ContentslistsavailableatScienceDirect
Journal
of
Molecular
Catalysis
B:
Enzymatic
jo u r n al h om ep ag e :w w w . e l s e v i e r . c o m / l o c a t e / m o l c a t b
␣-Rhamnosidase
activity
in
the
marine
isolate
Novosphingobium
sp.
PP1Y
and
its
use
in
the
bioconversion
of
flavonoids
Viviana
Izzo
a,c,
Pietro
Tedesco
a,
Eugenio
Notomista
a,
Eduardo
Pagnotta
b,
Alberto
Di
Donato
a,
Antonio
Trincone
b,
Annabella
Tramice
b,∗aDipartimentodiBiologia,UniversitàdiNapoliFedericoII,ComplessoUniversitariodiMonteS.Angelo,ViaCinthia4,80126Naples,Italy bIstitutodiChimicaBiomolecolare,ConsiglioNazionaledelleRicerche,ViaCampiFlegrei34,80072Pozzuoli,Naples,Italy
cDipartimentodiMedicinaeChirurgia,UniversitàdegliStudidiSalerno,ViaS.Allende,84081Baronissi,Salerno,Italy
a
r
t
i
c
l
e
i
n
f
o
Articlehistory: Received3January2014
Receivedinrevisedform6March2014 Accepted5April2014
Availableonline18April2014 Keywords:
␣-l-rhamnosidase Novosphingobiumsp.PP1Y Flavonoidsbioconversion
a
b
s
t
r
a
c
t
CrudeproteinextractsofNovosphingobiumsp.PP1Y,amicroorganismisolatedfrompollutedmarine watersinPozzuoli(Italy),wereanalyzedforthepresenceofglycosidaseactivities.Particularattention wasdevotedtoa␣-L-rhamnosidaseactivityabletohydrolyzeseveralflavonoidsofinterestforthe phar-maceuticalandfoodindustries.ThisactivityhadanalkalinepHoptimumandamoderatetolerancetothe presenceoforganicsolvents,appealingfeaturesforitspossiblebiotechnologicaluses.Anincreaseofthe ␣-L-rhamnosidaseactivityinPP1Ycrudeextractswasinducedbyaddingnaringintothegrowthmedium, suggestingthepossibilitytousematerialfromCitrusindustrialwastetoinducetheglycosidaseactivity expressedbystrainPP1Yandproducesimultaneouslyhigh-added-valuemoleculesfromthehydrolysisof theirflavonoids.InordertoinvestigateontheenzymaticmechanismofPP1Y␣-L-rhamnosidaseactivity, hydrolysisproductsofPNP-␣-L-rhamnopyranosidewereanalyzedby1H-NMRexperiments.Thekinetic
behaviourclearlyindicatedaninvertingmechanismofhydrolysisforthisnovelenzymaticactivity. ©2014ElsevierB.V.Allrightsreserved.
1. Introduction
Biocatalysisrepresentsnowadaysaversatileandvaluabletool forindustrialbiotechnologies.Theuseofenzymesasbiocatalysts canhavesignificantbenefitscomparedtoconventionalchemical technologies,forachievinghighreactionselectivity,higher reac-tionrate,improvedproductpurity,andasignificantdecreasein chemicalwasteproduction.Awidevarietyofchemicalsubstances is already produced in industrial processes through theuse of enzymes[1,2].
Withinthisframework,␣-l-rhamnosidases[E.C.3.2.1.40]have attractedgreatattentioninthelastdecadeduetotheirapplication asbiocatalystsinavarietyoffood,pharmaceuticalandchemical industrialprocesses[3].
␣-l-Rhamnosidases(fromnowonindicatedas␣-RHAs)area classofglycosylhydrolasesthatspecificallycleaveterminal ␣-l-rhamnosefromalargenumberofnaturalproducts,whichinclude flavonoids,someterpenylglycosides[4,5]andmanyothernatural glycosidescontainingaterminalrhamnose,suchasglycopeptides antibioticsandglycolipids[6].Theseenzymeshaverecentlybeen
∗ Correspondingauthor.Tel.:+390818675070;fax:+390818041770. E-mailaddress:atramice@icb.cnr.it(A.Tramice).
thefocusofanincreasingscientificinterest.Asanexample,theuse of␣-RHAstoimprovethebioavailability,andthusthebiological activity,offlavonoidsbeneficialforhumanhealthasdirectdrugs orasnutritionalsupplements,hasbeenreported[3].
Moreover,l-rhamnosehasacentralroleintheorganicsynthesis asachiralintermediateofpharmaceuticallyimportantcompounds. Itsproductionusingtheenzymaticactivityof␣-RHAsinhydrolysis reactionsofglycosylatedcompoundsthatmightberecoveredfrom wastematerialoffoodprocessingindustry(e.g.citruspeel), repre-sentsaninterestingandusefulbiotechnologicalapplicationthese glycosidases[7].
Fungiarethemainsourceof␣-RHAs.However,theseenzymes havebeenisolatedalsofromanimaltissues,suchastheliverofboth themarinegastropodTurbocornutus[8]andpig[9],andfromplants suchasRhamnusdaurica[10]andFagopyrumesculentum[11].
Bacteriarepresentayetunexploredreservoirof␣-RHAs,which mightshownovelinterestingproperties.Ananalysisofseveral ␣-RHAsisolatedfromvariousmicrobialsourcesreveals,forexample, thatoneofthemaindifferencesfoundbetweenfungaland bacte-rialenzymesistheiroptimalpH,withthefungalenzymesshowing more acidic pHoptimacompared tobacterialcounterparts, for whichneutralandalkalineoptimalpHvalueshavegenerallybeen reported.Thischaracteristicsuggestsdifferentpotential applica-tionsforfungalandbacterialenzymes,makingbacterial␣-RHAs
http://dx.doi.org/10.1016/j.molcatb.2014.04.002 1381-1177/©2014ElsevierB.V.Allrightsreserved.
suitableinbiotechnologicalprocessesrequiring goodactivityin more basicsolutions such as theproduction of l-rhamnose by hydrolysisofnaringinorhesperidin,compoundswhosesolubility stronglyincreasesathigherpHvalues[3,12].
