. 2015 Jun 17;6:441. doi: 10.3389/fpls.2015.00441

Table 1.

Differentially abundant proteins during E. arvense spore germination.

Spot No.⁽^a⁾	Protein name⁽^b⁾	Subcellular location⁽^c⁾	Plant species⁽^d⁾	Gi No.⁽^e⁾	Thr. MW(Da)/pI⁽^f⁾	Exp. MW(Da)/pI⁽^g⁾	Cov (%)⁽^h⁾	Sco⁽ⁱ⁾	QM⁽^j⁾
PHOTOSYNTHESIS (17)
121	Chlorophyll a/b binding protein (CAB)	Chl	Hedera helix	12,582	20,759/4.83	25,376/4.71	10	57	3
346	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Eryngium bourgatii	1,292,976	53,093/5.56	28,686/6.28	6	59	3
763	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Donatia fascicularis	1,304,292	49,896/6.32	134,736/5.48	8	55	5
902	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Grammitis diminuta	340,031,166	45,938/6.26	50,502/6.31	5	61	2
117	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Equisetum telmateia	16,565,336	48,750/6.26	52,974/6.47	15	57	7
196	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	E. telmateia	16,565,336	48,750/6.26	51,502/6.47	16	52	6
194	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	E. telmateia	16,565,336	48,750/6.26	51,418/6.33	13	53	6
400	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	E. telmateia	16,565,336	48,750/6.26	49,452/6.31	11	53	5
23	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	E. bourgatii	1,292,976	53,093/5.56	50,872/5.02	4	78	2
528	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Equisetum arvense	1,352,773	52,493/5.86	67,620/4.64	7	60	3
100	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL)	Chl	Isoetes capensis	83,032,384	47,561/6.30	42,425/5.47	6	55	3
496	Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit-binding protein subunit beta (RBP)	Chl	Solanum lycopersicum	460,379,814	64,527/5.46	71,249/5.21	4	61	2
34	Ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA)	Chl	Gossypium hirsutum	12,620,883	48,609/5.06	48,999/5.19	11	98	4
184	Ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA)	Chl	Hordeum vulgare	100,614	47,496/5.64	47,356/6.31	11	94	4
125	Ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA)	Chl	Musa acuminata subsp. malaccensis	695,062,479	47,898/6.18	42,859/5.67	8	75	3
308	Transketolase (TK)	Chl	Spinacia oleracea	2,529,342	80,744/6.20	95,817/6.20	8	156	5
84	Transketolase (TK)	Chl	S. lycopersicum	460,388,792	80,615/6.26	85,056/6.11	8	90	7
CARBOHYDRATE AND ENERGY METABOLISM (9)
685	Unknown, pyruvate dehydrogenase E1 component subunit beta^* (PDH)	Chl	Glycine max	255,647,166	44,596/6.28	27,410/6.46	4	60	2
160	Malate dehydrogenase (MDH)	^#Chl, Cyt, Mit, Pox	Arabidopsis thaliana	15,219,721	35,890/6.11	46,411/4.98	12	74	3
503	Malate dehydrogenase (MDH)	^#Chl, Cyt, Mit, Pox	A. thaliana	15,219,721	35,890/6.11	42,425/5.53	6	57	2
260	Malate dehydrogenase (MDH)	^#Chl, Cyt, Mit, Pox	A. thaliana	11,133,509	35,548/6.11	29,729/6.41	6	59	3
164	Malate dehydrogenase (MDH)	^#Chl, Cyt, Mit, Pox	Beta vulgaris subsp. vulgaris	731,361,010	41,677/5.74	36,353/5.84	12	193	4
163	Malate dehydrogenase (MDH)	Chl	Brachypodium distachyon	357,147,942	41,864/6.97	38,560/5.94	10	60	4
486	Enolase	Cyt	Tarenaya hassleriana	729,317,446	51,639/5.91	48,823/5.62	3	54	2
489	6-phosphogluconate dehydrogenase (6-PGDH)	^#Chl, Cyt	G. max	356,513,305	54,116/6.25	24,817/5.21	12	53	5
192	Fructokinase (FK)	Chl	Lycopersicon esculentum	23,476,263	40,620/5.41	37,710/4.91	8	129	3
OTHER METABOLISMS (5)
