Inactive enzymatic mutant proteins (phosphoglycerate mutase and enolase) as sugar binders for ribulose-1,5-bisphosphate regeneration reactors
© De et al; licensee BioMed Central Ltd. 2005
Received: 01 December 2004
Accepted: 02 February 2005
Published: 02 February 2005
Carbon dioxide fixation bioprocess in reactors necessitates recycling of D-ribulose1,5-bisphosphate (RuBP) for continuous operation. A radically new close loop of RuBP regenerating reactor design has been proposed that will harbor enzyme-complexes instead of purified enzymes. These reactors will need binders enabling selective capture and release of sugar and intermediate metabolites enabling specific conversions during regeneration. In the current manuscript we describe properties of proteins that will act as potential binders in RuBP regeneration reactors.
We demonstrate specific binding of 3-phosphoglycerate (3PGA) and 3-phosphoglyceraldehyde (3PGAL) from sugar mixtures by inactive mutant of yeast enzymes phosphoglycerate mutase and enolase. The reversibility in binding with respect to pH and EDTA has also been shown. No chemical conversion of incubated sugars or sugar intermediate metabolites were found by the inactive enzymatic proteins. The dissociation constants for sugar metabolites are in the micromolar range, both proteins showed lower dissociation constant (Kd) for 3-phosphoglycerate (655–796 μM) compared to 3-phosphoglyceraldehyde (822–966 μM) indicating higher affinity for 3PGA. The proteins did not show binding to glucose, sucrose or fructose within the sensitivity limits of detection. Phosphoglycerate mutase showed slightly lower stability on repeated use than enolase mutants.
The sugar and their intermediate metabolite binders may have a useful role in RuBP regeneration reactors. The reversibility of binding with respect to changes in physicochemical factors and stability when subjected to repeated changes in these conditions are expected to make the mutant proteins candidates for in-situ removal of sugar intermediate metabolites for forward driving of specific reactions in enzyme-complex reactors.
One of the potential use of sugar and sugar intermediate binding proteins and binders of intermediate sugar metabolites derived from microbes is in new and expanding area of environmental biotechnology particularly in carbon dioxide fixation bioprocess reactors [1, 2]. Accelerated consumption of fossil fuels and other anthropogenic activities have resulted in increased atmospheric levels of the greenhouse gas carbon dioxide (CO2). Sustained increase of atmospheric CO2 has already initiated a chain of events with unintended ecological consequences [3–7]. The reduction in atmospheric carbon dioxide level is highly desirable lest it will have a catastrophic impact upon both the environment and the economy on a global scale [5–7].
Biotechnological process with recombinant catalytic proteins offer contained handling of carbon dioxide and could be one method of abatement of carbon dioxide pollution [8, 9]. Recent advances in biotechnological methods makes possible efficient capture  and fixation of CO2 at emission source/site into concatenated carbon compounds [9, 11]. Such a process starts with initial capture of the carbon dioxide solublized as carbonic acid or bicarbonate . After adjustment of pH using controllers and pH-stat the solution is fed to immobilized Rubisco reactors  where acceptor D-Ribulose-1,5-bisphosphate (RuBP) after CO2 fixation is converted into 3-phosphoglycerate [8, 9]. We have invented a novel scheme which proceeds with no loss of CO2 (unlike cellular biochemical systems) in 11 steps in a series of bioreactors .
For starting up the process, however, a different scheme was used to generate RuBP from D-glucose rather than from 3-PGA . The linear combination of reactors in the 11 step RuBP regeneration process requires large volume and weight and are unsuitable for use in mobile CO2 emitters leaving only the stationary source of emission to be controlled using this technology [8, 9]. These problems are circumvented in a new scheme where enzyme-complex reactors instead of linear combination of purified single enzyme reactors were proposed [1, 2]. In this scheme, the catalytic enzymes have been used as functionally interacting complexes/interactomes.
