Supporting Information for Proteomics DOI 10.1002/pmic.200600043 Yuzo Nozu, Akira Tsugita and Kenichi Kamijo Proteomic analysis of rice leaf, stem and root tissues during growth course ª 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Supplementary Table 1. Observed unique leaf, stem and root proeins during the course of growth. Protein identificationa) N-terminalb) c) sequence L1 L2 L4 L8 L10 S2 S4 S8 catalase isozyme A X X X X X X X X superoxide dismutase, [Mn] X X X X X X X X L-ascorbate peroxidase AKNYPVV/ X X X X X X X X actin 1 X X X X X X X X ascorbate peroxidase X X X X X X X X peroxiredoxin APVAVXD/ X X X X X X X X glyoxalase I X X X X X X X X ATP synthase beta subunit, mitochondrial X X X X X X X X cytosolic glyceraldehyde-3-phosphate dehydrogenase GKIKIXI/ X X X X X X X X cytosolic glyceraldehyde-3-phosphate dehydrogenase VALQSEL/ X S-adenosyl methionine synthetase 1 X X X X X X X X fructose-bisphosphate aldolase isoenzyme C-1 X X X X X X X X cysteine synthase X X X X X X X X plastidic cysteine synthase 1 AVAAEVE/ X X X X X X X X nucleoside diphosphate kinase X X X X X X X X malate dehydrogenase SSASGQP/ X X X X X X X X 2,3-bisphosphoglycerate-independent phosphoglycerate mutase X X X X X X X X fructokinase II PLGDGAA/ X X X X X X X X cytosolic triosephosphate isomerase GRKFXVG/ X X X X X X X X cytosolic triosephosphate isomerase (#46->) YVFLPXY/ cytosolic triosephosphate isomerase (#34->) STDVVEV/ mitochondrial chaperonine-60 kDa DAKDIAF/ X X X X X X X X - 1 - isoflavone reductase X X X X X X X X Rubisco acrtivase (#46->) KELDEGK/ X X X X X X X X Rubisco acrtivase (#87->) FQAPTGD/ X X X X X X X X Rubisco large subunit X X X X X X X X Rubisco large subunit (#180->) LSAKNYG/ X Rubisco large subunit (#320->) XSGXDHI/ X ＦＡＲＥＬＧＶ Rubisco large subunit (#256->) X / Rubisco large subunit (#41->) RVTPQXX/ X ATP synthase beta subunit MRTNPTT/ X X X X X X X X glyceraldehyde-3-phosphate dehydrogenase AKIKIGI/ X X X X X X X glyceraldehyde-3-phosphate dehydrogenase SKIKIXI/ EFVVESG/ glyceraldehyde-3-phosphate dehydrogenase (#143->) nucleoside diphosphate kinase I X X X X X X X formate dehydrogenase AHTSAGS/ X X X X X X X X chaperonin 60 kDa beta subunit AKELHFN/ X X X X X X X X translational elongation factor Tu ARGKFER/ X X X X X X X X heat shock protein 70 kDa AVQAAIL/ X X X X X cyclophilin 2 X X X X X heat shock 70 kDa protein, mitochodrial X X X X X heat shock protein cognate 70 kDa X X reversibly glycosylated polypeptide X X X X X X tubulin beta chain MREILHI/ X X X X X actin depolymerizing factor X X X X X glycine-rich protein X X X X X osr40c1 X X X X - 2 - glutamine synthetase shoot isozyme X X X X X S-adenosyl methionine synthetase 2 X X X X X glyoxysomal malate dehydrogenase RAKGXAP/ X X X X cytoplasmic malate dehydrogenase AKEPMRV/ X X X X X X dihydrolipoamide dehydrogenase AAVAGEE/ X X X X X dehydrogenase ALREDGP/ X X X X X X reductase X X X X X chalcon isomerase X X X X dihydrolipoamide acyltransferase ASDNGDQ/ X X X X glutamate dehydrogenase X X X X X coproporphyrinogen III oxidase X X X X aspartate aminotransferase ALAVDVX/ X X X X X X aminomethyl transferase AGAAEAA/ X X X X malate dehydrogenase SAAAAAE/ X X X 20S