Succinyl-proteome profiling of a high taxol containing hybrid Taxus. species (Taxus media) revealed involvement of succinylation in

Transcription

1 Succinyl-proteome profiling of a high taxol containing hybrid Taxus species (Taxus media) revealed involvement of succinylation in multiple metabolic pathways Chenjia Shen 1, Jie Xue 1, Tao Sun 1, Hong Guo 1, Lei Zhang 2, Yijun Meng 1,*, Huizhong Wang 1,* 1 College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou , China. 2 Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina Yijun Meng mengyijun@zju.edu.cn Huizhong Wang: whz62@163.com

2 Fig.S1: Representative MS/MS spectra of succinyl peptides from TCA cycle related enzyme IDH1 (Contig24602). (a) Succinyl-peptide _EPILCK(su)NVPR_ with succinylation site at K117 in TCA cycle related enzyme IDH1. (b) Succinyl-peptide _LK(su)LVFVPEK_ with succinylation site at K155 in TCA cycle related enzyme IDH1.

3

4 Fig.S2: Representative MS/MS spectra of succinyl peptides from TCA cycle related enzyme LSC1 (Contig4446). (a) Succinyl-peptide _GGVHIVK(su)TEK_ with succinylation site at K97 in TCA cycle related enzyme LSC1. (b) Succinyl-peptide _TEK(su)AEDIAGK_ with succinylation site at K100 in TCA cycle related enzyme LSC1. (c) Succinyl-peptide _K(su)GGTSIEDLAEK_ with succinylation site at K160 in TCA cycle related enzyme LSC1. (d) Succinyl-peptide _PVNK(su)VYLCQK_ with succinylation site at K127 in TCA cycle related enzyme LSC1. (e) Succinyl-peptide _QK(su)EIFALR_ with succinylation site at K259 in TCA cycle related enzyme LSC1.

5 Fig.S3: Representative MS/MS spectra of succinyl peptides from TCA cycle related enzyme LSC2 (Contig18557). Succinyl-peptide _VICQGITGK(su)NGTFHTEQAIEYGTK_ with succinylation site at K55 in TCA cycle related enzyme LSC2.

6 Fig.S4: Top seven clusters of highly interconnected lysine-succinylated protein networks. Interaction network of lysine-succinylated oxidative phosphorylation proteins (listed in gene names) was analyzed by the Cytoscape software (version 3.0.1).

7 Fig.S5: Top seven clusters of highly interconnected lysine-succinylated protein networks. Interaction network of lysine-succinylated photosynthesis-associated proteins (listed in gene names) was analyzed by the Cytoscape software (version 3.0.1).

8 Fig.S6: Top seven clusters of highly interconnected lysine-succinylated protein networks. Interaction network of lysine-succinylated RNA degradation-related proteins (listed in gene names) was analyzed by the Cytoscape software (version 3.0.1).

9 Fig.S7: Top seven clusters of highly interconnected lysine-succinylated protein networks. Interaction network of lysine-succinylated ribosome-associated proteins (listed in gene names) was analyzed by the Cytoscape software (version 3.0.1).

10 Fig.S8: Top seven clusters of highly interconnected lysine-succinylated protein networks. Interaction network of lysine-succinylated TCA cycle-related proteins (listed in gene names) was analyzed by the Cytoscape software (version 3.0.1).

11 Table S1. The information of succinylated peptides from histone proteins. Protein Localization prob PEP Modified sequence Modification (K) Probabilities Position Mass error [ppm] Peptide Score Contig _EIAQDFK(su)TDLR_ EIAQDFK(1)TDLR

12 Table S2. The information of succinylated sites in each succinylated protein. Protein Localization prob PEP Modified sequence Modification (K) Probabilities Position Mass error [ppm] Peptide Score Contig _RPQAK(su)AHFAK_ RPQAK(1)AHFAK Contig _AVEQK(su)QVAQQEAER_ AVEQK(1)QVAQQEAER Contig _LIFAGK(su)QLEDGR_ LIFAGK(1)QLEDGR Contig _TVTLEQK(su)IDR_ TVTLEQK(1)IDR Contig _K(su)FLLNIR_ K(1)FLLNIR Contig _GDVNSITVGSGTNIQDNTLVHVAK(su)SNLGGK_ GDVNSITVGSGTNIQDNTLVHVAK(1)SNLGGK Contig _ESK(su)AFQK_ ESK(1)AFQK Contig _IAGVYNPK(su)R_ IAGVYNPK(1)R Contig _ISFTK(su)EETEYLTNR_ ISFTK(1)EETEYLTNR Contig _LKK(su)ELQGSIDK_ LK(0.107)K(0.893)ELQGSIDK Contig _EEPSEIK(su)DLKR_ EEPSEIK(0.956)DLK(0.044)R Contig _FK(su)DEIIPVETK_ FK(1)DEIIPVETK Contig _LVDPK(su)TGDEK_ LVDPK(1)TGDEK Contig _K(su)MGWDEK_ K(1)MGWDEK Contig _YQVK(su)GIDNLR_ YQVK(1)GIDNLR Contig _LK(su)TPVENSLR_ LK(1)TPVENSLR Contig _DPSFSK(su)IEPR_ DPSFSK(1)IEPR Contig _TLK(su)EVQIIPPNVPYR_ TLK(1)EVQIIPPNVPYR Contig _IMALDLPHGGHLSHGYQTDTK(su)K_ IMALDLPHGGHLSHGYQTDTK(1)K Contig _VLELAHIAANK(su)NTVPGDVSAMVPGGIR_ VLELAHIAANK(1)NTVPGDVSAMVPGGIR Contig _LYVCK(su)AQAGDK_ LYVCK(1)AQAGDK Contig _LNSGK(su)VVAVGPGAR_ LNSGK(1)VVAVGPGAR Contig _NK(su)EGNIIPVSLK_ NK(1)EGNIIPVSLK Contig _SFEDVK(su)IADR_ SFEDVK(1)IADR Contig _YAPTAK(su)DLASR_ YAPTAK(1)DLASR Contig _AVAVLK(su)GNSK_ AVAVLK(1)GNSK Contig _FYIK(su)FYDVK_ FYIK(1)FYDVK Contig _AAALNPVDYK(su)IR_ AAALNPVDYK(1)IR Contig _EAFK(su)HLESGR_ EAFK(1)HLESGR Contig _LLK(su)QEPR_ LLK(1)QEPR Contig _NIANMVPPYQK(su)K_ NIANMVPPYQK(1)K Contig _AYEK(su)GISK_ AYEK(1)GISK Contig _EYVWK(su)TLK_ EYVWK(1)TLK Contig _TLK(su)SGQVVPGYGHGVLR_ TLK(1)SGQVVPGYGHGVLR Contig E-08 _VK(su)NPWPNVDAHSGVLLNHFGLTEDR_ VK(1)NPWPNVDAHSGVLLNHFGLTEDR Contig _FLM(ox)K(su)TLQQLGSK_ FLMK(1)TLQQLGSK

