583 Regeneration of cofactors for use in biocatalysis Huimin Zhao and Wilfred A van der Donky Cofactor-dependent enzymes catalyze many synthetically useful reactions. The high cost of cofactors, however, necessitates in situ cofactor regeneration for preparative applications. After two decades of research, several cofactors can now be effectively regenerated using enzyme or whole-cell based methods. Significant advances have been made in this area in the past three years and include the development of novel or improved methods for regenerating ATP, sugar nucleotides and 3-phosphoadenosine-50 -phosphosulphate. These approaches have found novel applications in biocatalysis. Addresses Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA e-mail: [email protected] y Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA e-mail: [email protected] Current Opinion in Biotechnology 2003, 14:583–589 This review comes from a themed issue on Chemical biotechnology Edited by Frances H Arnold and Anton Glieder 0958-1669/$ – see front matter ß 2003 Elsevier Ltd. All rights reserved. DOI 10.1016/j.copbio.2003.09.007 Abbreviations AdK ADP AMP ATP CMP-NeuAc CTP GDP-Fuc NTP PAP PAPS PEP PPK TTN UDP-Gal UDP-GlcNAc UTP adenylate kinase adenosine 50 -diphosphate adenosine 50 -monophosphate adenosine 50 -triphosphate cytidine 50 -monophosphate N-acetylneuraminic acid cytidine 50 -triphosphate GDP-fucose nucleoside triphosphate polyphosphate:AMP phosphotransferase 3-phosphoadenosine-50 -phosphosulfate phosphoenolpyruvate polyphosphate kinase total turnover number UDP-galactose UDP-N-acetylglucosamine uridine 50 -triphosphate Introduction With recent advances in genomics and genetic engineering, the use of biocatalysis for industrial synthetic chemistry is growing rapidly [1,2,3,4]. Most of the biocatalysts in current use, however, are limited to cofactor-independent enzymes such as hydrolases, which perform relatively simple chemistry. In comparison, cofactor-dependent www.current-opinion.com enzymes, such as oxidoreductases and transferases, are capable of performing much more complex chemistry and catalyzing a large number of synthetically useful reactions. Cofactors are low molecular weight compounds that are essential for enzymatic reactions. Certain cofactors such as pyridoxal phosphate and biotin are tightly bound to the enzymes and are essentially self-regenerating. Others, such as pyridine nucleotides and nucleoside triphosphates (NTPs), act as functional group transfer agents and are cosubstrates that must be used in stoichiometric amounts [5]. As these cofactors are too expensive to be used as stoichiometric agents for preparative applications, they must be regenerated in situ. Cofactor regeneration can also reduce the cost of synthesis by driving the reaction to completion, simplifying product isolation, and preventing the accumulation of inhibitory cofactor by-products [3]. A practically useful cofactor regeneration method must fulfill several requirements. The enzymes, reagents and equipment required should be readily available, inexpensive, easily manipulated and stable under the operational conditions. The energetics of the regeneration step should be favorable both kinetically and thermodynamically. Any reagents or by-products of the regeneration step should not interfere with product isolation and should be compatible with the rest of the reaction system. Most importantly, the ‘total turnover number’ (TTN) of the cofactor should be high [5]. TTN is defined as the total number of moles of product formed per mole of cofactor during the course of a complete reaction [6]. This number reflects several factors including the loss of cofactor due to degradation or incorrect regiochemistry of regeneration, the reaction time, and the catalyst turnover number (kcat). As a rule of thumb, TTNs of 103 to 105 can be sufficient to make a process economically viable depending on the value of the reaction product. In the past two decades, many chemical, enzymatic and electrochemical methods have been investigated to regenerate various cofactors [5,7]. Compared with enzymatic methods, chemical and electrochemical strategies often lack the high selectivity required to achieve high TTNs, and are frequently incompatible with the other components of the enzymatic reactions. Thus, enzymatic