D-Ribulose production by a mutant of Aerobacter aerogens

A review on selective l-fucose/d-arabinose isomerases for biocatalytic production of l-fuculose/d-ribulose

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.

Isolation of an operon involved in xylitol metabolism from a xylitol-utilizing Pantoea ananatis mutant

An operon involved in cryptic xylitol metabolism of Pantoea ananatis was cloned by transposon tagging. A xylitol negative mutant with a transposon insertion in the xylitol 4-dehydrogenase gene (xdh) was isolated and genomic DNA around the transposon was sequenced. Consequently, six consecutive genes, xytB-G are located downstream of xdh in the same strand. These seven genes are cotranscribed as a single transcript in a P. ananatis xylitol-utilizing mutant, suggesting that they comprise an operon. In addition to xdh, xytF also encodes oxidoreductase that is a member of the short-chain dehydrogenase/reductase family. Recombinant Escherichia coli that heterologously expresses the Xdh protein converts xylitol to xylulose as expected. On the other hand, the recombinant XytF protein has activity with l-arabitol but not with xylitol. XytB, xytD and xytE have significant sequence similarities to genes encoding the substrate-binding, ATP-binding and permease subunits, respectively, of ATP-binding cassette transporters. Although the physiological role of the operon remains unknown, the operon appears to be involved in uptake and metabolism of a various sugar alcohols. A gene encoding a DeoR-type transcriptional regulator, xytR, is located upstream of the operon in the opposite strand and a single nucleotide substitution that could cause a nonsense mutation is present in the xytR gene of the xylitol-utilizing mutant. This result suggests that the product of xytR negatively controls expression of the operon like other DeoR regulators.

Cloning and expression of a xylitol-4-dehydrogenase gene from Pantoea ananatis

The Pantoea ananatis ATCC 43072 mutant strain is capable of growing with xylitol as the sole carbon source. The xylitol-4-dehydrogenase (XDH) catalyzing the oxidation of xylitol to L-xylulose was isolated from the cell extract of this strain. The N-terminal amino acid sequence of the purified protein was determined, and an oligonucleotide deduced from this peptide sequence was used to isolate the xylitol-4-dehydrogenase gene (xdh) from a P. ananatis gene library. Nucleotide sequence analysis revealed an open reading frame of 795 bp, encoding the xylitol-4-dehydrogenase, followed by a 5' region of another open reading frame encoding an unknown protein. Results from a Northern analysis of total RNA isolated from P. ananatis ATCC 43072 suggested that xdh is transcribed as part of a polycistronic mRNA. Reverse transcription-PCR analysis of the transcript confirmed the operon structure and suggested that xdh was the first gene of the operon. Homology searches revealed that the predicted amino acid sequence of the P. ananatis XDH shared significant identity (38 to 51%) with members of the short-chain dehydrogenase/reductase family. The P. ananatis xdh gene was successfully overexpressed in Escherichia coli, XDH was purified to homogeneity, and some of its enzymatic properties were determined. The enzyme had a preference for NAD+ as the cosubstrate, and in contrast to previous reports, the enzyme also showed a side activity for the D-form of xylulose. Xylitol was converted to L-xylulose with a high yield (>80%) by the resting recombinant cells, and the L-xylulose was secreted into the medium. No evidence of D-xylulose being synthesized by the recombinant cells was found.

Molecular cloning of the Escherichia coli B L-fucose-D-arabinose gene cluster

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.

Isolation and characterization of Escherichia coli mutants able to utilize the novel pentose L-ribose

Wild-type strains of Escherichia coli were unable to utilize L-ribose for growth. However, L-ribose-positive mutants could be isolated from strains of E. coli K-12 which contained a ribitol operon. L-ribose-positive strains of E. coli, isolated after 15 to 20 days, had a growth rate of 0.22 generation per h on L-ribose. Growth on L-ribose was found to induce the enzymes of the L-arabinose and ribitol pathways, but only ribitol-negative mutants derived from strains originally L-ribose positive lost the ability to grow on L-ribose, showing that a functional ribitol pathway was required. One of the mutations permitting growth on L-ribose enabled the mutants to produce constitutively an NADPH-linked reductase which converted L-ribose to ribitol. L-ribose is not metabolized by an isomerization to L-ribulose, as would be predicted on the basis of other pentose pathways in enteric bacteria. Instead, L-ribose was metabolized by the reduction of L-ribose to ribitol, followed by the conversion to D-ribulose by enzymes of the ribitol pathway.

