nitrogen'source and mineral optimization enhance d-xylose

12
Appl Microbiol Biotechnol (2006) 72: 1285-1296 DOl 10.1007/s00253-006-0435-1 9434 -- -------- --- - - -- - ,.------- APPLIED MICROBIAL AND CELL PHYSIOLOGY Patricia J. Slininger. Bruce S. Dien . StevenW. Gorsich. ZonglinL. Lin Nitrogen'source and mineral optimization enhance D-xylose conversion to ethanol by the yeast Pichia stipitis NRRLY-7124 Received: 31 December 2005 / Revised: 20 March 2006 / Accepted: 24 March 2006 / Published online: 5 May 2006 (g Springer-Verlag2006 Abstract Nutrition-based strategies to optimize xylose to ethanol conversion by Pichia stipitis were identified in growing and stationary-phase cultures provided with a defined medium varied in nitrogen, vitamin, purine/py- rimidine, and mineral content via full or partial factorial designs. It is surprising to note that stationary-phase cultures were unable to ferment xylose (or glucose) to ethanol without the addition of a nitrogen source, such as amino acids. Ethanol accumulation increased with argi- nine, alanine, aspartic acid, glutamic acid, glycine, histi- dine, leucine, and tyrosine, but declined with isoleucine. Ethanol production from 150 gli xylose was maximized (61:1:9g/l) by providing C:N in the vicinity of -57-126:1 and optimizing the combination of urea and amino acids to supply 40-80 % nitrogen from urea and 60-20 % from amino acids (casamino acids supplemented with trypto- phan and cysteine). When either urea or amino acids were used as sole nitrogen source, ethanol accumulation dropped to 11 or 24 g/l, respectively, from the maximum of 46 g/l for the optimal nitrogen combination. The interaction of minerals with amino acids and/or urea was key to optimizing ethanol production by cells in both growing and stationary-phase cultures. In nongrowing cultures supplied with nitrogen as amino acids, ethanol concentra- tion increased from 24 to 54 g/l with the addition of an optimized mineral supplement of Fe, Mn, Mg, Ca, Zn, and others. The mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. P. J. Slininger (IBJ) . B. S. Dien . S. W. Gorsich . Z. L. Uu U. S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, IL 61604, USA e-mail: [email protected] Tel.: +1-309-6816596 Introduction Various sources of lignocellulosic biomass such as agricultural residues, wood, municipal solid wastes, and wastes from pulp and paper industry can serve as low-cost and abundant feedstocks for the production of fuel ethanol or value-added chemicals. It is estimated that approxi- mately 50 billion gallons of ethanol could be produced annually from current biomass wastes in our country while dedicated energy farms offer the potential to produce up to 350 billion gallons (Wyman 1994). However, there are many technological hurdles to leap to have an economical biomass-to-ethanol process-one being the efficient fer- mentation of biomass-derived sugars to ethanol. Sugars from biomass include both hexoses and pentoses. Pichia stipitis and Candida shehatae strains are known to ferment the pentose D-xylose to ethanol more efficiently than other natural yeasts previously described (prior et al. 1989). P. stipitis NRRL Y-7124 is particularly useful because it accumulates 50-60 g/l ethanol at a yield ofOAI gig xylose with almost no xylitol as a fermentation by-product (Slininger et al. 1985). The genome of P. stipitis strain NRRL Y-11545 has now been sequenced for use in continuing research toward engineering a more efficient fermentation of hemicellulose hydrolysates (Jeffries et al. 2005). Improvement goals for this yeast will include minimizing oxygen demand, increasing nongrowth-asso- ciated ethanol production, increasing fermentation rates four- to fivefold, and improving ethanol and inhibitor tolerances. In the absence of cell growth and maintenance, the theoretical yield of ethanol from xylose in yeasts has generally been considered to be 0.51 g ethanol/g xylose consumed, assuming that xylose is converted to xylulose without xylitol accumulation, that xylulose-5-phosphate is converted to fructose-6-phosphate and glyceraldehyde-3- phosphate via the pentose phosphate pathway without oxidative recycling or cofactor imbalance, and that these intermediates are converted to ethanol and carbon dioxide via glycolysis and ethanolic fermentation. Thus, 3 mol xylose can potentially give rise to 5 mol each of ethanol

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Page 1: Nitrogen'source and mineral optimization enhance D-xylose

Appl Microbiol Biotechnol (2006) 72: 1285-1296DOl 10.1007/s00253-006-0435-1

9434

-- ----------- - - -- - ,.-------

APPLIED MICROBIAL AND CELL PHYSIOLOGY

Patricia J. Slininger.BruceS. Dien.StevenW. Gorsich. ZonglinL. Lin

Nitrogen'source and mineral optimization enhance D-xyloseconversion to ethanol by the yeast Pichia stipitis NRRLY-7124

Received: 31 December 2005 / Revised: 20 March 2006 / Accepted: 24 March 2006 / Published online: 5 May 2006(g Springer-Verlag2006

Abstract Nutrition-based strategies to optimize xylose toethanol conversion by Pichia stipitis were identified ingrowing and stationary-phase cultures provided with adefined medium varied in nitrogen, vitamin, purine/py-rimidine, and mineral content via full or partial factorialdesigns. It is surprising to note that stationary-phasecultures were unable to ferment xylose (or glucose) toethanol without the addition of a nitrogen source, such asamino acids. Ethanol accumulation increased with argi-nine, alanine, aspartic acid, glutamic acid, glycine, histi-dine, leucine, and tyrosine, but declined with isoleucine.Ethanol production from 150 gli xylose was maximized(61:1:9g/l) by providing C:N in the vicinity of -57-126:1and optimizing the combination of urea and amino acids tosupply 40-80 % nitrogen from urea and 60-20 % fromamino acids (casamino acids supplemented with trypto-phan and cysteine). When either urea or amino acids wereused as sole nitrogen source, ethanol accumulation droppedto 11 or 24 g/l, respectively, from the maximum of 46 g/lfor the optimal nitrogen combination. The interaction ofminerals with amino acids and/or urea was key tooptimizing ethanol production by cells in both growingand stationary-phase cultures. In nongrowing culturessupplied with nitrogen as amino acids, ethanol concentra-tion increased from 24 to 54 g/l with the addition of anoptimized mineral supplement of Fe, Mn, Mg, Ca, Zn, andothers.