135	Enoyl-acyl carrier protein reductase (EAR)	Chl	Oryza sativa subsp. japonica	75,225,229	39,277/8.81	32,651/6.16	5	21	2
197	Hypothetical protein PHAVU_001G035500g, glycine decarboxylase^* (GDC)	Mit	Phaseolus vulgaris	593,795,946	116,167/6.65	117,088/6.30	11	157	12
362	3-isopropylmalate dehydrogenase (IPMDH)	Chl	A. thaliana	15,241,338	44,305/5.75	28,512/4.87	23	67	7
445	Hypothetical protein SELMODRAFT_406755, containing cd00517 ATP-sulfurylase domain^* (ATPS)	Chl	Selaginella moellendorffii	302,763,978	56,179/6.69	26,370/5.59	5	60	3
190	Predicted protein, pyridoxal biosynthesis protein PDX1^*	Cyt	Physcomitrella patens	168,019,502	33,769/6.03	29,893/5.82	15	324	8
SIGNALING AND VESICLE TRAFFICKING (8)
282	Unknown, containing PLN02804 chalcone isomerase domain^* (CHI)	Chl	Picea sitchensis	116,784,316	23,688/5.23	23,141/4.75	7	56	2
1063	Hypothetical protein SELMODRAFT_151778, containing cd00200 WD40 domain^* (WD40)	Nuc	S. moellendorffii	302,791,020	37,267/5.65	36,189/5.74	6	84	2
207	14-3-3 protein	Cyt	S. oleracea	440,573,600	30,029/4.84	27,277/4.79	16	79	6
276	Unknown, containing cd00877 Ran GTPase domain^* (RAN)	Nuc	P. sitchensis	116,794,384	25,374/6.30	27,727/6.65	20	52	4
317	GTP-binding nuclear protein Ran/TC4 (RAN)	Nuc	Vicia faba	585,783	25,274/6.39	27,750/6.73	27	187	6
340	Unknown, containing cd00877 Ran GTPase domain^* (RAN)	Nuc	P. sitchensis	116,794,384	25,374/6.30	30,115/5.59	24	53	5
764	Unknown, containing cd00877 Ran GTPase domain^* (RAN)	Nuc	P. sitchensis	116,794,384	25,374/6.30	44,900/6.58	30	51	6
123	ADP-ribosylation factor (ARF)	Gol	Chlamydomonas reinhardtii	1,703,374	20,747/6.92	19,121/6.71	29	92	4
CELL STRUCTURE (5)
397	Os03g0718100, actin^*	Cyt	O. sativa subsp. japonica	115,454,971	42,014/5.30	32,585/4.95	9	82	3
554	Reversibly glycosylated polypeptide (RGP)	Cyt	Ricinus communis	223,546,230	41,557/5.82	39,973/5.41	14	105	5
118	Reversibly glycosylated polypeptide (RGP)	Cyt	Solanum tuberosum	34,582,499	42,146/5.71	35,827/5.36	24	74	8
299	Unknown protein, rhamnose biosynthetic enzyme 1^* (RBE)	^#Cyt	A. thaliana	8,493,590	33,861/5.73	29,119/6.48	7	127	4
482	Caffeoyl-CoA O-methyltransferase (CCoAOMT)	^#Cyt	Eucalyptus gunnii	3,023,419	28,010/5.02	29,0934.81	11	73	2
CELL CYCLE (2)
104	Cell division cycle protein 48 homolog (CDC48)	Cyt	T. hassleriana	729,396,339	89,888/5.09	103,252/5.22	21	119	14
139	Proliferation-associated protein 2G4-like (PA2G4)	Nuc	Nicotiana tomentosiformis	697,180,533	43,837/5.96	55,758/6.73	5	52	2
TRANSCRIPTION RELATED (1)
938	Predicted protein, containing cd00771 threonyl-tRNA synthetase class II core catalytic domain^* (ThrRS)	Cyt	P. patens	168,012,416	71,002/5.96	80,637/6.37	3	54	2
PROTEIN SYNTHESIS (10)
83	Predicted protein, 40S ribosomal protein SA (RPSA)	Cyt	P. patens	168,017,628	31,539/4.72	43,804/4.58	7	101	2
454	Hypothetical protein AMTR_s00087p00135370, containing cd08065 eukaryotic translation initiation factor 3^* (eIF3)	^#Chl, Cyt, Mit, Nuc	Amborella trichopoda	548,842,775	44,710/5.17	39,587/4.64	5	82	2
66	Hypothetical protein, eukaryotic initiation factor 4A^* (eIF4A)	Cyt	P. patens	168,026,095	47,119/5.46	48,999/5.32	25	162	11
878	Eukaryotic initiation factor 4A (eIF4A)	Cyt	Nicotiana. tabacum	1,170,511	47,098/5.37	49,134/5.23	14	118	6
94	OSJNBa0020P07.3, elongation factor 2^* (EF2)	Cyt	O. sativa subsp. japonica	38,344,860	94,939/5.85	115,425/6.42	9	111	7
538	Hypothetical protein SELMODRAFT_411087, elongation factor 2^* (EF2)	Cyt	S. moellendorffii	302,773,640	94,568/6.00	114,195/6.33	5	167	5