Despitetheverylimitednumberofbacterial␣-RHAsthathas beendescribedsofar,datainliteraturesuggestthatthisenzymatic activityis widelydistributed over a diverserangeof ecological niches.␣-RHAshavebeendetectedandcharacterizedinthehuman intestinalbacteriumBacteroidesJY-6[13],incold-adapted Pseu-doalteromonasspecies and Ralstoniapickettii isolatedin thesea waterofsubAntarcticenvironment[14],alsoinsoilbacteriasuchas Bacillussp.GL1[15,16],SphingomonaspaucimobilisFP2001[17]and Sphingomonassp.R1[18]andfinallyinwinestrainsofOenococcus oeni[19].
␣-RHAsfromLactobacillusspecieswereidentifiedand investi-gatedfortheirpotentialbiotechnologicalusetode-rhamnosylate flavonoidspresentinfrequentlyconsumedfoodcommodities[20]. Moreover,␣-RHAsgeneshavebeenclonedandexpressedfrom thermophilic bacteriasuch asClostridiumstercorarium [21] and fromthebacteriumPRI-1686,whichisamemberofthephylum ofThermomicrobia[22].
Recently, the crystal structure of Streptomyces avermitilis ␣-l-rhamnosidase(SaCBM67)wasreported[23];itsstructure pre-sentedanovelcatalyticcarbohydrate-bindingmoduleandresulted different from the only two structures of ␣-l-rhamnosidases (GH78)previouslyreported:theBsRhaBisolatedfromBacillussp. GL1[24] and theputative␣-l-rhamnosidase BT1001from Bac-teroidesthetaiotaomicronVPI-5482[25].
Itgoeswithoutsayingthatthebiotechnologicalpotentialof bac-terial␣-RHAs,whosestructural,functionalandmolecularbiology aspectshavenotbeensufficientlyinvestigated,isstrictlyrelated totheacquisitionofnewinformationontheenzymaticsystems isolatedfromnewbacterialsources.
Recently, Novosphingobium sp. PP1Y, an organic solvent-resistant, biofilm-forming marine microorganism, was isolated fromthesurfacewatersofadockingbayintheharbourof Poz-zuoli(Naples,Italy),anareaheavilypollutedwithhydrocarbons
[26].Theanalysisofitsgenome,confirmedthepresenceofseveral genomicfeaturesofinterestforthebiotechnologicalpotentialof thismicroorganism,andmorespecificallyforitsexploitationasa sourceofenzymesactiveoncarbohydrates.StrainPP1Yshowsin factauniqueabundanceamongSphingomonadalesofgenes encod-ingforglycosyl hydrolases(53orfs)[27],whichare distributed among27differentfamilies.Thispromptedourinterestin investi-gatingthepresenceof␣-RHAactivitiesinthecrudeproteinextract ofstrainPP1Y.
Inthiswork,cellextractsobtainedfromNovosphingobiumsp. PP1Ycellsgrowninminimalmediumweretestedforthepresence ofglycosidase activities;in particular␣-RHAand -glucosidase activitiesweredetectedandpartiallycharacterized.
This ␣-RHA activity was successfully used in bioconversion studiesofflavonoidiccompounds,thussuggestingitspotentialuse asaneco-friendlytooltomodulatethebiologicaland pharmacolog-icalpropertiesofthesemolecules.Itwasfurtherdemonstratedby
1H-NMRexperimentsthat␣-RHAactivityfromNovosphingobium
sp.PP1Yfunctionedwithaninvertingmechanism,inagreement withtheenzymaticmechanismalreadyproposedforother␣-RHAs previouslydescribed.
2. Materialsandmethods
2.1. General
Novosphingobiumsp.PP1Ywasisolatedaspreviouslyreported
[26].AllreagentswerepurchasedfromSigma-Aldrichandused
withoutany furtherpurification. Silica gel, reverse-phasesilica gelC-18andTLCsilicagelplateswerefromE.Merck(Darmstadt, Germany).Allotherchemicalswereofanalyticalgrade.Compounds onTLCplateswerevisualizedunderUVlightorcharringwith ␣-naphtholreagent.
TLCsolventsystemsusedwere(A)EtOAc:MeOH:H2O,70:20:10
and(B)EtOAc:AcOH:2-Propanol:HCOOH:H2O,25:10:5:1:15. 1H-,13C-and2D-NMRspectrawereacquiredbytheNMRService
oftheIstitutodiChimicaBiomolecolareoftheNationalResearch CouncilofItaly(C.N.R.-Pozzuoli,Naples,Italy)andrecordedona BrukerDRX-600spectrometer,equippedwithaTCICryoProbeTM,
fitted with a gradient along the Z-axis, and on other Bruker instrumentswithfieldsat400and/or300MHz.SamplesforNMR analysisweredissolvedintheappropriatesolvent;spectrainD2O
were referenced to internal sodium
3-(trimethyl-silyl)-(2,2,3,3-2H
4) propionate (Aldrich, Milwaukee, WI); for other solvents
downfieldshiftofthesignalofthesolventwasusedasinternal standard.
Inthebioconversionstudiesfollowedby1H-NMRexperiments,
reportedin paragraph2.8 and 2.9,the selectedsignals integral valuesofproductsand reagentsresultedaffectedbyanerrorin integration(<5%)whichdependeduponinstrumentoptimization. Proteinconcentrationwasroutinelyestimatedusingthe Bio-Rad Protein System [28]; bovine serum albumin was used as standard.
2.2. Bacterialgrowth
Novosphingobium sp. PP1Y wasroutinely grown in minimal medium. Potassium phosphate minimal medium (PPMM) con-tained 20mM potassium phosphate pH 6.9, 1g/L NH4Cl and
100mMNaCl.Afterautoclaving,5mLofatraceelementsolution wasaddedtoeachlitreofcooledPPMM.Thetraceelement solu-tioncontainedina0.92%solutionofHCl:30.1g/LMgSO4,4.75g/L
FeSO4×7H2O, 5.4g/L MgO, 1.0g/L CaCO3, 0.72g/L ZnSO4×7
H2O, 0.56g/L MnSO4×H2O, 0.125g/L CuSO4×5 H2O, 0.14g/L
CoSO4×7H2O,0.03g/LH3BO3,0.004g/LNiCl2×6H2O,0.006g/L
Na2MoO4×2H2O. When usingPPMM as growthmedium, 0.4%
(w/v)of glutamic acid, preparedin deionized water and steril-izedbyfiltrationwitha0.22mMilliporemembrane,wasused asuniquecarbonandenergysourceandaddedtotheautoclaved media. Cultures were incubated at 30◦C with orbital shaking (220rpm).
