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Sun L, Sun B, Zhang Y, Chen K. Kinetic properties of glucose 6-phosphate dehydrogenase and inhibition effects of several metal ions on enzymatic activity in vitro and cells. Sci Rep 2024; 14:5806. [PMID: 38461203 PMCID: PMC10924972 DOI: 10.1038/s41598-024-56503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
Due to the non-degradable and persistent nature of metal ions in the environment, they are released into water bodies, where they accumulate in fish. In order to assess pollution in fish, the enzyme, glucose 6-phosphate dehydrogenase (G6PD), has been employed as a biomarker due to sensitivity to various ions. This study investigates the kinetic properties of the G6PD enzyme in yellow catfish (Pelteobagrus fulvidraco), and analyzes the effects of these metal ions on the G6PD enzyme activity in the ovarian cell line (CCO) of channel catfish (Ictalurus punctatus). IC50 values and inhibition types of G6PD were determined in the metal ions Cu2+, Al3+, Zn2+, and Cd2+. While, the inhibition types of Cu2+ and Al3+ were the competitive inhibition, Zn2+ and Cd2+ were the linear mixed noncompetitive and linear mixed competitive, respectively. In vitro experiments revealed an inverse correlation between G6PD activity and metal ion concentration, mRNA levels and enzyme activity of G6PD increased at the lower metal ion concentration and decreased at the higher concentration. Our findings suggest that metal ions pose a significant threat to G6PD activity even at low concentrations, potentially playing a crucial role in the toxicity mechanism of metal ion pollution. This information contributes to the development of a biomonitoring tool for assessing metal ion contamination in aquatic species.
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Affiliation(s)
- Lindan Sun
- School of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Binbin Sun
- School of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, China
| | - Yulei Zhang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212000, Jiangsu, China.
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Alomar HA, Elkady WM, Abdel-Aziz MM, Ibrahim TA, Fathallah N. Anti- Heliobacter pylori and Anti-Inflammatory Potential of Salvia officinalis Metabolites: In Vitro and In Silico Studies. Metabolites 2023; 13:136. [PMID: 36677061 PMCID: PMC9865027 DOI: 10.3390/metabo13010136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/08/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Due to its rising antibiotic resistance and associated inflammations, Helicobacter pylori poses a challenge in modern medicine. Salvia officinalis, a member of the Lamiaceae family, is a promising medicinal herb. In this regard, a phytochemical screening followed by GC-MS and LC-MS was done to evaluate the chemical profile of the total ethanolic extract (TES) and the essential oil, respectively. The anti-H. pylori and the anti-inflammatory activities were evaluated by a micro-well dilution technique and COX-2 inhibition assay. Potential anti-H. pylori inhibitors were determined by an in silico study. The results revealed that the main metabolites were flavonoids, sterols, volatile oil, saponins, and carbohydrates. The LC-MS negative ionization mode demonstrated 12 compounds, while GC-MS showed 21 compounds. Carnosic acid (37.66%), epirosmanol (20.65%), carnosol1 (3.3%), and 12-O-methyl carnosol (6.15%) were predominated, while eucalyptol (50.04%) and camphor (17.75%) were dominant in LC-MS and GC-MS, respectively. TES exhibited the strongest anti-H. pylori activity (3.9 µg/mL) asymptotic to clarithromycin (0.43 µg/mL), followed by the oil (15.63 µg/mL). Carnosic acid has the best-fitting energy to inhibit H. pylori (-46.6769 Kcal/mol). TES showed the highest reduction in Cox-2 expression approaching celecoxib with IC50 = 1.7 ± 0.27 µg/mL, followed by the oil with IC50 = 5.3 ± 0.62 µg/mL. Our findings suggest that S. officinalis metabolites with anti-inflammatory capabilities could be useful in H. pylori management. Further in vivo studies are required to evaluate and assess its promising activity.
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Affiliation(s)
- Hatun A. Alomar
- Pharmacology and Toxicology Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Wafaa M. Elkady
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
| | - Marwa M. Abdel-Aziz
- Regional Center for Mycology and Biotechnology (RCMB), Al-Azhar University, Cairo 11651, Egypt
| | - Taghreed A. Ibrahim
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Noha Fathallah
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
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Shah BA, Kasarlawar ST, Phale PS. Glucose-6-Phosphate Dehydrogenase, ZwfA, a Dual Cofactor-Specific Isozyme Is Predominantly Involved in the Glucose Metabolism of Pseudomonas bharatica CSV86 T. Microbiol Spectr 2022; 10:e0381822. [PMID: 36354357 PMCID: PMC9769727 DOI: 10.1128/spectrum.03818-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 11/12/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (Zwf) is an important enzyme in glucose metabolism via the Entner-Doudoroff pathway and the first enzyme in the oxidative pentose-phosphate pathway. It generates NAD(P)H during the conversion of glucose-6-phosphate (G6P) to 6-phosphogluconolactone, thus aiding in anabolic processes, energy yield, and oxidative stress responses. Pseudomonas bharatica CSV86T preferentially utilized aromatic compounds over glucose and exhibited a significantly lower growth rate on glucose (0.24 h-1) with a prolonged lag phase (~10 h). In strain CSV86T, glucose was metabolized via the intracellular phosphorylative route only because it lacked an oxidative (gluconate and 2-ketogluconate) route. The genome harbored three genes zwfA, zwfB, and zwfC encoding three Zwf isozymes. The present study aimed to understand gene arrangement, gene expression profiling, and molecular and kinetic properties of the purified enzymes to unveil their physiological significance in the strain CSV86T. The zwfA was found to be a part of the zwfA-pgl-eda operon, which was proximal to other glucose transport and metabolic clusters. The zwfB was found to be arranged as a gnd-zwfB operon, while zwfC was present independently. Among the three, zwfA was transcribed maximally, and the purified ZwfA displayed the highest catalytic efficiency, cooperativity with respect to G6P, and dual cofactor specificity. Isozymes ZwfB and ZwfC were NADP+-preferring and NADP+-specific, respectively. Among other functionally characterized Zwfs, ZwfA from strain CSV86T displayed poor catalytic efficiency and the further absence of oxidative routes of glucose metabolism reflected its lower growth rate on glucose compared to P. putida KT2440 and could be probable reasons for the unique carbon source utilization hierarchy. IMPORTANCE Pseudomonas bharatica CSV86T metabolizes glucose exclusively via the intracellular phosphorylative Entner-Doudoroff pathway leading the entire glucose flux through Zwf as the strain lacks oxidative routes. This may lead to limiting the concentration of downstream metabolic intermediates. The strain CSV86T possesses three isoforms of glucose-6-phosphate dehydrogenase, ZwfA, ZwfB, and ZwfC. The expression profile and kinetic properties of purified enzymes will help to understand glucose metabolism. Isozyme ZwfA dominated in terms of expression and displayed cooperativity with dual cofactor specificity. ZwfB preferred NADP+, and ZwfC was NADP+ specific, which may aid in redox cofactor balance. Such beneficial metabolic flexibility facilitated the regulation of metabolic pathways giving survival/fitness advantages in dynamic environments. Additionally, multiple genes allowed the distribution of function among these isoforms where the primary function was allocated to one of the isoforms.
