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Supporting Information for Proteomics DOI 10.1002/Pmic.200600526

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Supporting Information for Proteomics DOI 10.1002/Pmic.200600526 Supporting Information for Proteomics DOI 10.1002/pmic.200600526 Servet zcan, Volkan Yldrm, Levent Kaya, Dirk Albrecht, Drte Becher, Michael Hecker and Gulay Ozcengiz Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Figure S1. Predicted 2-D gel separation of the P. chrysosporium proteome. The rectangle indicates the analytical window of the experimental master gel. Figure S2. Comparison of the theoretical and experimental molecular weights (A) and pI (B) of the identified proteins in the P. chrysosporium master gel. The migration distances of the spots were measured by Delta2-D as Y and X-axis coordinates of the spot centers on the gel image, respectively. Table 1. List of protein identifications according to accession number*** ) % ( e g pI/Mr Hit Number of matched Number of matched peptides in PMF Subcellular localization* of Number multiple spots Modification** peptide Signal Relative abundancy Phosohorylation Sequence covera Accession number (kDa) score Putative function Identified peptides by MS/MS K.YLVDVGAGR.M 62 5.65/36.2 134 26S proteasome regulatory subunit rpn-8. C 0.041 30 R.VSEQLASLR.G R.ASDQEINDLLKR.Y 8 R.SEISNPPAFGAR.I K.LILGEDSPVIAAGR.V 265 6.43/45.8 199 Aspartate/other aminotransferase C 0.22 38 R.VGALHLVAPTTEAAAR.V 14 361 5.29/46.7 127 AAA ATPase N 0.023 21 R.EAVELPLTHFDLYR.K 23 425 7.76/28.8 139 Short-chain dehydrogenase/reductase SDR M + 0.017 35 R.NAGHIINIGSIAGR.E 11 K.ILAPFKGDK.K 465 4.61/31.5 88 DNA-directed RNA polymerase N 0.119 24 K.AEAAPAEAAPAPAAEAPKEEK.K 8 R.YLNESKR.L 503 8.97/26.7 78 Glutathione S-transferase, C-terminal C 0.12 24 R.TGLDLDEFPNVK.A K.GREYILGTYGIADIK.I 4 511 5.66/41.2 108 Enoyl-CoA hydratase/isomerase C 0.08 15 R.EASEAPGLFR.G K.IGYTPDVGATFFLSR.L 13 R.CHPFAVLR.G + Carbamidomethyl (C) Pyruvate dehydrogenase E1 component alpha R.SSSNTEYFTR.G 563 8.41/44.2 122 subunit M 3 C-M 0.336 + 32 K.GPILLEFVTYR.Y 16 582 6.39/57.7 87 Anthranilate synthase. C 0.058 19 K.LKEHIVAGDIIQAVPSQR.L 12 843 6.76/18.1 203 TonB-dependent receptor protein N 0.047 52 R.LFDEAFNNR.V R.VGGSQGQGNSGQLQR.R 6 871 5.13/30.0 105 E3 binding C 0.186 40 K.TAPAPPLDGPAIR.R 10 K.HLLPPLTR.E K.VVQDGTTADQIFTVR.Q 1076 6.65/32.6 178 Fumarylacetoacetate (FAA) hydrolase