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Sabotič J, Bayram E, Ezra D, Gaudêncio SP, Haznedaroğlu BZ, Janež N, Ktari L, Luganini A, Mandalakis M, Safarik I, Simes D, Strode E, Toruńska-Sitarz A, Varamogianni-Mamatsi D, Varese GC, Vasquez MI. A guide to the use of bioassays in exploration of natural resources. Biotechnol Adv 2024; 71:108307. [PMID: 38185432 DOI: 10.1016/j.biotechadv.2024.108307] [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: 07/24/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.
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Affiliation(s)
- Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia.
| | - Engin Bayram
- Institute of Environmental Sciences, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - David Ezra
- Department of Plant Pathology and Weed Research, ARO, The Volcani Institute, P.O.Box 15159, Rishon LeZion 7528809, Israel
| | - Susana P Gaudêncio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; UCIBIO - Applied Biomolecular Sciences Unit, Department of Chemistry, Blue Biotechnology & Biomedicine Lab, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Berat Z Haznedaroğlu
- Institute of Environmental Sciences, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Nika Janež
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Leila Ktari
- B3Aqua Laboratory, National Institute of Marine Sciences and Technologies, Carthage University, Tunis, Tunisia
| | - Anna Luganini
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
| | - Ivo Safarik
- Department of Nanobiotechnology, Biology Centre, ISBB, CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Dina Simes
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal; 2GenoGla Diagnostics, Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Evita Strode
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Riga LV-1007, Latvia
| | - Anna Toruńska-Sitarz
- Department of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, 81-378 Gdynia, Poland
| | - Despoina Varamogianni-Mamatsi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
| | | | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 3036 Limassol, Cyprus
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Majumdar A, Kar RK. Orchestration of Cu-Zn SOD and class III peroxidase with upstream interplay between NADPH oxidase and PM H +-ATPase mediates root growth in Vigna radiata (L.) Wilczek. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:248-256. [PMID: 30537611 DOI: 10.1016/j.jplph.2018.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Post-germination plant growth depends on the regulation of reactive oxygen species (ROS) metabolism, spatiotemporal pH changes and Ca+2 homeostasis, whose potential integration has been studied during Vigna radiata (L.) Wilczek root growth. The dissipation of proton (H+) gradients across plasma membrane (PM) by CCCP (protonophore) and the inhibition of PM H+-ATPase by sodium orthovanadate repressed SOD (superoxide dismutase; EC 1.15.1.1) activity as revealed by spectrophotometric and native PAGE assay results. Similar results derived from treatment with DPI (NADPH oxidase inhibitor) and Tiron (O2- scavenger) denote a functional synchronization of SOD, PM H+-ATPase and NOX, as the latter two enzymes are substrate sources for SOD (H+ and O2-, respectively) and are involved in a feed-forward loop. After SOD inactivation, a decline in apoplastic H2O2 content was observed in each treatment group, emerging as a possible cause of the diminution of class III peroxidase (Prx; EC 1.11.1.7), which utilizes H2O2 as a substrate. In agreement with the pivotal role of Ca+2 in PM H+-ATPase and NOX activation, Ca+2 homeostasis antagonists, i.e., LaCl3 (Ca+2 channel inhibitor), EGTA (Ca+2 chelator) and LiCl (endosomal Ca+2 release blocker), inhibited both SOD and Prx. Finally, a drastic reduction in apoplastic OH (hydroxyl radical) concentrations (induced by each treatment, leading to Prx inhibition) was observed via fluorometric analysis. A consequential inhibition of root growth observed under each treatment denotes the importance of the orchestrated functioning of PM H+-ATPase, NOX, Cu-Zn SOD and Prx during root growth. A working model demonstrating postulated enzymatic synchronization with an intervening role of Ca+2 is proposed.
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Affiliation(s)
- Arkajo Majumdar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Visva-Bharati University, Santiniketan, 731235, West Bengal, India; Department of Botany, City College, 102/1 Raja Rammohan Sarani, Kolkata, 700009, West Bengal, India
| | - Rup Kumar Kar
- Plant Physiology and Biochemistry Laboratory, Department of Botany, Visva-Bharati University, Santiniketan, 731235, West Bengal, India.
