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Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate
Microbial Cell Factories volume 3, Article number: 7 (2004)
Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology. The fixation of carbon dioxide at emission source has recently emerged as a technology with potentially significant implications for environmental biotechnology. Carbon dioxide is fixed onto a five carbon sugar D-ribulose-1,5-bisphosphate. We present a review of enzymatic and non-enzymatic binding proteins, for 3-phosphoglycerate (3PGA), 3-phosphoglyceraldehyde (3PGAL), dihydroxyacetone phosphate (DHAP), xylulose-5-phosphate (X5P) and ribulose-1,5-bisphosphate (RuBP) which could be potentially used in reactors regenerating RuBP from 3PGA. A series of reactors combined in a linear fashion has been previously shown to convert 3-PGA, (the product of fixed CO2 on RuBP as starting material) into RuBP (Bhattacharya et al., 2004; Bhattacharya, 2001). This was the basis for designing reactors harboring enzyme complexes/mixtures instead of linear combination of single-enzyme reactors for conversion of 3PGA into RuBP. Specific sugars in such enzyme-complex harboring reactors requires removal at key steps and fed to different reactors necessitating reversible sugar binders. In this review we present an account of existing microbial sugar binding proteins and their potential utility in these operations.
Rapid industrialization has led to a dramatically accelerated consumption of fossil fuels with a consequent increase in atmospheric levels of the greenhouse gas carbon dioxide (CO2). This sustained increase of atmospheric CO2 has already initiated a chain of events with negative ecological consequences [1–3]. Failure to reduce these greenhouse gas emissions will have a catastrophic impact upon both the environment and the economy on a global scale [4, 5]. The reduction has to be brought about by global concerted effort by all countries in order to be effective and meaningful.
At one end of the spectrum – that of generation and utilization of energy resulting in generation of carbon dioxide – hydrocarbons serve as intermediaries for energy storage. Hydrocarbons are not energy by themselves but store energy in their bonds, which is released during combustion. They are thus intermediates for obtaining stored bond energy within them and carbon dioxide is emitted as a consequence of combustion to extract this stored energy. In recent times hydrogen has received renewed attention as the potential replacement for hydrocarbons [6–10]. However, hydrogen too is an intermediary for obtaining stored bond energy. Recent reports suggest that hydrogen as intermediary may not be entirely free from problems. Also, the problems from use of hydrogen as fuel are yet to be fully realized or foreseen [11, 12]. In all these endeavors a key question, that whether the hydrocarbons will be still retained as intermediaries in energy utilization and the problem of air pollution caused as a result of their combustion can be technologically ameliorated, has not been looked in as much detail as perhaps it should have been. This can possibly be achieved by contained handling of carbon dioxide. The contained handling and fixation of CO2 can be achieved biotechnologically, chemically or by a combination of both.
Sugar binding proteins derived from microbial and other sources have been used for various applications such as diagnostics and affinity purification [13, 14], however they have not been used in environmental biotechnological applications. The possibility of their potential application in environmental biotechnology and review of a few potential candidates is presented here.
The methods in environmental biotechnology that enables efficient capture  and fixation of CO2 at emission source/site into concatenated carbon compounds has been pioneered by our group [16–19]. The first part in the biocatalytic carbon dioxide fixation is the capture of gaseous CO2. We have pioneered novel reactors employing immobilized carbonic anhydrase for this purpose . Subsequent to capture the carbon dioxide becomes 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 [16, 17]. However, inasmuch as the recycling of acceptor RuBP is central to continuous CO2 fixation, we have invented a novel scheme (Figure 1), which proceeds with no loss of CO2 (unlike cellular biochemical systems) in 11 steps in a series of bioreactors . This scheme is very different from generation of RuBP from D-glucose for start-up process  and employing 11 steps in different reactors requiring large volume and weight. The linear combination of reactors with large volume and weight are unsuitable for use with mobile CO2 emitters leaving only the stationary source of emission to be controlled using this technology . To circumvent these problems we have devised a new scheme presented in Figure 2. Based on this scheme, we have designed enzymes as functionally interacting complexes/interactomes or successive conversion in radial flow with layers of uniformly oriented enzymes in concentric circle with axial collection flow system for three enzymes in first reactor for the scheme presented in Figure 2. The four reactors harboring enzymatic complexes/mixtures replace the current 11 reactors. This leads to a faster conversion rate and requires less volume and material weight. However, 4 sugar moieties [3-phosphoglyceraldehyde (3PGAL), Dihydroxyacetone phosphate (DHAP), Xylulose-5-phosphate (X5P) and Ribulose-1, 5-bisphosphate (RuBP)] must be separated at four key steps, as illustrated in Figure 2. In figure 2, using four symbols with solid for bound state and empty for released state, for potential binders: plus for 3PGA, circle for DHAP, cylinder for X5P and box for RuBP, the possible place for utility of these binders have been depicted. In the course of this review, we will consider the availability of enzymatic proteins and non-enzymatic proteins that would be potentially useful as specific binders for these sugar molecules. With a recombinant mutant enzyme we illustrate that such an approach has potential to be used as an in-situ reversible binding matrix for sugar binding and release.