P + 0.056 13 R.FVAAETSQVHLGEPVDR.W 3 26S proteasome non-ATPase regulatory subunit K.DAATLLFFR.T 1148 5.43/32.1 104 Nin1/mts3 N 0.497 23 K.LITVNLQYAR.E 6 K.VNHGIISGVR.Y K.ASLGIVPGASGPATGPR.V 1157 8.91/84.1 358 RHO protein GDP dissociation inhibitor M 0.204 8 K.TVDEYAQLDAEDESLAR.W 10 1164 5.74/23.3 109 Uracil phosphoribosyl transferase C 0.028 48 K.LHVLAHPVINAR.L 8 1173 6.35/42.3 63 Oxidoreductase, N-terminal M + 0.125 + 24 K.GLVLYPYQNR.R 7 K.YFAYGISR.S R. 1293 5.48/85.0 142 Peptidase S9A, prolyl oligopeptidase M 0.019 5 YGAVLAVPNIR.G 15 RNA-binding region RNP-1 1311 10.12/19.1 96 (RNA recognition motif) N 0.119 32 R.DYDGPSTSAPPASNGEPR.W 6 R.RGAALHGLR.R 1324 5.58/64.2 65 TPR repeat, heat shock chaperonin-binding C 2 C 0.037 11 K.LAEQSFAQDPR.L 14 1333 6.44/48.8 139 NAD-dependent epimerase/dehydratase N 0.089 22 R.VAETLTYGFHR.Q 15 RNA-binding region RNP-1 (RNA recognition K.EVGGRPIAVK.V K.GYGFVDVGDEANQAK.A 1407 9.18/36.2 330 motif) C 2 M 0.495 + 49 R.SAGYGFVSLNTAEAAQK.A 12 K.YQLAYVR.S 1474 5.05/47.0 224 Proteasome component region PCI C_N 2 C-M 0.271 48 K.LSQTSQTFHIVR.A 16 1585 5.45/33.5 164 Proteasome endopeptidase complex M + 0.083 + 18 K.GNTEEFPSTDLDILDR.S 6 R.HNNVDFAIIR.E Isocitrate dehydrogenase NAD-dependent, R.EYALFEPGCR.H + Carbamidomethyl (C) 1651 9.07/40.6 104 mitochondrial M + 0.097 8 K.LGDGLFLNTFR.R 4 1661 7.28/28.4 85 Puromycin N-acetyltransferase M 0.085 6 R.AGYHLQLIGVHPDHQR.R 2 R.YLTVFSPEGR.L R.LANINQVYTQR.A 1827 6.34/31.3 203 20S proteasome, A and B subunits M 2 C 0.152 29 K.YGYEITPDALAR.R 9 R.YALQLLTPASILAR.L R.GTTDIVAPHGIPVDLLDR.C 1962 5.81/50.0 146 Replication factor C conserved region M 0.05 14 K.GLGLNPEGYANVDGAGFVGQVNAR.E 8 2075 5.62/15.7 72 Ubiquitin-conjugating enzymes C 0.802 25 R.QNSIETVLVEIR.R 3 2311 4.94/18.8 109 Tropomyosins N 0.275 50 12 K.IAVHVTIR.G K.VKEYELR.R 2657 10.36/20.1 91 Mitochondrial ribosomal protein L5 M 0.239 44 K.QRFDGIILK.- 9 2729 6.23/57.0 180 Probable oxidoreductase C + 0.027 26 13 K.VLHQGYFDNR.R Zinc-containing alcohol dehydrogenase K.VLHQGYFDNRR.A 2822 7.78/38.4 306 superfamily C 0.027 39 K.EIVHVFGNVHVPEQR.A 14 K.LLSHPSASTFDITALVR.N R.NVDNAIFEADKEGYCR.A + Carbamidomethyl 2920 5.36/37.7 53 Putative dyhydroflavanol-4-reductase C + 0.09 22 (C) 11 2978 5.20/61.5 95 Chaperonin ATPase. C 0.087 9 R.QQFLLATQLVR.A 15 Nucleotidyl transferase, Mannose-6-phosphate 3052 6.35/53.9 96 isomerase, type II Cs 2 C 0.203 6 R.EIPGFYVVIPAGGAGTR.L 9 K.AASEAAPFFR.D R.DVHDFIFGR.T 