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Carrillo JB, Gomez-Casati DF, Busi MV, Martín M. Development of fast and simple chromogenic methods for glucan phosphatases in-gel activity assays. Anal Biochem 2017; 517:36-39. [PMID: 27836260 DOI: 10.1016/j.ab.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
Glucan phosphatases are essential for normal starch degradation in plants and glycogen metabolism in mammals. Here we develop two chromogenic methods for the detection of glucan phosphatase activity in situ after non denaturing poliacrylamide gel electrophoresis; one method uses pNPP and the second one applies BCIP/NBT. The assays are sensitive, fast, simple, reliable and cost-effective preventing the use of radioactive or fluorogenic compounds. Taking advantage of an efficient separation method combined with the reported assays it is possible to obtain information about oligomeric state of the active enzymes as well as to simultaneously detect glucan substrate binding and phosphatase activity.
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Affiliation(s)
- Julieta B Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Maria V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
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Auslender EL, Dorion S, Dumont S, Rivoal J. Expression, purification and characterization of Solanum tuberosum recombinant cytosolic pyruvate kinase. Protein Expr Purif 2015; 110:7-13. [PMID: 25573389 DOI: 10.1016/j.pep.2014.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022]
Abstract
The cDNA encoding for a Solanum tuberosum cytosolic pyruvate kinase 1 (PKc1) highly expressed in tuber tissue was cloned in the bacterial expression vector pProEX HTc. The construct carried a hexahistidine tag in N-terminal position to facilitate purification of the recombinant protein. Production of high levels of soluble recombinant PKc1 in Escherichia coli was only possible when using a co-expression strategy with the chaperones GroES-GroEL. Purification of the protein by Ni(2 +) chelation chromatography yielded a single protein with an apparent molecular mass of 58kDa and a specific activity of 34unitsmg(-1) protein. The recombinant enzyme had an optimum pH between 6 and 7. It was relatively heat stable as it retained 80% of its activity after 2min at 75°C. Hyperbolic saturation kinetics were observed with ADP and UDP whereas sigmoidal saturation was observed during analysis of phosphoenolpyruvate binding. Among possible effectors tested, aspartate and glutamate had no effect on enzyme activity, whereas α-ketoglutarate and citrate were the most potent inhibitors. When tested on phosphoenolpyruvate saturation kinetics, these latter compounds increased S0.5. These findings suggest that S. tuberosum PKc1 is subject to a strong control by respiratory metabolism exerted via citrate and other tricarboxylic acid cycle intermediates.
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Affiliation(s)
- Evgenia L Auslender
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Qc H1X 2B2, Canada
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Qc H1X 2B2, Canada
| | - Sébastien Dumont
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Qc H1X 2B2, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Qc H1X 2B2, Canada.
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Kumari U, Vishwakarma RK, Sonawane P, Abbassi S, Khan BM. Biochemical characterization of recombinant mevalonate kinase from Bacopa monniera. Int J Biol Macromol 2014; 72:776-83. [PMID: 25281875 DOI: 10.1016/j.ijbiomac.2014.09.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
Mevalonate kinase (MK; ATP: mevalonate 5-phosphotransferase; EC 2.7.1.36) plays a key role in isoprenoid biosynthetic pathway in plants. MK catalyzes the phosphorylation of mevalonate to form mevalonate-5-phosphate. The recombinant BmMK was cloned and over-expressed in E. coli BL21 (DE3), and purified to homogeneity by affinity chromatography followed by gel filtration. Optimum pH and temperature for forward reaction was found to be 7.0 and 30 °C, respectively. The enzyme was most stable at pH 8 at 25 °C with deactivation rate constant (Kd*) 1.398 × 10(-4) and half life (t1/2) 49 h. pH activity profile of BmMK indicates the involvement of carboxylate ion, histidine, lysine, arginine or aspartic acid at the active site of enzyme. Activity of recombinant BmMK was confirmed by phosphorylation of RS-mevalonate in the presence of Mg(2+), having Km and Vmax 331.9 μM and 719.1 pKat μg(-1), respectively. The values of kcat and kcat/Km for RS-mevalonate were determined to be 143.82 s(-1) and 0.43332 M(-1) s(-1) and kcat and kcat/Km values for ATP were found 150.9 s(-1) and 1.023 M(-1) s(-1). The metal ion studies suggested that BmMK is a metal dependent enzyme and highly active in the presence of MgCl2.
