D-Xylose metabolism by cell-free extracts of Penicillium chrysogenum

The Weimberg pathway: an alternative for Myceliophthora thermophila to utilize D-xylose

BACKGROUND

With D-xylose being the second most abundant sugar in nature, its conversion into products could significantly improve biomass-based process economy. There are two well-studied phosphorylative pathways for D-xylose metabolism. One is isomerase pathway mainly found in bacteria, and the other one is oxo-reductive pathway that always exists in fungi. Except for these two pathways, there are also non-phosphorylative pathways named xylose oxidative pathways and they have several advantages over traditional phosphorylative pathways. In Myceliophthora thermophila, D-xylose can be metabolized through oxo-reductive pathway after plant biomass degradation. The survey of non-phosphorylative pathways in this filamentous fungus will offer a potential way for carbon-efficient production of fuels and chemicals using D-xylose.

RESULTS

In this study, an alternative for utilization of D-xylose, the non-phosphorylative Weimberg pathway was established in M. thermophila. Growth on D-xylose of strains whose D-xylose reductase gene was disrupted, was restored after overexpression of the entire Weimberg pathway. During the construction, a native D-xylose dehydrogenase with highest activity in M. thermophila was discovered. Here, M. thermophila was also engineered to produce 1,2,4-butanetriol using D-xylose through non-phosphorylative pathway. Afterwards, transcriptome analysis revealed that the D-xylose dehydrogenase gene was obviously upregulated after deletion of D-xylose reductase gene when cultured in a D-xylose medium. Besides, genes involved in growth were enriched in strains containing the Weimberg pathway.

CONCLUSIONS

The Weimberg pathway was established in M. thermophila to support its growth with D-xylose being the sole carbon source. Besides, M. thermophila was engineered to produce 1,2,4-butanetriol using D-xylose through non-phosphorylative pathway. To our knowledge, this is the first report of non-phosphorylative pathway recombinant in filamentous fungi, which shows great potential to convert D-xylose to valuable chemicals.

Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds

The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.

d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review

Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.

Enhanced biosynthesis of 3,4-dihydroxybutyric acid by engineered Escherichia coli in a dual-substrate system

3,4-Dihydroxybutyric acid (3,4-DHBA), a versatile platform four carbon (C4) chemical, can be used as a precursor in the production of many commercially important chemicals. Here, a dual-substrate biosynthesis system was developed for 3,4-DHBA production via a synthetic pathway established in an engineered Escherichia coli, and using xylose as a synthetic substrate and glucose as a cell growth substrate. The deletion of genes xylA, yjhH and yagE and others encoding for alcohol dehydrogenases in E. coli is essential for the production of 3,4-DHBA. Blocking competing pathway by removing the gene yiaE encoding for a 2-keto-3-deoxy-D-xylonate reductase also facilitated carbon flow towards the synthesis of 3,4-DHBA. Furthermore, regulation the availability of NAD⁺ resulted in further improved 3,4-DHBA production. The combinational optimization of the biosynthesis system led to a production of 0.38g/L 3,4-DHBA. This study provides an alternative 3,4-DHBA biosynthesis approach with the possibility of utilizing hydrolysates of lignocellulosic biomass as substrates.

Arabinose and xylose fermentation by recombinant Saccharomyces cerevisiae expressing a fungal pentose utilization pathway

Background

Sustainable and economically viable manufacturing of bioethanol from lignocellulose raw material is dependent on the availability of a robust ethanol producing microorganism, able to ferment all sugars present in the feedstock, including the pentose sugars L-arabinose and D-xylose. Saccharomyces cerevisiae is a robust ethanol producer, but needs to be engineered to achieve pentose sugar fermentation.

Results

A new recombinant S. cerevisiae strain expressing an improved fungal pathway for the utilization of L-arabinose and D-xylose was constructed and characterized. The new strain grew aerobically on L-arabinose and D-xylose as sole carbon sources. The activities of the enzymes constituting the pentose utilization pathway(s) and product formation during anaerobic mixed sugar fermentation were characterized.

Conclusion

Pentose fermenting recombinant S. cerevisiae strains were obtained by the expression of a pentose utilization pathway of entirely fungal origin. During anaerobic fermentation the strain produced biomass and ethanol. L-arabitol yield was 0.48 g per gram of consumed pentose sugar, which is considerably less than previously reported for D-xylose reductase expressing strains co-fermenting L-arabinose and D-xylose, and the xylitol yield was 0.07 g per gram of consumed pentose sugar.

Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains

BACKGROUND

Ethanolic fermentation of lignocellulosic biomass is a sustainable option for the production of bioethanol. This process would greatly benefit from recombinant Saccharomyces cerevisiae strains also able to ferment, besides the hexose sugar fraction, the pentose sugars, arabinose and xylose. Different pathways can be introduced in S. cerevisiae to provide arabinose and xylose utilisation. In this study, the bacterial arabinose isomerase pathway was combined with two different xylose utilisation pathways: the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways, respectively, in genetically identical strains. The strains were compared with respect to aerobic growth in arabinose and xylose batch culture and in anaerobic batch fermentation of a mixture of glucose, arabinose and xylose.

RESULTS

The specific aerobic arabinose growth rate was identical, 0.03 h-1, for the xylose reductase/xylitol dehydrogenase and xylose isomerase strain. The xylose reductase/xylitol dehydrogenase strain displayed higher aerobic growth rate on xylose, 0.14 h-1, and higher specific xylose consumption rate in anaerobic batch fermentation, 0.09 g (g cells)-1 h-1 than the xylose isomerase strain, which only reached 0.03 h-1 and 0.02 g (g cells)-1h-1, respectively. Whereas the xylose reductase/xylitol dehydrogenase strain produced higher ethanol yield on total sugars, 0.23 g g-1 compared with 0.18 g g-1 for the xylose isomerase strain, the xylose isomerase strain achieved higher ethanol yield on consumed sugars, 0.41 g g-1 compared with 0.32 g g-1 for the xylose reductase/xylitol dehydrogenase strain. Anaerobic fermentation of a mixture of glucose, arabinose and xylose resulted in higher final ethanol concentration, 14.7 g l-1 for the xylose reductase/xylitol dehydrogenase strain compared with 11.8 g l-1 for the xylose isomerase strain, and in higher specific ethanol productivity, 0.024 g (g cells)-1 h-1 compared with 0.01 g (g cells)-1 h-1 for the xylose reductase/xylitol dehydrogenase strain and the xylose isomerase strain, respectively.

CONCLUSION

The combination of the xylose reductase/xylitol dehydrogenase pathway and the bacterial arabinose isomerase pathway resulted in both higher pentose sugar uptake and higher overall ethanol production than the combination of the xylose isomerase pathway and the bacterial arabinose isomerase pathway. Moreover, the flux through the bacterial arabinose pathway did not increase when combined with the xylose isomerase pathway. This suggests that the low activity of the bacterial arabinose pathway cannot be ascribed to arabitol formation via the xylose reductase enzyme.

Identification in the mould Hypocrea jecorina of a gene encoding an NADP(+): d-xylose dehydrogenase

A gene coding for an NADP⁺-dependent d-xylose dehydrogenase was identified in the mould Hypocrea jecorina (Trichoderma reesei). It was cloned from cDNA, the active enzyme was expressed in yeast and a histidine-tagged enzyme was purified and characterized. The enzyme had highest activity with d-xylose and significantly smaller activities with other aldose sugars. The enzyme is specific for NADP⁺. The K_m values for d-xylose and NADP⁺ are 43 mM and 250 μM, respectively. The role of this enzyme in H. jecorina is unclear because in this organism d-xylose is predominantly catabolized through a path with xylitol and d-xylulose as intermediates and the mould is unable to grow on d-xylonic acid.

POLYOL METABOLISM IN THE BASIDIOMYCETE SCHIZOPHYLLUM COMMUNE

Niederpruem, Donald J. (Indiana University Medical Center, Indianapolis), Amtul Hafiz, and Lyle Henry. Polyol metabolism in the basidiomycete Schizophyllum commune. J. Bacteriol. 89:954-959. 1965.-The polyol metabolism of intact cells and extracts of the wood-rotting mushroom Schizophyllum commune was investigated during the developmental cycle. Exogenous polyols stimulated the cellular respiration of germlings, but were without effect on that of ungerminated basidiospores. Requisite enzymes of polyol metabolism were demonstrated in extracts of spores and of subsequent stages of development. Oxidation of mannitol and sorbitol appeared to be coupled to nicotinamide adenine dinucleotide (NAD) reduction and was favored in alkaline medium. Ketohexose formation was shown during mannitol oxidation, and the NAD-dependent oxidation of xylitol yielded ketopentose. Xylitol oxidation with nicotinamide adenine dinucleotide phosphate (NADP) as hydrogen acceptor led to pentose formation. Oxidation of reduced NAD was enhanced by fructose but not by sorbose. Reduction of aldohexose and pentose was dependent upon reduced NADP, and pentose reductase was maximal at pH 6.8. The specific activity of mannitol dehydrogenase was highest in extracts of vegetative mycelium. Growth in either glucose or xylose media had no significant effect on enzymes of polyol metabolism.