13 Contig _LSEEEASK(su)LR_ LSEEEASK(1)LR Contig _ALCTGEK(su)GFGYK_ ALCTGEK(1)GFGYK Contig _GFGYK(su)GSSFHR_ GFGYK(1)GSSFHR Contig _K(su)TCKIVDSGELP_ K(0.873)TCK(0.127)IVDSGELP Contig _VVAVSK(su)TKPVSLIR_ VVAVSK(0.999)TK(0.001)PVSLIR Contig _GDLK(su)TDHYLPIHR_ GDLK(1)TDHYLPIHR Contig _GVQK(su)VLQNYK_ GVQK(1)VLQNYK Contig _IMNVIGEPIDEK(su)GDLK_ IMNVIGEPIDEK(1)GDLK Contig _SIEFK(su)DR_ SIEFK(1)DR Contig _VCAIK(su)APGFGENR_ VCAIK(1)APGFGENR Contig _VTMGPK(su)GR_ VTMGPK(1)GR Contig _DVDFDK(su)IAR_ DVDFDK(1)IAR Contig _LVFVTNNSTK(su)SR_ LVFVTNNSTK(1)SR Contig _VEGGWK(su)LDGQK_ VEGGWK(1)LDGQK Contig _AYPK(su)AFVR_ AYPK(1)AFVR Contig _EGHK(su)SPGYYDGR_ EGHK(1)SPGYYDGR Contig _QIDYLLK(su)NK_ QIDYLLK(1)NK Contig _DDFIEK(su)DR_ DDFIEK(1)DR Contig _DKLNK(su)YGR_ DKLNK(1)YGR Contig _GHYLNATAGTCEEMMK(su)R_ GHYLNATAGTCEEMMK(1)R Contig _LGLSAK(su)NYGR_ LGLSAK(1)NYGR Contig _PK(su)LGLSAK_ PK(1)LGLSAK Contig _TETK(su)ASVGFK_ TETK(1)ASVGFK Contig _EIEK(su)DLGR_ EIEK(1)DLGR Contig _SFLGK(su)ICGR_ SFLGK(1)ICGR Contig _AIK(su)YYCELR_ AIK(1)YYCELR Contig _SENLEK(su)QCLAK_ SENLEK(1)QCLAK Contig _LEAK(su)TVYGALR_ LEAK(1)TVYGALR Contig _AQVLDSEGK(su)R_ AQVLDSEGK(1)R Contig _IVPEK(su)IAYVVER_ IVPEK(1)IAYVVER Contig _FVFYDEK(su)K_ FVFYDEK(1)K Contig _K(su)LEPTPGDMVR_ K(1)LEPTPGDMVR Contig _EDLLAK(su)PENIR_ EDLLAK(1)PENIR Contig _ETLQQNK(su)ILK_ ETLQQNK(1)ILK Contig _VEK(su)VVVSDR_ VEK(1)VVVSDR Contig _EVAQQIESINK(su)K_ EVAQQIESINK(1)K Contig _YHVGK(su)IGK_ YHVGK(1)IGK