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Affiliation(s)
- Uma Kumari
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Rishi K Vishwakarma
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Prashant Sonawane
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Shakeel Abbassi
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
| | - Bashir M Khan
- Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India.
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Li Y, Deng D, Zhang X, Zhang H, Wang C, Chen P. Direct detection of rutin-degrading isozymes with polyacrylamide gel electrophoresis. Anal Biochem 2013; 443:240-2. [DOI: 10.1016/j.ab.2013.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/02/2013] [Accepted: 09/09/2013] [Indexed: 11/16/2022]
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Guerrero-Mendiola C, Oria-Hernández J, Ramírez-Silva L. Kinetics of the thermal inactivation and aggregate formation of rabbit muscle pyruvate kinase in the presence of trehalose. Arch Biochem Biophys 2009; 490:129-36. [PMID: 19703407 DOI: 10.1016/j.abb.2009.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/19/2009] [Accepted: 08/19/2009] [Indexed: 11/29/2022]
Abstract
In a previous study we found that 30-40% dimethylsulfoxide induces the active conformation of rabbit muscle pyruvate kinase. Because dimethylsulfoxide is known to perturb structure and function of many proteins, we have explored the effect of trehalose on the kinetics of thermal inactivation and stability of pyruvate kinase; this is because trehalose, in contrast to dimethyl sulfoxide, is totally excluded from the hydration shell of proteins. The results show that 600 mM trehalose inhibits the activity of pyruvate kinase by about 20% at 25 degrees C, however, trehalose protects pyruvate kinase from thermal inactivation at 60 degrees C, increases the Tm(app) of unfolding by 7.2 degrees C, induces a more compact state, and stabilizes its tetrameric structure. The inactivation process is irreversible due to the formation of protein aggregates. Trehalose diminishes the rate of formation of intermediates with propensity to aggregate, but does not affect the extent of aggregation. Remarkably, trehalose affects the aggregation process by inducing aggregates with amyloid-like characteristics.
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Affiliation(s)
- Carlos Guerrero-Mendiola
- Departamento de Bioquímica, Facultad de Medicina, Apartado Postal 70-159, Universidad Nacional Autónoma de México, 04510 México, DF, Mexico
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Müller K, Doubnerová V, Synková H, Cerovská N, Ryslavá H. Regulation of phosphoenolpyruvate carboxylase in PVY(NTN)-infected tobacco plants. Biol Chem 2009; 390:245-51. [PMID: 19090725 DOI: 10.1515/bc.2009.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The effect of viral infection on the regulation of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) in Nicotiana tabacum L. leaves was studied. PEPC activity was 3 times higher in infected plant leaves compared to healthy plants. Activity of plant PEPC can be regulated, e.g., by de novo synthesis or reversible phosphorylation. The reason for the increase of PEPC activity as a consequence of PVY(NTN) infection was studied. The amount of PEPC determined by Western blot analysis or by relative estimation of PEPC mRNA by real-time PCR did not differ in control and PVY(NTN)-infected plants. Changes in posttranslational modification of PEPC by phosphorylation were evaluated by comparing activity of the native and the dephosphorylated enzyme. The infected plants were characterized by a higher decrease of the enzyme activity after its dephosphorylation, which indicated a higher phosphorylation level. Immunochemical detection of phosphoproteins by Western blot analysis showed a more intensive band corresponding to PEPC from the infected material. This strengthens the hypothesis of an infection-related phosphorylation, which could be part of the plant's response to pathogen attack. The physiological implications of the increase in PEPC activity during PVY(NTN) infection are discussed.
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Affiliation(s)
- Karel Müller
- Department of Biochemistry, Faculty of Natural Science, Charles University, Hlavova 2030, CZ-128 00 Prague 2, Czech Republic.
