Data set for the proteomic inventory and quantitative analysis of chicken eggshell matrix proteins during the primary events of eggshell mineralization and the active growth phase of calcification

Da a A icle Da a se o he p o eomic in en o y and quan i a i e analysis o chicken eggshell ma ix p o eins du ing he p ima y e en s o eggshell mine aliza ion and he ac i e g ow h phase o calcifica ion Pauline Ma ie a , Valé ie Labas b , Au élien B ionne a , G égoi e Ha ichaux b , Ch is elle Henneque -An ie a , Alejand o B. Rod iguez-Na a o c , Y es Nys a , Joël Gau on a, n a INRA, UR83 Reche ches a icoles, Fonc ion e Régula ion des p o éines de l'œu , F-37380 Nouzilly, F ance b INRA, UMR INRA85, UMR CNRS 7247; Uni e si é de Tou s; IFCE, Physiologie de la Rep oduc ion e des Compo emen s, Pla e- o me d'Analyse In ég a i e des Biomolécules, Labo a oi e de Spec omé ie de Masse, F-37380 Nouzilly, F ance c Depa men o de Mine alogia y Pe ologia, Uni e sidad de G anada, Campus Fuen e Nue a s/n, 18002 G anada, Spain a icle in o A icle his o y: Recei ed 15 June 2015 Recei ed in e ised o m 26 June 2015 Accep ed 29 June 2015 A ailable online 7 July 2015 Keywo ds: Chicken Eggshell Biomine alisa ion Quan i a i e p o eomics Eggshell ma ix abs ac Chicken eggshell is a biomine al composed o 95% calci e calcium ca bona e mine al and o 3.5% o ganic ma ix p o eins. The assembly o mine al and i s s uc u al o ganiza ion is con olled by i s o ganic ma ix. In a ecen s udy [1], we ha e used quan i a i e p o eomic, bioin o ma ic and unc ional analyses o explo e he dis ibu ion o 216 eggshell ma ix p o eins a ou key s ages o shell mine aliza ion defined as: (1) widesp ead deposi- ion o amo phous calcium ca bona e (ACC), (2) ACC ans o ma- ion in o c ys alline calci e agg ega es, (3) o ma ion o la ge calci e c ys al uni s and (4) apid g ow h o calci e as columna s uc u e wi h p e e en ial c ys al o ien a ion. The cu en a icle de ailed he quan i a i e analysis pe o med a he ou s ages o Con en s lis s a ailable a ScienceDi ec jou nal homepage: www.else ie .com/loca e/dib Da a in B ie h p://dx.doi.o g/10.1016/j.dib.2015.06.019 2352-3409/&2015 The Au ho s. Published by Else ie Inc. This is an open access a icle unde he CC BY license (h p://c ea i ecommons.o g/licenses/by/4.0/). DOI o o iginal a icle: h p://dx.doi.o g/10.1016/j.jp o .2015.05.034 n Co esponding au ho . E-mail add ess: [email p o ec ed] (J. Gau on). Da a in B ie 4 (2015) 430–436 shell mine aliza ion o de e mine he p o eins which a e he mos abundan . Addi ionally, we epo ed he en iched GO e ms and desc ibed he p esence o 35 an imic obial p o eins equally dis ibu ed a all s ages o keep he egg ee o bac e ia and o 81 p o eins, he unc ion o which could no be asc ibed. &2015 The Au ho s. Published by Else ie Inc. This is an open access a icle unde he CC BY license (h p://c ea i ecommons.o g/licenses/by/4.0/). Specifica ions able Subjec a ea Biology Mo e specific subjec a ea Lis and pu a i e unc ions o eggshell ma ix p o eins p esen a ini ial and mid phases o eggshell o ma ion. Type o da a Raw and p ocessed/analyzed mass spec ome y da a ob ained by nanoliquid ch oma og aphy combined o high esolu ion andem mass spec ome y,.xls ables wi h iden ified/ alida ed and quan ified p o eins ables wi h in eg a i e