14 Contig _DGPADTTALAK(su)WR_ DGPADTTALAK(1)WR Contig _WAFK(su)LLQR_ WAFK(1)LLQR Contig _MEK(su)FYWAPTR_ MEK(1)FYWAPTR Contig E-08 _AASANPNK(su)LHIGDVAIPR_ AASANPNK(1)LHIGDVAIPR Contig _CLEQQPK(su)IK_ CLEQQPK(1)IK Contig _EVAQQIK(su)SINK_ EVAQQIK(1)SINK Contig _HALSAVGEMFK(su)R_ HALSAVGEMFK(1)R Contig _IEK(su)GSSANIYVNNEAYR_ IEK(1)GSSANIYVNNEAYR Contig _IENVELDK(su)CLGK_ IENVELDK(1)CLGK Contig _SEK(su)NM(ox)AFLALR_ SEK(1)NMAFLALR Contig _NDNNIVLK(su)TEGK_ NDNNIVLK(1)TEGK Contig _GQLEEEK(su)GGIK_ GQLEEEK(1)GGIK Contig _ALTYPVK(su)LIAK_ ALTYPVK(1)LIAK Contig _LAAK(su)VDAIR_ LAAK(1)VDAIR Contig _GK(su)FDESR_ GK(1)FDESR Contig _SVITALK(su)R_ SVITALK(1)R Contig _TSVDILK(su)VGGYK_ TSVDILK(1)VGGYK Contig _AHIAGLHDK(su)GK_ AHIAGLHDK(1)GK Contig _ASHLLIK(su)HQGSR_ ASHLLIK(1)HQGSR Contig _YYM(ox)LGGK(su)GGVGK_ YYMLGGK(1)GGVGK Contig _GADLQVLSAK(su)LAADK_ GADLQVLSAK(1)LAADK Contig _ILLEDVK(su)K_ ILLEDVK(1)K Contig _LAVEAWGLK(su)NCTQR_ LAVEAWGLK(1)NCTQR Contig _SPAVPALTK(su)ILLEDVKK_ SPAVPALTK(0.999)ILLEDVK(0.001)K Contig _VAGK(su)VFR_ VAGK(1)VFR Contig _VK(su)AVCIVHNETATGVTNNLAAVR_ VK(1)AVCIVHNETATGVTNNLAAVR Contig _QLSYTFK(su)R_ QLSYTFK(1)R Contig _YLLYK(su)DVNR_ YLLYK(1)DVNR Contig _VICQGITGK(su)NGTFHTEQAIEYGTK_ VICQGITGK(1)NGTFHTEQAIEYGTK Contig _SPNFAGVK(su)ECVGNDR_ SPNFAGVK(1)ECVGNDR Contig _DYNPEQNK(su)DNVLAR_ DYNPEQNK(1)DNVLAR Contig _VK(su)FLDDQNR_ VK(1)FLDDQNR Contig _TTFLSDPEVK(su)R_ TTFLSDPEVK(1)R Contig _IIK(su)VTGPR_ IIK(1)VTGPR Contig _SK(su)AGIPSLPR_ SK(1)AGIPSLPR Contig _NTGVK(su)PEILK_ NTGVK(1)PEILK Contig E-15 _NVGK(su)AITSLPETFNPHR_ NVGK(1)AITSLPETFNPHR

15 Contig _FDALLK(su)EAK_ FDALLK(1)EAK Contig _K(su)EFLNLR_ K(1)EFLNLR Contig _TYEEVK(su)R_ TYEEVK(1)R Contig _GVVESLK(su)IITR_ GVVESLK(1)IITR Contig _K(su)TDGLFLQCCR_ K(1)TDGLFLQCCR Contig _VAEYAFHYAK(su)THGR_ VAEYAFHYAK(1)THGR Contig E-08 _GLSLIGEDVK(su)ILAR_ GLSLIGEDVK(1)ILAR Contig E-08 _LNAIQEASGGK(su)R_ LNAIQEASGGK(1)R Contig _VDK(su)LMELR_ VDK(1)LMELR Contig _ASK(su)QVYNISGSR_ ASK(1)QVYNISGSR Contig _SLSAISAEVK(su)ELADK_ SLSAISAEVK(1)ELADK Contig _AVVAK(su)NLQNR_ AVVAK(1)NLQNR Contig _SIPTVMLFK(su)SGEK_ SIPTVMLFK(1)SGEK Contig _VIK(su)VVSDR_ VIK(1)VVSDR Contig _VLDQK(su)FGIIK_ VLDQK(1)FGIIK Contig _IAGLEVK(su)R_ IAGLEVK(1)R Contig _YLAEFK(su)TGNER_ YLAEFK(1)TGNER Contig _ASGLK(su)PIVDDDK_ ASGLK(1)PIVDDDK Contig _LAK(su)VDLGR_ LAK(1)VDLGR Contig _FTEK(su)AIK_ FTEK(1)AIK Contig _DHIVK(su)GILIGLR_ DHIVK(1)GILIGLR Contig _EIAQDFK(su)TDLR_ EIAQDFK(1)TDLR Contig _GK(su)GVYQFTNK_ GK(1)GVYQFTNK Contig _PGTFK(su)QTTLCIR_ PGTFK(1)QTTLCIR Contig _AMK(su)QVAGK_ AMK(1)QVAGK Contig _VGSAAQMK(su)AM(ox)K_ VGSAAQMK(1)AMK Contig _VCAAALNPVDFK(su)R_ VCAAALNPVDFK(1)R Contig _MVLLK(su)GVDER_ MVLLK(1)GVDER Contig _LSK(su)VLDVYEER_ LSK(1)VLDVYEER Contig _HEEIVDLAK(su)K_ HEEIVDLAK(1)K Contig _VVVIK(su)ELK_ VVVIK(1)ELK Contig _TLAK(su)VVGSEEEAK_ TLAK(1)VVGSEEEAK Contig _MEGK(su)LTGSGHSIAAAR_ MEGK(1)LTGSGHSIAAAR Contig _HYIQDPPTVEK(su)CHELSK_ HYIQDPPTVEK(1)CHELSK Contig _EPILCK(su)NVPR_ EPILCK(1)NVPR Contig _LK(su)LVFVPEK_ LK(1)LVFVPEK Contig _LEQETLK(su)WCR_ LEQETLK(1)WCR

