The Proteomic Changes in Cynara Cardunculus L. var. altilis DC Following the Etiolation Phenomena Using De Novo Sequence Analysis

Table 1

Constantly and differently expressed proteins in green and etiolated fleshy stalks classified according to functional categories. (a) Differentially expressed proteins and (b) constantly expressed proteins. Spot number, experimental 𝑝𝐼 and 𝑀_𝑟 values, protein description, accession number, hortologous organism, peptide sequences, and conserved domain are listed. Increasing/decreasing index (fold change) was calculated as the ratio of spot intensities (relative volumes) for green and etiolated fleshy stalks. Proteins were considered as differentially expressed when a relative fold change >2.0 or <0.5 was measured. (c) Abbreviated names of organisms: AT: Arabidopsis thaliana; CI × CE: Cichorium intybus × Cichorium endivia; CJ: Cercidiphyllum japonicum; CR: Catharanthus roseus; CS: Cucumis sativus; DC: Daucus carota; FB: Flaveria bidentis; GM: Glycine max; HA: Helianthus annuus; LS: Lactuca sativa; MT: Medicago truncatula; NP: Narcissus pseudonarcissus; NPl: Nicotiana plumbaginifolia; NS: Nicotiana sylvestris; NT: Nicotiana tabacum; OS: Oryza sativa; OSj: Oryza sativa japonica; OT: Ostreococcus tauri; PB: Pimpinella brachycarpa; PG: Panax ginseng; PS: Pisum sativum; PT: Populus trichocarpa; SA: Sinapis alba; SP: Schizosaccharomyces pombe; ST: Solanum tuberosum; TA: Triticum aestivum; TS: Tsuga heterophylla; VV: Vitis vinifera; ZH: Zinnia elegans.

Carbon ⧵ Nitrogen metabolism or energy
Spot	𝑝𝐼 /𝑀𝑟 (kDa)	Relative Fold change Green/Etiolated	Description	Accession number	Hortologous Organisms (c)	Exact Match sequence	“de novo” sequence	Conserved domains
(a) Differentially expressed proteins
10	6.1/30	5.30	Triosephosphate isomerase cytosolic	P48493	LS	(K)VASPAQAQEVHAGLR(K); (K)VIACmVGETLEQR(E); (L)AYEPVWAIGTGK(V); (R)EAGTTMoxEVVAAQTK(A); (R)IIYGGSVSGSNCmK(E)	N(I/L)SADVAGDTR; VASPA(Q/K)A(Q/K)EVYAE(I/L)R	cd00311
16	5.7/56	0.40	Malate dehydrogenase cytoplasmic	Q7XDC8	OSj	(E)FISTVQQR(G); (R)ALGQISEK(L)	(Q/K)G(I/L)(Q/K)(I/L)DEFSRARMDA
25	5.7/10	3.00	Vacuolar membrane ATPase subunit G	AAD54418.1	AT	—	R(I/L)E(Q/K)ETDE(Q/K)(I/L)AG(I/L)(I/L)TR; EAGAA(I/L)EA(Q/K)(Q/K)(I/L)VNAAR; (Q/K)(I/L)TETSGDSGANV(Q/K)R; (I/L)SSDVVEMox(I/L)(I/L)K; A(Q/K)MEADY(Q/K)R