The mention of trade names or commercial products in this article issolely for the purpose of providing specific information and does notimply recommendation or endorsement by the U.S. Department ofAgriculture.

P. J. Slininger (IBJ) . B. S. Dien . S. W. Gorsich . Z. L. UuU. S. Department of Agriculture, Agricultural Research Service,National Center for Agricultural Utilization Research,1815 N. University Street,Peoria, IL 61604, USAe-mail: [email protected].: +1-309-6816596

Introduction

Various sources of lignocellulosic biomass such asagricultural residues, wood, municipal solid wastes, andwastes from pulp and paper industry can serve as low-costand abundant feedstocks for the production of fuel ethanolor value-added chemicals. It is estimated that approxi-mately 50 billion gallons of ethanol could be producedannually from current biomass wastes in our country whilededicated energy farms offer the potential to produce up to350 billion gallons (Wyman 1994). However, there aremany technological hurdles to leap to have an economicalbiomass-to-ethanol process-one being the efficient fer-mentation of biomass-derived sugars to ethanol. Sugarsfrom biomass include both hexoses and pentoses. Pichiastipitis and Candida shehatae strains are known to fermentthe pentose D-xylose to ethanol more efficiently than othernatural yeasts previously described (prior et al. 1989).P. stipitis NRRL Y-7124 is particularly useful because itaccumulates 50-60 g/l ethanol at a yield ofOAI gig xylosewith almost no xylitol as a fermentation by-product(Slininger et al. 1985). The genome of P. stipitis strainNRRL Y-11545 has now been sequenced for use incontinuing research toward engineering a more efficientfermentation of hemicellulose hydrolysates (Jeffries et al.2005). Improvement goals for this yeast will includeminimizing oxygen demand, increasing nongrowth-asso-ciated ethanol production, increasing fermentation ratesfour- to fivefold, and improving ethanol and inhibitortolerances.

In the absence of cell growth and maintenance, thetheoretical yield of ethanol from xylose in yeasts hasgenerally been considered to be 0.51 g ethanol/g xyloseconsumed, assuming that xylose is converted to xylulosewithout xylitol accumulation, that xylulose-5-phosphate isconverted to fructose-6-phosphate and glyceraldehyde-3-phosphate via the pentose phosphate pathway withoutoxidative recycling or cofactor imbalance, and that theseintermediates are converted to ethanol and carbon dioxidevia glycolysis and ethanolic fermentation. Thus, 3 molxylose can potentially give rise to 5 mol each of ethanol

Page 2: Nitrogen'source and mineral optimization enhance D-xylose

1286

and carbon dioxide (Slininger et al. 1985; Prior et al. 1989;Hahn-Hagerdal et al. 1994). The observed ethanol yieldachieved on xylose is usually less as carbon goes to cellmass and as pentose phosphate cycling occurs to supply theNADPH demands of biosynthesis. Under aerobic condi-tions, the diversion of acetyl phosphate via conversion toacetyl CoA to feed the tricarboxylic acid cycle may furtherlessen the carbon flow to ethanol. Culture nutrition,including nitrogen and carbon sources, growth factors,and minerals, is expected to impact ethanol yield byinfluencing the efficiency of biosynthesis, cell preservationand maintenance, and the redox balance involving NAD/NADH and NADPINADPH cofactors.

This paper focuses on P. stipitis strain Y-7124 and theimportance of nutrition to the efficient conversion ofconcentrated xylose substrates to product streams havinginhibitory ethanol concentrations. Other researchers havereported the great importance of nutrient limitation to high-gravity brewing wort-seeing significantly increased cellmass and higher fermentation rates as a result of yeastextract, ergosterol, oleic acid, or soy flour additions (Caseyet al. 1984; Viegas et al. 1985; O'Connor-Cox et al. 1991).Although there have been several publications on thesubject of P. stipitis nutrition (reviewed by Prior et al.1989), the research reported in this study fills gaps inknowledge about the required carbon to nitrogen ratio foroptimal ethanol production and key combinations ofnitrogen sources and other nutrient groups that interact toimpact ethanol production efficiency from xylose. Full andpartial factorial designs were applied to examine the impactof nutrient combinations on biomass and ethanol accumu-lations in growing compared to nongrowing stationary-phase cultures of P. stipitis. The investigation into thequestion of whether there are different nutrient require-ments for growth vs nongrowth-associated ethanolproduction is also novel. Such comparative studies ofphase-dependent nutrition for ethanologenic yeasts aresparse in the literature, yet they are pertinent to thedesign of cost-effective media and feeding strategies foroptimizing growth and ethanol productivity. The resultsof such studies will also provide valuable insight into thedesign of defined media for experiments, such asgenome-wide micro array, to troubleshoot metabolicbottlenecks and investigate mechanisms by which yeastsare able to tolerate stress factors, such as high sugar andethanol concentrations.

Precultures were shaken at 150 rpm (1-in. stroke) for48 h at 25°C in a New Brunswick Psychrotherm. Testcultures with low initial yeast biomass concentration(A62o,o=0.1absorbance units) were inoculated with buff-er-washed cells of P. stipitis NRRL Y-7124 fromprecultures grown in 125-ml flasks, having 50-ml Difcoyeast nitrogen base (YNB) medium with 50 to 150 g/lxylose added as needed to equal the sugar content ofsubsequent test cultures. To assess stationary-phase ethanolproduction independently of cell growth, test cultures wereinoculated to a high initial biomass concentration(A620,o=20) with buffer-washed stationary yeast fromprecultures that had been grown 72 h in Fembach flaskson 1.5-1 Difco YNB medium. Yeast-cell washing wasaccomplished by centrifuging 200-ml culture aliquots for5 min at 7,000 rpm (7,974xg) and 4 DC in a Sorvalcentrifuge equipped with GSA rotor, resuspending pelletsin pH 7 sterile buffer (1 g/l each ofKH2P04 and K2HP04),pooling buffered cells, and centrifuging and resuspendingthe pooled pellets to about l/15th of the original culturevolume in buffer.

