Faculty & Staff

  • Image of Thomas W. Jeffries

    Thomas W. Jeffries

    Professor of Bacteriology, Emeritus

    1531 Microbial Sciences Building
    Office: (608) 698-4470


Ph.D. 1975 Rutgers University
Postdoctoral Research: Columbia University

Areas of Study

Bioconversion of renewable resources
metabolic engineering of pentose fermenting yeasts

Research Overview

Our research interests are in the areas of microbial physiology, metabolic regulation and metabolic engineering as they apply to the utilization of lignocellulosic materials. This involves genetic engineering of novel yeasts, strain screening, scale-up, microbial biochemistry, and molecular genetics. Areas of emphasis are the fermentation of xylose by yeasts and metabolic pathway engineering. Research activities include metabolic engineering in the xylose-fermenting yeast, Pichia stipitis; optimization of metabolic pathways in Saccharomyces cerevisiae; determination of rate-limiting steps in yeast fermentation and growth; and alteration of intermediary metabolism to regulate energetics.


  • Microbiology 632: Industrial Microbiology


Research Papers

  • Su YK, Willis LB, Rehmann L, Smith DR, Jeffries TW (2018) Spathaspora passalidarum selected for resistance to AFEX hydrolysate shows decreased cell yield. FEMS Yeast Res. 18(6): 10.1093/femsyr/foy011 · Pubmed

    This study employed cell recycling, batch adaptation, cell mating and high-throughput screening to select adapted Spathaspora passalidarum strains with improved fermentative ability. The most promising candidate YK208-E11 (E11) showed a 3-fold increase in specific fermentation rate compared to the parental strain and an ethanol yield greater than 0.45 g/g substrate while co-utilizing cellobiose, glucose and xylose. Further characterization showed that strain E11 also makes 40% less biomass compared to the parental strain when cultivated in rich media under aerobic conditions. A tetrazolium agar overlay assay in the presence of respiration inhibitors, including rotenone, antimycin A, KCN and salicylhydroxamic acid elucidated the nature of the mutational events. Results indicated that E11 has a deficiency in its respiration system that could contribute to its low cell yield. Strain E11 was subjected to whole genome sequencing and an ∼11 kb deletion was identified; the open reading frames absent in strain E11 code for proteins with predicted functions in respiration, cell division and the actin cytoskeleton, and may contribute to the observed physiology of the adapted strain. Results of the tetrazolium overlay also suggest that cultivation on xylose affects the respiration capacity in the wild-type strain, which could account for its faster fermentation of xylose as compared to glucose. These results support our previous finding that S. passalidarum has highly unusual physiological responses to xylose under oxygen limitation.

  • Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW (2016) Comparative genomics of biotechnologically important yeasts. Proc. Natl. Acad. Sci. U.S.A. 113(35):9882-7 (PMC5024638) · Pubmed

    Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

  • Hittinger CT, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP (2015) Genomics and the making of yeast biodiversity. Curr. Opin. Genet. Dev. 35:100-9 (PMC4771062) · Pubmed

    Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.

  • Calvey CH, Su YK, Willis LB, McGee M, Jeffries TW (2015) Nitrogen limitation, oxygen limitation, and lipid accumulation in Lipomyces starkeyi. Bioresour. Technol. 200:780-8 · Pubmed

    Lipid production by oleaginous yeasts is optimal at high carbon-to-nitrogen ratios. In the current study, nitrogen and carbon consumption by Lipomyces starkeyi were directly measured in defined minimal media with nitrogen content and agitation rates as variables. Shake flask cultures with an initial C:N ratio of 72:1 cultivated at 200rpm resulted in a lipid output of 10g/L, content of 55%, yield of 0.170g/g, and productivity of 0.06g/L/h. All of these values decreased by ≈50-60% when the agitation rate was raised to 300rpm or when the C:N ratio was lowered to 24:1, demonstrating the importance of these parameters. Under all conditions, L. starkeyi cultures tolerated acidified media (pH≈2.6) without difficulty, and produced considerable amounts of alcohols; including ethanol, mannitol, arabitol, and 2,3-butanediol. L. starkeyi also produced lipids from a corn stover hydrolysate, showing its potential to produce biofuels from renewable agricultural feedstocks.

  • Damiani AL, He QP, Jeffries TW, Wang J (2015) Comprehensive evaluation of two genome-scale metabolic network models for Scheffersomyces stipitis. Biotechnol. Bioeng. 112(6):1250-62 · Pubmed

    Genome-scale metabolic network models represent the link between the genotype and phenotype of the organism, which are usually reconstructed based on the genome sequence annotation and relevant biochemical and physiological information. These models provide a holistic view of the organism's metabolism, and constraint-based metabolic flux analysis methods have been used extensively to study genome-scale cellular metabolic networks. It is clear that the quality of the metabolic network model determines the outcome of the application. Therefore, it is critically important to determine the accuracy of a genome-scale model in describing the cellular metabolism of the modeled strain. However, because of the model complexity, which results in a system with very high degree of freedom, a good agreement between measured and computed substrate uptake rates and product secretion rates is not sufficient to guarantee the predictive capability of the model. To address this challenge, in this work we present a novel system identification based framework to extract the qualitative biological knowledge embedded in the quantitative simulation results from the metabolic network models. The extracted knowledge can serve two purposes: model validation during model development phase, which is the focus of this work, and knowledge discovery once the model is validated. This framework bridges the gap between the large amount of numerical results generated from genome-scale models and the knowledge that can be easily understood by biologists. The effectiveness of the proposed framework is demonstrated by its application to the analysis of two recently published genome-scale models of Scheffersomyces stipitis.

  • Su YK, Willis LB, Jeffries TW (2015) Effects of aeration on growth, ethanol and polyol accumulation by Spathaspora passalidarum NRRL Y-27907 and Scheffersomyces stipitis NRRL Y-7124. Biotechnol. Bioeng. 112(3):457-69 · Pubmed

    Spathaspora passalidarum NN245 (NRRL-Y27907) is an ascomycetous yeast that displays a higher specific fermentation rate with xylose than with glucose. Previous studies have shown that its capacity for xylose fermentation increases while cell yield decreases with decreasing aeration. Aeration optimization plays a crucial role in maximizing bioethanol production from lignocellulosic hydrolysates. Here, we compared the kinetics of S. passalidarum NN245 and Scheffersomyces (Pichia) stipitis NRRL Y-7124 fermenting 15% glucose, 15% xylose, or 12% xylose plus 3% glucose under four different aeration conditions. The maximum specific fermentation rate for S. passalidarum was 0.153 g ethanol/g CDW · h with a yield of 0.448 g/g from 150 g/L xylose at an oxygen transfer rate of 2.47 mmol O2 /L h. Increasing the OTR to 4.27 mmol O2 /L h. decreased the ethanol yield from 0.46 to 0.42 g/g xylose while increasing volumetric ethanol productivity from 0.52 to 0.8 g/L h. Both yeasts had lower cells yields and higher ethanol yields when growing on xylose than when growing on glucose. Acetic acid accretions of both strains correlated positively with increasing aeration. S. passalidarum secreted lower amounts of polyols compared to S. stipitis under most circumstances. In addition, the composition of polyols differed: S. passalidarum accumulated mostly xylitol and R,R-2,3-butanediol (BD) whereas S. stipitis accumulated mostly xylitol and ribitol when cultivated in xylose or a mixture of 12% xylose and 3% glucose. R,R-2,3-BD accumulation by S. passalidarum during xylose fermentation can be as much as four times of that by S. stipitis, and R,R-2,3-BD is also the most abundant byproduct after xylitol. The ratios of polyols accumulated by the two species under different aeration conditions and the implications of these observations for strain and process engineering are discussed.

  • Calvey CH, Willis LB, Jeffries TW (2014) An optimized transformation protocol for Lipomyces starkeyi. Curr. Genet. 60(3):223-30 · Pubmed

    We report the development of an efficient genetic transformation system for Lipomyces starkeyi based on a modified lithium acetate transformation protocol. L. starkeyi is a highly lipogenic yeast that grows on a wide range of substrates. The initial transformation rate for this species was extremely low, and required very high concentrations of DNA. A systematic approach for optimizing the protocol resulted in an increase in the transformation efficiency by four orders of magnitude. Important parameters included cell density, the duration of incubation and recovery periods, the heat shock temperature, and the concentration of lithium acetate and carrier DNA within the transformation mixture. We have achieved efficiencies in excess of 8,000 transformants/µg DNA, which now make it possible to screen libraries in the metabolic engineering of this yeast. Metabolic engineering based on this transformation system could improve lipogenesis and enable formation of higher value products.

  • Cheng J, Leu SY, Zhu JY, Jeffries TW (2014) Ethanol production from non-detoxified whole slurry of sulfite-pretreated empty fruit bunches at a low cellulase loading. Bioresour. Technol. 164:331-7 · Pubmed

    Sulfite pretreatment to overcome the recalcitrance of lignocelluloses (SPORL) was applied to an empty fruit bunches (EFB) for ethanol production. SPORL facilitated delignification through lignin sulfonation and dissolution of xylan to result in a highly digestible substrate. The pretreated whole slurry was enzymatically saccharified at a solids loading of 18% using a relatively low cellulase loading of 15 FPU/g glucan and simultaneously fermented without detoxification using Saccharomyces cerevisiae of YRH400. An ethanol yield of 217 L/tonne EFB was achieved at titer of 32 g/L. Compared with literature studies, SPORL produced high ethanol yield and titer with much lower cellulase loading without detoxification.

  • Scalcinati G, Otero JM, Van Vleet JR, Jeffries TW, Olsson L, Nielsen J (2012) Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. FEMS Yeast Res. 12(5):582-97 · Pubmed

    Industrial biotechnology aims to develop robust microbial cell factories, such as Saccharomyces cerevisiae, to produce an array of added value chemicals presently dominated by petrochemical processes. Xylose is the second most abundant monosaccharide after glucose and the most prevalent pentose sugar found in lignocelluloses. Significant research efforts have focused on the metabolic engineering of S. cerevisiae for fast and efficient xylose utilization. This study aims to metabolically engineer S. cerevisiae, such that it can consume xylose as the exclusive substrate while maximizing carbon flux to biomass production. Such a platform may then be enhanced with complementary metabolic engineering strategies that couple biomass production with high value-added chemical. Saccharomyces cerevisiae, expressing xylose reductase, xylitol dehydrogenase and xylulose kinase, from the native xylose-metabolizing yeast Pichia stipitis, was constructed, followed by a directed evolution strategy to improve xylose utilization rates. The resulting S. cerevisiae strain was capable of rapid growth and fast xylose consumption producing only biomass and negligible amount of byproducts. Transcriptional profiling of this strain was employed to further elucidate the observed physiology confirms a strongly up-regulated glyoxylate pathway enabling respiratory metabolism. The resulting strain is a desirable platform for the industrial production of biomass-related products using xylose as a sole carbon source.

