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Iqbal MW, Riaz T, Mahmood S, Ali K, Khan IM, Rehman A, Zhang W, Mu W. A review on selective l-fucose/d-arabinose isomerases for biocatalytic production of l-fuculose/d-ribulose. Int J Biol Macromol 2020; 168:558-571. [PMID: 33296692 DOI: 10.1016/j.ijbiomac.2020.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
L-Fuculose and D-ribulose are kinds of rare sugars used in food, agriculture, and medicine industries. These are pentoses and categorized into the two main groups, aldo pentoses and ketopentoses. There are 8 aldo- and 4 ketopentoses and only fewer are natural, while others are rare sugars found in a very small amount in nature. These sugars have great commercial applications, especially in many kinds of drugs in the medicine industry. The synthesis of these sugars is very expensive, difficult by chemical methods due to its absence in nature, and could not meet industry demands. The pentose izumoring strategy offers a complete enzymatic tactic to link all kinds of pentoses using different enzymes. The enzymatic production of L-fuculose and D-ribulose through L-fucose isomerase (L-FI) and D-arabinose isomerase (D-AI) is the inexpensive and uncomplicated method up till now. Both enzymes have similar kinds of isomerizing mechanisms and each enzyme can catalyze both L-fucose and D-arabinose. In this review article, the enzymatic process of biochemically characterized L-FI & D-AI, their application to produce L-fuculose and D-ribulose and its uses in food, agriculture, and medicine industries are reviewed.
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Affiliation(s)
- Muhammad Waheed Iqbal
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tahreem Riaz
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shahid Mahmood
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Khubaib Ali
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Abdur Rehman
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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Kemble H, Eisenhauer C, Couce A, Chapron A, Magnan M, Gautier G, Le Nagard H, Nghe P, Tenaillon O. Flux, toxicity, and expression costs generate complex genetic interactions in a metabolic pathway. SCIENCE ADVANCES 2020; 6:eabb2236. [PMID: 32537514 PMCID: PMC7269641 DOI: 10.1126/sciadv.abb2236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Our ability to predict the impact of mutations on traits relevant for disease and evolution remains severely limited by the dependence of their effects on the genetic background and environment. Even when molecular interactions between genes are known, it is unclear how these translate to organism-level interactions between alleles. We therefore characterized the interplay of genetic and environmental dependencies in determining fitness by quantifying ~4000 fitness interactions between expression variants of two metabolic genes, starting from various environmentally modulated expression levels. We detect a remarkable variety of interactions dependent on initial expression levels and demonstrate that they can be quantitatively explained by a mechanistic model accounting for catabolic flux, metabolite toxicity, and expression costs. Complex fitness interactions between mutations can therefore be predicted simply from their simultaneous impact on a few connected molecular phenotypes.
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Affiliation(s)
- Harry Kemble
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | | | - Alejandro Couce
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Audrey Chapron
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Mélanie Magnan
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Gregory Gautier
- Centre de Recherche sur l'Inflammation, INSERM, UMRS 1149, 75018 Paris, France
- Laboratoire d’Excellence INFLAMEX, Université de Paris, Sorbonne Paris Cité, 75018 Paris, France
| | - Hervé Le Nagard
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
| | - Philippe Nghe
- Laboratory of Biochemistry (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL University, CNRS, 75005 Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université de Paris, Université Paris Nord, 75018 Paris, France