Test cultures, experiment design, and data analysis

Nutritional requirements for growth and ethanol productionwere assessed in either 125- or 500-ml shake flasks with75- or 400-ml filter-sterilized defined medium formula-tions, respectively, incubated at 150 rpm and optimalconditions of 25 DCand initial pH 6.5 to minimize xylitolproduction (Slininger et al. 1990a). Each defined mediumformulation was tested in duplicate cultures. Factorial orpartial factorial experiment designs were applied to test thedependence of biomass and ethanol accumulations on theculture nutrients in base defined (BD) medium used forcommercial optimization described by Zabriskie et al.(1980) (Table 1). The presence vs absence of wholenutrient groups-amino acids, purines and pyrimidines,vitamins, and minerals-was first tested using 22 and 23full factorial designs. The presence(+)/absence(-) ofindividual nutrients within groups having significantimpact on ethanol production were studied in follow-upexperiments using a 16-combination 29 fractional factorialdesign described by the following treatment (rows 1-16) xingredients (columns A-I) matrix (Webb 1971):

A c F G HB D E

Materials and methods1 - +2 - - - + + + +3 - + - + - + +

Yeast inoculum preparation 4 + + + + - - +5 + - + + - + -

Lyophilized P. stipitis NRRL Y-7124 (CBS 5773) was6 + - + + + - +7 + + - + + - +

acquired from the ARS Culture Collection (National 8 + + + +Center for Agricultural Utilization Research, Peoria, IL, 9 + - - - + + +

USA). Stock cultures were maintained in 10 % glycerol at 10 + - - + + + +

-80 DC and were used to inoculate yeast malt agar plates11 + - + - + + +12 + - + + + -

that were incubated 48 h at 25 DC before loop transfer to 13 + + - + + +precultures.

Page 3: Nitrogen'source and mineral optimization enhance D-xylose

A B C D E F G H

141516

+++

+++

+ +++

+++ + + + +

Vitamins, amino acids, and minerals tested using thisdesign are listed in A-I order in Tables 3, 5, and 6,respectively. The SAS program was applied to perform ananalysis of variance on experiment results and to determinethe significance of nutrient variations effecting the cultureproduct accumulations. Significant effects of variableswere indicated if reported P values were less than 0.05.Additional experiments involving concentration serieswere run to find the optimum concentrations of keynutrients needed to maximize ethanol production.

Culture sampling and analyses

Samples were drawn daily or twice daily as needed toassess the time courses of yeast biomass, substrate, andfermentation product concentrations. Sample absorbance at620 nm (A620)was measured in l-cm pathlength cuvettesusing a Bausch and Lomb Spectronic 2000 spectropho-tometer. Samples were diluted such that absorbance fell in

Table 1 Base defined (BD) medium in which all ingredientconcentrations represent "I x base" level

Nutrient Concentration (g/I)

Buffer

K2HP04

KH2P04Minerals

FeS04[7H2O]

MgS04[7H2O]NaCI

Purines and pyrimidinesAdenine

CytosineGuanine

Uracil

ThymineVitamins

Thiamine

Riboflavin

Calcium pantothenateNiacin

PyridoxamineThioctic acidFolic acid

Biotin

B12Amino acids

Vitamin-free cas amino acids

0.01

0.1

0.01

0.01

0.01

0.01

0.01

0.01

0.0005

0.0005

0.0005

0.0005

0.0005

0.0005

0.00005

0.00005

0.00005

5

0.05

0.2

Tryptophan

Cysteine

1287

the range, 0.05<A620<0.5units, where Beer's law is linearwith biomass concentration (b). The product of absorbancex dilution factor is reported and indicates biomass concen-tration. For P stipitis, b=kA, where k=0.167 g/l.

Samples were centrifuged, and the supernatant wasstored at -20°C until analysis. Xylose, xylitol, ribitol, andethanol were analyzed using a Waters High PerformanceLiquid Chromatographic system equipped with a BioradHPX-87H Aminex ion exclusion column and a refractiveindex detector. The column was operated at room temper-ature with acidified water (0.0017 N H2SO4) as mobilephase. Ethanol concentration was determined using aPackard Model 428 Gas Chromatograph equipped with a6-ft Poropak Q column operating at 150°C.

Results

Vitamins and amino acids but not purinesand pyrimidines impacted growth and ethanolaccumulation

Including vitamins in the BD medium (Table 1) improvedcell biomass accumulation, but the addition of purines andpyrimidines, either alone or in combination with vitamins,had no significant impact on the growth of strain Y-7124 onxylose (Table 2). Although biotin was the key vitaminresponsible for growth improvement, it had little impact onethanol accumulation by stationary-phase cells (Table 3).Neither the vitamin nor the purine/pyrimidine group, eitheralone or in combination, influenced ethanol accumulationby a large stationary-phase population (Table 4).

Amino acids were a sufficient source of nitrogen tosupport growth ofY-7l24 (data not shown). It is interestingto note, however, that the presence of amino acids (the solenitrogen source) was key to maintaining ethanol produc-tion by high densities of stationary-phase Y-7124, and thiswas true regardless of whether the carbon source providedwas xylose or glucose (Table 4). Eight of the 18 aminoacids tested significantly affected yeast biomass accumula-tions, while nine of 18 influenced ethanol production(Table 5). Arginine, histidine, isoleucine, and proline had apositive effect on growth, while alanine, glutamic acid,leucine, and tyrosine had a negative impact. Additions ofalanine, arginine, aspartic acid, glutamic acid, glycine,histidine, leucine, and tyrosine improved ethanol accumu-lation, but isoleucine reduced it. Arginine and histidine

Table 2 Significance (P<0.05) of growth factor effects on P stipitisNRRL Y-7124 biomass accumulation determined using a 22complete factorial experiment design to test presence vs absenceof purines/pyrimidines and vitamins in the BD medium (Table I)prepared with 50 g/I xylose and inoculated to A62o=0.1O

Maximum biomass accumulation (A620)

