Protein Name. IFLENVIR,DSVTYTEHAK,TV TALDVVYALK,KTVTALDVV YALK,TVTALDVVYALKR,IF LENVIRDSVTYTEHAK gi Histone H2B

Transcription

1 Table 1. A functional category list of proteins (Lentinula edodes) identified by 1-DGE and nesi-lc-ms/ms. The table lists indicated fraction numbers, matching peptides, scores, accession numbers, protein names, theoretical mass (molecular weight, Da), theoretical pi and analyzed peptides; left to right. Fraction Matching Peptide Score Accession Protein Name Analytical MW Theoretical pi Peptide Chromatin structure and dynamics gi Histone H2B* AMAILNSFVNDIFER gi 3142 Histone H4.2* TVTALDVVYALKR gi Histone H2B AMAILNSFVNDIFER gi 3142 Histone H IFLENVIR,DSVTYTEHAK,TV TALDVVYALK,KTVTALDVV YALK,TVTALDVVYALKR,IF LENVIRDSVTYTEHAK gi Histone H2B LILPGELAK,AMAILNSFVNDI FER Cell division and chromosome partitioning gi α tubulin* LIAQVVSSITASLR,FDGSLNV DLNEFQTNLVPFPR,AFVHW YVGEGMEEGEFSEAREDLAA gi CDC (cell division control protein) 12* LTVIDTPGFGDYVNNR gi Septin* STLINTLFSAHLMDSK Transcription gi Pre-mRNA splicing factor* SATTNLSTADVVNNLKR gi AP-1 like bzip transcriptional activator* ASCYHILEEISSLPK Translation, ribosomal structure and biogenesis gi GNVASDSKNDPAK,EHALLA Τranslation elongation factor FTLGVR,AGMIVTFAPSNVTT 1-α EVK gi Τranslation elongation factor 1 α gi 5059 Ribosomal protein L3* HGSLGFLPR gi Cytoplasmic asparaginyltrna synthetase* FLAWLCAR gi gi gi gi gi gi gi Translation elongation factor 2* Translation elongation factor 2* Translation elongation factor 2* Translation elongation factor 2* Τranslation elongation factor 1-α Τranslation elongation factor 1-α Τranslation elongation factor 1-α EHALLAFTLGVR,YVVTVIDA PGHRDFIK IKPVVIINK,FSVSPVVQVAVE VK IQGPNYIPGK,FSVSPVVQVA VEVK ILADEFGWDVTDAR VLADEFGWDVTDAR ETKAGNAK,GITIDIALWK,Y AWVLDKLK,YVVTVIDAPGH R,EHALLAFTLGVR,ERGITIDI ALWK,YVVTVIDAPGHRDFI KEAAELGK,ERGITIDIALWK, YAWVLDKLK EHALLAFTLGVR,SVEMHHE QLEQGTPGDNVGFNV