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Heterologous expression of d-xylulokinase from Pichia stipitis enables high levels of xylitol production by engineered Escherichia coli growing on xylose. Metab Eng 2009; 11:48-55. [DOI: 10.1016/j.ymben.2008.07.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 07/02/2008] [Accepted: 07/29/2008] [Indexed: 11/20/2022]
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Murray JS, Wong ML, Miyada CG, Switchenko AC, Goodman TC, Wong B. Isolation, characterization and expression of the gene that encodes D-arabinitol dehydrogenase in Candida tropicalis. Gene X 1995; 155:123-8. [PMID: 7698655 DOI: 10.1016/0378-1119(94)00900-d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The gene (ARD) that encodes NAD-dependent D-arabinitol dehydrogenase (ArDH) in the pathogenic fungus Candida tropicalis (Ct) was cloned by transforming Escherichia coli (Ec) BW31M (araCc) with a plasmid library of Ct genomic DNA and selecting for D-arabinitol-utilizing (D-arab+) clones. Plasmid DNA from a D-arab+ clone retransformed fresh Ec BW31M cells to D-arab+; these cells produced both ArDH catalytic activity and a 31-kDa protein recognized by antibodies to native Ct ArDH. The plasmid contained an 846-bp open reading frame (ORF) that encoded a deduced protein of 282 amino acids (aa) (30,748 Da). Four partial aa sequences from Ct ArDH were present in the deduced aa sequence, thus verifying that Ct ARD had been cloned. Ct ArDH was 95% identical to ArDH from Candida albicans (Ca), 85% identical to a xylitol dehydrogenase (XDH) from Pichia stipitis (Ps) and 20-25% identical to many other short-chain dehydrogenases. Ct ArDH, Ca ArDH and Ps XDH were typical short-chain dehydrogenases except that they lacked an N-terminal Gly that is conserved in other members of this family. Thus, these enzymes may represent a subclass of closely-related fungal pentitol dehydrogenases. Large amounts of recombinant ArDH (re-ArDH) were produced in Ec and purified by dye ligand affinity chromatography. The physical and catalytic properties of re-ArDH were similar to those of native Ct ArDH, and re-ArDH and native ArDH performed similarly in an automated enzymatic assay for D-arabinitol in human serum.
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Affiliation(s)
- J S Murray
- Department of Internal Medicine, University of Cincinnati College of Medicine, OH 45267-0560, USA
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Elsinghorst EA, Mortlock RP. Molecular cloning of the Escherichia coli B L-fucose-D-arabinose gene cluster. J Bacteriol 1994; 176:7223-32. [PMID: 7961494 PMCID: PMC197110 DOI: 10.1128/jb.176.23.7223-7232.1994] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To metabolize the uncommon pentose D-arabinose, enteric bacteria often recruit the enzymes of the L-fucose pathway by a regulatory mutation. However, Escherichia coli B can grow on D-arabinose without the requirement of a mutation, using some of the L-fucose enzymes and a D-ribulokinase that is distinct from the L-fuculokinase of the L-fucose pathway. To study this naturally occurring D-arabinose pathway, we cloned and partially characterized the E. coli B L-fucose-D-arabinose gene cluster and compared it with the L-fucose gene cluster of E. coli K-12. The order of the fucA, -P, -I, and -K genes was the same in the two E. coli strains. However, the E. coli B gene cluster contained a 5.2-kb segment located between the fucA and fucP genes that was not present in E. coli K-12. This segment carried the darK gene, which encodes the D-ribulokinase needed for growth on D-arabinose by E. coli B. The darK gene was not homologous with any of the L-fucose genes or with chromosomal DNA from other D-arabinose-utilizing bacteria. D-Ribulokinase and L-fuculokinase were purified to apparent homogeneity and partially characterized. The molecular weights, substrate specificities, and kinetic parameters of these two enzymes were very dissimilar, which together with DNA hybridization analysis, suggested that these enzymes are not related. D-Arabinose metabolism by E. coli B appears to be the result of acquisitive evolution, but the source of the darK gene has not been determined.