D-arabinose metabolism in Escherichia coli B: induction and cotransductional mapping of the L-fucose-D-arabinose pathway enzymes

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.

Inducible xylitol dehydrogenases in enteric bacteria

Morganella morganii ATCC 25829, Providencia stuartii ATCC 25827, Serratia marcescens ATCC 13880, and Erwinia sp. strain 4D2P were found to induce a xylitol dehydrogenase when grown on a xylitol-containing medium. The xylitol dehydrogenases were partially purified from the four strains, and those from M. morganii ATCC 25829, P. stuartii ATCC 25827, and S. marcescens ATCC 13880 were all found to oxidize xylitol to D-xylulose. These three enzymes had KmS for xylitol of 7.1 to 16.4 mM and molecular weights ranging from 130,000 to 155,000. In contrast, the xylitol dehydrogenase from Erwinia sp. strain 4D2P oxidized xylitol at the C-4 position to produce L-xylulose, had a Km for xylitol of 72 mM, and had a molecular weight of 102,000.

Characterization of xylitol-utilizing mutants of Erwinia uredovora

Of the four pentitols ribitol, xylitol, D-arabitol, and L-arabitol, Erwinia uredovora was able to utilize only D-arabitol as a carbon and energy source. Although attempts to isolate ribitol- or L-arabitol-utilizing mutants were unsuccessful, mutants able to grow on xylitol were isolated at a frequency of 9 X 10(-8). Xylitol-positive mutants constitutively synthesized both a novel NAD-dependent xylitol-4-dehydrogenase, which oxidized xylitol to L-xylulose, and an L-xylulokinase. The xylitol dehydrogenase had a Km for xylitol of 48 mM and showed best activity with xylitol and D-threitol as substrates. However, D-threitol was not a growth substrate for E. uredovora, and its presence did not induce either dehydrogenase or kinase activity. Attempts to determine the origin of the xylitol catabolic enzymes were unsuccessful; neither enzyme was induced on any growth substrate or in the presence of any polyol tested. Analysis of xylitol-negative mutants isolated after Tn5 mutagenesis suggested that the xylitol dehydrogenase and the L-xylulokinase structural genes were components of two separate operons but were under common regulatory control.

Production of D- and L-xylulose by mutants of Klebsiella pneumoniae and Erwinia uredovora

D-Xylulose and L-xylulose were produced biologically by the oxidation of a corresponding pentitol. A Klebsiella pneumoniae mutant was constructed for the oxidation of D-arabitol to D-xylulose. This mutant constitutively synthesized the D-arabitol permease system and D-arabitol dehydrogenase but was unable to produce the D-xylulokinase of the D-arabitol pathway or the D-xylose isomerase and D-xylulokinase of the D-xylose pathway. An Erwinia uredovora mutant which constitutively synthesized a novel xylitol-4-dehydrogenase but could not synthesize L-xylulokinase was used for the oxidation of xylitol to L-xylulose. Washed cell suspensions of either mutant incubated with 0.5% pentitol would oxidize 60 to 65% of the pentitol to the corresponding ketopentose in 18 h and excrete the ketopentose into the medium. Ketopentoses were rapidly purified from the remaining pentitol by hydroxyl affinity chromatography.

Directed evolution of a second xylitol catabolic pathway in Klebsiella pneumoniae