proteasome subunit alpha-6 X X X X X X 20S proteasome subunit alpha-5 X X X X X X disulfide-isomerase DDVLALT/ X X X X X voltage-dependent anion channel VGPGLYP/ X X X X voltage-dependent anion channel X X X X X X H+exporting ATPase X X X X X X X translationally controlled tumor protein MLVYQDL/ X X X X X abscisic acid- and stress-induced protein QGVDSYG/ X X X X X glutathione peroxidase 1 X X X X methylmalonate-semialdehyde dehydrogenase X X X X cystathionine gamma-synthase X X dehydroascorbate reductase X X X X X disulfide isomerase X X X X X X - 3 - 26S protasome regulatory particle triple-A ATPase subunit 3 X X X X X X nascent polypepteide associated complex alpha chain X X X X X X elongation factor 1-beta' X X X X salt-stress induced protein TLVKIXP/ X X X X drought-induced S-like ribonuclease DSPFDFY/ X X X X X X glutathione S-transferase X X X X X carboxymethylene butenolidase X X dnaK-type molecular chaperone hsp 70 kDa X X X thioredoxin H-type X X X X X proteasome endopeptidase complex alpha chain X X X X dnaK-type molecular chaperone Bip (K)EXTKKL/ X X X X 20S proteasome subunit beta-1 X X X 20S proteasome subunit alpha-2 X X X X X 20S proteasome subunit beta-3 X X Protein identificationa) N-terminalb) c) sequence L1 L2 L4 L8 L10 S2 S4 S8 glutathione S-transferase II APMKLYG/ X X X X 20S proteasome beta 6 subunit X X X X superoxide dismutase, [Cu-Zn] ATKTAVA/ X X X X X X X X Rubisco small subunit XQVXPIE/ X X X X X X X X photosystem II oxygen-evolving complex protein 1 EGVPRRL/ X X X X X X X X X photosystem II oxygen-evolving complex protein 2 AYGEAAN/ X X X X X X X phosphoribulokinase SVDKPVV/ X X X X X X X X VSTETTG/ glutamine synthetase shoot isozyme, chloroplast X X X X X X X X - 4 - chloroplast fructose-bisphosphate aldolase GAXDDEL/ X X X X X X X X 3-beta hydroxysteroid dehydrogenase/isomerase X X X X X X X X peptidyl-prolyl cis-trans isomerase X X X X X X X X 50S ribosomal protein L10 X X X X X X X X glycine dehydrogenase VSASALA/ X X X X X X ferredoxin-NADP reductase, leaf isozyme X X X X X X ribulose-phosphate 3-epimerase XSRVDKF/ X X X X X X X glycolate oxidase X X X X X X glyceraldehyde-3-phosphate dehydrogenase KLKVAIN/ X X X X X X X chloroplast photosystem I reaction center subunit II X X X X X X ATP synthase gamma-subunit X X X X X X X quinone oxidoreductase X X X X X X X sedoheptulose-1,7-bisphophatase EIGDSLE/ X X X X X X ribosomal protein X X X X X X X thioredoxin M-type X X X X X X ferritin X X X X r40c1 protein X X X germin-like protein 5 LTQDFXV/ X X X X X X transketolase AAVETLE/ X X triose phosphate isomerase, chloroplast AGSGXFF/ X X X epimerase/dehydratase X X X X ATP dependent Clp protease ATP-binding subunit XFERFTE/ X X X 70 kDa peptidylpropyl isomerase X X X chloroplast peptidyl-prolyl cis-trans isomerase VLISGPG/ X X - 5 - 20 kDa chaperonin, chloroplast ATVVTXK/ X X ribosomal protein SWDGPLS/ X X X X thioredoxin peroxidase X X X salt-induced protein X X X X X X heat shock-related protein X X X X glyceraldehyde-3-phosphate dehydrogenase X X X X ATP synthetase epsilon subunit X X peroxidase X X cell death associated protein X X thioredoxin peroxidase AGGVDDA/ X X photosystem I 9 kDa protein (fragment) X