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Aranda-Caraballo J, Saenz RA, López-Zavala AA, Velazquez-Cruz B, Espinosa-Barrera L, Cárdenas-Conejo Y, Zárate-Romero A, Linares-Vergara O, Osuna-Castro JA, Bonales-Alatorre E, Centeno-Leija S, Serrano-Posada H. Binding Specificity of a Novel Cyclo/Maltodextrin-Binding Protein and Its Role in the Cyclodextrin ABC Importer System from Thermoanaerobacterales. Molecules 2023; 28:6080. [PMID: 37630332 PMCID: PMC10458862 DOI: 10.3390/molecules28166080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Extracellular synthesis of functional cyclodextrins (CDs) as intermediates of starch assimilation is a convenient microbial adaptation to sequester substrates, increase the half-life of the carbon source, carry bioactive compounds, and alleviate chemical toxicity through the formation of CD-guest complexes. Bacteria encoding the four steps of the carbohydrate metabolism pathway via cyclodextrins (CM-CD) actively internalize CDs across the microbial membrane via a putative type I ATP-dependent ABC sugar importer system, MdxEFG-(X/MsmX). While the first step of the CM-CD pathway encompasses extracellular starch-active cyclomaltodextrin glucanotransferases (CGTases) to synthesize linear dextrins and CDs, it is the ABC importer system in the second step that is the critical factor in determining which molecules from the CGTase activity will be internalized by the cell. Here, structure-function relationship studies of the cyclo⁄maltodextrin-binding protein MdxE of the MdxEFG-MsmX importer system from Thermoanaerobacter mathranii subsp. mathranii A3 are presented. Calorimetric and fluorescence studies of recombinant MdxE using linear dextrins and CDs showed that although MdxE binds linear dextrins and CDs with high affinity, the open-to-closed conformational change is solely observed after α- and β-CD binding, suggesting that the CM-CD pathway from Thermoanaerobacterales is exclusive for cellular internalization of these molecules. Structural analysis of MdxE coupled with docking simulations showed an overall architecture typically found in sugar-binding proteins (SBPs) that comprised two N- and C-domains linked by three small hinge regions, including the conserved aromatic triad Tyr193/Trp269/Trp378 in the C-domain and Phe87 in the N-domain involved in CD recognition and stabilization. Structural bioinformatic analysis of the entire MdxFG-MsmX importer system provided further insights into the binding, internalization, and delivery mechanisms of CDs. Hence, while the MdxE-CD complex couples to the permease subunits MdxFG to deliver the CD into the transmembrane channel, the dimerization of the cytoplasmatic promiscuous ATPase MsmX triggers active transport into the cytoplasm. This research provides the first results on a novel thermofunctional SBP and its role in the internalization of CDs in extremely thermophilic bacteria.
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Affiliation(s)
- Jorge Aranda-Caraballo
- Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico; (J.A.-C.); (B.V.-C.); (L.E.-B.); (O.L.-V.)
| | - Roberto A. Saenz
- Facultad de Ciencias, Universidad de Colima, Bernal Díaz del Castillo 340, Colima 28045, Mexico;
| | - Alonso A. López-Zavala
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo 83000, Mexico;
| | - Beatriz Velazquez-Cruz
- Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico; (J.A.-C.); (B.V.-C.); (L.E.-B.); (O.L.-V.)
| | - Laura Espinosa-Barrera
- Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico; (J.A.-C.); (B.V.-C.); (L.E.-B.); (O.L.-V.)
| | - Yair Cárdenas-Conejo
- Consejo Nacional de Humanidades, Ciencias y Tecnologías, Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico;
| | - Andrés Zárate-Romero
- Consejo Nacional de Humanidades, Ciencias y Tecnologías, Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 CarreteraTijuana-Ensenada, Ensenada 22860, Mexico;
| | - Oscar Linares-Vergara
- Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico; (J.A.-C.); (B.V.-C.); (L.E.-B.); (O.L.-V.)
