D-

Xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon atoms and includes an aldehyde functional g ...

is a five-carbon aldose (

pentose In chemistry, a pentose is a monosaccharide (simple sugar) with five carbon atoms. The chemical formula of many pentoses is , and their molecular weight is 150.13 g/mol.monosaccharide) that can be catabolized or metabolized into useful products by a variety of organisms. There are at least four different pathways for the catabolism of D-xylose: An oxido-reductase pathway is present in eukaryotic microorganisms. Prokaryotes typically use an isomerase pathway, and two oxidative pathways, called Weimberg and Dahms pathways respectively, are also present in prokaryotic microorganisms.

Pathways

The oxido-reductase pathway

This pathway is also called the “Xylose Reductase-Xylitol Dehydrogenase” or XR-XDH pathway.

Xylose reductase Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon atoms and includes an aldehyde functional g ...

(XR) and xylitol dehydrogenase (XDH) are the first two enzymes in this pathway. XR is reducing D-xylose to

xylitol Xylitol is a chemical compound with the formula , or HO(CH2)(CHOH)3(CH2)OH; specifically, one particular stereoisomer with that structural formula. It is a colorless or white crystalline solid that is freely soluble in water. It can be classifi ...

using

NADH Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an aden ...

or NADPH.

Xylitol Xylitol is a chemical compound with the formula , or HO(CH2)(CHOH)3(CH2)OH; specifically, one particular stereoisomer with that structural formula. It is a colorless or white crystalline solid that is freely soluble in water. It can be classifi ...

is then oxidized to D-xylulose by XDH, using the cofactor NAD. In the last step D-xylulose is phosphorylated by an ATP utilising kinase, XK, to result in D-xylulose-5-phosphate which is an intermediate of the

pentose phosphate pathway The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt and the HMP Shunt) is a metabolic pathway parallel to glycolysis. It generates NADPH and pentoses (5-carbon sugars) as well as ribose 5-pho ...

The isomerase pathway

In this pathway the enzyme

xylose isomerase In enzymology, a xylose isomerase () is an enzyme that catalyzes the interconversion of D-xylose and D-xylulose. This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ket ...

converts D-xylose directly into D-xylulose. D-xylulose is then phosphorylated to D-xylulose-5-phosphate as in the oxido-reductase pathway. At equilibrium, the isomerase reaction results in a mixture of 83% D-xylose and 17% D-xylulose because the conversion of xylose to xylulose is energetically unfavorable.

Weimberg pathway

The Weimberg pathway is an oxidative pathway where the D-xylose is oxidized to D-xylono-lactone by a D-xylose dehydrogenase followed by a

lactonase Lactonase (EC 3.1.1.81, acyl-homoserine lactonase; systematic name ''N''-acyl-L-homoserine-lactone lactonohydrolase) is a metalloenzyme, produced by certain species of bacteria, which targets and inactivates acylated homoserine lactones (AHLs). I ...

to hydrolyze the lactone to D-xylonic acid. A xylonate dehydratase is splitting off a water molecule resulting in 2-keto 3-deoxy-xylonate. 2-keto-3-deox-D-xylonate dehydratase forms the α-ketoglutarate semialdehyde. This is subsequently oxidised via α-ketoglutarate semialdehyde dehydrogenase to yield 2-ketoglutarate which serves as a key intermediate in the citric acid cycle.

Dahms pathway

The Dahms pathway starts as the Weimberg pathway but the 2-keto-3 deoxy-xylonate is split by an aldolase to pyruvate and

glycolaldehyde Glycolaldehyde is the organic compound with the formula . It is the smallest possible molecule that contains both an aldehyde group () and a hydroxyl group (). It is a highly reactive molecule that occurs both in the biosphere and in the inters ...

Biotechnological applications

It is desirable to ferment D-xylose to ethanol. This can be accomplished either by native xylose fermenting yeasts such as ''Scheffersomyces Pichia stipitis'' or by metabolically engineered strains of ''Saccharomyces cerevisiae''. '' Pichia stipitis'' is not as ethanol tolerant as the traditional ethanol producing yeast ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have b ...

''. ''S. cerevisiae'' on the other hand can not ferment D-xylose to ethanol. In attempts to generate ''S. cerevisiae'' strains that are able to ferment D-xylose the ''XYL1'' and ''XYL2'' genes of ''P. stipitis'' coding for the D-xylose reductase (XR) and xylitol dehydrogenase (XDH), respectively were introduced in S. cerevisiae by means of genetic engineering. XR catalyze the formation of

from D-xylose and XDH the formation of D-xylulose from xylitol. ''Saccharomyces cerevisiae'' can naturally ferment D-xylulose through the

. In another approach, bacterial xylose isomerases have been introduced into ''S. cerevisiae''. This enzyme catalyze the direct formation of D-xylulose from D-xylose. Many attempts at expressing bacterial isomerases were not successful due to misfolding or other problems, but a xylose isomerase from the anaerobic fungus '' Piromyces'' Sp. has proven effective. One advantage claimed for ''S. cerevisiae'' engineered with the xylose isomerase is that the resulting cells can grow anaerobically on xylose after evolutionary adaptation. Studies on flux through the oxidative

during D-xylose metabolism have revealed that limiting the rate of this step may be beneficial to the efficiency of fermentation to ethanol. Modifications to this flux that may improve ethanol production include deleting the GND1 gene, or the ZWF1 gene. Since the pentose phosphate pathway produces additional NADPH during metabolism, limiting this step will help to correct the already evident imbalance between NAD(P)H and NAD+ cofactors and reduce xylitol byproduct formation. Another experiment comparing the two D-xylose metabolizing pathways revealed that the XI pathway was best able to metabolize D-xylose to produce the greatest ethanol yield, while the XR-XDH pathway reached a much faster rate of

ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an alcohol with the chemical formula . Its formula can be also written as or (an ethyl group linked to a ...

production. Overexpression of the four genes encoding non-oxidative

enzymes

Transaldolase Transaldolase is an enzyme () of the non-oxidative phase of the pentose phosphate pathway. In humans, transaldolase is encoded by the ''TALDO1'' gene. The following chemical reaction is catalyzed by transaldolase: : sedoheptulose 7-phosph ...

Transketolase Transketolase (abbreviated as TK) is an enzyme that is encoded by the TKT gene. It participates in both the pentose phosphate pathway in all organisms and the Calvin cycle of photosynthesis. Transketolase catalyzes two important reactions, whic ...

, Ribulose-5-phosphate epimerase and Ribose-5-phosphate ketol-isomerase led to both higher D-xylulose and

D-xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon atoms and includes an aldehyde functional gro ...

fermentation rate. The aim of this genetic recombination in the laboratory is to develop a

yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constit ...

strain that efficiently produces ethanol. However, the effectiveness of D-xylose metabolizing laboratory strains do not always reflect their metabolism abilities on raw xylose products in nature. Since D-xylose is mostly isolated from agricultural residues such as wood stocks then the native or genetically altered yeasts will need to be effective at metabolizing these less pure natural sources. Varying expression of the XR and XDH enzyme levels have been tested in the laboratory in the attempt to optimize the efficiency of the D-xylose metabolism pathway.

References

{{Carbohydrate metabolism Monosaccharides Metabolism