glucose pyrophosphorylase from wheat endosperm controls starch synthesis in seeds and has unique regulatory properties compared to others from this family. It comprises two types of subunits, but despite its importance little is known about their roles. Here, we synthesized de novo the wheat endosperm ADP-glucose pyrophosphorylase small (S) and large (L) subunit genes, heterologously expressed them in Escherichia coli, and kinetically characterized the recombinant proteins. To understand their distinct roles, we co-expressed them with well characterized subunits from the potato tuber enzyme to obtain hybrids with one S subunit from one source and an L subunit from the other. After kinetic analyses of these hybrids, we concluded that the unusual insensitivity to activation of the wheat endosperm enzyme is caused by a pre-activation of the L subunit. In addition, the heat stability and sensitivity to phosphate are given by the S subunit.
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Affiliation(s)
- Danisa M. L. Ferrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET – UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Matias D. Asencion Diez
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET – UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | | | - Claudia V. Piattoni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET – UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Alberto A. Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET – UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- *Correspondence: Alberto A. Iglesias, Miguel A. Ballicora,
| | - Miguel A. Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
- *Correspondence: Alberto A. Iglesias, Miguel A. Ballicora,
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Hill BL, Figueroa CM, Asencion Diez MD, Lunn JE, Iglesias AA, Ballicora MA. On the stability of nucleoside diphosphate glucose metabolites: implications for studies of plant carbohydrate metabolism. J Exp Bot 2017; 68:3331-3337. [PMID: 28859372 PMCID: PMC5853320 DOI: 10.1093/jxb/erx190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/25/2017] [Indexed: 05/25/2023]
Abstract
Nucleoside diphosphate sugars (NDP-sugars) are the substrates for biosynthesis of oligo- and polysaccharides, such as starch and cellulose, and are also required for biosynthesis of nucleotides, ascorbic acid, several cofactors, glycoproteins and many secondary metabolites. A controversial study that questions the generally accepted pathway of ADP-glucose and starch synthesis in plants is based, in part, on claims that NDP-sugars are unstable at alkaline pH in the presence of Mg2+ and that this instability can lead to unreliable results from in vitro assays of enzyme activities. If substantiated, this claim would have far-reaching implications for many published studies that report on the activities of NDP-sugar metabolizing enzymes. To resolve this controversy, we investigated the stability of UDP- and ADP-glucose using biophysical, namely nuclear magnetic resonance (NMR), and highly specific enzymatic methods. Results obtained with both techniques indicate that NDP-sugars are not as unstable as previously suggested. Moreover, their calculated in vitro half-lives are significantly higher than estimates of their in planta turnover times. This indicates that the physico-chemical stability of NDP-sugars has little impact on their concentrations in vivo and that NDP-sugar levels are determined primarily by the relative rates of enzymatic synthesis and consumption. Our results refute one of the main arguments for the controversial pathway of starch synthesis from imported ADP-glucose produced by sucrose synthase in the cytosol.
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Affiliation(s)
- Benjamin L Hill
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, IL, USA
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Matías D Asencion Diez
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam-Golm, Germany
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, IL, USA
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20
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Patel HP, Dobrzynski E, Liu D, Ballicora MA. Role of the inter‐subunit surface interaction in the regulation of the ADP‐glucose pyrophosphorylase from
Agrobacterium tumefaciens. FASEB J 2017. [DOI: 10.1096/fasebj.31.1_supplement.765.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hiralben P. Patel
- Department of Chemistry and BiochemistryLoyola University of ChicagoChicagoIL
| | - Emily Dobrzynski
- Department of Chemistry and BiochemistryLoyola University of ChicagoChicagoIL
| | - Dali Liu
- Department of Chemistry and BiochemistryLoyola University of ChicagoChicagoIL