Sugar and their intermediate metabolites binding proteins derived from microbial and other sources despite being used for various applications [15, 16] have not yet been used in environmental biotechnological applications. However, they are potentially applicable in RuBP recycling. In this report we demonstrate the utility of two inactive mutants of enzymatic proteins: phosphoglycerate mutase (PGDM) and enolase. The inactive mutants of yeast enzymes PGDM [17–19] and enolase [20, 21] were characterized for properties that may render them potentially useful in reactors. We report determination of the enzymatic activity, sugar binding capacity, specificity in binding for different sugar and their metabolites and reversibility in binding with respect to changes in physicochemical factors and stability on repeatedly subjecting to these changes using purified proteins.
Purity of proteins
Chromatographic detection of sugars and intermediate metabolites
Paper chromatography was used for initial qualitative detection of sugars or sugar metabolites (Figure 3A) subsequently thin layer chromatography (Figure 3B) was used for detection and determination of modification as well as for measurements. Relative measurements of spot area with respect to the controls allowed determination of binding as described in methods.
The binding constants of proteins for sugar metabolites.
10 mM Tris-Cl pH 7.5, 50 mM NaCl
655 ± 33
822 ± 42
10 mM Tris-Cl pH 4.0, 50 mM NaCl
10 mM Tris-Cl pH 7.5, 10 mM NaCl, 10 mM MgCl2
676 ± 28
835 ± 38
10 mM Tris-Cl pH 7.5, 10 mM NaCl, 1 mM MgCl2, 15 mM EDTA
10 mM Tris-Cl pH 7.5, 10 mM NaCl, 10 mM MgCl2
796 ± 23
966 ± 31
10 mM Tris-Cl pH 7.5, 10 mM NaCl, 1 mM MgCl2, 15 mM EDTA
Reversibility in binding and repeated use
The stability of proteins with use-cycles.
Number of Cycle when still active*
Microbes (as well as higher organisms) produce a number of binding and metabolizing proteins for sugar and other intermediate metabolic products of sugar metabolism pathways. Complex conversion necessitated using binding entities to enhance reactor performance as well as obtaining converted compounds in purified state.
In the biocatalytic CO2 fixation bioprocess, three modular reactors enables continuous fixation. The first module is Rubisco reactor where CO2 is fixed onto RuBP and converted into 3PGA, the second involves regeneration of ATP which acts as a cofactor for subsequent process and the third being RuBP regeneration [8, 9]. Recently an added module has been devised for efficient capture of CO2, which is constructed before first module . However, the generation of RuBP from converted 3PGAL requires a series of conversion in 11 reactors [8, 9]. In many reactors in this series, the sugar or intermediate metabolites are generated that are not substrates for immediate subsequent reactors. Thus a specific capture and delivery will help eliminate dilution as well as interference in reactors where sugar intermediates are not direct substrate. Towards this goal, three different entities divided into biological and chemical moieties have potential for use. The biological entities include lectins or sugar binding proteins or non-immunogenic origin and inactive mutants of sugar binding enzymes. The chemical entities include the entities that recognize and binds aldehyde, ketones and alcohols. However, most of the biological entities provides high specificity, strong binding, reversible with respect to select physico-chemical conditions. They are also compatible with buffer systems with respect to conversion reactors in the loop where they are likely to be used. For 3PGAL and 3PGA as test sugars we have attempted using PGDM and inactive yeast enolase mutants (S39A, H159A) here. The determination of binding strength by these entities will enable their pilot tests in novel reactors in close loop with 3PGA to RuBP conversion reactors. It appears that the PGDM and enolase mutants are reversible binders and are stable with respect to repeated use-cycles. However, the binding is moderate at best (Kd values are in the range of 655–966 μM). Similar measurements for enolase provides 500 ± 28 and 673 ± 32 μM for binding with 3PGA and 3PGAL indicating that wild type enolase has slightly higher binding affinity for these metabolites. Further enhancement in binding by screening other different inactive enzyme mutants or that from different sources may help find more suitable entities.