Bacterial growth was monitored by measuring the optical densityat600nm(OD600).Apre-inoculuminrichmediumwas
pre-paredbytransferring50Lfromaglycerolstockstoredat−80◦C
toa50mLFalcontubecontaining12.5mLofsterileLBmedium.LB waspreparedaccordingtoSambrooketal.[29].Thepre-inoculum wasallowedtogrowat30◦Cforatleast14hat220rpmandthen usedtoinoculate1LofapreparativegrowthinPPMMmediumat aninitialcellconcentrationof0.01–0.02OD600/mL.Cellswere
usu-allyharvestedafter24hatafinalopticaldensityofca.1OD600/mL.
Itisworthytonotethat,whenfollowingthegrowthformorethan 24h,theformationofflockswasobserved,thushamperingacorrect estimationoftheturbidityofthecellsuspension.
2.3. PreparationofNovosphingobiumsp.PP1Ycrudeprotein extract
Cellcultureswereharvestedbycentrifugationat5,524×gfor 30minat4◦C.Cellpelletsweresuspendedin25mMMOPSatpH 7.0anddisruptedbysonication(30total,30sONand30sOFF)in anice-waterbath.Cellsuspensionwascentrifugedat17,418×gat 4◦Cfor60min.Thesolublefractionobtainedaftercentrifugation wasfilteredona0.45mmMilliporemembrane,dividedinaliquots andstoredat−80◦C.Whenusedforthescreeningofglycosidase
Table1
Evaluationofdifferentsubstratesbioconversionbyusingglycosidaseactivitiesin thecrudeextractofNovosphingobiumsp.PP1Ycells.
Substratesa CrudeextractofPP1YcellsgrowninPPMMmedium Hydrolysisb Transglycosylationc 3h 24h 3h 24h PNP-␣-d-Glcp + + − +/− PNP--d-Glcp + ++ + ++ PNP-␣-d-Galp +/− + − +/− PNP--d-Galp + ++ + ++ PNP-␣-d-Manp − − − − PNP--d-Manp − − − − PNP-␣-d-Xylp − − − − PNP--d-Xylp + ++ +/− + PNP-␣-l-Fucp − − − − PNP--d-Fucp + ++ + ++ PNP␣-d-NAGp − − − − PNP-d-NAGp +/− + +/− +/− PNP-␣-l-Rhap ++ +++ − +/− PNP-␣-l-Araf − − − −
Note:−/+:percentageofproductsbelow10%;+:10–30%ofproducts;++:30–70%of products;+++:percentageofproductshigherthan70%.
aAraf,arabinofuranose;Fucp,fucopyranose;Galp,galactopyranose;Glcp,
glu-copyranose;Manp,mannopyranose;NAGp,N-acetylglucosaminopyranose;Rhap, Rhamnopyranose;Xylp,xylopyranose.
bHydrolysisproductswereanalyzedbycomparingRfvalueswithappropriate
standardsinTLCsolventsystemA.
c Due to self-transglycosylation reactions, products showed positive UV
absorbanceandlowerRfthanthecorrespondingarylsubstratesintheselectedTLC solventsystemA.
activities(Section2.4),thesolublefractionwasdialyzedagainst 20mMpotassiumphosphateatpH7,andthendividedinaliquots andstoredat−80◦C.PP1Ycrudeextractswereassayedfortheir
totalproteincontent.
Withoutanydifferentindication,allexperimentsreportedinthe followingsections,wereperformedusingacrudeextractobtained froma2LcultureofPP1YcellsgrowninPPMMmediumandwith a proteinconcentrationof 3.72mgtotal protein/mL. Cellswere recoveredafter24hatanopticaldensityof1.02OD600/mL.
2.4. Glycosidaseactivitiesscreening
PP1Ycrudeproteinextract,preparedasdescribedinthe previ-ousparagraph,wastestedforthepresenceofglycosidaseactivities byusingseveralpNP-␣-andpNP--substrates(Table1)ata20mM concentrationin0.6mLof50mMNa-phosphatebufferpH7,at 35◦Candundermagneticstirring.Allreactionswerecarriedout using4.42mgof totalprotein/mmol ofreagent. Reactionswere monitoredovertime(0–24h)byTLCanalysis(systemsolventA).
Moreover,hydrolysisreactionswithmaltose,lactose,cellobiose, sucrose,raffinose,laminaripentaose,laminarin,curdlan,-glucan frombarley,xylan frombirchwood, pullulan, amylopectin and starchassubstrateswerecarriedoutusingcrudeextractsofPP1Y cellsgrowninPPMM.Eachsubstrate(10mg)wassuspendedin 1mLof50mMNa-phosphatebufferpH7,containing41.6gof totalprotein/mLofreactionmixture.Reactionswereperformedat 35◦C.HydrolysisproductsweremonitoredbyTLCanalysis(system solventsAandB).
Flavonoidicsubstratessuch asnaringin, diosmin, rutin, hes-peridin,neohesperidindihydrochalcone,quericitrin,weretested. Tothispurpose,a2mMsolutionofeachcompoundpreparedin afinalvolumeof1mLof50mMNa-phosphatebufferpH7was incubatedat35◦Cinthepresenceof100LofPP1Ycrudeextract obtainedfromcellsgrowninPPMM(3.72mgoftotalprotein/mL) for24h.ReactionswerecheckedovertimebyTLCanalysis(solvent systemA).
Rutinosehydrolysiswasalsoinvestigated.Inthiscase,0.5mLof asolutioncontaining6mMrutinose,0.25mLofPP1Ycrudeextract in50mMofTris/HClbufferatpH8.5wasincubatedat35◦Cunder magneticstirringandmonitoredbyTLCanalysis(solventsystem A)for24h.
Inallexperiments,TLCstandardsolutionsofpurereagentsand productswereusedforcomparison.
2.5. ˛-l-rhamnosidaseactivityassay
␣-RHA activity was determined using p-nitrophenyl- ␣-l-rhamnopyranoside(pNPR)assubstrate.Theassaywasperformed in0.5mLof50mMpotassiumacetatebufferpH5.5,containinga variableamountofPP1YcrudeextractandpNPRatafinal concen-trationof0.28mM.Theassaymixturewasincubatedfor30min atroomtemperature;afterwards,0.5mLofa1Msodium carbon-atesolutionwereaddedandthesampleabsorbancewasrecorded spectrophotometricallyat405nm(ε405=0.0182M−1cm−1).One
milliunit of enzymatic activity was defined as the amount of enzymethatreleases1nmolofp-nitrophenolpermin.