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Affiliation(s)
- Bhavik A. Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Mumbai, Mumbai, India
| | - Sravanti T. Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Mumbai, Mumbai, India
| | - Prashant S. Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Mumbai, Mumbai, India
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Ortiz-Ramírez P, Hernández-Ochoa B, Ortega-Cuellar D, González-Valdez A, Martínez-Rosas V, Morales-Luna L, Arreguin-Espinosa R, Castillo-Rodríguez RA, Canseco-Ávila LM, Cárdenas-Rodríguez N, Pérez de la Cruz V, Montiel-González AM, Gómez-Chávez F, Gómez-Manzo S. Biochemical and Kinetic Characterization of the Glucose-6-Phosphate Dehydrogenase from Helicobacter pylori Strain 29CaP. Microorganisms 2022; 10:microorganisms10071359. [PMID: 35889079 PMCID: PMC9323780 DOI: 10.3390/microorganisms10071359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) has been proposed as the foremost risk factor for the development of gastric cancer. We found that H. pylori express the enzyme glucose-6-phosphate dehydrogenase (HpG6PD), which participates in glucose metabolism via the pentose phosphate pathway. Thus, we hypothesized that if the biochemical and physicochemical characteristics of HpG6PD contrast with the host G6PD (human G6PD, HsG6PD), HpG6PD becomes a potential target for novel drugs against H. pylori. In this work, we characterized the biochemical properties of the HpG6PD from the H.pylori strain 29CaP and expressed the active recombinant protein, to analyze its steady-state kinetics, thermostability, and biophysical aspects. In addition, we analyzed the HpG6PD in silico structural properties to compare them with those of the HsG6PD. The optimal pH for enzyme activity was 7.5, with a T1/2 of 46.6 °C, at an optimum stability temperature of 37 °C. The apparent Km values calculated for G6P and NADP+ were 75.0 and 12.8 µM, respectively. G6P does not protect HpG6PD from trypsin digestion, but NADP+ does protect the enzyme from trypsin and guanidine hydrochloride (Gdn-HCl). The biochemical characterization of HpG6PD contributes to knowledge regarding H. pylori metabolism and opens up the possibility of using this enzyme as a potential target for specific and efficient treatment against this pathogen; structural alignment indicates that the three-dimensional (3D) homodimer model of the G6PD protein from H. pylori is different from the 3D G6PD of Homo sapiens.
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Affiliation(s)
- Paulina Ortiz-Ramírez
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (P.O.-R.); (V.M.-R.); (L.M.-L.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City 06720, Mexico;
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (P.O.-R.); (V.M.-R.); (L.M.-L.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (P.O.-R.); (V.M.-R.); (L.M.-L.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Angélica Castillo-Rodríguez
- Programa Investigadoras e Investigadores por México, CONACYT-Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Luis Miguel Canseco-Ávila
- Facultad de Ciencias Químicas, Campus IV, Universidad Autónoma de Chiapas, Tapachula City 30580, Mexico;
| | - Noemi Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Verónica Pérez de la Cruz
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico;
| | - Alba Mónica Montiel-González
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, Aut. San Martín Texmelucan-Tlaxcala Km 10.5, San Felipe Ixtacuixtla, Tlaxcala 90120, Mexico;
| | - Fernando Gómez-Chávez
- Laboratorio de Enfermedades Osteoarticulares e Inmunológicas, Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (P.O.-R.); (V.M.-R.); (L.M.-L.)
- Correspondence: ; Tel.: +52-55-1084-0900 (ext. 1442)
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Investigation into the suitability of screen printed graphene-melanin pH sensors for use in bacterial culturing applications. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2021.115868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hou L, Jia L, Morrison HM, L-W Majumder E, Kumar D. Enhanced polyhydroxybutyrate production from acid whey through determination of process and metabolic limiting factors. BIORESOURCE TECHNOLOGY 2021; 342:125973. [PMID: 34563817 DOI: 10.1016/j.biortech.2021.125973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
To sustainably produce biodegradable polyhydroxybutyrate (PHB), this study investigated effects of process and metabolic limiting factors during bioconversion of acid whey (AW) to PHB, offering economic and environmental advantages for dairy industry. Recombinant Escherichia coli LSBJ was used to achieve high PHB yields by utilizing both lactose and lactic acid as carbon source. Up to 85% PHB accumulation was achieved during growth on the synthetic AW. Growth on raw AW had the highest PHB yield of 4 g/L and a high substrate utilization efficiency (95%). Notably, ratios of lactate: lactose and C/N impacted metabolic flux and PHB yields. Maintaining the fermentation pH enhanced PHB production. Furthermore, additives of inorganic nitrogen sources, minerals and trace metals promoted PHB production from AW. The study improves the understanding of factors affecting utilization of AW and demonstrated the high PHB yields using recombinant E. coli that could be leveraged to design a sustainable process.
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Affiliation(s)
- Liyuan Hou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Linjing Jia
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Hailee M Morrison
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA.
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Hernández-Ochoa B, Navarrete-Vázquez G, Aguayo-Ortiz R, Ortiz-Ramírez P, Morales-Luna L, Martínez-Rosas V, González-Valdez A, Gómez-Chávez F, Enríquez-Flores S, Wong-Baeza C, Baeza-Ramírez I, Pérez de la Cruz V, Gómez-Manzo S. Identification and In Silico Characterization of Novel Helicobacter pylori Glucose-6-Phosphate Dehydrogenase Inhibitors. Molecules 2021; 26:molecules26164955. [PMID: 34443540 PMCID: PMC8401736 DOI: 10.3390/molecules26164955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/24/2022] Open
Abstract
Helicobacter pylori (H. pylori) is a pathogen that can remain in the stomach of an infected person for their entire life. As a result, this leads to the development of severe gastric diseases such as gastric cancer. In addition, current therapies have several problems including antibiotics resistance. Therefore, new practical options to eliminate this bacterium, and its induced affections, are required to avoid morbidity and mortality worldwide. One strategy in the search for new drugs is to detect compounds that inhibit a limiting step in a central metabolic pathway of the pathogen of interest. In this work, we tested 55 compounds to gain insights into their possible use as new inhibitory drugs of H. pylori glucose-6-phosphate dehydrogenase (HpG6PD) activity. The compounds YGC-1; MGD-1, MGD-2; TDA-1; and JMM-3 with their respective scaffold 1,3-thiazolidine-2,4-dione; 1H-benzimidazole; 1,3-benzoxazole, morpholine, and biphenylcarbonitrile showed the best inhibitory activity (IC50 = 310, 465, 340, 204 and 304 μM, respectively). We then modeled the HpG6PD protein by homology modeling to conduct an in silico study of the chemical compounds and discovers its possible interactions with the HpG6PD enzyme. We found that compounds can be internalized at the NADP+ catalytic binding site. Hence, they probably exert a competitive inhibitory effect with NADP+ and a non-competitive or uncompetitive effect with G6P, that of the compounds binding far from the enzyme’s active site. Based on these findings, the tested compounds inhibiting HpG6PD represent promising novel drug candidates against H. pylori.
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Affiliation(s)
- Beatriz Hernández-Ochoa
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (B.H.-O.); (V.M.-R.)
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico
| | - Gabriel Navarrete-Vázquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico;
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Paulina Ortiz-Ramírez
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (P.O.-R.); (L.M.-L.)
| | - Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (P.O.-R.); (L.M.-L.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Víctor Martínez-Rosas
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (B.H.-O.); (V.M.-R.)
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (P.O.-R.); (L.M.-L.)