In the present report we demonstrate binding without chemical modification of 3PGA and 3PGAL by inactive yeast mutant enzymatic proteins PGDM and enolase. The binding seems to be specific as the proteins were not found to bind other sugars (glucose, fructose or sucrose in mixtures that were subjected to incubation). The binding is reversible with respect to pH and EDTA and proteins retain activity even after repeated use. The MgCl2 cycling seems to have less effect on protein stability with respect to binding and release and could be more suitable for use in larger reactors. While these criteria are suitable for use of the proteins for in-situ separation of sugar metabolites in reactors, but high micromolar dissociation constants (655–966 μM) suggest the moderate or even low binding strength. Finding inactive enzymes with high binding affinity or engineering them for this purpose will improve their utility.
Purified yeast PGDM and recombinant cultures for inactive yeast enolase mutants (S39A and H159A) were obtained from Dr. J. Nairn and Prof. J. M. Brewer as research gift respectively. The enolase mutants were purified following suitable modifications of published protocols [20, 21]. Briefly, the overnight grown yeast cultures were harvested when absorbance values reached 12. The cells were harvested by centrifugation at 4000 × g and disrupted using sonication for 10 min with 20 sec gap and burst cycles and centrifuged at 12000 × g for 20 min. This crude protein solution was subjected to ammonium sulphate precipitation at 75% saturation. After ammonium sulphate precipiration the protein was dialyzed for 16 hours in a dialysis bag (molecular weight cutoff 3000) in 0.1 M Tris-Cl (pH8.5) containing 0.1 M NaCl and 0.1 mM MgCl2, with three changes in buffer solution. Enolase mutants were subjected to ion exchange chromatography for further purification on Acta prime protein purification system (Amersham Pharmacia Biotech, CA) using Q Sepharose column at a flow rate of 0.5 ml /minute at 4°C. Protein was eluted using a NaCl gradient (0.1 M to 0.3 M), about 95 fractions containing 8.6 ml each were collected. The proteins eluted in about conductivity equivalent of 0.1–0.15 M NaCl (fractions 5 to 9). This purified protein was temporarily stored at 4°C and used for subsequent experiments. Proteins were estimated using Bradford's method  using BSA (1 mg/ml) as standard. 10%SDS-PAGE was prepared and subjected to Coomassie blue staining.
Paper and thin layer chromatography
Paper and thin layer chromatography was performed to demonstrate that the purified mutant proteins lacked any sugar modification capacity. Sugar mixtures in appropriate concentration were incubated with Proteins (PGDM or enolase mutants S39A and H159A) for up to 16 hours. At the end of incubation (every 2 hours), the mixtures were centrifuges and the aliquots from experimental mixtures were spotted onto the filter paper chromatograms (Whatman; 3 mm) or on TLC plates. The TLC analyses were performed on Plastic backed 20 cm × 20 cm Silica Gel 60 F254 plates with 0.2 mm layer thickness (Merck). After spotting with an applicator the samples were air-dried and placed in a TLC tank (27 cm × 24 cm × 7 cm) containing the solvent system. For both chromatography, the spots were air-dried and the chromatograms were dipped in the solvent system [60% v/v n-propanol/30% v/v conc.ammonia/10% v/v distilled water] and allowed to run for 5 hours. The chromatograms were removed from the solvent system and subjected to staining. Three different staining techniques were used to detect sugars, ammonium molybdate, silver nitrate and alpha-naphthol staining [23, 24]. For ammonium molybdate staining, the paper chromatogram was dipped in the solution contianing: 5 ml 60 per cent w/w perchloric acid,10 ml and 0.1 N hydrochloric acid,25 ml, 0.4 per cent w/v ammonium molybdate, and made the volume to 100 ml with distilled water. The paper, after drying in a current of warm air for a few minutes to remove excess water, was subjected to heating at 85°C for 7 min in a water-jacketed oven. The spots in the chromatogram were also visualized using alkaline silver oxide reagent. This reagent was composed of two parts: first part containing 0.1 ml saturated aqueous silver nitrate plus 19 ml acetone and second part containing 0.5 g NaOH dissolved in 5 ml water and finally these two parts are added to 100 ml with ethanol. First part was mixed immediately before use and a few drops of water were added, with stirring, until all the AgNO3 is dissolved. The dried chromatogram was then dipped through the silver reagent and allowed to air dry for 10 min and subsequently dipped into ethanolic sodium hydroxide and again allowed to air dry. After the spots are visible, the paper was soaked in dilute (5 mg/l) sodium thiosulfate for 1 minute and rinsed in tap water. The last step dissolves the dark background and allows obtaining a permanent record. For staining with alphanapthol, paper chromatogram was dipped in the following solution: 1 per cent w/v alpha-napthol, 10 per cent v/v orthophosphoric acid and distilled water to make up the volume. The air-dried paper or TLC plate was heated for a few minutes at 85°C in a water-jacketed oven for color development.
