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
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Chapter 5
Database mining and transcriptional analysis of genes encoding inulin modifying enzymes of
Aspergillus niger
XiaoLianYuan*,CoenieGoosen*,HarrieKools,MarcJ.E.C.vanderMaarel,
CeesA.M.J.JvandenHondel,LubbertDijkhuizenandArthurF.J.Ram
*Theseauthorscontributedequallytothiswork
PublishedinMicrobiology.2006Oct;152(Pt10):30613073
Abstract
As a soil fungus, Aspergillusniger is able to metabolize a wide variety of carbon sources,
employingsetsofenzymesabletodegradeplantderivedpolysaccharides.Inthisstudy,we
have surveyed the genome sequence of A. niger strain CBS513.88, to analyze the
gene/enzyme network involved in utilization of the plant storage polymer inulin, and of
sucrose, the substrate for inulin synthesis in plants. In addition to three known activities,
encodedbythesuc1gene(invertaseactivity;designatedsucA),theinuEgene(exoinulinase
activity)andtheinuA/inuBgenes(endoinulinaseactivity),twonewputativeinvertaselike
proteinswereidentified.ThesetwoputativeproteinslackNterminalsignalsequencesand
thereforeareexpectedtobeintracellularenzymes.Oneofthesetwogenes,designatedsucB,
is expressed at a low level, and its expression is upregulated when A.niger is grown on
sucrose or inulincontaining media. Transcriptional analysis of the genes encoding the
sucrose (sucA) and inulin hydrolyzing enzymes (inuA and inuE) indicated that they are
similarly regulated and all strongly induced on sucrose and inulin. Analysis of a creA
mutantstrainofA.nigerrevealedthatexpressionoftheextracellularinulinolyticenzymesis
undercontrolofthecataboliterepressorCreA.Expressionoftheinulinolyticenzymeswas
notinducedbyfructose,noteveninthecreAbackground,indicatingthatfructosedidnot
actasaninducer.Weprovideevidencethatsucrose,orasucrosederivedintermediate,but
notfructose,actsasaninducerfortheexpressionofinulinolyticgenesinA.niger.
Introduction
Inulins are linear polymers of fructose residues (fructans), which are primarily linked by
2,1glycosidicbonds,andusuallyfollowedbyaterminalglucosemoiety.Inulinispresent
asstoragepolysaccharideinrootsandtubersofplantssuchasJerusalemartichoke,chicory
and dahlia (Cairns, 2003). Its presence has also been implicated in protection against water
deficitindryandcoldconditions(Hendry&Wallace,1993;PilonSmitsetal.,1995).Inulin
inplantsissynthesizedbytheconcertedactionoftwofructosyltransferases,withsucroseas
theprimaryfructosyldonor(seeforreviewRitsema&Smeekens,2003).Inulinhasattracted
considerable research attention because it is a relatively inexpensive and abundant
substratefortheproductionoffructoserichsyrups,aswellasasourcefortheproductionof
fructooligosaccharides (FOS). Both fructose syrups and FOS are regarded as ‘functional
foods’ since they positively influence the composition of the intestinal microflora (Yun,
1996;Roberfroid&Delzenne,1998;Kaplan&Hutkins,2003).
Yeasts and filamentous fungi have been shown to employ various enzymes to
degrade inulin and sucrose (Pandey et al., 1999). Apart from displaying substrate
hydrolysis, some of these enzymes can also perform transfructosylation reactions,
producingthetrisaccharide1kestosefromsucrose(Rehmetal.,1998;Sangeethaetal.,2004;
Yanai et al., 2001) and even longer fructooligosaccharides (Heyer & Wendenburg, 2001).
Currently,allknownfungalinulinmodifyingenzymesaregroupedtogetherinfamily32of
glycoside hydrolases (GH32) (http://afmb.cnrsmrs.fr/CAZY/index.html, Coutinho &
Henrissat, 1999). Members of this family GH32 share conserved amino acid motifs and
possessasimilarthreedimensionalproteinstructure(Ponsetal.,1998;Albertoetal.,2004;
Nagemetal.,2004).