16 Contig _TASK(su)SVSSSPWYGPDR_ TASK(1)SVSSSPWYGPDR Contig _ELAK(su)EGINAEVINLR_ ELAK(1)EGINAEVINLR Contig _IISSIEQK(su)EESR_ IISSIEQK(1)EESR Contig _EK(su)GIFTNVTSPSAK_ EK(1)GIFTNVTSPSAK Contig _TIAFK(su)VR_ TIAFK(1)VR Contig _TQVAYGSK(su)NEIIR_ TQVAYGSK(1)NEIIR Contig _VIK(su)NVDDR_ VIK(1)NVDDR Contig _GLCGGFNNMVLK(su)R_ GLCGGFNNMVLK(1)R Contig E-11 _GILAM(ox)DESNATCGK(su)R_ GILAMDESNATCGK(1)R Contig _TAK(su)TVASPGR_ TAK(1)TVASPGR Contig _ILDVEQCK(su)ELK_ ILDVEQCK(1)ELK Contig _K(su)NEVFTK_ K(1)NEVFTK Contig _EVANK(su)LER_ EVANK(1)LER Contig _IENVGLDK(su)CLGR_ IENVGLDK(1)CLGR Contig _NDAVGTIK(su)HVEK_ NDAVGTIK(1)HVEK Contig _TPPLK(su)LSK_ TPPLK(1)LSK Contig E-08 _SMTQHNVGALLVVK(su)PGAEK_ SMTQHNVGALLVVK(1)PGAEK Contig _DGVYPEK(su)ANPGR_ DGVYPEK(1)ANPGR Contig _FK(su)INYQFYR_ FK(1)INYQFYR Contig _VPAEVIESIK(su)R_ VPAEVIESIK(1)R Contig _VLVTDQK(su)ISTIK_ VLVTDQK(1)ISTIK Contig _LK(su)HGEALVQNEGDSDISK_ LK(1)HGEALVQNEGDSDISK Contig _LPK(su)NVVYR_ LPK(1)NVVYR Contig _SLFK(su)GAGANILR_ SLFK(1)GAGANILR Contig _TIK(su)SDGVAGLYR_ TIK(1)SDGVAGLYR Contig _VK(su)LLIQNQDEMLK_ VK(1)LLIQNQDEMLK Contig _SQSPWK(su)R_ SQSPWK(1)R Contig _VLSVVK(su)SFPK_ VLSVVK(1)SFPK Contig _VPNTK(su)NLGLEEVGVK_ VPNTK(1)NLGLEEVGVK Contig _ALNDHHVLLEGTLLK(su)PNMVTPGSDAPK_ ALNDHHVLLEGTLLK(1)PNMVTPGSDAPK Contig _LVAQK(su)GLHLIR_ LVAQK(1)GLHLIR Contig _AMK(su)FSVSPVVR_ AMK(1)FSVSPVVR Contig _GYVASDSK(su)NDPAK_ GYVASDSK(1)NDPAK Contig _QTVAVGVIK(su)AVEK_ QTVAVGVIK(1)AVEK Contig _EPAGEDRPSDK(su)PR_ EPAGEDRPSDK(1)PR Contig _ELK(su)LDLEK_ ELK(1)LDLEK Contig _TALSDEYFVK(su)R_ TALSDEYFVK(1)R

17 Contig _EFEK(su)EAK_ EFEK(1)EAK Contig _SPAYYK(su)R_ SPAYYK(1)R Contig _ESGLYGICGDK(su)DMR_ ESGLYGICGDK(1)DMR Contig _IFLEDGHQIACAQSFAK(su)NM(ox)GLYGQR_ IFLEDGHQIACAQSFAK(1)NMGLYGQR Contig _DDELLATDTK(su)SVPR_ DDELLATDTK(1)SVPR Contig _IAGLDVK(su)R_ IAGLDVK(1)R Contig _NPK(su)VIENSEGAR_ NPK(1)VIENSEGAR Contig _SCLK(su)DAGVTVK_ SCLK(1)DAGVTVK Contig _SESIDLSK(su)DR_ SESIDLSK(1)DR Contig _TKEPCK(su)SCLK_ TKEPCK(1)SCLK Contig _EK(su)VVIPK_ EK(1)VVIPK Contig _TCEK(su)SPIPR_ TCEK(1)SPIPR Contig _NFHK(su)FLEVR_ NFHK(1)FLEVR Contig _AEFLK(su)AVENNR_ AEFLK(1)AVENNR Contig _IADVVK(su)LR_ IADVVK(1)LR Contig _MYK(su)TLLGK_ MYK(1)TLLGK Contig _VEEISK(su)GVGDK_ VEEISK(1)GVGDK Contig _LNVFK(su)PDK_ LNVFK(1)PDK Contig _K(su)NKFVEEWGAAR_ K(0.857)NK(0.143)FVEEWGAAR Contig _NK(su)FVEEWGAAR_ NK(1)FVEEWGAAR Contig _HVIGEDNQFIGK(su)K_ HVIGEDNQFIGK(1)K Contig _TIQDEINDLK(su)K_ TIQDEINDLK(1)K Contig _NIWK(su)VINWK_ NIWK(1)VINWK Contig _NLAPVK(su)EGGGEPPK_ NLAPVK(1)EGGGEPPK Contig _NVRPDYLK(su)NIWK_ NVRPDYLK(1)NIWK Contig _GLLGK(su)NITER_ GLLGK(1)NITER Contig _VLDVYDK(su)R_ VLDVYDK(1)R Contig _YIAQK(su)YETR_ YIAQK(1)YETR Contig _GSDLSGK(su)DFSGK_ GSDLSGK(1)DFSGK Contig _SLDEVIK(su)R_ SLDEVIK(1)R Contig _VEK(su)LGTELK_ VEK(1)LGTELK Contig _FYKEEEK(su)NDPEFAK_ FYK(0.001)EEEK(0.999)NDPEFAK Contig _GVTPK(su)YSLKPLVPR_ GVTPK(1)YSLKPLVPR Contig _YSLK(su)PLVPR_ YSLK(1)PLVPR Contig _AMK(su)QVCGSLK_ AMK(1)QVCGSLK Contig _GK(su)LTNEIEMK_ GK(1)LTNEIEMK Contig _ITDYSTDLK(su)VDEIGR_ ITDYSTDLK(1)VDEIGR