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Affiliation(s)
- E A Elsinghorst
- Section of Microbiology, Cornell University, Ithaca, New York 14853
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Wong B, Murray JS, Castellanos M, Croen KD. D-arabitol metabolism in Candida albicans: studies of the biosynthetic pathway and the gene that encodes NAD-dependent D-arabitol dehydrogenase. J Bacteriol 1993; 175:6314-20. [PMID: 8407803 PMCID: PMC206728 DOI: 10.1128/jb.175.19.6314-6320.1993] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Candida albicans produces large amounts of the pentitol D-arabitol in culture and in infected mammalian hosts, but the functional and pathogenic significance of D-arabitol in C. albicans is not known. In this study, we sought to elucidate the pathway by which C. albicans synthesizes D-arabitol and to identify and characterize key enzymes in this pathway. C. albicans B311 produced D-[14C-1]arabitol from [14C-2]glucose; this finding implies on structural grounds that D-ribulose-5-PO4 from the pentose pathway is the major metabolic precursor of D-arabitol. NAD- or NADP-dependent pentitol dehydrogenases catalyze the final steps in D-arabitol biosynthesis in other fungi; therefore, lysates of C. albicans B311 were tested for enzymes of this class and were found to contain a previously unknown NAD-dependent D-arabitol dehydrogenase (ArDH). The ArDH structural gene was cloned by constructing a new D-arabitol utilization pathway in Escherichia coli. The C. albicans ArDH gene expressed in E. coli and Saccharomyces cerevisiae an enzyme that catalyzes the reaction D-arabitol + NAD <-->D-ribulose + NADH; this gene was present as a single copy per haploid genome, and its deduced peptide sequence was homologous with sequences of several members of the short-chain dehydrogenase family of enzymes. These results suggest that (i) C. albicans synthesizes D-arabitol by dephosphorylating and reducing the pentose pathway intermediate D-ribulose-5-PO4 and (ii) ArDH catalyzes the final step in this pathway.
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Affiliation(s)
- B Wong
- Department of Internal Medicine, University of Cincinnati College of Medicine, Ohio 45267-0560
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Elsinghorst EA, Mortlock RP. D-arabinose metabolism in Escherichia coli B: induction and cotransductional mapping of the L-fucose-D-arabinose pathway enzymes. J Bacteriol 1988; 170:5423-32. [PMID: 3056899 PMCID: PMC211633 DOI: 10.1128/jb.170.12.5423-5432.1988] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
D-Arabinose is degraded by Escherichia coli B via some of the L-fucose pathway enzymes and a D-ribulokinase which is distinct from the L-fuculokinase of the L-fucose pathway. We found that L-fucose and D-arabinose acted as the apparent inducers of the enzymes needed for their degradation. These enzymes, including D-ribulokinase, appeared to be coordinately regulated, and mutants which constitutively synthesized the L-fucose enzymes also constitutively synthesized D-ribulokinase. In contrast to D-arabinose-positive mutants of E. coli K-12, in which L-fuculose-1-phosphate and D-ribulose-1-phosphate act as inducers of the L-fucose pathway, we found that these intermediates did not act as inducers in E. coli B. To further characterize the E. coli B system, some of the L-fucose-D-arabinose genes were mapped by using bacteriophage P1 transduction. A transposon Tn10 insertion near the E. coli B L-fucose regulon was used in two- and three-factor reciprocal crosses. The gene encoding D-ribulokinase, designated darK, was found to map within the L-fucose regulon, and the partial gene order was found to be Tn10-fucA-darK-fucI-fucK-thyA.
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Affiliation(s)
- E A Elsinghorst
- Department of Microbiology, Cornell University, Ithaca, New York 14853
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Stayton MM, Fromm HJ. Purification, properties, and kinetics of D-ribulokinase from Aerobacter aerogenes. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50652-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Scangos GA, Reiner AM. A unique pattern of toxic synthesis in pentitol catabolism: implications for evolution. J Mol Evol 1979; 12:189-95. [PMID: 374747 DOI: 10.1007/bf01732338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
All of our Escherichia coli C mutants blocked in the first step of D-arabitol catabolism (D-arabitol dehydrogenase) became unable to grow in the presence of D-arabitol. We have shown that this sensitivity is eliminated by a defect in the second enzyme of the pathway (D-xylulokinase), leading to a pattern of toxicity and its relief which has not been previously reported. We have found a similar pattern of toxicity and its relief in the closely related ribitol pathway. The evolutionary significance of these findings is discussed.