2 gi Τranslation elongation factor EHALLAFTLGVR,AGMIVTFA α PSNVTTEVK gi 5059 Ribosomal protein L HGSLGFLPR gi Ribosomal protein L2* RLNLLQLAPGGHLGR LFAIGFTK,APSIFDVR,MFEI S-phase specific ribosomal gi MTR,SIYPLQNVYVR,IIEVSL protein cyc07* GDLNKEEEQSFR TSFFQALGIPTK,GNIGFVFTS gi L10e protein* GDLK APTGSNTVLLR,ILKAGGEVL gi S ribosomal protein L18* TLDQLALR gi Ribosomal protein S2* SMEEIYLFSLPVK gi Cytosolic small ribosomal subunit S4* TDPTYPAGFMDVISIEK gi Ribosomal protein S28* VSGVGLLALWK gi Ribosomal protein L12* ATGGEVGASSALAPK modification, protein gi 2551 Ubiquitin* ESTLHLVLR,IQDKEGIPPDQQ R,TITLEVESSDTIDNVK LYSLDMGALMAGAK,EFVTL gi Heat shock protein 100* FLQVLDDGR,TLATLLFDSPD NALEEYIYDTR,KNALEEYIY gi PSS1* DTR FELSGIPPAPR,DAGTIAGMN VLR,IINEPTAAAIAYGLDK,A gi Heat shock protein 70* TAGDTHLGGEDFDNR,IINEP TAAAIAYGLDKK,KSETFSTY ADNQPGVLIQVFEGER FELSGIPPAPR,LVSDFFNGKE gi Heat shock protein 70* PNK,ATAGDTHLGGEDFDNR, IINEPTAAAIAYGLDKK,TQD LLLLDVAPLSLGIETAGGVM TALIK,ATAGDTHLGGEDFD gi Heat shock protein 70* LVSDFFNGKEPNK,IINEPTAA AIAYGLDKK,KSETFSTFSDN QPGVLIQVFEGER,TLSSAAQ TSIEIDSLYEGIDFYTSITR FELSGIPPAPR,LVDHFIQEFK, gi Heat shock protein 70* IINEPTAAAIAYGLDK,ATAG DTHLGGEDFDNR,NQVAMNP HNTVFDAKR DSPFLEVLKK,HFSVEGQLEF gi Heat shock protein 90* KLGIHEDAQNR,GIVDSEDLPL gi Heat shock protein 90* NISR TIEDELEVTEGMR,VEFEKPLI gi Heat shock protein 60* LLSEK GFISPYFITDVK,VEFEKPLILL gi kda chaperonin* SEK gi 2908 Heat shock protein 70* TFSPQEISSMVLTK gi Heat shock protein 70* DAGTIAGLNILR gi kda cyclophilin* SLLAPLLLNSALAAIR gi S proteaseme regulatory subunit 7* TMLELINQLDGFDPR gi kda cyclophilin SLLAPLLLNSALAAIR gi Thioredoxin reductase Trr1* VVIIGSGPAGHTAAIYLAR gi S proteasome component α 1* LYQVEYAFK gi S proteasome subunit* YNDDLSLEDAIHTALLTLK

3 gi S proteasome component α 5* LFQVEYAIEAIK gi Cyclophilin (peptidyl-prolyl cis-trans isomerase)* IIPNFMIQGGDFTR Energy production and conversion gi Plasma membrane (H+) ATPase* GAADIVLTEPGLSTIVHAIR gi ATP citrate lyase (citrate synthetase)* SIAIIAEGVPER gi ATP citrate lyase (citrate synthetase) SIAIIAEGVPER gi Pyruvate carboxylase* VFEEYQGFLEK gi Pyruvate kinase* QIHLHR,NGVDMIFASFIR,IEN EQGVANFDEILK,GDLGIEIPA SQVFLAQK gi Isocitrate dehydrogenase* GLANPTALLLSSLMMLR gi Inorganic pyrophosphatase* VLGIMALLDEGETDWK gi NADH-ubiquinone oxidoreductase* VVYEPLQLTQAFR Carbohydrate transport gi phosphogluconate dehydrogenase* GILFVGSGVSGGEEGAR gi Glycogen synthase* GVDMFIESLAR gi Trehalose synthase* LADELREK,NNHNILQGVAD PSLR,IGFFSSTPQGGGVALM gi Phosphoglucomutase* FFGNLMDAGR VIPSLNGK,YDSVHGR,EISVF GEK,FKGTVETK,VVDLLVFA AK,SVNGNIIPSSTGAAK,VPT LDVSVVDLVCR,LIVDGKEIS gi Glyceraldehyde-3-phosphate VFGEK,LIAWYDNEWGYSGR dehydrogenase*,fgivealmttvhattatqk, VIHDKFGIVEALMTTVHATT ATQK,DAGAIPWSSVGAEYIV ESTGVFTTIEK,NALLNPEVN VVAVNDPFIALEYMVYMFK gi Glyceraldehyde-3-phosphate dehydrogenase* gi Transaldolase* gi Amino acid transport NAD-specific glutamate dehydrogenase* YDSVHGR,DPAAIPWGSVGA HYIVESTGVFTTIEK LLIEFGK,VSTEVDAR,IASTW EGIQAAR LGPAYLQLK,LPSGEIVLDGT DFR gi Tryptophan synthetase Trp 1* WFLGSLQDMLHAR gi Glutamine synthetase* gi Glutamine synthetase* gi deoxy-7- phosphoheptulonate synthase* KVTDIGQLR,RPASNIDPYR,R HDEHIAVYGEDNDLR,GGDN ILVLAETYNNDGTPNR KVTDIGQLR,RPASNIDPYR,H ETGHIGSFSSGVANR,VQAEY VWIDGDGGLR ELASGVSFPIGFK,VLGYDPL VQPALLR gi Endopeptidase* EPGLAFAFGK

