Identification and characterization of starch and inulin modifying network of Aspergillus niger by functional genomics
Yuan, X.L.
Citation
Yuan, X. L. (2008, January 23). Identification and characterization of starch and inulin modifying network of Aspergillus niger by functional genomics.
Institute of Biology Leiden (IBL), Group of Molecular Microbiology, Faculty of Science, Leiden University. Retrieved from
https://hdl.handle.net/1887/12572
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
Downloaded from: https://hdl.handle.net/1887/12572
Note: To cite this publication please use the final published version (if
applicable).
References
AkacheB,WuK,TurcotteB(2001)Phenotypicanalysisofgenesencodingyeastzincclusterproteins.
NucleicAcidsRes29:21812190
Akimoto H, Kushima T, Nakamura T, Ohta K (1999) Transcriptional analysis of two endoinulinase
genesinuAandinuBinAspergillusnigerandnucleotidesequencesoftheirpromoterregions.
JBiosciBioeng88:599604
AkimotoH,KiyotaN,KushimaT,NakamuraT,OhtaK(2000)Molecularcloningandsequenceanalysis
of an endoinulinase gene from Penicillium sp. strain TN88. Biosci Biotechnol Biochem
64:23282335
Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M (2004) The threedimensional crystal
structure of invertase (fructosidase) from Thermotoga maritima reveals a bimodular
arrangementandanevolutionaryrelationshipbetweenretainingandinvertingglycosidases.
JBiolChem279:18903–18910
Alberto F, Jordi E, Henrissat B, Czjzek M (2006) Crystal structure of inactivated Thermotoga maritima
invertaseincomplexwiththetrisaccharidesubstrateraffinose.Biochem.J.395:457462
ArandM,GolubevAM,NetoJR,PolikarpovI,WattiezR,KorneevaOS,EneyskayaEV,Kulminskaya
AA, Shabalin KA, Shishliannikov SM, Chepurnaya OV, Neustroev KN (2002) Purification,
charaterization,genecloningandpreliminaryXraydataoftheexoinulasefromAspergillus
awamori.BiochemistryJournal362:131135
ArcherDB,PeberdyJF(1997)Themolecularbiologyofsecretedenzymeproductionbyfungi.CritRev
Biotechnol.17(4):273306
ArguellesJC(2000)Physiologicalrolesoftrehaloseinbacteriaandyeasts:acomparativeanalysis.Arch
Microbiol174:217224
AsconeI,LenouvelF,SequevalD,DexpertH,FelenbokB(1997)Firstexperimentalevidenceofazinc
binuclearclusterinAlcRprotein,mutationalandXrayabsorptionstudies.BiochimBiophys
Acta.1343(2):211220
BaneyxF(1999)RecombinantproteinexpressioninEscherichiacoli.CurrOpinBiotechnol.10:411421
Bardalaye PC, Nordin JH (1977) Chemical structure of the galactomannan from the cell wall of
Aspergillusniger.J.Biol.Chem.252:25842591
BarkerSA,CarringtonTR(1953)StudiesofAspergillusniger.PartII.TransglycosylationbyAspergillus
niger.JChemSoc1953:35883593
Baker SE (2006) Aspergillus niger genomics: past, present and into the future. Med Mycol. 44: Suppl
1:S1721.Review
BauerS,VasuP,PerssonS,MortAJ,SomervilleCR(2006)Developmentandapplicationofasuiteof
polysaccharidedegradingenzymesforanalyzingplantcellwalls.ProcNatlAcadSciUSA
103:1141711422
BeauvaisA,LatgéJP(2001)MembraneandcellwalltargetsinAspergillusfumigatus.DrugResistUpdat
4:3849
BeauvaisA,MaubonD,ParkS,MorelleW,TanguyM,HuerreM,PerlinDS,LatgeJP(2005)Twoalpha
(13) glucan synthases with different functions in Aspergillus fumigatus. Appl. Environ.
Microbiol.71:15311538
BendtsenJD,NielsenH,VonHeijneG,BrunakS(2004)Improvedpredictionofsignalpeptides:SignalP
3.0.JMolBiol340:783795
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S (2004) Featurebased prediction of
nonclassicalandleaderlessproteinsecretion.ProteinEngDesSel17:349356
Benen JA, Kester HC, Visser J (1999) Kinetic characterization of Aspergillus niger N400
endopolygalacturonasesI,IIandC.Eur.J.Biochem.259:577585
Bennet JW, Lasure LL (1991) Growth media. In: Bennet JW and Lasure LL (eds) More gene
manipulationsinfungi.AcademicPress,SanDiego,pp.441447
BennettJW,LasureLL(1991)Moregenemanipulationsinfungi.AcademicPress,SanDiego
BergerH,PachlingerR,MorozovI,GollerS,NarendjaF,CaddickM,StraussJ(2006)TheGATAfactor
AreAregulateslocalizationandinvivobindingsiteoccupancyofthenitrateactivatorNirA.
MolMicrobiol.59(2):433446
Berges T, Barreau C, Peberdy JF, Boddy LM (1993) Cloning of an Aspergillusniger invertase gene by
expressioninTrichodermareesei.CurrGenet24:5359
Berka RM, DunnColeman NS, Ward M (1992) Industrial enzymes from Aspergilli. In: Bennett JW,
Klich MA (eds) Aspergillus, biology and industrial applications. ButterworthHeinemann,
London,pp155202
BhattiHN,AsgherM,AbbasA,NawazR,SheikhMA(2006)Studiesonkineticsandthermostabilityof
anovelacidinvertasefromFusariumsolani.J.Agric.FoodChem.54:46174623
BigelisRandLasureLL(1987)Fungalenzymesandprimarymetabolitesusedinfoodprocessing.In:
Food and beverage mycology. Beuchat, L.R (ed.) Van Nostrand Reinhold, New York, USA,
pp473516
BirneyE,ClampM,DurbinR(2004)GeneWiseandGenomewise.GenomeRes14:988995
BlumenthalHJ,RosemanS(1957)Quantitativeestimationofchitininfungi.J.Bacteriol.74:222224
Bobbitt TF, Nordin JH, Roux M, Revol JF, Marchessault RH (1977) Distribution and conformation of
crystalline nigeran in hyphal walls of Aspergillusniger and Aspergillusawamori. J. Bacteriol.
132:691703
Boddy LM, Berges T, Barreau C, Vainstein C, Dobson MJ, Balance DJ, Peberdy JF (1993) Purification
and characterization of an Aspergillus niger invertase and its DNA sequence. Curr Genet
24:6066
BoelE,BradyL,BrzozowskiAM,DerewendaZ,DodsonGG,JensenVJ,PetersenSB,SwiftH,ThimL,
Woldike HF (1990) Calcium binding in alphaamylases: an Xray diffraction study at 2.1A
resolutionoftwoenzymesfromAspergillusnigerBiochemistry29(26):62446249
Boel E, Hjort I, Svensson B, Norris F, Norris KE, Fiil NP (1984) Glucoamylases G1 and G2 from
Aspergillus nigerare synthesized from two different but closely related mRNAs. EMBO J
3:10971102
BorkovichKA,AlexLA,YardenO,FreitagM,TurnerGE,ReadND,SeilerS,BellPedersenD,PaiettaJ,
Plesofsky N, Plamann M, GoodrichTanrikulu M, Schulte U, Mannhaupt G, Nargang FE,
Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H,
AramayoR,PolymenisM,SelkerEU,SachsMS,MarzlufGA,PaulsenI,DavisR,EbboleDJ,
ZelterA,KalkmanER,ORourkeR,BowringF,YeadonJ,IshiiC,SuzukiK,SakaiW,PrattR
(2004)LessonsfromthegenomesequenceofNeurosporacrassa:tracingthepathfromgenomic
blueprinttomulticellularorganism.MicrobiolMolBiolRev68:1108.Review
Bos CJ, Debets AJ, Swart K, Huybers A, Kobus G, Slakhorst SM (1988) Genetic analysis and the
construction of master strains for assignment of genes to six linkage groups in Aspergillus
niger.CurrGenet14:437443
BradyRL,BrzozowskiAM,DerewendaZS,DodsonEJ,DodsonGG(1991)Solutionofthestructureof
Aspergillus niger acid alphaamylase by combined molecular replacement and multiple
isomorphousreplacementmethods.ActaCrystallogrB.47:527535
Brul S, King A, van der Vaart JM, Chapman J, Klis F, Verrips CT (1997) The incorporation of
mannoproteins in the cell wall of S. cerevisiae and filamentous Ascomycetes. Antonie Van
Leeuwenhoek72:229237.
Buckholz RG, Gleeson MA (1991) Yeast systems for the commercial production of heterologous
proteins.Biotechnology(NY).9(11):1067–1072
BurgerG,StraussJ,ScazzocchioC,LangBF(1991)nirA,thepathwayspecificregulatorygeneofnitrate
assimilation in Aspergillus nidulans, encodes a putative GAL4type zinc finger protein and
containsfourintronsinhighlyconservedregions.MolCellBiol11:57465755
Cahuzac B, Cerdan R, Felenbok B, Guittet E (2001) The solution structure of an AlcRDNA complex
sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein.