methods are presently preferred for cofactor regeneration. As listed in Table 1, many enzymatic approaches have been developed to effectively regenerate various cofactors, including adenosine 50 -triphosphate (ATP) regeneration in phosphoryl transfer reactions, NAD(P)þ or NAD(P)H regeneration in oxidoreductions, acetyl CoA regeneration in acyl transfer reactions, sugar nucleotide Current Opinion in Biotechnology 2003, 14:583–589 584 Chemical biotechnology Table 1 Common cofactors required for biotransformation and their representative in situ regeneration methods. Cofactor þ NAD NADH NADPþ NADPH ATP Sugar nucleotides CoA PAPS S-Adenosyl methionine Flavins Pyridoxal phosphate Biotin Metal porphyrin complexes Reaction type Representative regeneration method References Removal of hydrogen Addition of hydrogen Removal of hydrogen Addition of hydrogen Phosphoryl transfer Glycosyl transfer Acyl transfer Sulfuryl transfer Methyl transfer Oxygenation Transamination Carboxylation Peroxidation, oxygenation Glutamate dehydrogenase with a-ketoglutarate Formate dehydrogenase with formate Glutamate dehydrogenase with a-ketoglutarate Glucose dehydrogenase with glucose Acetate kinase with acetyl phosphate Bacterial coupling Phosphotransacetylase with acyl phosphate Aryl sulfotransferase IV with p-nitrophenyl sulfate No demonstrated method Self-regeneration Self-regeneration Self-regeneration Self-regeneration [43] [44] [43] [45] [46] [47] [48] [40] [3] [1] [1] [1] [1] Many flavin-dependent mono-oxygenases or di-oxygenases require additional NAD(P)H as an indirect reducing agent. A first example of direct regeneration of a flavin-dependent mono-oxygenase was reported recently [41] (see also Update). regeneration in glycosylations, and 3-phosphoadenosine50 -phosphosulfate (PAPS) regeneration in sulfuryl transfer reactions. Some of these have been successfully used in large-scale chemical syntheses [5,7]. In this review, we will discuss new developments in cofactor regeneration since 2000. We will focus on new and improved approaches for regeneration of ATP, sugar nucleotides and PAPS, and their applications in biocatalysis. We will not discuss the recent advances in pyridine nucleotide or nicotinamide cofactor regeneration as this topic has been reviewed recently [8]. ATP/NTP regeneration NTPs are required in many synthetically useful enzymecatalyzed phosphoryl transfer reactions. ATP is most frequently used as a phosphorylating agent and hence has received more attention than other NTPs such as uridine 50 -triphosphate (UTP) and cytidine 50 -triphosphate (CTP), which have been mainly used as sources of nucleoside phosphates rather than suppliers of phosphate or energy [6]. Several enzyme and whole-cell based methods have been developed to regenerate ATP from adenosine 50 -diphosphate (ADP) [6,9]. Three enzymatic methods are commonly employed: the use of phosphoenolpyruvate (PEP) as the phosphate donor in a coupled reaction catalyzed by pyruvate kinase; acetylphosphate coupled with acetate kinase; and polyphosphate coupled with polyphosphate kinase (PPK). It should be noted that because these three enzymes have broad substrate specificities, these ATP regeneration methods can also be used to replenish other NTPs including guanosine 50 triphosphate (GTP), UTP and CTP from their corresponding nucleoside diphosphates [6,9]. Although the above-mentioned ATP regeneration methods are effective for enzyme-catalyzed chemical synthesis, they are not well-suited for cell-free protein Current Opinion in Biotechnology 2003, 14:583–589 synthesis because of the high cost of substrates and enzymes and, more importantly, because of the degradation of the phosphate-containing substrates by uncoupled enzymes in the cell extracts. In addition, the accumulation of phosphates in the cell-free system will inhibit long-term protein synthesis [10]. To address these limitations, a novel ATP regeneration approach was developed for cell-free protein synthesis. This approach takes advantage of the endogenous enzymes present in cell extracts and uses glycolytic intermediates such as pyruvate and glucose-6-phosphate rather than PEP as energy sources. It was found that with the addition of NADþ, certain endogenous enzymes can convert pyruvate into acetylphosphate, which in turn is converted into