4 gi α-keto-β-hydroxylacyl reductoisomerase* Nucleotide transport gi 2977 ADP/ATP carrier protein* Inorganic ion transport DNGLNVIVGVR TIASDGIAGLYR,QFNGLVDV YRK gi Catalase* YNILDLTK,LFSYPDTHR gi Manganese superoxide dismutase* IALQAALK Cytoskeleton gi Actin* IVAPPERK,AVFPSIVGRPR,I WHHTFYNELR,SYELPDGQVI TIGNER,YPIEHGIVTNWDDM EK,VAPEEHPVLLTEAPLNPK, DLYGNVVLSGGTTMFPGIAD R,TTGIVLDSGDGVTHTVPIY gi Actin* IVAPPERK,VAPEEHPVLLTE APLNPK,FRAPEALFQPGFLG LESAGIHETTYNSIMK Cell envelope biogenesis, outer membrane gi Glutamine:fructose-6- phosphate amidotransferase* TIETLELELAAIMK gi gi gi Intracellular trafficking and secretion Mitochondrial processing peptidase β subunit* Ypt (yeast protein transport) 1 related protein* SAR small monomeric GTPase* gi Ran GTPase Spi1* gi gi Signal transduction CAP (adenyl cyclase associated protein)* Protein phosphatase regulatory subunit Pab1* DVPVAVDIISDILQNSK LLLIGDSGVGK,LQIWDTAGQ ER,FADDTYTESYISTIGVDFK LLFLGLDNAGK,LATLQPTLH PTSEELAIGNVK LVLVGDGGTGK,SNYNFEKP FLWLAR SFAGASVVEIVGLVEK SFFSEIISSISDVK gi Hhp1 protein kinase* TVLLLADQLISR NLLSVAYK,YLAEFATGDK,D gi protein* STLIMQLLR,PETREDSVYLA K,VASSDQELTVEER,QAFDD AIAELDTLSEESYK,DNLTLW TSDMQDSADKPAEKDEAAD APADE,QAFDDAIAELDTLSE ESYKDSTLIMQLLR TIIVWQLTR,DKTIIVWQLTR, DGITMLWDLNEGK,DGITML WDLNEGK,SIVDELKPAYAE Guanine nucleotide binding gi EGGR,SIVDELKPAYAEEGGR protein beta subunit*,fspnvmnpvivssgwdk,hl YSLEAGDIVNALVFSPNR,HL YSLEAGDIVNALVFSPNR,G gi Small GTPase CDC42* NVFDEAIVAALEPPVVK gi Ras * INVDQAFQDLVR

5 Asterisks indicate unique proteins identified from L.edodes fruiting body using 1-DGE and following LC-MS/MS. Commonly identified proteins from 1-DGE and 2-DGE analysis are shown in red letters.

6 Table 2. Proteins (Lentinula edodes) identified by 2-DGE and nesi-lc-ms/ms. The table lists indicated spot numbers, internal amino acid sequences analyzed by tandem MS, matching peptides, scores, accession numbers, protein names, sequence coverage, theoretical mass (molecular weight, kda), theoretical pi, function and N -terminal amino acid sequence analyzed; left to right. Spot Amino Acid Sequence Peptide Score Accession Protein Name Sequence Coverage Analytical MW Theoretical pi Functional Category N -terminal Amino Acid GFFHHESDEAQAYD 1 EAFVEVTK 1 40 gi Hypothetical protein 2% Unknown Q 2 Unanalyzed 3 4 IPTIGIGAGNGTSGQVLV QADMTGNFPPGR TEAILTPLQQAMRQK,QV KESWPSNPVDGYIQSIR, AGPGK 1 26 gi methyl-2-oxobutanoate hydroxymethyltransferase* 9% Coenzyme metabolism DGGME 3 0 gi Hypothetical protein 7% Unknown QGLNL 5 IEKDAVLK 1 39 gi Hypothetical protein 0% Unknown QLERG LYDDVVPK,IIPDFMLQG gi Cyclophilin* 13% modification, protein Blocked GDFTR 7 IDTGSPRYSFLDPR 1 24 gi Hypothetical protein 3% Unknown Unanalyzed 8 MYTTISPMLVVSLATLAF ISLFNIYR 1 25 gi Cytochrome P450 1* 5% Secondary metabolites biosynthesis, transport, and catabolism Unanalyzed 9 DATEAFEDVGHSDEAR 1 52 gi Hypothetical protein 10% Unknown Unanalyzed MPNLYETFVNSIAPSIYG 10 NEDIKK,LSSHFVSIR 2 36 gi Hypothetical protein 4% Unknown Unanalyzed 11 No significant hit found QPNEDR 12 DYGVLIEDEGIALR gi Hypothetical protein 7% Unknown QPXIY 13 KNGHVVIK,NRPCKIVDM Translation iniciation factor Translation, ribosomal 3 82 gi % STSK,VHLVA IDIFTGK 5A* structure and biogenesis Blocked 14 EFGIDQK 1 45 gi Hypothetical protein 1% Unknown Unanalyzed APTIKVGDTVPDGT 15 VEVDLASIPEGK 1 46 gi Hypothetical protein 5% Unknown F SPVKPTAAPITTTPSEPKV SPAK,VSLPR,MSVSQQQ SKQNDR,TEDEHNPMSAI 16 RPTMAPPIR,T AQPQRPAHPM DMAKYASGKI 5 0 gi Hypothetical protein 6% Unknown Unanalyzed PLHAYQHDNNSGG 17 FVNSIVSRLDAK 1 43 gi Hypothetical protein 4% Unknown PL 18 IALQAALK 1 49 gi Manganese superoxide Inorganic ion transport 5% dismutase* QGGPL