A. niger degrades inulin using both endoinulinases (EC 3.2.1.7), encoded by the
inuA and inuB genes (Ohta et al., 1998; Akimoto et al., 1999), and an exoinulinase (EC
3.2.1.80), encoded by the inuE gene (Moriyama et al., 2003). Endoinulinase hydrolyzes
inulininternallytoproducemainlyinulotrioseand–tetraose(Akimotoetal.,1999),whereas
exoinulinase hydrolyzes the terminal 2,1fructosidic bonds in both sucrose and inulin
(Arand et al., 2002; Kulminskaya et al., 2003; Moriyama et al., 2003). Invertase
(Efructofuranosidase, EC 3.2.1.26), encoded by the suc1 gene (Boddy et al., 1993),
hydrolyzesthe2,1glycosidicbondinsucrosetoproducefructoseandglucose(L’Hocine
et al., 2000). A specific fructosyltransferase activity (EC 2.4.1.9) without significant
invertase activity has been purified from A. niger strain AS0023. This enzyme transfers
fructose residues from the nonreducing terminal 2,1glycosidic bond in sucrose to
another sucrose or inulin molecule to form kestose or higher fructooligosaccharides
(L’Hocineetal.,2000).Unfortunately,thegeneencodingthisenzymeactivityhasnotbeen
identifiedandcharacterizedyet.
Recent advances made in the area of genome sequencing of A. niger opened
possibilitiestofurtherexploitthisfungustoidentifyadditionalinulinmodifyingenzymes.
The full genomic sequence of A.niger was made available to us by DSM Food Specialties
(http://www.dsm.com). Based on deduced amino acid similarities, we have identified six
putativeproteinsthatbelongtofamilyGH32.Apartfromthethreeknownfungalenzymes
(InuA/B, InuE and Suc1), three new putative inulin modifying enzymes were identified.
One of them appears to be a pseudogene (inuQ), while the other two encode intracellular
invertaselike proteins and were named SucB and SucC. The transcriptional regulation of
thesefiveputativeinulin/sucrosemodifyingproteinsinrelationtovariouscarbonsources
hasbeenstudiedinfurtherdetail.
Materials and methods
Strainsandcultureconditions
A.nigerstrainN402 used in thisstudy wasderived from the wildtypestrain A.nigervan
Tieghem (CBS 120.49, ATCC 9029) (Bos et al., 1988). The A. niger strain used for the
sequencingofthegenomebyDSMisCBS513.88(anaturalderivativeofstrainNRRL3122).
Strain AB4.1 is a pyrGderivative of N402 (van Hartingsveldt etal., 1987) and was used to
construct the creAdeletion strain. A.nigerstrains were grown in Minimal Medium (MM)
(Bennett & Lasure, 1991) containing 7 mM KCl, 11 mM KH2PO4, 70 mM NaNO3; 2mM
MgSO4, 76 nM ZnSO4, 178 nM H3BO3, 25 nM MnCl2, 18 nM FeSO4, 7.1 nM, CoCl2, 6.4nM
CuSO4,6.2nMNa2MoO4and174nMEDTA.Erlenmeyerflasksof300mlwereinoculated
with2x106spores/mlandincubatedat30°Cinarotaryshakerat300rpmfor21h.Each
flaskcontained100mlofMM(pH6.5)supplementedwith0.1%(w/v)casaminoacidsand
2% (w/v) carbon source. Glucose, sucrose (BDH Chemicals Ltd), xylose, fructose and
maltose (SigmaAldrich), inulin (Sensus, Frutafit® TEX, Cosun, The Netherlands) and
starch(Windmillstarch,Avebe,TheNetherlands)wereusedascarbonsources.Fortransfer
experiments, N402 was pregrown in MM supplemented with 2%(w/v)xylose or 2% (v/v)
glycerol and 0.1% (w/v) casamino acids for 18 h at 30 °C on a rotary shaker at 300 rpm.
MyceliumwasharvestedbysuctionoveranylonmembraneandwashedwithMMwithout
carbonsource.Aliquotsof1.5gwetweightofmyceliumweretransferredto70mlofMM
containing1%(w/v)variouscarbonsourcesandincubatedat30°Cwithagitation.Mycelial
samplesweretakenatdifferenttimepointsbyharvestingoveraMyraclothfilterfollowed
by freezing in liquid nitrogen. The samples were stored at 80 °C prior to the isolation of
total RNA. Conidiospores were obtained by harvesting spores from a complete medium
plate (minimal medium with 0.5% (w/v) yeast extract and 0.1% (w/v) casamino acids)
containing 1%(w/v) glucose, after 46 days of growth at 30 °C, using a 0.9% (w/v) NaCl
solution.