18 Contig _LTEVLK(su)QPQYSPLPIEK_ LTEVLK(1)QPQYSPLPIEK Contig _M(ox)ELTTLLEK(su)R_ MELTTLLEK(1)R Contig _TGSIVDVPVGK(su)ALLGR_ TGSIVDVPVGK(1)ALLGR Contig _VGSAAQLK(su)AM(ox)K_ VGSAAQLK(1)AMK Contig _AAAEK(su)IFSAK_ AAAEK(1)IFSAK Contig _AK(su)TLSGPVSSPK_ AK(1)TLSGPVSSPK Contig _HK(su)EHIAAYGEGNER_ HK(1)EHIAAYGEGNER Contig _WAFELLK(su)R_ WAFELLK(1)R Contig _VEK(su)HIQDAISK_ VEK(1)HIQDAISK Contig _NLGIK(su)CR_ NLGIK(1)CR Contig _FK(su)DIFEEEYEK_ FK(1)DIFEEEYEK Contig _MTK(su)DLAILVHGSR_ MTK(1)DLAILVHGSR Contig _LPPK(su)AISAAK_ LPPK(1)AISAAK Contig _IK(su)GYPLWPDANK_ IK(1)GYPLWPDANK Contig _LEICTEK(su)K_ LEICTEK(1)K Contig _SQGEIPTTWK(su)R_ SQGEIPTTWK(1)R Contig _ISK(su)AFFR_ ISK(1)AFFR Contig _SIK(su)SIQK_ SIK(1)SIQK Contig _INPDSAK(su)GYK_ INPDSAK(1)GYK Contig _ITTLVK(su)AANVK_ ITTLVK(1)AANVK Contig _ENNFK(su)QPGER_ ENNFK(1)QPGER Contig _THGGIDVIK(su)K_ THGGIDVIK(1)K Contig _GILAVDESNATCGK(su)R_ GILAVDESNATCGK(1)R Contig _SAEYYK(su)QGAR_ SAEYYK(1)QGAR Contig _GIPTFEK(su)TQQEGK_ GIPTFEK(1)TQQEGK Contig _EK(su)AGLYSDADR_ EK(1)AGLYSDADR Contig _EK(su)VTIDPDDPNAVSR_ EK(1)VTIDPDDPNAVSR Contig _K(su)EKVTIDPDDPNAVSR_ K(0.975)EK(0.025)VTIDPDDPNAVSR Contig _VK(su)SGLEDHLGAEK_ VK(1)SGLEDHLGAEK Contig _YEK(su)QLELDVAK_ YEK(1)QLELDVAK Contig _LIVIDYK(su)PMR_ LIVIDYK(1)PMR Contig _AEVTASLNQMK(su)K_ AEVTASLNQMK(1)K Contig _LQEEADAILK(su)AAR_ LQEEADAILK(1)AAR Contig _ACSVDAVK(su)YIR_ ACSVDAVK(1)YIR Contig _DVFLEK(su)HGVK_ DVFLEK(1)HGVK Contig _HGVK(su)LGFMSGFIK_ HGVK(1)LGFMSGFIK Contig _LNFAEIEK(su)TMSALAK_ LNFAEIEK(1)TMSALAK

19 Contig _QLEK(su)ELKER_ QLEK(1)ELKER Contig _VWK(su)GTAFGGFK_ VWK(1)GTAFGGFK Contig _AGFK(su)AIALTVDTPR_ AGFK(1)AIALTVDTPR Contig _DVK(su)WLQTITK_ DVK(1)WLQTITK Contig _SLSWK(su)DVK_ SLSWK(1)DVK Contig _EFLENLK(su)LGEGVK_ EFLENLK(1)LGEGVK Contig _LM(ox)K(su)VISDSVK_ LMK(1)VISDSVK Contig _MSK(su)SGRPIEPR_ MSK(1)SGRPIEPR Contig _IFK(su)IGGLGVK_ IFK(1)IGGLGVK Contig _IGGLGVK(su)TYR_ IGGLGVK(1)TYR Contig _TEEGK(su)PLILNVVR_ TEEGK(1)PLILNVVR Contig _EIK(su)VECTIPR_ EIK(1)VECTIPR Contig _VNAELK(su)TYMTR_ VNAELK(1)TYMTR Contig _IAIAK(su)AGYTGK_ IAIAK(1)AGYTGK Contig _GMFDK(su)EK_ GMFDK(1)EK Contig _M(ox)K(su)EGVLIVNNAR_ MK(1)EGVLIVNNAR Contig _VVGVFYK(su)ANEYASK_ VVGVFYK(1)ANEYASK Contig _YAAGVK(su)DMLDK_ YAAGVK(1)DMLDK Contig _SCLK(su)EPYK_ SCLK(1)EPYK Contig _LVAVGYGIK(su)K_ LVAVGYGIK(1)K Contig _HYK(su)NAFHALSR_ HYK(1)NAFHALSR Contig _AILDK(su)SEQK_ AILDK(1)SEQK Contig _DK(su)DLAHIESHMK_ DK(1)DLAHIESHMK Contig _DKDLAHIESHMK(su)NFK_ DKDLAHIESHMK(1)NFK Contig _GK(su)ECIPFLEK_ GK(1)ECIPFLEK Contig _K(su)TALYDFHVENGGK_ K(1)TALYDFHVENGGK Contig _TIGEITSGGFSPCLK(su)K_ TIGEITSGGFSPCLK(1)K Contig _EEDLK(su)GFR_ EEDLK(1)GFR Contig _HIEK(su)GAAVEAK_ HIEK(1)GAAVEAK Contig _TLISGK(su)FPEGWEK_ TLISGK(1)FPEGWEK Contig _AVSLVLPQLK(su)GK_ AVSLVLPQLK(1)GK Contig _VIK(su)VVSNR_ VIK(1)VVSNR Contig _NFNIIQK(su)QLGR_ NFNIIQK(1)QLGR Contig _LSDYIGK(su)K_ LSDYIGK(1)K Contig _LK(su)EYSINTK_ LK(1)EYSINTK Contig _AQDYYK(su)PGSMSK_ AQDYYK(1)PGSMSK Contig _GGVHIVK(su)TEK_ GGVHIVK(1)TEK