Determination of binding parameters
The dissociation constants for protein-sugar binding was estimated by measurements of area in chromatograms. For this purpose covalently immobilized protein A sepharose beads (Pharmacia Biotech, CA) was used. The proteins were immobilized on protein A using Amino link kit (Pierce Chemicals, CA). The known concentration of protein was incubated at room temperature (25°C) with varying concentration of sugar in the range of 1 μM to 1 mM in a 100 μl fixed volume. At the end of incubation (10 min), the mixture was centrifuged at 10000 × g and an aliquot of supernatant was spotted and chromatogram (TLC) was developed. A similar mixture but with BSA coupled beads served as control. Area calibration using varying concentration of sugar with a fixed aliquot spot volume was recorded under identical conditions. From the measurement of area in control and experimental set the free sugar was calculated such bound sugar is control minus sugar left in experimental set. The experimental data was used to draw a Scatchard type plot from where dissociation constant was calculated, represented by P as free protein, L as ligand and PL as the ligand-bound-protein, the dissociation constant is defined as Kd = [Pfree] [Lfree]/ [PL]. The dissociation constant Kd values for PGDM and S39A enolase for 3PGA and 3PGAL were calculated using experimental data using MS excel program.
We thank Dr. Nanasaheb P. Chougule, Mrs. Vaijyanti Thambane and Gauri Bhatt for their help with the experiments. We thank Mr. R. N. Ghosh for his timely administrative assistance.
- Bhattacharya SK: Use of enzyme mixtures for complex biosynthesis. Curr Opin Biotechnol. 2004, 15: 449-455. 10.1016/j.copbio.2004.08.012.View ArticleGoogle Scholar
- Mahato S, De D, Dutta D, Kundu M, Bhattacharya S, Schiavone MT, Bhattacharya SK: Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. Microb Cell Fact. 2004, 3: 7-10.1186/1475-2859-3-7.View ArticleGoogle Scholar
- Victor DG: Strategies for cutting Carbon. Nature. 1998, 395: 837-838. 10.1038/27532.View ArticleGoogle Scholar
- Joos F, Plattner G-K, Stocker TF, Marchal O, Schmittner A: Global warming and marine carbon cycle feedbacks on future atmospheric CO2. Science. 1999, 284: 464-467. 10.1126/science.284.5413.464.View ArticleGoogle Scholar
- Schnur R: The investment Forecast. Nature. 2002, 415: 483-484. 10.1038/415483a.View ArticleGoogle Scholar
- De Leo GA, Gatto M, Caizzi A, Cellina F: The ecological and economic consequences of global climate change. Recent Research Developments in Biotechnol. Bioeng. Edited by: Bhattacharya SK, Chakrabarti S, Mal TK. 2002, Research Signpost, Kerala, 163-183.Google Scholar
- De Leo GA, Rizzi L, Caizzi A, Gatto M: Carbon emissions. The economic benefits of the Kyoto Protocol. Nature. 2001, 413: 478-479. 10.1038/35097156.View ArticleGoogle Scholar
- Bhattacharya SK: Conversion of carbon dioxide from ICE exhausts by fixation. US patent number 6258335. 2001, 1-18.Google Scholar
- Bhattacharya S, Chakrabarti S, Bhattacharya SK: Bioprocess for recyclable CO2 fixation: A general description. Recent Research Developments in Biotechnol Bioeng. Edited by: Bhattacharya SK, Chakrabarti S, Mal TK. 2002, Research Signpost, Kerala, 109-120.Google Scholar