7 19 AATPK,IALQAALK 2 56 gi Manganese superoxide Inorganic ion transport 9% dismutase QNTLL 20 Unanalyzed 21 TTKATMAANAK 1 48 gi Hypothetical protein 10% Unknown QFGIE 22 SFGAEEGGSGK 1 44 gi Hypothetical protein 0% Unknown SFGIE 23 Unanalyzed 24 MSGLSKMEK 1 35 gi Ribosome biogenesis protein* 1% Translation, ribosomal structure and biogenesis QFGIE 25 QEQQHLWTR 1 41 gi Hypothetical protein 1% Unknown Unanalyzed 26 LQSTSFDKK,SYLTYLK 2 56 gi Cytoplasm protein* 9% Signal transduction MLLYS 27 QFHIFIVK 1 45 gi Hypothetical protein 7% Unknown Unanalyzed 28 GETVISPR 1 42 gi Hypothetical protein 0% Unknown Unanalyzed 29 FGSPALLLLVAR 1 48 gi Hypothetical protein 1% Unknown Unanalyzed 30 AANRAFASSAATLIK 1 50 gi Hypothetical protein 16% Unknown Unanalyzed 31 LVLVGDGGTGK,RHLTG EFEKK,FGGLR,NVPNWH R,VCENIPIVLCGNK,VDV K,TGAVTFHR,NLQYFEIS gi Small G protein RAN* 31% Intracellular trafficking and secretion 32 GLISEER 1 28 gi Hypothetical protein 0% Unknown Unanalyzed 33 SVYVIDPAKK 1 56 gi Hypothetical protein 3% Unknown Unanalyzed 34 SVYVIDPAKK 1 55 gi Hypothetical protein 3% Unknown QGQDL 35 SVYVIDPAKK 1 45 gi Hypothetical protein 3% Unknown XAPNT 36 NEENILPLPK 1 40 gi Hypothetical protein 1% Unknown Unanalyzed 37 ILCDISNISR 1 33 gi Hypothetical protein 2% Unknown Unanalyzed 38 Unanalyzed EIAPDGHCLFSAFADQLS 39 TLSIPLQQK 1 31 gi Hypothetical protein 4% Unknown Unanalyzed PETR,EDSVYLAK,LAEQ AER,YEEMVENMKR,VA SSDQELTVEER,NLLSVA YK,NVIGAR,IVSSIEQK,E ESK,GNEAQVSMIK,HLIP 40 SAASGESK,MMGDYHR, YLAEFATGDKR,ESADKS LEAYK,AASDVAVTELPP THPIR,DSTLIMQLLR,DN LTLWTSDMQDSADKPAE K,DEAADAPADE gi protein* 68% Signal transduction PETRE Blocked