20 Contig _TEK(su)AEDIAGK_ TEK(1)AEDIAGK Contig _K(su)GGTSIEDLAEK_ K(1)GGTSIEDLAEK Contig _PVNK(su)VYLCQK_ PVNK(1)VYLCQK Contig _QK(su)EIFALR_ QK(1)EIFALR Contig _EVLDIFK(su)AK_ EVLDIFK(1)AK Contig _ANSLTDEDIK(su)ALTK_ ANSLTDEDIK(1)ALTK Contig _GSDWIVNEM(ox)K(su)K_ GSDWIVNEMK(1)K Contig _MAFK(su)STR_ MAFK(1)STR Contig _TVPK(su)TVENFR_ TVPK(1)TVENFR Contig _AVLIDK(su)DQNPK_ AVLIDK(1)DQNPK Contig _FTTFK(su)PLGDR_ FTTFK(1)PLGDR Contig _VLIK(su)VQEAEEK_ VLIK(1)VQEAEEK Contig _AAQLGLK(su)TTCIEK_ AAQLGLK(1)TTCIEK Contig _TTCIEK(su)R_ TTCIEK(1)R Contig _GIEGLFK(su)K_ GIEGLFK(1)K Contig _GLGLEELGVK(su)LDK_ GLGLEELGVK(1)LDK Contig _IIAEK(su)ETDK_ IIAEK(1)ETDK Contig _SFQK(su)TLEK_ SFQK(1)TLEK Contig _MK(su)AVTGLTK_ MK(1)AVTGLTK Contig _NAELDPEK(su)R_ NAELDPEK(1)R Contig _AVIAK(su)SFER_ AVIAK(1)SFER Contig _LLNGEVGPK(su)TIHIPTGEK_ LLNGEVGPK(1)TIHIPTGEK Contig _NCDNFQVTK(su)ADVEK_ NCDNFQVTK(1)ADVEK Contig _YLLK(su)SGLQK_ YLLK(1)SGLQK Contig _GQK(su)EYLR_ GQK(1)EYLR Contig _HVLK(su)SEGGIR_ HVLK(1)SEGGIR Contig _IYENTK(su)TIK_ IYENTK(1)TIK Contig E-19 _ANIK(su)AIQEASESGVK_ ANIK(1)AIQEASESGVK Contig _GK(su)IPASEFR_ GK(1)IPASEFR Contig _ASCISFK(su)DSACR_ ASCISFK(1)DSACR

21 Table S3. The number of succinylated sites in each succinylated protein. Protein number of sites Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig454 1 Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig392 3 Contig

22 Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig

23 Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig

24 Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig136 2 Contig Contig Contig Contig

25 Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig Contig

26 Table S4: Information of succinylated proteins involved in glycolysis, pyruvate metabolism and TCA cycle. Protein Enzyme Nomenclature Abbreviation Function Sites Contig8976 EC: PGM Alpha-D-phosphohexomutase 1 Contig25672 EC: ALDO fructose-bisphosphate aldolase 2 Contig32731 EC: PGK phosphoglycerate kinase 3 Contig4152 EC: ENO enolase 1 Contig32010 EC: PDHB pyruvate dehydrogenase 1 Contig7916 EC: DLD dihydrolipoamide dehydrogenase 7 Contig21171 EC: DLAT pyruvate dehydrogenase 3 Contig32590 EC: ALDH aldehyde dehydrogenase 1 Contig38639 EC: frma S-(hydroxymethyl)glutathione dehydrogenase 1 Contig18385 EC: CS citrate synthase 4 Contig8619 EC: ACO aconitate hydratase 4 Contig24602 EC: IDH1 isocitrate dehydrogenase 2 Contig26853 EC: IDH3 isocitrate dehydrogenase (NAD+) 1 Contig2087 EC: OGDH 2-oxoglutarate dehydrogenase 2 Contig3710 EC: DLST 2-oxoglutarate dehydrogenase 3 Contig4446 EC: LSC1 succinyl-coa synthetase 5 Contig18557 EC: LSC2 succinyl-coa synthetase 1 Contig43437 EC: SDHA succinate dehydrogenase 1 Contig4938 EC: MDH2 malate dehydrogenase 1

27 Table S5: Information of succinylated proteins involved in carbon fixation. Protein Enzyme Nomenclature Function Sites Contig25672 EC: ALDO fructose-bisphosphate aldolase 2 Contig25407 EC: SBPase sedoheptulose-bisphosphatase 4 Contig42340 EC: Transketolase transketolase 3 Contig15471 EC: RBCS ribulose-bisphosphate carboxylase 3 Contig32731 EC: PGK phosphoglycerate kinase 3 Contig42616 EC: GAPA glyceraldehyde-3-phosphate dehydrogenase 2 Contig25672 EC: ALDO fructose-bisphosphate aldolase 2 Contig3195 EC: TPI triosephosphate isomerase 1 Contig29422 EC: GOT2 aspartate aminotransferase 1 Contig4938 EC: MDH1 malate dehydrogenase 1 Contig16825 EC: MDH2 malate dehydrogenase 2 Contig34715 EC: GGAT glutamate-glyoxylate aminotransferase 1