acetate with concurrent regeneration of ATP. Similarly, glucose-6phosphate can be first converted into pyruvate and then acetate, with concurrent ATP regeneration occurring in each step. As NADþ, pyruvate and glucose-6-phosphate are much cheaper than PEP, and as the protein synthesis yield using these substrates is either comparable to (for pyruvate/NADþ) or higher than (for glucose6-phosphate/NADþ) that using PEP, this new ATP regeneration approach can significantly improve the economic efficiency of cell-free protein synthesis [10]. Another important recent advance in ATP regeneration is the use of inorganic polyphosphate (poly(P)) to regenerate ATP from adenosine 50 -monophosphate (AMP) [11,12,13]. An efficient method for regenerating ATP from AMP is highly desirable, because many ATP-dependent enzymes produce AMP rather than ADP. Poly(P) consists of linear polymers of orthophosphate containing high-energy phospho anhydride linkages [14,15] and is used as a phosphate donor because of its high stability and low cost. Resnick and Zehnder [13] designed an ATP regeneration system using poly(P) and the enzymes polyphosphate:AMP phosphotransferase (PAP) and adenylate kinase (AdK) of Acinetobacter johnsonii. The system was www.current-opinion.com Regeneration of cofactors for use in biocatalysis Zhao and van der Donk 585 successfully applied to synthesize glucose-6-phosphate with hexokinase. In this process, hexokinase generates ADP, which is converted by AdK into ATP and AMP. In turn, the AMP is phosphorylated by PAP to ADP. The main advantage of this approach lies in the use of relatively inexpensive AMP as the initial nucleotide and poly(P) as the phosphoryl donor. Current drawbacks that are likely to be addressed in future research concern the low TTN (3–4) achieved in this preliminary study and the lack of a cloned gene encoding PAP. In conjugation with ATP-dependent light-emitting luciferase, this same system was also adapted to detect AMP for hygiene monitoring and RNA quantification [16]. Shiba and coworkers [11] developed a similar process in which PAP from Myxococcus xanthus and a recombinant PPK from Escherichia coli were used together to regenerate ATP from AMP and poly(P). This strategy was successfully used in combination with acetyl-CoA synthase to synthesize acetylCoA with the addition of inorganic pyrophosphatase (PPase) to alleviate the inhibitory effect of PPi and to provide an additional driving force (Figure 1). Compared with the PAP–AdK system, this approach appears to have several advantages, including a TTN for the ATP cofactor of 40 and the ability to regenerate GTP from GMP using the same system. PAP and PPK accept the low cost phosphate donor poly(P), but unfortunately they are both highly specific for their nucleotide substrate, AMP and ADP, respectively [17]; hence, ATP regeneration from AMP presently always requires two enzymes. As with the ATP regeneration methods from AMP, a novel enzymatic method using poly(P) as sole phosphorus donor has been developed to regenerate CTP from CMP [18]. In this strategy, the combined activity of PPK and cytidine 50 -monophosphate (CMP) kinase from E. coli converts CMP into CDP, while PPK by itself further phosphorylates CDP. This regeneration system was Figure 1 poly(P)n poly(P)n–1 ADP PPK PAP poly(P)n poly(P)n–1 ATP AMP + PPi Acetate + CoA PPase 2Pi Acetyl-CoA Acetyl-CoA synthase The PAP-PPK ATP regeneration system from AMP coupled with the acetyl-CoA synthetic reaction. PPase, inorganic pyrophosphatase. (Figure adapted from [11] with permission.) www.current-opinion.com coupled with cytidine 50 -monophosphate N-acetylneuraminic acid (CMP-NeuAc) synthetase of Haemophilus influenzae to synthesize CMP-NeuAc. It should be noted that CMP-NeuAc can also be produced by a novel recombinant E. coli strain containing an acetylphosphate/ acetate kinase-based ATP regeneration system [19]. These two studies will be further discussed below. Sugar nucleotide regeneration Oligosaccharides and polysaccharides have vital roles in a variety of biological processes including molecular recognition and cellular communication in bacterial and viral infection, cancer and the immune response. On this basis, they have been explored as potential pharmaceuticals [20,21]. Among the numerous methods developed for oligosaccharide