| | - Miguel A. Ballicora
- Department of Chemistry and BiochemistryLoyola University of ChicagoChicagoIL
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Hedin N, Barchiesi J, Gomez-Casati DF, Iglesias AA, Ballicora MA, Busi MV. Identification and characterization of a novel starch branching enzyme from the picoalgae Ostreococcus tauri. Arch Biochem Biophys 2017; 618:52-61. [DOI: 10.1016/j.abb.2017.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 01/26/2023]
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Barchiesi J, Hedin N, Iglesias AA, Gomez-Casati DF, Ballicora MA, Busi MV. Identification of a novel starch synthase III from the picoalgae Ostreococcus tauri. Biochimie 2016; 133:37-44. [PMID: 28003125 DOI: 10.1016/j.biochi.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 12/08/2016] [Indexed: 01/07/2023]
Abstract
Hydrosoluble glycogen is the major energy storage compound in bacteria, archaea, fungi, and animal cells. In contrast, photosynthetic eukaryotes have evolved to build a highly organized semicrystalline granule of starch. Several enzymes are involved in polysaccharide synthesis, among which glycogen or starch synthase catalyze the elongation of the α-1,4-glucan chain. Ostreococcus tauri, accumulates a single starch granule and contains three starch synthase III (SSIII) isoforms, known as OsttaSSIII-A, OsttaSSIII-B and OsttaSSIII-C. After amino acids sequence analysis we found that OsttaSSIII-C lacks starch-binding domains, being 49% identical to the catalytic region of the SSIII from Arabidopsis thaliana and 32% identical to the entire Escherichia coli glycogen synthase. The recombinant, highly purified OsttaSSIII-C exhibited preference to use as a primer branched glycans (such as rabbit muscle glycogen and amylopectin), rather than amylose. Also, the enzyme displayed a high affinity toward ADP-glucose. We found a marked conservation of the amino acids located in the catalytic site, and specifically determined the role of residues R270, K275 and E352 by site-directed mutagenesis. Results show that these residues are important for OsttaSSIII-C activity, suggesting a strong similarity between the active site of the O. tauri SSIII-C isoform and other bacterial glycogen synthases.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Nicolás Hedin
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (UNL-CONICET) & FBCB, Santa Fe, 3000, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 405 Flanner Hall, 1068 W Sheridan Road, Chicago, IL 60660, USA
| | - María V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Barchiesi J, Hedin N, Gomez-Casati DF, Ballicora MA, Busi MV. Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms. BMC Res Notes 2015; 8:613. [PMID: 26510916 PMCID: PMC4625611 DOI: 10.1186/s13104-015-1598-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Starch-binding domains are key modules present in several enzymes involved in polysaccharide metabolism. These non-catalytic modules have already been described as essential for starch-binding and the catalytic activity of starch synthase III from the higher plant Arabidopsis thaliana. In Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, there are three SSIII isoforms, known as Ostta SSIII-A, SSIII-B and SSIII-C. RESULTS In this work, using in silico and in vitro characterization techniques, we have demonstrated that Ostta SSIII-A, SSIII-B and SSIII-C contain two, three and no starch-binding domains, respectively. Additionally, our phylogenetic analysis has indicated that OsttaSSIII-B, presenting three N-terminal SBDs, is the isoform more closely related to higher plant SSIII. Furthermore, the sequence alignment and homology modeling data gathered showed that both the main 3-D structures of all the modeled domains obtained and the main amino acid residues implicated in starch binding are well conserved in O. tauri SSIII starch-binding domains. In addition, adsorption assays showed that OsttaSSIII-A D2 and SSIII-B D2 domains are the two that make the greatest contribution to amylose and amylopectin binding, while OsttaSSIII-B D1 is also important for starch binding. CONCLUSIONS The results presented here suggest that differences between OsttaSSIII-A and SSIII-B SBDs in the number of and binding of amino acid residues may produce differential affinities for each isoform to polysaccharides. Increasing the knowledge about SBDs may lead to their employment in biomedical and industrial applications.
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Affiliation(s)
- Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Nicolás Hedin
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 405 Flanner Hall, 1068 W Sheridan Road, Chicago, IL, 60660, USA.