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Oliver SN, Lunn JE, Urbanczyk-Wochniak E, Lytovchenko A, van Dongen JT, Faix B, Schmälzlin E, Fernie AR, Geigenberger P. Decreased expression of cytosolic pyruvate kinase in potato tubers leads to a decline in pyruvate resulting in an in vivo repression of the alternative oxidase. PLANT PHYSIOLOGY 2008; 148:1640-54. [PMID: 18829984 PMCID: PMC2577264 DOI: 10.1104/pp.108.126516] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 09/24/2008] [Indexed: 05/18/2023]
Abstract
The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo.
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Affiliation(s)
- Sandra N Oliver
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Feria AB, Alvarez R, Cochereau L, Vidal J, García-Mauriño S, Echevarría C. Regulation of phosphoenolpyruvate carboxylase phosphorylation by metabolites and abscisic acid during the development and germination of barley seeds. PLANT PHYSIOLOGY 2008; 148:761-74. [PMID: 18753284 PMCID: PMC2556803 DOI: 10.1104/pp.108.124982] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 08/14/2008] [Indexed: 05/20/2023]
Abstract
During barley (Hordeum vulgare) seed development, phosphoenolpyruvate carboxylase (PEPC) activity increased and PEPC-specific antibodies revealed housekeeping (103-kD) and inducible (108-kD) subunits. Bacterial-type PEPC fragments were immunologically detected in denatured protein extracts from dry and imbibed conditions; however, on nondenaturing gels, the activity of the recently reported octameric PEPC (in castor [Ricinus communis] oil seeds) was not detected. The phosphorylation state of the PEPC, as judged by l-malate 50% inhibition of initial activity values, phosphoprotein chromatography, and immunodetection of the phosphorylated N terminus, was found to be high between 8 and 18 d postanthesis (DPA) and during imbibition. In contrast, the enzyme appeared to be in a low phosphorylation state from 20 DPA up to dry seed. The time course of 32/36-kD, Ca(2+)-independent PEPC kinase activity exhibited a substantial increase after 30 DPA that did not coincide with the PEPC phosphorylation profile. This kinase was found to be inhibited by l-malate and not by putative protein inhibitors, and the PEPC phosphorylation status correlated with high glucose-6-phosphate to malate ratios, thereby suggesting an in vivo metabolic control of the kinase. PEPC phosphorylation was also regulated by photosynthate supply at 11 DPA. In addition, when fed exogenously to imbibing seeds, abscisic acid significantly increased PEPC kinase activity. This was further enhanced by the cytosolic protein synthesis inhibitor cycloheximide but blocked by protease inhibitors, thereby suggesting that the phytohormone acts on the stability of the kinase. We propose that a similar abscisic acid-dependent effect may contribute to produce the increase in PEPC kinase activity during desiccation stages.
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Affiliation(s)
- Ana-Belén Feria
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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Gennidakis S, Rao S, Greenham K, Uhrig RG, O'Leary B, Snedden WA, Lu C, Plaxton WC. Bacterial- and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:839-49. [PMID: 17894783 DOI: 10.1111/j.1365-313x.2007.03274.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Two classes of phosphoenolpyruvate carboxylase (PEPC) sharing the same 107-kDa catalytic subunit (p107) were previously purified from developing castor oil seed (COS) endosperm. The association of p107 with an immunologically unrelated 64-kDa polypeptide (p64) causes pronounced physical and kinetic differences between the Class-1 PEPC p107 homotetramer and Class-2 PEPC p107/p64 hetero-octamer. Tryptic peptide sequencing matched p64 to the deduced C-terminal half of several bacterial-type PEPCs (BTPCs) of vascular plants. Immunoblots probed with anti-(COS p64 peptide or p107)-IgG established that: (i) BTPC exists in vivo as an approximately 118-kDa polypeptide (p118) that is rapidly truncated to p64 by an endogenous cysteine endopeptidase during incubation of COS extracts on ice, and (ii) mature and germinated COS contain Class-1 PEPC and p107, but no detectable Class-2 PEPC nor p118. Non-denaturing PAGE, in-gel PEPC activity staining and immunoblotting of developing COS extracts demonstrated that p118 and p107 are subunits of the non-proteolysed approximately 910-kDa Class-2 PEPC complex. As total PEPC activity of clarified COS extracts was unaffected following p118 truncation to p64, the BTPC p118 may function as a regulatory rather than catalytic subunit of the Class-2 PEPC. Moreover, recombinant AtPPC3 and AtPPC4 (Arabidopsis orthologs of COS p107 and p118) expressed as active and inactive PEPCs, respectively. Cloning of cDNAs encoding p118 (RcPpc4) and p107 (RcPpc3) confirmed their respective designation as bacterial- and plant-type PEPCs. Levels of RcPpc3 and RcPpc4 transcripts generally mirrored the respective amounts of p107 and p118. The collective findings provide insights into the molecular features and functional significance of vascular plant BTPCs.