  • Long TM, Su YK, Headman J, Higbee A, Willis LB, Jeffries TW (2012) Cofermentation of glucose, xylose, and cellobiose by the beetle-associated yeast Spathaspora passalidarum. Appl. Environ. Microbiol. 78(16):5492-500 (PMC3406140) · Pubmed

    Fermentation of cellulosic and hemicellulosic sugars from biomass could resolve food-versus-fuel conflicts inherent in the bioconversion of grains. However, the inability to coferment glucose and xylose is a major challenge to the economical use of lignocellulose as a feedstock. Simultaneous cofermentation of glucose, xylose, and cellobiose is problematic for most microbes because glucose represses utilization of the other saccharides. Surprisingly, the ascomycetous, beetle-associated yeast Spathaspora passalidarum, which ferments xylose and cellobiose natively, can also coferment these two sugars in the presence of 30 g/liter glucose. S. passalidarum simultaneously assimilates glucose and xylose aerobically, it simultaneously coferments glucose, cellobiose, and xylose with an ethanol yield of 0.42 g/g, and it has a specific ethanol production rate on xylose more than 3 times that of the corresponding rate on glucose. Moreover, an adapted strain of S. passalidarum produced 39 g/liter ethanol with a yield of 0.37 g/g sugars from a hardwood hydrolysate. Metabolome analysis of S. passalidarum before onset and during the fermentations of glucose and xylose showed that the flux of glycolytic intermediates is significantly higher on xylose than on glucose. The high affinity of its xylose reductase activities for NADH and xylose combined with allosteric activation of glycolysis probably accounts in part for its unusual capacities. These features make S. passalidarum very attractive for studying regulatory mechanisms enabling bioconversion of lignocellulosic materials by yeasts.

  • Rodrigues RC, Kenealy WR, Dietrich D, Jeffries TW (2012) Response surface methodology (RSM) to evaluate moisture effects on corn stover in recovering xylose by DEO hydrolysis. Bioresour. Technol. 108:134-9 · Pubmed

    Response surface methodology (RSM), based on a 2(2) full factorial design, evaluated the moisture effects in recovering xylose by diethyloxalate (DEO) hydrolysis. Experiments were carried out in laboratory reactors (10 mL glass ampoules) containing corn stover (0.5 g) properly ground. The ampoules were kept at 160 °C for 90 min. Both DEO concentration and corn stover moisture content were statistically significant at 99% confidence level. The maximum xylose recovery by the response surface methodology was achieved employing both DEO concentration and corn stover moisture at near their highest levels area. We amplified this area by using an overlay plot as a graphical optimization using a response of xylose recovery more than 80%. The mathematical statistical model was validated by testing a specific condition in the satisfied overlay plot area. Experimentally, a maximum xylose recovery (81.2%) was achieved by using initial corn stover moisture of 60% and a DEO concentration of 4% w/w. The mathematical statistical model showed that xylose recovery increases during DEO corn stover acid hydrolysis as the corn stover moisture level increases. This observation could be important during the harvesting of corn before it is fully dried in the field. The corn stover moisture was an important variable to improve xylose recovery by DEO acid hydrolysis.

  • Koivistoinen OM, Arvas M, Headman JR, Andberg M, Penttilä M, Jeffries TW, Richard P (2012) Characterisation of the gene cluster for l-rhamnose catabolism in the yeast Scheffersomyces (Pichia) stipitis. Gene 492(1):177-85 · Pubmed

    In Scheffersomyces (Pichia) stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species. Our transcriptome analysis shows that all the catabolic genes and all genes of the cluster are up-regulated on L-rhamnose. Among genes that were also up-regulated on L-rhamnose were two transcription factors including the TRC1. In addition, in 16 out of the 32 analysed fungal species only RHA1, LRA2 and LRA3 are physically clustered. The clustering of RHA1, LRA3 and TRC1 is also conserved in species not closely related to S. stipitis. Since the LRA4 is often not part of the cluster and it has several paralogues in L-rhamnose utilising yeasts we analysed the function of one of the paralogues, LRA41 by heterologous expression and biochemical characterization. Lra41p has similar catalytic properties as the Lra4p but the transcript was not up-regulated on L-rhamnose. The RHA1, LRA2, LRA4 and LADH genes were previously characterised in S. stipitis. We expressed the L-rhamnonate dehydratase, Lra3p, in Saccharomyces cerevisiae, estimated the kinetic constants of the protein and showed that it indeed has activity with L-rhamnonate.

  • Sreenath HK, Jeffries TW (2011) Interactions of fungi from fermented sausage with regenerated cellulose casings. J. Ind. Microbiol. Biotechnol. 38(11):1793-802 · Pubmed

    This research examined cellulolytic effects of fungi and other microbes present in cured sausages on the strength and stability of regenerated cellulose casings (RCC) used in the sausage industry. Occasionally during the curing process, RCC would split or fail, thereby leading to loss of product. The fungus Penicillium sp. BT-F-1, which was isolated from fermented sausages, and other fungi, which were introduced to enable the curing process, produced small amounts of cellulases on RCC in both liquid and solid cultivations. During continued incubation for 15-60 days in solid substrate cultivation (SSC) on RCC support, the fungus Penicillium sp isolate BT-F-1 degraded the casings' dry weights by 15-50% and decreased their tensile strengths by ~75%. Similarly commercial cellulase(s) resulted in 20-50% degradation of RCC in 48 h. During incubation with Penicillium sp BT-F-1, the surface structure of RCC collapsed, resulting in loss of strength and stability of casings. The matrix of industrial RCC comprised 88-93% glucose polymer residues with 0.8-4% xylan impurities. Premature casing failure appeared to result from operating conditions in the manufacturing process that allowed xylan to build up in the extrusion bath. The sausage fungus Penicillium sp BT-F-1 produced xylanases to break down soft xylan pockets prior to slow cellulosic dissolution of RCC.

  • Rodrigues RC, Kenealy WR, Jeffries TW (2011) Xylitol production from DEO hydrolysate of corn stover by Pichia stipitis YS-30. J. Ind. Microbiol. Biotechnol. 38(10):1649-55 · Pubmed

    Corn stover that had been treated with vapor-phase diethyl oxalate released a mixture of mono- and oligosaccharides consisting mainly of xylose and glucose. Following overliming and neutralization, a D-xylulokinase mutant of Pichia stipitis, FPL-YS30 (xyl3-â

  • Lee JW, Zhu JY, Scordia D, Jeffries TW (2011) Evaluation of ethanol production from corncob using Scheffersomyces (Pichia) stipitis CBS 6054 by volumetric scale-up. Appl. Biochem. Biotechnol. 165(3-4):814-22 · Pubmed

    In scale-up, the potential of ethanol production by dilute sulfuric acid pretreatment using corncob was investigated. Pretreatments were performed at 170 °C with various acid concentrations ranging from 0% to 1.656% based on oven dry weight. Following pretreatment, pretreated biomass yield ranged from 59% to 67%. More than 90% of xylan was removed at 0.828% of sulfuric acid. At same pretreatment condition, the highest glucose yield obtained from pretreated biomass by enzymatic hydrolysis was about 76%, based on a glucan content of 37/100 g. In hydrolysate obtained by pretreatment, glucose concentration was low, while xylose concentration was significantly increased above 0.368% of sulfuric acid. At 1.656% of sulfuric acid, xylose and glucose concentration was highest. In subsequent, fermentation with hydrolysate, maximal ethanol yield was attained after 24 h with 0.368% of sulfuric acid. The fermentation efficiency of hydrolysate obtained by enzymatic hydrolysis reached a maximum of 75% at an acid charge of 0.368%.

  • Lee JW, Houtman CJ, Kim HY, Choi IG, Jeffries TW (2011) Scale-up study of oxalic acid pretreatment of agricultural lignocellulosic biomass for the production of bioethanol. Bioresour. Technol. 102(16):7451-6 · Pubmed

    Building on our laboratory-scale optimization, oxalic acid was used to pretreat corncobs on the pilot-scale. The hydrolysate obtained after washing the pretreated biomass contained 32.55g/l of xylose, 2.74g/l of glucose and low concentrations of inhibitors. Ethanol production, using Scheffersomyces stipitis, from this hydrolysate was 10.3g/l, which approached the predicted value of 11.9g/l. Diafiltration using a membrane system effectively reduced acetic acid in the hydrolysate, which increased the fermentation rate. The hemicellulose content of the recovered solids decreased from 27.86% before pretreatment to only 6.76% after pretreatment. Most of the cellulose remained in the pretreated biomass. The highest ethanol production after simultaneous saccharification and fermentation (SSF) of washed biomass with S. stipitis was 21.1g/l.

  • Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc. Natl. Acad. Sci. U.S.A. 108(32):13212-7 (PMC3156214) · Pubmed

    Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.

  • Lee JW, Jeffries TW (2011) Efficiencies of acid catalysts in the hydrolysis of lignocellulosic biomass over a range of combined severity factors. Bioresour. Technol. 102(10):5884-90 · Pubmed

    Dicarboxylic organic acids have properties that differ from those of sulfuric acid during hydrolysis of lignocellulose. To investigate the effects of different acid catalysts on the hydrolysis and degradation of biomass compounds over a range of thermochemical pretreatments, maleic, oxalic and sulfuric acids were each used at the same combined severity factor (CSF) values during hydrolysis. Xylose and glucose concentrations in hydrolysates were highest with maleic acid. Oxalic acid gave the next highest followed by sulfuric acid. This ranking was particularly true at low CSF values. The concentrations of glucose and xylose increased with oxalic and sulfuric acid pretreatments as the CSF increased, but they never attained the levels observed with maleic acid. Among sulfuric, oxalic and maleic acid treatments, the amount of xylose released as xylooligosaccharide was highest with sulfuric acid. The fraction of xylooligosaccharide was lowest with the maleic acid and the oligosaccharide fraction with oxalic acid fell in between. Furfural and hydroxymethyl furfural levels were also highest with maleic acid. In subsequent fermentations with pretreated biomass, the ethanol concentration was maximal at 19.2g/l at CSF 1.9 when maleic acid was used as the pretreatment catalyst. This corresponded to an ethanol volumetric production rate of 0.27 g ethanol/l per h. This was the same condition showing the highest xylose production in following pretreatment with various acid catalysts. These findings suggest that maleic and oxalic dicarboxylic acids degrade hemicelluloses more efficiently than does sulfuric acid.

  • Wang GS, Lee JW, Zhu JY, Jeffries TW (2011) Dilute Acid pretreatment of corncob for efficient sugar production. Appl. Biochem. Biotechnol. 163(5):658-68 · Pubmed

    Aqueous dilute acid pretreatments of corncob were conducted using cylindrical pressure vessels in an oil bath. Pretreatments were conducted in a temperature range of 160-190 °C with acid-solution-to-solid-corncob ratio of 2. The acid concentration (v/v) in the pretreatment solution was varied from 0% to 0.7%, depending on temperature. This gives acid charge on ovendry-weight corncob of 0-2.58%. It was found that optimal pretreatment temperature is between 160 and 170 °C based on total xylose and glucose yields and thermal energy consumption in pretreatment. At 170 °C and acid charge of 2.2% on cob, total glucose yield and xylose recovery were 97% and 75%, respectively, which resulted in an overall monomeric sugar recovery of about 88%. Xylose concentration in the hydrolysate was about 12%, with xylose-to-acetic-acid ratio of 8 and to furan (furfural and hydroxymethylfurfural) of about 15.