| | - Juan A. Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Autopista Colima-Manzanillo, Tecomán 28100, Mexico;
| | - Edgar Bonales-Alatorre
- Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Avenida 25 de julio 965, Colonia Villa de San Sebastián, Colima 28045, Mexico;
| | - Sara Centeno-Leija
- Consejo Nacional de Humanidades, Ciencias y Tecnologías, Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico;
| | - Hugo Serrano-Posada
- Consejo Nacional de Humanidades, Ciencias y Tecnologías, Laboratorio de Biología Sintética, Estructural y Molecular, Universidad de Colima, Carretera Los Limones-Loma de Juárez, Colima 28627, Mexico;
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TranNgoc K, Pham N, Lee C, Jang SH. Cloning, Expression, and Characterization of a Psychrophilic Glucose 6-Phosphate Dehydrogenase from Sphingomonas sp. PAMC 26621. Int J Mol Sci 2019; 20:E1362. [PMID: 30889888 PMCID: PMC6471386 DOI: 10.3390/ijms20061362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022] Open
Abstract
Glucose 6-phosphate dehydrogenase (G6PD) (EC 1.1.1.363) is a crucial regulatory enzyme in the oxidative pentose phosphate pathway that provides reductive potential in the form of NADPH, as well as carbon skeletons for the synthesis of macromolecules. In this study, we report the cloning, expression, and characterization of G6PD (SpG6PD1) from a lichen-associated psychrophilic bacterium Sphingomonas sp. PAMC 26621. SpG6PD1 was expressed in Escherichia coli as a soluble protein, having optimum activity at pH 7.5⁻8.5 and 30 °C for NADP⁺ and 20 °C for NAD⁺. SpG6PD1 utilized both NADP⁺ and NAD⁺, with the preferential utilization of NADP⁺. A high Km value for glucose 6-phosphate and low activation enthalpy (ΔH‡) compared with the values of mesophilic counterparts indicate the psychrophilic nature of SpG6PD1. Despite the secondary structure of SpG6PD1 being maintained between 4⁻40 °C, its activity and tertiary structure were better preserved between 4⁻20 °C. The results of this study indicate that the SpG6PD1 that has a flexible structure is most suited to a psychrophilic bacterium that is adapted to a permanently cold habitat.
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Affiliation(s)
- Kiet TranNgoc
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - Nhung Pham
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, Korea.
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Bian M, Li S, Wei H, Huang S, Zhou F, Zhu Y, Zhu G. Heteroexpression and biochemical characterization of a glucose-6-phosphate dehydrogenase from oleaginous yeast Yarrowia lipolytica. Protein Expr Purif 2018; 148:1-8. [PMID: 29580928 DOI: 10.1016/j.pep.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 01/08/2023]
Abstract
Yarrowia lipolytica, a nonpathogenic, nonconventional, aerobic and dimorphic yeast, is considered an oleaginous microorganism due to its excellent ability to accumulate large amounts of lipids. Glucose-6-phosphate dehydrogenase (G6PD) is one of two key enzymes involved in the lipid accumulation in this fungi, which catalyzes the oxidative dehydrogenation of glucose-6-phosphate to 6-phosphoglucono-δ-lactone with the reduction of NADP+ to NADPH. In this study, the full-length gene of G6PD from Y. lipolytica (YlG6PD) was cloned without intron and heterogeneously expressed in E. coli. Then, YlG6PD was purified and biochemically characterized in details. Kinetic analysis showed that YlG6PD was completely dependent on NADP+ and its apparent Km for NADP+ was 33.3 μM. The optimal pH was 8.5 and the maximum activity was around 47.5 °C. Heat-inactivation profiles revealed that it remained 50% of maximal activity after incubation at 48 °C for 20 min YlG6PD activity was competitively inhibited by NADPH with a Ki value of 56.04 μM. Most of the metal ions have no effect on activity, but Zn2+ was a strong inhibitor. Furthermore, the determinants in the coenzyme specificity of YlG6PD were investigated. Kinetic analysis showed that the single mutant R52D completely lost the ability to utilize NADP+ as its coenzyme, suggesting that Arg-52 plays a decisive role in NADP+ binding in YlG6PD. The identification of Y. lipolytica G6PD may provide useful scientific information for metabolic engineering of this yeast as a model for bio-oil production.
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Affiliation(s)
- Mingjie Bian
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Shan Li
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Huanhuan Wei
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Shiping Huang
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Feng Zhou
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China
| | - Youming Zhu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Stomatological Hospital, Anhui Medical University, No.81 Mei Shan Road, Hefei 230032, Anhui, China.
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology and the Research Center of Life Omics and Health, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, Anhui, China.
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Huang R, Chen H, Zhou W, Ma C, Zhang YHP. Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro. Appl Microbiol Biotechnol 2018; 102:3203-3215. [DOI: 10.1007/s00253-018-8798-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 10/17/2022]
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