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Affiliation(s)
- Sam Gennidakis
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Moellering ER, Ouyang Y, Mamedov TG, Chollet R. The two divergent PEP-carboxylase catalytic subunits in the green microalga Chlamydomonas reinhardtii respond reversibly to inorganic-N supply and co-exist in the high-molecular-mass, hetero-oligomeric Class-2 PEPC complex. FEBS Lett 2007; 581:4871-6. [PMID: 17888908 DOI: 10.1016/j.febslet.2007.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/07/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
Abstract
Our recent molecular studies revealed two divergent PEP-carboxylase (PEPC [Ppc]) encoding genes in the green microalga Chlamydomonas reinhardtii, CrPpc1 and CrPpc2, which are coordinately responsive to changes in inorganic-N and -C supply at the transcript level [Mamedov, T.G., Moellering, E.R. and Chollet, R. (2005) Identification and expression analysis of two inorganic C- and N-responsive genes encoding novel and distinct molecular forms of eukaryotic phosphoenolpyruvate carboxylase in the green microalga C. reinhardtii, Plant J. 42, 832-843]. Here, we report the distribution of these two encoded catalytic subunits in the minor Class-1 and predominant Class-2 PEPC enzyme-forms, the latter of which is a novel high-molecular-mass, hetero-oligomeric complex containing both CrPpc1 (p109) and CrPpc2 (p131) polypeptides. The Class-1 enzyme, however, is a typical PEPC homotetramer comprised solely of p109. We also document that the amount of both CrPpc1/2 catalytic subunits is up-/down-regulated by varying levels of NH(4)(+) supplied to the culture medium.
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Affiliation(s)
- Eric R Moellering
- Department of Biochemistry, University of Nebraska-Lincoln, George W. Beadle Center, Lincoln, NE 68588-0664, USA
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Andre C, Froehlich JE, Moll MR, Benning C. A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis. THE PLANT CELL 2007; 19:2006-22. [PMID: 17557808 PMCID: PMC1955724 DOI: 10.1105/tpc.106.048629] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Glycolysis is a ubiquitous pathway thought to be essential for the production of oil in developing seeds of Arabidopsis thaliana and oil crops. Compartmentation of primary metabolism in developing embryos poses a significant challenge for testing this hypothesis and for the engineering of seed biomass production. It also raises the question whether there is a preferred route of carbon from imported photosynthate to seed oil in the embryo. Plastidic pyruvate kinase catalyzes a highly regulated, ATP-producing reaction of glycolysis. The Arabidopsis genome encodes 14 putative isoforms of pyruvate kinases. Three genes encode subunits alpha, beta(1), and beta(2) of plastidic pyruvate kinase. The plastid enzyme prevalent in developing seeds likely has a subunit composition of 4alpha4beta(1), is most active at pH 8.0, and is inhibited by Glu. Disruption of the gene encoding the beta(1) subunit causes a reduction in plastidic pyruvate kinase activity and 60% reduction in seed oil content. The seed oil phenotype is fully restored by expression of the beta(1) subunit-encoding cDNA and partially by the beta(2) subunit-encoding cDNA. Therefore, the identified pyruvate kinase catalyzes a crucial step in the conversion of photosynthate into oil, suggesting a preferred plastid route from its substrate phosphoenolpyruvate to fatty acids.