Arbinose utilization by xylose-fermenting yeasts and fungi

Various wild-type yeasts and fungi were screened to evaluate their ability to ferment L-arabinose under oxygen-limited conditions when grown in defined minimal media containing mixtures of L-arabinose, D-xylose, and D-glucose. Although all of the yeasts and some of the fungi consumed arabinose, arabinose was not fermented to ethanol by any of the strains tested. Arabitol was the only major product other than cell mass formed from L-arabinose; yeasts converted arabinose to arabitol at high yield. The inability to ferment L-arabinose appears to be a consequence of inefficient or incomplete assimilation pathways for this pentose sugar.

Fusarium oxysporum: status in bioethanol production

Fermentation of lignocellulosic materials to ethanol and other solvents provides an alternative way of treating wastes and producing chemical feedstocks and fuel additives. Considerable efforts have been made in past 10 years to improve the process based on lignocellulosic biomass and hydrolysate that contains a complex mixture of sugars, decomposition products of sugars, and sometimes the inhibitory levels of soluble lignin. Despite the relative abundance of D-xylose in crop and forest residues it has not been found efficiently fermentable by most of the microorganisms. Recent research has revealed that D-xylose may be fermented to ethanol and organic acids. Recently, several strains of Fusarium oxysporum have been found to have potential for converting not only D-xylose, but also cellulose to ethanol in a one-step process. Distinguishing features of F. oxysporum for ethanol production in comparison to other organisms are identified. These include the advantage of in situ cellulase production and cellulose fermentation, pentose fermentation, and the tolerance of sugars and ethanol. The main disadvantage is the slow conversion rate when compared with yeast.

Conversion of pentoses to ethanol by yeasts and fungi

Fermentation of D-xylose is of interest in enhancing the yield of ethanol obtainable from lignocellulosic hydrolysates. Such hydrolysates can contain both pentoses and hexoses, and while technology to convert hexoses to ethanol is well established, the fermentation of pentoses had been problematical. To overcome the difficulty, yeasts and fungi have been sought and identified in recent years that can convert D-xylose into ethanol. However, operation of their cultures in the presence of the pentose to obtain rapid and efficient ethanol production is somewhat more complex than in the archetype alcoholic fermentation, Saccharomyces cerevisiae on D-glucose. The complexity stems, in part, from the association of ethanol accumulation in cultures where D-xylose is the sole carbon source with conditions that limit growth, by oxygen in particular, although limitation by other nutrients might also be implicated. Aspects of screening for appropriate organisms and of the parameters that play a role in determining culture variables, especially those associated with ethanol productivity, are reviewed. Performance with D-xylose as sole carbon source, in sugar mixtures, and in lignocellulosic hydrolysates is discussed. A model that involves biochemical considerations of D-xylose metabolism is presented that rationalizes the effects of oxygen on cultures where D-xylose is the sole carbon source, notably effects of the specific rate of oxygen use on the rate and extent of ethanol accumulation. Alternate methods to direct fermentation of D-xylose have been developed that depend on its prior isomerization to D-xylose, followed by fermentation of the pentulose by certain yeasts and fungi. Factors involved in the biochemistry, use, and performance of these methods, which with some organisms involves sensitivity to oxygen, are reviewed.

Identification of a salvage pathway for D-arabinose in Mycobacterium smegmatis

Extracts of Mycobacterium smegmatis, which was adapted to growth in synthetic medium containing D-arabinose as sole carbon source, catalyzed the NADPH-mediated reduction of D-arabinose to D-arabitol. When arabinose-adapted bacteria were transferred to glycerol medium, resumption of growth was accompanied by a sharp drop in the specific activity of this enzyme. Moreover, extracts of cells grown in D-arabinose medium contained large amounts of an NAD+-linked pentitol dehydrogenase, as compared to bacteria multiplying in glycerol medium. The specific activity of mycobacterial extracts was ten-fold higher for D-arabitol than for its L-isomer, and eight-fold higher than for xylitol (it was more than forty-fold lower in the case of glycerol-grown cells). The product of the pentitol dehydrogenase reaction was identified as D-xylulose by three different procedures. On the basis of these data, it is suggested that utilization of exogenous D-arabinose in mycobacteria involves two dehydrogenases that catalyze the reactions D-arabinose NADPH----D-arabitol NAD+----D-xylulose, by virtue of which an aldopentose is converted into a ketopentose. The alditol: NADP oxidoreductase was isolated from homogenates of D-arabinose-adapted mycobacteria, and purified by DEAE-cellulose chromatography. The enzymatic activity was restricted to a single band which, under denaturing conditions, comigrated with albumin (approximately 46 kDa). It was insensitive to 2-mercaptoethanol, EDTA and NaF, and was inactivated at 70 degrees C.