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Fernando Gómez-Chávez
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico;
- Cátedras CONACyT-Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
- Departamento de Formación Básica Disciplinaria, Escuela Nacional de Medicina y Homeopatía del Instituto Politécnico Nacional, Ciudad de México 07320, Mexico
| | - Sergio Enríquez-Flores
- Laboratorio de EIMyT, Grupo de Investigación en Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | - Carlos Wong-Baeza
- Laboratorio de Biomembranas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (C.W.-B.); (I.B.-R.)
| | - Isabel Baeza-Ramírez
- Laboratorio de Biomembranas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (C.W.-B.); (I.B.-R.)
| | - Verónica Pérez de la Cruz
- Neurochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Ciudad de México 14269, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (P.O.-R.); (L.M.-L.)
- Correspondence: ; Tel.: +52-55-1084-0900 (ext. 1442)
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Khan MR, Khan MS, Ahmed A, Malik A, Qamar W. Optimization of expression and purification of mitochondrial HSP 40 (Tid1-L) chaperone: Role of mortalin and tid1 in the reactivation and amyloid inhibition of proteins. Saudi J Biol Sci 2020; 27:3099-3105. [PMID: 33100870 PMCID: PMC7569118 DOI: 10.1016/j.sjbs.2020.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 11/26/2022] Open
Abstract
Stimulation of complex chaperone activity may be a viable means of therapy for neurodegenerative diseases. These chaperons execute reactivation of thermally and chemically aggregated protein substrates by cooperating with their partner co-chaperons. We optimized the expression and purification conditions of Tid1-L chaperone. Expression of Tid1-L in E. coli resulted in the formation of inclusion bodies which was further purified to soluble active form using 8 M urea and Ni-NTA column. Also, we investigated the events of the reactivation and disaggregation using aggregated G6PDH, luciferase and insulin as substrates. Incubation of aggregated/denatured enzymes with mortalin but not with Tid1 and/or Mge1 resulted in the initiation of the disaggregation reaction albeit very insignificantly. Under the same conditions coincubating the samples with chaperon and its assisted partners Tid1-L and nucleotide exchange factor Mge1 led to (40%) increase in enzyme activity of G6PDH. Similarly, luciferase activity was synergistically enhanced in the presence of mortlain/Tid1-L/Mge1 chaperones machinery. Chaperone-dependent disaggregation of thermally aggregated insulin showed that addition of Hsp70 and Hsp40 chaperones resulted in fast-track of renaissance reaction and inhibition of amyloid. The present study results conclude the quality of cell-control involves interaction of chaperon Hsp70 and its co-chaperones leading to complex formation with chemically/thermally aggregated substrate eventually causing its reactivation and disaggregation.
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Affiliation(s)
- Mohammad Rashid Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anwar Ahmed
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Wajhul Qamar
- Central Laboratory, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Unconventional biochemical regulation of the oxidative pentose phosphate pathway in the model cyanobacterium Synechocystis sp. PCC 6803. Biochem J 2020; 477:1309-1321. [PMID: 32227111 DOI: 10.1042/bcj20200038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023]
Abstract
Metabolite production from carbon dioxide using sugar catabolism in cyanobacteria has been in the spotlight recently. Synechocystis sp. PCC 6803 (Synechocystis 6803) is the most studied cyanobacterium for metabolite production. Previous in vivo analyses revealed that the oxidative pentose phosphate (OPP) pathway is at the core of sugar catabolism in Synechocystis 6803. However, the biochemical regulation of the OPP pathway enzymes in Synechocystis 6803 remains unknown. Therefore, we characterized a key enzyme of the OPP pathway, glucose-6-phosphate dehydrogenase (G6PDH), and related enzymes from Synechocystis 6803. Synechocystis 6803 G6PDH was inhibited by citrate in the oxidative tricarboxylic acid (TCA) cycle. Citrate has not been reported as an inhibitor of G6PDH before. Similarly, 6-phosphogluconate dehydrogenase, the other enzyme from Synechocystis 6803 that catalyzes the NADPH-generating reaction in the OPP pathway, was inhibited by citrate. To understand the physiological significance of this inhibition, we characterized succinic semialdehyde dehydrogenase (SSADH) from Synechocystis 6803 (SySSADH), which catalyzes one of the NAD(P)H generating reactions in the oxidative TCA cycle. Similar to isocitrate dehydrogenase from Synechocystis 6803, SySSADH specifically catalyzed the NADPH-generating reaction and was not inhibited by citrate. The activity of SySSADH was lower than that of other bacterial SSADHs. Previous and this studies revealed that unlike the OPP pathway, the oxidative TCA cycle is a pathway with low efficiency in NADPH generation in Synechocystis 6803. It has, thus, been suggested that to avoid NADPH overproduction, the OPP pathway dehydrogenase activity is repressed when the flow of the oxidative TCA cycle increases in Synechocystis 6803.
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Morales-Luna L, Hernández-Ochoa B, Ramírez-Nava EJ, Martínez-Rosas V, Ortiz-Ramírez P, Fernández-Rosario F, González-Valdez A, Cárdenas-Rodríguez N, Serrano-Posada H, Centeno-Leija S, Arreguin-Espinosa R, Cuevas-Cruz M, Ortega-Cuellar D, Pérez de la Cruz V, Rocha-Ramírez LM, Sierra-Palacios E, Castillo-Rodríguez RA, Vega-García V, Rufino-González Y, Marcial-Quino J, Gómez-Manzo S. Characterizing the Fused TvG6PD::6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP + Molecule on Enzyme Stability. Int J Mol Sci 2020; 21:E4831. [PMID: 32650494 PMCID: PMC7402283 DOI: 10.3390/ijms21144831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/30/2022] Open
Abstract
This report describes a functional and structural analysis of fused glucose-6-phosphate dehydrogenase dehydrogenase-phosphogluconolactonase protein from the protozoan Trichomonas vaginalis (T. vaginalis). The glucose-6-phosphate dehydrogenase (g6pd) gene from T. vaginalis was isolated by PCR and the sequence of the product showed that is fused with 6pgl gene. The fused Tvg6pd::6pgl gene was cloned and overexpressed in a heterologous system. The recombinant protein was purified by affinity chromatography, and the oligomeric state of the TvG6PD::6PGL protein was found as tetramer, with an optimal pH of 8.0. The kinetic parameters for the G6PD domain were determined using glucose-6-phosphate (G6P) and nicotinamide adenine dinucleotide phosphate (NADP+) as substrates. Biochemical assays as the effects of temperature, susceptibility to trypsin digestion, and analysis of hydrochloride of guanidine on protein stability in the presence or absence of NADP+ were performed. These results revealed that the protein becomes more stable in the presence of the NADP+. In addition, we determined the dissociation constant for the binding (Kd) of NADP+ in the protein and suggests the possible structural site in the fused TvG6PD::6PGL protein. Finally, computational modeling studies were performed to obtain an approximation of the structure of TvG6PD::6PGL. The generated model showed differences with the GlG6PD::6PGL protein (even more so with human G6PD) despite both being fused.