- Bhattacharya S, Nayak A, Schiavone M, Bhattacharya SK: Solubilization and Concentration of Carbon dioxide: Novel Spray reactors with immobilized Carbonic anhydrase. Biotechnol Bioeng. 2004, 86: 37-46. 10.1002/bit.20042.View ArticleGoogle Scholar
- Chakrabarti S, Bhattacharya S, Bhattacharya SK: Biochemical engineering: cues from cells. Trends Biotechnol. 2003, 21: 204-209. 10.1016/S0167-7799(03)00077-5.View ArticleGoogle Scholar
- Chakrabarti S, Bhattacharya S, Bhattacharya SK: Immobilization of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: A step toward carbon dioxide fixation bioprocess. Biotechnol Bioeng. 2003, 81: 705-711. 10.1002/bit.10515.View ArticleGoogle Scholar
- Bhattacharya S, Schiavone M, Gomes J, Bhattacharya SK: Cascade of bioreactors in series for conversion of 3-phospho-D-glycerate into D-ribulose-1,5-bisphosphate: kinetic parameters of enzymes and operation variables. J Biotechnol. 2004, 111: 203-217. 10.1016/j.jbiotec.2004.04.002.View ArticleGoogle Scholar
- Bhattacharya S, Nayak A, Gomes J, Bhattacharya SK: A continuous process for production of D-ribulose-1,5-bisphosphate from D-glucose. Biochem Eng J. 2004, 19: 229-235. 10.1016/j.bej.2004.02.002.View ArticleGoogle Scholar
- Raphael SJ: The meanings of markers: ancillary techniques in diagnosis of thyroid neoplasia. Endocr Pathol. 2002, 13: 301-311. 10.1385/EP:13:4:301.View ArticleGoogle Scholar
- Jackson A, Kemp P, Giddings J, Sugar R: Development and validation of a lectin-based assay for the quantitation of rat respiratory mucin. Novartis Found Symp. 2002, 248: 94-105.View ArticleGoogle Scholar
- Nairn J, Duncan D, Price NE, Kelly SM, Fothergill-Gilmore LA, Uhrinova S, Barlow PN, Rigden DJ, Price NC: Characterization of active-site mutants of Schizosaccharomyces pombe phosphoglycerate mutase. Elucidation of the roles of amino acids involved in substrate binding and catalysis. Eur J Biochem. 2000, 267: 7065-7074. 10.1046/j.1432-1327.2000.01802.x.View ArticleGoogle Scholar
- Nairn J, Price NC, Kelly SM, Rigden D, Fothergill-Gilmore LA, Krell T: Phosphoglycerate mutase from Schizosaccharomyces pombe: development of an expression system and characterisation of three histidine mutants of the enzyme. Biochim Biophys Acta. 1996, 296: 69-75.View ArticleGoogle Scholar
- Price RM, Nairn J, Price NC, Fothergill-Gilmore LA: The reaction of phosphoglycerate mutase from Schizosaccharomyces pombe with diethylpyrocarbonate. Biochem Soc Trans. 1996, 24: 324S-View ArticleGoogle Scholar
- Brewer JM, Glover CVC, Holland MJ, Lebioda L: Significance of the enzymatic properties of yeast S39A enolase to the catalytic mechanism. Biochimica et Biophysica Acta. 1998, 1383: S351-355.View ArticleGoogle Scholar
- Brewer JM, Glover CVC, Holland MJ, Lebioda L: Effect of site-directed mutagenesis of His 373 of yeast enolase on some its physical and enzymatic properties. Biochimica et Biophysica Acta. 1997, 1340: 88-96.View ArticleGoogle Scholar
- Bradford MM: A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976, 72: 248-254.View ArticleGoogle Scholar
- Hanes CS, Isherwood FA: Seperation of the phosphoric esters on the paper chromatogram. Nature. 1949, 164: 1107-1112.View ArticleGoogle Scholar
- Borders CL: Descending paper chromatography of oligosaccharides. Journal of Chemical Education. 1972, 437: 438-Google Scholar
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