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Affiliation(s)
- Carl Andre
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Tripodi KE, Turner WL, Gennidakis S, Plaxton WC. In vivo regulatory phosphorylation of novel phosphoenolpyruvate carboxylase isoforms in endosperm of developing castor oil seeds. PLANT PHYSIOLOGY 2005; 139:969-78. [PMID: 16169958 PMCID: PMC1256010 DOI: 10.1104/pp.105.066647] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Our previous research characterized two phosphoenolpyruvate (PEP) carboxylase (PEPC) isoforms (PEPC1 and PEPC2) from developing castor oil seeds (COS). The association of a shared 107-kD subunit (p107) with an immunologically unrelated bacterial PEPC-type 64-kD polypeptide (p64) leads to marked physical and kinetic differences between the PEPC1 p107 homotetramer and PEPC2 p107/p64 heterooctamer. Here, we describe the production of antiphosphorylation site-specific antibodies to the conserved p107 N-terminal serine-6 phosphorylation site. Immunoblotting established that the serine-6 of p107 is phosphorylated in COS PEPC1 and PEPC2. This phosphorylation was reversed in vitro following incubation of clarified COS extracts or purified PEPC1 or PEPC2 with mammalian protein phosphatase type 2A and is not involved in a potential PEPC1 and PEPC2 interconversion. Similar to other plant PEPCs examined to date, p107 phosphorylation increased PEPC1 activity at pH 7.3 by decreasing its K(m)(PEP) and sensitivity to L-malate inhibition, while enhancing glucose-6-P activation. By contrast, p107 phosphorylation increased PEPC2's K(m)(PEP) and sensitivity to malate, glutamic acid, and aspartic acid inhibition. Phosphorylation of p107 was promoted during COS development (coincident with a >5-fold increase in the I(50) [malate] value for total PEPC activity in desalted extracts) but disappeared during COS desiccation. The p107 of stage VII COS became fully dephosphorylated in planta 48 h following excision of COS pods or following 72 h of dark treatment of intact plants. The in vivo phosphorylation status of p107 appears to be modulated by photosynthate recently translocated from source leaves into developing COS.
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Affiliation(s)
- Karina E Tripodi
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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Saavedra E, Olivos A, Encalada R, Moreno-Sánchez R. Entamoeba histolytica: kinetic and molecular evidence of a previously unidentified pyruvate kinase. Exp Parasitol 2004; 106:11-21. [PMID: 15013784 DOI: 10.1016/j.exppara.2004.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2003] [Revised: 09/23/2003] [Accepted: 01/28/2004] [Indexed: 11/22/2022]
Abstract
We report the kinetic characterization of a previously unidentified pyruvate kinase (PK) activity in extracts from Entamoeba histolytica trophozoites. This activity was about 74% of the activity of pyruvate phosphate dikinase. EhPK differed from most PKs in that its pH optimum was 5.5-6.5 and was inhibited by high PEP concentrations (1-5mM); these are concentrations at which PK is usually assayed. The optimal temperature was above 40 degrees C with negligible activity below 20 degrees C. EhPK exhibited hyperbolic kinetics with respect to both PEP (K(m) = 0.018 mM) and ADP (K(m) = 1.05 mM). However, it exhibited a sigmoidal behavior with respect to PEP at sub-saturating ADP concentrations. EhPK did not require monovalent cations for activity. Fructose-1,6 bisphosphate was a potent non-essential activator; it increased the affinity for ADP without modification of the V(max) or the affinity for PEP. Phosphate, citrate, malate, and alpha-ketoglutarate significantly inhibited EhPK activity. A putative EhPK gene fragment found in EhDNA was analyzed. The data indicate that E. histolytica trophozoites contain an active PK, which might contribute to the generation of glycolytic ATP for parasite survival.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México D.F. 14080, Mexico.
