Supplementary table1 Summary of phosphopeptides characterised in Populus Leaf Protein excised from the leaf of Populus were analysed using NanoLC–ESI-MS/MS by TiO2/SCX enrichment. Observed, observed m/z. Mr(expt), molecular weight of the peptide calculated from the observed m/z. Mr(calc), theoretical molecular weight of the peptide. Score, Mascot Mowse score, the higher the mass, the more reliable the sequence.

JGI Protein ID / Protein description / Phosphopeptide sequence / Phosphorylation site / Mr(expt) / Mr(calc) / Score / Novel
Photosynthesis and calvin cycle
551203 / Photosystem II reaction center protein PsbP / K.pSIADYGSPEEFLSK.V / S146 / 1621.69 / 1621.69 / 66 / N
813989 / Manganese-stabilizing protein/photosystem II polypeptide / K.GpSGTANQCPTIDGGLDSFAFKPGK.Y / S107 / 2490.09 / 2490.09 / (56) / N
674736
569170 / Photosystem II 10 kDa polypeptide PsbR, Short-chain dehydrogenase/reductase SDR / K.TDTPYGpTGGGMNLR.D / T52 / 1518.63 / 1518.62 / 72 / N
716206 / photosystem II ,manganese ion binding / K.GSGpTANQCPTLDGGAESFAFKPGK.Y / T109 / 2462.06 / 2462.06 / 61 / Y,B
652073
568456 / Light-harvesting complex II protein Lhcb1 / K.pTTKPVPSGSPWYGPDR.V / T38 / 1866.83 / 1866.83 / 94 / Y,A
K.TpTKPVPSGSPWYGPDR.V / T39 / 1866.84 / 1866.83 / 73 / N
242776 / chloroplastic beta subunit of F1 ATP synthase / K.GRDTVSQQINVpTCEVQQLLGNNR.V / T62 / 2651.26 / 2651.25 / (74) / N
R.DpTVSQQINVTCEVQQLLGNNR.V / T54 / 2438.13 / 2438.13 / (117) / N
Metabolism and energy
815458 / Fructose-6-phosphate 2-kinase/fructose-2,6-bisphosphatase / R.FSNVDGPGNApSFSYK.D / S232 / 1668.68 / 1668.68 / 87 / N
835143 / GDP-mannose pyrophosphorylase / R.ISpSFEALQSATR.S / S217 / 1388.62 / 1388.63 / 61 / Y,A
423384 / GDP-mannose pyrophosphorylase / R.VSpSFEALQFSTR.H / S217 / 1450.64 / 1450.65 / 57 / Y,A
595429 / dTDP-glucose 4-6-dehydratase/UDP-glucuronic acid decarboxylase / K.VVGTQAPVQLGpSLR.A / S368 / 1503.78 / 1503.78 / 59 / Y,A
739764 / phosphoglycerate mutase / K.AHGTAVGLPSEDDMGNpSEVGHNALGAGR.I / S82 / 2798.23 / 2798.21 / 78 / Y,O,A
832763
822067 / Phosphoglucomutase / K.ApTGAFILTASHNPGGPNEDFGIK.Y / T116 / 2393.11 / 2393.11 / 54 / Y,O,A
R.ATGAFILpTASHNPGGPNEDFGIK.Y / T122 / 2393.12 / 2393.11 / 56 / Y,O,A
R.ATGAFILTApSHNPGGPNEDFGIK.Y / S124 / 2393.11 / 2393.11 / 103 / Y,O,A
230754 / Pyruvate dehydrogenase E1, alpha subunit / R.YHGHpSMSDPGSTYR.T / S291 / 1673.62 / 1673.63 / 69 / Y,O,A
723209 / Predicted dehydrogenase / K.LSSQISTAVQpTTSENTK.V / T247 / 1873.88 / 1873.87 / 100 / N
549130 / Predicted dehydrogenase / K.ISSQISTAVQpTTSEK.T / T440 / 1658.78 / 1658.78 / 76 / N
780407 / 5'-AMP-activated protein kinase / R.SIGFNPGNpSIGIGR.S / S340 / 1467.69 / 1467.69 / 72 / N
657667 / Asparagine synthase / _.MLGVFSSAIVSPPDELVAAGSRpTPSPK.I / T23 / 2834.39 / 2834.39 / 100 / N
568931 / Asparagine synthase / R.RGpSEANWTEWESHS.- / S244 / 1754.67 / 1754.67 / 70 / N
K.AFANPPEELNpSPASQR.S / S18 / 1806.79 / 1806.79 / 62 / N