30	6.8/11	3.60	Nucleoside diphosphate kinase B	Q39839	GM	(-)MDEQTFIMIKPDGVQR(G)	M(I/L)WEG(Q/K)NVV(I/L)TGR(Q/K)(I/L)(I/L)GATNPAASEPGT(I/L)R	cd04413
			Nucleoside diphosphate kinase B	P47920	FB	(E)IIGATNPAESAPGTIR(G); (E)IIGATNPAESAPGTIRGDFAIDIGR(N); (E)PGTIR(G); (K)NVVTTGR(E); (L)VGEILGRFEK(K); (R)GDFAIDIGR(N); (R)GDFAIDIGRNVIHGSDAVESAKK(E); (R)GLVGEIIGRFEK(K); (R)GLVGEILGR(F); (R)NVIHGSDAVESAK(K); (R)NVIHGSDAVESAKK(E); (V)IHGSDAVESAKK(E)
			RNA binding translational regulation protein of the SUA5 family ISS	CAL50272.1	OT	(R)EGLLGR(I)
21	4.3/11	0.08	Acyl CoA binding protein	BAB85987.1	PG	(K)QATVGPVNTSR(P); (K)TLPESSTTNENK(L); (K)LILYGL(Y)	G(I/L)(K/Q)EDFEEHAEK	cd00435
60	6.6/12	3.10	Nucleoside diphosphate kinase B	P47920	FB	(N)PAESAPGTIR(G); (V)IHGSDAVESAK(K); (A)TNPAESAPGTIR(G); (R)NVIHGSDAVESAK(K); (K)IIGATNPAESAPGTIR(G)		cd04413
36	5.8/27	2.40	Oxygen evolving enhancer protein 2, chloroplast	Q40407	NP	(K)EVEFPGQVLR(Y); (K)VDYLLGK(Q); (K)WNPSKEVEFPGQVLR(Y)	EATDFGPPEEMox(I/L)SK; AYGEAANVFG(Q/K)PK; GDDTAEHSHSAT(I/L)TATVSGGK	pfam01789
45	5.2/38	2.40	Oxygen-evolving enhancer protein 1, chloroplast	Q40459	NT	(R)GSSFLDPK(G); (K)RLTFDEIQSK(T)
46	5.3/38	2.40	Oxygen evolving enhancer protein 1, chloroplast	P26320	ST	(R)GGSTGYDNAVALPAGGR(G); (R)LTFDEIQSK(T); (R)VPFLFTIK(Q); (S)SFLDPK(E); (T)YLEVK(G); (V)PFLFTIK(Q)	GDEEE(I/L)(I/L)(Q/K)EN(I/L)K	pfam01716
47	5.4/38	2.30	Oxygen evolving enhancer protein 1, chloroplast	P26320	ST	(R)VPFLFTIK(Q); (K)RLTFDEIQSK(T); (K)FCmLEPTSFTVK(A)
Oxidative stress
38	6.0/32	3.10	Ascorbate peroxidase	AAF22246.1	PB	(K)EGLLQLPTDK(A); (K)TGGPFGTMR(L); (K)TGGPFGTMoxR(L)	WGEVRVD(Q/K)EEPP(Q/K)NGR; EEPP(I/L)EGR
55	7.0/80	0.40	Catalase 4	AAF61734.1	HA	(F)AYSDTQR(H); (K)YPINPAR(V); (L)GPNYLQLPVNAPK(C); (N)FPVFF(V); (N)FPVFFTR(D); (N)YLQLPVNAPK(C); (R)DEEVDYFPSR(Y); (R)EGNFDIVGNNFPVFFTR(D); (R)FSTVIHER(G); (R)LGPNYLQLPVNAPK(C); (S)SVNTLTLVNK(E); (Y)TLVNK(A)	APGV(Q/K)TPT(I/L)VR; S(Q/K)AD(Q/K)S(I/L)G(Q/K)K	cd00328
Stress and defense
17	5.1/51	0.09	beta-1,3-glucanase	CAA09765.1	CI×CE		YVAVGNEVDPNK
							(I/L)YDPD(Q/K)NT(I/L)(Q/K)A(I/L)(K
			beta-1,3-glucanase	CAB55309.1	CI×CE		DN(I/L)(Q/K)NYPDVK
18	5.0/51	0.03	beta-1,3-glucanase	BAA31142.1	CS	(R)TYNNNLIQHVK(Q)	—
48	5.5/30	3.00	Putative chaperonin 21	AAT80888.1	VV	(V)SPGNTVLYSK(Y)	YAGNDF(Q/K)GPDGS(I/L)F(I/L)DTR	cd00320
						(Y)TSLKPLGDR(V)	VGA(Q/K)VVYSK