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Affiliation(s)
- Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, 06720 Ciudad de México, Mexico;
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Edson Jiovany Ramírez-Nava
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Paulina Ortiz-Ramírez
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Fabiola Fernández-Rosario
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Miguel Cuevas-Cruz
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, 04530 Secretaría de Salud, Mexico;
| | - Verónica Pérez de la Cruz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaria de Salud, 14269 Ciudad de México, Mexico;
| | - Luz María Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Col Doctores, 06720 Delegación Cuauhtémoc, Mexico;
| | - Edgar Sierra-Palacios
- Colegio de Ciencias y Humanidades, Plantel Casa Libertad, Universidad Autónoma de la Ciudad de México, 09620 Ciudad de México, Mexico;
| | - Rosa Angélica Castillo-Rodríguez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Vanesa Vega-García
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Yadira Rufino-González
- Laboratorio de Parasitología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
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Biochemical comparison of two glucose 6-phosphate dehydrogenase isozymes from a cold-adapted Pseudomonas mandelii. Extremophiles 2020; 24:501-509. [DOI: 10.1007/s00792-020-01171-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
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12
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Ramírez-Nava EJ, Ortega-Cuellar D, González-Valdez A, Castillo-Rodríguez RA, Ponce-Soto GY, Hernández-Ochoa B, Cárdenas-Rodríguez N, Martínez-Rosas V, Morales-Luna L, Serrano-Posada H, Sierra-Palacios E, Arreguin-Espinosa R, Cuevas-Cruz M, Rocha-Ramírez LM, Pérez de la Cruz V, Marcial-Quino J, Gómez-Manzo S. Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter diazotrophicus PAL5. Int J Mol Sci 2019; 20:ijms20215279. [PMID: 31652968 PMCID: PMC6862599 DOI: 10.3390/ijms20215279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 11/17/2022] Open
Abstract
Gluconacetobacter diazotrophicus PAL5 (GDI) is an endophytic bacterium with potential biotechnological applications in industry and agronomy. The recent description of its complete genome and its principal metabolic enzymes suggests that glucose metabolism is accomplished through the pentose phosphate pathway (PPP); however, the enzymes participating in this pathway have not yet been characterized in detail. The objective of the present work was to clone, purify, and biochemically and physicochemically characterize glucose-6-phosphate dehydrogenase (G6PD) from GDI. The gene was cloned and expressed as a tagged protein in E. coli to be purified by affinity chromatography. The native state of the G6PD protein in the solution was found to be a tetramer with optimal activity at pH 8.8 and a temperature between 37 and 50 °C. The apparent Km values for G6P and nicotinamide adenine dinucleotide phosphate (NADP+) were 63 and 7.2 μM, respectively. Finally, from the amino acid sequence a three-dimensional (3D) model was obtained, which allowed the arrangement of the amino acids involved in the catalytic activity, which are conserved (RIDHYLGKE, GxGGDLT, and EKPxG) with those of other species, to be identified. This characterization of the enzyme could help to identify new environmental conditions for the knowledge of the plant–microorganism interactions and a better use of GDI in new technological applications.
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Affiliation(s)
- Edson Jiovany Ramírez-Nava
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico.
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud 04530, Mexico.
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico.
| | - Rosa Angélica Castillo-Rodríguez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de Mexico 04530, Mexico.
| | - Gabriel Yaxal Ponce-Soto
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, 52428 Jülich, Germany.
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de Mexico 06720, Mexico.
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico.
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico.
| | - Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico.
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, Colima 28629, Mexico.
| | - Edgar Sierra-Palacios
- Colegio de Ciencias y Humanidades, Plantel Casa Libertad, Universidad Autónoma de la Ciudad de México, Ciudad de Mexico 09620, Mexico.
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico.
| | - Miguel Cuevas-Cruz
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico.
| | - Luz María Rocha-Ramírez
- Departamento de Infectología, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Col Doctores, Delegación Cuauhtémoc 06720, Mexico.
| | - Verónica Pérez de la Cruz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Ciudad de Mexico 14269, Mexico.
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de Mexico 04530, Mexico.
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, 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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14
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Biochemical Characterization and Structural Modeling of Fused Glucose-6-Phosphate Dehydrogenase-Phosphogluconolactonase from Giardia lamblia. Int J Mol Sci 2018; 19:ijms19092518. [PMID: 30149622 PMCID: PMC6165198 DOI: 10.3390/ijms19092518] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/18/2018] [Accepted: 08/22/2018] [Indexed: 11/17/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is the first enzyme in the pentose phosphate pathway and is highly relevant in the metabolism of Giardialamblia. Previous reports suggested that the G6PD gene is fused with the 6-phosphogluconolactonase (6PGL) gene (6pgl). Therefore, in this work, we decided to characterize the fused G6PD-6PGL protein in Giardialamblia. First, the gene of g6pd fused with the 6pgl gene (6gpd::6pgl) was isolated from trophozoites of Giardialamblia and the corresponding G6PD::6PGL protein was overexpressed and purified in Escherichia coli. Then, we characterized the native oligomeric state of the G6PD::6PGL protein in solution and we found a catalytic dimer with an optimum pH of 8.75. Furthermore, we determined the steady-state kinetic parameters for the G6PD domain and measured the thermal stability of the protein in both the presence and absence of guanidine hydrochloride (Gdn-HCl) and observed that the G6PD::6PGL protein showed alterations in the stability, secondary structure, and tertiary structure in the presence of Gdn-HCl. Finally, computer modeling studies revealed unique structural and functional features, which clearly established the differences between G6PD::6PGL protein from G. lamblia and the human G6PD enzyme, proving that the model can be used for the design of new drugs with antigiardiasic activity. These results broaden the perspective for future studies of the function of the protein and its effect on the metabolism of this parasite as a potential pharmacological target.
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15
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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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16
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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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17
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Schüürmann J, Quehl P, Lindhorst F, Lang K, Jose J. Autodisplay of glucose-6-phosphate dehydrogenase for redox cofactor regeneration at the cell surface. Biotechnol Bioeng 2017; 114:1658-1669. [PMID: 28401536 DOI: 10.1002/bit.26308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/02/2017] [Accepted: 04/02/2017] [Indexed: 11/06/2022]
Abstract
Inherent cofactor regeneration is a pivotal feature of whole cell biocatalysis. For specific biotechnological applications, surface display of enzymes is emerging as a tool to circumvent mass transfer limitations or enzyme stability problems. Even complex reactions can be accomplished applying displayed enzymes. Yet, industrial utilization of the technique is still impeded by lacking cofactor regeneration at the cell surface. Here, we report on the surface display of a glucose-6-phoshate dehydrogenase (G6PDH) via Autodisplay to address this limitation and regenerate NADPH directly at the cell surface. The obtained whole cell biocatalyst demonstrated similar kinetic parameters compared to the purified enzyme, more precisely KM values of 0.2 mM for NADP+ and calculated total turnover numbers of 107 . However, the KM for the substrate G6P increased by a factor of 7 to yield 1.5 mM. The whole cell biocatalyst was cheaper to produce, easy to separate from the reaction mixture and reusable in consecutive reaction cycles. Furthermore, lyophilization allowed storage at room temperature. The whole cell biocatalyst displaying G6PDH was applicable for NADPH regeneration in combination with soluble as well as surface displayed enzymes and model reactions in combination with bacterial CYP102A1 and human CYP1A2 were realized. Biotechnol. Bioeng. 2017;114: 1658-1669. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jan Schüürmann
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Paul Quehl
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Fabian Lindhorst
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Kristina Lang
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, 48149 Münster, Germany
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18
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Kim EJ, Wu CH, Adams MWW, Zhang YHP. Exceptionally High Rates of Biological Hydrogen Production by Biomimetic In Vitro Synthetic Enzymatic Pathways. Chemistry 2016; 22:16047-16051. [PMID: 27605312 DOI: 10.1002/chem.201604197] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 11/08/2022]
Abstract
Hydrogen production by water splitting energized by biomass sugars is one of the most promising technologies for distributed green H2 production. Direct H2 generation from NADPH, catalysed by an NADPH-dependent, soluble [NiFe]-hydrogenase (SH1) is thermodynamically unfavourable, resulting in slow volumetric productivity. We designed the biomimetic electron transport chain from NADPH to H2 by the introduction of an oxygen-insensitive electron mediator benzyl viologen (BV) and an enzyme (NADPH rubredoxin oxidoreductase, NROR), catalysing electron transport between NADPH and BV. The H2 generation rates using this biomimetic chain increased by approximately five-fold compared to those catalysed only by SH1. The peak volumetric H2 productivity via the in vitro enzymatic pathway comprised of hyperthermophilic glucose 6-phosphate dehydrogenase, 6-phosphogluconolactonase, and 6-phosphogluconate dehydrogenase, NROR, and SH1 was 310 mmol H2 /L h-1 , the highest rate yet reported. The concept of biomimetic electron transport chains could be applied to both in vitro and in vivo H2 production biosystems and artificial photosynthesis.