510	Hypothetical protein SELMODRAFT_143627, elongation factor G^* (EF-G)	^#Chl, Mit	S. moellendorffii	302,765,284	75,483/5.31	119,422/6.41	6	75	4
942	Elongation factor Tu (EF-Tu)	Mit	Setaria italica	514,812,465	48,530/5.99	44,724/6.18	16	63	8
205	Uncharacterized protein LOC105056625, containing cd14275 elongation factor Ts domain^* (EF-Ts)	Chl	Elaeis guineensis	743,840,139	125,269/4.92	27,102/5.82	2	130	5
625	Tyrosine phosphorylated protein A (TypA)	Chl	Suaeda salsa	162,424,768	75,474/6.71	85,342/5.71	6	205	4
PROTEIN FOLDING AND PROCESSING (8)
542	Hypothetical protein SELMODRAFT_440382, containing pfam00012 heat shock protein 70 domain^* (HSP70)	Cyt	S. moellendorffii	302,770,212	71,931/5.17	80,237/5.18	13	295	7
1002	Heat shock protein 70 (HSP70)	Cyt	Populus trichocarpa	224,098,390	71,620/5.14	80,105/5.21	16	135	8
1566	Heat shock protein 70 (HSP70)	Cyt	Petunia × hybrida	20,559	71,137/5.07	106,146/6.34	4	92	2
314	Heat shock protein 70 (HSP70)	Cyt	Dactylis glomerata	188,011,548	72,002/5.03	86,310/5.38	21	338	13
928	Heat shock protein 70 like protein (HSP70)	Cyt	S. lycopersicum	460,394,037	72,308/5.16	91,122/5.25	7	122	5
598	Predicted protein, containing pfam00183 heat shock protein 90 domain^* (HSP90)	Cyt	P. patens	168,034,606	79,652/4.93	87,379/5.25	5	89	3
259	T-complex protein 1 subunit alpha (TCP1α)	Cyt	A. thaliana	135,535	59,477/5.93	66,881/6.22	8	246	4
106	Hypothetical protein VITISV_000290, T-complex protein 1 subunit gamma^* (TCP1γ)	Cyt	V. vinifera	147,784,740	61,064/6.06	72,989/6.14	5	94	3
PROTEIN DEGRADATION (8)
284	Alpha7 proteasome subunit (PSA7)	Cyt, Nuc	N. tabacum	14,594,925	27,466/6.11	25,449/5.20	8	79	2
199	Zinc dependent protease (ZDP)	Chl	Trifolium pratense	84,468,286	74,746/5.82	73,106/5.66	12	106	7
227	Zinc dependent protease (ZDP)	Chl	T. pratense	84,468,286	74,746/5.82	26,150/5.94	10	87	7
37	Zinc dependent protease (ZDP)	Chl	T. pratense	84,468,286	74,746/5.82	72,520/5.57	5	93	3
869	Zinc metalloprotease (ZMP)	Chl, Mit	A. thaliana	10,120,424	121,539/5.39	131,816/5.10	1	44	2
354	Predicted protein, containing pfam06480 FtsH extracellular domain^* (FtsH)	Chl	Micromonas pusilla CCMP1545	303,275,720	77,421/5.29	75,882/5.26	6	113	4
508	Predicted protein, ATP-dependent zinc metalloprotease FtsH^* (FtsH)	Chl	P. patens	168,001,910	68,933/5.23	108,174/5.50	3	75	2
59	ATP-dependent Clp protease ATP-binding subunit ClpC (CLPC)	Chl	A. thaliana	9,758,239	103,616/6.36/	94,506/5.45/	9	415	9
STRESS AND DEFENSE (7)
414	Hypothetical protein MIMGU_mgv1a021611mg, containing cd03015 2-cys peroxiredoxin domain^* (Prx)	Chl, Cyt	Erythranthe guttata	604,334,612	21,153/4.98	21,812/4.68	17	132	4
92	2-cys peroxiredoxin-like protein (Prx)	Chl, Cyt	Hyacinthus orientalis	47,027,073	21,956/4.93	22,930/5.24	12	58	3
166	Ascorbate peroxidase (APX)	Cyt	Eucalyptus grandis	702,241,628	27,613/6.07	25,671/5.66	7	104	2
244	Dehydroascorbate reductase-like protein (DHAR)	Cyt	S. tuberosum	76,573,291	23,610/6.32	24,534/5.60	11	147	3
361	Dehydroascorbate reductase-like protein (DHAR)	Cyt	S. tuberosum	76,573,291	23,610/6.32	24,783/5.64	11	105	3
899	Dehydroascorbate reductase-like protein (DHAR)	Cyt	S. tuberosum	76,160,951	23,596/6.09	44,783/6.60	11	92	3
294	Chloroplast drought-induced stress protein of 32 kDa (CDSP32)	Chl, Cyt	S. tuberosum	2,582,822	33,779/8.07	31,436/6.26	8	87	3