  • Kim HY, Lee JW, Jeffries TW, Choi IG (2011) Response surface optimization of oxalic acid pretreatment of yellow poplar (Liriodendron tulipifera) for production of glucose and xylose monosaccarides. Bioresour. Technol. 102(2):1440-6 · Pubmed

    The primary goal of this study was to determine the optimal condition to obtain fermentable monosaccharides (xylose and glucose) from hydrolysates of yellow poplar (Liriodendron tulipifera) by oxalic acid pretreatment as a potential bio-ethanol source. Based on 2(3) factorial design, fifteen operations were performed by varying on acid loading, reaction time and temperature, and the components of the solid and liquid fractions were analyzed. The sugar concentration (g/L) in hydrolysates and xylose solubilization (%) were applied to response surface methodology. The optimal condition for producing sugars was 151 °C, 0.042 g/g (weight of oxalic acid/dry matter), 13 min with predicted yield of 37.4 g/L, and for the xylose solubilization was 158 °C, 0.037 g/g, 13 min yielding 72.0% of the predicted value. Severe conditions generated inhibitors. By measuring the concentrations, the possibility utilizing hydrolysates for fermentation were estimated.

  • Jeffries TW (2010) A new generation. J. Ind. Microbiol. Biotechnol. 37(7):641-2 · Pubmed

    No abstract available.

  • Scordia D, Cosentino SL, Jeffries TW (2010) Second generation bioethanol production from Saccharum spontaneum L. ssp. aegyptiacum (Willd.) Hack. Bioresour. Technol. 101(14):5358-65 · Pubmed

    Saccharum (Saccharum spontaneum L. ssp. aegyptiacum (Willd.) Hack.), is a rapidly growing, wide ranging high-yield perennial, suitable for second generation bioethanol production. This study evaluated oxalic acid as a pretreatment for bioconversion. Overall sugar yields, sugar degradation products, enzymatic glucan hydrolysis and ethanol production were studied as effects of temperature (150-190 degrees C), reaction time (10-40 min) and oxalic acid concentration 2-8% (w/w). Time and temperature were combined into a single parameter, Severity Factor (SF) [Log(R(0))], and related to oxalic acid using a response surface methodology. Maximum total sugar yield was attained at a SF of 2.93 and 6.79% (w/w) oxalic acid, while maximum formation of sugar degradation products was observed at the highest SF (4.05) and 5% (w/w) oxalic acid. These were also the conditions for maximum simultaneous saccharification and fermentation (SSF) of the residual solids. Commercial cellulases and Saccharomyces cerevisiae attained 89.9% glucan conversion and 17.8 g/l ethanol. Pichia stipitis CBS 6054 fermented hemicellulosic hydrolysates from less severe conditions to ethanol with a yield of 0.35 (g(e)/g(s)). Maximal product yields were 69% of theoretical value and 90% of the SSF conversion efficiency for hydrolysate fermentation and SSF, respectively.

  • Lee JW, Rodrigues RC, Kim HJ, Choi IG, Jeffries TW (2010) The roles of xylan and lignin in oxalic acid pretreated corncob during separate enzymatic hydrolysis and ethanol fermentation. Bioresour. Technol. 101(12):4379-85 · Pubmed

    High yields of hemicellulosic and cellulosic sugars are critical in obtaining economical conversion of agricultural residues to ethanol. To optimize pretreatment conditions, we evaluated oxalic acid loading rates, treatment temperatures and times in a 2(3) full factorial design. Response-surface analysis revealed an optimal oxalic acid pretreatment condition to release sugar from the cob of Zea mays L. ssp. and for Pichia stipitis CBS 6054. To ferment the residual cellulosic sugars to ethanol following enzymatic hydrolysis, highest saccharification and fermentation yields were obtained following pretreatment at 180 degrees C for 50 min with 0.024 g oxalic acid/g substrate. Under these conditions, only 7.5% hemicellulose remained in the pretreated substrate. The rate of cellulose degradation was significantly less than that of hemicellulose and its hydrolysis was not as extensive. Subsequent enzymatic saccharification of the residual cellulose was strongly affected by the pretreatment condition with cellulose hydrolysis ranging between 26.0% and 76.2%. The residual xylan/lignin ratio ranged from 0.31 to 1.85 depending on the pretreatment condition. Fermentable sugar and ethanol were maximal at the lowest ratio of xylan/lignin and at high glucan contents. The model predicts optimal condition of oxalic acid pretreatment at 168 degrees C, 74 min and 0.027 g/g of oxalic acid. From these findings, we surmised that low residual xylan was critical in obtaining maximal glucose yields from saccharification.

  • Lee JW, Rodrigues RC, Jeffries TW (2009) Simultaneous saccharification and ethanol fermentation of oxalic acid pretreated corncob assessed with response surface methodology. Bioresour. Technol. 100(24):6307-11 · Pubmed

    Response surface methodology was used to evaluate optimal time, temperature and oxalic acid concentration for simultaneous saccharification and fermentation (SSF) of corncob particles by Pichia stipitis CBS 6054. Fifteen different conditions for pretreatment were examined in a 2(3) full factorial design with six axial points. Temperatures ranged from 132 to 180 degrees C, time from 10 to 90 min and oxalic acid loadings from 0.01 to 0.038 g/g solids. Separate maxima were found for enzymatic saccharification and hemicellulose fermentation, respectively, with the condition for maximum saccharification being significantly more severe. Ethanol production was affected by reaction temperature more than by oxalic acid and reaction time over the ranges examined. The effect of reaction temperature was significant at a 95% confidence level in its effect on ethanol production. Oxalic acid and reaction time were statistically significant at the 90% level. The highest ethanol concentration (20 g/l) was obtained after 48 h with an ethanol volumetric production rate of 0.42 g ethanol l(-1) h(-1). The ethanol yield after SSF with P. stipitis was significantly higher than predicted by sequential saccharification and fermentation of substrate pretreated under the same condition. This was attributed to the secretion of beta-glucosidase by P. stipitis. During SSF, free extracellular beta-glucosidase activity was 1.30 pNPG U/g with P. stipitis, while saccharification without the yeast was 0.66 pNPG U/g.

  • Jeffries TW, Van Vleet JR (2009) Pichia stipitis genomics, transcriptomics, and gene clusters. FEMS Yeast Res. 9(6):793-807 (PMC2784038) · Pubmed

    Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose-fermenting yeast Pichia stipitis. These studies have provided an insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the result of several gene products acting together. When coinheritance is necessary for the overall physiological function, recombination and selection favor colocation of these genes in a cluster. These are particularly evident in strongly conserved and idiomatic traits. In some cases, the functional clusters consist of multiple gene families. Phylogenetic analyses of the members in each family show that once formed, functional clusters undergo duplication and differentiation. Genome-wide expression analysis reveals that regulatory patterns of clusters are similar after they have duplicated and that the expression profiles evolve along with functional differentiation of the clusters. Orthologous gene families appear to arise through tandem gene duplication, followed by differentiation in the regulatory and coding regions of the gene. Genome-wide expression analysis combined with cross-species comparisons of functional gene clusters should reveal many more aspects of eukaryotic physiology.

  • Van Vleet JH, Jeffries TW (2009) Yeast metabolic engineering for hemicellulosic ethanol production. Curr. Opin. Biotechnol. 20(3):300-6 · Pubmed

    Efficient fermentation of hemicellulosic sugars is critical for the bioconversion of lignocellulosics to ethanol. Efficient sugar uptake through the heterologous expression of yeast and fungal xylose/glucose transporters can improve fermentation if other metabolic steps are not rate limiting. Rectification of cofactor imbalances through heterologous expression of fungal xylose isomerase or modification of cofactor requirements in the yeast oxidoreductase pathway can reduce xylitol production while increasing ethanol yields, but these changes often occur at the expense of xylose utilization rates. Genetic engineering and evolutionary adaptation to increase glycolytic flux coupled with transcriptomic and proteomic studies have identified targets for further modification, as have genomic and metabolic engineering studies in native xylose fermenting yeasts.

  • Van Vleet JH, Jeffries TW, Olsson L (2008) Deleting the para-nitrophenyl phosphatase (pNPPase), PHO13, in recombinant Saccharomyces cerevisiae improves growth and ethanol production on D-xylose. Metab. Eng. 10(6):360-9 · Pubmed

    Overexpression of D-xylulokinase in Saccharomyces cerevisiae engineered for assimilation of xylose results in growth inhibition that is more pronounced at higher xylose concentrations. Mutants deficient in the para-nitrophenyl phosphatase, PHO13, resist growth inhibition on xylose. We studied this inhibition under aerobic growth conditions in well-controlled bioreactors using engineered S. cerevisiae CEN.PK. Growth on glucose was not significantly affected in pho13Delta mutants, but acetate production increased by 75%. Cell growth, ethanol production, and xylose consumption all increased markedly in pho13Delta mutants. The specific growth rate and rate of specific xylose uptake were approximately 1.5 times higher in the deletion strain than in the parental strain when growing on glucose-xylose mixtures and up to 10-fold higher when growing on xylose alone. In addition to showing higher acetate levels, pho13Delta mutants also produced less glycerol on xylose, suggesting that deletion of Pho13p could improve growth by altering redox levels when cells are grown on xylose.

  • Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 18(10):1638-42 (PMC2556265) · Pubmed

    Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.

  • Jeffries TW, Yang VW, Davis MW (2008) Comparative study of xylanase kinetics using dinitrosalicylic, arsenomolybdate, and ion chromatographic assays. Appl. Biochem. Biotechnol. 70-72:257-65 · Pubmed

    Xylanases are commonly assayed by the dinitrosalicylic acid (DNS) or the arsenomolybdate (ARS) method. However, specific activities are many times higher with DNS than with ARS. This is because the DNS assay is more reactive and the ARS assay is less reactive with xylooligosaccharides than with xylose. Xylose is often used as a standard, even though oligosaccharides are prevalent, so the DNS method overestimates and the ARS method underestimates specific activity. Ion chromatography, with pulsed amperometric detection, separates and measures all products and intermediates, but quantitation on a molar basis is difficult, because few xylooligosaccharide response factors are known. This report directly compares these three assay methods for the assay of xylanase activities.

  • Sreenath HK, Jeffries TW (2008) Diminished respirative growth and enhanced assimilative sugar uptake result in higher specific fermentation rates by the mutant Pichia stipitis FPL-061. Appl. Biochem. Biotechnol. 63-65:109-16 · Pubmed

    A mutant strain of Pichia stipitis, FPL-061, was obtained by selecting for growth on L-xylose in the presence of respiratory inhibitors. The specific fermentation rate of FPL-061, was higher than that of the parent,Pichia stipitis CBS 6054, because of its lower cell yield and growth rate and higher specific substrate uptake rate. With a mixture of glucose and xylose, the mutant strain FPL-061 produced 29.4 g ethanol/L with a yield of 0.42 g ethanol/g sugar consumed. By comparison, CBS 6054 produced 25.7 g ethanol/L with a yield of 0.35 gJg. The fermentation was most efficient at an aeration rate of 9.2 mmoles O2 L-1 h-1. At high aeration rates (22 mmoles O2 L-1 h-1), the mutant cell yield was less than that of the parent. At low aeration rates, (1.1 to 2.5 O2 L-1 h-1), cell yields were similar, the ethanol formation rates were low, and xylitol accumulation was observed in both the strains. Both strains respired the ethanol once sugar was exhausted. We infer from the results that the mutant, P. stipitis FPL-061, diverts a larger fraction of its metabolic energy from cell growth into ethanol production.