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Affiliation(s)
- Eui-Jin Kim
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China.
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Talbert JN, Alcaine SD, Nugen SR. Engineering bacteriophage for a pragmatic low-resource setting bacterial diagnostic platform. Bioengineered 2016; 7:132-6. [PMID: 27246532 PMCID: PMC4927197 DOI: 10.1080/21655979.2016.1184386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022] Open
Abstract
Bacteriophages represent multifaceted building blocks that can be incorporated as substitutes for, or in unison with other detection methods, to create powerful new diagnostics for the detection of bacteria. The ease of phage manipulation, production, and detection speed clearly highlights that there remains unrealized opportunities to leverage these phage-based components in diagnostics amenable to resource-limited settings. The passage of regulations like the Food Safety Modernization act, and the ever increasing extent of global trade and travel, will create further demand for these types of diagnostics. While phage-based diagnostics have begun to entering the market place, further research is needed to ensure the potential benefits of phage-based technologies for public health are fully realized. We are just beginning to explore the possibilities that phage-based detection can offer us in the future. The combination of engineered phages as well as engineered enzymes could result in ultrasensitive detection systems for low-resource settings. Because the reporter enzyme is synthesized in vivo, we need to consider the options outside of normal enzyme reporters. In this case, common enzyme issues such as purification and long-term stability are less important. Phage-based diagnostics were conceptualized from out-of-the box thinking and the evolution of these systems should be as well.
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Affiliation(s)
- Joey N. Talbert
- Department of Food Science and Nutrition, Iowa State University, Ames, IA
| | | | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY, USA
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
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Fuentealba M, Muñoz R, Maturana P, Krapp A, Cabrera R. Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies. PLoS One 2016; 11:e0152403. [PMID: 27010804 PMCID: PMC4807051 DOI: 10.1371/journal.pone.0152403] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 03/14/2016] [Indexed: 11/25/2022] Open
Abstract
Glucose 6-Phosphate Dehydrogenases (G6PDHs) from different sources show varying specificities towards NAD+ and NADP+ as cofactors. However, it is not known to what extent structural determinants of cofactor preference are conserved in the G6PDH family. In this work, molecular simulations, kinetic characterization of site-directed mutants and phylogenetic analyses were used to study the structural basis for the strong preference towards NADP+ shown by the G6PDH from Escherichia coli. Molecular Dynamics trajectories of homology models showed a highly favorable binding energy for residues K18 and R50 when interacting with the 2'-phosphate of NADP+, but the same residues formed no observable interactions in the case of NAD+. Alanine mutants of both residues were kinetically characterized and analyzed with respect to the binding energy of the transition state, according to the kcat/KM value determined for each cofactor. Whereas both residues contribute to the binding energy of NADP+, only R50 makes a contribution (about -1 kcal/mol) to NAD+ binding. In the absence of both positive charges the enzyme was unable to discriminate NADP+ from NAD+. Although kinetic data is sparse, the observed distribution of cofactor preferences within the phylogenetic tree is sufficient to rule out the possibility that the known NADP+-specific G6PDHs form a monophyletic group. While the β1-α1 loop shows no strict conservation of K18, (rather, S and T seem to be more frequent), in the case of the β2-α2 loop, different degrees of conservation are observed for R50. Noteworthy is the fact that a K18T mutant is indistinguishable from K18A in terms of cofactor preference. We conclude that the structural determinants for the strict discrimination against NAD+ in the case of the NADP+-specific enzymes have evolved independently through different means during the evolution of the G6PDH family. We further suggest that other regions in the cofactor binding pocket, besides the β1-α1 and β2-α2 loops, play a role in determining cofactor preference.
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Affiliation(s)
- Matias Fuentealba
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rodrigo Muñoz
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Maturana
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Adriana Krapp
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Li Z, Jiang N, Yang K, Zheng J. Cloning, expression, and characterization of a thermostable glucose-6-phosphate dehydrogenase from Thermoanaerobacter tengcongensis. Extremophiles 2016; 20:149-56. [DOI: 10.1007/s00792-016-0808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022]
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Ibrahim MA, Ghazy AHM, Salem AMH, Ghazy MA, Abdel-Monsef MM. Biochemical characterization of buffalo liver glucose-6-phosphate dehydrogenase isoforms. Protein J 2016; 34:193-204. [PMID: 25980795 DOI: 10.1007/s10930-015-9615-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is a key regulatory enzyme involved in the pentose phosphate pathway. This works represents purification of two buffalo liver glucose-6-phosphate dehydrogenases (BLG6PD1 and BLG6PD2) using combination of ammonium sulfate precipitation and several chromatographic columns. Both enzymes (BLG6PD1 and BLG6PD2) were homogenous on both native PAGE as well as 12% SDS PAGE with molecular weights of 28 and 66 kDa. The molecular weight of BLG6PD1 and BLG6PD2 native forms were determined to be 28 and 66 kDa by gel filtration; indicating monomeric proteins. The K(m) values for BLG6PD1 and BLG6PD2 estimated to be 0.059 and 0.06 mM of β-nicotinamide adenine dinucleotide phosphate. The optimum activity of BLG6PD1 and BLG6PD2 were displayed at pH 8.0 and 8.2 with an isoelectric point (pI) of pH 7.7-7.9 and 5.7-5.9. The divalent cations MgCl2, and CoCl2 act as activators, on the other hand, FeCl2, CuCl2 and ZnCl2 are potent inhibitors of BLG6PD1 and BLG6PD2 activity. NADPH inhibited both isoenzymes competitively with Ki values of 0.012 and 0.030 mM. This study describes a reproducible purification scheme of G6PD from the liver of buffalo as a rich source.