Structure9(9):827836
Cairns,A.J.(2003).Fructanbiosynthesisintransgenicplants.JExpBot54,549567
CareyM,KakidaniH,LeatherwoodJ,MostashariF,PtashneM(1989)Anaminoterminalfragmentof
GAL4bindsDNAasadimer.JMolBiol.209(3):423432
Carpita NC, Kanabus J, Housley TL (1989) Linkage structure of fructans and fructan oligomers from
TriticumaestivumandFestucaarundinaceaeleaves.JPlantPhysiol134:162168
Cazelle B, Pokorska A, Hull E, Green PM, Stanway G, Scazzocchio C (1998) Sequence, exonintron
organization, transcription and mutational analysis of prnA, the gene encoding the
transcriptionalactivatoroftheprngeneclusterinAspergillusnidulans.MolMicrobiol28:355
370
Chang CT, Lo HF, Chi MC, Yao CY, Hsu WH, Lin LL (2003) Identification of essential histidine
residues in a recombinant alphaamylase of thermophilic and alkaliphilic Bacillussp. strain
TS23.Extremophiles7:505509
Chavez FP, Pons T, Delgado JM, Rodriguez L (1998) Cloning and sequence analysis of the gene
encodinginvertase(INV1)fromtheyeastCandidautilis.Yeast14,12231232
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple
sequencealignmentwiththeClustalseriesofprograms.NucleicAcidsRes31:34973500
Chiou CY,WangHH,ShawGC(2002)Identificationand characterizationofthenonPTSfrulocusof
BacillusmegateriumATCC14581.MolGenetGenomics268:240248
Christgau S, Sandal T, Kofod LV, Dalboge H (1995) Expression cloning, purification and
characterizationofabeta1,4galactanasefromAspergillusaculeatus.CurrGenet.27(2):135141
Coussement PAA (1999) Inulin and oligofructose: safe intakes and legal status. J. Nutr. 129:1412S
1417S
Coutinho PM, Henrissat B (1999) Carbohydrateactive enzymes: an integrated database approach. In:
Gilbert HJ, Davies GJ, Henrissat B, Svensson B (eds) Recent Advances in Carbohydrate
Bioengineering.TheRoyalSocietyofChemistry,Cambridge,pp.312
CrabeelM,deRijckeM,SenecaS,HeimbergH,PfeifferI,MatisovaA(1995)Furtherdefinitionofthe
sequenceandpositionrequirementsoftheargininecontrolelementthatmediatesrepression
andinductionbyarginineinSaccharomycescerevisiae.Yeast11:13671380
Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome
Res.14:11881190
Cubero B, Scazzocchio C (1994) Two different, adjacent and divergent zinc finger binding sites are
necessary for CREAmediated carbon catabolite repression in the proline gene cluster of
Aspergillusnidulans.EMBOJ.13:407415
Da Silva NA, Bailey JE (1991) Influence of plasmid origin and promoter strength in fermentations of
recombinantyeast.BiotechnologyandBioengineering37:318324
DalbøgeH,HeldtHansenHP(1994)Anovelmethodforefficientexpressioncloningoffungalenzyme
genes.MolGenGenet.243:253260
DamveldRA,VankuykPA,ArentshorstM,KlisFM,vandenHondelCA,RamAF(2005)Expressionof
agsA,oneoffive1,3alphadglucansynthaseencodinggenesinAspergillusniger,isinduced
inresponsetocellwallstress.FungalGenetBiol42:165177
Damveld RA, Arentshorst M, VanKuyk PA, Klis FM, van den Hondel CA, Ram AF (2005)
Characterisation of CwpA, a putative glycosylphosphatidylinositolanchored cell wall
mannoproteininthefilamentousfungusAspergillusniger.Fungal.Genet.Biol.42:873885
DarwenCWE,JohnP(1989)Localisationoftheenzymesoffructanmetabolisminvacuolesisolatedby
a mechanical method from tubers of Jerusalem artichoke (Helianthus tuberosus L.) Plant
Physiol89:658663
Davies RW (1994) Heterologous gene expression and protein secretion in Aspergillus niger. Prog Ind
Microbiol.29:527560.Review
Davies GJ, Wilson KS, Henrissat B (1997) Nomenclature for sugarbinding subsites in glycosyl
hydrolases.Biochem.J.321:557559
DeGrootPW,HellingwerfKJandKlisFM(2003)GenomewideidentificationoffungalGPIproteins.
Yeast20:781796
deRuiterJacobsYM,BroekhuijsenM,UnklesSE,CampbellEI,KinghornJR,ContrerasR,PouwelsPH,
vandenHondelCA(1989)AgenetransfersystembasedonthehomologouspyrGgeneand
efficientexpressionofbacterialgenesinAspergillusoryzae.CurrGenet16:159163
DeVriesRP(2003)RegulationofAspergillusgenesencodingplantcellwallpolysaccharidedegrading
enzymes;relevanceforindustrialproduction.ApplMicrobiolBiotechnol.61:10–20
deVriesRP,FrisvadJC,vandeVondervoortPJ,BurgersK,KuijpersAF,SamsonRA,VisserJ(2005a)
Aspergillus vadensis, a new species of the group of black Aspergilli. Antonie Van
Leeuwenhoek.87(3):195203
de Vries, R. P., van Grieken, C., van Kuyk, P. A. & Wösten, H. A. B. (2005b). The value of genome
sequences in the rapid identification of novel genes encoding specific plant cell wall
degradingenzymes.CurrGenom6,157187
De Vries RP, Visser J (2001) Aspergillus enzymes involved in degradation of plant cell wall
polysaccharides.MicrobiolMolBiolRev65:497522
denHerderIF,RosellAM,vanZuilenCM,PuntPJ,vandenHondelCA(1992)Cloningandexpression
of a member of the Aspergillus niger gene family encoding alphagalactosidase. Mol Gen
Genet233:404410
Diep CQ, Peng G, Bewley M, Pilauri V, Ropson I, Hopper JE (2006) Intragenic suppression of Gal3C
interactionwithGal80intheSaccharomycescerevisiaeGALgeneswitch.Genetics.172(1):7787
DowzerCE&KellyJM(1991)AnalysisofthecreAgene,aregulatorofcarboncataboliterepressionin
Aspergillusnidulans.MolCellBiol.11:57015709
Drysdale MR, Kolze SE, Kelly JM (1993) The Aspergillus niger carbon catabolite repressor encoding
gene,creA.Gene130:241245
Duarte JC, CostaFerreira M (1994) Aspergilli and lignocellulosics: enzymology and biotechnological
applications.FEMSMicrobiol.Rev.13:377386
Durbin R, Eddy S (1998) Biological Sequence analysis: Probabilistic Models of Proteins and Nucleic
acids. A tutorial introduction to hidden Markov models and other probabilistic modeling
approachesincomputationalsequenceanalysis.CambridgeUniversityPress,Cambridge
EddySR(1998)ProfilehiddenMarkovmodels.Bioinformatics14:755763
Eisenhaber B, Schneider G, Wildpaner M, Eisenhaber F (2004) A sensitive predictor for potential GPI
lipid modification sites in fungal protein sequences and its application to genomewide
studiesforAspergillusnidulans,Candidaalbicans,Neurosporacrassa,Saccharomycescerevisiaeand
Schizosaccharomycespombe.JMolBiol337:243253
El Alami M, Feller A, Pierard A, Dubois E (2000) Characterization of a tripartite nuclear localization
sequenceintheregulatoryproteinLys14ofSaccharomycescerevisiae.CurrGenet38:7886
EspesoEA,TilburnJ,SanchezPulidoL,BrownCV,ValenciaA,ArstHNJr,PenalvaMA(1997)Specific
DNArecognitionbytheAspergillusnidulansthreezincfingertranscriptionfactorPacC.JMol
Biol.274(4):466480
FakhouryAM,WoloshukCP(1999)Amy1,thealphaamylasegeneofAspergillusflavus:Involvementin
aflatoxinbiosynthesisinmaizekernels.Phytopathology89:908914
FelenbokB,FlipphiM,NikolaevI(2001)EthanolcatabolisminAspergillusnidulans:amodelsystemfor
studyinggeneregulation.ProgNucleicAcidResMolBiol.69:149204.Review
Fillinger S, Felenbok B (1996) A newly identified gene cluster in Aspergillus nidulans comprises five
novelgeneslocalizedinthealcregionthatarecontrolledbothbythespecifictransactivator
AlcRandthegeneralcarboncataboliterepressorCreA.MolMicrobiol.20:47588
Flipphi M, Kocialkowska J, Felenbok B (2002) Characteristics of physiological inducers of the ethanol
utilization(alc)pathwayinAspergillusnidulans.BiochemJ.364:2531
Flynn PJ, Reece RJ (1999) Activation of transcription by metabolic intermediates of the pyrimidine
biosyntheticpathway.MolCellBiol19:882888
FontaineT,SimenelC,DubreucqG,AdamO,DelepierreM,LemoineJ,VorgiasCE,DiaquinM,Latgé
JP (2000) Molecular organization of the alkaliinsoluble fraction of Aspergillusfumigatus cell
wall.JBiolChem275:41528
FowlerT,BerkaRM,WardM(1990)RegulationoftheglaAgeneofAspergillusniger.CurrGenet18:537
545
FranckA(2002)Technologicalfunctionalityofinulinandoligofructose.Br.J.Nutr.87Suppl2:S287291
Frost GM, Moss DA (1987) Production of enzymes by fermentation. In: Rehm HJ, Reed G (eds)
Biotechnology,vol7a.VCH,Weinheim,pp65102
GalaganJE,CalvoSE,CuomoC,MaLJ,WortmanJR,BatzoglouS,LeeSI,BasturkmenM,SpevakCC,
ClutterbuckJ,KapitonovV, JurkaJ,ScazzocchioC,FarmanM, ButlerJ, PurcellS,HarrisS,
Braus GH, Draht O, Busch S, dEnfert C, Bouchier C, Goldman GH, BellPedersen D,
GriffithsJones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB,
Penalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman
WC,DenningDW,CaddickM,HynesM,PaolettiM,FischerR,MillerB,DyerP,SachsMS,
Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis
withA.fumigatusandA.oryzae.Nature438:11051115
Gangwani L, Mikrut M, GalchevaGargova Z, Davis RJ (1998) Interaction of ZPR1 with translation
elongationfactor1alphainproliferatingcells.JCellBiol143:14711484
Gascon, S. and J. O. Lampen. 1968. Purification of the internal invertase of yeast. J. Biol. Chem.