| | - María V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Filippova EV, Kuhn ML, Osipiuk J, Kiryukhina O, Joachimiak A, Ballicora MA, Anderson WF. A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure. J Mol Biol 2015; 427:1316-1334. [PMID: 25623305 DOI: 10.1016/j.jmb.2015.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 01/20/2023]
Abstract
Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60626, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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' CC 242, S3000ZAA, Santa Fe, Argentina; Department of Chemistry and Biochemistry, Loyola University Chicago, 1068, W Sheridan Rd., Chicago, IL, 60660, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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:
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Ballicora MA, Diez MA, Iglesias AA. Pyruvate Revisited as a Synergistic Secondary Activator of the
Escherichia coli
ADP‐glucose Pyrophosphorylase. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1004.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hill BL, Wong J, Frisby‐zedan J, May B, Ballicora MA. The Importance of a Loop Structure in ATP Apparent Affinity and Allosteric Activation of
Escherichia coli
ADP‐Glucose Pyrophosphorylase. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1004.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin L. Hill
- Dept. of Chemistry and BiochemistryLoyola University ChicagoChicagoIL
| | - Jennifer Wong
- Dept. of Chemistry and BiochemistryLoyola University ChicagoChicagoIL
| | | | - Brian May
- Dept. of Chemistry and BiochemistryLoyola University ChicagoChicagoIL
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Asención Diez MD, Demonte AM, Naleway C, Iglesias AA, Ballicora MA. Monofluorophosphate inhibits the key step of internal polysaccharide biosynthesis in
Streptococcus mutans. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.560.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ana M. Demonte
- Universidad Nacional del Litoral (Argentina)Santa FeArgentina
| | - Conrad Naleway
- Dept. of Chemistry and BiochemistryLoyola University ChicagoChicagoIL
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Kuhn ML, Figueroa CM, Iglesias AA, Ballicora MA. The ancestral activation promiscuity of ADP-glucose pyrophosphorylases from oxygenic photosynthetic organisms. BMC Evol Biol 2013; 13:51. [PMID: 23433303 PMCID: PMC3585822 DOI: 10.1186/1471-2148-13-51] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/13/2013] [Indexed: 11/30/2022] Open
Abstract
Background ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA) and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum) tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP), fructose-6-phosphate, and glucose-6-phosphate. Results The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer), O. tauri, and potato tuber was considerably higher than for other activators. O. tauri and potato tuber enzymes were heterotetramers comprising homologous small and large subunits. Conversely, the O. tauri small subunit (OtaS) homotetramer was more promiscuous because its FBP specificity constant was similar to that for 3-PGA. To explore the role of both OtaS and OtaL (O. tauri large subunit) in determining the specificity of the heterotetramer, we knocked out the catalytic activity of each subunit individually by site-directed mutagenesis. Interestingly, the mutants OtaSD148A/OtaL and OtaS/OtaLD171A had higher specificity constants for 3-PGA than for FBP. Conclusions After gene duplication, OtaS seemed to have lost specificity for 3-PGA compared to FBP. This was physiologically and evolutionarily feasible because co-expression of both subunits restored the specificity for 3-PGA of the resulting heterotetrameric wild type enzyme. This widespread promiscuity seems to be ancestral and intrinsic to the enzyme family. Its presence could constitute an efficient evolutionary mechanism to accommodate the ADP-Glc PPase regulation to different metabolic needs.
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Affiliation(s)
- Misty L Kuhn
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W, Sheridan Rd, Chicago, IL 60660, USA
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Figueroa CM, Asención Diez MD, Kuhn ML, McEwen S, Salerno GL, Iglesias AA, Ballicora MA. The unique nucleotide specificity of the sucrose synthase from Thermosynechococcus elongatus. FEBS Lett 2012. [PMID: 23196182 DOI: 10.1016/j.febslet.2012.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Sucrose synthase catalyzes the reversible conversion of sucrose and UDP into fructose and UDP-glucose. In filamentous cyanobacteria, the sucrose cleavage direction plays a key physiological function in carbon metabolism, nitrogen fixation, and stress tolerance. In unicellular strains, the function of sucrose synthase has not been elucidated. We report a detailed biochemical characterization of sucrose synthase from Thermosynechococcus elongatus after the gene was artificially synthesized for optimal expression in Escherichia coli. The homogeneous recombinant sucrose synthase was highly specific for ADP as substrate, constituting the first one with this unique characteristic, and strongly suggesting an interaction between sucrose and glycogen metabolism.