						(K)YTSLKPLGDR(V)
			Putative chaperonin 21	BAD35227.1	OSj	—	E(Q/K)PS(I/L)GTV(I/L)AVGPGP(I/L)DDEG(Q/K)R
			Triose phosphate isomerase	AAB23371.1	LS	(R)IIYGGSVSGSNCmK(E)
						(R)EAGTTMoxEVVAAQTK(A)
Miscellaneous
5	4.9/29	2.50	Proteasome subunit alpha type	Q9M4T8	GM	(K)EGVVLAVEK(R); (R)TLVEHAR(V); (K)VTPNNVDIAK(V); (R)TEYDRGVNTFSPEGR(L); (K)QVMoxEEKVTPNNVDIAK(V); (R)ITSPLLEPSSVEK(I); (R)FGEGDEESMoxSRPF(G)	T(Q/K)DGVV(I/L)AVE(Q/K)R; DGVV(I/L)AVE(Q/K)R; VAPTYH(I/L)YTPAEVEAV(I/L)SRL; DET(Q/K)F(Q/K)(Q/K)EYYN(Q/K)A(I/L) CmD(I/L)PSR	cd03753
12	6.6/19	2.50	Transcription factor	CAA70323.1	NPI	(R)LQSTLKR(L); (K)TTTTDDKRLQSTLKR(I); (Q)ANTWVVSGSPQTK(N)	(Q/K)(I/L)GPDN(I/L)DN(I/L)R
24	5.4/12	4.30	Glycine rich RNA binding protein	Q03878	DC	(I)NDRETGR(S); (I)INDRETGR(S); (R)EGGGGGYGGGGGYGGR(R); (R)CmFVGGLAWATNDE(S)	AAADVEYR; (I/L)DGRN(I/L)TVNEA(Q/K)SR
Unidentified proteins
3	5.3/23	0.40	Unidentified proteins				(I/L)APYFCR; TPPN(I/L)DPPR; PYVR; YMPAVFPEVF(Q/K)ADK; PEVTK; PFP(I/L)(I/L)V; TPS(Q/K)YF(Q/K)T(Q/K)MDYPPPGGTK; T(I/L)DAGGSWY(I/L)VT(I/L)VEN
4		0.20	Unidentified proteins				PVP(Q/K)K; SEFT(Q/K)K
6	4.6/30	2.50	Unidentified proteins				AANNETGR; GEFSPYGESYPCR; PVP(Q/K)K
8	4.4/45	13.00	Unidentified proteins				MSCVSACGANFCK; S(I/L)NYGAAMER; CGPCNSDFR
(b) Constantly expressed proteins
15	5.8/72	2.00	Mitochondrial processing peptidase	CAA56520.1	ST	(R)IVLAASGVEHEELLK(V)	DV(I/L)S(I/L)PTYDVVN; EVEA(I/L)GGNVTASASR
35	6.5/29	0.50	Triosephosphate isomerase cytosolic	P48493	LS	(K)VASPAQAQEVHAGLRK(W); (K)VASPAQAQEVHAGLR(K); (L)AYEPVWAIGTGK(V); (K)ISSWDNVVLAYEPVWAIGTGK(V); (R)ALLNETNEFVGDKVAYALSQGLK(V); (K)AIADKISSWDNVVLAYEPVWAIGTGK(V)		cd00311
39	5.9/29	0.60	Triosephosphate isomerase cytosolic	P48493	LS	(K)VASPAQAQEVH(A); (A)YEPVWAIGTGK(V); (R)IIYGGSVSGSNCmK(E); (K)VIACmVGETLEQR(E); (R)ALLNETNEFVGDK(V); (R)EAGTTMoxEVVAAQTK(A); (V)AAQTK(A)	MoxYEVHAG(I/L)R	cd00311
			Triosephosphate isomerase cytosolic	P21820	OSj	(F)VGGNWK(C)	PCmGTSEDV(Q/K)K
40	5.4/19	0.80	ATP synthase D chain	Q9FT52	AT	(K)SLKESERLEK(E); (K)FDALLVELK(E); (L)LVELK(E); (I)ADVAFK(A); (K)LSTMoxTADEYFEK(H)	FS(Q/K)EPEP(I/L)DWEYYRK; VTDEA(Q/K)R; (Q/K)VADVAFK
41	5.3/20	1.90	ATP synthase D chain	Q9FT52	AT	(R)TIDWDGMoxAK(V); (L)LVELKEAEQK(S); (I)ADVAFK(A); (K)LSTMoxTADEYFEK(H); (K)MoxLVSDEAR(K); (K)MoxLVSDEARK(E)	SVE(I/L)PK; FS(Q/K)EPEP(I/L)DWEYYRK; FS(Q/K)EPEP(I/L)DWEYYR