synthesis, glycosyltransferase-mediated methodology is recognized as one of the most practical approaches for large-scale preparation, owing to the high regioselectivity and stereoselectivity of these enzymes [20]. However, glycosyltransferases require a sugar nucleotide as donor substrate that must be generated in situ for preparative applications by recycling of the nucleotide moiety. Although many glycosyltransferases are involved in the biosynthesis of oligosaccharides, only nine sugar nucleotides are used in mammalian systems, including uridine 50 -diphosphoglucose (UDP-Glc), UDPgalactose (UDP-Gal), UDP-glucuronic acid (UDPGlcUA), CMP-NeuAc, guanosine 50 -diphosphomannose (GDP-Man), GDP-fucose (GDP-Fuc), UDP-N-acetylglucosamine (UDP-GlcNAc), uridine 50 -diphospho-a-Dxylose (ADP-Xyl) and UDP-N-acetylgalactosamine (UDP-GalNAc) [22]. The enzymatic synthesis of these compounds has been reviewed [23]. Recently, several new approaches have been developed to regenerate sugar nucleotides including UDP-Gal, UDPGlc, UDP-GlcNAc, CMP-NeuAc and GDP-Fuc for preparative applications. One notable approach is bacterial coupling, which uses a combination of batches of different strains of whole cells. For instance Corynebacterium ammoniagenes, which efficiently produces UTP from orotic acid, has been coupled with recombinant E. coli strains expressing the enzymes required for sugar nucleotide generation. Importantly, this strategy does not require enzyme purification or the addition of nucleotides. The approach has been successfully used for large-scale production of sugar nucleotides including CMP-NeuAc (17 g l1), UDP-GlcNAc (7.4 g l1) and GDP-Fuc (18.4 g l1) [24,25,26]. As illustrated in Figure 2, CMP-NeuAc can be obtained by the combination of C. ammoniagenes and two E. coli strains expressing CTP synthetase (converting UTP to CTP) and CMP-NeuAc synthase (converting NeuAc and CTP to CMP-NeuAc), respectively [24]. Further coupling of the CMP-NeuAc or GDP-Fuc regeneration systems with recombinant E. coli strain(s) over-expressing desired glycosyltransferase(s) led to largescale production of several important oligosaccharides Current Opinion in Biotechnology 2003, 14:583–589 586 Chemical biotechnology Figure 2 Recombinant E. coli #2 NeuAc neuA Lac CMP-NeuAc CTP Recombinant E. coli #1 pyrG Recombinant E. coli #3 α-2,3-Sialyltransferase CTP UTP CMP CDP 3′ -Sialyllactose UDP Orotic acid UMP C. ammoniagenes Current Opinion in Biotechnology The CMP-NeuAc regeneration system using bacterial coupling. The system consists of C. ammoniagenes, which converts orotic acid into UTP, and two recombinant E. coli strains expressing the CTP synthetase gene (pyrG) from E. coli K12 and the CMP-NeuAc synthetase gene (neuA) from E. coli K1, respectively. Further coupling of a recombinant E. coli strain overexpressing the a-(2!3)-sialyltransferase gene from Neisseria gonorrhoeae led to the large-scale production of 30 -sialyllactose using NeuAc, orotic acid and lactose (Lac) as substrates. including globotriose, 3’-sialyllactose and Lewis X [24,26]. The same strategy was also used to produce the sialyl-Tn epitope of the tumor-associated carbohydrate antigen [27] and NeuAc [28]. Owing to the low cost of enzymes and starting materials, bacterial coupling is a cost-effective method for sugar nucleotide regeneration. However, because multiple strains are used simultaneously, the transport of reaction intermediates between strains and the maintenance of cell growth of different strains may be problematic for certain applications. To overcome these limitations, a new approach using a single recombinant bacterial strain (‘superbug’) containing all the necessary enzymes for sugar nucleotide regeneration and oligosaccharide synthesis has been recently demonstrated [19,29,30]. Kim and coworkers [19] developed a CMP-NeuAc regeneration method by co-expressing CMP kinase, sialic acid aldolase and CMP-NeuAc synthetase in a single E. coli strain. In related work, Wang and coworkers [29] introduced an artificial biosynthetic pathway consisting of the genes encoding a galactosyltransferase, a UDP-galactose 4-epimerase from E. coli K-12 ( galE), and a sucrose synthase from Anabaena sp. PCC 7119 (susA) into a single E. coli strain. By choosing different galactosyltransferases, these recombinant strains