Present Absent PNutrient group

Purines/Pyrimidines 14.8

Vitamins 28.8

17.5

3.50.068

<0.001

Page 4: Nitrogen'source and mineral optimization enhance D-xylose

1288

Table 3 Significance (P<0.05) of vitamin effects on biomass accumulation (A620initially 0.1) and on ethanol accumulation by stationary-phase P stipitis NRRL Y-7124 (A620initially 20) when the initial xylose concentration is 50 g/l. In both growing and stationary cellexperiments, a 29 fractional factorial design matrix was applied to test the benefit of adding each vitamin to BD medium (Table 1)

improved both growth and ethanol accumulation. Alanine,glutamic acid, leucine, and tyrosine improved ethanol atthe expense of reducing biomass. Isoleucine improvedgrowth at the expense of reducing ethanol. Proline onlyimproved growth, while aspartic acid and glycine onlyimproved ethanol accumulation. None of the amino acidstested had a negative impact on both growth and ethanolproduction. While many of the individual amino acidsimproved growth and/or ethanol production, no singleamino acid was an absolute requirement for either growthor ethanol production.

Adjustment of amino acid but not biotin levelsoptimized ethanol accumulation per xylose loading

BD medium was adjusted to search for biotin and aminoacid combinations optimizing ethanol production trom 50,100, and 150 g/l xylose (Fig. 1). Ethanol and biomassaccumulations generated by random combinations of biotin(0.1 to 30x base concentration) and amino acids (0.5 to 15xbase) were independent of biotin, provided that the level ofamino acids supplied was more than 0.5x base concentra-tion. Amino acids in the 1 to 12.5x, 2 to 12.5x, and 2 to 8xbase concentration ranges optimized ethanol accumula-tions, averaging 18.1,29.9, and 34.5 g/l trom 50, 100, and150 g/l xylose, respectively. In this experiment, ethanolaccumulation was a linear function of xylose consumed

(R2=0.7), and so the slope, i.e., the ethanol yield per xylose(averaging 0.35 gig), was rather insensitive to the aminoacid level. The optimum amino acid range becamenarrower with increasing initial xylose. The nitrogenanalysis ofBacto Vitamin Assay Casamino Acids indicatedthat amino nitrogen comprised 4 % and C comprised 53 %.Therefore, the corresponding optimum carbon to nitrogenratio ranges were 127:1 to 24:1,126:1 to 33:1, and 182:1 to57:1 for 50, 100, and 150 g/l xylose, respectively. Thisindicates that while the minimum amount of nitrogenrequired for optimum ethanol production increased withincreasing sugar concentration, the relative carbon tonitrogen ratio also increased. Furthermore, there was amaximum limit on nitrogen supply above which ethanolaccumulation decreased. This nitrogen limit decreased (i.e.,minimum C:N increased) as the sugar supply increased.With regard to maximum yeast biomass accumulations(data not shown), the cultures given with 50, 100, and150 g/l initial xylose reached average A620maxima of 29,43, and 39, respectively, as the amino acids supplied to thecultures reached ~6x, ~6x, and ~2-8x, respectively.Although maximum ethanol accumulation improved, themaximum biomass accumulation was not improved byincreasing xylose concentration above 100 g/l, despiteincreasing amino acid levels up to 15x base concentration;the volumetric ethanol productivity at peak ethanol fellfrom 0.21 to 0.16 to 0.14 g/l/h as xylose increased trom 50to 100 to 150 g/l.

Table 4 Significance (P<0.05) of nutrient group effects on maximum ethanol accumulation by stationary-phaseP stipitis NRRL Y-7124detennined using a complete 23 factorial design to test presence vs absence of amino acids, purines/pyrimidines, and vitamins in BDmedium (Table 1) prepared with 50 g/l xylose and inoculated to A620=20.Numbers in parentheses are comparable values for cultures given50 g/l glucose instead of xylose

Nutrient group P

Maximum ethanol accumulation (g/l)Present Absent

Amino acids

Purines/PyrimidinesVitamins

18.3 (18.1)12.3 (9.9)12.0 (9.1)

5.7 (1.1)11.6 (9.4)11.9 (10.1)

<0.001 «0.001)0.406 (0.397)

0.845 (0.111)

Maximum biomass (A620) Maximum ethanol accumulation (g/l)Vitamin Present Absent P Present Absent P

Thiamine 21.5 19.9 0.204 16.7 16.2 0.567Riboflavin 20.2 21.2 0.431 16.2 16.7 0.541Calcium pantothenate 21.1 20.3 0.541 15.9 17.0 0.232Niacinamide 20.6 20.8 0.822 16.2 . 16.6 0.821Pyridoxamine 20.9 20.5 0.761 16.5 16.4 0.844Thioctic acid 21.6 19.8 0.153 15.9 17.0 0.224Folic acid 20.9 20.5 0.694 16.5 16.4 0.933Biotin 26.3 15.1 <0.001 16.0 16.8 0.544BI2 20.7 20.7 0.988 16.7 16.2 0.531

Page 5: Nitrogen'source and mineral optimization enhance D-xylose

1289

'Concentration of each amino acid is given in parentheses after its name

Combinations of urea and arriino acids maximizedethanol accumulation and productivity

Optimal accumulation of 46 g/l ethanol on 0.15 M nitrogenwas obtained by supplying 80 % of nitrogen as 3.65 g/lurea and 20 % as 2x base amino acids in BD medium(Fig. 2). This was an 11-g/1 higher level of ethanolproduction than observed at optimal 3x to 8x levels ofamino acids with no urea present (Fig. 1). Supplying 100 %of the 0.15 M nitrogen as either amino acids (correspond-ing to lOx base) or urea (4.56 g/l) led to relatively lowethanol accumulations, 23.6 or 11.8 g/l, respectively.Biomass accumulation declined gradually as the percent-age of nitrogen supplied by urea increased, but thevolumetric ethanol productivity (calculated at the time ofpeak ethanol) nevertheless increased from 0.080 g/Vh for100 % of nitrogen from amino acids to 0.19-0.210 g/l/h for40-80 % nitrogen from urea, and then fell to 0.038 g/l/hwhen the percent nitrogen from urea was 100 %.