Transformation of A.nigerAB4.1wasasdescribedbyPunt&vandenHondel(1992)
usinglysingenzymes(L1412,SigmaAldrich)forprotoplastformation.Thebacterialstrain
used for transformation and amplification of recombinant DNA was Escherichia coli
XL1Blue(Stratagene,U.S.A).TransformationofXL1Bluewasperformedaccordingtothe
heatshockprotocolasdescribedbyInoueetal.,1990.
Table1.FungalfamilyGH32proteinsusedformultiplesequencealignmentinFigs.1and2
Name Main activity Acc. No. Organism Reference
AngSucAp Invertase DQ233218 Aspergillus niger CBS 513.88 This study
AngSuc1p Invertase S33920 Aspergillus niger B60 Boddy et al., 1993 AsySftAp Fructosyltransferase CAB89083 Aspergillus sydowii IAM 2544 Heyer & Wendenburg, 2001 AjaFopAp Fructosyltransferase BAB67771 Aspergillus japonicus ATCC 20611 Yanai et al., 2001 AngSucBp Putative invertase DQ233219 Aspergillus niger CBS 513.88 This study AngSucCp Putative invertase DQ233220 Aspergillus niger CBS 513.88 This study AngInuEp Exo-inulinase DQ233222 Aspergillus niger CBS 513.88 This study Afo1-Sstp Fructosyltransferase CAA04131 Aspergillus foetidus NRRL 337 Rehm et al.,1998
Ang12InuEp Exo-inulinase BAD01476 Aspergillus niger 12 Moriyama et al., 2003 Aawinu1p Exo-inulinase CAC44220 Aspergillus awamori var. 2250 Arand et al., 2002 PspInuDp Exo-inulinase BAC16218 Penicillium sp. TN-88 Moriyama et al., 2002 AngInuAp Endo-inulinase DQ233221 Aspergillus niger CBS 513.88 This study
AfiInu2p Endo-inulinase CAA07345 Aspergillus ficuum ATCC 16882 Uhm et al., 1998 Ang12InuAp Endo-inulinase BAA33797 Aspergillus niger 12 Ohta et al., 1998 Ang12InuBp Endo-inulinase BAA33798 Aspergillus niger 12 Ohta et al., 1998 PpuInuAp Endo-inulinase BAA12321 Penicillium purpurogenum Onodera et al., 1996 PspInuCp Endo-inulinase BAB19132 Penicillium sp. TN-88 Akimoto et al., 2000 KmaInu1p Inulinase CAA40488 Kluyveromyces marxianus ATCC 12424 Laloux et al., 1991 SceSuc2p Invertase P00724 Saccharomyces cerevisiae Taussig & Carlson, 1983 PjaInv1p Invertase CAA73208 Pichia jadinii NRRL-Y1084 Chávez et al., 1998 PanInv1p Invertase CAA56684 Pichia anomala CBS5759 Pérez et al., 1996 SpoInv1p Invertase BAA25684 Schizosaccharomyces pombe TP4 Tanaka et al., 1998
DatabaseminingofA.nigergenome
The A. niger CBS513.88 genome has been determined by random sequencing of selected
BACs to a 7.5fold coverage. The resulting genome sequence (35.9 Mb) consists of
approximately400contigs,whichareassembledinto19supercontigs(Dr.N.vanPeij,DSM,
personal communication). The sequence of the A. niger genome is currently available to
academic groups and nonprofit organizations on request (hans.roubos@dsm.com) after
signingaMaterialTransferAgreementandwillbegenerallyavailableafterpublicationof
theA.nigergenomesequence(H.Peletal.,inpreparation).Accessionnumbersofcurrently
describedfamiliesGH32andGH68memberswereselectedfromtheCarbohydrateActive
Enzymes server at URL: http://afmb.cnrsmrs.fr/CAZY/ (Coutinho & Henrissat, 1999), and
the corresponding protein sequences were extracted from the GenBank/GenPept database
and SwissProt database released at URL: http://www.ncbi.nlm.nih.gov/entrez/ and URL:
http://www.expasy.org/sprot/. Sequences were aligned with the ClustalW program
(Thompson et al., 1994; Chenna et al., 2003) and transformed in a Hidden Markov Model
(HMM) profile (Eddy, 1998) with the HMMbuild program from the HMMer package
obtainedatURL:http://hmmer.wustl.edu/.SubsequentlytheA.nigergenomewassearched
using the HMM profiles and the wise2 package from URL: http://www.ebi.ac.uk/Wise2/.