have been used for large-scale production of the biomedically important trisaccharides Gala1,4Lac (globotriose) and Gala1,3Lac (a-Gal epitope) with the concurrent regeneration of UDP-Gal in a twostep process. The first step entailed the fermentation of the engineered recombinant strain and the second step Current Opinion in Biotechnology 2003, 14:583–589 involved the use of permeabilized harvested cells as whole-cell biocatalysts for oligosaccharide synthesis. In the same manner, an artificial gene cluster encoding all five enzymes in the biosynthetic pathway of Gala1,3Lac was transferred into an E. coli strain to produce the a-Gal epitope [30]. Compared with the above-mentioned whole-cell based approaches for sugar nucleotide regeneration and oligosaccharide synthesis, enzymatic methods can offer more flexibility in certain cases. In particular, greater productivity and a simpler process for product isolation can be achieved when immobilized enzymes are used. Wang and coworkers [31,32] developed a new enzymatic method for cost-effective UDP-Gal regeneration by immobilizing seven enzymes involved in the biosynthesis of UDP-Gal onto nickel agarose beads. The genes encoding all of the enzymes were cloned and expressed individually, and the corresponding enzymes were immobilized through their hexahistidine tags to the beads [33]. The formation of UDP-Gal was achieved using a combination of stoichiometric amounts of UMP and galactose with catalytic quantities of ATP and glucose-1-phosphate, resulting in a 50% yield based on UMP. In a subsequent study, the methodology was used to prepare several oligosaccharides including globotriose and the a-Gal epitope [32]. Although this approach has many advantages, the authors point out that, to date, bacterial coupling is still more cost effective. Ishige and coworkers [18] described a new efficient enzymatic method for CMP-NeuAc regeneration based on purified enzymes. In this method, the www.current-opinion.com Regeneration of cofactors for use in biocatalysis Zhao and van der Donk 587 gene encoding a novel CMP-NeuAc synthetase of H. influenzae was cloned and the corresponding enzyme was coupled with an enzymatic CTP regeneration system discussed in the previous section. aryl sulfotransferase IV with p-nitrophenyl sulfate as the sulfate donor. This method proved to be most practical in the preparative synthesis of carbohydrate sulfates [40]. Conclusions In addition to the nine sugar nucleotides involved in mammalian glycobiology, the dTDP- and UDP-activated deoxyhexoses involved in secondary metabolism in bacteria and plants [34] have received much attention in recent years for their potential application in reprogramming of the structures of antibiotics that are decorated with carbohydrates [35]. Many of the glycosyltransferase genes have been cloned and chemoenzymatic syntheses of various pyrimidine diphosphosugars with sugar nucleotide regeneration have been reported [36–38]. PAPS regeneration The cofactor PAPS is the universal sulfate donor in biological systems and is required in the sulfotransferasecatalyzed synthesis of many biologically or therapeutically important sulfated carbohydrates and glycopeptides. The high cost and instability of PAPS and the production inhibition problem caused by 30 -phosphoadenosine 50 -sulfate requires in situ regeneration of PAPS for preparative applications. The first enzymatic PAPS regeneration method was based on a complex multi-enzyme system consisting of ATP sulfurylase, adenosine-50 -phosphosulfate (APS) kinase, 30 -nucleotidase, myokinase and pyruvate kinase [39]. In this process, which mimics the natural metabolic cycle, the product generated after sulfate transfer is first converted to ATP using the latter three enzymes; ATP is subsequently transformed to PAPS by ATP sulfurylase and APS kinase. Recently, a much simpler, one-enzyme PAPS regeneration method has been developed (Figure 3) [40]. This method uses a recombinant rat liver Figure 3 Substrate Sulfated product NH2 NH2 PAPS N N N Target sulfotransferase N O – O O S O– N O O P O O P O N N N O O– O O O– OH O P O– O OH O P O– O– Aryl sulfotransferase O– O– O2N OH O 2N O S O O p-Nitrophenyl sulfate Much of the recent progress in cofactor regeneration has focused on nicotinamide cofactors, ATP, sugar nucleotides and PAPS. In