Minerals significantly impacted biomass and ethanolaccumulations

Iron sulfate, manganese chloride, and magnesium sulfatewere identified as key to maximizing both biomass andethanol production, while calcium chloride and zinc sulfatehad significant impact on either biomass or ethanol

accumulation, respectively (Table 6). The macromineralmagnesium sulfate presence vs absence had the mostprofound effect on both dependent variables. To elucidateoptimum levels of these minerals, four-level concentrationseries were tested including zero, the 5x base control levelslisted in Table 6, and two otherlevels-2.5x and 7.5x, or 1xand 3x in the cases where an inhibitory effect was seen inthe presence/absence testing. However, in BD mediummodified to contain 3x amino acids, lOx biotin, and 150 g/lxylose, only small changes in biomass and ethanolaccumulations were observed as a result of the variationin each mineral series-1 to 6 % improvement in thebiomass accumulation and 0 to 5 % improvement in theethanol compared to that in cultures with minerals atthe control levels. An optimized mineral compositioncompared to that of control cultures was obtained basedfirst on ethanol and then biomass benefit priorities, asfollows: reducing ZnS04 (7H2O) from 11 to 5.5 mg/limproved ethanol accumulation by 0.4 % and biomass by4 %; reducing CoCh (6H2O) from 8 to 1.6 mg/l improvedethanol accumulation by 4 %; decreasing MnCh (4H2O)from 25 to 12.5 mg/l increased ethanol accumulation by5 %; decreasing H3B03 from 6 to 0 mg/l improved ethanoland biomass accumulations both by 1 % (and by 11 and3 %, respectively, in Table 6); increasing MgS04 (7H2O)from 500 to 750 mg/l improved biomass accumulation by6 % with no further improvement to ethanol; andmaintaining the control levels of all other minerals provided

Table 5 Significance (P<0.05) of amino acid effects on biomass and ethanol accumulation by P. stipitis NRRL Y-7124, when initiallyA62o=0.1Oand xylose concentration=50 g/l. The BD medium was applied except that the amino acids below replaced the "amino acidsgroup" given in Table l. The presence of amino acids in the experiment Group I was varied according to the 29 tractional factorial designmatrix when all Group II amino acids were present; then GroupII componentpresence was varied while all Group I amino acids were present

Maximum biomass (A620) Maximum ethanol accumulation (g/I)

Amino acid (mg/lt Present Absent P Present Absent P

Group IAlanine (130) 24.3 25.3 0.033 14.4 13.5 0.014Arginine (185) 25.4 24.1 0.008 14.8 13.1 <0.001Aspartic acid (285) 24.8 24.7 0.835 14.5 13.4 0.005Cystine (15) 24.6 24.9 0.589 14.2 13.7 0.147Glutamic acid (1,000) 23.8 25.7 <0.001 15.2 12.7 <0.001Glycine (50) 24.4 25.1 0.117 14.5 13.4 0.006Histidine (110) 25.3 24.3 0.033 14.5 13.4 0.003Leucine (529) 24.1 25.5 0.006 14.5 13.4 0.004Isoleucine (240) 25.3 24.2 0.026 13.1 14.8 <0.001

Group IILysine (340) 35.4 34.5 0.105 5.41 4.54 0.078Methionine (140) 34.7 35.2 0.345 5.28 4.67 0.179Phenylalanine (275) 35.1 34.9 0.661 5.14 4.82 0.367Proline (485) 36.2 33.5 <0.001 5.47 4.41 0.063Serine (280) 35.1 34.8 0.445 5.31 4.64 0.146Threonine (215) 34.9 35 0.823 4.73 5.27 0.329Tyrosine (220) 34.2 35.8 0.010 5.87 3.95 0.006Tryptophan (110) 34.6 35.3 0.211 4.85 5.12 0.592Valine (310) 35 34.9 0.879 5.52 4.43 0.147

Page 6: Nitrogen'source and mineral optimization enhance D-xylose

1290

Fig. 1 Surface of maximumethanol accumulation byP stipitis NRRL Y-7l24 gener-ated as a function of randomamino acid-biotin variations ofBD medium. Culture maximaoccurred 87, 188, and 210-240 h after inoculation, respec-tively, for initial xylose concen-trations of a 50, b 10O,andc 150 g/l at initial A62o=0.1O

a

351::J]! 30''0c:

~ 251UjE 20:JE'x 151\1~

b

35

::J~ 3010c:~ 25UjE 20:J

.~ 15

~.~ \

10 \u515

Xylose =50 g/L

40

10

12 .9 -

11l11il)oIIciC/ l. 6 3evel/J( ""

I. oClSe)

3025 "-

20 <Q~se\

15 Ne' "'"10 .~"e~\o~

0

Xylose =100 g/L

40

12 -9 -

11l11il)oIIciC/ l. 6 3eVel/J( n

I- oClSe)

30

25 l<Ji:I20 <Q'ti

15 Ne' "'"10 .~"e~\o~

0

optimum product accumulations-50 mg/l FeS04 (7H2O),5 mg/l (NH4)6M07024(4H2O), 8 mg/l CUS04 (5H2O), and28 mg/l CaCh (2H2O).

Minerals interacted with amino acids to boost yeastand ethanol production

production were both functions of a significant three-wayinteractionof minerals,urea, and amino acids (P<O.OOI)(Fig. 3). In the absence of urea, both biomass and ethanolproduction were negligible unless amino acids were addedbecause cell growth required the presence of a nitrogensource. In the presence of urea, biomass and ethanolproductions remained near or at zero, respectively, unlessminerals were added. Both product accumulations weresignificantly improved by the addition of amino acids (at10 % of total nitrogen). The addition of minerals boosted

An analysis of variance conducted on data from a 23 fullfactorial experiment showed that biomass and ethanol

Page 7: Nitrogen'source and mineral optimization enhance D-xylose

Fig. 1 (continued) c

1291

Xylose =150 g/L

40

351:::r

]! 30.'0c:2 25Lii

e 20='e'x 1511!Z

10

accumulations, but significantly greater impact of mineralswas observed when amino acids were absent compared towhen they were present. Regardless of whether urea waspresent or absent, 49 g/l ethanol was accumulated whenboth minerals and amino acids were present. In a follow-upexperiment, it was interesting to find that the significantinteraction of amino acids and the optimized minerals wasagain key to maintaining successful nongrowth-associatedethanol production by stationary-phaseyeast (P<O.OO1)(Fig. 4), allowing a further improved ethanol accumulationof 54 g/l (0.36 g ethanol/g xylose consumed).