Assigned spot number as indicated in Figure 3.

The name and functional category of the proteins identified by ESI-Q-TOF and ESI-Q-Trap tandem mass spectrometry. Protein names marked with an asterisk (^*) have been edited by us depending on searching against NCBI non-redundant protein database for functional domain. The abbreviations for the protein names are indicated in the bracket after protein names.

Protein subcellular localization predicted by softwares (YLoc, LocTree3, Plant-mPLoc, ngLOC, and TargetP). Only the consistent predictions from at least two tools were accepted as a confident result. Pounds (#) indicate prediction results were inconsistent among five tools. The subcellular localizations were predicted based on literature listed in Supplementary Table S4. Chl, chloroplast; Cyt, cytoplasm; Gol, Golgi apparatus; Mit, mitochondria; Nuc, nucleus; Pox, peroxisome.

The plant species that the peptides matched from.

Database accession number from NCBI non-redundant protein database.

^f,g

Theoretical (f) and experimental (g) molecular weight (Da) and pI of identified proteins. Theoretical values were retrieved from the protein database. Experimental values were calculated using ImageMaster 2D version 5.0.

The amino acid sequence coverage for the identified proteins.

ⁱ

The Mascot score obtained after searching against the NCBI non-redundant protein database.

The number of matched peptides for each protein.

The mean values of protein spot volumes relative to total volume of all the spots. Five spore germination stages, MS, mature spores; RS, rehydrated spores, DCS, double-celled spores, GS, germinated spores; and SPC, spores with protonemal cells were performed. Error bar indicates ± standard deviation (SD). Letters indicate statistically significant differences (p <0.05) among five stages of spore germination as determined by One-Way ANOVA.