and unc ional analysis o p o ein sequences. How da a was acqui ed LC–MS/MS using a LTQ O bi ap Velos mass spec ome e . Da a o ma Raw da a: aw.mzml and P ocessed and analyzed da a using Masco Sea ch engine:.da . Analyzed: Fu he assembled sequences using Clus al Omega mul i-alignmen algo i hm and BLASTþsui e. GO e ms ex ac ed om sequences and en ichmen de e mina ion. Expe imen al ac o s S age o eggshell o ma ion. Expe imen al ea u es Eggshell ma ix samples we e collec ed a ou s ages o eggshell mine aliza ion and diges ed in gel using ypsin. Resul ing pep ides we e analyzed by LC–MS/MS and u he ea ed using da a mining and bioin o ma ic analysis. Da a sou ce loca ion Nouzilly, F ance, INRA Cen e Val de Loi e. Da a accessibili y Da a ha e been deposi ed in o he P o eomeXchange Conso ium [2] ia he PRIDE pa ne eposi o y wi h he da ase iden ifie PXD001450. Value o he da a [desc ibe in 3–5 bulle ed poin s why his da a is o alue o he scien ific communi y]  P o eomic analysis o 216 chicken eggshell ma ix p o eins.  Gene On ology e ms en ichmen s in es iga ing po en ial unc ions o eggshell ma ix p o eins.  Quan i a i e da a on p o ein abundances acco ding o s ages o eggshell o ma ion.  Anno a ion on quan ified eggshell ma ix p o eins. 1. Collec ion o eggshell ma ix samples and p epa a ion o MS analyses Eggs we e collec ed on b own-laying hens a 5, 6, 7 and 16 h a e p e ious o iposi ion as desc ibed in [1]. These ime in e als co espond espec i ely o he p ima y e en s o mine aliza ion wi h widesp ead deposi ion o amo phous calcium ca bona e (ACC), ACC ans o ma ion in o c ys alline calci e agg ega es, o ma ion o la ge calci e c ys al uni s and apid g ow h o calci e and de elopmen o a columna s uc u e wi h p e e en ial c ys al o ien a ion [3]. Eggs we e b oken and o ming eggshells we e washed wi h wa e , ai d ied and s o ed a 20 1C un il p o ein ex ac ion. Eggshell ma ix p o eins we e ex ac ed as desc ibed in [1]. A o al o 24 indi idual eggshell p o ein ex ac s we e used. Six samples collec ed a he same ime poin we e pooled in equal amoun s o each ime (5 h p.o., 6 h p.o., 7 h p.o. and 16 h p.o.). The ou pooled samples (51 m g o p o eins/sample) we e ac iona ed on a 4–20% SDS-PAGE gel (8.3 cm 7.3 cm 1.5 mm). P o eins we e s ained wi h Coomassie blue and he en i e SDS-PAGE lanes we e sec ioned in o 15 bands o each indi idual pooled sample. Excised p o eins we e in-gel P. Ma ie e al. / Da a in B ie 4 (2015) 430–436 431 diges ed wi h bo ine ypsin (Roche Diagnos ics GmbH, Mannhiem, Ge many) as p e iously desc ibed [4] and analyzed by nanoscale liquid ch oma og aphy- andem mass spec ome y (nanoLC–MS/MS). 2. Nano LC MS/MS analyses All expe imen s we e pe o med on a linea ion ap Fou ie T ans o m Mass Spec ome e (FT-MS) LTQ O bi ap Velos (The mo Fishe Scien ific, B emen, Ge many) coupled o an Ul ima e s 3000 RSLC Ul a-High P essu e Liquid Ch oma og aphe (Dionex, Ams e dam, The Ne he lands) as p e iously desc ibed in [1,4]. Raw da a files we e con e ed o MGF as p e iously desc ibed [4]. The iden ifica ion o p o eins was es ablished using MASCOT sea ch engine ( 2.3, Ma ix Science, London, UK). The pep ide and agmen masses ob ained we e ma ched au oma ically agains he cho da a sec ion o n NCBI da abase (2132453 sequences, downloaded on 2013/05/13). Enzyme