243:15671572
GasconS,NeumannNP,LampenJO(1968)Comparativestudyofthepropertiesofthepurifiedinternal
andexternalinvertasesfromyeast.J.Biol.Chem.243:15731577
Geber A, Williamson PR, Rex JH, Sweeney EC, Bennett JE (1992) Cloning and characterization of a
Candidaalbicansmaltasegeneinvolvedinsucroseutilization.JBacteriol174:69926996
Gellissen G, Melber K, Janowicz ZA, Dahlems UM, Weydemann U, Piontek M, Strasser AW,
HollenbergCP(1992)Heterologousproteinproductioninyeast.AntonieVanLeeuwenhoek.
62(12):7993.Review
GeysensS,PakulaT,UusitaloJ,DewerteI,PenttilaM,ContrerasR(2005)Cloningandcharacterization
oftheglucosidaseIIalphasubunitgeneofTrichodermareesei:aframeshiftmutationresultsin
the aberrant glycosylation profile of the hypercellulolytic strain RutC30. Appl Environ
Microbiol71:29102924
Gielkens MM, Dekkers E, Visser J, de Graaff LH (1999) Two cellobiohydrolaseencoding genes from
AspergillusnigerrequireDxyloseandthexylanolytictranscriptionalactivatorXlnRfortheir
expression.ApplEnvironMicrobiol65:43404345
GomezD,CuberoB,CecchettoG,ScazzocchioC(2002)PrnA,aZn2Cys6activatorwithauniqueDNA
recognitionmode,requiresinducerforinvivobinding.MolMicrobiol44:585597
GomiK,AkenoT,MinetokiT,OzekiK,KumagaiC,OkazakiN,IimuraY(2000)Molecularcloningand
characterization of a transcriptional activator gene, amyR, involved in the amylolytic gene
expressioninAspergillusoryzae.BiosciBiotechnolBiochem.64(4):81627
GoosenC,YuanXL,vanMunsterJM,RamAF,vanderMaarelMJ,DijkhuizenL(2007)Molecularand
biochemical characterization of a novel intracellular invertase from Aspergillus niger with
transfructosylatingactivity.EukaryotCell6:674681
Gouka RJ, Hessing JG, Stam H, Musters W, van den Hondel CA. (1995) A novel strategy for the
isolationofdefinedpyrGmutantsandthedevelopmentofasitespecificintegrationsystem
forAspergillusawamori.CurrGenet.27(6):536540.
GrassinC,FauguenbergueP(1999)Enzymes,fruitjuiceprocessing.In:FlickingerMC,DrewSW(eds)
Encyclopediaofbioprocesstechnology:fermentation,biocatalysis,andbioseparation.Wiley
&Sons,Inc,NewYork
GronenbornAM(2005)TheDNAbindingdomainofGATAtranscriptionfactorsaprototypicaltype
IV Cys2Cys2 Zinc finger. In zinc finger proteins: from atomic contact to cellular function.
IuchiSandKuldellN(eds).LandesBioscience,Georgetown,TX.pp.2630
Grootwassink JWD, Hewitt GM (1983) Inducible and constitutive formation of fructofuranosidase
(inulase)inbatchandcontinuousculturesoftheyeastKluyveromycesfragilis.JGenMicrobiol
129:3141
GrünCH,HochstenbachF,HumbelBM,VerkleijAJ,SietsmaJH,KlisFM,KamerlingJP,Vliegenthart
JF(2005)Thestructureofcellwallalphaglucanfromfissionyeast.Glycobiology15:245257
Guasconi V, Yahi H, AitSiAli S (2002) Transcription factors. Atlas Genet Cytogenet Oncol
Haematol.URL:
http://www.infobiogen.fr/services/chromcancer/Deep/TranscripFactorsID20043.html
GuptaAKandKaurN(1997)Fructanstoringplantsapotentialsourceofhighfructosesyrups.JSci
IndRes56:447–452
Gupta AK and Kaur N (eds) (2000) Fructan metabolism in Jerusalem artichoke and chicory; in
Carbohydrate reserves in plants – synthesis and regulation (The Netherlands: Elsevier
Science)pp223–248
HannigG,MakridesSC(1998)StrategiesforoptimizingheterologousproteinexpressioninEscherichia
coli.TrendsBiotechnol,16:5460
Hartley JL, Temple GF, Brasch MA (2000) DNA cloning using in vitro sitespecific recombination.
GenomeRes.10:17881795
HasperAA,TrindadeLM,vanderVeenD,vanOoyenAJ,deGraaffLH(2004)Functionalanalysisof
thetranscriptionalactivatorXlnRfromAspergillusniger.Microbiology150:13671375
HataY,IshidaH,KojimaY,IshikawaE,KawatoA,SuginamiK,ImayasuS(1997)Comparisonoftwo
glucoamylasesproducedbyAspergillusoryzaeinsolidstate(koji)andinsubmergedculture.
J.Ferment.Bioeng.84:532537
HataY,KitamotoK,GomiK,KumagaiC,TamuraG(1992)Functionalelementsofthepromoterregion
oftheAspergillusoryzaeglaAgeneencodingglucoamylase.CurrGenet.22(2):8591
HataY,TsuchiyaK,KitamotoK,GomiK,KumagaiC,TamuraG,HaraS(1991)Nucleotidesequence
and expression of the glucoamylaseencoding gene (glaA) from Aspergillusoryzae. Gene
108:145150
Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited.
Mycol.Res.105:14221432
Hayashida S, Kuroda K, Ohta K, Kuhara S, Fukuda K and Sakaki Y (1989) Molecular cloning of the
glucoamylase I gene of Aspergillus awamori var. kawachi for localization of the rawstarch
affinitysite.Agric.Biol.Chem.53:923929
Hendry G (1993) Evolutionary origins and natural functions of fructans: A climatological,
biogeographicandmechanisticappraisal.NewPhytol.123:3–14
HendryGAF,WallaceRK(1993)Theorigin,distributionandevolutionarysignificanceoffructans.In
Scienceandtechnologyoffructans.pp 119139. Edited by Suzuki, M. & Chatterton, N. J. Boca
Raton,FL:CRCPress
Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities.
BiochemJ.280:309316
HenrissatB,BairochA(1993)Newfamiliesintheclassificationofglycosylhydrolasesbasedonamino
acidsequencesimilarities.BiochemJ.293:781788
HesseSJ,RuijterGJ,DijkemaC,VisserJ(2002)IntracellularpHhomeostasisinthefilamentousfungus
Aspergillusniger.Eur.J.Biochem.269:34853494
Heyer AG, Wendenburg R (2001) Gene cloning and functional characterization by heterologous
expressionofthefructosyltransferaseofAspergillussydowiIAM2544.ApplEnvironMicrobiol
67:363370
Hirayama M, Sumi N, Hidaka H (2006) Purification and characterization of a fructooligosaccharide
producing betafructofuranosidase from Aspergillus niger ATCC 20611. Agric. Biol. Chem.