2.6. Inductionof˛-l-rhamnosidaseactivity
Toevaluatethepossibleinfluenceofnaringin onthe expres-sionoftheintracellular␣-rhamnosidaseactivityofthestrainPP1Y, wecomparedthespecificactivityincellextractsobtainedfrom growthsinPPMMtowhichincreasingconcentrationsofnaringin wereadded.Tothispurpose,four250mL-Erlenmeyerflaskswere prepared,eachcontaining250mLofPPMMmediumand0.4% glu-tamicacidasuniquecarbonandenergysource.Variableamounts ofnaringinwereaddedtoautoclavedmedia,inordertohavefinal concentrationsof0.1–0.2–0.3mM.Thefourflaskswereinoculated withanovernightcultureofPP1YinLB,asdescribedinparagraph 2.2.Theinitialcellconcentrationsintheflaskswerecomparable andintherange0.02–0.04OD600/mL.
2.7. InfluenceofpHandorganicsolventson˛-l-rhamnosidase andˇ-glucosidaseactivities
InexperimentsofpHmonitoring,2mMsolutionsofnaringin werepreparedinHCl/KCl,Na-acetate,Na-phosphate,Tris/HCl, Na-carbonatebuffers,inordertocoverthepHrangebetween2.2and 10.9(Table2).100LofPP1Ycrudeextractwereaddedto0.5mL ofeachsolutionandincubatedat35◦Cundermagneticstirring. Reactionswerecheckedevery20minbyTLCanalyses(solvent sys-temA)andnaringinconsumptionwasevaluatedbyusingsolutions ofpurenaringin,narigenin,rhamnoseandglucoseas chromato-graphicstandards.BlankreactionsatdifferentpHswereperformed toevaluatethechemicaldegradationoftheflavanoneglycoside, occurringpreferentiallyinstronglybasicconditions.
Similarly,solutionsof2mMnaringinin50mMTris/HClbuffer pH8.5containing1,10and50%v/vofDMSOorCH3CN(Table2)
wereplacedunderconstantagitationat35◦Cinthepresenceof 200LofPP1Ycrudeenzymaticextract(0.74mgtotalprotein)/mL ofreaction.Aspreviouslyreported,reactionsweremonitoredby TLCanalysis(solventsystemA).
2.8. Stereochemicalcourseof˛-l-rhamnosidaseactivityin hydrolysisreactions
To the purpose, 800L of a 6mM pNPR solution prepared in 50mM Tris/HCl buffer pH7 was freeze-dried, re-suspended threetimesinD2Oandre-freeze-driedtoexchangethe1Hatoms
involvedinlabilelinkagesfor2Hones.Asimilarprocedureofproton
isotopeexchangewasappliedto200LofPP1Ycrudeextract.Just priortothe1H-NMRexperiment,thepreviouslyexchangedpNPR
Table2
TheinfluenceofpHandorganicsolventspresenceonnaringinhydrolysisby␣-RHA activityinPP1Ycrudeproteinextract.
pHvalues Naringinhydrolysis Time(min) 60 120 140 180 2.2 − − − − 3.6 − − − − 5.4 − − − − 5.9 − − − −/+ 6.1 − −/+ −/+ + 7.2 −/+ + ++ ++ 8.1 − ++ ++ ++ 8.3 + ++ +++ +++ 8.5 + +++ +++ +++ 8.8 + ++ +++ +++ 9.1a − − + + 9.9a − − + + 10.9a − − + + %oforganicsolvent DMSO1% + ++ ++ +++ DMSO10% + + ++ +++ DMSO50% − − − − CH3CN1% − − − −/+ CH3CN10% − − − − CH3CN50% − − − −
Note:−nohydrolysis;−/+:percentageofhydrolysisbelow10%;+:10–30%of hydrol-ysis;++:30–70%ofhydrolysis;+++:percentageofhydrolysishigherthan70%.
aIntheseconditionsapartialchemicaldegradationofnaringinwasobserved
whichwassuggestedbythepresenceonTLC,alongwiththedisappearanceofthe substrate,ofaproductmorepolarthannaringinandtheabsenceofrhamnoseand glucosespots,thusconfirmingtheabsenceofanenzymatichydrolysis.
solutionwasdissolvedin0.75mLofD2O,equilibratedat35◦Cina
NMRtubeinsidethespectrometerprobe,andaninitialspectrumof solutionwithoutenzymewasrecorded(T0).Thealiquotof
freeze-driedcrudeextractwassuspendedin50LofD2Oandaddedtothe
solution.Startingfromthatmoment(T0withenzyme),the
stereo-chemicalcourseofhydrolysiswasfollowedbyrecording1H-NMR
spectraatcloseintervalsduringtheincubationtime (from0to 60min).
A6mMsolutionoffreerhamnosedissolvedin50mMTris/HCl bufferpH7wastreatedandmonitoredby1H-NMRexperimentsas
previouslyreported.
2.9. Bioconversionstudiesfollowedby1H-NMRanalyses
pNPR, naringin, rutin and neohesperidin dihydrochalcone bioconversionswereperformedandcomparedby1H-NMR
spec-troscopicanalyses.
In particular,11.4mol of each substrate weredissolved in 1.9mLofNa-phosphatebuffer(50mM,pH8.5orpH7) contain-ing1mLofPP1Ycrudeextract.Reactionswereincubatedat35◦C, underconstantmagneticstirringfor3h.Aliquotsof380Lwere withdrawnfromeachreactionatdifferenttimeintervalsfrom0 to173min.Enzymaticreactionswerestoppedbyboilingat100◦C for2minandsampleswerefreeze-dried.Collectedaliquotswere dissolvedinMeODorD2O,asforpNPR,andanalyzedby1H-NMR
experiments.ThesereactionswerealsomonitoredbyTLC analy-sis(systemsolventA).ThesereactionswerealsomonitoredbyTLC analysis(systemsolventA).