8 PETR,EDSVYLAK,LAEQ AER,YEEMVENMKR,VA SSDQELTVEER,NLLSVA YK,NVIGAR,IVSSIEQK,E ESK,GNEAQVSMIK,HLIP SAASGESK,MMGDYHR, 41 YLAEFATGDKR,ESADKS gi protein 72% Signal transduction PETRE LAYK,AASDVAVTELPPT HPIR,LGLALNFSVFYYEI LNSPDR,DSTLIMQLLR,D NLTLWTSDMQDSADKP AEK PETR,EDSVYLAK,LAEQ AER,YEEMVENMKR,VA SSDQELTVEER,NLLSVA YK,NVIGARR,IVSSIEQK, EESK,GNEAQVSMIK,HLI PSAASGESK,MMGDYHR, 42 YLAEFATGDKR,ESADKS gi protein 78% Signal transduction QEDIE LEAYK,AASDVAVTELPP THPIR,QAFDDAIAELDTL SEESYK,DSTLIMQLLR,D NLTLWTSDMQDSADKP AEK,DEAADAPADE LAEQAERYEEMVENMK, VASSDQELTVEER,NLLS 43 VAYK,ICEDILDVLDK,YL gi protein 22% Signal transduction QPREE AEFATGDK VASSDQELTVEER,NLLS 44 VAYK,ICEDILDVLDK gi protein 12% Signal transduction ATELI NLLSVAYK,ICEDILDVLD 45 K 2 63 gi protein 7% Signal transduction QYCES 46 EVDLSK 1 41 gi Hypothetical protein 2% Unknown Unanalyzed 47 ELEEELK 1 49 gi Hypothetical protein 0% Unknown Unanalyzed Cell division and Cytoplasmic dynein 48 EEIEEELR 1 44 gi % chromosome QPLPP intermediate chain * partitioning 49 FLGSLTGHK,GWVTAIAT SSENPDMILTASR,DKTII VWQLTR,DDDSYGYPKR, LWDLNTGLTTR,QIVSGS R,LWNTLGECK,YDIK,DD GHSEWVSCVR,FSPNVM NPVIVSSGWDK,VWELSK,TNHYGHTGYINTVSVSP DGSLAASGGK,DGITML WDLNEGK,YWLCAATAS CVK,SIVDELKPAYAEEG GR,VWTVTS gi Guanine nucleotide binding protein beta subunit* 61% Signal transduction QGIEQ

9 50 NSLRIAR 1 53 gi MPENFTYKPK 1 42 gi ATP synthase δ chain, mitochondrial precursor* MAPK activated protein kinase Cmk2* 4% Energy production and conversion QGE 1% Signal transduction Unanalyzed IIAIDVKDPLASK,HLPGL 52 LRATNEWFR,KYADEVIR 3 52 gi Hypothetical protein 12% Unknown QSQYS IIAIDVKDPLASK,HLPGL 53 LR 2 47 gi Hypothetical protein 6% Unknown Unanalyzed 54 HIDTAAVYGTEK,YGKTG Carbohydrate transport 2 55 gi Aldehyde reductase* 8% AQVALAWG ITK QYLET GSVANMSLGGGK,KIVE 55 AGSYK RADGIHLLNIGK,FTPGSF 2 63 gi Hypothetical protein 3% Unknown DEILV 56 TNYITR,SFKEPR,VDHQA 4 60 gi Hypothetical protein 13% Unknown Unanalyzed 57 IR GVFAAGDVQDKR 1 94 gi Hypothetical protein 3% Unknown Unanalyzed 58 DMLASNMLEAVSKPK 1 50 gi Hypothetical protein 0% Unknown QTPLD 59 Unanalyzed 60 QALISNGLK 1 47 gi Palmitoyltransferase* 1% Lipid metabolism Unanalyzed SYWPLDEPSINMLAVSTS KK YDSVHGR,LIVDG K,EISVFGEK,LTGLAFR,V VDLLVFAAK 1 27 gi Hypothetical protein 2% Unknown Unanalyzed 4 43 gi Glyceraldehyde-3-phosphate dehydrogenase* 11% Carbohydrate transport 63 CTS IACFLHAK 1 48 gi Aspartyl proteinase* 6% Amino acid transport Blocked 64 THDGAVAVR 1 36 gi Hypothetical protein 5% Unknown Unanalyzed VTDIGQLR,GGFPGPQGP YYCGAGTGK,DLIEAHYR TTTVSK,KVTDIGQLR,GG FPGPQGPYYCGAGTGK,D LIEAHYR,RHDEHIAVYG EDNDLR,RPASNIDPYR LQDYFK,DNGLNVIVGVR K,EVYSDLYGER GVAEVKLSMFESALK,TS EQTSGALGEDHGPKK 3 69 gi Glutamine synthetase* 9% gi Glutamine synthetase 18% Amino acid transport Amino acid transport 3 98 gi Hypothetical protein 4% Unknown IKTLD QVLRP GILDI QNRVY 2 29 gi Hypothetical protein 3% Unknown QAYKI