53:667673
Hochstenbach F, Klis FM, Van Den EH, van DE, Peters PJ, Klausner RD (1998) Identification of a
putative alphaglucan synthase essential for cell wall construction and morphogenesis in
fissionyeast.ProcNatlAcadSciUSA95:91619166
Holz C, Prinz B, Bolotina N, Sievert V, Büssow K, Simon B, Stahl U, Lang C (2003) Establishing the
yeast Saccharomyces cerevisiae as a system for expression of human proteins on a
proteomescale.JStructFunctGenomics,4:97108
HorisbergerM,LewisBA,SmithF(1972)Structureofa(1,3)aDglucan(pseudonigeran)ofAspergillus
nigerNNRL326cellwall.CarbohydrRes23:183188
Hoshiko S, Makabe O, Nojiri C, Katsumata K, Satoh E, Nagaoka K (1987) Molecular cloning and
characterization of the Streptomyceshygroscopicus alphaamylase gene. J. Bacteriol. 169:1029
1036
Hull EP, Green PM, Arst HN, Jr., Scazzocchio C (1989) Cloning and physical characterization of the
LprolinecatabolismgeneclusterofAspergillusnidulans.MolMicrobiol3:553559
InoueH,NojimaH,OkayamaH(1990)HighefficiencytransformationofEscherichiacoliwithplasmids.
Gene96:2328
Ito T, Tani S, Itoh T, Tsukagoshi N, Kato M, Kobayashi T (2004) Mode of AmyR binding to the
CGGN8AGG sequence in the Aspergillusoryzae taaG2 promoter. Biosci Biotechnol Biochem
68:19061911
Jespersen HM, MacGregor EA, Sierks MR, Svensson B (1991) Comparison of the domainlevel
organizationofstarchhydrolasesandrelatedenzymes.Biochem.J.280:5155.Review
JohnstonIR(1965)ThecompositionofthecellwallofAspergillusniger.BiochemJ96:651658
Johnston M (1987) A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces
cerevisiae.MicrobiolRev.51(4):458476
JohnstonIR(1965)ThecompositionofthecellwallofAspergillusniger.Biochem.J.96:651658
Kaneko A, Sudo S, Sakamoto Y, Tamura G, Ishikawa T, Ohba T (1996) Molecularcloning and
determination of the nucleotidesequence of a gene encoding an acidstable alphaamylase
fromAspergilluskawachii.J.Ferment.Bioeng.81:292298
Kang HK, Lee JH, Kim D, Day DF, Robyt JF, Park KH, Moon TW (2004) Cloning and expression of
Lipomyces starkeyi alphaamylase in Escherichia coli and determination of some of its
properties.FEMSMicrobiol.Lett.233:5364
Kaper T, van der Maarel MJ, Euverink GJ, Dijkhuizen L (2004) Exploring and exploiting
starchmodifyingamylomaltasesfromthermophiles.Biochem.Soc.Trans.32:279282
KaplanH,HutkinsRW(2003)MetabolismoffructooligosacchridesbyLactobacillusparacasei1195.Appl
EnvironMicrobiol69,22172222
KarnaoukhovaL,TaylorM,NeiditchB(2003)ConstructionofcDNAlibrariesbyrecombinationusing
theCloneMiner™cDNALibraryConstructionKit.FOCUS25.2:320324
KatoM,KatoY,KinT,KokubunA,MaedaH,MaeyamaN,MaruyamaJ,NagasakiH,NakajimaT,Oda
K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y,
WortmanJR,YamadaO,YamagataY,AnazawaH,HataY,KoideY,KomoriT,KoyamaY,
Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H (2005)
GenomesequencingandanalysisofAspergillusoryzae.Nature438:11571161
Kato M, Sekine K, Tsukagoshi N (1996) Sequencespecific binding sites in the Takaamylase A G2
promoter for the CreA repressor mediating carbon catabolite repression. Biosci Biotechnol
Biochem.60:17761779
Kato N, Murakoshi Y, Kato M, Kobayashi T, Tsukagoshi N (2002a) Isomaltose formed by
alphaglucosidasestriggersamylaseinductioninAspergillusnidulans.CurrGenet42:4350
KatoN,SuyamaS,ShirokaneM,KatoM,KobayashiT,TsukagoshiN(2002b)Novelalphaglucosidase
from Aspergillus nidulans with strong transglycosylation activity. Appl Environ Microbiol
68:12501256
Kaur N, Gupta AK (2002) Applications of inulin and oligofructose in health and nutrition. J Biosci
27:703714
KellerNP,HohnTM.(1997)Metabolicpathwaygeneclustersinfilamentousfungi.Fungal.Genet.Biol.
21:1729
Kelly R, KwonChung KJ (1992) A zinc finger protein from Candida albicans is involved in sucrose
utilization.JBacteriol174:222232
KellyJM,HynesMJ(1985)TransformationofAspergillusnigerbytheamdSgeneofAspergillusnidulans.
EMBOJ.4:475479
Kim HY, Choi YJ (2001) Molecular characterization of cycloinulooligosaccharide fructanotransferase
fromBacillusmacerans.ApplEnvironMicrobiol67:9951000
Kimura A, Takata M, Sakai O, Matsui H, Takai N, Takayanagi T, Nishimura I, Uozumi T, Chiba S
(1992)CompleteaminoacidsequenceofcrystallinealphaglucosidasefromAspergillusniger.
Biosci.Biotechnol.Biochem.56:13681370
KirkpatrickCR,SchimmelP(1995)DetectionofleucineindependentDNAsiteoccupancyoftheyeast
Leu3ptranscriptionalactivatorinvivo.MolCellBiol15:40214030
Kitamoto HK, Ohmomo S, Iimura Y (1998) Isolation and nucleotide sequence of the gene encoding
phosphoenolpyruvatecarboxykinasefromKluyveromyceslactis.Yeast14:963967
Kohlhaw GB (2003) Leucine biosynthesis in fungi: entering metabolism through the back door.
MicrobiolMolBiolRev67:115
Kolar M, Punt PJ, van den Hondel CA, Schwab H (1988) Transformation of Penicillium chrysogenum
usingdominantselectionmarkersandexpressionofanEscherichiacolilacZfusiongene.Gene
62:127134
Korman DR, Bayliss FT, Barnett CC, Carmona CL, Kodama KH, Royer TJ, Thompson SA, Ward M,
WilsonLJ,BerkaRM(1990)Cloning,characterization,andexpressionoftwoalphaamylase
genesfromAspergillusnigervar.awamori.CurrGenet17:203212
Kralj S, van GeelSchutten GH, van der Maarel MJ, Dijkhuizen L (2004) Biochemical and molecular
characterizationofLactobacillusreuteri121reuteransucrase.Microbiology150:20992112
Kralj S, van GeelSchutten GH, Dondorff MM, Kirsanovs S, van der Maarel MJ, Dijkhuizen L (2004)
GlucansynthesisinthegenusLactobacillus:isolationandcharacterizationofglucansucrase
genes,enzymesandglucanproductsfromsixdifferentstrains.Microbiology150:36813690
KrappmannS,BrausGH(2005)NitrogenmetabolismofAspergillusanditsroleinpathogenicity.Med
Mycol.43Suppl1:S3140.Review
Kulmburg P, Mathieu M, Dowzer C, Kelly J, Felenbok B (1993) Specific binding sites in the alcR and
alcA promoters of the ethanol regulon for the CREA repressor mediating carbon catabolite
repressioninAspergillusnidulans.MolMicrobiol.7:847857
Kulmburg P, Prangé T, Mathieu M, Sequeval D, Scazzocchio C, Felenbok B (1991) Correct intron
splicinggeneratesanewtypeofaputativezincbindingdomaininatranscriptionalactivator
ofAspergillusnidulans.FEBSLett.280(1):1116
Kulmburg P, Sequeval D, Lenouvel F, Mathieu M, Felenbok B (1992) Identification of the promoter
region involved in the autoregulation of the transcriptional activator ALCR in Aspergillus
nidulans.MolCellBiol12:19321939
KulminskayaAA,ArandM,EneyskayaEV,IvanenDR,ShabalinKA,ShishlyannikovSM,SavelievAN,
Korneeva OS, Neustroev KN (2003) Biochemical characterization of Aspergillus awamori
exoinulinase: substrate binding characteristics and regioselectivity of hydrolysis. Biochim
BiophysActa1650,2229
Kumar S, Tamura K, Nei M (1993) MEGA: Molecular Evolutionairy Analysis, version 1.01., The
PennsylvaniaStateUniversity,UniversityPark,PA
KurikiT,ImanakaT(1999)Theconceptofthealphaamylasefamily:structuralsimilarityandcommon
catalyticmechanism.J.Biosci.Bioeng.87:557565
LaemmliUK(1970)Cleavageofstructuralproteinsduringtheassemblyoftheheadofbacteriophage
T4.Nature227:680685
LalouxO,CassartJP,DelcourJ,VanBeeumenJ,VandenhauteJ(1991)Cloningandsequenceanalysis
ofthegeneencodinginvertasefromtheyeastKluyveromycesmarxianusvar.marxianusATCC
12424.FEBSLett289,6468
Laughon A, Gesteland RF (1982) Isolation and prelim inary characterization of the GAL4 gene, a
positiveregulatoroftranscriptioninyeast.ProcNatlAcadSciUSA.79(22):68276831
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC (1993) Detecting subtle
sequencesignals:aGibbssamplingstrategyformultiplealignment.Science262:208–214
LeGalCoeffetMF,JacksAJ,SorimachiK,WilliamsonMP,WilliamsonG,ArcherDB(1995)Expression
in Aspergillus niger of the starchbinding domain of glucoamylase. Comparison with the
proteolyticallyproducedstarchbindingdomain.Eur.J.Biochem.233:561567
Leandro MJ, Goncalves P, SpencerMartins I (2006) Two glucose/xylose transporter genes from the
yeast Candida intermedia: first molecular characterization of a yeast xyloseH+ symporter.