Multiple sequence alignment of known fungal fructan modifying enzymes, based on full
length predicted proteinsequences (Table 1), was performed using the ClustalW interface
inMega3.1(www.megasoftware.com)withgapopeningandextensionpenaltiesof10and
0.2, respectively. Bootstrap test of phylogeny was performed by the Neighbor Joining
methodusing1000replicates.
Northernanalysis
Total RNA wasisolatedbygrindingfrozen(80°C)myceliuminliquidnitrogenwithapestle
and mortar. Powdered mycelium (200 mg) was extracted with 1 ml TRIzol Reagent
(Invitrogen,U.S.A)inaccordancewiththesupplier’sinstructions.ForNorthernanalysis,5
Pg of total RNA was incubated with 3.3 Pl 6 M glyoxal, 10Pl DMSO and 2 Pl 0.1M
phosphatebuffer(pH7)inatotalvolumeof20Plfor1hat50°CtodenatureRNA.RNA
electrophoresiswasperformedinaSEA2000electrophoresisapparatus(ElchromScientific,
Switzerland) at 10 °C. The RNA samples were separated on 1.5% (w/v) agarose gel using
0.01M phosphate buffer (pH 5) and transferred to HybondN filters (Amersham, UK) by
capillaryblotting.Filterswereprehybridizedat65°Cfor2hinasolutionof0.9MNaCl,90
mMNa3citrate,1.0%(w/v)ficoll,1.0%(w/v)polyvinylpyrolidone,1.0%(w/v)bovineserum
albumin,10mMEDTA,0.5%(w/v)SDSand100Pg/mlsinglestrandedherringspermDNA.
Hybridizationswereperformedat42°Cfor18hinasolutionof50%(v/v)formamide,10%
(w/v) dextran sulphate, 0.9M NaCl, 90mM Na3citrate, 0.2% (w/v) ficoll, 0.4% (w/v)
polyvinylpyrolidone, 0.4% (w/v) bovine serum albumin, 0.4% (w/v) SDS and 100 g/ml
singlestrandedherringspermDNA.Blotswerewashedtwiceinhighstringencywashing
buffer(30mMNaCl,3mMNa3citrateand0.5%(w/v)SDS)for20minat65°C.Probesfor
thedetectionofthesix(putative)sucroseandfructanmodifyingenzymesofA.niger,were
generated using six pairsofoligonucleotide primers by PCR using A.nigerN402 genomic
DNA as template (Supplementary Table 1). The PCRamplified fragments were run onan
agarose gel and purified from the gel. The purified DNA fragments were cloned into
plasmid pGEMTeasy and sequenced to confirm their identity. Probes were generated by
digestionofthepGEMTeasyvectorcontainingtheinulinolyticenzymeencodinggenewith
EcoRI.Fragmentswerepurifiedfromgeland[32P]dCTPlabeledprobesweresynthesized
usingRediprimeIIDNAlabelingSystem(AmershamPharmaciaBiotech,UK)accordingto
theinstructionsofthemanufacturer.
DisruptionofthecarboncataboliterepressorCreAinA.niger
TheplasmidusedtodisruptthecreAgenewasconstructedasfollows.TheDNAfragments
flankingthecreAORFwereamplifiedbyPCRusingN402genomicDNAastemplate:1.4kb
of 5’ flanking DNA and 0.9 kb of 3’flanking DNA was amplified by PCR using primers
CreAP1fandCreAP2r,CreAP3fandCreAP4r(SupplementaryTable1),respectively.Each
primerwasadaptedwitharestrictionsiteforfurthercloning.TheamplifiedPCRfragments
weredigestedwithNotIandBamHIorBamHIandKpnIrespectively,andclonedintopBlue
ScriptII SK to obtain plasmids pF5 and pF3. Subsequently, pF3 was digested with BamHI
andKpnI,andtheobtainedfragmentwasligatedintoBamHIandKpnIdigestedpF5togive
pF53. pF53 was digested with SalI and BamHI and inserted with the SalIBamHI fragment
containing A. oryzae pyrG gene, obtained from plasmid pAO413 (de RuiterJacobs et al.,
1989) and resulted in the creA disruption plasmid, pXY1.1. The plasmid pXY1.1 was
linearized with NotI and transformed to AB4.1. Uridine prototrophic transformants were
selected by incubating protoplasts on agar plates containing MM without uridine.