10 69 AGFAGDDAPR,AVFPSIV GRPR,HQGVMVGMGQK, DSYVGDEAQSK,RGILTL K,YPIEHGIVTNWDDMEK,IWHHTFYNELR,VAPEE HPVLLTEAPLNPK,LDLA GR,DLTDFLIK,NLMER,G gi β-actin* 56% Cytoskeleton QTMNY 70 YPFTTTAER,LCYVALDF EQELQTAAQSSALEK,SY ELPDGQVITIGNER,CDLD IR,DLYGNVVLSGGTTMF PGIADR,VKIVAPPER,QE YDESGPGIVHRK DLTDFLIK,LCYVALDFE QELQTAAQSSALEK,SYE LPDGQVITIGNER,DLYG gi β-actin 18% Cytoskeleton QPGAK NVVLSGGTTMFPGIADR MQK 71 AAVPSGASTGIHEAVELR,EIDDFLIK,LDGTPNK,YD LDFK,IKTAIEK,KACNGL LLK,SGETEDVTIADLVV GLGVGIIKTGAPCR gi Hypothetical protein 18% Unknown QPNKD AAVPSGASTGIHEAVELR 72,EIDDFLIK 2 84 gi Hypothetical protein 5% Unknown Unanalyzed 73 KDDGTSAIVLENPK 1 52 gi Hypothetical protein 2% Unknown Unanalyzed 74 VLHMDR,DR,DYAVDLIP K,SPLMGLFEK,KVIGDPS YFGAGK 5 82 gi Hypothetical protein 8% Unknown Unanalyzed ILSTLDR,GVLLYGPPGTG K,TMLVK,VVGSEFVQK, YLGEGPR,ENSPAIIFIDEI DAIATK,VIMATNR TGTLSSTGGGGGGGPERP PFAR VWELSK,SIVDELKPAYA EEGGR SPYLYPLYGLGELPQGFT R gi Protease regulatory subunit 6B homolog* 15% modification, protein Blocked 1 28 gi Hypothetical protein 2% Unknown Unanalyzed 2 49 gi Guanine nucleotide binding protein beta subunit 7% Signal transduction Unanalyzed 1 42 gi Hypothetical protein 4% Unknown Unanalyzed 79 ELAALKGK 1 48 gi Hypothetical protein 3% Unknown Unanalyzed DYAVDLIPK,SPLMGLFE gi Hypothetical protein 6% Unknown Unanalyzed K,KVIGDPSYFGAGK 81 GRPI LSIPK 1 41 gi Putative monooxygenase* 1% Secondary metabolites biosynthesis, transport, and catabolism Blocked

11 82 YAWVLDK,YVTVIDAPG HR 2 42 gi Translation elongation factor 1-α 22% Translation, ribosomal structure and biogenesis QVAFE 83 VVDLLAPYAR,IGLFGGA GVGK,VALVFGQMNEPP GAR,FTQAGSEVSALLGR gi Hypothetical protein 14% Unknown Unanalyzed,IPSAVGYQPTLSTDMGG MQER,ITTTK,MLDPR 84 GIAELGIYPAVDPLDSK 1 56 gi Hypothetical protein 3% Unknown Unanalyzed 85 DATDPPDK 1 34 gi Hypothetical protein 1% Unknown Unanalyzed 86 LGRVELLK,GGSEAVISK, RVFNDPPALTANHDPNG MR 3 45 gi Hypothetical protein 1% Unknown Unanalyzed TAVALDTILNQK,ASLAY RQLSLMLR SLFHPETLLTGK,EDAAS NYAR,GHYTIGK,YMACA LLYR,LGICNEPPAHVPG GDLAK,SMCMLSNTTAIS SAWSR,LDHKFDLLYSKR,EDLAALEK NMIYGK,FFGNLMDAGR, LSICGEESFGTGSDHIR 2 78 gi ATPase 1 α subunit* 4% gi α tubulin* 20% gi Phosphoglucomutase* 5% Energy production and conversion Cell division and chromosome partitioning Carbohydrate transport Blocked MREVI QGAIS 90 SGAITGITLKDXK 1 67 gi Integrase* 11% Translation, ribosomal structure and biogenesis MLAGT 91 DAGAIAGLDVLR 1 86 gi Hypothetical protein 1% Unknown Unanalyzed 92 VEIIANDQGNR,TTPSYV AFTEGER,TFSPQEISAMV LTK,KAVVTVPAYFNDSQ gi Hypothetical protein 12% Unknown QGLVA R,LDISDDAR,VDDIVLVG GSTR,DAEQFK 93 IINEPTAAAIAYGLDR 1 77 gi Heat shock protein Ssa2* 2% modification, protein Unanalyzed NQVAMNPHNTVFDAKR, FDDAEVQSDMK,IINEPT AAAIAYGLDKK,ATAGDT HLGGEDFDNR,SINPDEA 94 VAYGAAVQAAILSGDTS EK,NTTVPTK,TKDNNLL GK,FELSGIPPAPR,EGIEW LDSNTTASTDELKDK gi Hypothetical protein 20% Unknown Unanalyzed