706715 / Predicted carbonic anhydrase / R.VCPpSHVLDFQPGEAFVLR.N / S160 / 2092.99 / 2092.98 / 49 / N
565688 / pyruvate,orthophosphate dikinase / R.GGMpTSHAAVVAR.G / T581 / 1235.54 / 1235.55 / 93 / Y
816402 / Phosphoenolpyruvate carboxykinase [ATP] / R.KKpSAPTpTPIKGAQGAFNAISEEER.Q / S66,T70 / 2689.26 / 2689.25 / 153 / Y,Y,A
K.APDNGEFSFASNpTPR.S / T17 / 1688.71 / 1688.68 / 65 / N
786314 / Octicosapeptide/Phox/Bem1p (PB1) domain-containing protein / K.ESLSSSMpSLPR.Q / S284 / 1272.55 / 1272.54 / 72 / N
294045 / K+-channel ERG and related proteins, contain PAS/PAC sensor / R.LTPVNVSQpSPTTFPDAAK.N / S269 / 1951.93 / 1951.93 / 66 / N
287942 / Phosphatidylinositol transfer protein SEC14 and related proteins / K.KVPLTLVSFKEEpSNALADLSHIER.R / S50 / 2775.42 / 2775.42 / 56 / N
250392 / Membrane coat complex Retromer / R.SpSSSDSSQSFSISR.S / S116 / 1540.61 / 1540.60 / 79 / N
R.SLpSTASNSSSDFMK.I / S131 / 1540.64 / 1540.61 / 79 / N
797875 / ER-Golgi vesicle-tethering protein p115 / K.SGGASpTPPDVEAIR.A / T842 / 1435.63 / 1435.63 / 60 / N
Nucleic acid binding and gene expression
Transcription
642381 / Global transcription factor group E / R.ASpSPTSGPASASAR.A / S182 / 1325.56 / 1325.56 / 60 / N
669671 / Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins / R.GHpSPPPPGPHAPPSGPPHREPPPPGPR.A / S39 / 2782.32 / 2782.32 / 121 / N
826637 / CREB/ATF family transcription factor / R.SKGpSLGSLNMITGK.N / S145 / 1471.71 / 1471.71 / 72 / Y,O,A
247052 / CCAAT-binding factor / M.ADpSDNEpSGGHNAVSELSAK.E / S4,S8 / 2008.81 / 2008.80 / 141 / N
422794 / CCCH-type Zn-finger protein / K.EIPQLGFQSFSSpSPR.F / S27 / 1758.80 / 1758.80 / 64 / N
588050 / Conserved Zn-finger protein / R.SQYEKPSYGDDpSPKR.S / S343 / 1835.76 / 1835.77 / 111 / N
K.YGDDNpSDDDAEK.K / S397 / 1422.46 / 1422.45 / 66 / N
566362 / Zn-finger / R.DVFGDpSEDEEEDAYAVR.N / S177 / 2024.78 / 2024.75 / 105 / N
660535 / Zinc finger / R.ADpSIEGTVIDR.D / S128 / 1254.56 / 1254.55 / 85 / N
729872 / HMG-I and HMG-Y, DNA-binding, Protein of unknown function DUF296 / K.LPpSPVGASVPSFGFR.S / S284 / 1596.78 / 1596.77 / 69 / N
251538 / Same as HMGA905 / R.pSDSNANITTTTPTVSTSPTQIQPQYAVPVSSAPPEQK.R / S117 / 3921.87 / 3921.85 / 64 / N
585498 / KEKE-like motif-containing transcription regulator (Rlr1)/suppressor of sin4 / K.VGPPpSPNLVNSVK.S / S186 / 1386.69 / 1386.69 / 54 / N
818339 / Nuclear localization sequence binding protein / K.TPVpTPVTSENAGSK.T / T384 / 1466.67 / 1466.67 / 76 / N
649767 / Calcium-responsive transcription coactivator / R.LFLFPVNPpSPASFGSDGGR.S / S149 / 2043.95 / 2043.95 / 116 / N
819443 / Predicted MutS-related protein involved in mismatch repair / R.SGYVLTEQQEPpSPR.H / S144 / 1669.74 / 1669.73 / 73 / N
RNA processing
593806 / RNA-binding protein LARP/SRO9 and related La domain proteins / M.ATLTNSNPNSIAAADHpSPR.H / S18 / 2057.92 / 2057.92 / 79 / N
203151 / RNA-binding protein RBM8 / K.SAITGGSApSPSLSAPK.K / S50 / 1509.70 / 1509.71 / 73 / N