  • Bae JY, Laplaza J, Jeffries TW (2008) Effects of gene orientation and use of multiple promoters on the expression of XYL1 and XYL2 in Saccharomyces cerevisiae. Appl. Biochem. Biotechnol. 145(1-3):69-78 · Pubmed

    Orientation of adjacent genes has been reported to affect their expression in eukaryotic systems, and metabolic engineering also often makes repeated use of a few promoters to obtain high expression. To improve transcriptional control in heterologous expression, we examined how these factors affect gene expression and enzymatic activity in Saccharomyces cerevisiae. We assembled D-xylose reductase (XYL1) and D-xylitol dehydrogenase (XYL2) in four ways. Each pair of genes was placed in two different tandem (1-->2--> or <--1<--2), convergent (1--><--2), and divergent (<--1 2-->) orientations in autonomous plasmids. The TEF1 promoter was used to drive XYL1 and the TDH3 promoter to drive XYL2 in each of the constructs. The effects of gene orientation on growth, transcription, and enzyme activity were analyzed. The transcription level as measured by quantitative PCR (q-PCR) correlated with enzyme activities, but our data did not show a significant effect of gene orientation. To test the possible dilution of promoter strength due to multiple use of the same promoter, we examined the level of expression of XYL1 driven by either the TEF1 or TDH3 promoter when carried on a single copy plasmid. We then co-expressed XYL2 from either a single or multicopy plasmid, which was also driven by the same promoter. XYL2 transcript and enzyme expression increased with plasmid copy number, while the expression of XYL1 was constant regardless of the number of other TEF1 or TDH3 promoters present in the cell. According to our data, there is no significant effect of gene orientation or multiple promoter use on gene transcription and translation when genes are expressed from plasmids; however, other factors could affect expression of adjacent genes in chromosomes.

  • Rodrigues RC, Lu C, Lin B, Jeffries TW (2008) Fermentation kinetics for xylitol production by a Pichia stipitis D: -xylulokinase mutant previously grown in spent sulfite liquor. Appl. Biochem. Biotechnol. 148(1-3):199-209 · Pubmed

    Spent sulfite pulping liquor (SSL) contains lignin, which is present as lignosulfonate, and hemicelluloses that are present as hydrolyzed carbohydrates. To reduce the biological oxygen demand of SSL associated with dissolved sugars, we studied the capacity of Pichia stipitis FPL-YS30 (xyl3Delta) to convert these sugars into useful products. FPL-YS30 produces a negligible amount of ethanol while converting xylose into xylitol. This work describes the xylose fermentation kinetics of yeast strain P.stipitis FPL-YS30. Yeast was grown in rich medium supplemented with different carbon sources: glucose, xylose, or ammonia-base SSL. The SSL and glucose-acclimatized cells showed similar maximum specific growth rates (0.146 h(-1)). The highest xylose consumption at the beginning of the fermentation process occurred using cells precultivated in xylose, which showed relatively high specific activity of glucose-6-phosphate dehydrogenase (EC However, the maximum specific rates of xylose consumption (0.19 g(xylose)/g(cel) h) and xylitol production (0.059 g(xylitol)/g(cel) h) were obtained with cells acclimatized in glucose, in which the ratio between xylose reductase (EC and xylitol dehydrogenase (EC was kept at higher level (0.82). In this case, xylitol production (31.6 g/l) was 19 and 8% higher than in SSL and xylose-acclimatized cells, respectively. Maximum glycerol (6.26 g/l) and arabitol (0.206 g/l) production were obtained using SSL and xylose-acclimatized cells, respectively. The medium composition used for the yeast precultivation directly reflected their xylose fermentation performance. The SSL could be used as a carbon source for cell production. However, the inoculum condition to obtain a high cell concentration in SSL needs to be optimized.

  • Agbogbo FK, Coward-Kelly G, Torry-Smith M, Wenger K, Jeffries TW (2007) The effect of initial cell concentration on xylose fermentation by Pichia stipitis. Appl. Biochem. Biotechnol. 137-140(1-12):653-62 · Pubmed

    Xylose was fermented using Pichia stipitis CBS 6054 at different initial cell concentrations. A high initial cell concentration increased the rate of xylose utilization, ethanol formation, and the ethanol yield. The highest ethanol concentration of 41.0 g/L and a yield of 0.38 g/g was obtained using an initial cell concentration of 6.5 g/L. Even though more xylitol was produced when the initial cell concentrations were high, cell density had no effect on the final ethanol yield. A two-parameter mathematical model was used to predict the cell population dynamics at the different initial cell concentrations. The model parameters, a and b correlate with the initial cell concentrations used with an R(2) of 0.99.

  • Ni H, Laplaza JM, Jeffries TW (2007) Transposon mutagenesis to improve the growth of recombinant Saccharomyces cerevisiae on D-xylose. Appl. Environ. Microbiol. 73(7):2061-6 (PMC1855673) · Pubmed

    Saccharomyces cerevisiae L2612 transformed with genes for xylose reductase and xylitol dehydrogenase (XYL1 and XYL2) grows well on glucose but very poorly on d-xylose. When a gene for d-xylulokinase (XYL3 or XKS1) is overexpressed, growth on glucose is unaffected, but growth on xylose is blocked. Spontaneous or chemically induced mutants of this engineered yeast that would grow on xylose could, however, be obtained. We therefore used insertional transposon mutagenesis to identify two loci that can relieve this xylose-specific growth inhibition. One is within the open reading frame (ORF) of PHO13, and the other is approximately 500 bp upstream from the TAL1 ORF. Deletion of PHO13 or overexpression of TAL1 resulted in a phenotype similar to the insertional mutation events. Quantitative PCR showed that deletion of PHO13 increased transcripts for TAL1, indicating that the growth inhibition imposed by the overexpression of XYL3 on xylose can be relieved by an overexpression of transcripts for downstream enzymes. These results may be useful in constructing better xylose-fermenting S. cerevisiae strains.

  • Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat. Biotechnol. 25(3):319-26 · Pubmed

    Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions.

  • Jeffries TW (2006) Engineering yeasts for xylose metabolism. Curr. Opin. Biotechnol. 17(3):320-6 · Pubmed

    Technologies for the production of alternative fuels are receiving increased attention owing to concerns over the rising cost of petrol and global warming. One such technology under development is the use of yeasts for the commercial fermentation of xylose to ethanol. Several approaches have been employed to engineer xylose metabolism. These involve modeling, flux analysis, and expression analysis followed by the targeted deletion or altered expression of key genes. Expression analysis is increasingly being used to target rate-limiting steps. Quantitative metabolic models have also proved extremely useful: they can be calculated from stoichiometric balances or inferred from the labeling of intermediate metabolites. The recent determination of the genome sequence for P. stipitis is important, as its genome characteristics and regulatory patterns could serve as guides for further development in this natural xylose-fermenting yeast or in engineered Saccharomyces cerevisiae. Lastly, strain selection through mutagenesis, adaptive evolution or from nature can also be employed to further improve activity.

  • Jin YS, Cruz J, Jeffries TW (2005) Xylitol production by a Pichia stipitis D-xylulokinase mutant. Appl. Microbiol. Biotechnol. 68(1):42-5 · Pubmed

    Xylitol production by Pichia stipitis FPL-YS30, a xyl3-delta1 mutant that metabolizes xylose using an alternative metabolic pathway, was investigated under aerobic and oxygen-limited culture conditions. Under both culture conditions, FPL-YS30 (xyl3-delta1) produced a negligible amount of ethanol and converted xylose mainly into xylitol with comparable yields (0.30 and 0.27 g xylitol/g xylose). However, xylose consumption increased five-fold under aerobic compared to oxygen-limited conditions. This suggests that the efficiency of the alternative route of xylose assimilation is affected by respiration. As a result, the FPL-YS30 strain produced 26 g/l of xylitol, and exhibited a higher volumetric productivity (0.22 g xylitol l(-1) h(-1)) under aerobic conditions.

  • Jeffries TW (2005) Ethanol fermentation on the move. Nat. Biotechnol. 23(1):40-1 · Pubmed

    No abstract available.

  • Jin YS, Laplaza JM, Jeffries TW (2004) Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response. Appl. Environ. Microbiol. 70(11):6816-25 (PMC525251) · Pubmed

    Native strains of Saccharomyces cerevisiae do not assimilate xylose. S. cerevisiae engineered for d-xylose utilization through the heterologous expression of genes for aldose reductase (XYL1), xylitol dehydrogenase (XYL2), and d-xylulokinase (XYL3 or XKS1) produce only limited amounts of ethanol in xylose medium. In recombinant S. cerevisiae expressing XYL1, XYL2, and XYL3, mRNA transcript levels for glycolytic, fermentative, and pentose phosphate enzymes did not change significantly on glucose or xylose under aeration or oxygen limitation. However, expression of genes encoding the tricarboxylic acid cycle, respiration enzymes (HXK1, ADH2, COX13, NDI1, and NDE1), and regulatory proteins (HAP4 and MTH1) increased significantly when cells were cultivated on xylose, and the genes for respiration were even more elevated under oxygen limitation. These results suggest that recombinant S. cerevisiae does not recognize xylose as a fermentable carbon source and that respiratory proteins are induced in response to cytosolic redox imbalance; however, lower sugar uptake and growth rates on xylose might also induce transcripts for respiration. A petite respiration-deficient mutant (rho degrees ) of the engineered strain produced more ethanol and accumulated less xylitol from xylose. It formed characteristic colonies on glucose, but it did not grow on xylose. These results are consistent with the higher respiratory activity of recombinant S. cerevisiae when growing on xylose and with its inability to grow on xylose under anaerobic conditions.

  • Jin YS, Jeffries TW (2004) Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae. Metab. Eng. 6(3):229-38 · Pubmed

    Metabolic pathway engineering is constrained by the thermodynamic and stoichiometric feasibility of enzymatic activities of introduced genes. Engineering of xylose metabolism in Saccharomyces cerevisiae has focused on introducing genes for the initial xylose assimilation steps from Pichia stipitis, a xylose-fermenting yeast, into S. cerevisiae, a yeast traditionally used in ethanol production from hexose. However, recombinant S. cerevisiae created in several laboratories have used xylose oxidatively rather than in the fermentative manner that this yeast metabolizes glucose. To understand the differences between glucose and engineered xylose metabolic networks, we performed a flux balance analysis (FBA) and calculated extreme pathways using a stoichiometric model that describes the biochemistry of yeast cell growth. FBA predicted that the ethanol yield from xylose exhibits a maximum under oxygen-limited conditions, and a fermentation experiment confirmed this finding. Fermentation results were largely consistent with in silico phenotypes based on calculated extreme pathways, which displayed several phases of metabolic phenotype with respect to oxygen availability from anaerobic to aerobic conditions. However, in contrast to the model prediction, xylitol production continued even after the optimum aeration level for ethanol production was attained. These results suggest that oxygen (or some other electron accepting system) is required to resolve the redox imbalance caused by cofactor difference between xylose reductase and xylitol dehydrogenase, and that other factors limit glycolytic flux when xylose is the sole carbon source.