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Affiliation(s)
- Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas (UNL), Ciudad Universitaria, S3000ZAA Santa Fe, Argentina
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Kuhn ML, Figueroa CM, Aleanzi M, Olsen KW, Iglesias AA, Ballicora MA. Bi-national and interdisciplinary course in enzyme engineering. Biochem Mol Biol Educ 2010; 38:370-379. [PMID: 21567865 DOI: 10.1002/bmb.20438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Higher education institutions and scientific funding agencies are emphasizing international projects that involve the integration and synergy between research groups, particularly if different disciplines are involved. Students with an education that reflects these trends will have more tools to succeed in the future, but it is challenging to provide this type of learning experience. Here we present the organization of a bi-national course with the goals to teach students protein structure/function relationships, which give them actual research experience in both computational and experimental laboratories, and engage them in an international networking experience. Two collaborative learning courses were organized at Loyola University Chicago (USA) and Universidad Nacional del Litoral (Argentina) for graduate and advanced undergraduate students. Multiple instructors at different stages in their careers gave lectures during the course and were able to interact with students on a one-on-one basis. Nearly every student from both institutions thoroughly enjoyed this approach, and they learned more about protein structure and gained important tools for their own research. We believe that this type of course design is applicable and transferable to other institutions and areas of science. We found that the combination of international networking and incorporation of actual research projects ignited the enthusiasm of students and instructors. Due to the success of these courses, we planned to incorporate them as regular series in our curriculum.
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Affiliation(s)
- Misty L Kuhn
- Department of Chemistry, Loyola University Chicago, 6525 N. Sheridan Road, Chicago, Illinois 60626, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Misty L Kuhn
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
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Ziegler AJ, Florián J, Ballicora MA, Herlinger AW. Alkaline phosphatase inhibition by vanadyl-β-diketone complexes: electron density effects. J Enzyme Inhib Med Chem 2008; 24:22-8. [DOI: 10.1080/14756360701841426] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Amanda J. Ziegler
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
| | - Jan Florián
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
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Ventriglia T, Kuhn ML, Ruiz MT, Ribeiro-Pedro M, Valverde F, Ballicora MA, Preiss J, Romero JM. Two Arabidopsis ADP-glucose pyrophosphorylase large subunits (APL1 and APL2) are catalytic. Plant Physiol 2008; 148:65-76. [PMID: 18614708 PMCID: PMC2528121 DOI: 10.1104/pp.108.122846] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 06/30/2008] [Indexed: 05/17/2023]
Abstract
ADP-glucose (Glc) pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in starch biosynthesis. Higher plant ADP-Glc PPase is a heterotetramer (alpha(2)beta(2)) consisting of two small and two large subunits. There is increasing evidence that suggests that catalytic and regulatory properties of the enzyme from higher plants result from the synergy of both types of subunits. In Arabidopsis (Arabidopsis thaliana), two genes encode small subunits (APS1 and APS2) and four large subunits (APL1-APL4). Here, we show that in Arabidopsis, APL1 and APL2, besides their regulatory role, have catalytic activity. Heterotetramers formed by combinations of a noncatalytic APS1 and the four large subunits showed that APL1 and APL2 exhibited ADP-Glc PPase activity with distinctive sensitivities to the allosteric activator (3-phosphoglycerate). Mutation of the Glc-1-P binding site of Arabidopsis and potato (Solanum tuberosum) isoforms confirmed these observations. To determine the relevance of these activities in planta, a T-DNA mutant of APS1 (aps1) was characterized. aps1 is starchless, lacks ADP-Glc PPase activity, APS1 mRNA, and APS1 protein, and is late flowering in long days. Transgenic lines of the aps1 mutant, expressing an inactivated form of APS1, recovered the wild-type phenotype, indicating that APL1 and APL2 have catalytic activity and may contribute to ADP-Glc synthesis in planta.