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Affiliation(s)
- Mahmoud A Ibrahim
- Molecular Biology Department, National Research Centre, El-Tahrir St., Dokki, Cairo, 12311, Egypt,
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Ibrahim MA, Ghazy AHM, Salem AMH, Ghazy MA, Abdel-Monsef MM. Purification and characterization of glucose-6-phosphate dehydrogenase from camel liver. Enzyme Res 2014; 2014:714054. [PMID: 25610637 PMCID: PMC4290037 DOI: 10.1155/2014/714054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/23/2014] [Indexed: 12/02/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase from camel liver was purified to homogeneity by ammonium sulfate precipitation and a combination of DEAE-cellulose, Sephacryl S-300 gel filtration, and 2', 5' ADP Sepharose 4B affinity chromatography columns. The specific activity of camel liver G6PD is increased to 1.80438 units/mg proteins with 63-fold purification. It turned out to be homogenous on both native PAGE and 12% SDS PAGE, with a molecular weight of 64 kDa. The molecular weight of the native form of camel liver G6PD was determined to be 194 kDa by gel filtration indicating a trimeric protein. The K m value was found to be 0.081 mM of NADP(+). Camel liver G6PD displayed its optimum activity at pH 7.8 with an isoelectric point (pI) of pH 6.6-6.8. The divalent cations MgCl2, MnCl2, and CoCl2 act as activators; on the other hand, CaCl2 and NiCl2 act as moderate inhibitors, while FeCl2, CuCl2, and ZnCl2 are potent inhibitors of camel liver G6PD activity. NADPH inhibited camel liver G6PD competitively with K i value of 0.035 mM. One binding site was deduced for NADPH on the enzyme molecule. This study presents a simple and reproducible purification procedure of G6PD from the camel liver.
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Affiliation(s)
- Mahmoud A. Ibrahim
- Molecular Biology Department, National Research Center, Dokki, Cairo 12311, Egypt
| | - Abdel-Hady M. Ghazy
- Molecular Biology Department, National Research Center, Dokki, Cairo 12311, Egypt
| | - Ahmed M. H. Salem
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Ghazy
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
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Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R. Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli. MICROBIOLOGY-SGM 2014; 160:2780-2793. [PMID: 25246670 DOI: 10.1099/mic.0.082180-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In Escherichia coli, the oxidative branch of the pentose phosphate pathway (oxPPP) is one of the major sources of NADPH when glucose is the sole carbon nutrient. However, unbalanced NADPH production causes growth impairment as observed in a strain lacking phosphoglucoisomerase (Δpgi). In this work, we studied the metabolic response of this bacterium to the replacement of its glucose-6-phosphate dehydrogenase (G6PDH) by an NADH-producing variant. The homologous enzyme from Leuconostoc mesenteroides was studied by molecular dynamics and site-directed mutagenesis to obtain the NAD-preferring LmG6PDH(R46E,Q47E). Through homologous recombination, the zwf loci (encoding G6PDH) in the chromosomes of WT and Δpgi E. coli strains were replaced by DNA encoding LmG6PDH(R46E,Q47E). Contrary to some predictions performed with flux balance analysis, the replacements caused a substantial effect on the growth rates, increasing 59 % in the Δpgi strain, while falling 44 % in the WT. Quantitative PCR (qPCR) analysis of the zwf locus showed that the expression level of the mutant enzyme was similar to the native enzyme and the expression of genes encoding key enzymes of the central pathways also showed moderate changes among the studied strains. The phenotypic and qPCR data were integrated into in silico modelling, showing an operative G6PDH flux contributing to the NADH pool. Our results indicated that, in vivo, the generation of NADH by G6PDH is beneficial or disadvantageous for growth depending on the operation of the upper Embden-Meyerhof pathway. Interestingly, a genomic database search suggested that in bacteria lacking phosphofructokinase, the G6PDHs tend to have similar preferences for NAD and NADP. The importance of the generation of NADPH in a pathway such as the oxPPP is discussed.
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Affiliation(s)
- K Olavarria
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - J De Ingeniis
- Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
| | - D C Zielinski
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - M Fuentealba
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - R Muñoz
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - D McCloskey
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - A M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - R Cabrera
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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25
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Laass S, Kleist S, Bill N, Drüppel K, Kossmehl S, Wöhlbrand L, Rabus R, Klein J, Rohde M, Bartsch A, Wittmann C, Schmidt-Hohagen K, Tielen P, Jahn D, Schomburg D. Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. J Biol Chem 2014; 289:13219-31. [PMID: 24648520 DOI: 10.1074/jbc.m113.545004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Metabolic flexibility is the key to the ecological success of the marine Roseobacter clade bacteria. We investigated the metabolic adaptation and the underlying changes in gene expression of Dinoroseobacter shibae DFL12(T) to anoxic life by a combination of metabolome, proteome, and transcriptome analyses. Time-resolved studies during continuous oxygen depletion were performed in a chemostat using nitrate as the terminal electron acceptor. Formation of the denitrification machinery was found enhanced on the transcriptional and proteome level, indicating that D. shibae DFL12(T) established nitrate respiration to compensate for the depletion of the electron acceptor oxygen. In parallel, arginine fermentation was induced. During the transition state, growth and ATP concentration were found to be reduced, as reflected by a decrease of A578 values and viable cell counts. In parallel, the central metabolism, including gluconeogenesis, protein biosynthesis, and purine/pyrimidine synthesis was found transiently reduced in agreement with the decreased demand for cellular building blocks. Surprisingly, an accumulation of poly-3-hydroxybutanoate was observed during prolonged incubation under anoxic conditions. One possible explanation is the storage of accumulated metabolites and the regeneration of NADP(+) from NADPH during poly-3-hydroxybutanoate synthesis (NADPH sink). Although D. shibae DFL12(T) was cultivated in the dark, biosynthesis of bacteriochlorophyll was increased, possibly to prepare for additional energy generation via aerobic anoxygenic photophosphorylation. Overall, oxygen depletion led to a metabolic crisis with partly blocked pathways and the accumulation of metabolites. In response, major energy-consuming processes were reduced until the alternative respiratory denitrification machinery was operative.
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Affiliation(s)
- Sebastian Laass
- From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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Basner A, Antranikian G. Isolation and biochemical characterization of a glucose dehydrogenase from a hay infusion metagenome. PLoS One 2014; 9:e85844. [PMID: 24454935 PMCID: PMC3891874 DOI: 10.1371/journal.pone.0085844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/02/2013] [Indexed: 11/19/2022] Open
Abstract
Glucose hydrolyzing enzymes are essential to determine blood glucose level. A high-throughput screening approach was established to identify NAD(P)-dependent glucose dehydrogenases for the application in test stripes and the respective blood glucose meters. In the current report a glucose hydrolyzing enzyme, derived from a metagenomic library by expressing recombinant DNA fragments isolated from hay infusion, was characterized. The recombinant clone showing activity on glucose as substrate exhibited an open reading frame of 987 bp encoding for a peptide of 328 amino acids. The isolated enzyme showed typical sequence motifs of short-chain-dehydrogenases using NAD(P) as a co-factor and had a sequence similarity between 33 and 35% to characterized glucose dehydrogenases from different Bacillus species. The identified glucose dehydrogenase gene was expressed in E. coli, purified and subsequently characterized. The enzyme, belonging to the superfamily of short-chain dehydrogenases, shows a broad substrate range with a high affinity to glucose, xylose and glucose-6-phosphate. Due to its ability to be strongly associated with its cofactor NAD(P), the enzyme is able to directly transfer electrons from glucose oxidation to external electron acceptors by regenerating the cofactor while being still associated to the protein.