  • Jeffries TW, Lynd LR (2004) Introduction to microbial catalysis and engineering. Appl. Biochem. Biotechnol. 113-116:323-4 · Pubmed

    No abstract available.

  • Jeffries TW, Jin YS (2004) Metabolic engineering for improved fermentation of pentoses by yeasts. Appl. Microbiol. Biotechnol. 63(5):495-509 · Pubmed

    The fermentation of xylose is essential for the bioconversion of lignocellulose to fuels and chemicals, but wild-type strains of Saccharomyces cerevisiae do not metabolize xylose, so researchers have engineered xylose metabolism in this yeast. Glucose transporters mediate xylose uptake, but no transporter specific for xylose has yet been identified. Over-expressing genes for aldose (xylose) reductase, xylitol dehydrogenase and moderate levels of xylulokinase enable xylose assimilation and fermentation, but a balanced supply of NAD(P) and NAD(P)H must be maintained to avoid xylitol production. Reducing production of NADPH by blocking the oxidative pentose phosphate cycle can reduce xylitol formation, but this occurs at the expense of xylose assimilation. Respiration is critical for growth on xylose by both native xylose-fermenting yeasts and recombinant S, cerevisiae. Anaerobic growth by recombinant mutants has been reported. Reducing the respiration capacity of xylose-metabolizing yeasts increases ethanol production. Recently, two routes for arabinose metabolism have been engineered in S. cerevisiae and adapted strains of Pichia stipitis have been shown to ferment hydrolysates with ethanol yields of 0.45 g g(-1) sugar consumed, so commercialization seems feasible for some applications.

  • Dien BS, Cotta MA, Jeffries TW (2003) Bacteria engineered for fuel ethanol production: current status. Appl. Microbiol. Biotechnol. 63(3):258-66 · Pubmed

    The lack of industrially suitable microorganisms for converting biomass into fuel ethanol has traditionally been cited as a major technical roadblock to developing a bioethanol industry. In the last two decades, numerous microorganisms have been engineered to selectively produce ethanol. Lignocellulosic biomass contains complex carbohydrates that necessitate utilizing microorganisms capable of fermenting sugars not fermentable by brewers' yeast. The most significant of these is xylose. The greatest successes have been in the engineering of Gram-negative bacteria: Escherichia coli, Klebsiella oxytoca, and Zymomonas mobilis. E. coli and K. oxytoca are naturally able to use a wide spectrum of sugars, and work has concentrated on engineering these strains to selectively produce ethanol. Z. mobilis produces ethanol at high yields, but ferments only glucose and fructose. Work on this organism has concentrated on introducing pathways for the fermentation of arabinose and xylose. The history of constructing these strains and current progress in refining them are detailed in this review.

  • Kenealy WR, Jeffries TW (2003) Rapid 2,2'-bicinchoninic-based xylanase assay compatible with high throughput screening. Biotechnol. Lett. 25(19):1619-23 · Pubmed

    High-throughput screening requires simple assays that give reliable quantitative results. A microplate assay was developed for reducing sugar analysis that uses a 2,2'-bicinchoninic-based protein reagent. Endo-1,4-beta-D-xylanase activity against oat spelt xylan was detected at activities of 0.002 to 0.011 IU ml(-1). The assay is linear for sugar concentrations from 0 to 86 microg ml(-1) and can also be used to assay protein concentrations (0 to 143 microg ml(-1)) on the same plate. A variety of temperatures and pH conditions can be used and, after incubation, the assay requires only one detection reagent and one heating step.

  • Jeffries TW, Jin YS (2003) Ethanol and thermotolerance in the bioconversion of xylose by yeasts. Adv. Appl. Microbiol. 47:221-68 · Pubmed

    The mechanisms underlying ethanol and heat tolerance are complex. Many different genes are involved, and the exact basis is not fully understood. The integrity of cytoplasmic and mitochondrial membranes is critical to maintain proton gradients for metabolic energy and nutrient uptake. Heat and ethanol stress adversely affect membrane integrity. These factors are particularly detrimental to xylose-fermenting yeasts because they require oxygen for biosynthesis of essential cell membrane and nucleic acid constituents, and they depend on respiration for the generation of ATP. Physiological responses to ethanol and heat shock have been studied most extensively in S. cerevisiae. However, comparative biochemical studies with other organisms suggest that similar mechanisms will be important in xylose-fermenting yeasts. The composition of a cell's membrane lipids shifts with temperature, ethanol concentration, and stage of cultivation. Levels of unsaturated fatty acids and ergosterol increase in response to temperature and ethanol stress. Inositol is involved in phospholipid biosynthesis, and it can increase ethanol tolerance when provided as a supplement. Membrane integrity determines the cell's ability to maintain proton gradients for nutrient uptake. Plasma membrane ATPase generates the proton gradient, and the biochemical characteristics of this enzyme contribute to ethanol tolerance. Organisms with higher ethanol tolerance have ATPase activities with low pH optima and high affinity for ATP. Likewise, organisms with ATPase activities that resist ethanol inhibition also function better at high ethanol concentrations. ATPase consumes a significant fraction of the total cellular ATP, and under stress conditions when membrane gradients are compromised the activity of ATPase is regulated. In xylose-fermenting yeasts, the carbon source used for growth affects both ATPase activity and ethanol tolerance. Cells can adapt to heat and ethanol stress by synthesizing trehalose and heat-shock proteins, which stabilize and repair denatured proteins. The capacity of cells to produce trehalose and induce HSPs correlate with their thermotolerance. Both heat and ethanol increase the frequency of petite mutations and kill cells. This might be attributable to membrane effects, but it could also arise from oxidative damage. Cytoplasmic and mitochondrial superoxide dismutases can destroy oxidative radicals and thereby maintain cell viability. Improved knowledge of the mechanisms underlying ethanol and thermotolerance in S. cerevisiae should enable the genetic engineering of these traits in xylose-fermenting yeasts.

  • Jin YS, Jeffries TW (2003) Changing flux of xylose metabolites by altering expression of xylose reductase and xylitol dehydrogenase in recombinant Saccharomyces cerevisiae. Appl. Biochem. Biotechnol. 105 -108:277-86 · Pubmed

    We changed the fluxes of xylose metabolites in recombinant Saccharomyces cerevisiae by manipulating expression of Pichia stipitis genes (XYL1 and XYL2) coding for xylose reductase (XR) and xylitol dehydrogenase (XDH), respectively. XYL1 copy number was kept constant by integrating it into the chromosome. Copy numbers of XYL2 were varied either by integrating XYL2 into the chromosome or by transforming cells with XYL2 in a multicopy vector. Genes in all three constructs were under control of the strong constitutive glyceraldehyde-3-phosphate dehydrogenase promoter. Enzymatic activity of XR and XDH in the recombinant strains increased with the copy number of XYL1 and XYL2. XR activity was not detected in the parent but was present at a nearly constant level in all of the transformants. XDH activity increased 12-fold when XYL2 was on a multicopy vector compared with when it was present in an integrated single copy. Product formation during xylose fermentation was affected by XDH activity and by aeration in recombinant S. cerevisiae. Higher XDH activity and more aeration resulted in less xylitol and more xylulose accumulation during xylose fermentation. Secretion of xylulose by strains with multicopy XYL2 and elevated XDH supports the hypothesis that D-xylulokinase limits metabolic flux in recombinant S. cerevisiae.

  • Kang MH, Ni H, Jeffries TW (2003) Molecular characterization of a gene for aldose reductase ( CbXYL1) from Candida boidinii and its expression in Saccharomyces cerevisiae. Appl. Biochem. Biotechnol. 105 -108:265-76 · Pubmed

    Candida boidinii produces significant amounts of xylitol from xylose, and assays of crude homogenates for aldose (xylose) reductase (XYL1p) have been reported to show relatively high activity with NADH as a cofactor even though XYL1p purified from this yeast does not have such activity. A gene coding for XYL1p from C. boidinii (CbXYL1) was isolated by amplifying the central region using primers to conserved domains and by genome walking. CbXYL1 has an open reading frame of 966 bp encoding 321 amino acids. The C. boidinii XYL1p is highly similar to other known yeast aldose reductases and is most closely related to the NAD(P)H-linked XYL1p of Kluyveromyces lactis. Cell homogenates from C. boidinii and recombinant Saccharomyces cerevisiae were tested for XYL1p activity to confirm the previously reported high ratio of NADH:NADPH linked activity. C. boidinii grown under fully aerobic conditions showed an NADH:NADPH activity ratio of 0.76, which was similar to that observed with the XYL1p from Pichia stipitis XYL1, but which is much lower than what was previously reported. Cells grown under low aeration showed an NADH:NADPH activity ratio of 2.13. Recombinant S. cerevisiae expressing CbXYL1 showed only NADH-linked activity in cell homogenates. Southern hybridization did not reveal additional bands. These results imply that a second, unrelated gene for XYL1p is present in C. boidinii.

  • Jin YS, Ni H, Laplaza JM, Jeffries TW (2003) Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate D-xylulokinase activity. Appl. Environ. Microbiol. 69(1):495-503 (PMC152454) · Pubmed

    D-Xylulokinase (XK) is essential for the metabolism of D-xylose in yeasts. However, overexpression of genes for XK, such as the Pichia stipitis XYL3 gene and the Saccharomyces cerevisiae XKS gene, can inhibit growth of S. cerevisiae on xylose. We varied the copy number and promoter strength of XYL3 or XKS1 to see how XK activity can affect xylose metabolism in S. cerevisiae. The S. cerevisiae genetic background included single integrated copies of P. stipitis XYL1 and XYL2 driven by the S. cerevisiae TDH1 promoter. Multicopy and single-copy constructs with either XYL3 or XKS1, likewise under control of the TDH1 promoter, or with the native P. stipitis promoter were introduced into the recombinant S. cerevisiae. In vitro enzymatic activity of XK increased with copy number and promoter strength. Overexpression of XYL3 and XKS1 inhibited growth on xylose but did not affect growth on glucose even though XK activities were three times higher in glucose-grown cells. Growth inhibition increased and ethanol yields from xylose decreased with increasing XK activity. Uncontrolled XK expression in recombinant S. cerevisiae is inhibitory in a manner analogous to the substrate-accelerated cell death observed with an S. cerevisiae tps1 mutant during glucose metabolism. To bypass this effect, we transformed cells with a tunable expression vector containing XYL3 under the control of its native promoter into the FPL-YS1020 strain and screened the transformants for growth on, and ethanol production from, xylose. The selected transformant had approximately four copies of XYL3 per haploid genome and had moderate XK activity. It converted xylose into ethanol efficiently.