Potential utilizable sugar binding proteins in RuBP regeneration
Three categories of binding proteins can be potentially employed for differential absorption of sugars and for subsequent elution and feeding the reactors downstream in conversion cascade. These are: mutant enzymatic proteins that retain the ability of binding but completely lack any catalytic activity, lectins or proteins of non-immunogenic origin  having more than one binding site for the sugar (in nature they cause agglutination of due to sugar binding at multiple sites) and mutant or wild type receptors that binds sugars but are incapable of eliciting further biological activities. The desirable proteins in all these categories are those for which binding affinity is high in a condition close to pH of the emanating solution from the reactor and other conditions for reactor effluent, ability to bind reversibly with respect to some simple but easily manipulable physicochemical parameter (such as temperature, pH, salt concentration), and the ability to be easily attached to a matrix using simple chemistry without loss of binding ability and a long shelf life.
We undertook this review because, although the comprehensive information on a large number of enzymes have been accumulated in BRENDA database [24, 25], but the systematic information on their mutants is lacking and non-enzymatic binders of sugar ligands are not identified / listed in the database.
Proteins that bind 3-phosphoglycerate/3-phosphoglyceraldehye
Both enzymatic and non-enzymatic proteins bind these sugar entities. A number of mutants of many enzymes that bind to either 3-phosphoglycerate or 3-phosphoglyceraldehyde are also known, for example, Phosphoglyceromutase (EC 188.8.131.52), Enolase (EC 184.108.40.206), Mannosyl-3-phosphoglycerate phosphatase (EC 220.127.116.11), Mannosyl-3-phosphoglycerate synthase (EC 18.104.22.168), Phosphoglycerate kinase, (EC 22.214.171.124), Bisphosphoglycerate mutase (EC 126.96.36.199), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 188.8.131.52), D-3-phosphoglycerate dehydrogenase 2 (EC 184.108.40.206), Cyclic 2,3-diphosphoglycerate-synthetase, Phosphoglycerate dehydrogenase, Transketolase, and Triosephosphate isomerase, BRENDA database shows only three enzymes: Phosphoglycerate dehydrogenase, Mannosyl-3-phosphoglycerate synthase and Phosphoglycerate kinase. A number of mutants of enzymes that binds 3-phosphoglycerate and shows some change in enzymatic activity or kinetic parameters are listed in Table 1. Many of these proteins are reported to retain ligand binding ability with varying degree of loss in catalytic ability (inactive mutants are in bold face), the non-enzymatic protein that also has been reported in literature has been placed towards the bottom part of Table 1. The proteins which retain binding ability but with complete loss in catalytic activity are the ones which warrant further investigation in batch and continuous processes for exploring their suitability as binding proteins in continuous RuBP regenerating reactors (Figure 2). A number of non-enzymatic protein summarized in Table 1 also warrant further exploration. The only binding entity of significance for 3-phosphoglyceraldehyde is 3-phosphoglyceraldehyde dehydrogenase (EC 220.127.116.11) and has not been reviewed.
Proteins that bind dihydroxyacetone phosphate
Several enzymes: dihydroxyacetone phosphate acyltransferase, Glycerol-3-phosphate dehydrogenase, Aldolase A, fructose-bisphosphatase, Aldolase B, fructose-bisphosphatase, L-aspartate oxidase, Quinolinate synthetase A, Dihydroxyacetone kinase 1 (Glycerone kinase 1), Glycerol-3-phosphate acyltransferase, NAD(P)H-dependent dihydroxyacetone-phosphate reductase, Dihydroxyacetone phosphate acyltransferase, Alkyl-dihydroxyacetonephosphate synthase, Dihydroxyacetone kinase isoenzyme I, Alpha-glycerophosphate oxidase and Triose phosphate isomerase binds DHAP (Table 2), however, BRENDA shows only four of these proteins, glycerol-3-phosphate dehydrogenase (EC 18.104.22.168), acylglycerone-phosphate reductase (EC 22.214.171.124), glycerone-phosphate O-acyltransferase (EC 126.96.36.199) and alkylglycerone-phosphate synthase (188.8.131.52). The mutants of enzymes with no chemical conversion ability but with high affinity for binding dihydroxyacetone phosphate but very low affinity for other proteins and reversible binding with respect to temperature, salt or pH are desirable properties for the binders.