2.10. Pruninproduction
Thereactionwasperformedusing2mLofPP1Ycrudeextract whichwerepreviouslylyophilizedandthenresuspendedina1mL solutionofNa-phosphatebuffer(50mM,pH8.5)containing10% ofDMSO.72.5mgofnaringin(0.125mmol)wereaddedandthe
samplewasincubatedat35◦C,undermagneticstirring.Reaction wasstoppedafter72hbyheatingthesampleat100◦Cfor2min andpruninwasisolatedbysilicagelpurificationwithEtOAc:MeOH 9:1(v/v)asmobilephase.1Dand2DNMRanalysesconfirmedits structure.
3. ResultsandDiscussion
3.1. Glycosidaseactivitiesscreening
Glycosidaseactivitiesincrudeproteinextractof Novosphingob-iumsp.PP1Ycellscollectedaftera24hgrowthinPPMMmedium (Section2.2)werepreliminaryinvestigatedfortheirhydrolyticand transglycosylationpotentials,asdescribedinSection2.4.Reaction productswereanalyzedovertimebyTLCanalysisusingsolvent systemASection2.1, andtheresultswerereportedinTable1. Dataindicatedthat␣-l-rhamnosidaseand-glycosylhydrolases activitiesresultedthemostabundantones.After3h,30–70%of PNP-␣-l-Rhapand 10–30%of PNP--d-Glcp,PNP--d-Galp, and PNP--d-Xylpwerehydrolyzed.Hydrolysisreactionswereallowed toproceedfor24h.Atthistime,analmostcompleteconversionof PNP-␣-l-Rhapwasobserved.
Transglycosylationreactionsresultedmoreinterestingbyusing PNP--glycosides as substrates, suggesting a better attitude of -glycosyl hydrolases to transfer monosaccharidic units in self-condensationreactionsthanthe␣-l-rhamnosidaseactivity; aryl--oligosaccharideswerepresentinthereactionmediaupto 24h.
Polysaccharidesandoligosaccharideswerealsotestedas pos-siblesubstratesfortheenzymaticactivitiespresentinPP1Ycrude extracts.ProductsformationwasmonitoredbyTLCanalysis (sys-tem solvents A and B, Section 2.1), using pure compounds as chromatographic standards. After24hof reaction, curdlan and laminarinwereonlyslightlyconsumedwhereaslaminaripentaose resultedthebesthydrolyzedoligosaccharide,resultinginthemajor productionofglucose;cellobiose,instead,wasnotagoodsubstrate (datanotshown).
␣-glucanslikepullulan,amylopectin,starchandmaltosewere partiallyoralmosttotallyhydrolyzedtoglucose,maltoseorlarger oligosaccharides,suggestingthepossiblepresenceof␣-glucanase activities(datanotshown).
Thesepreliminarydataconfirmedthebiotechnological poten-tialofPP1Ystrainasasourceofawidearrayofenzymaticactivities thatcanbeusedforthemodificationofcarbohydratesand glyco-conjugates.
3.2. HydrolyticbehaviourofPP1Ycrudeextractenzymeson flavonoids:description,pHdependenceandtolerancetoorganic solvents
ThesimultaneouspresenceinPP1Ycrudeextractof␣-RHAand -glucosidaseactivitiespromptedustoinvestigatethe possibil-itytohydrolyzeselectedflavonoidiccompounds,havingintheir chemicalstructureboth␣-rhamnoseand-glucoseunits,suchas naringin,diosmin, rutin,hesperidin,neohesperidin dihydrochal-cone and quericitrin (Fig. 1).It is worth tonote that chemical modificationofthesecompounds,whichareendowedwith ther-apeuticpotential [12]is important tomodulatetheirbiological activity.
InthereactionconditionsreportedinSection2.4,after3hof incubation, complete conversionof naringin,rutin and neohes-peridin dihydrochalcone was detectedby TLCanalysis (system solventA,Fig.2):spotsofrhamnose,glucoseandthecorresponding aglyconewereobservedforeachreaction.
Fig.1. Chemicalstructureofflavonoidiccompoundsusedassubstrates.Chemicalshiftvaluesofsignalsthatareintegratedinbioconversionreactionsarereported.
Ontheotherhand,diosmin,hesperidinand quericitrinwere nothydrolyzed;after24hasobservedbyTLCinvestigations (sys-temsolventA)rhamnose and glucosespots, atRf0.56 and 0.3 respectively,wereabsentonTLCplatesofdiosminandhesperidin
reactions.Quericitrinwassopoorlyconsumed(yieldbelow3%)that itshydrolysiswasconsiderednegligible;indeed,averyscarce pres-enceofquercetinandrhamnose,atRf0.88and0.56respectively, wasobserved.
Fig.2.FlavonoidshydrolysisfollowedbyTLC(systemsolventA).TLCstandard solutionsataconcentrationof2mMwereused.Nar:naringin,R-nar:naringin reaction;rut:rutin,R-rut:rutinreaction;neohe:nehoesperidindihydrochalcone; R-neohe:nehoesperidindihydrochalconereaction;glu:glucose,rha:rhamnose;es: enzymaticsolution.
Thesedatagavesomeindicationonthesubstratepreferenceof the␣-RHAactivityexpressedbystrainPP1Yunderour experimen-talconditions.
Diosminandhesperidin(Fig.1),whichcontainedtherutinose disaccharide (␣-l-Rhamnopyranosyl-(1→6)--d-glucopyranose) linked to the phenolic portion of the molecules, were not hydrolyzed. Rutin, whose rutinosideportion was linked tothe quercetin3-enol position,wasinsteadconverted. Undersimilar reaction conditions, flavonoids with the neohesperidose disac-charide 2-O-(6-deoxy-␣-l-mannopyranosyl)--d-glucopyranose) linkedtothephenolicportion(naringinandneohesperidin dihy-drochalcone)werecompletelytransformed.
These data suggested that the ␣-RHA activity was able to hydrolyzeboth␣,1-2and␣,1-6interglycosidiclinkages.Mostof the␣-RHAsreportedinliteraturearemainlyactiveon␣-1,2 gly-cosidiclinkages,toasmallerextenton␣-1,6linkages,andeven lessonotherglycosidicbonds[30].Interestingly,theenzymatic activityexpressedbystrainPP1Ywasspecificfor␣,1-2 intergly-cosidicbondswhenthedisaccharideunitofrutinosewaslinked tothephenolichydroxylgroups.Infact,diosminandhesperidin, whichsharedthepresenceofa␣,1-6interglycosidicbondinthe disaccharideunitslinkedtoaphenolicsite,werenothydrolyzed. The␣,1-6interglycosidicbondwasinsteadhydrolyzedwhenthe rutinoseunitwaslinkedto3-enolpositionofrutin.Thishydrolytic behaviourmightbeaconsequenceofadifferentstericeffect deriv-ingfromtheattachmentofthedisaccharidicunitstodifferentsites oftheaglycons[3].