  • Shi NQ, Cruz J, Sherman F, Jeffries TW (2002) SHAM-sensitive alternative respiration in the xylose-metabolizing yeast Pichia stipitis. Yeast 19(14):1203-20 · Pubmed

    SHAM-sensitive (STO) alternative respiration is present in the xylose-metabolizing, Crabtree-negative yeast, Pichia stipitis, but its pathway components and physiological roles during xylose metabolism are poorly understood. We cloned PsSTO1, which encodes the SHAM-sensitive terminal oxidase (PsSto1p), by genome walking from wild-type CBS 6054 and subsequently deleted PsSTO1 by targeted gene disruption. The resulting sto1-delta deletion mutant, FPL-Shi31, did not contain other isoforms of Sto protein that were detectable by Western blot analysis using an alternative oxidase monoclonal antibody raised against the Sto protein from Sauromatum guttatum. Levels of cytochromes b, c, c(1) and a.a(3) did not change in the sto1-delta mutant, which indicated that deleting PsSto1p did not alter the cytochrome pool. Interestingly, the sto1-delta deletion mutant stopped growing earlier than the parent and produced 20% more ethanol from xylose. Heterologous expression of PsSTO1 in Saccharomyces cerevisiae increased its total oxygen consumption rate and imparted cyanide-resistant oxygen uptake but did not enable growth on ethanol, indicating that PsSto1p is not coupled to ATP synthesis. We present evidence that the mitochondrial NADH dehydrogenase complex (Complex I) was present in wild-type CBS 6054 but was bypassed in the cells during xylose metabolism. Unexpectedly, deleting PsSto1p led to the use of Complex I in the mutant cells when xylose was the carbon source. We propose that the non-proton-translocating NAD(P)H dehydrogenases are linked to PsSto1p in xylose-metabolizing cells and that this non-ATP-generating route serves a regulatory function in the complex redox network of P. stipitis.

  • Jin YS, Jones S, Shi NQ, Jeffries TW (2002) Molecular cloning of XYL3 (D-xylulokinase) from Pichia stipitis and characterization of its physiological function. Appl. Environ. Microbiol. 68(3):1232-9 (PMC123745) · Pubmed

    XYL3, which encodes a D-xylulokinase (EC, was isolated from Pichia stipitis CBS 6054 genomic DNA by using primers designed against conserved motifs. Disruption of XYL3 eliminated D-xylulokinase activity, but D-ribulokinase activity was still present. Southern analysis of P. stipitis genomic DNA with XYL3 as a probe confirmed the disruption and did not reveal additional related genes. Disruption of XYL3 stopped ethanol production from xylose, but the resulting mutant still assimilated xylose slowly and formed xylitol and arabinitol. These results indicate that XYL3 is critical for ethanol production from xylose but that P. stipitis has another pathway for xylose assimilation. Expression of XYL3 using its P. stipitis promoter increased Saccharomyces cerevisiae D-xylulose consumption threefold and enabled the transformants to produce ethanol from a mixture of xylose and xylulose, whereas the parental strain only accumulated xylitol. In vitro, D-xylulokinase activity in recombinant S. cerevisiae was sixfold higher with a multicopy than with a single-copy XYL3 plasmid, but ethanol production decreased with increased copy number. These results confirmed the function of XYL3 in S. cerevisiae.

  • Baerends RJ, Sulter GJ, Jeffries TW, Cregg JM, Veenhuis M (2002) Molecular characterization of the Hansenula polymorpha FLD1 gene encoding formaldehyde dehydrogenase. Yeast 19(1):37-42 · Pubmed

    Glutathione-dependent formaldehyde dehydrogenase (FLD) is a key enzyme required forthe catabolism of methanol as a carbon source and certain primary amines, such as methylamine as nitrogen sources in methylotrophic yeasts. Here we describe the molecular characterization of the FLD1 gene from the yeast Hansenula polymorpha. Unlike the recently described Pichia pastoris homologue, the H. polymorpha gene does not contain an intron. The predicted FLD1 product (Fld1p) is a protein of 380 amino acids (ca. 41 kDa) with 82% identity to P. pastoris Fld1p, 76% identity to the FLD protein sequence from n-alkane-assimilating yeast Candida maltosa and 63-64% identity to dehydrogenase class III enzymes from humans and other higher eukaryotes. The expression of FLD1 is strictly regulated and can be controlled at two expression levels by manipulation of the growth conditions. The gene is strongly induced under methylotrophic growth conditions; moderate expression is obtained under conditions in which a primary amine, e.g. methylamine, is used as nitrogen source. These properties render the FLD1 promoter of high interest for heterologous gene expression. The availability of the H. polymorpha FLD1 promoter provides an attractive alternative for expression of foreign genes besides the commonly used alcohol oxidase promoter.

  • Jeffries TW, Shi NQ (1999) Genetic engineering for improved xylose fermentation by yeasts. Adv. Biochem. Eng. Biotechnol. 65:117-61 · Pubmed

    Xylose utilization is essential for the efficient conversion of lignocellulosic materials to fuels and chemicals. A few yeasts are known to ferment xylose directly to ethanol. However, the rates and yields need to be improved for commercialization. Xylose utilization is repressed by glucose which is usually present in lignocellulosic hydrolysates, so glucose regulation should be altered in order to maximize xylose conversion. Xylose utilization also requires low amounts of oxygen for optimal production. Respiration can reduce ethanol yields, so the role of oxygen must be better understood and respiration must be reduced in order to improve ethanol production. This paper reviews the central pathways for glucose and xylose metabolism, the principal respiratory pathways, the factors determining partitioning of pyruvate between respiration and fermentation, the known genetic mechanisms for glucose and oxygen regulation, and progress to date in improving xylose fermentations by yeasts.

  • Shi NQ, Davis B, Sherman F, Cruz J, Jeffries TW (1999) Disruption of the cytochrome c gene in xylose-utilizing yeast Pichia stipitis leads to higher ethanol production. Yeast 15(11):1021-30 · Pubmed

    The xylose-utilizing yeast, Pichia stipitis, has a complex respiratory system that contains cytochrome and non-cytochrome alternative electron transport chains in its mitochondria. To gain primary insights into the alternative respiratory pathway, a cytochrome c gene (PsCYC1, Accession No. AF030426) was cloned from wild-type P. stipitis CBS 6054 by cross-hybridization to CYC1 from Saccharomyces cerevisiae. The 333 bp open reading frame of PsCYC1 showed 74% and 69% identity to ScCYC1 and ScCYC7, respectively, at the DNA level. Disruption of PsCYC1 resulted in a mutant that uses the salicylhydroxamic acid (SHAM)-sensitive respiratory pathway for aerobic energy production. Cytochrome spectra revealed that cytochromes c and a.a(3) both disappeared in the cyc1-Delta mutant, so no electron flow through the cytochrome c oxidase was possible. The cyc1-Delta mutant showed 50% lower growth rates than the parent when grown on fermentable sugars. The cyc1-Delta mutant was also found to be unable to grow on glycerol. Interestingly, the mutant produced 0.46 g/g ethanol from 8% xylose, which was 21% higher in yield than the parental strain (0.38 g/g). These results suggested that the alternative pathway might play an important role in supporting xylose conversion to ethanol under oxygen-limiting conditions.

  • Jeffries TW, Schartman R (1999) Bioconversion of secondary fiber fines to ethanol using counter-current enzymatic saccharification and co-fermentation. Appl. Biochem. Biotechnol. 77-79:435-44 · Pubmed

    This research examined several enzymatic and microbial process for the conversion of waste cellulosic fibers into ethanol. The first was a one-stage process in which pulp fines were contacted with commercial enzyme solutions. The second process used sequential, multistage saccharification. The third used sequential enzyme addition in a countercurrent mode. Experiments compared the results with various feedstocks, different commercial enzymes, supplementation with beta-glucosidase, and saccharification combined with fermentation. The highest saccharification (65%) from a 4% consistency pulp and the highest sugar concentration (5.4%) from an 8% consistency pulp were attained when 5 FPU/g plus 10 IU/g of beta-glucosidase were used. Sequential addition of enzyme to the pulp in small aliquots produced a higher overall sugar yield/U enzyme than the addition of the same total amount of enzyme in a single dose. In the saccharification and fermentation experiments, we produced 2.12% ethanol from a 5.4% sugar solution. This represents 78% of the theoretical maximum. This yield could probably be increased through optimization of the fermentation step. Even when little saccharification occurred, the enzyme facilitated separation of water, fiber, and ash, so cellulase treatment could be an effective means for dewatering pulp sludges.

  • Cho JY, Jeffries TW (1999) Transcriptional control of ADH genes in the xylose-fermenting yeast Pichia stipitis. Appl. Environ. Microbiol. 65(6):2363-8 (PMC91349) · Pubmed

    We studied the expression of the genes encoding group I alcohol dehydrogenases (PsADH1 and PsADH2) in the xylose-fermenting yeast Pichia stipitis CBS 6054. The cells expressed PsADH1 approximately 10 times higher under oxygen-limited conditions than under fully aerobic conditions when cultivated on xylose. Transcripts of PsADH2 were not detectable under either aeration condition. We used a PsADH1::lacZ fusion to monitor PsADH1 expression and found that expression increased as oxygen decreased. The level of PsADH1 transcript was repressed about 10-fold in cells grown in the presence of heme under oxygen-limited conditions. Concomitantly with the induction of PsADH1, PsCYC1 expression was repressed. These results indicate that oxygen availability regulates PsADH1 expression and that regulation may be mediated by heme. The regulation of PsADH2 expression was also examined in other genetic backgrounds. Disruption of PsADH1 dramatically increased PsADH2 expression on nonfermentable carbon sources under fully aerobic conditions, indicating that the expression of PsADH2 is subject to feedback regulation under these conditions.

  • Shi NQ, Jeffries TW (1998) Anaerobic growth and improved fermentation of Pichia stipitis bearing a URA1 gene from Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 50(3):339-45 · Pubmed

    Respiratory and fermentative pathways coexist to support growth and product formation in Pichia stipitis. This yeast grows rapidly without ethanol production under fully aerobic conditions, and it ferments glucose or xylose under oxygen-limited conditions, but it stops growing within one generation under anaerobic conditions. Expression of Saccharomyces cerevisiae URA1 (ScURA1) in P. stipitis enabled rapid anaerobic growth in minimal defined medium containing glucose when essential lipids were present. ScURA1 encodes a dihydroorotate dehydrogenase that uses fumarate as an alternative electron acceptor to confer anaerobic growth. Initial P. stipitis transformants grew and produced 32 g/l ethanol from 78 g/l glucose. Cells produced even more ethanol faster following two anaerobic serial subcultures. Control strains without ScURA1 were incapable of growing anaerobically and showed only limited fermentation. P. stipitis cells bearing ScURA1 were viable in anaerobic xylose medium for long periods, and supplemental glucose allowed cell growth, but xylose alone could not support anaerobic growth even after serial anaerobic subculture on glucose. These data imply that P. stipitis can grow anaerobically using metabolic energy generated through fermentation but that it exhibits fundamental differences in cofactor selection and electron transport with glucose and xylose metabolism. This is the first report of genetic engineering to enable anaerobic growth of a eukaryote.