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Affiliation(s)
- Alexander Basner
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
- * E-mail:
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Kouril T, Esser D, Kort J, Westerhoff HV, Siebers B, Snoep JL. Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus. FEBS J 2013; 280:4666-80. [PMID: 23865479 DOI: 10.1111/febs.12438] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/04/2013] [Accepted: 07/11/2013] [Indexed: 01/22/2023]
Abstract
Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature instability of the pathway intermediates to carbon loss from the system. The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of fructose 6-phosphate over a 1-h period. Cofactors ATP and NADPH were regenerated via pyruvate kinase and glucose dehydrogenase. A mathematical model was constructed on the basis of the kinetics of the purified enzymes and the measured half-life times of the pathway intermediates. The model quantitatively predicted the system fluxes and metabolite concentrations. Relative enzyme concentrations were chosen such that half the carbon in the system was lost due to degradation of the thermolabile intermediates dihydroxyacetone phosphate, glyceraldehyde 3-phosphate and 1,3-bisphosphoglycerate, indicating that intermediate instability at high temperature can significantly affect pathway efficiency.
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Affiliation(s)
- Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Germany
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Wang Y, Zhang YHP. Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration. Microb Cell Fact 2009; 8:30. [PMID: 19497097 PMCID: PMC2701922 DOI: 10.1186/1475-2859-8-30] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 06/04/2009] [Indexed: 11/29/2022] Open
Abstract
Background Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes. Results An open reading frame TM0438 from a hyperthermophilic bacterium Thermotoga maritima putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in E. coli. The purified protein was confirmed to have 6PGDH activity with a molecular mass of 53 kDa. The kcat of this enzyme was 325 s-1 and the Km values for 6-phosphogluconate, NADP+, and NAD+ were 11, 10 and 380 μM, respectively, at 80°C. This enzyme had half-life times of 48 and 140 h at 90 and 80°C, respectively. Through numerous approaches including expression vectors, hosts, cultivation conditions, inducers, and codon-optimization of the 6pgdh gene, the soluble 6PGDH expression levels were enhanced to ~250 mg per liter of culture by more than 500-fold. The recombinant 6PGDH accounted for >30% of total E. coli cellular proteins when lactose was used as a low-cost inducer. In addition, this enzyme coupled with glucose-6-phosphate dehydrogenase for the first time was demonstrated to generate two moles of NADPH per mole of glucose-6-phosphate. Conclusion We have achieved a more than 500-fold improvement in the expression of soluble T. maritima 6PGDH in E. coli, characterized its basic biochemical properties, and demonstrated its applicability for NADPH regeneration by a new enzyme cocktail. The methodology for over-expression and simple purification of this thermostable protein would be useful for the production of other thermostable proteins in E. coli.
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Affiliation(s)
- Yiran Wang
- Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Polytechnic Institute and State University, Blacksburg, Virgina 24061, USA.
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Hong SY, Cho KM, Kim YH, Hong SJ, Cho SJ, Cho YU, Kim H, Yun HD. Cloning and Identification of Essential Residues for Thermostable β-glucosidase (BgIB) from Thermotoga maritima. ACTA ACUST UNITED AC 2006. [DOI: 10.5352/jls.2006.16.7.1148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hansen T, Arnfors L, Ladenstein R, Schönheit P. The phosphofructokinase-B (MJ0406) from Methanocaldococcus jannaschii represents a nucleoside kinase with a broad substrate specificity. Extremophiles 2006; 11:105-14. [PMID: 17021658 DOI: 10.1007/s00792-006-0018-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 07/04/2006] [Indexed: 12/01/2022]
Abstract
Recently, unusual non-regulated ATP-dependent 6-phosphofructokinases (PFK) that belong to the PFK-B family have been described for the hyperthermophilic archaea Desulfurococcus amylolyticus and Aeropyrum pernix. Putative homologues were found in genomes of several archaea including the hyperthermophilic archaeon Methanocaldococcus jannaschii. In this organism, open reading frame MJ0406 had been annotated as a PFK-B sugar kinase. The gene encoding MJ0406 was cloned and functionally expressed in Escherichia coli. The purified recombinant enzyme is a homodimer with an apparent molecular mass of 68 kDa composed of 34 kDa subunits. With a temperature optimum of 85 degrees C and a melting temperature of 90 degrees C, the M. jannaschii nucleotide kinase represents one of the most thermoactive and thermostable members of the PFK-B family described so far. The recombinant enzyme was characterized as a functional nucleoside kinase rather than a 6-PFK. Inosine, guanosine, and cytidine were the most effective phosphoryl acceptors. Besides, adenosine, thymidine, uridin and xanthosine were less efficient. Extremely low activity was found with fructose-6-phosphate. Further, the substrate specificity of closely related PFK-Bs from D. amylolyticus and A. pernix were reanalysed.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
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Ulusu NN, Tandogan B. Purification and kinetics of sheep kidney cortex glucose-6-phosphate dehydrogenase. Comp Biochem Physiol B Biochem Mol Biol 2006; 143:249-55. [PMID: 16406826 DOI: 10.1016/j.cbpb.2005.11.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 11/24/2005] [Accepted: 11/24/2005] [Indexed: 10/25/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G-6-PD) is one of the important enzymes, which is responsible for the production of NADPH and ribose-5-phosphate. NADPH is used for the biosynthetic reactions and protection of the cells from free radicals. We have investigated some properties and kinetic mechanism of the sheep kidney cortex G-6-PD. This enzyme has been purified 1,384-fold with a yield of 16.96% and had a specific activity of 27.69 U/mg protein. The purification procedure consists of 2', 5'-ADP-Sepharose 4B affinity chromatography after ultracentrifugation. The sheep kidney cortex G-6-PD was found to operate according to a Ping Pong Bi Bi mechanism. The kinetic parameters from sheep K(m) values for G-6-P and NADP(+) and V(m) were determined to be 0.041+/-0.0043 mM, 0.0147+/-0.001 mM and 28.23+/-0.86 microMol min(-1) mg protein(-1), respectively. The pH optimum was 7.4 and the optimum temperature was 45 degrees C. In our previous study we have found that lamb kidney cortex G-6-PD enzyme obeys 'Ordered Bi Bi' mechanism. We suggest that kinetic mechanism altered due to the aging since sheep G-6-PD uses a 'ping pong' mechanism.
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Affiliation(s)
- Nuray N Ulusu
- Hacettepe University, Faculty of Medicine, Department of Biochemistry, 06100 Ankara, Turkey.