3168 6.03/49.9 227 Transforming growth factor beta C 0.015 24 R.LPPTFIEQAR.H 10 K.TLAGPPYPYR.E 3179 5.83/26.2 56 Hypothetical protein C 0.136 21 R.ADGTDVFLGDIDVHR.C 7 tRNA synthetases, class-II (G, H, P and S), C, K.TATPVPVVVIAR.E 3216 5.85/78.8 141 Prolyl-tRNA synthetase C 3 C-M + 0.092 10 K.FAGGLYTTTVEGFIPTSGR.A 16 K.TFTTQETITNATSAR.D 3583 6.17/61.8 58 Phosphoglucose isomerase (PGI) C 0.042 9 K.TEEEVRQELGPNASEPLVK.S 12 Hypothetical protein, elongation factor EF-Tu, K.EILAGFAGAFVDR.E 3623 4.62/13.1 144 tufA N 0.035 39 K.EILAGFAGAFVDREVETR.G 5 3711 6.80/38.2 64 GDP-L-fucose synthetase C 0.221 24 K.NGTPFIVGGTGKPLR.Q 9 K.VVETPQSETTPFYPR.S R.LHHLYEDQHERPNK.F 3727 6.61/42.9 61 GDP-mannose 4,6-dehydratase C 2 C 0.239 23 R.YFRPAEVDLLHGNPAK.A 10 4077 6.51/46.7 122 Adenylosuccinate synthetase C 0.058 27 R.YGHFEYDTEGEIVR.Y 12 Metalloenzyme, phosphoglycerate mutase, 2,3- 4270 5.62/57.8 162 bisphosphoglycerate-independent C 2 C-M 0.164 + 24R.IKDGDTLFFFNYR.S 16 4311 4.93/23.0 111 Amidase from nicotinamidase family C + 0.033 21 R.NAPHPPLIIHVR.N 6 4345 6.81/36.0 153 Arp2/3 complex, 34kDa subunit p34-Arc N 0.018 45 K.VFLQEFVDAR.R 14 4500 6.48/62.8 105 G-protein beta WD-40 repeat, corin like proteinon E + 0.016 28 K.AITALAPTSSSGTFIAGLADGR.V 13 Adipophilin (adipose differentiation-related R.VHPLLEATQAR.A 4580 6.37/37.6 83 protein) C 0.029 45 R.TPALTVVQGIDQR.F 14 Zinc-containing alcohol dehydrogenase K.SINIIGSYVGNR.Q 4796 7.54/37.9 189 superfamily C 2 C-M 0.445 54 K.AAVVDAHGAPLEIR.D 14 K.LFDDTFNVNVK.V K.SEQLIQFFANLHPQK.R 4883 5.79/27.2 336 Short-chain dehydrogenase/reductase SDR M 2 C-M 0.072 34 K.GVNVNAIAPGPVDTDLFR.A 5 5061 5.57/82.5 136 Dipeptidyl-peptidase V precursor E 3 C-M + 0.169 13 R.NSLTSPNDAFVLR.N 8 5153 5.75/37.6 146 Putative dyhydroflavanol-4- reductase C + 0.036 36 R.TYIVSPGTIYGLAR.G 11 K.HIVPDPAR.A K.VAEYAEEETSKR.A 5211 5.43/21.6 111 Suppressor protein SRP40 M + 0.143 22 R.APIPEPEGAANDEASATPSANDDSAK.V 3 R.VHHFDESYFR.A R.VAFSEDDEQVVCVTEQR.M + Carbamidomethyl 5240 5.96/37.4 182 G-protein beta WD-40 repeat N 0.207 43 (C) 14 R.IPLPIDDASR.F K.ELILEYYSLVR.A C, M R.SLVLLSAAGCEYAEYNR.Q + Carbamidomethyl 5348 5.55/35.6 58 Hypothetical protein M 4 C-M + 0.365 + 35 (C) 10 R.EPNQDHHAHH.