  • Shen S, Sulter G, Jeffries TW, Cregg JM (1998) A strong nitrogen source-regulated promoter for controlled expression of foreign genes in the yeast Pichia pastoris. Gene 216(1):93-102 · Pubmed

    In methylotrophic yeasts, glutathione-dependent formaldehyde dehydrogenase (FLD) is a key enzyme required for the metabolism of methanol as a carbon source and certain alkylated amines such as methylamine as nitrogen sources. We describe the isolation and characterization of the FLD1 gene from the yeast Pichia pastoris. The gene contains a single short intron with typical yeast-splicing signals near its 5' end, the first intron to be demonstrated in this yeast. The predicted FLD1 product (Fld1p) is a protein of 379 amino acids (approx. 40 kDa) with 71% identity to the FLD protein sequence from the n-alkane-assimilating yeast Candida maltosa and 61-65% identity with dehydrogenase class III enzymes from humans and other higher eukaryotes. Using beta-lactamase as a reporter, we show that the FLD1 promoter (PFLD1) is strongly and independently induced by either methanol as sole carbon source (with ammonium sulfate as nitrogen source) or methylamine as sole nitrogen source (with glucose as carbon source). Furthermore, with either methanol or methylamine induction, levels of beta-lactamase produced under control of PFLD1 are comparable to those obtained with the commonly used alcohol oxidase I gene promoter (PAOX1). Thus, PFLD1 is an attractive alternative to PAOX1 for expression of foreign genes in P. pastoris, allowing the investigator a choice of carbon (methanol) or nitrogen source (methylamine) regulation with the same expression strain.

  • Cho JY, Jeffries TW (1998) Pichia stipitis genes for alcohol dehydrogenase with fermentative and respiratory functions. Appl. Environ. Microbiol. 64(4):1350-8 (PMC106154) · Pubmed

    Two genes coding for isozymes of alcohol dehydrogenase (ADH); designated PsADH1 and PsADH2, have been identified and isolated from Pichia stipitis CBS 6054 genomic DNA by Southern hybridization to Saccharomyces cerevisiae ADH genes, and their physiological roles have been characterized through disruption. The amino acid sequences of the PsADH1 and PsADH2 isozymes are 80.5% identical to one another and are 71.9 and 74.7% identical to the S. cerevisiae ADH1 protein. They also show a high level identity with the group I ADH proteins from Kluyveromyces lactis. The PsADH isozymes are presumably localized in the cytoplasm, as they do not possess the amino-terminal extension of mitochondrion-targeted ADHs. Gene disruption studies suggest that PsADH1 plays a major role in xylose fermentation because PsADH1 disruption results in a lower growth rate and profoundly greater accumulation of xylitol. Disruption of PsADH2 does not significantly affect ethanol production or aerobic growth on ethanol as long as PsADH1 is present. The PsADH1 and PsADH2 isozymes appear to be equivalent in the ability to convert ethanol to acetaldehyde, and either is sufficient to allow cell growth on ethanol. However, disruption of both genes blocks growth on ethanol. P. stipitis strains disrupted in either PsADH1 or PsADH2 still accumulate ethanol, although in different amounts, when grown on xylose under oxygen-limited conditions. The PsADH double disruptant, which is unable to grow on ethanol, still produces ethanol from xylose at about 13% of the rate seen in the parental strain. Thus, deletion of both PsADH1 and PsADH2 blocks ethanol respiration but not production, implying a separate path for fermentation.

  • Lu P, Davis BP, Hendrick J, Jeffries TW (1998) Cloning and disruption of the beta-isopropylmalate dehydrogenase gene (LEU2) of Pichia stipitis with URA3 and recovery of the double auxotroph. Appl. Microbiol. Biotechnol. 49(2):141-6 · Pubmed

    Transformation of Pichia stipitis is required to advance genetic studies and development of xylose metabolism in this yeast. To this end, we used P. stipitis URA3 (PsURA3) to disrupt P. stipitis LEU2 in a P. stipitis ura3 mutant. A highly fermentative P. stipitis mutant (FPL-DX26) was selected for resistance to 5'-fluoroorotic acid to obtain P. stipitis FPL-UC7 (ura3-3). A URA3:lacZ "pop-out" cassette was constructed containing PsURA3 flanked by direct repeats from segments of the lacZ reading frame. The P. stipitis LEU2 gene (PsLEU2) was cloned from a P. stipitis CBS 6054 genomic library through homology to Saccharomyces cerevisiae LEU2, and a disruption cassette was constructed by replacing the PsLEU2 reading sequence with the PsURA3:lacZ cassette. FPL-UC7 (ura3-3) was transformed with the disruption cassette, and a site-specific integrant was identified by selecting for the Leu- Ura+ phenotype. The ura3 marker was recovered from this strain by plating cells onto 5'-fluoroorotate and screening for spontaneous URA3 deletion mutants. Excision of the flanked PsURA3 gene resulted in the Leu- Ura- phenotype. The double auxotrophs are stable and can be transformed at a high frequency by PsLEU2 or PsURA3 carried on autonomous-replication-sequence-based plasmids.

  • Lu P, Davis BP, Jeffries TW (1998) Cloning and characterization of two pyruvate decarboxylase genes from Pichia stipitis CBS 6054. Appl. Environ. Microbiol. 64(1):94-7 (PMC124677) · Pubmed

    In Pichia stipitis, fermentative and pyruvate decarboxylase (PDC) activities increase with diminished oxygen rather than in response to fermentable sugars. To better characterize PDC expression and regulation, two genes for PDC (PsPDC1 and PsPDC2) were cloned and sequenced from P. stipitis CBS 6054. Aside from Saccharomyces cerevisiae, from which three PDC genes have been characterized, P. stipitis is the only organism from which multiple genes for PDC have been identified and characterized. PsPDC1 and PsPDC2 have diverged almost as far from one another as they have from the next most closely related known yeast gene. PsPDC1 contains an open reading frame of 1,791 nucleotides encoding 597 amino acids. PsPDC2 contains a reading frame of 1,710 nucleotides encoding 570 amino acids. An 81-nucleotide segment in the middle of the beta domain of PsPDC1 codes for a unique segment of 27 amino acids, which may play a role in allosteric regulation. The 5' regions of both P. stipitis genes include two putative TATA elements that make them similar to the PDC genes from S. cerevisiae, Kluyveromyces marxianus, and Hanseniaspora uvarum.

  • Yang VW, Jeffries TW (1997) Regulation of phosphotransferases in glucose- and xylose-fermenting yeasts. Appl. Biochem. Biotechnol. 63-65:97-108 · Pubmed

    This research examined the titers of hexokinase (HK), phosphofructokinase (PFK), and xylulokinase (XUK) in Saccharomyces cerevisiae and two xylose fermenting yeasts, Pachysolen tannophilus and Candida shehatae, following shifts in carbon source and aeration. Xylose-grown C. shehatae, glucose-grown P. tannophilus, and glucose-grown S. cerevisiae, had the highest specific activities of XUK, HK, and PFK, respectively. XUK was induced by xylose to moderate levels in both P. tannophilus and C. shehatae, but was present only in trace levels in S. cerevisiae. HK activities in P. tannophilus were two to three fold higher when cells were grown on glucose than when grown on xylose, but HK levels were less inducible in C. shehatae. The PFK activities in S. cerevisiae were 1.5 to 2 times higher than in the two xylose-fermenting yeasts. Transfer from glucose to xylose rapidly inactivated HK in P. tannophilus, and transfer from xylose to glucose inactivated XUK in C. shehatae. The patterns of induction and inactivation indicate that the basic regulatory mechanisms differ in the two xylose fermenting yeasts.

  • Dahn KM, Davis BP, Pittman PE, Kenealy WR, Jeffries TW (1996) Increased xylose reductase activity in the xylose-fermenting yeast Pichia stipitis by overexpression of XYL1. Appl. Biochem. Biotechnol. 57-58:267-76 · Pubmed

    The Pichia stipitis xylose reductase gene (XYL1) was inserted into an autonomous plasmid that P. stipitis maintains in multicopy. The plasmid pXOR with the XYL1 insert or a control plasmid pJM6 without XYL1 was introduced into P. stipitis. When grown on xylose under aerobic conditions, the strain with pXOR had up to 1.8-fold higher xylose reductase (XOR) activity than the control strain. Oxygen limitation led to higher XOR activity in both experimental and control strains grown on xylose. However, the XOR activities of the two strains grown on xylose were similar under oxygen limitation. When grown on glucose under aerobic or oxygen-limited conditions, the experimental strain had XOR activity up to 10 times higher than that of the control strain. Ethanol production was not improved, but rather it decreased with the introduction of pXOR compared to the control, and this was attributed to nonspecific effects of the plasmid.

  • Jeffries TW (1996) Biochemistry and genetics of microbial xylanases. Curr. Opin. Biotechnol. 7(3):337-42 · Pubmed

    Xylanases are classified into two major families (10 or F and 11 or G) of glycosyl hydrolases. Both use ion pair catalytic mechanisms and both retain anomeric configuration following hydrolysis. Family 10 xylanases are larger, more complex and produce smaller oligosaccharides; Family 11 xylanases are more specific for xylan. Alkaline-active and extreme-thermophilic enzymes are of particular interest. Such xylanases are being commercialized for bleaching pulps and other applications.

  • Yang VW, Marks JA, Davis BP, Jeffries TW (1994) High-efficiency transformation of Pichia stipitis based on its URA3 gene and a homologous autonomous replication sequence, ARS2. Appl. Environ. Microbiol. 60(12):4245-54 (PMC201976) · Pubmed

    This paper describes the first high-efficiency transformation system for the xylose-fermenting yeast Pichia stipitis. The system includes integrating and autonomously replicating plasmids based on the gene for orotidine-5'-phosphate decarboxylase (URA3) and an autonomous replicating sequence (ARS) element (ARS2) isolated from P. stipitis CBS 6054. Ura- auxotrophs were obtained by selecting for resistance to 5-fluoroorotic acid and were identified as ura3 mutants by transformation with P. stipitis URA3. P. stipitis URA3 was cloned by its homology to Saccharomyces cerevisiae URA3, with which it is 69% identical in the coding region. P. stipitis ARS elements were cloned functionally through plasmid rescue. These sequences confer autonomous replication when cloned into vectors bearing the P. stipitis URA3 gene. P. stipitis ARS2 has features similar to those of the consensus ARS of S. cerevisiae and other ARS elements. Circular plasmids bearing the P. stipitis URA3 gene with various amounts of flanking sequences produced 600 to 8,600 Ura+ transformants per micrograms of DNA by electroporation. Most transformants obtained with circular vectors arose without integration of vector sequences. One vector yielded 5,200 to 12,500 Ura+ transformants per micrograms of DNA after it was linearized at various restriction enzyme sites within the P. stipitis URA3 insert. Transformants arising from linearized vectors produced stable integrants, and integration events were site specific for the genomic ura3 in 20% of the transformants examined. Plasmids bearing the P. stipitis URA3 gene and ARS2 element produced more than 30,000 transformants per micrograms of plasmid DNA. Autonomously replicating plasmids were stable for at least 50 generations in selection medium and were present at an average of 10 copies per nucleus.