specifici y was se o ypsin wi h wo missed clea ages using ca bamidome hylcys eine, oxida ion o me hionine and N- e minal p o ein ace yla ion as a iable modifica ions. The ole ance o he ions was se o 5 ppm o pa en and 0.8 Da o agmen ion ma ches. Masco esul s ob ained om he a ge and decoy da abase we e inco po a ed in Sca old 3 so wa e ( e sion 3.4, P o eome So wa e, Po land, USA). Pep ide iden ifica ions we e accep ed i hey could be es ablished a g ea e han 95.0% p obabili y as specified by he Pep ide P ophe algo i hm [5]. Pep ides we e conside ed dis inc i hey di e ed in sequence. P o ein iden ifica ions we e accep ed i hey could be es ablished a g ea e han 95.0% p obabili y as specified by he P o ein P ophe algo i hm [6] and con ained a leas one sequence- unique pep ide o global in en o y and a leas wo sequence-unique pep ides o quan i a i e analysis. A alse disco e y a e was calcula ed as o1% a he pep ide o p o ein le el. The abundance o iden ified p o eins was es ima ed by calcula ing he emPAI using Sca old 4 Qþso wa e ( e sion 4.2, P o eome So wa e, Po land, USA). Addi ionally, label- ee quan i a i e p o eomic analyses based on spec al coun ing me hod, Sca old 3 Qþso wa e ( e sion 3.4, P o eome So wa e, Po land, USA) was used o quan i y he p o eins a he ou di e en s ages o calcifica ion. All p o eins wi h g ea e han wo sequence-unique pep ides, iden ified in da abase wi h high confidence we e conside ed o p o ein quan ifica ion. To elimina e quan i a i e ambigui y wi hin p o ein g oups, we igno ed all he spec a ma ching any pep ide which is sha ed be ween p o eins. The eby, quan ifica ion pe o med wi h no malized spec al coun s was ca ied ou on dis inc p o eins. The mass spec ome y p o eomic da a ha e been deposi ed in o he P o eomeXchange Conso ium [2] ia he PRIDE pa ne eposi o y wi h he da ase iden ifie PXD001450. 3. Da a se analysis o a ian eggshell ma ix p o eins A o al o 261 p o eins we e iden ified using n NCBI da abase. Ke a ins and bo ine ypsin we e elimina ed om he lis as hey appea ed o be con aminan s o esul ing om he diges ion p ocess. P o ein sequences we e aligned o elimina e all edundancies. P o ein g oups we e de e mined using Clus al Omega mul i-alignmen algo i hm [7]. Sequences we e blas ed agains n NCBI da abase limi ed o Gallus gallus axon using he blas p p og am (BLASTþsui e) [8]. This was pe o med using R language (h p://c an. -p ojec .o g). A o al o 216 non- edundan eggshell ma ix p o ein sequences we e iden ified. The esul ing file (Supplemen a y Table 1) is made o En ezGene Ids, GI numbe s, p o ein symbols, sho desc ip ions, in o ma ion on hei p e ious iden ifica ion in he shell and in he u e ine fluid, mean quan i a i e alues and emPAI alues a each ime poin . We compa ed ou lis wi h he p e iously published p o eomes o eggshell ma ix p o eins [9–15]. Ou o he 216 p o eins, 24 p o eins a e no el compa ed o p e ious s udies and a e highligh ed (Supplemen a y Table 1). In o de o de e mine he po en ial unc ions o he 216 eggshell ma ix p o eins, 3231 GO e ms we e ex ac ed om he p o ein sequences using GORe ie e (h p://agbase.mss a e.edu/). Ca eGO ize (h p://www.animalgenome.o g/ ools/ca ego/) was hen used o g oup he GO e ms in 91 di e en pa en e m ca ego ies using a GO slim2 me hod. Finally, GO