Freerutinosedisaccharidewasalsoexaminedasapossible sub-strate,resultinginaverylowyieldofproducts(datanotshown), thus suggesting the importance of thearomatic portionof the flavonoidicmoietyintherecognitionmechanismoftheenzymes involved.
Moreover,quercitrin,thequercetin3-␣-l-rhamnoside,inwhich l-rhamnoseisdirectlylinkedtotheaglycon,wasnothydrolyzed. ItshouldbenotedthatamarkedpreferencefortheofPNP- ␣-l-Rhap(fromnowonindicatedaspNPR)incomparisontoquercitrin, roboninorrutinhasbeenreportedalsoforothercharacterized ␣-RHAs[3].
The solubility of flavonoids (typically polyphenols) is pH-dependentand generallyincreasesinalkalinemedia,whichare oftennotcompatible withtheenzymatic activitiesusedin bio-processes. Using naringin as the most water-soluble available flavonoid(0.5g/Lat20◦C)[31],theinfluenceofpHandorganic sol-ventsonthehydrolyticbehaviouroftheenzymespresentinPP1Y crudeextractswasinvestigated.
ResultsoftheseexperimentswerereportedinTable2.Ahigher yieldofnaringinhydrolysisproductswasobtainedatalkalinepH valuesrangingfrom7.2to8.8(Na-phosphateandTris/HClbuffers) andanoptimumpHvalueof8.5wasdetermined.Inthiscase,after 3hofreaction,substrate spotswereabsentonTLCplates,thus suggestingasubstratecompletedepletion.
Withinareactiontimeof3h,TLCanalysesofreactionsystemsin thepHrange8.2–8.8showedthepresenceofaproductwithanRf valuehigherthanthatofnaringin.Freeglucoseandthenarigenin aglyconewerealmostabsent.
ThesedatasuggestedtheoccurrenceatthesebasicpHvaluesof amarkeddecreaseofthe-glucosidaseactivity,whichshouldbe responsiblefortheproductionoffreeglucoseandnarigenin agly-cone,andthepermanenceofthe␣-RHAactivity.Thishypothesis wasconfirmedbytheconcomitantaccumulationofacompound which wasidentified as prunin (Fig. 1), the de-rhamnosylated product ofnaringin, a moleculeof biotechnologicalimportance endowed with anti-inflammatory and antiviral activity against DNA/RNAviruses[32,33].
Itisworthtonotethatbacterial␣-RHAshavingapHoptimum valueat8–8.5havenotbeenoftenreportedinliterature[30].
Pruninstructure(Fig.1)wasconfirmedbya2DNMR spectro-scopicinvestigation.Thepresenceof the-glucoseresidue was establishedbythevalueoftheanomericpositionsignalin13CNMR
spectrum(inMeOD)at101.25ppmwhichresultedcorrelatedin HSQCspectrumtothediastereoisomericanomericprotonsH-1at 5.01(J=6.90Hz),and4.99(J=6.90Hz)ppm.Thefollowingsignals (inppm):C-274.66(H-2:3.48),C-377.82(H-3:3.47),C-471.16 (H-4:3.41),C-5 78.28(H-5:3.42),C-6 62.34(H-6-H-6:3.90, 3.72)confirmedtheglucosestructureofpruninsaccharidicportion. Aglyconestructurewasconfirmedbythe13Cspectrumsignalsat
80.69ppm(C-2),44.19ppm(C-3),166.98and167.05ppm(C-7,the glycosylationsite),129.12ppm(C-2-C6),116.33ppm(C-3-C5) andin1H-NMRspectrumbytheprotonsignalsat7.35ppm
(H-2-H6)and6.85ppm(H-3-H5).Theothersignalsinthespectra wereinagreementwithdatapreviouslyreported[34].Theincrease ofthe␣-RHAactivitypresentinPP1Yproteinextractsobservedat alkalinepHvalueswasalsoconfirmedbythepNPRbioconversion studyfollowedbyNMRanalysisreportedinSection3.3.
ThepHvariationisnottheuniquestrategythathasbeenusedto overcomethepoorhydrosolubilityofflavonoids;theuseof water-miscibleorganicco-solvents,infact,hasalsobeensuggested[31]. However,itshouldbenotedthatthisstrategyhasseveral draw-backs,suchastoxicityproblemsderivedfromtheuseofanorganic solventinabioprocess,andthepossibledecreaseintheenzymatic activitiesemployed[35].
Inthisstudy,theinfluenceofthepresenceoforganicsolvents onthehydrolysis of naringinwas evaluatedby TLCanalysisof
reactionmixturescontainingfrom1to50%v/vDMSOorCH3CN
(Table2).After90min,inthepresenceof1%and10%ofDMSO, naringinwasalmosttotallyconsumedandtracesofpruninwere detected,suggestingatoleranceofthe␣-RHAactivitytothe pres-enceoforganicsolventsalongwithadetrimentaleffectofDMSO onthe-glucosidaseactivity,asfreeglucosewasalmostabsentin thereactionmixtures.
Finally,inthepresenceofeither50%DMSOoranyconcentration ofCH3CN,de-rhamnosylationandde-glucosylationreactionsdid
notproceedevenafter10h.
Usingtheapparentbestexperimentalconditionsreportedin
Table2(pHvalueof8.5and10%DMSO),andstartingfroma125mM naringinsolution(Section2.10),pruninwasproducedwithayield of32.1%,correspondingtoafinalconcentrationof0.02Mandan amountof17.4mgofrecoveredproduct.