809716 / RNA-binding protein Sam68 and related KH domain proteins / M.SGFYTHNFpSPVR.A / S10 / 1532.65 / 1532.64 / 74 / N
554708 / RNA-binding protein Bicaudal-C / R.IEEGDNNLENpSNGEEGFVR.E / S169 / 2200.90 / 2200.89 / 65 / N
820878 / RNA-binding protein Bicaudal-C / K.SAMLPLpSPSPTVPAK.S / S246 / 1574.77 / 1574.78 / 59 / N
567751 / RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains / K.MVDGpSDSEDSNER.T / S136 / 1519.52 / 1519.51 / 73 / N
556597 / FOG: RRM domain/glycine-rich protein / K.TLTLAELSNYPpSAK.Q / S75 / 1586.75 / 1586.76 / 63 / N
781843 / K-homology type RNA binding proteins / R.KLEDLEPETLEEAEPSPADEQEPEEDGKADDVEDGGpSPDSKR.L / S57 / 4661.08 / 4660.98 / 54 / N
729865 / PolyC-binding proteins alpha CP-1 and related KH domain proteins / R.IIDGLDSDSSNpTPPTSGAK.V / T81 / 1953.86 / 1953.86 / 67 / N
653761 / Alternative splicing factor SRp20/9G8 / R.pSVENENRpSLpSPEPK.S / S10;S12;S21 / 1824.67 / 1824.67 / 52 / N,N,N
423773 / Splicing factor 1/branch point binding protein / R.DYpSGGEEETTSR.R / S25 / 1409.50 / 1409.50 / 84 / Y,A,O
823076 / RNA recognition motif / R.KApSPIRESLVLHVDSLTR.N / S100 / 2100.10 / 2100.11 / 63 / N
R.QREPpSPHRKPLApSPR.R / S226,S234 / 1914.88 / 1914.90 / 50 / N
Translation and posttranslational modification
717121 / Translation initiation factor 5A / M.pSDEEHHFESK.A / S2 / 1365.46 / 1365.49 / 47 / Y, M
832971 / 60S acidic ribosomal protein P2 / K.KEEKVEEKEEpSDDDMGFSLFD.- / S103 / 2585.05 / 2585.04 / 92 / Y,O
552351 / 60S acidic ribosomal protein P1 / K.KKEEVKEEpSEDEDMGFSLFD.- / S99 / 2470.02 / 2470.01 / 60 / Y,O,P
227384 / 26S proteasome regulatory complex, ATPase RPT4 / R.WGGLVTDMpSDDQQDITR.G / S80 / 2015.83 / 2015.83 / (54) / N
729432 / Calreticulin / R.DEEESKEDPADpSDAEEEDEAGDAEGEDpSDAETK.A / S379,S395 / 3702.27 / 3702.24 / 65 / Y,Y,A
554508 / Hypothetical protein / K.SVpSFHTLEELEAK.I / S121 / 1568.71 / 1568.71 / 49 / N
782441 / Molecular chaperone (small heat-shock protein Hsp26/Hsp42) / K.IEGAEDDNLpSPR.T / S204 / 1394.58 / 1394.57 / 60 / N
Signal transduction
413197 / Ste20-like serine/threonine protein kinase / K.SApSVGEWMFEPK.Q / S541 / 1446.59 / 1446.59 / 77 / N
582750 / Serine/threonine protein kinase / R.LSFPLTQGIGpSFK.W / S475 / 1896.86 / 1896.89 / 75 / N
554898 / Serine/threonine protein phosphatase / K.VSGMIEGLIWpSPR.R / S131 / 1523.72 / 1523.72 / 87 / N
832575 / Regulatory protein MLP and related LIM proteins / R.SPpSKAAGMFSGTQEK.C / S95 / 1604.70 / 1604.69 / 65 / Y,M
180526 / Predicted regulator of the ubiquitin protein (contains UAS and UBX domains) / R.EAGVVEApSPPSpSPGR.S / S338;S342 / 1598.64 / 1598.64 / 56 / N,N
736382 / Ca2+-binding protein, EF-Hand protein superfamily / R.KQpSYEEEGEGYGGR.S / S268 / 1710.67 / 1710.65 / 58 / N
798347 / Synaptic vesicle protein EHS-1 and related EH domain proteins / R.FDSFSMNEGGFpSPR.E / S876 / 1656.64 / 1656.63 / 62 / N
R.AASEpSPSQDFADVFAK.N / S747 / 1748.73 / 1748.73 / 80 / N