28 Table S6: The information of 162 succinylated proteins that involved in Protein-protein interactions (PPIs) network. Node name Protein No. of modegree MCODE_ Subcellular Locati 3694.grail Contig mitochondria 3694.gw1.X Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XVII1357 Contig mitochondria 3694.grail Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_I2224 Contig mitochondria 3694.gw Contig plasma membrane 3694.estExt_fgenesh4_pg.C_LG_XVI0781 Contig chloroplast 3694.estExt_fgenesh4_kg.C_LG_IX0036 Contig mitochondria 3694.eugene Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_VIII0532 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_XVIII0241 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_VIII0144 Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_XIV0805 Contig cytosol 3694.estExt_Genewise1_v1.C_LG_IV0774 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_IX0030 Contig chloroplast 3694.eugene Contig chloroplast 3694.eugene Contig chloroplast 3694.eugene Contig cytosol 3694.eugene Contig cytosol 3694.estExt_Genewise1_v1.C_LG_VIII1306 Contig chloroplast 3694.gw Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_X1053 Contig mitochondria 3694.gw1.XIV Contig mitochondria 3694.estExt_fgenesh4_pm.C_LG_XII0223 Contig mitochondria 3694.fgenesh4_pg.C_LG_X Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_X0655 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_IX1362 Contig chloroplast 3694.gw Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_V0707 Contig chloroplast 3694.gw Contig chloroplast 3694.grail Contig cytosol 3694.gw1.XIV Contig chloroplast 3694.grail Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XVI2794 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_I8285 Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_I1607 Contig cytosol 3694.estExt_fgenesh4_pm.C_ Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_VIII0227 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_XIII0026 Contig chloroplast 3694.fgenesh4_pg.C_LG_III Contig mitochondria 3694.grail Contig chloroplast 3694.eugene Contig cytosol 3694.estExt_fgenesh4_pg.C_ Contig mitochondria 3694.estExt_Genewise1_v1.C_ Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_I0780 Contig chloroplast

29 3694.estExt_fgenesh4_pm.C_LG_I0166 Contig mitochondria 3694.estExt_Genewise1_v1.C_LG_III2625 Contig chloroplast 3694.gw1.XVII Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XI2343 Contig nuclear 3694.estExt_fgenesh4_pg.C_LG_XIII0274 Contig cytosol 3694.eugene Contig cytosol 3694.gw Contig cytosol 3694.eugene Contig cytosol 3694.estExt_Genewise1_v1.C_LG_X3287 Contig cytosol 3694.estExt_Genewise1_v1.C_LG_XI0817 Contig cytosol 3694.estExt_Genewise1_v1.C_LG_XI2803 Contig mitochondria 3694.grail Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_I0194 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XIV0188 Contig mitochondria 3694.estExt_fgenesh4_pg.C_LG_II2062 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_V0127 Contig mitochondria 3694.gw1.X Contig mitochondria 3694.gw1.VII Contig chloroplast 3694.eugene Contig chloroplast 3694.gw1.III Contig cytosol 3694.estExt_fgenesh4_pg.C_ Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_X0942 Contig mitochondria 3694.estExt_fgenesh4_pm.C_ Contig chloroplast 3694.gw1.VIII Contig cytoskeleton 3694.gw1.X Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_XVII0246 Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_VIII0421 Contig chloroplast,mitochon 3694.grail Contig cytosol 3694.eugene Contig cytosol 3694.gw1.X Contig chloroplast 3694.fgenesh4_pm.C_LG_XIV Contig chloroplast 3694.grail Contig chloroplast 3694.eugene Contig plasma membrane 3694.eugene Contig plasma membrane 3694.gw Contig extracellular 3694.gw Contig mitochondria 3694.estExt_fgenesh4_pm.C_LG_IX0400 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_VI0678 Contig chloroplast 3694.eugene Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_X0989 Contig cytosol 3694.grail Contig cytosol 3694.gw Contig cytosol 3694.eugene Contig chloroplast 3694.gw1.XVIII Contig cytosol 3694.estExt_fgenesh4_pg.C_ Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XVI3692 Contig extracellular

30 3694.fgenesh4_pm.C_LG_I Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_II1218 Contig chloroplast 3694.eugene Contig chloroplast,mitochon 3694.fgenesh4_pg.C_LG_IV Contig mitochondria 3694.estExt_fgenesh4_pm.C_LG_II0915 Contig mitochondria 3694.estExt_fgenesh4_pm.C_ Contig cytosol 3694.gw1.VII Contig chloroplast 3694.eugene Contig cytosol 3694.estExt_Genewise1_v1.C_LG_II2125 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_IV0266 Contig cytosol 3694.eugene Contig cytosol 3694.estExt_fgenesh4_kg.C_LG_IV0030 Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_II1351 Contig chloroplast 3694.gw1.VII Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_VII1183 Contig nuclear 3694.estExt_fgenesh4_pg.C_LG_II1684 Contig chloroplast 3694.eugene Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_X0463 Contig mitochondria 3694.eugene Contig chloroplast 3694.eugene Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_I0932 Contig chloroplast 3694.estExt_fgenesh4_pg.C_ Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_I1460 Contig mitochondria 3694.estExt_Genewise1_v1.C_LG_XIII3158 Contig mitochondria 3694.fgenesh4_pm.C_scaffold_ Contig cytosol 3694.fgenesh4_pm.C_LG_I Contig mitochondria 3694.estExt_fgenesh4_pg.C_LG_X2033 Contig chloroplast 3694.grail Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_V0695 Contig peroxisome 3694.grail Contig nuclear 3694.eugene Contig chloroplast 3694.grail Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_X0791 Contig nuclear 3694.estExt_fgenesh4_pg.C_LG_XIV1000 Contig mitochondria 3694.estExt_Genewise1_v1.C_LG_I2532 Contig chloroplast 3694.gw1.XVIII Contig chloroplast 3694.gw Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_VII0233 Contig chloroplast 3694.gw1.VI Contig chloroplast 3694.eugene Contig nuclear 3694.eugene Contig nuclear 3694.estExt_fgenesh4_pm.C_LG_XIV0571 Contig chloroplast 3694.eugene Contig cytosol 3694.eugene Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_VI1023 Contig chloroplast 3694.eugene Contig chloroplast