BiochemJ395:543549
LeemhuisH,WehmeierUF,DijkhuizenL(2004)Singleaminoacidmutationsinterchangethereaction
specificities of Cyclodextrin Glycosyltransferase and the acarbosemodifying enzyme
AcarviosylTransferase.Biochemistry43:1320413213
LHocine L, Wang W, Jiang B, Xu S (2000) Purification and partial characterization of
fructosyltransferaseandinvertasefromAspergillusnigerAS0023.JBiotechnol81:7384
LieblW,BremD,GotschlichA.(1998)Analysisofthegeneforbetafructosidase(invertase,inulinase)
ofthehyperthermophilicbacteriumThermotogamaritima,andcharacterisationoftheenzyme
expressedinEscherichiacoli.Appl.Microbiol.Biotechnol.50:5564
Lockington R, Scazzocchio C, Sequeval D, Mathieu M, Felenbok B (1987) Regulation of alcR, the
positive regulatory gene of the ethanol utilization regulon of Aspergillus nidulans. Mol
Microbiol.1:27581
MaJ,PtashneM(1987)DeletionanalysisofGAL4definestwotranscriptionalactivatingsegments.Cell.
48(5):847853
MacGregorEA,JanecekS,SvenssonB(2001)Relationshipofsequenceandstructuretospecificityinthe
alphaamylasefamilyofenzymes.BiochimBiophysActa1546:120
MachidaM,AsaiK,SanoM,TanakaT,KumagaiT,TeraiG,KusumotoK,ArimaT,AkitaO,Kashiwagi
Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW,
Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE,
Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K,
Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J,
NagasakiH,NakajimaT,OdaK,OkadaK,PaulsenI,SakamotoK,SawanoT,TakahashiM,
TakaseK,TerabayashiY,WortmanJR,YamadaO,YamagataY,AnazawaH,HataY,Koide
Y,KomoriT,KoyamaY,MinetokiT,SuharnanS,TanakaA,IsonoK,KuharaS,Ogasawara
N,KikuchiH(2005)GenomesequencingandanalysisofAspergillusoryzae.Nature438:1157
1161
MarchlerBauerA,BryantSH(2004)CDSearch:proteindomainannotationsonthefly.NucleicAcids
Res32:W327W331
MarionCL,RappleyeCA,EngleJT,GoldmanWE(2006)Analpha(1,4)amylaseisessentialforalpha
(1,3)glucanproductionandvirulenceinHistoplasmacapsulatum.MolMicrobiol62:970983
Marmorstein R, Carey M, Ptashne M, Harrison SC (1992) DNA recognition by GAL4: structure of a
proteinDNAcomplex.Nature.356(6368):408414
MartensUzunovaES,ZandlevenJS,BenenJA,AwadH,KoolsHJ,BeldmanG,VoragenAG,Vanden
Berg JA, Schaap PJ (2006) A new group of exoacting family 28 glycoside hydrolases of
Aspergillusnigerthatareinvolvedinpectindegradation.BiochemJ.400:4352
MartinI,DebarbouilleM,FerrariE,KlierA,RapoportG(1987)Characterizationofthelevanasegeneof
Bacillussubtiliswhichshowshomologytoyeastinvertases.MolGenGenet208,177184
MathieuM,FillingerS,FelenbokB(2000)Invivostudiesofupstreamregulatorycisactingelementsof
thealcRgeneencodingthetransactivatoroftheethanolreguloninAspergillusnidulans.Mol
Microbiol.36(1):123131
MathieuM,NikolaevI,ScazzocchioC,FelenbokB(2005)Patternsofnucleosomalorganizationinthe
alc regulon of Aspergillusnidulans: roles of the AlcR transcriptional activator and the CreA
globalrepressor.MolMicrobiol.56(2):535548
Matsubara T, Ben Ammar Y, Anindyawati T, Yamamoto S, Ito K, Iizuka M, Minamiura N (2004)
Molecular cloning and determination of the nucleotide sequence of raw starch digesting
alphaamylasefromAspergillusawamoriKT11.J.Biochem.Mol.Biol.37:429438
MatteyM,AllanA(1990)GlycogenaccumulationinAspergillusniger.BiochemSocTrans.18:10201021
MayT,MackieRI,FaheyC,CreminJC,GarlebKA(1994)Effectoffibersourceonshortchainfattyacid
production and on the growth and toxin production by Clostridium difficile. Scand. J.
Gastroenterol.29:916922
MeeuwsenPJ,VinckenJP,BeldmanG,VoragenAG.(2000)Auniversalassayforscreeningexpression
librariesforcarbohydrases.JBiosciBioeng.89(1):107109
MegnegneauB,DebetsF,HoekstraRF(1993)Geneticvariabilityandrelatednessinthecomplexgroup
of black Aspergilli based on random amplification of polymorphic DNA. Curr Genet.
23(4):323329
Meng G, Futterer K (2003) Structural framework of fructosyl transfer in Bacillussubtilislevansucrase.
NatStructBiol10,935941
Merika M, Orkin SH (1993) DNAbinding specificity of GATA family transcription factors. Mol Cell
Biol.13(7):39994010
Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F (1997) MIPS: a database for protein
sequences,homologydataandyeastgenomeinformation.NucleicAcidsRes25:2830
Meyer V, Arentshorst M, ElGhezal A, Drews AC, Kooistra R, van den Hondel CA, Ram AF (2007)
HighlyefficientgenetargetingintheAspergillusnigerkusAmutant.J.Biotechnol.128:770775
Miller J, McLachlan AD, Klug A (1985) Repetitive zincbinding domains in the protein transcription
factorIIIAfromXenopusoocytes.EMBOJ.4(6):1609–1614
MinetokiT,GomiK,KitamotoK,KumagaiC,TamuraG(1995)Nucleotidesequenceandexpressionof
alphaglucosidaseencodinggene(agdA)fromAspergillusoryzae.Biosci.Biotechnol.Biochem.
59(8):15161521
MoritaT,TanakaN,HosomiA,GigaHamaY,TakegawaK(2006)Analphaamylasehomologue,aah3,
encodes a GPIanchored membrane protein required for cell wall integrity and
morphogenesisinSchizosaccharomycespombe.BiosciBiotechnolBiochem70:14541463
Moriyama S, Tanaka H, Uwataki M, Muguruma M, Ohta K (2003) Molecular cloning and
characterizationofanexoinulinasegenefromAspergillusnigerstrain12anditsexpressionin
Pichiapastoris.JBiosciBioeng96:324331
Moriyama S, Akimoto H, Suetsugu N, Kawasaki S, Nakamura T, Ohta K (2002) Purification and
properties of an extracellular exoinulinase from Penicillium sp. strain TN88 and sequence
analysisoftheencodinggene.Biosci.Biotechnol.Biochem.66,18871896
MoriyamaS,MugurumaM,OhtaK(2006)Quantitativeexpressionanalysisofinulinasegeneclusterof
Penicilliumsp.strainTN88.JBiosciBioeng101:277–279
Morkeberg R, Carlsen M, Nielsen J (1995) Induction and repression of alphaamylase production in
batchandcontinuousculturesofAspergillusoryzae.Microbiology.141:24492454
MouynaI,FontaineT,VaiM,MonodM,FonziWA,DiaquinM,PopoloL,HartlandRP,LatgeJP(2000)
Glycosylphosphatidylinositolanchored glucanosyltransferases play an active role in the
biosynthesisofthefungalcellwall.J.Biol.Chem.275:1488214889
Mouyna I, Morelle W, Vai M, Monod M, Léchenne B, Fontaine T, Beauvais A, Sarfati J, Prévost MC,
Henry C, Latgé JP (2005) Deletion of GEL2 encoding for a beta(13)glucanosyltransferase
affectsmorphogenesisandvirulenceinAspergillusfumigatus.Mol.Microbiol.56:16751688
MuramatsuM,NakakukiT(1995)Enzymaticsynthesisofnovelfructosylandoligofructosyltrehaloses
byAspergillussydowibetafructofuranosidase.Biosci.Biotechnol.Biochem.59:208212
MyersAM,MorellMK,JamesMG,BallSG(2000)Recentprogresstowardsunderstandingbiosynthesis
oftheamylopectincrystal.PlantPhysiol.122:989–997
Nagem RA, Rojas AL, Golubev AM, Korneeva OS, Eneyskaya EV, Kulminskaya AA, Neustroev KN,
PolikarpovI(2004)Crystalstructureofexoinulinasefrom Aspergillusawamori:Theenzyme
foldandstructuraldeterminantsofsubstraterecognition.JMolBiol344:471480
Nakajima T, Imanaka T, Aiba S (1986) Comparison of amino acid sequences of eleven different