- K.NEADAFLELCER.E + 5470 6.54/19.5 149 ATP synthase subunit h M 0.152 12 Carbamidomethyl (C) 4 R.NTLEGYLYR.L 5586 6.32/92.9 116 Heat shock protein Hsp70 E.R. + 0.016 + 15 R.LFGSDAFNIAGR.F 19 5721 5.93/121.8 111 Glycosyl S-transferase 35 C 0.072 22 8 Required for invasion and pseudohyphae R.AAYDYAVAHAR.A 5811 4.82/76.5 53 formation in response to nitrogen starvation N 0.507 + 5 K.NKPVHAYEHALNGLLAR.L 5 Elongation factor 1, beta/beta'/delta chain, K.LVPIGYGIR.K 5826 4.55/25.3 193 inorganic pyrophosphatase C 0.039 33 K.AITSAPDASLVSVNR.W 7 5864 6.25/52.3 129 Glutamine synthetase, catalytic region M 0.048 21 R.LSPYAPGHATVFGYFQYK.V 11 K.AFGNIYSR.I 5957 5.97/46.7 83 O-acetylhomoserine/O-acetylserine sulfhydrylase C 0.134 27 R.FPSFTKPSEGYHGLK.F 16 R.EGIAPVPVDAPR.L 6010 5.74/63.8 81 Glucose-methanol-choline oxidoreductase C 0.066 12 R.LVVVSAGTFGSPAILER.S 11 K.IGIQLAHAGR.K 6330 6.27/44.8 213 NADH flavin oxidoreductase/NADH oxidase C + 0.064 28 R.GPGLTFFEATAVSPEGR.I 13 R.DYFGAHTFR.V R.SEVVPANLIQAQR.D 6357 6.35/54.1 177 6-phosphogluconate dehydrogenase, C-terminal C 2 C 0.424 36 K.GLLFVGSGVSGGEEGAR.Y 17 6364 5.50/29.4 53 6-phosphogluconolactonase C 0.059 + 44 R.LTLTFPVINHAAR.V 10 K.EGIAIVFPDTSPR.G 6460 6.32/31.8 100 Esterase/lipase/thioesterase M 0.023 36 K.VIQEAGLPIDFSR.Q 9 Translation elongation factor Tu, protein K.YSPQIFLR.T 6570 8.36/51.8 177 synthesis factor M 0.05 20 K.FTDYNEIDKAPEER.A 17 R.GITINSAHVEYETDNR.H Rab GDI protein, probable secretory pathway C, K.QIAGSFVYR.D 6612 5.44/50.2 123 GDP dissociation inhibitor 1 C 3 C-M 0.376 + 38 K.FRPDQAPPAELGR.D 18 R.LIYFYLDER.G Phosphoglucomutase/phosphomannomutase C K.LPPSLAAHLKPGQR.A 6660 5.96/59.4 172 terminal C 0.051 24 R.NAGVTTTPILHYLVR.A 13 6715 6.00/32.9 66 Aldose 1-epimerase P + 0.011 46 K.YICVEPGYVR.G + Carbamidomethyl (C) 11 Ribosomal protein S3, C-terminal, 6737 8.72/29.2 103 Eukaryotic/archaeal ribosomal protein S3 M 0.052 42 R.FKFPENSLELYAEK.V 11 R.VYEIGPVFR.A 6758 6.05/62.7 230 Aspartyl-tRNA synthetase class IIb N 2 C-M 0.226 5 K.LQHAIGHLFR.D 20 Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen, similar to K.VGRPIVLFFYPK.S 6867 5.36/25.2 144 peroxiredoxin Q M + 0.051 39 K.LTYPVLSDSAGEAR.K 7 6915 4.68/34.9 60 F-actin capping protein, alpha subunit N 0.048 31 8 R.LLEFNNGR.V Glycyl-tRNA synthetase, alpha2 dimer, tRNA R.FFYAPAFEIYR.G 7072 5.92/73.8 156 synthetases, class-II (G, H, P and S) C 0.029 12 R.EFTPNVIEPSFGLGR.I 13 R.EFLQSIEDR.K 2Fe-2S ferredoxin, iron-sulfur binding site, R.CHTIFNCSR.T + 2 Carbamidomethyl (C) 7113 8.99/31.1 86 Ferredoxin M + 0.025 10 K.IKNEIDPTLTFR.R 3 R.SQFEGLVSNLIQR.T C, R.VINEPTAAALAYGLDR.A
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