Fig. 2 Variationof BD mediumto find the optimum combina-tion of urea and amino acids tomaximize ethanol accumulationby P. stipitis NRRL Y-7124.Cultures were provided initialconditions of A62o=0.1O,150 g/lxylose, lOx base biotin, and100 % nitrogen set at 0.15 M Nas either 4.56 g ureall or lOxbase amino acids

12 9

4fr1if/o 4cicJ l. 6 3

e"e/ (J( Base) 0

Ethanol production improved by combining optimalnitrogen and mineral conditions

Based on the above findings, BD medium (Table 1) wasoptimized for ethanol production on 150 g/l xylose bymaking the following substitutions: 2x base amino acids,including 10 g/l Difco vitamin-free casamino acids, 0.1 g/ltryptophan, 0.4 g/l cysteine, and 3.56 g/l urea to supply C:N 37:1 and 0.15 M N with 20 % N from amino acids;0.0005 g/l biotin (lOx base) for cell production; optimumminerals including 50 mg/l FeS04 (7H2O), 750 mg/lMgS04 (7H2O), 10 mg/l NaCl, 5.5 mg/l ZnS04 (7H2O),1.6 mg/l CoCh (6H2O), 12.5 mg/l MnCh (4H2O), 5 mg/l(NH4)6M07024 (4H2O), 8 mg/l CUS04 (5H2O), 28 mg/lCaCh (2H2O), and 250 mg/l EDTA. All other ingredients

20 30 40 50 60 70 80

80

L60 20

I50

I4070 30

Percent of Total Nitrogen

50

45

40

+35,

0 30('II<0 25<I:E=' 20E'x 15ma

10

5

0L--....L

0 10

L-....L100 90

50

-, 0.5 1

40 +

:20.4 :::J

::J30 'S:

03 :g'0 ::Ic: "0m 0.l::

a:20 w

0.2 '0E c:::I mE .l::'x W

10 m .a 0.1a;E='

0 J 0.0 g90 100 Urea

-L--..J Amino10 0 Acids

Page 8: Nitrogen'source and mineral optimization enhance D-xylose

1292

Table 6 Significance of mineral effects on maximum biomass and ethanol accumulation by P. stipitis NRRL Y-7124 (P<0.05). A 29fractional factorial design was applied to test the benefit of adding each mineral to culturesinitially providedA62o:::0.10andBD mediumwith 150 g/l xylose, 3x base amino acids, lOx base biotin, and the following minerals at 5x base

"The mineral concentration is given in parentheses after its formula

(buffer, purines and pyrimidines, and vitamins) are thesame as in Table 1 for BD medium. Given these nutrients,maximum (::!:SD)biomass reached 25::!:6absorbance units(620 nm) (or 4.2::!:1g dry cells/I); maximum ethanolaccumulation averaged 61::!:9g/l with a yield of 0.41::!:0.06 gig xylose consumed; and the volumetric ethanolproductivity at the time of peak ethanol averaged 0.38::!:0.06 g/l/h across four replicate fermentations supplied with150 g/l xylose.

Urea=0

~ 60~~ 50'0

~ 40J:W 30

§ 20

.~ 10co:; 0

~0 "5X"

Minerals Level1Amino Acids = 0 --- Amino Acids = 3X1:i' 60t;,~ 50'0~ 40~ 30E 20'".5 10><:!¥ 0

Urea =15 g/L

...

0 "5X"Minerals Level

I Amino Acids = 0 ---Amino Acids= 3X 1

a

Fig. 3 Dependence of P. stipitis NRRL Y-7124 a ethanol andb biomass production on the significant interactionof amino acids xminerals in the absence or presence of urea. Effects of urea, aminoacids, and minerals were studied using a 23 factorial design andinitial conditions ofA62o=0.1O,150 g/l xylose, and BD medium with

Discussion

Nitrogen is required for nongrowth-associated ethanolproduction

The notable finding of a strict nitrogen requirement fornongrowth-associated ethanol production by stationary-phase P. stipitis was unexpected (Table 4, Fig. 4). Noethanol was produced from xylose or glucose when a

Urea =0

'" 60~ 50E.2 ~ 4010°E ~ 30",<E ~ 20'x~ 10

0

~.......

0 "5X"

Minerals level

1-.- Amino Acids = 0 --II-- Amino Acids = 3X I

Urea=15 g/L

'" 60'"~ 50

~6.40E ~30" <E ~20.~ 10:; 0

-II--

0 "5X"Minerals Level

1-.- AminoAcids = 0 --II-- AminoAcids = 3X1b

lOx base biotin. Presence/absence of 3x base amino acids in BDmedium (Table 1) and 5x base minerals (Table 6) were tested. Pointsplotted represent means of duplicate cultures generated by three-wayANOVA. Nonparallel lines indicate a significant interaction(P<0.05)

Maximum biomass (A620) Maximum ethanol (g/l)Mineral (mg/l)a Present Absent P Present Absent P

FeS04[7H2O] (50) 33.5 27.1 0.021 34.5 20.1 <0.001ZnS04[7H2O] (11) 32.8 27.9 0.069 31.6 23 0.004CoCI216H2O](8) 28.4 32.3 0.147 28.4 26.3 0.452MnCI2[4H2O](25) 36.8 23.8 <0.001 32.2 22.5 0.002(NH4)6Mo7024[4H2O](5) 32.2 28.5 0.167 28.3 26.3 0.464CuS04[5H2O] (8) 28.2 32.4 0.114 28.3 26.3 0.474CaCI2[2H2O](28) 34.9 25.7 0.002 29.2 25.5 0.189H3B03 (6) 29.9 30.7 0.775 25.9 28.7 0.312MgS04[7H2O] (500) 47.4 13.2 <0.001 44.1 10.5 <0.001