alphaamylases.ApplMicrobiolBiotechnol23:355360
NakamuraA,NishimuraI,YokoyamaA,LeeDG,HidakaM,MasakiH,KimuraA,ChibaS,UozumiT
(1997) Cloning and sequencing of an alphaglucosidase gene from Aspergillus niger and its
expressioninA.nidulans.JBiotechnol53:7584
Nakamura T, Maeda Y, Tanoue N, Makita T, Kato M, Kobayashi T (2006) Expression profile of
amylolyticgenesinAspergillusnidulans.BiosciBiotechnolBiochem70:23632370
Nakamura A, Haga K, Yamane K (1993) Three histidine residues in the active center of cyclodextrin
glucanotransferase from alkalophilic Bacillus sp. 1011: effects of the replacement on pH
dependenceandtransitionstatestabilization.Biochemistry32:66246631
Nakao M, Nakayama T, Kakudo A, Inohara M, Harada M, Omura F, Shibano Y(1994) Structure and
expression of a gene coding for thermostable alphaglucosidase with a broad substrate
specificityfromBacillussp.SAM1606.EurJBiochem220:293300
NarendjaF,GollerSP,WolschekM,StraussJ(2002)NitrateandtheGATAfactorAreAarenecessary
for in vivo binding of NirA, the pathwayspecific transcriptional activator of Aspergillus
nidulans.MolMicrobiol.44(2):573583
NaumoffDG(2001)betafructosidasesuperfamily:homologywithsomealphaLarabinasesandbeta
Dxylosidases.Proteins42:6676
Nguyen QD, Mattes F, Hoschke A, Rezessyszabó J, Bhat MK (1999) Production, purification and
identificationoffructooligosaccharidesproducedbybetafructofuranosidasefromAspergillus
nigerIMI303386.Biotechnol.Lett.21:183186
Ni BF, Needleman RB (1990) Identification of the upstream activating sequence of MAL and the
bindingsitesfortheMAL63activatorofSaccharomycescerevisiae.MolCellBiol10:37973800
NiermanWC,PainA,AndersonMJ,WortmanJR,KimHS,ArroyoJ,BerrimanM,AbeK,ArcherDB,
BermejoC,BennettJ,BowyerP,ChenD,CollinsM,CoulsenR,DaviesR,DyerPS,Farman
M,FedorovaN,FedorovaN,FeldblyumTV,FischerR,FoskerN,FraserA,GarciaJL,Garcia
MJ,GobleA,GoldmanGH,GomiK,GriffithJonesS,GwilliamR,HaasB,HaasH,HarrisD,
HoriuchiH,HuangJ,HumphrayS,JimenezJ,KellerN,KhouriH,KitamotoK,KobayashiT,
Konzack S, Kulkarni R, Kumagai T, Lafon A, Latgé JP, Li W, Lord A, Lu C, Majoros WH,
MayGS,MillerBL,MohamoudY,MolinaM,MonodM,MouynaI,MulliganS,MurphyL,
ONeilS,PaulsenI,PenalvaMA,PerteaM,PriceC,PritchardBL,QuailMA,Rabbinowitsch
E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de CS,
RodriguezPena JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, SanchezFerrero JC,
Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de
AldanaCR,WeidmanJ,WhiteO,WoodwardJ,YuJH,FraserC,GalaganJE,AsaiK,Machida
M,HallN,BarrellB,DenningDW(2005)Genomicsequenceofthepathogenicandallergenic
filamentousfungusAspergillusfumigatus.Nature438:11511156
NikolaevI,LenouvelF,FelenbokB(1999)UniqueDNAbindingspecificityofthebinuclearzincAlcR
activatoroftheethanolutilizationpathwayinAspergillusnidulans.JBiolChem.274(14):9795
9802
NinessKR(1999)InulinandOligofructose:WhatAreThey?J.Nutr.129:1402S1406S
NunbergJH,MeadeJH,ColeG,LawyerFC,McCabeP,SchweickartV,TalR,WittmanVP,Flatgaard
JE, Innis MA (1984) Molecular cloning and characterization of the glucoamylase gene of
Aspergillusawamori.Mol.Cell.Biol.4(11):23062315
OharaO,TempleG(2001)DirectionalcDNAlibraryconstructionassistedbytheinvitrorecombination
reaction.NucleicAcidsResearch,29:E22
Ohta K, Akimoto H, Matsuda S, Toshimitsu D, Nakamura T (1998) Molecular cloning and sequence
analysis of two endoinulinase genes from Aspergillus niger. Biosci Biotechnol Biochem
62:17311738
Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM
(1993)NMRstructureofaspecificDNAcomplexofZncontainingDNAbindingdomainof
GATA1.Science261:438446
Onodera S, Murakami T, Ito H, Mori H, Matsui H, Honma M, Chiba S, Shiomi N (1996) Molecular
cloning and nucleotide sequences of cDNA and gene encoding endoinulinase from
Penicilliumpurpurogenum.BiosciBiotechnolBiochem60:17801785
Orlean P (1997) Biogenesis of yeast wall and surface components. In: Pringle J, Broach JR, Jones EW
(eds)CellCycleandCellBiology.ColdSpringHarborLaboratoryPress,NewYork,pp.229
362
Ozimek LK, Kralj S, van der Maarel MJ, Dijkhuizen L (2006) The levansucrase and inulosucrase
enzymes of Lactobacillus reuteri 121 catalyse processive and nonprocessive
transglycosylationreactions.Microbiology.152:11871196
Paldi T, Levy I, Shoseyov O (2003) Glucoamylase starchbinding domain of Aspergillus niger B1:
molecularcloningandfunctionalcharacterization.Biochem.J.372:905910
PandeyA,SoccolCR,SelvakumarP,SoccolVT,KriegerN,FontanaJD(1999)Recentdevelopmentsin
microbial inulinases. Its production, properties, and industrial applications. Appl Biochem
Biotechnol81,3552
PanozzoC,CapuanoV,FillingerS,FelenbokB(1997)ThezincbinuclearclusteractivatorAlcRisable
to bind to single sites but requires multiple repeated sites for synergistic activation of the
alcAgeneinAspergillusnidulans.JBiolChem.272(36):2285922865
ParenicováL,BenenJAE,SamsonRA,VisserJ(1997)EvaluationofRFLPanalysisoftheclassification
ofselectedblackaspergilli.Mycol.Res.101:810814
Parenicova L, Benen JA, Kester HC, Visser J (1998) pgaE encodes a fourth member of the
endopolygalacturonasegenefamilyfromAspergillusniger.Eur.J.Biochem.251:7280
PelHJ,deWindeJH,ArcherDB,DyerPS,HofmannG,SchaapPJ,TurnerG,deVriesRP,AlbangR,
AlbermannK,AndersenMR,BendtsenJD,BenenJA,vandenBergM,BreestraatS,Caddick
MX,ContrerasR,CornellM,CoutinhoPM,DanchinEG,DebetsAJ,DekkerP,vanDijckPW,
vanDijkA,DijkhuizenL,DriessenAJ,dEnfertC,GeysensS,GoosenC,GrootGS,deGroot
PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA,
vanderHeijdenRT,vanderKaaijRM,KlisFM,KoolsHJ,KubicekCP,vanKuykPA,Lauber
J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG,
OlsthoornM,PalK,vanPeijNN,RamAF,RinasU,RoubosJA,SagtCM,SchmollM,SunJ,
UsseryD,VargaJ,VerveckenW,vandeVondervoortPJ,WedlerH,WostenHA,ZengAP,
vanOoyenAJ,VisserJ,StamH(2007)Genomesequencingandanalysisoftheversatilecell
factoryAspergillusnigerCBS513.88.NatBiotechnol.25(2):221231.
PenalvaMA,ArstHNJr(2002)RegulationofgeneexpressionbyambientpHinfilamentousfungiand
yeasts.MicrobiolMolBiolRev.66(3):426446. Review
Penalva MA, Arst HN Jr. (2004) Recent advances in the characterization of ambient pH regulation of
geneexpressioninfilamentousfungiandyeasts.AnnuRevMicrobiol.58:425451. Review
Penalva MA, Arst H (2002). Regulation of gene expression by ambient pH in filamentous fungi and
yeasts.MicrobiolMolBiolRev66,426446
PerezJA,RodriguezJ,RodriguezL,RuizT(1996)Cloningandsequenceanalysisoftheinvertasegene
INV1fromtheyeastPichiaanomala.CurrGenet29,234240
PetersD(2006)Carbohydratesforfermentation.BiotechnolJ1:806814
Petersen KL, Lehmbeck J, Christensen T (1999) A new transcriptional activator for amylase genes in
Aspergillus.MolGenGenet262:668676
Pilauri V, Bewley M, Diep C, Hopper J (2005) Gal80 dimerization and the yeast GAL gene switch.