e ms en ichmen s we e de e mined using Gene se en ichmen ools om Genoma ix sui e (www.genoma ix.de). When P. Ma ie e al. / Da a in B ie 4 (2015) 430–436432 conside ing GO e ms associa ed o Molecula Func ion (MF) and Biological P ocess (BP), a o al o 71 GO e ms we e ound o be significan ly en iched (p- alues anges om 9.92 10 3 o 2.96 10 7 ). They we e g ouped in 18 main ca ego ies (Table 1). G oups o impo ance we e composed o eggshell ma ix p o eins in ol ed in binding and anspo ac i i y (41 p o eins) and o 27 p o eins ela ed o he biology o de elopmen . Addi ionally, we also epo ed p o eins in ol ed in esponse o ex e nal s imulus (13 p o eins), in he egula ion o biological quali y (15 p o eins), exhibi ing enzyme egula o ac i i y (13 p o eins). Also we e p esen p o eins ela ed o p o ein pos - ansla ional olding (9 p o eins), homeos asis main enance (9 p o eins), mul i-o ganism p ocess (8 p o eins), nu i ion and diges ion (7 p o eins), he ex acellula o ganiza ion (4 p o eins), he cell–cell adhesion (5 p o eins), he oxido educ ase ac i i y (3 p o eins), he coagula ion p ocess (2 p o eins), he egula ion o p o ein phospho yla ion (2 p o eins), he glyce ol e he me abolic p ocess (2 p o eins) and he shell calcifica ion (2 p o eins). 4. Quan i a i e da ase o a ian eggshell ma ix p o eins Two di e en me hods we e applied o disce n he ela i e abundance o he p o eins a he di e en s ages o eggshell o ma ion, fi s ly he emPAI was calcula ed o all p o eins a each indi idual s age and secondly, GeLC–MS/MS analyses combined wi h label ee spec al coun ing me hod we e ca ied ou o de e mine quan i a i e alues a he ou s ages o mine aliza ion o he 216 unique p o eins. Table 1 GO e ms significan ly en iched in he 216 iden ified eggshell ma ix p o eins. Desc ip ions Numbe o p o eins Symbols Response o ex e nal s imulus 13 AVBD11, HSPA5, RBP4, FN1, LCN8, ALB, OC-17, CTSD, HIST1H2B7, LYZ, APOA1, TTR, LY86 Ex acellula o ganiza ion 4 ANXA2, LOXL2, VMO1, COL2A1 Nu i ion and diges ion 7 HSPA5, ALB, CTSD, RBP4, APOA1, VTG1, VTG2 Oocy e o ma ion 3 RBP4, VMO1, TTR P o ein pos ansla ional olding 9 PDIA3, PPIB, QSOX1, P4HB, HSPA5, DNAJC3, HSP90B1, HSP90AA1, DNAJB6 Homeos asis main enance 9 PDIA3, RBP4, CALB1, QSOX1, LCN8, COL2A1, P4HB, APOA1, CALM De elopmen 27 HSPA5, SPP1, RBP4, SEMA3C, DKK3, ACTA1, ANXA2, LOXL2, CALB1, YWHAE, FN1, ATP5B, LCN8, CDH2, TSKU, OC-17, GSN, DNAJB6, COCH, COL2A1, FST, SDF4, OC- 116, APOA1, CNTN1, CA2, TTR Enzyme egula o ac i i y 13 HSP90AA1, ANXA2, OVM, OVST, OVAY, SERPINI1, DNAJB6, APOA1, OIH, OVAX, TIMP2, CST3, CALM Binding and anspo ac i i y 41 DNAJC3, DNAJB6, CALB1, APOA1, GPC1, CNTN1, ALB, LCN8, HSPA5, SPP1, RBP4, HSP90B1, PTN, HSP90AA1, ANXA2, LOXL2, OVM, YWHAE, RDX, ANXA5, CDH2, GSN, COL2A1, FST, YWHAZ, HIST1H2B7, OIH, LYZ, HBG2, CDH1, TTR, CALM, FBLN1, SDF4, SPARC, OC-17, PLOD1, HBAA, HBAD, VTG1, VTG2 Oxido educ ase ac i i y 3 PDIA3, QSOX1, P4HB Coagula ion p ocess 2 ANXA2, ANXA5 Cell–cell adhesion 5 CDH2, DNAJB6, COL2A1, APOA1, CDH1 Ca ilage me abolism 2 LOXL2, LCN8, CDH2, COL2A1 Glyce ol e he me abolic p ocess 2 PDIA3, P4HB Regula ion o biological quali y 15 PDIA3, RBP4, ANXA2, ALB, CALB1, FN1, QSOX1, RDX, LCN8, GSN, COCH, COL2A1, P4HB, APOA1, CALM Mul i-o ganism p ocess 8 RBP4, ALB, AVBD11, LCN8, OC-17, HIST1H2B7, LYZ, TTR