Transformants were purified and genomic DNA was isolated and analyzed by PCR to
identifypossiblecreAstrains.Primerpairsusedtoidentifyhomologousrecombinationof
thecreAdeletionconstructonthecreAlocuswerecreAP5fandPAO10orPAO9andcreA6f.
Primer pairs used in the PCR to analyze the presence of the wild type creA gene were
creAP5f and creAP7r, creAP8f and creAP6r (Supplementary Table 1). Three independent
creAdeletionstrainswithidenticalphenotypeswereobtainedanddesignatedXY1.1,XY1.2
andXY1.3.StrainXY1.1wasfurtherusedforanalysisoftheexpressionofinulinmodifying
enzymesandwewillrefertothisstrainasthecreAstrainintheremainingofthepaper.
ForcomplementationofthecreAstrain,thecreAgene,including1.3kbpromoterand0.8
kbofterminatorsequences,wasamplifiedbyPCRusingprimerscreAP1fandcreAP6r.The
PCR product of 3.5 kb was cloned into pGEMTeasy (Promega) and cotransformed with
pAN7.1(Puntetal.,1987)tocreAstrainXY1.1togenerateXY1.1CreA.
Nucleotideaccessionnumbers
TheA.nigerCBS513.88DNAsequencesencodingfamilyGH32members,including1000bp
up and downstream of open reading frame and their predicted protein sequences were
obtainedfromDSM(Dr.G.Groot).ThesequencedatahavebeensubmittedtotheGenBank
database under accession numbers DQ233218 (sucA), DQ233219 (sucB), DQ233220 (sucC),
DQ233221(inuA),DQ23322(inuE)andDQ233223(inuQ).
Results
IdentificationofGlycosideHydrolasefamily32membersintheA.nigergenome
Glycoside hydrolase families GH32 and GH68 include invertase, levanase, inulinase and
levansucraseenzymesfrombacterial,fungalandplantorigin(Coutinho&Henrissat1999;
Ponsetal.,1998).Bothfamiliesarestructurallysimilar(clanGHJ),sharingasimilar5fold
propeller fold (Meng & Futterer, 2003; Nagem et al., 2004). Protein sequences from
members of families GH32 and GH68 were extracted from GenBank/GenPept and
SwissProt databases and were used to construct HMM profiles to identify additional
members in the genome of A. niger CBS513.88. Family GH68 profiles did not return any
significant matches. The family GH32 profile did return five significant sequences. In
addition to three family GH32 members already described for A. niger (invertase (Suc1,
Boddy et al., 1993), exoinulinase (InuE, Moriyama et al., 2003) and endoinulinases
(InuA/InuB,Ohtaetal.,1998),twonewmemberswereidentifiedwhichwerenamedSucB
andSucC.
Ang12InuAp AfiInu2p
AngInuAp Ang12InuBp
PpuInuAp PspInuCp PspInuDp AawInu1p Ang12InuEp Afo1-Sstp AngInuEp
SceSuc2p KmaInu1p SpoInv1p PjaInv1p
PanInv1p AngSucCp AngSucBp AsySftAp AjaFopAp AngSuc1p AngSucAp 100 89
100
92 100 100
93 74 100
100 100
100
100 79
100
100
100
99 89
Ang12InuAp AfiInu2p
AngInuAp Ang12InuBp
PpuInuAp PspInuCp PspInuDp AawInu1p Ang12InuEp Afo1-Sstp AngInuEp
SceSuc2p KmaInu1p SpoInv1p PjaInv1p
PanInv1p AngSucCp AngSucBp AsySftAp AjaFopAp AngSuc1p AngSucAp 100 89
100
92 100 100
93 74 100
100 100
100
100 79
100
100
100
99 89
Filamentous fungi Invertase Exo-inulinase/
Fructosyltransferases Endo-inulinase
Yeast Invertase/inulinase
Fig. 1. Neighbourjoining tree of functionally characterized GH32 family members from filamentous
fungi and yeast species. GH32 proteins identified in the genome of A.niger CBS513.88 are shown in
bold.Theproteins,theirmainactivities,accessionnumbers,andthesource(organisms)oftheprotein
sequencesusedinthisalignment,arelistedinTable1.Bootstrapvaluesareindicatedonthe node of
eachbranch.ThetreewascreatedwithMega3.1usingdefaultsettingsforgapandextensionpenalties.
Barindicates10%aminoacidsequencedifference.