Proteins binding xylulose-5-phosphate
As shown in Table 3 several enzymatic proteins binds to xylulose-5-phosphate. Xylulose-5-phosphate phosphoketolase, Dihydroxyacetone synthase, xylulose kinase, Protein phosphatase 2A B alpha isoform, Xylulose 5-phosphate-activated protein phosphatase, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, 1-deoxy-D-xylulose 5-phosphate synthase 1 and 2 are examples of such enzymes. The non-enzymatic xylulose-5-phosphate binders are shown in the bottom part of Table 3. BRENDA database shows following five proteins, 1-deoxy-D-xylulose-5-phosphate reductoisomerase (EC 184.108.40.2067), formaldehyde transketolase (EC 220.127.116.11), 1-deoxy-D-xylulose 5-phosphate synthase (EC 18.104.22.168), Phosphoketolase (EC 22.214.171.124), Ribulose-phosphate 3-epimerase (EC 126.96.36.199).
Proteins binding D-Ribulose-1,5-bisphosphate
A number of Ribulose-1,5-bisphosphate and metabolizing enzymes such as Ribulose phosphate kinase and their mutants binds D-ribulose-1,5-bisphosphate. The RuBP binding entities devoid of any enzymatic activities are very valuable in reactors necessitating extraction and separation of RuBP from other sugar compounds (Table 4). Very few non-enzymatic proteins bind RuBP and none of them are microbial sources, and hence have not been incorporated in this review, Rubisco associated protein from soybean is one of them, that show significant RuBP binding .
In order to illustrate the utility of non-catalytic enzymatic mutants as specific sugar binders for in-situ separation in reactors, recombinant Saccharomyces cerevisiae 3-phosphoglycerate kinase mutant R38Q  was prepared. Mutagenesis was carried out using wild type protein construct in plasmid pET19b as a template. The R38Q mutant was constructed with the Quickchange/Chameleon site-directed mutagenesis kit from stategene using primers as described elsewhere . DNA sequencing of the plasmid identified the mutant. Recombinant wild-type and mutant (R38Q) 3-phosphoglycerate kinase (PGK) were purified to apparent homogeneity as described previously  have been shown in Figure 3A. The wild-type and mutant protein was incubated with 10 mM 3-phosphoglycerate barium salt (3PGA) in 50 mM Tris-Cl buffer, pH 7.5 containing 50 mM NaCl for overnight at room temperature. No modification of 3PGA was observed after incubation with R38Q mutant protein (data not shown). The R38Q was coupled with Protein A sepharose beads using dimethylpimelimidate. The recombinant R38Q mutant protein beads (R38Q-PGK) was incubated overnight at room temperature with a mixture of sugars, 3-phosphoglycerate, barium salt (3PGA), ribulose-5-phosphate (R5P), Glucose-6-phosphate (G6P) and Fructose-6-posphate (F1,6-bP) each at a concentration of 10 mM in a volume of 200 μl. After incubation they were washed with 1.5 ml of 180 mM NaCl in 50 mM Tris-Cl buffer, pH 7.5. They were subjected to elution with 1 M NaCl. Lane 1, mixture of sugar prior to incubation with R38Q-PGK and Lane-2 after elution with 1 M NaCl.
The enzyme-mutants lacking catalytic activity represent an important group of proteins that could be used for development of sugar-binding proteins reversible with respect to physicochemical parameters such as pH or salt concentration. Nevertheless, the non-enzymatic proteins also represent a suitable repertoire of such potential scaffolds, which could be used for development as sugar-binding proteins to be used in reactors for simultaneous separation of sugars that would be used in subsequent conversion steps. We have developed a RuBP production scheme from 3PGA [16, 17] and also a de novo RuBP production scheme from D-glucose  for continuous CO2 fixation and for start-up of the fixation respectively employing series of reactors. Both systems for production of RuBP will benefit from specific sugar binders but besides their use in environmental biotechnology, they will find application in diagnostics, separation technologies and also as research reagents.
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We thank Dr. Paramita Ray for help with literature search and Dr. Surabhi Choudhuri for her comments on the manuscript.
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Mahato, S., De, D., Dutta, D. et al. Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. Microb Cell Fact 3, 7 (2004). https://doi.org/10.1186/1475-2859-3-7
- Dihydroxyacetone Phosphate
- Phosphoglycerate Mutase
- Phosphoglycerate Dehydrogenase
- Sugar Binding Protein
- Dihydroxyacetone Kinase