12 95 96 NQVAMNPHNTVFDAKR, KFDDAEVQSDMK,IINEP TAAAIAYGLDKK,ATAGD THLGGEDFDNR,NTTVPT KK,TKDNNLLGK,FELSGI PPAPR VEIIANDQGNR,NQVAM NPHNTVFDAKR,IINEPTA AAIAYGLDK,ATAGDTHL GGEDFDNR,DLSSNPR,L VSFFNGK,TKDNNLLGK,I TITNDKGR,LTDEK,LADK gi Hypothetical protein 13% Unknown Unanalyzed gi HSS1 (HSP 70)* 16% modification, protein TLDEQADSAAR,LTIGPR, Carbohydrate transport gi Trehalose phosphorylase* 4% EESNS NNHNILQGVASPDLR 98 TPDILNK 1 45 gi Hypothetical protein 1% Unknown Unanalyzed EIISNASDALDK,YESLSD PSKLDSGK,DTGIGMTK,E TLQQNK,LGIHEDAQNR, AQALR LIPVYK,FPTTTIG SFPQTK,GMLTGPVTILN WSFPR,AIQVDEPAIR,EG LPLR,LDADVISIEASK GVSYLK,AIDINK,DVILK, VAGILTVK,FAEEVK,SQF T ITPGSEQVR,KGEANSIITS YNR,CTTDHISAGGPWLK EHAALEPR IHETNLKK 6 96 gi Heat shock protein 90* 8% gi methyltetrahydropteroyltriglut amate-homocysteine S- methyltransferase* 8% gi Aconitase* 10% modification, protein Amino acid transport Energy production and conversion 102 EVLEILKK 1 41 gi Hypothetical protein 0% Unknown Unanalyzed 103 YK,IDVLSNPK,K NALEEYIYDTR gi Pss1* 3% modification, protein Asterisks indicate unique proteins identified from L. edodes fruiting body using 2-DGE and LC-MS/MS analysis. (In case of overlapping among Table 2, Table 3 and 4, astertisks added to protein name prior Table 2 to Table 3 and 4) Commonly identified proteins from 1-DGE and 2-DGE analysis are shown in red letters. Blue letters indicates consensus amino acid sequences between analyzed protein and matched protein. QGEAT QNAEE QASEV QTAAP Blocked