Klebsiella pneumoniae PRL-R3 has inducible catabolic pathways for the degradation of ribitol and D-arabitol but cannot utilize xylitol as a growth substrate. A mutation in the rbtB regulatory gene of the ribitol operon permits the constitutive synthesis of the ribitol catabolic enzymes and allows growth on xylitol. The evolved xylitol catabolic pathway consists of an induced D-arabitol permease system that also transports xylitol, a constitutively synthesized ribitol dehydrogenase that oxidizes xylitol at the C-2 position to produce D-xylulose, and an induced D-xylulokinase from either the D-arabitol or D-xylose catabolic pathway. To investigate the potential of K. pneumoniae to evolve a different xylitol catabolic pathway, strains were constructed which were unable to synthesize ribitol dehydrogenase or either type of D-xylulokinase but constitutively synthesized the D-arabitol permease system. These strains had an inducible L-xylulokinase; therefore, the evolution of an enzyme which oxidized xylitol at the C-4 position to L-xylulose would establish a new xylitol catabolic pathway. Four independent xylitol-utilizing mutants were isolated, each of which had evolved a xylitol-4-dehydrogenase activity. The four dehydrogenases appeared to be identical because they comigrated during nondenaturing polyacrylamide gel electrophoresis. This novel xylitol dehydrogenase was constitutively synthesized, whereas L-xylulokinase remained inducible. Transductional analysis showed that the evolved dehydrogenase was not an altered ribitol or D-arabitol dehydrogenase and that the evolved dehydrogenase structural gene was not linked to the pentitol gene cluster. This evolved dehydrogenase had the highest activity with xylitol as a substrate, a Km for xylitol of 1.4 M, and a molecular weight of 43,000.

D-Arabitol catabolic pathway in Klebsiella aerogenes

Klebsiella aerogenes strain W70 has an inducible pathway for the degradation of d-arabitol which is comparable to the one found in Aerobacter aerogenes strain PRL-R3. The pathway is also similar to the pathway of ribitol catabolism in that it is composed of a pentitol dehydrogenase, d-arabitol dehydrogenase (ADH), and a pentulokinase, d-xylulokinase (DXK). These two enzymes are coordinately controlled and induced in response to d-arabitol, the apparent inducer of synthesis of these enzymes. We obtained mutants which lacked a functional d-xylose pathway and were constitutive for the ribitol catabolic pathway. These mutants were able to grow on the unusual pentitol, xylitol, only if they contained the functional DXK of the d-arabitol pathway. This provided us with a specific selection technique for DXK(+) transductants. As in A. aerogenes, mutants constitutive for ADH were able to use this enzyme to convert the hexitol d-mannitol to d-fructose. With mutants blocked in the normal d-mannitol catabolic pathway, growth on d-mannitol became a test for ADH constitutivity. Growth of such mutants on xylitol, d-arabitol, and d-mannitol was utilized to classify transductants in mapping, by transductional analysis, the loci involved in d-arabitol utilization. Three-point crosses gave the order dalK-dalD-dalC, where dalK is the DXK structural gene, dalD is the ADH structural gene, and dalC is a regulatory site controlling synthesis of both enzymes.

Ribitol catabolic pathway in Klebsiella aerogenes

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.

Close genetic linkage of the determinants of the ribitol and D-arabitol catabolic pathways in Klebsiella aerogenes

Klebsiella aerogenes strain W70 has separate inducible pathways for the degradation of the pentitols ribitol and d-arabitol. These pathways are closely linked genetically as determined by transduction with phage PW52. There are two regulatory sites for the ribitol catabolic pathway as defined by loci for mutations to constitutive synthesis of ribitol dehydrogenase and d-ribulokinase, rbtB and rbtC. The two control sites are separated by a site represented by the dalB22 mutation. This mutation deprives the cell of the ability to induce synthesis of d-arabitol dehydrogenase and d-xylulokinase activities. Two additional regulatory mutations for the d-arabitol pathway, dalC31 and dalC37, map to the opposite side of rbtB13 relative to dalB22. The order of the genetic sites thus far determined for this region is dalK-dalD-dalC31, dalC37-rbtB13-dalB22-rbtC14-rbtD-rbtK, where dalK and dalD represent structural genes for the kinase and dehydrogenase of the d-arabitol pathway, respectively, and rbtK and rbtD represent the corresponding genes for the ribitol pathway. The two mutations that lead to constitutive synthesis of the d-arabitol-induced enzymes, dalC31 and dalC37, have different phenotypes with regard to their response to xylitol. The growth of dalC31 is inhibited by xylitol, but the toxicity can be reduced by increasing the levels of ribitol dehydrogenase either by induction with ribitol or by selection of a ribitol dehydrogenase-constitutive mutation.