X oxalate oxidase X X X cytosolic monodehydroascorbate reductase GADSKNI/ X X transcription factor APFI X X 3'(2'),5'bisphosphate nucleotidase X X caffeoyl-CoA O-methyltransferase 1 X X X cytosolic 6-phosphogluconate dehydrogenase X X X enoyl-[acyl-career-protein] reductase AXESGPQ/ X X X UDP-glucuronic acid decarboxylase X X X aldehyde dehydrogenase X X X eukaryotic initiation factor 4A X X X 60S acidic ribosomal protein P0 X X X mannose-binding rice lectin X X X enolase X X UDP-glucose pyrophosphorylase X X 26S proteasome regulatory subunit 6A X X X prepro-glutelin X X X - 6 - translation initiatiom factor 5A X X X 40S ribosomal protein S12 X X X DEAD BOX RNA helicase X X X GF14-c protein X X GDP dissociation inhibitor protein X X alpha-tubulin X X Sgt1 X fatty acid alpha-oxidase X cysteine synthase X X adenosine kinase X X 3-isopropylmalate dehydrogenase AAKRSYN/ X X Rubisco subunit binding-protein beta subunit AKELYFN/ X caffeic acid 3-O-methyltransferase STAADMA/ X X 26S proteasome regulatory particle triple-A ATPase subunit 6 X vacuolar ATPase B subunit X X prohibitin homologue X superoxide dismutase, (Cu-Zn) 1 X secretory peroxidase X receptor-like protein kinase X X guanine nucleotide-binding protein beta subunit X r40g2 protein AAPSDXN/ X X ATP synthase alpha chain, mitochondrial X X ATP synthase delta' chain, mitochondrial X X alpha-soluble NSF attachment protein X isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase X methylenetetrahydrofolate dehydrogenase X X - 7 - UDP-glucose dehydrogenasee X X cysteine synthase, 5'-partial X glycine hydroxy methyltransferase X carbonic anhydrase/acetyltransferase X X inorganic pyrophosphatase X Protein identificationa) N-terminalb) c) sequence L1 L2 L4 L8 L10 S2 S4 S8 phosphoenolpyruvate phosphonomutase X xyloglucan endotransglycosylase X 26S proteasome regulatory particle triple-A ATPase subunit 4 X X 20S proteasome subunit alpha-1 X X ６０ kDa chaperonin alpha subunit X endoplasmic reticulum membrane fusion protein X ATPase with chaperone activity X aminoacylase X translational elongation factor Tu, mitochondrial X susceptibility homeodomain transcription factor X X nuclear transport factor 2 X gamma hydroxybutylate dehydrogenase X 20S proteasome subunit alpha-3 X X mitochondrial processing peptidase alpha-II chain elongation factor-1 alpha X X X X X - 8 - phosphoserine aminotransferase X 40S ribosomal protein S21 X orthophosphate dikinase X X X chaperonine 60 kDa alpha subunit X X X peroxidase X 1,4 benzoquinone reductase AVKVYVV/ X X porin-like protein X peroxidase X IAA-amino acid hydrolase X tyrosine phosphatase X X X X X GTP-binding protein X X X X mRNA binding protein X X X X X peptidyl-prolyl cis-trans isomerase X X X X heat shock protein HSP 70 kDa homolog* DRQALXX/ X heat shock protein 26 kDa X heat shock protein 70 kDa EKVVGIL/ X X zinc-binding protein DAHKSEV/ X guanine nucleotide-binding protein beta subunit X calcium-dependent protein kinase (fragment) RPVAVXD/ X GTP-binding protein SUP1,EF-1-alpha-related SQADIXA/ X calcium-dependent protein kinase X ethylene responsive factor X tau-tubulin kinase family member* RFTKGXX/ X ethylene-inducible protein X X receptor-like