49	6.6/51	1.00	Malate dehydrogenase	Q7XDC8	OS	(K)NVSIYK(A); (R)ALGQISEK(L); (A)SSACmDHIR(-)	F(I/L)STV(Q/K)(Q/K)R
			Malate dehydrogenase	AAP70009.1	TA	(R)LGVQVSDVK(N)
			Malate dehydrogenase	BAA97412.1	AT	(Q)ASALEK(H)
			Malate dehydrogenase	AAF69802.1	VV	(K)TFYAGK(A)
50	6.6/51	0.90	Malate dehydrogenase	AAF69802.1	VV	(L)FGVTTLDVVR(A); (T)FYAGK(A); (R)LFGVTTLDVVR(A); (R)TQDGGTEVVEAK(A); (T)EVVEAK(A); (K)TFYAGK(A); (S)SLSLYDIAGTPGVAADVSHINTR(S); (K)VAVLGAAGGIGQPLALLMoxK(L)	R(I/L)FGVDS(I/L)DVVR; RT(Q/K)DGGTEVVEAK; A(I/L)EGADVV(I/L)(I/L)PAGVPR; SMCmTA(I/L)AK; (I/L)FGVTT(I/L)DVVR; AGA(I/L)FADACm(I/L)K; N(I/L)SNEE(I/L)VA(I/L)TK; NGVEEV(I/L)G(I/L)GS(I/L)SDYEK	cd01337
53	6.9/52	0.80	Malate dehydrogenase	AAC19244.1	GM	(R)LFGVTTLDVVR(A); (R)DDLFNINAGIVK(T); (K)ALEGADVVIIPAGVPR(K)		cd01337
			Malate dehydrogenase	BAA97412.1	AT	(K)ASALEK(G); (K)SQASALEK(H); (K)NVSIYK(A)	F(I/L)STV(Q/K)(Q/K)R
			Malate dehydrogenase	Q7XDC8	OS	(R)ALGQISEK(L)
			Malate dehydrogenase	AAP70009.1	TA	(R)LGVQVSDVK(N)
54	7.0/53	0.50	Malate dehydrogenase	AAF69802.1	VV	(R)TQDGGTEVVEAK(A); (R)DDLFNINAGIVK(T); (K)TFYAGK(A); (K)RTQDGGTEVVEAK(A); (K)SDYEK(M); (R)FYAGK(V); (C)TAIAK(Y)	VSS(I/L)S(I/L)YD(I/L)AGTPGVAADVSHMNAPA; NGVEEV(I/L)G(I/L)GS(I/L)SDYEK	cd01337
			Malate dehydrogenase	AAD56659.1	GM	(N)VPVAGVNVPVVGGH(A); (K)ALEGADVVIIPAGVPR(K); (N)VPVAGV(N)	SEVVGY(Q/K)GDEEMGK
56	5.5/74	0.50	ATPase beta subunit	AAD03393.1	NS	(R)IINVIGEPIDER(G); (R)EAPAFVEQATEQQILVTGIK(V); (R)DAEGQDVLLFIDNIFR(F); (I)GLFGGAGVGK(T); (G)SPITVPVGR(A); (N)VIGEPIDER(G); (Y)GQMoxNEPPGAR(A); (R)TIAMoxDGTEGLVR(G); (R)VLNTGSPITVPVGR(A); (K)TVLIMoxELINNVAK(A); (R)FTQANSEVSALLGR(I); (K)CmALVYGQMoxNEPPGAR(A); (R)IPSAVGYQPTLATDLGGLQER(I); (L)GEDHYNTAR(G)	(Q/K)NVA(Q/K)H(I/L)GYMoxMR	cd01133
			Ribulose bisphosphate carboxylase RuBisCO large subunit	Q05987	CJ	(R)MSGGDHLHSGTVVGK(L); (L)GLSAK(N)
Oxidative stress
34	6.2/30	1.90	Glutathione S transferase PM24	P46422	AT	(G)EHKKEPFLSR(N)	A(I/L)T(Q/K)Y(I/L)AHRYEG(Q/K)GTN(I/L)(I/L)PADSK	cd03053
Stress and defence
33	6.9/20	0.70	Pathogenesis-related protein 5-1	AAM21199.1	HA	(R)NNCmPYTVWAGAVPGGGR(Q)	AVFT(I/L)RNNCPYTVWAGAVPGGGR; TGCmNFDGSGR	pfam00314
42	5.0/16	0.70	Pathogenesis-related protein	BAC10911.1	ZH	(K)VFSDFDNIAPK(V); (L)FTFGDAVPFTSGK(C); (K)QTIVYNCK(G); (K)LFTFGDAVPFTSGK(C)
43	4.8/16	1.70	Pathogenesis-related protein	BAC10911.1	ZH	(K)VFSDFDNIAPK(V); (K)QTIVYNCK(G)	—