570193 / Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain / K.IASQNAENLSSpSPK.G / S29 / 1524.68 / 1524.68 / 67 / N
666576 / Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain / K.TASQNADNLLSpSSPK.G / S29 / 1611.72 / 1611.71 / 61 / N
Transporter
826518 / Autoinhibited H+ ATPase (AHA) transporter / K.NLDLNLIQTAHpTV.- / T949 / 1530.74 / 1530.74 / 69 / N
825159 / White-brown-complex ABC transporter / K.FDLDDVSSGAALpSR.A / S93 / 1531.67 / 1531.66 / 67 / N
756426 / Predicted transporter / R.KPFLHTGpSWYR.M / S23 / 1470.68 / 1470.68 / 46 / N
Other and unknown function
818784 / Nucleolar GTPase/ATPase p130 / K.FEGLGSTApSLNR.S / S477 / 1330.60 / 1330.59 / 73 / N
559737 / von Willebrand factor and related coagulation proteins / R.AAAESQATSQLSpSPSR.A / S93 / 1669.73 / 1669.73 / 85 / N
552310 / von Willebrand factor and related coagulation proteins / K.GAFMEVIRpSPK.K / S350 / 1313.62 / 1313.62 / 53 / N
K.SVTVTSSVQNpSPATK.A / S200 / 1584.75 / 1584.74 / 58 / N
718854 / Acinus (induces apoptotic chromatin condensation) / R.SEpSSVSEEAPK.E / S378 / 1228.49 / 1228.49 / 58 / N
558581 / Acinus (induces apoptotic chromatin condensation) / R.SDpSSVSEEAPK.E / S472 / 1214.47 / 1214.47 / 55 / N
591823 / Auxilin-like protein and related proteins containing DnaJ domain / R.SSFAETTDpSFVSR.S / S65 / 1512.62 / 1512.61 / 60 / N
752753 / GYF domain containing proteins / K.ITSSGALNNpSFR.E / S375 / 1345.60 / 1345.60 / 59 / N
410339 / Predicted methyltransferase / K.YVDEWIGPGpSPR.I / S208 / 1454.62 / 1454.62 / 76 / N
570481 / Protein phosphatase inhibitor 2 / K.TPYHPMIDVDDDSLpSPR.R / S46 / 2079.87 / 2079.86 / 71 / Y,A,O
569930 / PAF1 Complex Component B / R.EVEPDPGEpSEGER.E / S81 / 1508.57 / 1508.57 / 57 / N
657068 / Uncharacterized conserved protein / K.ADpSPEHTEESDLR.Y / S361 / 1564.60 / 1564.60 / 61 / N
R.ESpSPGFDVLVDNELR.D / S258 / 1755.78 / 1755.77 / 85 / Y,A
658643 / Uncharacterized conserved protein / K.ADpSPEHIEGSDLR.Y / S376 / 1504.63 / 1504.62 / 53 / N
R.ESpSPGFDVLVDDELR.D / S273 / 1756.76 / 1756.76 / 108 / Y,A
561367 / Uncharacterized protein CLU1/cluA/TIF31 / K.AAPTApSPISVQSAGK.I / S327 / 1463.70 / 1463.70 / 73 / N
553878 / FOG: Low-complexity / R.NApSPENDLIASR.L / S489 / 1365.59 / 1365.59 / 64 / N
561476 / Protein of unknown function / K.TTFpSVLEGVGR.T / S193 / 1244.57 / 1244.58 / 61 / N
583281 / Uncharacterized conserved protein / R.LADIpSDGESDEGGR.R / S415 / 1499.59 / 1499.58 / 60 / N
584641 / Unknown / R.AYFDpSADWALGK.Q / S19 / 1422.59 / 1422.59 / 76 / Y, O,A,
709976 / Unknown / R.YSIGSENSMEQpSPIHNHAR.I / S146 / 2235.93 / 2235.94 / 92 / N
570271 / Unknown / K.AKPFETSpSPADQAEIEKLEER.A / S134 / 2454.14 / 2454.13 / 76 / N
561661 / Unknown / R.LKpSISLYSYR.S / S76 / 1308.65 / 1308.65 / 56 / N

N, the phosphorylation site had not been identified in other species; Y, the phosphorylation site had been identified in other species. O, Oryza sativa; A, Arabidopsis thaliana; M, Medicago truncatula; B, Brassica napus; P, Populus simonii Populus nigra.