Furthermore,free l-rhamnose wasproduced as a secondary productataconcentrationof6g/L.Theyieldofproductsobtained inthisexperimentwascomparabletothatreportedfora recombi-nant␣-RHAfromClostridiumstercorariumusedforthehydrolysis ofcitruspeelwastenaringin[7]andtoothersimilarprocesses[30]. 3.3. BioconversionexperimentsfollowedbyNMR
Toconfirmandbetterdetailtheobservationsonthesubstrate preference of the␣-RHA activityin Novosphingobium sp. PP1Y crudeproteinextractsdescribedinthepreviousparagraph, bio-conversionreactionsofpNPR,naringin,rutin andneohesperidin dihydrochalconewereperformedusingPP1Ycellextracts(Section
2.9),andmonitoredovertimeby1H-NMR.
Basedondiagnosticsignalsofreagentsandproductsforeach reaction,substrateconversionswerecalculatedbymeasuringthe percentageratiobetweentheintegralsofdiagnosticsignalsofthe productsandthesumoftheintegrationvaluesofselectedsignals ofreagentsandfinalproducts.ResultswerereportedinFig.3.
The highest yield of bioconversion in a shortest time was obtainedwithrutin.After20min76.2%ofthesubstratewas con-sumed.Atthesametime,30–35%ofpNPR,26%ofnaringin,and7% ofneohesperidindihydrochalconeweretransformed.
After 173min, naringin and neohesperidin dihydrochalcone reachedbioconversionsyields(95.6and86%,respectively)similar torutin(89.4%).Undertheseconditions,3.1–3.3g/Lofflavonoids wereconverted toproductsand, although the flavonoidic sub-strateswerenottotallyhydrolyzedtoaglycone,freel-rhamnose wasreleasedintothereactionmediaataconcentrationofabout 0.77–0.86g/L.
ItshouldbeaddedthatpNPRbioconversionwasperformednot onlyatpH8.5butalsoatpH7,lookingforapossiblepHinfluenceon PP1Y␣-RHAactivity(seeSection3.2).Intheexperimentinwhich naringinwasusedasasubstrate,thereactioncoursewas evalu-atedbycomparingin1H-NMRspectratheintegralvaluesoftwo
aromaticprotonssinglets(Fig.1)H6–H8inringBat6.19ppmand 6.28ppm,whichwereattributedavalueof2,totheintegrationof thecorrespondingprotonsofthefinalproductnarigenin(aglycon) at5.78and5.8ppm.1H-NMRspectrainMeODofnaringin,
narin-geninandprunin(H6–H8signalsat6.22–6.24,respectively)ofpure solutionsconfirmedtheidentityofnarigeninintegratedsignals.
Whenrutinwasusedassubstrate,aromaticprotonsignalH6 ofthereagentat6.18ppmwasselectedasreferenceforthe inte-gration(Fig.1).Asforthereactionproducts,anaromaticsignalat 6.13ppm,whichincreasedovertime,wasselectedforevaluating rutinbioconversion.
After10minofreaction,theanomericprotonof-glucosein rutinat5.07ppm(d,J=7.61Hz)almostdisappeared(72%of con-version)andananomericprotonsignalat5.035ppm(d,J=8.07Hz), possiblycorrespondingtothe-anomericprotonofquercetin3- -glucoside,appeared;anomericsignalsoffreeglucosewereabsent.
On theotherhand,in1H-NMRspectraat173min,anomeric
protonsregionwasmorecrowdedwithsignalsduetothe pres-enceoffreeglucose(␣-protonat5.13ppmJ=3.91Hz;-protonat 4.50ppm,J=7.8Hz)andasignalat5.023ppmoffreerhamnose ␣-proton(withthe-anomericprotonoverlappedbythesolvent residualwatersignal).
Thesedatasuggestedafasthydrolysisoftheinterglycosidic link-ageinsidetherutinoseunit(␣-l-Rha-(1→6)--d-Glu)withthe productionoffreerhamnoseatthebeginningofthereaction,as confirmedbythepresenceofafurthermethylsignalat1.27ppm after10minofreaction,correspondingtoprotonsatposition6of freerhamnose,andthesubsequentreleaseofflavonolquercetin andglucose.
TheNeohesperidin dihydrochalconebioconversionwas eval-uated by 1H-NMR using the aromatic signals at 6.049ppm,
corresponding totwo overlapped aromaticprotons H2 and H6 (Fig.1)linkedtothesaccharidicportion,asthereagentreference signals,withaintegralvalueof1,andasignalat6.077ppm, belong-ingtothereactionproduct.
Anevaluationoftheanomericsignalsintherange4.45:5.2ppm of1H-NMRexperimentshowed,after173minofreaction,the
pres-enceofthe␣-protonsignaloflinkedrhamnoseat5.28ppmandthe anomericsignalof -glucoseat5.065ppm(d,J=7.63Hz)which belongedto thesubstrate, the␣- and -anomericprotons sig-nalsoffreeglucoseat5.13ppm(d,J=3.81Hz)and4.50ppm(d, J=7.63Hz)respectively.Moreover,anintensesignalat5.03ppm ofthe␣-anomericprotonoffreerhamnose,asignalat4.95ppm (d,J=7.31Hz)almostasintenseastheprevioussignal,whichwas partiallycoveredbyresidualH2OsignalinMeOD,corresponding
to-glucoseH1signalofneohesperidindihydrochalconewithout rhamnosewerealsoobserved.Onthecontrary,thefreerhamnose -anomericsignalwastotallyoverlappedbyresidualH2Osignalin
MeOD.
Thehighintensityofthe␣-anomericprotonoffreerhamnose andthescarcepresenceofanomericsignalsoffreeglucose,ledusto supposethatthemainreactionproductwasthede-rhamnosylated neohesperidindihydrochalcone.
InexperimentsusingpNPRassubstrate,theintegralvalueof aromaticprotonsignalat7.23ppmwassetto1andthesignalof p-nitrophenolat6.69ppmproducedbythehydrolysisofglycosidic linkagewasselectedfor theassessment ofpNPRbioconversion. ThisbioconversionwasperformedattwopHvalues;asreportedin
Fig.2,after60min,theconversionofpNPRwasofabout61%atpH 7,whereasathigherpHitreached97%,thusconfirmingthetrendof theexperimentsinwhichnaringinwasusedassubstratedescribed inSection3.2.