13 Table 3. Phosphoproteins (Lentinula edodes) identified by 2-DGE, Pro-Q DPGS staining, and nesi-lc-ms/ms. The table lists indicated spot numbers, matching peptide, scores, accession numbers, protein names, analytical mass (molecular weight, kda), theoretical pi, internal amino acid sequence and function; left to right. Spot Matching Peptide Score Accession Protein Name Analytical MW Theoretical pi Peptide Functional Category P1 P gi Hypothetical protein P gi Ring zinc finger transcription negative regulator factor* P4 (13) 3 82 gi Translation initiation factor 5A IGSSPVGAAESSTIR,DT GFDEHARIEIADQSR Unknown LIASGQGGGNFSNIR Transcription KNGHVVIK,NRPCKIV DMSTSK,VHLVA IDIFTGK Translation, ribosomal structure and biogenesis P5 (15) 1 45 gi Hypothetical protein EFGIDQK Unknown P6 P7 (22) 1 44 gi Hypothetical protein SFGAEEGGSGK Unknown P8 P9 P10 P11 (56) 4 60 gi Hypothetical protein RADGIHLLNIGK,FTPG SFTNYITR,SFKEPR,VD HQAIR Unknown P12 P13 (60) 1 47 gi Palmitoyltransferase QALISNGLK Lipid metabolism P14 P15 P16 P17 (75) gi ILSTLDR,GVLLYGPPG 26S protease regulatory TGK,TMLVK,VVGSEF modification, protein subunit 6B homolog VQK,YLGEGPR,ENSPA IIFIDEIDAIATK,VIMAT P18 P19 (89) 3 95 gi Phosphoglucomutase NMIYGK,FFGNLMDAG Carbohydrate transport R,LSICGEESFGTGSDHI R P gi Trehalose phosphorylase TLDEQADSAAR,GIPN VIDSYAR,NNHNILQG Carbohydrate transport VASPDLR,IGFFSSTPQ GGGVALMR,SDLVHIA GSPQEEVWK P gi Trehalose phosphorylase P gi Trehalose phosphorylase P23 (99) 6 96 gi Heat shock protein IGFFSSTPQGGGVALM R,NNHNILQGVASPDL R,SDLVHIAGSPQEEV WK,GIPNVIDSYAR,IAL QLSTR Carbohydrate transport TLDEQADSAARK,LTIG PR,IGFFSSTPQGGGVA LMR,NNHNILQGVASP Carbohydrate transport DLR,VRPELPIIYR,GIP NVIDSYAR,IALQLSTR, EGFEVK EIISNASDALDK,YESL SDPSKLDSGK,DTGIG modification, protein MTK,ETLQQNK,LGIHE DAQNR,AQALR Asterisks indicate unique proteins identified from L. edodes fruiting body using 2-DGE and LC-MS/MS analysis. (In case of overlapping among Table 2, Table 3 and 4, astertisks added to protein name prior Table 2 to Table 3 and 4) in parenthesis of Spot correspond to spot number of Figure 3 and Table 2.

14 Table 4. Glycoproteins (Lentinula edodes) identified by 2-DGE, Pro-Q EGGS, and nesi-lc-ms/ms. The table lists indicated spot numbers, matching peptide, scores, accession numbers, protein names, analytical mass (molecular weight, kda), theoretical pi, internal amino acid sequence and function; left to right. Spot Matching Peptide Score Accession Protein Name Analytical MW Theoretical pi Peptide Functional Category G1 (85) 1 34 gi Hypothetical protein DATDPPDK Unknown G2 (80) 3 63 gi Hypothetical protein DYAVDLIPK,SPLMGLFEK,KVI GDPSYFGAGK Unknown G3 (73) 1 52 gi Hypothetical protein KDDGTSAIV LENPK Unknown G4 G gi Hypothetical protein EQFLDDLEQALYASK,DYFGA HTFR Unknown G6 (41) gi protein PETREDSVYLAK,LAEQAER,Y EEMVENMKR,VASSDQELTVE ER,NLLSVAYK,NVIGARR,IVSS IEQK,EESK,GNEAQVSMIK,HLI PSAASGESK,MMGDYHR,YLAE Signal transduction FATGDKR,ESADKSLEAYK,AA SDVAVTELPPTHPIR,LGLALNF SVFYYEILNSPDR,DSTLIMQLL R,DNLTLWTSDQDSADKPAEK G gi Ras protein* TGEGFLLVYSITSR Signal transduction G8 (22) 1 44 gi Hypothetical protein SFGAEEGGSGK Unknown G9 (19) 2 56 gi Manganese superoxide Inorganic ion transport and AATPK,IALQAALK dismutase metabolism G10 (15) 1 46 gi Hypothetical protein VEVDLASIPEGK Unknown G11 (11) G12 (6)

15 Asterisks indicate unique proteins identified from L. edodes fruiting body using 2-DGE and LC-MS/MS analysis. (In case of overlapping among Table 2, Table 3 and 4, astertisks added to protein name prior Table 2 to Table 3 and 4) in parenthesis of Spot correspond to spot number of Figure 3 and Table 2. Commonly identified proteins from 1-DGE and 2-DGE analysis are shown in red letters.