Shell calcifica ion 2 OC-17, OC-116 Regula ion o p o ein Dephospho yla ion 2 YWHAE, CALM P. Ma ie e al. / Da a in B ie 4 (2015) 430–436 433 In he fi s app oach, emPAI om he p o eins was calcula ed amongs he p o eins e ealed a a pa icula s age o shell o ma ion a 5, 6, 7 and 16 h p.o. The aim was o classi y he ela i e abundance o he p o eins wi hin one indi idual s age and o de e mine hose which we e he mos abundan ones. EmPAI alues we e epo ed o he 216 eggshell ma ix p o eins a each s age, a nume ical alue di e en om ze o being in oduced when he p o ein was p esen (Supplemen a y Table 1). EmPAI alues we e also used o de e mine he numbe o p o eins p esen a a pa icula s age (Supplemen a y Table 2). The numbe s o p o eins showing an emPAI di e en om ze o we e 91, 132, 178 and 184 a 5, 6, 7 and 16 h p.o., espec i ely. In he second app oach, GeLC–MS/MS combined wi h label ee quan i a i e analyses based on a spec al coun ing me hod we e used o compa e he abundances o he di e en p o eins be ween he ou s ages o eggshell o ma ion (Supplemen a y Tables 1 and 2). One way ANOVA was pe o med on quan i a i e alues o p o ein abundance in o de o e eal p o eins which we e a a di e en concen a ion be ween a leas one s age ela i e o ano he one. Di e ences we e conside ed o be s a is ically significan o p- alueo0.01. Amongs he 216 p o eins, 175 showed di e en ial abundance acco ding o he ou s ages o shell calcifica ion. The mean abundance pe s age o shell calcifica ion was s anda dized o each p o ein on mean alues pe s age and was calcula ed o pe o m hie a chical clus e ing analysis. A o al o en clus e s we e highligh ed and de ailed in [1]. They we e g ouped in fi e main p o ein p ofiles associa ed wi h he di e en e en s which occu du ing eggshell calcifica ion [1,3]: o e abundance du ing he p ima y e en s o widesp ead deposi ion o amo phous calcium ca bona e, o aling 27 p o eins (5–6 h p.o.), o e abundance du ing ans o ma ion o ACC in o c ys alline calci e agg ega es, o aling 13 p o eins (6 h p.o.), o e - abundance du ing he o ma ion o la ge calci e c ys al uni s, o aling 47 p o eins (6–7 h p.o.), o e abundance du ing apid g ow h o calci e and de elopmen o a columna s uc u e wi h p e e en ial o ien a ion o calci e, o aling 70 p o eins (16 h p.o.). The las g oup co esponded o o e abundance h oughou he h ee la e s ages o calcifica ion (6–7 o 16 h p.o.), o alising 18 p o eins. 5. Supplemen a y unc ional anno a ions o a ian eggshell ma ix p o eins Po en ial unc ions o p o eins we e de e mined acco ding o he li e a u e, da a anno a ions and unc ional domain da abase and highligh ed 77 p o eins wi h po en ial unc ions ela ed o a mine aliza ion p ocess [1]. Beside hese p o eins, we iden ified 35 p o eins wi h po en ial an imic obial unc ions p esen a a ious s ages o mine aliza ion (Supplemen a y Table 3). These an imic obial p o eins we e p esen a qui e equally numbe h oughou he di e en s ages o shell o ma ion. The mos abundan p o ein in he shell ma ix is lysozyme, which is known o hyd olyze 1–4 be a linkages be ween N-ace yl mu amic acid and N-ace yl- D -glucosamine esidues in pep idoglycans o G am-posi i e bac e ia [16]. Ano he no able p o eins is OVAX, which exhibi s an imic obial p ope ies agains Lis e ia monocy ogenes and