Genetics169:19031914
PilonSmits EA, Ebskamp MJ, Paul MJ, Jeuken MJ, Weisbeek PJ, Smeekens SC (1995) Evaluation of
safetyoninulinandoligofructoseasdietaryfiber.PlantPhysiol107:125130
Pina C, Goncalves P, Prista C, LoureiroDias MC (2004) Ffz1, a new transporter specific for fructose
fromZygosaccharomycesbailii.Microbiology150:24292433
PollockCJ,ChattertonNJ(1988)Fructans.InTheBiochemistryofPlants(Stumpf,P.K.andConn,E.E.,
eds),Vol.14,Carbohydrates(Preiss,J.,ed.).London:AcademicPress,pp.109140
PonsT,NaumoffDG,MartinezFleitesCM,HernándezL(2004).Threeacidicresiduesareattheactive
siteofabetapropellerarchitectureinglycosidehydrolasefamilies32,43,62and68.Proteins
54,424432
Pons T, Olmea O, Chinea G, Beldarrain A, Marquez G, Acosta N, Rodriguez L, Valencia A (1998)
Structuremodelforfamily32ofglycosylhydrolaseenzymes.Proteins33,383395
PopoloL,VaiM,GattiE,PorelloS,BonfanteP,BalestriniR,AlberghinaL(1993)Physiologicalanalysis
ofmutantsindicatesinvolvementoftheSaccharomycescerevisiaeGPIanchoredproteingp115
inmorphogenesisandcellseparation.J.Bacteriol.175:18791885
Punt PJ, Oliver RP, Dingemanse MA, Pouwels PH, van den Hondel CA (1987) Transformation of
Aspergillus based on the hygromycin B resistance marker from Escherichiacoli. Gene 56:117
124
PuntPJ,StraussJ,SmitR,KinghornJR,vandenHondelCA,ScazzocchioC(1995)Theintergenicregion
between the divergently transcribed niiA and niaD genes of Aspergillus nidulans contains
multipleNirAbindingsiteswhichactbidirectionally.MolCellBiol15:56885699
PuntPJ,vanBiezenN,ConesaA,AlbersA,MangnusJ,vandenHondelC(2002)Filamentousfungias
cellfactoriesforheterologousproteinproduction.TrendsBiotechnol.20(5):200206
PuntPJ,vandenHondelCA(1992)TransformationoffilamentousfungibasedonhygromycinBand
phleomycinresistancemarkers.MethodsEnzymol216:447457
Raina S and Missiakas D (1997) Making and breaking disulfide bonds. Annu. Rev. Microbiol. 51:179
202
RamAFandKlisFM(2006)Identificationoffungalcellwallmutantsusingsusceptibilityassaysbased
onCalcofluorWhiteandCongoRed.NatureProtocols1:22532256
RamAF,WoltersA,TenHoopenR,KlisFM(1994)Anewapproachforisolatingcellwallmutantsin
Saccharomycescerevisiae by screening for hypersensitivity to calcofluor white. Yeast 10:1019
1030
RaperKB,FennellDI(1955)NewspeciesandvarietiesofAspergillus.Mycologia47:6889
RaperKB,FennellDI(1965)ThegenusAspergillus.WilliamsandWilkins,Baltimore
RappleyeCA,EngleJT,GoldmanWE(2004)RNAinterferenceinHistoplasmacapsulatumdemonstrates
aroleforalpha(1,3)glucaninvirulence.MolMicrobiol53:153165
Rappleye CA, Goldman WE (2006) Defining virulence genes in the dimorphic fungi. Annu Rev
Microbiol60:281303
RappleyeCA,EngleJT,GoldmanWE(2004)RNAinterferenceinHistoplasmacapsulatumdemonstrates
aroleforalpha(1,3)glucaninvirulence.Mol.Microbiol.53:153165
Ravagnani A, Gorfinkiel L, Langdon T, Diallinas G, Adjadj E, Demais S, Gorton D, Arst HN,
ScazzocchioC(1997)Subtlehydrophobicinteractionsbetweentheseventhresidueofthezinc
finger loop and the first base of an HGATAR sequence determine promoterspecific
recognitionbytheAspergillusnidulansGATAfactorAreA.EMBOJ.16:39743986
ReddyA,MaleyF(1996)StudiesonidentifyingthecatalyticroleofGlu204intheactivesiteofyeast
invertase.J.Biol.Chem.271:1395313957
Reese AJ, Doering TL (2003) Cell wall alpha1,3glucan is required to anchor the Cryptococcus
neoformanscapsule.Mol.Microbiol.50:14011409
Rehm J, Wilimitzer L, Heyer LG (1998) Production of 1kestose in transgenic yeast expressing a
fructosyltransferasefromAspergillusfoetidus.JBacteriol180,13051310
RitsemaT,SmeekensS(2003)Fructans:beneficialforplantsandhumans.CurrOpinPlantBiol6,223
230
RoberfroidMB,DelzenneNM(1998)Dietaryfructans.AnnuRevNutr18,117143
RobytJF(1998)EssentialsofCarbohydrateChemistry.Springer,NewYork.
RubioMC,MaldonadoMC(1995)PurificationandcharacterizationofinvertasefromAspergillusniger.
Curr.Microbiol.31:8083
RueppA,ZollnerA,MaierD,AlbermannK,HaniJ,MokrejsM,TetkoI,GuldenerU,MannhauptG,
Munsterkotter M, Mewes HW (2004) The FunCat, a functional annotation scheme for
systematicclassificationofproteinsfromwholegenomes.NucleicAcidsRes32:55395545
RuijterGJ,VisserJ(1997)CarbonrepressioninAspergilli.FEMSMicrobiolLett151:103114
Sambrook J , Fritsch E, and Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring
HarborLaboratoryPress,ColdSpringHarbor.
SangeethaPT,RameshMN,PrapullaSG(2004)ProductionoffructosyltransferasebyAspergillusoryzae
CFR 202 in solidstate fermentation using agricultural byproducts. Appl Microbiol
Biotechnol65,530537
Sasangka P, Matsuno A, Tanaka A, Akasaka Y, Suyama S, Kano S, Miyazaki M, Akao T, Kato M,
Kobayashi T, Tsukagoshi N (2002) Structural features of the glycogen branching enzyme
encodinggenesfromAspergilli.Microbiol.Res.157:337344
Sauer J, Sigurskjold BW, Christensen U, Frandsen TP, Mirgorodskaya E, Harrison M, Roepstorff P,
Svensson B (2000) Glucoamylase: structure/function relationships, and protein engineering.
BiochimBiophysActa1543:275293
ScazzocchioC(2000)ThefungalGATAfactors.CurrOpinMicrobiol.3(2):126131
Schjerling P, Holmberg S (1996) Comparative amino acid sequence analysis of the C6 zinc cluster
familyoftranscriptionalregulators.NucleicAcidsRes24:45994607
SchusterE,DunnColemanN,FrisvadJC,vanDijckPWM(2002)OnthesafetyofAspergillusniger–a
review.Appl.Microbiol.Biotechnol59:426435
SemovaN,StormsR,JohnT,GaudetP,UlycznyjP,MinXJ,SunJ,ButlerG,TsangA(2006)Generation,
annotation,andanalysisofanextensiveAspergillusnigerESTcollection.BMCMicrobiol.6:7
SghirA,ChowJM,MackieRI(1998)Continuouscultureselectionofbifidobacteriaandlactobacillifrom
humanfaecalsamplesusingfructooligosaccharideasselectivesubstrate.J.Appl.Microbiol.
85:769777
Sharrocks AD (2000) Introduction: the regulation of eukaryotic transcription factor function, CMLS
Cell.Mol.LifeSci.(57)11471148
Shibuya I, Gomi K, Iimura Y, Takahashi K, Tamura G, Hara S (1990) Molecular cloning of the
glucoamylase gene of Aspergillus shirousami and its expression in Aspergillus oryzae. Agric.
Biol.Chem.54(8):19051914
Shibuya I, Tamura G, Ishikawa T, Hara S (1992) Cloning of the alphaamylase cDNA of Aspergillus
shirousamii and its expression in Saccharomycescerevisiae. Biosci Biotechnol Biochem. 56:174
179
ShroffRA,OConnorSM,HynesMJ,LockingtonRA,KellyJM(1997)NullallelesofcreA,theregulator
ofcarboncataboliterepressioninAspergillusnidulans.FungalGenetBiol22:2838
SilAK,AlamS,XinP,MaL,MorganM,LeboCM,WoodsMP,HopperJE.(1999)TheGal3pGal80p
Gal4p Transcription Switch of Yeast: Gal3p Destabilizes the Gal80pGal4p Complex in
ResponsetoGalactoseandATP.MolCellBiol.19(11):78287840
SomiariR, BrzeskiH,TateR, BieleckS,PolakJ(1997)Cloningand sequencingof anAspergillusniger
genecodingforbetafructofuranosidase.Biotechnol.Lett.19:12431247
SouthallSM,SimpsonPJ,GilbertHJ,WilliamsonG,WilliamsonMP(1999)Thestarchbindingdomain
fromglucoamylasedisruptsthestructureofstarch.FEBSLetters447:5860
StaggCM,FeatherMS(1973)ThecharacterizationofachitinassociatedDglucanfromthecellwallsof
Aspergillusniger.Biochim.Biophys.Acta.320:6472
Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B (2006) Dividing the large glycoside
hydrolase family 13 into subfamilies: towards improved functional annotations of
alphaamylaserelatedproteins.ProteinEngDesSel19:555562
Steup,M(1988)Starchdegradation.InTheBiochemistryofPlants(Stumpf,P.K.andConn,E.E.,eds),
Vol.14,Carbohydrates(Preiss,J.,ed.).London:AcademicPress,pp.255–296
Stryer,L(1999)Biochemistry,fourthedition.W.H.FreemanandCompany,NewYork,pp.998999
Suzuki M and Yagi N (1994) DNA recognition code of transcription factors in the helixturnhelix,
probe helix, hormone receptor, and zinc finger families. Proc Natl Acad Sci U S A.