the case of ATP regeneration, the use of inexpensive poly(P) as sole phosphorus donor coupled with PAP and PPK/AdK enables the regeneration of ATP from AMP. Because PPK catalyzes the NTP regeneration reaction using poly(P) only, it might also be worthwhile engineering or discovering PPK with novel nucleotide monophosphate (NMP) specificity for the construction of an NTP regeneration method from NMP. In addition, a novel ATP regeneration method using glycolytic intermediates such as pyruvate and glucose-6-phosphate rather than PEP as energy sources was developed for the costeffective synthesis of proteins in a cell-free system. Among the several newly developed sugar nucleotide regeneration methods, whole-cell approaches using bacterial coupling or a single genetically engineered bacterial strain represent the most efficient and cost-effective routes for production of sugar nucleotides and pharmaceutically important oligosaccharides. With the discovery of more bacterial glycosyltransferases from genomics- and proteomics-related research and the development of better protein expression systems, the whole-cell approaches will receive much attention in glycobiotechnology in the near future. Furthermore, the development of a novel one-enzyme based PAPS regeneration method enables the cost-effective large-scale production of sulfated carbohydrates. In conjugation with the newly developed sugar nucleotide regeneration methods, this PAPS regeneration system is expected to facilitate the production of more complex carbohydrates of biological and therapeutic importance. Although much progress has been made in the past two decades, further improvement of the existing regeneration methods for nicotinamide cofactors, ATP/NTP, sugar nucleotides and PAPS will be required for their expected increased application in biocatalysis. Along this line, modern protein engineering and metabolic engineering techniques will be increasingly used, taking advantage of the advances in genomics, proteomics and bioinformatics. Future efforts should also focus on the development of new methods for cost-effective regeneration of S-adenosyl methionine (SAM), which currently is an unsolved problem on a preparative scale. It is expected that, with the development of inexpensive and efficient in situ regeneration methods for various cofactors, the applications of biocatalysis in the pharmaceutical and chemical industries will be greatly expanded in the coming years. Current Opinion in Biotechnology Update A novel PAPS regeneration method comprising a recombinant aryl sulfotransferase and p-nitrophenyl sulfate. www.current-opinion.com Hollmann and coworkers [41] recently developed a novel chemo-enzymatic approach to directly regenerate Current Opinion in Biotechnology 2003, 14:583–589 588 Chemical biotechnology flavin-dependent styrene monooxygenase (StyA) for the first time by means of an organometallic complex [CpRh(bpy)(H2O)]2þ). This organometallic complex can catalyze the transhydrogenation reaction between formate and isoalloxazine-based cofactors such as FAD and FMN, and thereby substitutes for the native reductase (StyB), the nicotinamide coenzyme (NAD), and an enzymatic NADH regeneration system such as formate dehydrogenase in StyA-catalyzed epoxidation reactions. Similarly, Wagenknecht and coworkers [42] developed a simple system based on ruthenium (II) and rhodium (III) organometallic complexes for the direct coupling of hydrogen to nicotinamide cofactor regeneration under conditions appropriate for in situ coupling with enzymatic reductions. The use of hydrogen as a reducing agent is advantageous compared with other reducing agents; however, the TTNs of the catalysts are very low. Bommarius and coworkers [43] demonstrated for the first time that NADH oxidase from Lactobacillus sanfranciscensis can be used to regenerate both NADþ from NADH and NADPþ from NADPH with concomitant reduction of O2 to innocuous H2O. Currently, the turnover number of the enzyme is still low, but is likely to be amenable to improvement. Acknowledgements We thank Biotechnology Research and Development Consortium (BRDC) for supporting our work on developing a phosphite dehydrogenase-based nicotinamide cofactor regeneration system for reductive biocatalysis. 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