3.4. Inductionof˛-RHAactivityinPP1Ycellextracts
␣-RHAactivitycanbespecificallyinducedbyseveralflavonoids
[36,37]amongwhichnaringinisofparticularinterestbecausethis compound can be abundantly recoveredin citrus solid wastes. Thesewastesarequiteinterestingbecausetheycanbeusedeither asanenergeticsourceforgrowingmicroorganisms,duetotheir content in carbon and othernutrient components,and/or as a specificinducerforthebiosynthesisofglycosidasesduetothe pres-enceofflavonoids.It goeswithoutsayingthattheuseofcitrus wasteasstartingmaterialinbioconversionprocessesisan advan-tageforindustrialcompaniesbecause,amongothers,itdecreases theexpensesforwastedisposal.Thepossibleroleofnaringinas an inducerof the␣-RHA activity[37] in PP1Y protein extracts wasinvestigatedusingPP1YcellsgrowninPPMMmedium sup-plementedwithnaringinatdifferentinitialconcentrationsupto 0.3mM,asdescribedindetailinSection2.6.
Fig.3.Bioconversionsofnaringin䊉,rutin,neohesperidindihydrochalcone—,p-nitrophenyl-␣-l-rhamnopyranosideatpH7and8.5.
Theeffectofnaringincouldnotbeevaluatedatconcentrations higherthan0.3mMduetoitspoorsolubilityunderthe experimen-talconditionsused.
Theeffectofnaringincouldnotbeinvestigatedat concentra-tionvalueshigherthan0.3mMduetoitspoorsolubilityunderthe experimentalconditionsused.ResultswerereportedinFig.4and confirmedthatnaringinactsasaninducerleading,ata concentra-tionof0.3mM,toamaximum5-foldincreaseofthe␣-RHAactivity (15.2mU/mg)detectedinthecrudeextractof PP1Ycells.These dataencourageafuturebiotechnologicaluseofPP1Ystrainandof its␣-RHAactivityfortheuseofagro-industryvegetableresidues. 3.5. Stereochemicalcourseof˛-RHAactivityinhydrolysis
reactions
Toshed light onthetype of enzymatic mechanism of PP1Y ␣-RHA activity,hydrolysis products of pNPRwere analyzed by recording 1H-NMR spectra over time. The integration of the
anomericprotonsignalsofreagentandproductswasinvestigated; theanalysiswasperformedtakingintoaccountthattheanomeric protonoffree rhamnoseshows peaksat5.06ppm (␣-anomeric form)and4.83ppm(-anomericform).Resultswerereportedin
Fig.5,wherethereactiontime-dependentchangesinamplitude ofH-1 signalsfrom substrate,␣-1(S) (5.68ppm),and products,
Fig.4.␣-RHAspecificactivityinthecellextractofstrainPP1Yisexpressedas mU/mgoftotalproteins(Y-axis).Specificactivityisreportedasafunctionofthe concentrationofnaringininitiallyaddedtothegrowthmedium.
␣-1(P),and-1(P),wereplottedas%oftotalanomeric(H-1)signals. Att0,theonly␣-anomericprotonsignalpresentwasthatofpNPR
at5.68ppm(␣-1(S)).Duringthefirstminutesofreactionasignal at4.83ppm,correspondingtothe-l-Rhapanomericproton(-1 (P)),appearedonlyslightlyearlierthantheappearanceofafurther signalat5.06ppm,correspondingtothe␣-l-Rhapanomericproton (␣-1(P)).
These signals increased in intensity over time, while the anomericsignalofpNPRdecreasedconcomitantly,asitisevident fromFig.5.NMRanalysisdidnotgaveevidencefortheonsetof mutarotationequilibrationduringthefirstminutesofreaction.
Laterintheincubation,mutarotationoftheinitiallyreleased -l-Rhapincreasedtheratiobetweentheintensitiesofthe␣-and -anomerprotonssignals.After7min,ataconversionpercentage of7.5%,therelativeintensitiesofthe␣-and-anomerresonances (calculatedfrompeaksintegration)wereina ratioofabout1:3 (25%ofthe␣-and75%forthe-anomer).After20min,ata con-versionpercentageof29%,the␣-/-anomerratiowasofabout1:2 (32%ofthe␣-and68%forthe-anomer).After60min,ata con-versionpercentageof61.5%,the␣/ratiovalueincreasedtoabout 1:1.Thisratiowaskeptconstantalsoafter80min,whenthe inte-grationvaluesshowedthattheyieldofpNPRconsumptionwasof
0 10 20 30 40 50 60 70 80 90 100 2 7 10 12 20 40 60 80 pe rcentage % time (min)
PNP-αα- Rha hydrolysis
Fig.5. %oftotalanomericsignalsinp-nitrophenyl-␣-l-rhamnopyranoside hydrol-ysisreaction:signalsfromsubstrate,␣-1(S),andproducts,␣-1(P),and-1(P) ,areplottedas%oftotalanomeric(H-1)signals.
about86%,andwasmaintainedupto18h,thusrepresentingthe equilibriumvalueoftheratiobetweenbothanomericformsof l-rhamnopyranose.Asolutionoffreerhamnoseusedin thesame experimentalconditionsandmonitoredby1H-NMRreachedthe
mutarotationalequilibriumafter1–2minandtheconcentrations ratioof␣-and-rhamnosewas1:1.
ThekineticbehavioursuggestedbytheseexperimentsforPP1Y ␣-RHAactivitywasaninvertingmechanismofhydrolysisinwhich -rhamnosewasformedfromthe␣-rhamnoseviaa single dis-placementmechanismandwasthenspontaneouslyconvertedby mutarotationtothe␣-anomericform.
4. Conclusions
Bacterialglycosylhydrolasesarethefocusofanincreasing num-berofresearchesbecauseoftheirkeyroleinfundamentalbiological processesandtheirbiotechnologicalapplications.Here,the atten-tionwasfocusedonanovel␣-RHAactivityfromNovosphingobium sp.PP1Y,whichresultedinterestingforitsalkalinepHoptimum andmoderatetolerancetoorganicsolvents.
This␣-RHAwasused,evenwithoutanyfurtherpurificationof PP1Ycrudeproteinextract,forthebioconversionofflavonoids use-fulforthefoodandpharmaceuticalindustries.However,afuture detailedbiochemicalcharacterizationofthisenzymeisnow cru-cial for a better understanding of its effective biotechnological potential.
Acknowledgments
WethankD.Melck,E.CastelluccioandA.Esposito(NMRservice ofIstitutodiChimicaBiomolecolare,CNR,Pozzuoli,Italy)fortheir skilfulassistance.
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