Salmonella en e i idis [17].A ian βde ensin 11, belonging o a ian β de ensin amily, is a ca ionic pep ides wi h h ee s anded βshee s uc u e connec ed wi h βhai pin loop ha p o ec agains G am-posi i e and G am-nega i e bac e ia [18].O ocledin-17, a C- ype lec in p o ein which exhibi s an imic obial p ope ies agains Bacillus sub ilis,S aphylococcus au eus and Pseudomonas ae uginosa is also a majo eggshell p o ein [19]. Ano he g oup is cons i u ed o an imic obial p o eins by dep i ing bac e ia o essen ial nu ien s. O o ans e in, i ellogenin-1 and 2 and MFI2 a e an imic obial by hei capaci y o chela e i on ions, essen ial o bac e ial g ow h [20].GC, a g oup-specific componen and ibofla in p o ein bind i amins which a e dep i ing bac e ia om i amin D. We epo o ocalyxin-36,BPIFCB and o oglobulinG2 ype AA, which belong o he LBP/BPI/PLUNC amily known o bind o he lipid A po ion o lipopolysaccha ide cell wall in G am-nega i e bac e ia leading o he dea h o bac e ia [21]. The s udy also e ealed p o ease inhibi o s which can be po en ially an imic obial by hei abili y o inhibi p o eases sec e ed by some bac e ia. O oinhibi o ,o omucoid,SPARC, ollis a in, ollis a in-like 1and IGFBP7 exhibi Kazal like p o ease inhibi o domains. Mo eo e , o oinhibi o was showed o P. Ma ie e al. / Da a in B ie 4 (2015) 430–436434 inhibi Bacillus hu ingiensis g ow h [22].O ocalyxin-32 p esen s homology wi h la exin, a ca boxypep idase inhibi o , and has been shown o inhibi B. sub ilis g ow h [23].SERPIND1,SERPINF2, SERPINE2,SERPING1 and SERPINI1 belong o SERPIN amily, a known amily o se ine p o ease inhibi o s [16].O ocalyxin-25 con ains wo inhibi o p o ease domains, a WAP and a Kuni z-like domain [24].Cys a in C is a cys eine p o ease inhibi o , and o os a in is known o inhibi all ou classes o p o eases [16]. Finally ou s udy e ealed se e al agmen o immunoglobulin (Ig-ligh -2,Ig-gamma-hea y,Ig- lambda-1,Ig-lambda-2,Ig-ligh -1,Ig-mu-hea y and Ig-alpha-hea y). Finally, ou o he 175 eggshell ma ix p o eins showing significan a ia ion o abundance acco ding o he ou s ages o shell calcifica ion, 81 could no be asc ibed o any o hese unc ional g oups and we e classified as “o he o unknown ole”(Supplemen a y Table 4). Conflic o in e es Au ho s claim no conflic o in e es . Acknowledgmen s This esea ch was unded by he F ench Na ional Resea ch Agency ANR (ANR-13-BSV6-0007-01, ANR-13-BSV6-0007-02 and ANR-13-BSV6-0007-05). The high esolu ion mass spec ome e was financed (SMHART p ojec , 35069) by he Eu opean Regional De elopmen Fund (ERDF), he Conseil Régional du Cen e, he F ench Na ional Ins i u e o Ag icul u al Resea ch (INRA) and he F ench Na ional Ins i u e o Heal h and Medical Resea ch (Inse m). ARN acknowledges unding h ough G an s CGL2011-25906 (Minis e io de Economia, Spain). The au ho s a e g a e ul o he expe imen al uni s (UE-PEAT) o ca e o bi ds, and o he geno oul bioin o ma ics pla o m Toulouse Midi-Py enees o p o iding help and/o compu ing and/o s o age esou ces. Appendix A. Suppo ing in o ma ion Supplemen a y da a associa ed wi h his a icle can be ound in he online e sion a h p://dx.doi. o g/10.1016/j.dib.2015.06.019. Re e ences [1] P. Ma ie, V. Labas, A. B ionne, G. Ha ichaux, C. Henneque -An ie , A.B. 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