Page 9: Nitrogen'source and mineral optimization enhance D-xylose

nitrogen source was absent even though a large stationary-phase yeast population was present and able to function toproduce ethanol once nitrogen was added. The additions ofvitamins, purines and pyrimidines, and minerals did notalleviate this nitrogen requirement. The Saccharomycesliterature teaches that amino nitrogen enhances fermenta-tion through increased growth and cell numbers, but thatthe use of high cell densities (high pitching rates)eliminates need for nitrogen supplementation to obtainrapid fermentation rates (O'Connor-Cox and Ingledew1991; Thomas and Ingledew 1990). It is well known thatlarge immobilized populations of Saccharomyces cerevisiaeand xylose-fermenting Pachysolen tannophilus NRRLY-2460 are able to continuously produce ethanol fromnitrogen-free feed streams containing only 1.2 g/l KH2P04,0.5 g/l MgS04, 3.0 g/l CaCI, and 50-100 g/1of glucose orxylose (see, for example, Slininger et al. 1982; Slininger andBothast 1988, and others). A significant level of mainte-nance ethanol productivity has been observed in continuousculture studies of P stipitis, and data support ethanolproductivity models which include both growth-associatedand nongrowth-associated production terms (Slininger et al.1990b). Our current findings show that this yeast still needsa nitrogen source to support nongrowth-associated mainte-nance ethanol production. The reason for this nitrogenrequirement by P stipitis and not by other yeasts, includingother pentose-fermenting yeasts, is not known, but worthyof further investigation.

Carbon to nitrogen ratio impacts ethanol accumulation

An optimum carbon to nitrogen ratio range was observed,which increased somewhat with the xylose concentrationsupplied. The C:N ratio in the vicinity of ~57:l to ~126:lencompassed optimum ethanol accumulation for the xylosesupplied in the 50-150 g/l range. Xylose uptake andethanol accumulation were dependent on nitrogen avail-ability though the ethanol yield remained around 0.35 gigin this experiment. Insufficient or very excessive nitrogenled to residual xylose and lower ethanol accumulation. Theexistence of a maximum nitrogen supply may be the resultof osmotic inhibition by the combined nitrogen and xyloseconcentrations (see Slininger et al. 1990b, 1991 on xyloseinhibition). The limitation of xylose uptake and ethanolaccumulation at the lower amino acid concentrations mayrelate to the balance of C and N needed to support growthand ethanol production with a favorable redox balance.Aon and Cortassa (2001) have presented evidence that inSaccharomyces, the trigger for ethanol production isglucose flux rate, which is dependent on the kind ofnitrogen available and the C:N ratio. The nitrogen sourceand C:N ratio are involved in setting the anabolic andcatabolic fluxes. In our system, if low nitrogen concentra-tion limits the C and N flux rates, then the trigger forethanol production may not be reached. Alternatively, thetrigger may be reached, but for Y-7l24, ethanol productionwould be cut short when the nitrogen source is gone even ifxylose still remains.

1293

Need for amino acids and urea, not just -NH2,is demonstrated

In other pentose fermentation studies, it has been reportedthat C. shehatae and P stipitis strains are unable to usenitrate, but that nitrogen sources such as yeast extract,peptone, and casamino acids stimulate ethanol production(Prior et al. 1989; Tran and Chambers 1986; Dellweg et al.1984; Du Preez et al. 1984; Jeffries 1986). Comparativeenzyme induction in the presence of ammonia, urea, aminoacids, and peptone indicated that organic sources of -NH2were generally superior to ammonia in supporting enzymeinductions (Jeffries et al. 1986).

Several of our experiments indicated that amino acidsplaya greater role in improving ethanol productivity thanmerely as a source of amino nitrogen (-NH2). Urea as soleamino nitrogen source allowed ethanol accumulations ofabout half of that when amino acids were supplied alone,but a quarter of that when nitrogen was optimally supplied80 % by urea and 20 % by amino acids (Fig. 2). Whilemany of the individual amino acids improved growth and!or ethanol production, no single amino acid was anabsolute requirement for either growth or ethanol produc-tion in the presence of other amino acids to supply nitrogen(Table 5), suggesting that amino acids are used in diverseapplications in the cell and that P stipitis is able to use themdirectly in protein building or to break them down ormodify them for use in other nitrogenous compounds asneeded. Girbes and Parrilla (1986) showed that thesensitivity of different yeast strains to ethanol may be aresult of perturbation of nutrient (sugar and amino acids)transport systems and may also be dependent on the proteinsynthetic machinery (Girbes and Parrilla 1983). Thus, asupply of amino acids would help to alleviate theseproblems. However, aside from supplying nitrogen andbuilding proteins, there are numerous reports in theliterature that amino acids may function in other ways toprotect cells against various stress factors that wouldreduce ethanol production capacity.

Studies of Mauricio et al. (2001) with S. cerevisiae havesuggested that amino acids may be used not only asnitrogen sources, but also as redox agents to balance theoxidation-reduction potential under conditions of restrictedoxygen, when electron transport along the respiratory chainmay be hindered. For example, when amino acids areabundant, excess NAD(P)H could be produced by degra-dation of L-proline, or L-arginine might be oxidized in theformation of higher alcohols from ketoacids of thecorresponding amino acids. In amino acid-deficient mustor wine, excess NAD(P)H from the biosynthesis of aminoacids could be diverted to the production of specific aminoacids, such as L-threonine, L-cysteine, L-methionine, andL-tryptophan, which could regenerate NAD(P)+ as a result.