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Hansen T, Schlichting B, Grötzinger J, Swan MK, Davies C, Schönheit P. Mutagenesis of catalytically important residues of cupin type phosphoglucose isomerase from Archaeoglobus fulgidus. FEBS J 2005; 272:6266-75. [PMID: 16336264 DOI: 10.1111/j.1742-4658.2005.05007.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Recently, cupin type phosphoglucose isomerases have been described as a novel protein family representing a separate lineage in the evolution of phosphoglucose isomerases. The importance of eight active site residues completely conserved within the cPGI family has been assessed by site-directed mutagenesis using the cPGI from Archaeoglobus fulgidus (AfcPGI) as a model. The mutants T63A, G79A, G79L, H80A, H80D, H82A, E93A, E93D, Y95F, Y95K, H136A, and Y160F were constructed, purified, and the impact of the respective mutation on catalysis and/or metal ion binding as well as thermostability was analyzed. The variants G79A, G79L, and Y95F exhibited a lower thermostability. The catalytic efficiency of the enzyme was reduced by more than 100-fold in the G79A, G79L, H80A, H80D, E93D, Y95F variants and more than 15-fold in the T63A, H82A, Y95K, Y160F variants, but remained about the same in the H136A variant at Ni2+ saturating conditions. Further, the Ni2+ content of the mutants H80A, H80D, H82A, E93A, E93D and their apparent Ni2+ binding ability was reduced, resulting in an almost complete loss of activity and thus underlining the crucial role of the metal ion for catalysis. Evidence is presented that H80, H82 and E93 play an additional role in catalysis besides metal ion binding. E93 appears to be the key catalytic residue of AfcPGI, as the E93A mutant did not show any catalytic activity at all.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany
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Saavedra L, Sesma F. Atypical Genetic Locus Associated with the zwf Gene Encoding the Glucose 6-Phosphate Dehydrogenase from Enterococcus mundtii CRL35. Curr Microbiol 2005; 51:148-52. [PMID: 16091851 DOI: 10.1007/s00284-004-4454-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 10/20/2004] [Indexed: 11/29/2022]
Abstract
The zwf gene encoding glucose 6-phosphate dehydrogenase (G6PD, EC.1.1.1.49) from Enterococcus mundtii CRL35 was cloned as a 4921 bp EcoRI fragment and analyzed. The predicted zwf gene product consists of 506 residues with a molecular mass of 58.4 kDa, and is fully active in Escherichia coli as demonstrated by its heterologous expression in the zwf-negative mutant E. coli Su294. It shows a high degree of sequence identity (40-60%) to G6PDs described in other bacteria. Upstream of the zwf gene, a homolog of the DtxR family was identified (ORF D). Analysis of the 5' sequence of ORF D revealed a potential promoter sequence, which would suggest the presence of an operon-like structure between ORF D and the zwf gene. Finally, it was found that Fe2+ levels have an important role as a modulator of G6PD activity. This is the first report of this type of regulation of G6PD activity. A possible involvement in oxidative stress is discussed.
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Affiliation(s)
- Lucila Saavedra
- Centro de Referencia para Lactobacilos (CONICET), Chacabuco , 145 (4000), Tucumán, Argentina
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Hansen T, Schlichting B, Felgendreher M, Schönheit P. Cupin-type phosphoglucose isomerases (Cupin-PGIs) constitute a novel metal-dependent PGI family representing a convergent line of PGI evolution. J Bacteriol 2005; 187:1621-31. [PMID: 15716432 PMCID: PMC1063998 DOI: 10.1128/jb.187.5.1621-1631.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cupin-type phosphoglucose isomerases (cPGIs) were identified in some archaeal and bacterial genomes and the respective coding function of cpgi's from the euryarchaeota Archaeoglobus fulgidus and Methanosarcina mazei, as well as the bacteria Salmonella enterica serovar Typhimurium and Ensifer meliloti, was proven by functional overexpression. These cPGIs and the cPGIs from Pyrococcus and Thermococcus spp. represent the cPGI family and were compared with respect to kinetic, inhibitory, thermophilic, and metal-binding properties. cPGIs showed a high specificity for the substrates fructose-6-phosphate and glucose-6-phosphate and were inhibited by millimolar concentrations of sorbitol-6-phosphate, erythrose-4-phosphate, and 6-phosphogluconate. Treatment of cPGIs with EDTA resulted in a complete loss of catalytic activity, which could be regained by the addition of some divalent cations, most effectively by Fe2+ and Ni2+, indicating a metal dependence of cPGI activity. The motifs TX3PX3GXEX3TXGHXHX6-11EXY and PPX3HX3N were deduced as the two signature patterns of the novel cPGI family. Phylogenetic analysis suggests lateral gene transfer for the bacterial cPGIs from euryarchaeota.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
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Hansen T, Urbanke C, Schönheit P. Bifunctional phosphoglucose/phosphomannose isomerase from the hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles 2004; 8:507-12. [PMID: 15290326 DOI: 10.1007/s00792-004-0411-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Accepted: 06/14/2004] [Indexed: 11/29/2022]
Abstract
ORF PAE1610 from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was first annotated as the conjectural pgi gene coding for hypothetical phosphoglucose isomerase (PGI). However, we have recently identified this ORF as the putative pgi/pmi gene coding for hypothetical bifunctional phosphoglucose/phosphomannose isomerase (PGI/PMI). To prove its coding function, ORF PAE1610 was overexpressed in Escherichia coli, and the recombinant enzyme was characterized. The 65-kDa homodimeric protein catalyzed the isomerization of both glucose-6-phosphate and mannose-6-phosphate to fructose-6-phosphate at similar catalytic rates, thus characterizing the enzyme as bifunctional PGI/PMI. The enzyme was extremely thermoactive; it had a temperature optimum for catalytic activity of about 100 degrees C and a melting temperature for thermal unfolding above 100 degrees C.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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Hansen T, Wendorff D, Schönheit P. Bifunctional Phosphoglucose/Phosphomannose Isomerases from the Archaea Aeropyrum pernix and Thermoplasma acidophilum Constitute a Novel Enzyme Family within the Phosphoglucose Isomerase Superfamily. J Biol Chem 2004; 279:2262-72. [PMID: 14551194 DOI: 10.1074/jbc.m309849200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic crenarchaeon Aeropyrum pernix contains phosphoglucose isomerase (PGI) activity. However, obvious homologs with significant identity to known PGIs could not be identified in the sequenced genome of this organism. The PGI activity from A. pernix was purified and characterized. Kinetic analysis revealed that, unlike all known PGIs, the enzyme catalyzed reversible isomerization not only of glucose 6-phosphate but also of epimeric mannose 6-phosphate at similar catalytic efficiency, thus defining the protein as bifunctional phosphoglucose/phosphomannose isomerase (PGI/PMI). The gene pgi/pmi encoding PGI/PMI (open reading frame APE0768) was identified by matrix-assisted laser desorption ionization time-of-flight analyses; the gene was overexpressed in Escherichia coli as functional PGI/PMI. Putative PGI/PMI homologs were identified in several (hyper)thermophilic archaea and two bacteria. The homolog from Thermoplasma acidophilum (Ta1419) was overexpressed in E. coli, and the recombinant enzyme was characterized as bifunctional PGI/PMI. PGI/PMIs showed low sequence identity to the PGI superfamily and formed a distinct phylogenetic cluster. However, secondary structure predictions and the presence of several conserved amino acids potentially involved in catalysis indicate some structural and functional similarity to the PGI superfamily. Thus, we propose that bifunctional PGI/PMI constitutes a novel protein family within the PGI superfamily.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
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Hansen T, Schönheit P. ATP-dependent glucokinase from the hyperthermophilic bacterium Thermotoga maritima represents an extremely thermophilic ROK glucokinase with high substrate specificity. FEMS Microbiol Lett 2003; 226:405-11. [PMID: 14553940 DOI: 10.1016/s0378-1097(03)00642-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The gene (open reading frame (ORF) Tm1469, glk) encoding ATP-dependent ROK (repressors, ORFs, sugar kinases) glucokinase (ATP-GLK, EC 2.7.1.2) of the hyperthermophilic bacterium Thermotoga maritima was cloned and functionally expressed in Escherichia coli. The purified recombinant enzyme is a homodimer with an apparent molecular mass of 80 kDa composed of 36-kDa subunits. Rate dependence (at 80 degrees C) on glucose and ATP followed Michaelis-Menten kinetics with apparent Km values of 1.0 and 0.36 mM, respectively; apparent Vmax values were about 370 U mg(-1). The enzyme was highly specific for glucose as phosphoryl acceptor. Besides glucose only 2-deoxyglucose was phosphorylated to some extent, whereas mannose and fructose were not used. With a temperature optimum of 93 degrees C the enzyme is the most thermoactive bacterial ATP-GLK described.
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Affiliation(s)
- Thomas Hansen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany.
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