  • Elegir G, Szakács G, Jeffries TW (1994) Purification, Characterization, and Substrate Specificities of Multiple Xylanases from Streptomyces sp. Strain B-12-2. Appl. Environ. Microbiol. 60(7):2609-15 (PMC201691) · Pubmed

    The endoxylanase complex from Streptomyces sp. strain B-12-2 was purified and characterized. The organism forms five distinct xylanases in the absence of significant cellulase activity when grown on oat spelt xylan. This is the largest number of endoxylanases yet reported for a streptomycete. On the basis of their physiochemical characteristics, they can be divided into two groups: the first group (xyl 1a and xyl 1b) consists of low-molecular-mass (26.4 and 23.8 kDa, respectively) neutral- to high-pI (6.5 and 8.3, respectively) endoxylanases. Group 1 endoxylanases are unable to hydrolyze aryl-beta-d-cellobioside, have low levels of activity against xylotetraose (X(4)) and limited activity against xylopentaose, produce little or no xylose, and form products having a higher degree of polymerization with complex substrates. These enzymes apparently carry out transglycosylation. The second group (xyl 2, xyl 3, and xyl 4) consists of high-molecular-mass (36.2, 36.2, and 40.5 kDa, respectively), low-pI (5.4, 5.0, and 4.8, respectively) xylanases. Group 2 endoxylanases are able to hydrolyze aryl-beta-d-cellobioside, show higher levels of activity against X(4), and hydrolyze xylopentaose completely with the formation of xylobiose and xylotriose plus limited amounts of X(4) and xylose. The enzymes display intergroup synergism when acting on kraft pulp. Despite intragroup similarities, each enzyme exhibited a unique action pattern and physiochemical characteristic. xyl 2 was highly glycosylated, and xyl 1b (but no other enzyme) was completely inhibited by p-hydroxymercuribenzoate.

  • Perez J, Jeffries TW (1993) Role of organic acid chelators in manganese regulation of lignin degradation by Phanerochaete chrysosporium. Appl. Biochem. Biotechnol. 39-40:227-38 · Pubmed

    Nitrogen, carbon, and manganese are potent regulators of lignin degradation, but although nitrogen and carbon elicit a generalizated response when cells are starved, manganese is a relatively specific regulator of lignin and manganese peroxidase (LiP and MnP, respectively). At high manganese levels, MnP is induced, and LiP is repressed. At low Mn levels, MnP is repressed, and LiP is induced. Organic acid chelators are very important in attaining LiP repression with high Mn. Both mineralization and lignin depolymerization are regulated by manganese in the presence of organic acid chelators. As long as the chelators keep Mn(II) and Mn(III) in solution, repression is observed, but eventually, dismutation reactions cause the formation and precipitation of Mn (IV) as MnO2. Repression is immediately relieved, and depolymerization and mineralization proceed at a high rate.

  • Grabski AC, Forrester IT, Patel R, Jeffries TW (1993) Characterization and N-terminal amino acid sequences of beta-(1-4)endoxylanases from Streptomyces roseiscleroticus: purification incorporating a bioprocessing agent. Protein Expr. Purif. 4(2):120-9 · Pubmed

    Streptomyces roseiscleroticus produces extracellular xylanases when cultured on a liquid xylan medium. Purified xylanases are used to facilitate bleaching of kraft pulps in the pulp and paper industry. Downstream processing and purification of xylanases from S. roseiscleroticus is difficult unless red pigments produced by the bacterium are removed. We report that the bioprocessing agent, Biocryl BPA-1000, removes these pigments allowing purification of four xylanases by HPLC employing cation exchange, hydrophobic interaction, and gel filtration. The xylanases have been named Xyl1, Xyl2, Xyl3, and Xyl4 according to their order of elution from the cation exchange column. The purified xylanases have been characterized according to their molecular weights, pH and temperature stabilities, N-terminal amino acid sequences, and hydrolysis action patterns on oat spelt xylan. The molecular weights by mass spectroscopy for Xyl1-Xyl4 are 33,647, 33,655, 21,070, and 46,855, respectively. All four xylanases exhibit pH optima between 5.0 and 7.0 and temperature optima between 50 and 60 degrees C. The N-terminal amino acid sequences are compared to sequences from Streptomyces lividans, Streptomyces 36A, and a Chainia sp. The N-terminal amino acid sequence of Xyl1 appears to be unique, but sequences from Xyl2, 3, and 4 bear strong homology to xylanases cloned from S. lividans. Xyl3 is also homologous to xylanases from Streptomyces 36A, and a Chainia sp. Predominant products of arabinoxylan hydrolysis by the purified xylanases included xylotriose, tetraose, and pentaose. None of the xylanases purified from S. roseiscleroticus produced xylose.

  • Perez J, Jeffries TW (1992) Roles of manganese and organic acid chelators in regulating lignin degradation and biosynthesis of peroxidases by Phanerochaete chrysosporium. Appl. Environ. Microbiol. 58(8):2402-9 (PMC195794) · Pubmed

    We studied the effect of manganese and various organic chelators on the distribution, depolymerization, and mineralization of synthetic 14C-labeled lignins (DHP) in cultures of Phanerochaete chrysosporium. In the presence of high levels of manganese [Mn(II) or Mn(III)], along with a suitable chelator, lignin peroxidase (LiP) production was repressed and manganese peroxidase (MnP) production was stimulated. Even though partial lignin depolymerization was observed under these conditions, further depolymerization of the polymer to smaller compounds was more efficient when low levels of manganese were present. LiPs were prevalent under these latter conditions, but MnPs were also present. Mineralization was more efficient with low manganese. These studies indicate that MnP performs the initial steps of DHP depolymerization but that LiP is necessary for further degradation of the polymer to lower-molecular-weight products and mineralization. We also conclude that a soluble Mn(II)-Mn(III) organic acid complex is necessary to repress LiP.

  • Grabski AC, Jeffries TW (1991) Production, Purification, and Characterization of beta-(1-4)-Endoxylanase of Streptomyces roseiscleroticus. Appl. Environ. Microbiol. 57(4):987-92 (PMC182834) · Pubmed

    Twelve species of Streptomyces that formerly belonged to the genus Chainia were screened for the production of xylanase and cellulase. One species, Streptomyces roseiscleroticus (Chainia rosea) NRRL B-11019, produced up to 16.2 IU of xylanase per ml in 48 h. A xylanase from S. roseiscleroticus was purified and characterized. The enzyme was a debranching beta-(1-4)-endoxylanase showing high activity on xylan but essentially no activity against acid-swollen (Walseth) cellulose. It had a very low apparent molecular weight of 5,500 by native gel filtration, but its denatured molecular weight was 22,600 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It had an isoelectric point of 9.5. The pH and temperature optima for hydrolysis of arabinoxylan were 6.5 to 7.0 and 60 degrees C, respectively, and more than 75% of the optimum enzyme activity was retained at pH 8.0. The xylanase had a K(m) of 7.9 mg/ml and an apparent V(max) of 305 mumol . min . mg of protein. The hydrolysis rate was linear for xylan concentrations of less than 4 mg/ml, but significant inhibition was observed at xylan concentrations of more than 10 mg/ml. The predominant products of arabinoxylan hydrolysis included arabinose, xylobiose, and xylotriose.

  • Perez J, Jeffries TW (1990) Mineralization of C-Ring-Labeled Synthetic Lignin Correlates with the Production of Lignin Peroxidase, not of Manganese Peroxidase or Laccase. Appl. Environ. Microbiol. 56(6):1806-12 (PMC184514) · Pubmed

    Recently, Mn(II) has been shown to induce manganese peroxidases (MnPs) and repress lignin peroxidases (LiPs) in defined liquid cultures of several white rot organisms. The present work shows that laccase is also regulated by Mn(II). We therefore used Mn(II) to regulate production of LiP, MnP, and laccase activities while determining the effects of Mn(II) on mineralization of ring-labeled synthetic lignin. At a low Mn(II) level, Phanerochaete chrysosporium and Phlebia brevispora produced relatively high titers of LiPs but only low titers of MnPs. At a high Mn(II) level, MnP titers increased 12- to 20-fold, but LiPs were not detected in crude broths. P. brevispora formed much less LiP than P. chrysosporium, but it also produced laccase activity that increased more than sevenfold at the high Mn(II) level. The rates of synthetic lignin mineralization by these organisms were similar and were almost seven times higher at low than at high Mn(II). Increased synthetic lignin mineralization therefore correlated with increased LiP, not with increased MnP or laccase activities.

  • Bonnarme P, Jeffries TW (1990) Mn(II) Regulation of Lignin Peroxidases and Manganese-Dependent Peroxidases from Lignin-Degrading White Rot Fungi. Appl. Environ. Microbiol. 56(1):210-7 (PMC183274) · Pubmed

    Two families of peroxidases-lignin peroxidase (LiP) and manganese-dependent lignin peroxidase (MnP)-are formed by the lignin-degrading white rot basidiomycete Phanerochaete chrysosporium and other white rot fungi. Isoenzymes of these enzyme families carry out reactions important to the biodegradation of lignin. This research investigated the regulation of LiP and MnP production by Mn(II). In liquid culture, LiP titers varied as an inverse function of and MnP titers varied as a direct function of the Mn(II) concentration. The extracellular isoenzyme profiles differed radically at low and high Mn(II) levels, whereas other fermentation parameters, including extracellular protein concentrations, the glucose consumption rate, and the accumulation of cell dry weight, did not change significantly with the Mn(II) concentration. In the absence of Mn(II), extracellular LiP isoenzymes predominated, whereas in the presence of Mn(II), MnP isoenzymes were dominant. The release of CO(2) from C-labeled dehydrogenative polymerizate lignin was likewise affected by Mn(II). The rate of CO(2) release increased at low Mn(II) and decreased at high Mn(II) concentrations. This regulatory effect of Mn(II) occurred with five strains of P. chrysosporium, two other species of Phanerochaete, three species of Phlebia, Lentinula edodes, and Phellinus pini.

  • Alexander MA, Chapman TW, Jeffries TW (1989) Continuous-Culture Responses of Candida shehatae to Shifts in Temperature and Aeration: Implications for Ethanol Inhibition. Appl. Environ. Microbiol. 55(9):2152-4 (PMC203048) · Pubmed

    Temperature and aeration shifts were used to perturb steady-state continuous cultures to determine the effects of ethanol on xylose metabolism by Candida shehatae. The accumulation of ethanol exerted a delayed inhibitory effect on the specific rate of substrate utilization. A second effect was also observed in which the specific rate of xylitol production increased at the expense of the specific rate of ethanol production. Both effects were enhanced at higher temperature. Inhibitory effects also occurred in glucose metabolism.

  • Jeffries TW, Sreenath HK (1988) Fermentation of hemicellulosic sugars and sugar mixtures by Candida shehatae. Biotechnol. Bioeng. 31(5):502-6 · Pubmed

    No abstract available.

  • Alexander MA, Chapman TW, Jeffries TW (1987) Continuous ethanol production from D-xylose by Candida shehatae. Biotechnol. Bioeng. 30(5):685-91 · Pubmed

    No abstract available.