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Affiliation(s)
- Tiziana Ventriglia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla-CSIC, 41092-Sevilla, Spain
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Kuhn ML, Falaschetti CA, Chaparro‐Krueger C, Ballicora MA. Synthesis of the
Ostreococcus tauri
ADP‐glucose pyrophosphorylase genes and characterization of their expressed subunits. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.841.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Misty L Kuhn
- Chemistry DepartmentLoyola University ChicagoChicagoIL
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Ballicora MA, Erben ED, Yazaki T, Bertolo AL, Demonte AM, Schmidt JR, Aleanzi M, Bejar CM, Figueroa CM, Fusari CM, Iglesias AA, Preiss J. Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis. J Bacteriol 2007; 189:5325-33. [PMID: 17496097 PMCID: PMC1951854 DOI: 10.1128/jb.00481-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 04/30/2007] [Indexed: 11/20/2022] Open
Abstract
ADP-glucose pyrophosphorylase (ADP-Glc PPase) is the enzyme responsible for the regulation of bacterial glycogen synthesis. To perform a structure-function relationship study of the Escherichia coli ADP-Glc PPase enzyme, we studied the effects of pentapeptide insertions at different positions in the enzyme and analyzed the results with a homology model. We randomly inserted 15 bp in a plasmid with the ADP-Glc PPase gene. We obtained 140 modified plasmids with single insertions of which 21 were in the coding region of the enzyme. Fourteen of them generated insertions of five amino acids, whereas the other seven created a stop codon and produced truncations. Correlation of ADP-Glc PPase activity to these modifications validated the enzyme model. Six of the insertions and one truncation produced enzymes with sufficient activity for the E. coli cells to synthesize glycogen and stain in the presence of iodine vapor. These were in regions away from the substrate site, whereas the mutants that did not stain had alterations in critical areas of the protein. The enzyme with a pentapeptide insertion between Leu(102) and Pro(103) was catalytically competent but insensitive to activation. We postulate this region as critical for the allosteric regulation of the enzyme, participating in the communication between the catalytic and regulatory domains.
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Ventriglia T, Ballicora MA, Crevillén P, Preiss J, Romero JM. Regulatory Properties of Potato–Arabidopsis Hybrid ADP-Glucose Pyrophosphorylase. ACTA ACUST UNITED AC 2007; 48:875-80. [PMID: 17452341 DOI: 10.1093/pcp/pcm047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In higher plants, ADP-glucose pyrophosphorylase (ADPGlc-PPase) is a heterotetrameric enzyme comprised of two small and two large subunits. Potato-Arabidopsis hybrid ADPGlc-PPases were generated and their regulatory properties analyzed. We show that ADPGlc-PPase subunits from two different species can interact, producing active enzymes with new regulatory properties. Depending on the subunit combinations, hybrid heterotetramers showed responses to allosteric effectors [3-phosphoglycerate (3-PGA) and Pi] in the micromolar or millimolar range. While hybrid potato small subunit (PSS) and the Arabidopsis large subunit APL1 showed an extremely sensitive response to 3-PGA and Pi, hybrid PSS/Arabidopsis APL2 was very insensitive to them. Intermediate responses were determined for other subunit combinations.
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Affiliation(s)
- Tiziana Ventriglia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla-CSIC, c/Americo Vespucio No. 49, 41092-Sevilla, Spain
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Kuhn ML, Ballicora MA. Phylogenetic analysis of starch synthetic enzymes. FASEB J 2007. [DOI: 10.1096/fasebj.21.6.lb38-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Misty Lee Kuhn
- Dept. of ChemistryLoyola University Chicago1068 W. Sheridan Rd.ChicagoIL60626
| | - Miguel A. Ballicora
- Dept. of ChemistryLoyola University Chicago1068 W. Sheridan Rd.ChicagoIL60626
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Yep A, Ballicora MA, Preiss J. The ADP-glucose binding site of the Escherichia coli glycogen synthase. Arch Biochem Biophys 2006; 453:188-96. [PMID: 16919233 DOI: 10.1016/j.abb.2006.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Revised: 07/01/2006] [Accepted: 07/06/2006] [Indexed: 10/24/2022]
Abstract
Bacterial glycogen/starch synthases are retaining GT-B glycosyltransferases that transfer glucosyl units from ADP-Glc to the non-reducing end of glycogen or starch. We modeled the Escherichia coli glycogen synthase based on the coordinates of the inactive form of the Agrobacterium tumefaciens glycogen synthase and the active form of the maltodextrin phosphorylase, a retaining GT-B glycosyltransferase belonging to a different family. In this model, we identified a set of conserved residues surrounding the sugar nucleotide substrate, and we replaced them with different amino acids by means of site-directed mutagenesis. Kinetic analysis of the mutants revealed the involvement of these residues in ADP-Glc binding. Replacement of Asp21, Asn246 or Tyr355 for Ala decreased the apparent affinity for ADP-Glc 18-, 45-, and 31-fold, respectively. Comparison with other crystallized retaining GT-B glycosyltransferases confirmed the striking similarities among this group of enzymes even though they use different substrates.