Regulation of D-xylose and D-arabitol catabolism by Aerobacter aerogenes

Aerobacter aerogenes strain PRL-R3 possesses inducible enzyme pathways for the catabolism of d-xylose and d-arabitol. d-Xylose is the apparent inducer for d-xylose isomerase and d-xylulokinase. d-Arabitol is the apparent inducer for d-arabitol dehydrogenase and a separate d-xylulokinase. Both kinases had similar K(m) values and substrate specificities, and could not be separated by sucrose gradient centrifugation or polyacrylamide gel electrophoresis. They could be differentiated, however, by their separate regulation, their inhibition by antisera, and by the cold sensitivity of the kinase of the d-arabitol catabolic pathway.

Growth of Aerobacter aerogenes on D-arabinose: origin of the enzyme activities

Mutants of Aerobacter aerogenes can be selected which are capable of utilizing d-arabinose as a sole source of carbon and energy for growth. Mutants can also be selected which are capable of using l-xylose. The mutational event permitting the utilization of d-arabinose results in the constitutive synthesis of certain enzymes of the l-fucose catabolic pathway. l-Fucose isomerase catalyzes the first reaction in the degradation of d-arabinose: the isomerization of d-arabinose to d-ribulose. No other type of mutation appears to be required to initiate growth on d-arabinose, and wild-type cells induced for the enzymes of the l-fucose catabolic pathway are capable of growth on d-arabinose. The first reaction in the catabolism of l-xylose, the isomerization of l-xylose to l-xylulose, also appears to be catalyzed by constitutively synthesized l-fucose isomerase.

Metabolism of D-arabinose by Aerobacter aerogenes: purification of the isomerase

In Aerobacter aerogenes, the mutational event permitting the utilization of d-arabinose as a source of carbon and energy is a regulatory mutation resulting in the constitutive synthesis of certain enzymes of the l-fucose catabolic pathway. l-Fucose isomerase catalyzes the isomerization of d-arabinose to d-ribulose. This enzyme was purified to homogeneity as indicated by a single band in disc-gel electrophoretic columns and single peaks with column chromatography and ultracentrifugation from the wild-type PRL-R3 strain, induced with l-fucose and two constitutive mutants, 502 and 510. The ratios of the activities of this isomerase on d-arabinose and l-fucose remained constant throughout all purifications. The apparent K(m) of the isomerase from the wild-type strain induced with l-fucose and from the constitutive mutant strains was 5.0 x 10(-2)m for l-fucose and 1.5 x 10(-1)m for d-arabinose. A strain 531 possessing an apparent alteration in the isomerase was isolated from the strain 502. This altered isomerase exhibited a lowered K(m) for d-arabinose.

Metabolism of D-arabinose: origin of a D-ribulokinase activity in Escherichia coli

The kinase responsible for the phosphorylation of d-ribulose was purified 45.5-fold from a strain of Escherichia coli K-12 capable of growth on d-arabinose with no separation of d-ribulo- or l-fuculokinase activities. Throughout the purification, the ratios of activities remained essentially constant. A nonadditive effect of combining both substrates in an assay mixture; identical K(m) values for adenosine triphosphate with either l-fuculose or d-ribulose as substrate; and, the irreversible loss of activity on both substrates, after removal of magnesium ions from the enzyme preparation, suggest that the dual activity is due to the same enzyme. A fourfold greater affinity of the enzyme for l-fuculose than for d-ribulose, as well as a higher relative activity on l-fuculose, suggest that the natural substrate for this enzyme is l-fuculose. The product of the purified enzyme, with d-ribulose as substrate, was prepared. The ratio of total phosphorous to ribulose phosphate was 1.01:1, indicating that the product was ribulose monophosphate. The behavior of the kinase product in the cysteine-carbazole and orcinol reactions, as well as the results of periodate oxidation assays, provided evidence that it was not d-ribulose-5-phosphate. Reaction of this compound with a cell-free extract of E. coli possessing l-fuculose-l-phosphate aldolase activity resulted in the production of dihydroxyacetone phosphate and glycolaldehyde. The kinase product failed to reduce 2,3,5-triphenyltetrazolium and possessed a half-life of approximately 1.5 min in the presence of 1 n HCl at 100 C. These properties suggested that the phosphate group was attached to carbon atom 1 of d-ribulose.