91(26):12357–12361
SuzukiM,PollockCJ(1986)Extractionandcharacterizationoftheenzymesoffructanbiosynthesisin
timothygrass(PhleumpratenseL.).CanJBot64:18841887
Tada S, Iimura Y, Gomi K, Takahashi K, Hara S and Yoshizawa K (1989) Cloning and nucleotide
sequence of the genomic Takaamylase A gene of Aspergillus oryzae. Agric. Biol. Chem.
53:593599
Takaha T, Yanase M, Okada S, Smith SM (1993) Disproportionating enzyme (4alpha
glucanotransferase;EC2.4.1.25)ofpotato.Purification,molecularcloning,andpotentialrole
instarchmetabolism.J.Biol.Chem.268:13911396
Tanaka N, Ohuchi N, Mukai Y, Osaka Y, Ohtani Y, Tabuchi M, Bhuiyan MS, Fukui H, Harashima S,
Takegawa K (1998) Isolation and characterization of an invertase and its repressor genes
fromSchizosaccharomycespombe.BiochemBiophysResCommun245:246253
TaniS,ItohT,KatoM,KobayashiT,Tsukagoshi N(2001)InvivoandinvitroanalysesoftheAmyR
bindingsiteoftheAspergillusnidulansagdApromoter;requirementoftheCGGdirectrepeat
forinductionandhighaffinitybindingofAmyR.BiosciBiotechnolBiochem65:15681574
Tani S, Katsuyama Y, Hayashi T, Suzuki H, Kato M, Gomi K, Kobayashi T, Tsukagoshi N (2001a)
CharacterizationoftheamyRgeneencodingatranscriptionalactivatorfortheamylasegenes
inAspergillusnidulans.CurrGenet39:1015
TannockGW(1997)Probioticpropertiesoflacticacidbacteria:plentyofscopeforfundamentalR&D.
TrendsBiotechnol.15:270274
TaussigR,CarlsonM(1983)NucleotidesequencesoftheyeastSUC2geneforinvertase.NucleicAcids
Res11:19431954
Teste MA, Enjalbert B, Parrou JL, Francois JM (2000) The Saccharomyces cerevisiae YPR184w gene
encodestheglycogendebranchingenzyme.FEMSMicrobiolLett193:105110
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting, positionspecific gap penalties
andweightmatrixchoice.NucleicAcidsRes22:46734680
TilburnJ,SarkarS,WiddickDA,EspesoEA,OrejasM,MungrooJ,PeñalvaMA,ArstHNJr.(1995)The
AspergillusPacC zinc finger transcription factor mediates regulation of both acid and
alkalineexpressedgenesbyambientpH.EMBOJ.14:779790
Todd RB, Andrianopoulos A (1997) Evolution of a fungal regulatory gene family: the Zn(II)2Cys6
binuclearclusterDNAbindingmotif.FungalGenetBiol21:388405
TsujiG,KenmochiY,TakanoY,SweigardJ,FarrallL,FurusawaI,HorinoO,KuboY(2000)Novel
fungal transcriptional activators, Cmr1p of Colletotrichum lagenarium and pig1p of
Magnaporthe grisea, contain Cys2His2 zinc finger and Zn(II)2Cys6 binuclear cluster
DNAbinding motifs and regulate transcription of melanin biosynthesis genes in a
developmentallyspecificmanner.MolMicrobiol38:940954
TsukagoshiN,KobayashiT,KatoM(2001)Regulationoftheamylolyticand(hemi)cellulolyticgenes
inAspergilli.JGenApplMicrobiol47:119
TsukamotoA,KimuraK,IshiiY,TakanoT,YamaneK(1988)Nucleotidesequenceofthemaltohexaose
producing amylase gene from an alkalophilic Bacillus sp. #707 and structural similarity to
liquefyingtypealphaamylases.BiochemBiophysResCommun151:2531
UhmT,ChaeS,LeeD,KimS,CassartP,VandenhauteJ(1998)Cloningandnucleotidesequenceofthe
endoinulinaseencodinggene,inu2,fromAspergillusficuum.BiotechnolLett20:809812
UitdehaagJC,MosiR,KalkKH,vanderVeenBA,DijkhuizenL,WithersSG,DijkstraBW(1999)Xray
structuresalongthereactionpathwayofcyclodextringlycosyltransferaseelucidatecatalysis
inthealphaamylasefamily.NatStructBiol6:432436
Vainstein MH, Peberdy JF (1990) Solubilisation of a cell wall bound invertase in Aspergillusnidulans.
FEMSMicrobiolLett59,265269
Vainstein MH, Peberdy JF (1991) Regulation of invertase in Aspergillus nidulans: effect of different
carbonsources.JGenMicrobiol137,315321
ValleeBL,ColemanJE,andAuldDS(1991)Zincfingers,zincclusters,andzinctwistsinDNAbinding
proteindomains.Proc.Natl.Acad.Sci.USA.Vol89:9991003
van der Kaaij RM, Yuan XL, Franken A, Ram AFJ, Punt PJ, Maarel MJEC, Dijkhuizen L (2007a) Two
novel, putatively cell wallassociated and glycosylphosphatidylinositolanchored alpha
glucanotransferaseenzymesofAspergillusniger.EukaryotCell6:11781188
VanderKaaijRM,JanecekS,vanderMaarelMJEC,DijkhuizenL(2007b)Phylogeneticandbiochemical
characterization of a novel cluster of intracellular fungal amylase enzymes. Microbiology
153:40034015
van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L (2002) Properties and
applicationsofstarchconvertingenzymesoftheamylasefamily.JournalofBiotechnology
94:137155
van der VlugtBergmans CJB and van Ooyen AJJ (1999) Expression cloning in Kluyveromyces lactis.
Biotechnol.Technol.13:87–92
vanDijckPW,SeltenGC,HempeniusRA(2003)OnthesafetyofanewgenerationofDSMAspergillus
nigerenzymeproductionstrains.Regul.Toxicol.Pharmacol.38:2735
Van Gorcom RFM, van Hartingsveldt W, van Paridon PA, Veenstra AE, Luiten RGM, Selten GCM
(1991)Cloningandexpressionofmicrobialphytase.EuropeanPatentApplication0.420.358
vanHartingsveldtW,MatternIE,vanZeijlCM,PouwelsPH,vandenHondelCA(1987)Development
of a homologous transformation system for Aspergillus niger based on the pyrG gene. Mol
GenGenet206:7175
van Hartingsveldt W, van Zeijl CM, Harteveld GM, Gouka RJ, Suykerbuyk ME, Luiten RG, van
Paridon PA, Selten GC, Veenstra AE, van Gorcom RFM, van den Hondel (1993) Cloning,
characterizationandoverexpressionofthephytaseencodinggene(phyA)ofAspergillusniger.
Gene.127(1):8794
vanHartingsveldtW,MatternIE,vanZeijlCM,PouwelsPH,vandenHondelCA(1987)Development
ofahomologoustransformationsystemforAspergillusnigerbasedonthepyrGgene.MolGen
Genet206:7175
Van Loo J, Coussement P, DeLeenheer L, Hoebregs H, Smits G (1995) On the presence of inulin and
oligofructose as natural ingredients in the Western diet. CRC Crit. Rev. Food Sci. Nutr.
35:525552
van Peij NN, Gielkens MM, de Vries RP, Visser J, de Graaff LH (1998b) The transcriptional activator
XlnRregulatesbothxylanolyticandendoglucanasegeneexpressioninAspergillusniger.Appl
EnvironMicrobiol64:36153619
vanPeijNN,VisserJ,deGraaff LH(1998a)IsolationandanalysisofxlnR,encodingatranscriptional
activatorcoordinatingxylanolyticexpressioninAspergillusniger.MolMicrobiol27:131142
Vandamme EJ, Derycke DG (1983) Microbial inulinase: fermentation process, properties, and
applications.Adv.Appl.Microbiol29:139176
Vankuyk PA, Diderich JA, MacCabe AP, Hererro O, Ruijter GJ, Visser J (2004) Aspergillusniger mstA
encodes a highaffinity sugar/H+ symporter which is regulated in response to extracellular
pH.BiochemJ379:375383
VargaJ,KeveiF,VriesemaA,DebetsF,KozakiewiczZ,CroftJH(1994)MitochondrialDNArestriction
fragment length polymorphisms in field isolates of the Aspergillus niger aggregate. Can J
Microbiol.40(8):612621