31 3694.grail Contig chloroplast 3694.estExt_fgenesh4_pg.C_ Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_II2900 Contig chloroplast 3694.gw1.II Contig cytosol 3694.estExt_Genewise1_v1.C_LG_XI3916 Contig chloroplast 3694.grail Contig chloroplast 3694.eugene Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_IX3737 Contig cytosol 3694.gw Contig nuclear 3694.eugene Contig chloroplast 3694.eugene Contig nuclear 3694.eugene Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_XIX0169 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_II0162 Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_VI0717 Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_IV1470 Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_III1822 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_I0264 Contig chloroplast 3694.fgenesh4_pm.C_LG_X Contig chloroplast 3694.gw1.X Contig cytosol 3694.fgenesh4_pm.C_scaffold_ Contig chloroplast 3694.estExt_fgenesh4_kg.C_LG_X0015 Contig cytosol 3694.gw Contig cytosol 3694.fgenesh4_pg.C_scaffold_ Contig chloroplast 3694.grail Contig cytosol

32 Table S7: The list of the proteins that classed into cluster 1. Node name Protein No. of moddegree MCODE_ Subcellular Location 3694.grail Contig mitochondria 3694.gw1.X Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XVII1357 Contig mitochondria 3694.grail Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_I2224 Contig mitochondria 3694.gw Contig plasma membrane 3694.estExt_fgenesh4_pg.C_LG_XVI0781 Contig chloroplast 3694.estExt_fgenesh4_kg.C_LG_IX0036 Contig mitochondria 3694.eugene Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_VIII0532 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_XVIII0241 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_VIII0144 Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_XIV0805 Contig cytosol 3694.estExt_Genewise1_v1.C_LG_IV0774 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_IX0030 Contig chloroplast 3694.eugene Contig chloroplast 3694.eugene Contig chloroplast 3694.eugene Contig cytosol 3694.eugene Contig cytosol 3694.estExt_Genewise1_v1.C_LG_VIII1306 Contig chloroplast 3694.gw Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_X1053 Contig mitochondria 3694.gw1.XIV Contig mitochondria 3694.estExt_fgenesh4_pm.C_LG_XII0223 Contig mitochondria 3694.fgenesh4_pg.C_LG_X Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_X0655 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_IX1362 Contig chloroplast 3694.gw Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_V0707 Contig chloroplast

33 Table S8: The list of the proteins that classed into cluster 2. Node name Protein No. of moddegree MCODE_SSubcellular Location 3694.gw Contig chloroplast 3694.grail Contig cytosol 3694.gw1.XIV Contig chloroplast 3694.grail Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XVI2794 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_I8285 Contig chloroplast 3694.estExt_fgenesh4_pg.C_LG_I1607 Contig cytosol 3694.estExt_fgenesh4_pm.C_ Contig cytosol 3694.estExt_fgenesh4_pg.C_LG_VIII0227 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_XIII0026 Contig chloroplast 3694.fgenesh4_pg.C_LG_III Contig mitochondria 3694.grail Contig chloroplast 3694.eugene Contig cytosol

34 Table S9: The list of the proteins that classed into cluster 3. Node name Protein No. of moddegree MCODE_Score Subcellular Location 3694.estExt_fgenesh4_pg.C_ Contig mitochondria 3694.estExt_Genewise1_v1.C_ Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_I0780 Contig chloroplast 3694.estExt_fgenesh4_pm.C_LG_I0166 Contig mitochondria 3694.estExt_Genewise1_v1.C_LG_III2625 Contig chloroplast 3694.gw1.XVII Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XI2343 Contig nuclear 3694.estExt_fgenesh4_pg.C_LG_XIII0274 Contig cytosol

35 Table S10: The list of the proteins that classed into cluster 4. Node name Protein No. of sites Degree MCODESubcellular Location 3694.eugene Contig cytosol 3694.gw Contig cytosol 3694.eugene Contig cytosol 3694.estExt_Genewise1_v1.C_LG_X3287 Contig cytosol 3694.estExt_Genewise1_v1.C_LG_XI0817 Contig cytosol

36 Table S11: The list of the proteins that classed into cluster 5. Node name Protein No. of sites Degree MCODESubcellular Location 3694.estExt_Genewise1_v1.C_LG_XI2803 Contig mitochondria 3694.grail Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_I0194 Contig chloroplast 3694.estExt_Genewise1_v1.C_LG_XIV0188 Contig mitochondria 3694.estExt_fgenesh4_pg.C_LG_II2062 Contig cytosol 3694.estExt_fgenesh4_pm.C_LG_V0127 Contig mitochondria 3694.gw1.X Contig mitochondria 3694.gw1.VII Contig chloroplast

37 Table S12: Comparison of Taxus media succinylated proteins with different reported species. organism no. of succinylated proteins no. of succinylated sites sites per protein Taxus media Mycobacterium tuberculosis E.Coli Toxoplasma gondii S. cerevisiae