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Affiliation(s)
- Alejandra Yep
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Iglesias AA, Ballicora MA, Sesma JI, Preiss J. Domain swapping between a cyanobacterial and a plant subunit ADP-glucose pyrophosphorylase. Plant Cell Physiol 2006; 47:523-30. [PMID: 16501256 DOI: 10.1093/pcp/pcj021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the regulatory step in the pathway for synthesis of bacterial glycogen and starch in plants. ADP-Glc PPases from cyanobacteria (homotetramer) and from potato (Solanum tuberosum) tuber (heterotetramer) are activated by 3-phosphoglycerate and inhibited by inorganic orthophosphate. To study the function of two putative domains, chimeric enzymes were constructed. PSSANA contained the N-terminus (292 amino acids) of the potato tuber ADP-Glc PPase small subunit (PSS) and the C-terminus (159 residues) of the Anabaena PCC 7120 enzyme. ANAPSS was the inverse chimera. These constructs were expressed separately or together with the large subunit of the potato tuber ADP-Glc PPase (PLS), to obtain homo- and heterotetrameric chimeric proteins. Characterization of these forms showed that the N-terminus determines stability and regulatory redox-dependent properties. The chimeric forms exhibited intermediate 3-phosphoglycerate activation properties with respect to the wild-type homotetrameric enzymes, indicating that the interaction between the putative N- and C-domains determines the affinity for the activator. Characterization of the chimeric heterotetramers showed the functionality of the large subunit, mainly in modulating regulation of the enzyme by the coordinate action of 3-phosphoglycerate and inorganic orthophosphate.
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Affiliation(s)
- Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral. Paraje El Pozo, CC 242, S3000ZAA, Santa Fe, Argentina
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Bejar CM, Ballicora MA, Iglesias AA, Preiss J. ADPglucose pyrophosphorylase's N-terminus: structural role in allosteric regulation. Biochem Biophys Res Commun 2006; 343:216-21. [PMID: 16530732 DOI: 10.1016/j.bbrc.2006.02.123] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 02/08/2006] [Indexed: 12/01/2022]
Abstract
We studied the functional role of the Escherichia coli ADPglucose pyrophosphorylase's N-terminus in allosteric regulation, and the particular effects caused by its length. Small truncated mutants were designed, and those lacking up to 15-residues were active and highly purified for further kinetic analyses. Ndelta3 and Ndelta7 did not change the kinetic parameters with respect to the wild-type. Ndelta11 and Ndelta15 enzymes were insensitive to allosteric regulation and highly active in the absence of the activator. Co-expression of two polypeptides corresponding to the N- and C-termini generated an enzyme with activation properties lower than those of the wild-type [C.M. Bejar, M.A. Ballicora, D.F. Gómez Casati, A.A. Iglesias, J. Preiss, The ADPglucose pyrophosphorylase from Escherichia coli comprises two tightly bound distinct domains, FEBS Lett. 573 (2004) 99-104]. Here, we characterized a Ndelta15 co-expression mutant, in which the allosteric regulation was restored to wild-type levels. Unusual allosteric effects caused by either an N-terminal truncation or co-expression of individual domains may respond to structural changes favoring an up-regulated or a down-regulated conformation rather than specific activator or inhibitor sites' disruption.