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Saint Martin EJ, Mortlock RP. Natural and altered induction of the L-fucose catabolic enzymes in Klebsiella aerogenes. J Bacteriol 1976; 127:91-7. [PMID: 179982 PMCID: PMC233037 DOI: 10.1128/jb.127.1.91-97.1976] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutants of Klebsiella aerogenes W70 were isolated that had gained the ability to utilize the uncommon pentose D-arabinose as their sole source of carbon and energy. In contrast to the D-arabinose-negative, parent strain, these mutants were found to be either constitutive for certain enzymes of the L-fucose catabolic pathway or inducible for such enzymes when incubated in the presence of D-arabinose. The mutants used L-fucose isomerase to convert D-arabinose to D-ribulose, which is an intermediate and inducer of the ribitol catabolic pathway. The D-ribulokinase of the ribitol pathway was then induced. This enzyme catalyzed the phosphorylation of D-ribulose at the 5-carbon position. Mutants that were negative for D-ribulokinase could still dissimilate D-arabinose slowly by using all three enzymes, the isomerase, kinase, and aldolase, of the L-fucose pathway. Using condition negative mutants, we were able to demonstrate that the natural induction of the L-fucose pathway enzymes by L-fucose required the activity of a functional L-fucose isomerase and a functional L-fuculokinase but not an L-fuculose-1-phosphate aldolase. A metabolic intermediate, L-fuculose-1-phosphate, was thereby shown to be a probable inducer of at least the isomerase and kinase of the L-fucose catabolic pathway. Similar experiments, with D-arabinose-positive mutants, which were induced for the L-fucose pathway enzymes upon incubation with D-arabinose, revealed that the activities of the L-fucose isomerase and the L-fuculokinase were also required for the induction of the L-fucose enzymes. These D-arabinose-positive mutants apparently produced an altered regulatory protein that accepted both L-fuculose-1-phosphate and D-ribulose-1-phosphate as inducers. Examination of constitutive mutants revealed that L-fucose isomerase and L-fuculokinase were both synthesized constitutively, with the aldolase apparently under separate control.
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Abstract
In Klebsiella aerogenes W70, there is an inducible pathway for the catabolism of ribitol consisting of at least two enzymes, ribitol dehydrogenase (RDH) and d-ribulokinase (DRK). These two enzymes are coordinately controlled and induced in response to d-ribulose, an intermediate of the pathway. Whereas wild-type K. aerogenes W70 are unable to utilize xylitol as a carbon and energy source, mutants constitutive for the ribitol pathway are able to utilize RDH to oxidize the unusual pentitol, xylitol, to d-xylulose. These mutants are able to grow on xylitol, presumably by utilization of the d-xylulose produced. Mutants constitutive for l-fucose isomerase can utilize the isomerase to convert d-arabinose to d-ribulose. In the presence of d-ribulose, RDH and DRK are induced, and such mutants are thus able to phosphorylate the d-ribulose by using the DRK of the ribitol pathway. Derivatives of an l-fucose isomerase-constitutive mutant were plated on d-arabinose, ribitol, and xylitol to select and identify mutations in the ribitol pathway. Using the transducing phage PW52, we were able to demonstrate genetic linkage of the loci involved. Three-point crosses, using constitutive mutants as donors and RDH(-), DRK(-) double mutants as recipients and selecting for DRK(+) transductants on d-arabinose, resulted in DRK(+)RDH(+)-constitutive, DRK(+)RDH(+)-inducible, and DRK(+)RDH(-)-inducible transductants but no detectable DRK(+)RDH(-) constitutive transductants, data consistent with the order rbtC-rbtD-rbtK, where rbtC is a control site and rbtD and rbtK correspond to the sites for the sites for the enzymes RDH and DRK, respectively.
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LeBlanc DJ, Mortlock RP. Regulation of the L-arabinose catabolic pathway in Aerobacter aerogenes. Arch Biochem Biophys 1973; 156:390-6. [PMID: 4718778 DOI: 10.1016/0003-9861(73)90287-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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