Another interesting function of proline is indicated byChen and Dickman (2005) who showed that prolinesuppresses apoptotic-like death in the fungal pathogenColletotrichum trifolii and have related this behavior toproline's potential ability to scavenge intracellular reactiveoxygen species (ROS) and thereby inhibit ROS-mediated

Page 10: Nitrogen'source and mineral optimization enhance D-xylose

1294

60

::I:g 50

g 40'".s:W 30

E

E 20'x

:e 10

~0

0 Optimum

Minerals Level

I-.lr-Amino Acids = 0 -ll-Amino Acids = 3X 1

Fig. 4 Dependenceof ethanolaccumulationof stationary-phaseP. stipitis NRRLY-7l24 on the significant interactionof aminoacids x minerals. Independent variables were studied using a 22factorial design in cultures with initial conditions A620=20,150 g/lxylose, and BD medium with lOx base biotin. Presence/absence of3x base amino acids in BD medium (Table 1) and optimizedminerals were tested. Points plotted represent means of duplicatecultures generated by two-way ANOVA.Nonparallel lines indicatea significant interaction (P<0.05)

apoptosis. In addition to its well-established role as anosmolyte, proline's function as a potent antioxidant andinhibitor of programmed cell death could explain its broad-based function in responding to cellular stresses thatproduce ROS, such as cold, heat, salt, drought, UV, andheavy metals.

The abilities to act as redox agents and as ROSscavengers may allow amino acids to protect P. stipitisfrom oxidation/reduction imbalance and cellular stressfactors imposed in xylose fennentations. In fennentation ofacid hydrolyzates of biomass, amino acids may similarlyguard cells against redox imbalance and ROS damageoccurring from exposure to furfural and 5-hydroxymethyl-furfural and the subsequent detoxification reactions whichconsume reducing equivalents. Gorsich et al. (2006)showed that the NADH-mediated conversion of furfuralto less- toxic furfuryl alcohol was dependent on a fullyfunctional pentose phosphate pathway in S. cerevisiaewhich could supply reducing equivalents. A similarcircumstance in yeasts occurs with the NADPH-mediateddetoxification of 5-hydroxymethylfurfural by conversionto 2,5-bis-hydroxymethylfuran in yeasts (Liu et al. 2004,2005).

Interactionof mineralswith urea and aminoacidsoptimizesethanolproduction

In our experiments, several minerals, particularly thosesupplying magnesium, iron, zinc, manganese, and calcium,were found to have significant benefit to yeast biomass andor/ethanol productivity, with magnesium having the mostprofound effect. Adding unoptimized minerals to definedmedium with casamino acids nitrogen source resulted in adoubling of ethanol (24 to 49 g/l) and biomass accumula-tions, while adding them to defined medium with urea wascrucial to obtain any significant growth and ethanolproduction (Fig. 3). When optimal mineral levels were

established and applied, a significant interaction ofmineralswith aminoacidswasobservedto further improveethanol accumulations of nongrowing stationary-phasecells by a factor of 2.3 from 24 to 54 g/l, suggesting thatthere was a notable benefit attributable to the mineraloptimization (Fig. 4) and also that the minerals are key toethanol production itself and not just to yeast growth. It isalso interesting to note that mineral supplementation hadless impact on ethanol accumulation in cultures withcombined urea and amino acids (90 % N from urea, 10 % Nfrom amino acids) than in cultures with one or the othernitrogen source alone (Fig. 3a).

The impact of magnesium on ethanol production byS. cerevisiae has been well documented. Dombek andIngram (1986) have shown that supplementing S. cerevi-siae fennentations with magnesium at a level of 0.5 mMprolonged exponential growth, increased yeast cell massaccumulation, and reduced the decline in fennentation rateduring the completion of batch fennentations. Thomas andIngledew (1990) postulated that Mg was a key element inyeast extract responsible for its efficacy in enhancingethanol yield in addition to amino acid and vitamin content.Our finding of750 mg/l MgS04 (7H2O)(4 mM Mg) as theoptimum .level for growth and ethanol production agreeswith that previously reported by Mahler and Guebel(1994).

Implications for medium design and future work

In their review of the literature on natural xylose-fennenting yeasts, Prior et al. 1989 point out that theefficacy of xylose conversion to ethanol is influenced bynutritional factors including vitamins and nitrogen sources,but that this dependence varies dramatically by genus andspecies (c. shehatae, P. stipitis, and P. tannophilus) andeven by strain within the same genus and species. Forexample, we have found that P. stipitis Y-7124 needsvitamins (particularly biotin) for growth but not ethanolproduction. Others have found that P. tannophilus IfGB0101 required only biotin and thiamine for growth, whileP. stipitis strain 5776 required neither (Dellweg et al. 1984).C. shehatae CSIR-Y492 required both biotin and thiaminefor optimal fennentation of xylose while P. stipitis CSIR-Y633 also benefited from the addition of these vitamins(Du Preez et al. 1985, 1986). Maximum specific growthrate of P. stipitis CSIR-Y633 was not impacted by vitaminsbeing present or absent, although biotin significantlyincreased the growth rate of C. shehatae CSIR-Y492 (DuPreez et al. 1985, 1986). Such diversity of nutrientrequirements implies that optimization of individual strainsis needed to design an appropriate defined medium forexperimental applications or to pursue an economicalcomplex medium for commercial consideration.

Having detennined the nutrient requirements ofP. stipitis Y-7124, it is possible to search industrial supplierdatabases to detennine potential low-cost complex mediaingredients for further perfonnance testing. For example,Kadam and Newman (1997) showed that a low-cost

Page 11: Nitrogen'source and mineral optimization enhance D-xylose

medium of 0.3 % com steep and 2.5 mM MgS04 (7H2O)(at $0.5/1,000 1)was similar in performance to a nutrient-rich medium containing yeast extract and peptone (at$27.86/1,000 1)for the fermentation of biomass to ethanolby S. cerevisiae DsA. More importantly, knowledge of thenutritional requirements of P stipitis Y-7124 will be ofgreat value in designing defined experiments aimed atstrain improvement to further optimize this importantbiocatalyst. The unique nutritional dependencies reportedfor biomass and ethanol production are expected to impactfuture investigations. For example, genome-wide micro-array experiments are expected to be useful in trouble-shooting metabolic bottlenecks, which are known to beinfluenced by nutrition, and also to investigate mechanismsby which yeasts are able to tolerate stress factors, such ashigh ethanol concentrations and biomass hydrolyzateinhibitors, including furfural and 5-hydroxymethylfurfural.As implied by our research results in the context of theavailable literature, nutritional components, such as aminoacids and minerals, may play key roles in yeast stresstolerance.

Acknowledgements We thank Maureen Shea-Andersh and LindaEricsson for their excellent technical assistance.

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Peoria, Illinois