Hydrolysis of xylan and fermentation of xylose to ethanol

The focus in the development of pulping processes has usually been exclusively on cellulose. However, hemicellulose could serve as a valuable source of hexose and pentose sugars. Consequently, it should not be destroyed in a process designed for very high cellulose fibre yields. Novel procedures developed for production of ethanol by the fermentation of pentoses as well as hexoses provide new possibilities of hemicellulose utilization. Many fungi produce extracellular hemicellulases. In the present work the production of xylanase and beta-xylosidase with strains of Aspergillus and Trichoderma was studied. The enzymes were used for the hydrolysis of xylan. Xylose was fermented to ethanol by the mold Fusarium oxysporum.

Identification of reduced nicotinamide adenine dinucleotide phosphate-dependent aldehyde reductase in a Rhodotorula strain

Reduced nicotinamide adenine dinucleotide phosphate (NADPH)-aldehyde reductase was isolated in 24% yield and 66-fold purification from a dl-glyceraldehyde-grown Rhodotorula species. This enzyme was specific for NADPH, and d-, l-, or dl-glyceraldehyde were equally good substrates. Other substrates had activities as follows: methylglyoxal, 50%; fructose, 33%; d- and l-arabinose, 12%; d-xylose, 8%; d-glucose, 5%; d-erythrose and d-threose, 0 to 5%. The product from the reduction of dl-glyceraldehyde was glycerol, as shown by high voltage electrophoresis, paper chromatography, and direct enzymatic analysis. Kinetic studies gave K(m) values of 0.89 mm and 0.013 mm for dl-glyceraldehyde and NADPH, respectively. An optimal pH range of 6.3 to 6.7 was found for maximal activity. Reduction of NADP(+) by glycerol was not demonstrable. This Rhodotorula NADPH-aldehyde reductase activity was compared to similar enzymes from other sources.

SEQUENTIAL PRIMARY AND SECONDARY SHUNT METABOLISM IN PENICILLIUM CHRYSOGENUM

Penicillium chrysogenum was grown on a rich medium and on a more sparse medium which favored penicillin production. Mycelia grown on both media were examined for changes in lipid, mannitol, erythritol, glycerol, pentitol, trehalose, and residual mycelium, and the filtrates were examined for penicillin. Penicillin production took place after the bulk of trehalose, polyol, and lipid had accumulated, and hence the sequential pattern of primary and secondary shunt metabolism, as observed in the case of ergot alkaloid production by Claviceps purpurea, was demonstrated in this example of penicillin production.

ENZYME SYSTEMS IN THE MYCOBACTERIA XV

Goldman, Dexter S. (Veterans Administration Hospital, Madison, Wis.). Enzyme systems in the mycobacteria. XV. Initial steps in the metabolism of glycerol. J. Bacteriol. 86: 30–37. 1963.—In cell-free extracts of strain H37Ra of Mycobacterium tuberculosis , glycerol is metabolized first by oxidation to dihydroxyacetone. A kinase was partially purified and shown to phosphorylate dihydroxyacetone; in the presence of the glyceraldehyde-3-phosphate dehydrogenase system, the product of the kinase reaction was further oxidized to 3-phosphoglycerate. The role of α-glycerol phosphate in the metabolism of strain H37Ra is discussed.

Fatty Acid Oxidation by Spores of Penicillium roqueforti

When 1 μ m sodium octanoate was the substrate for spores, most of the molecule was recovered as CO 2 and no ketone was produced. However, when larger concentrations (20 μ m ) were used as substrate, part of the molecule was converted to methyl ketone and part was completely oxidized. Optimal conditions for the production of 2-heptanone were determined because of the importance of this compound in giving aroma and flavor to mold-ripened cheeses. Optimal ketone formation was not dependent upon the temperature and length of time at which the spores were stored. The spore suspensions were stored for over 36 months at 4 C without losing their ability to convert octanoic acid to 2-heptanone. The oxidation of octanoic acid was inhibited by cyanide, carbon monoxide, mercury, 2,3-dimercapto-1-propanol, and α, α-dipyridyl. No ketone was produced under anaerobic conditions. Although no intermediates of fatty acid oxidation were isolated, since an active cell-free preparation could not be obtained, this investigation has yielded some evidence for the beta oxidation of the fatty acids by spores of Penicillium roqueforti .

SOME PROPERTIES OF THE D-YLULOKINASE OF AEROBACTER AEROGENES

The D-xylulokinase of Aerobacler aerogenes is an inducible enzyme specific for its substrate. The optimum pH for activity lies between 7.5 and 8.7. At 30 °C the enzyme is most stable between pH 6.0 and 9.5 and is inactivated at pH 4.6 and 11.5 within 15 minutes. At 61 °C, pH 7.8, 41% of the enzyme is inactivated in 15 minutes and at 66 °C completely inactivated. Magnesium ions, although required for activity, labilize the enzyme, while D-xylulose, adenosine triphosphate, EDTA, and glycerol protect the enzyme. The enzyme is sensitive to heavy metals and sulphhydryl reagents. ITP and GTP are about 25% and UTP about 14% as effective as ATP as phosphate donors.