59	5.1/100	1.50	Stromal 70 kDa heat shock related protein	Q02028	PS	(R)IPAVQELVK(K); (T)TLPTSK(S); (K)NQADSVVYQTEK(Q); (K)GPEGDVIDADFTDSK(-); (R)QAVVNPENTFFSVK(R); (R)IINEPTAA(S); (R)IINEPTAASLAYGFER(K); (V)PAYFNDSQR(T)	NTT(I/L)PTSK; MoxVSEAE(Q/K)FAK; (Q/K)VSYTVVRDDNNNV(Q/K)(I/L)ECPA(I/L)GK; (I/L)PAV(Q/K)EVVK	COG0443
51	6.6/42	1.00	Phenylcoumaran benzylic ether reductase	CAA06706.1	PT	(K)ILIIGGTGYIGK(F); (I)LGDGNAK(A); (F)IVEASAK(S); (I)ILGDGNAK(A); (V)VEASAK(S)	(I/L)VA(I/L)K; DVSDPSK; D(Q/K)VV(I/L)(I/L)GDGNAK; SFNE(I/L)VS(I/L)WEK; (I/L)PT(I/L)A(Q/K)PAADGPPR
52	6.7/42	0.50	Phenylcoumaran benzylic ether reductase homolog TH2	AAF64177.1	TH	(K)VVILGDGNAK(A); (L)GDGNAK(A); (R)DKVVILGDGNAK(A); (I)LGDGNAK(A); (V)ILGDGNAK(A)	(I/L)VA(I/L)K; FGNDVDR; YTTVDEY(I/L)TR
			Miscellaneous
26	5.7/13	1.10	Glycine rich RNA binding protein	Q03878	DC	(I)NDRETGR(S); (I)INDRETGR(S); (K)IINDRETGR(S)	DV(I/L)DS(Q/K)(I/L)(I/L)TDR; DA(I/L)EGMSGEE(I/L)DGR; TAFA(Q/K)YGDV(I/L)DSK; GFGFVTF(Q/K)DE(Q/K)SMR; N(I/L)TVNEA(Q/K)SR; CmFVGG(I/L)AWATGDAE	pfam00076
			Glycine rich RNA binding protein GRP2A	P49311	SA	(M)ASPDVEYR(C)
			RNA binding glycine rich protein 1 RGP 1a	BAA03743.1	NS	(G)SGGGGGGGGFRGGRREGGG(G)	T(I/L)GEAFS(Q/K)FGE(I/L)(I/L)DSK
27	5.9/17	0.70	Protein At5g10860 mitochondrial precursor	Q9LEV3	AT	(R)AMoxQLMoxTDNR(I)	H(I/L)R(Q/K)(I/L)(I/L)V(Q/K)GR; VGD(I/L)MoxTEEN(Q/K)(I/L)(I/L)TVTPDTK; TVTPDTK
			Regulator of ribonuclease like protein 1	Q9M8R9	AT	(R)VLVVDGGGSLR(C)	VFEDNV(I/L)(I/L)R
						(R)ALQPVFQIYGR(R)
			Eukaryotic translation initiation factor 5A 1 eIF 5A 1	Q9XI91	AT	(K)VVEVSTSK(T); (K)TYPQQAGTIR(K)
37	5.8/30	1.40	Proteasome subunit alpha type 2A subunit B	O23708	AT	(K)ASNGVVLATEK(K); (T)AVGSGQTSLGIK(A); (K)EPIPVTQLVR(E); (D)DKGPQLYQVDPSGSYFSWK(A); (R)YTEDMELDDAIHTAILTLK(E)	EGFEG(Q/K)(I/L)SGK; PAAPS(I/L)(I/L)VDETEG(Q/K)K; (I/L)YEEP(I/L)PVT(Q/K)(I/L)VR; ACmSNCmSESMTTFSPSGK	cd03750
			Triosephosphate isomerase cytosolic	P48493	LS	(R)IIYGGSVSGSNCmK(E); (R)EAGTTMoxEVVAAQTK(A)
57	5.4/68	1.30	26S protease regulatory subunit 6A homolog	O04019	AT	(K)LAGPQLVQMoxFIGDGAK(L); (Q)MoxFIGDGAK(L); (K)GVLLYGPPGTGK(T)		COG1222
44	5.0/41	1.40	atranbp1b (Ran-binding protein)	CAA66046.1	AT	(K)LYRFDK(D); (R)FGSVENCmK(A)
			Unidentified proteins
58	5.0/64	0.70	Unidentified proteins				APDK; DDPGR