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Affiliation(s)
- C M Bejar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Kuhn M, Ballicora MA. Homology model of starch synthases. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.a904-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Misty Kuhn
- Dept. of ChemistryLoyola University Chicago1068 W Sheridan Rd.ChicagoIL60626
| | - Miguel A. Ballicora
- Dept. of ChemistryLoyola University Chicago1068 W Sheridan Rd.ChicagoIL60626
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Bejar CM, Ballicora MA, Preiss J. Molecular architecture of the glucose 1‐phosphate site of ADP‐glucose pyrophosphorylases. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a475-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Clarisa Maria Bejar
- Dept. of Biochemistry and Molecular BiologyMichigan State University309 BiochemistryEast LansingMI48824
| | - Miguel A. Ballicora
- Dept.of ChemistryLoyola University405 Flanner Hall, 1068 W. Sheridan Rd.ChicagoIL60626
| | - Jack Preiss
- Dept. of Biochemistry and Molecular BiologyMichigan State University309 BiochemistryEast LansingMI48824
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Jin X, Ballicora MA, Preiss J, Geiger JH. Crystal structure of potato tuber ADP-glucose pyrophosphorylase. EMBO J 2005; 24:694-704. [PMID: 15692569 PMCID: PMC549618 DOI: 10.1038/sj.emboj.7600551] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Accepted: 12/20/2004] [Indexed: 11/08/2022] Open
Abstract
ADP-glucose pyrophosphorylase catalyzes the first committed and rate-limiting step in starch biosynthesis in plants and glycogen biosynthesis in bacteria. It is the enzymatic site for regulation of storage polysaccharide accumulation in plants and bacteria, being allosterically activated or inhibited by metabolites of energy flux. We report the first atomic resolution structure of ADP-glucose pyrophosphorylase. Crystals of potato tuber ADP-glucose pyrophosphorylase alpha subunit were grown in high concentrations of sulfate, resulting in the sulfate-bound, allosterically inhibited form of the enzyme. The N-terminal catalytic domain resembles a dinucleotide-binding Rossmann fold and the C-terminal domain adopts a left-handed parallel beta helix that is involved in cooperative allosteric regulation and a unique oligomerization. We also report structures of the enzyme in complex with ATP and ADP-glucose. Communication between the regulator-binding sites and the active site is both subtle and complex and involves several distinct regions of the enzyme including the N-terminus, the glucose-1-phosphate-binding site, and the ATP-binding site. These structures provide insights into the mechanism for catalysis and allosteric regulation of the enzyme.
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Affiliation(s)
- Xiangshu Jin
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Miguel A Ballicora
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jack Preiss
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. Tel.: +1 517 353 3137; Fax: +1 517 353 9334; E-mail:
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA. Tel.: +1 517 355 9715 Ext. 234; Fax: +1 517 353 1793; E-mail:
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Abstract
In the post-genomic era, functional prediction of genes is largely based on sequence similarity searches, but sometimes the homologues bear different roles because of evolutionary adaptations. For instance, the existence of enzyme and non-enzyme homologues poses a difficult case for function prediction and the extent of this phenomenon is just starting to be surveyed. Different evolutionary paths are theoretically possible for the loss or acquisition of enzyme function. Here we studied the ancestral role of a model non-catalytic modulatory subunit. With a rational approach, we "resurrected" enzymatic activity from that subunit to experimentally prove that it derived from a catalytic ancestor. We show that this protein (L subunit ADP-glucose pyrophosphorylase) evolved to have a regulatory role, losing catalytic residues more than 130 million years ago, but preserving, possibly as a by-product, the substrate site architecture. Inactivation of catalytic subunits could be the consequence of a general evolutionary strategy to explore new regulatory roles in hetero-oligomers.
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Affiliation(s)
- Miguel A Ballicora
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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50
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Yep A, Bejar CM, Ballicora MA, Dubay JR, Iglesias AA, Preiss J. An assay for adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase that measures the synthesis of radioactive ADP-glucose with glycogen synthase. Anal Biochem 2004; 324:52-9. [PMID: 14654045 DOI: 10.1016/j.ab.2003.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the conversion of glucose 1-phosphate and adenosine 5'-triphosphate to ADP-glucose and pyrophosphate. We present a radioactive assay of this enzyme with a higher signal/noise ratio. After stopping the reaction that uses [14C]glucose 1-phosphate as a substrate, the ADP-[14C]glucose formed as a product is converted to [14C]glycogen by the addition of glycogen synthase and nonradioactive glycogen as primer. The final product is precipitated and washed, and the radioactivity is measured in a scintillation counter. The [14C]glucose 1-phosphate that did not react is easily eliminated during the washes. We have found that this assay produces much lower blanks than previously described radioactive methods based on binding of ADP-[14C]glucose to O-(diethylaminoethyl)-cellulose paper. In addition, we tested the kinetic parameters for the effectors of the Escherichia coli ADP-Glc PPase and both assays yielded identical results. The presented method is more suitable for Km or S(0.5) determinations of ADP-Glc PPases having high apparent affinity for glucose 1-phosphate. It is possible to use a higher specific radioactivity to increase the sensitivity at lower concentrations of [14C]glucose 1-phosphate without compromising the blanks obtained at higher concentrations.
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Affiliation(s)
- Alejandra Yep
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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