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Blonde JD, Plaxton WC. Structural and kinetic properties of high and low molecular mass phosphoenolpyruvate carboxylase isoforms from the endosperm of developing castor oilseeds. J Biol Chem 2003; 278:11867-73. [PMID: 12519778 DOI: 10.1074/jbc.m211269200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is believed to play an important role in producing malate as a substrate for fatty acid synthesis by leucoplasts of the developing castor oilseed (COS) endosperm. Two kinetically distinct isoforms of COS PEPC were resolved by gel filtration chromatography and purified. PEPC1 is a typical 410-kDa homotetramer composed of 107-kDa subunits (p107). In contrast, PEPC2 exists as an unusual 681-kDa hetero-octamer composed of the same p107 found in PEPC1 and an associated 64-kDa polypeptide (p64) that is structurally and immunologically unrelated to p107. Relative to PEPC1, PEPC2 demonstrated significantly enhanced thermal stability and a much lower sensitivity to allosteric activators (Glc-6-P, Glc-1-P, Fru-6-P, glycerol-3-P) and inhibitors (Asp, Glu, malate) and pH changes within the physiological range. Nondenaturing PAGE of clarified extracts followed by in-gel PEPC activity staining indicated that the ratio of PEPC1:PEPC2 increases during COS development such that only PEPC1 is detected in mature COS. Dissimilar developmental profiles and kinetic properties support the hypotheses that (i) PEPC1 functions to replenish dicarboxylic acids consumed through transamination reactions required for storage protein synthesis, whereas (ii) PEPC2 facilitates PEP flux to malate in support of fatty acid synthesis. Interestingly, the respective physical and kinetic properties of COS PEPC1 and PEPC2 are remarkably comparable with those of the homotetrameric low M(r) Class 1 and heteromeric high M(r) Class 2 PEPC isoforms of unicellular green algae.
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Affiliation(s)
- James D Blonde
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Tang GQ, Hardin SC, Dewey R, Huber SC. A novel C-terminal proteolytic processing of cytosolic pyruvate kinase, its phosphorylation and degradation by the proteasome in developing soybean seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:77-93. [PMID: 12662311 DOI: 10.1046/j.1365-313x.2003.01711.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cytosolic pyruvate kinase (ATP:pyruvate 2-O-phosphotransferase, EC 2.7.1.40) is an important glycolytic enzyme, but the post-translational regulation of this enzyme is poorly understood. Sequence analysis of the soybean seed enzyme suggested the potential for two phosphorylation sites: site-1 (FVRKGS220DLVN) and site-2 (VLTRGGS407TAKL). Sequence- and phosphorylation state-specific antipeptide antibodies established that cytosolic pyruvate kinase (PyrKinc) is phosphorylated at both sites in vivo. However, by SDS-PAGE, the phosphorylated polypeptides were found to be smaller (20-51 kDa) than the full length (55 kDa). Biochemical separations of seed proteins by size exclusion chromatography and sucrose-density gradient centrifugation revealed that the phosphorylated polypeptides were associated with 26S proteasomes. The 26S proteasome particle in developing seeds was determined to be of approximately 1900 kDa. In vitro, the 26S proteasome degraded associated PyrKinc polypeptides, and this was blocked by proteasome-specific inhibitors such as MG132 and NLVS. By immunoprecipitation, we found that some part of the phosphorylated PyrKinc was conjugated to ubiquitin and shifted to high molecular mass forms in vivo. Moreover, recombinant wild-type PyrKinc was ubiquitinated in vitro to a much greater extent than the S220A and S407A mutant proteins, suggesting a link between phosphorylation and ubiquitination. In addition, during seed development, a progressive accumulation of a C-terminally truncated polypeptide of approximately 51 kDa was observed that was in parallel with a loss of the full-length 55 kDa polypeptide. Interestingly, the C-terminal 51 kDa truncation showed not only pyruvate kinase activity but also activation by aspartate. Collectively, the results suggest that there are two pathways for PyrKinc modification at the post-translational level. One involves partial C-terminal truncation to generate a 51 kDa pyruvate kinase subunit which might have altered regulatory properties and the other involves phosphorylation and ubiquitin conjugation that targets the protein to the 26S proteasome for complete degradation.
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Affiliation(s)
- Guo-Qing Tang
- US Department of Agriculture, Agricultural Research Service, North Carolina State University, Raleigh, NC 27695-7631, USA
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