Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum)

Pinzón-Latorre, David; Deyholos, Michael K

doi:10.1186/1471-2164-14-742

Table 3 Important features of LuPMEIs

From: Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum)

LuPMEI	Mature prot.			Subcellular localization				Conserved residues							Expression
LuPMEI	AA	Kda	pI	SP	TM	WolF PSORT	Plant-mPLoc	*	§	□	£2	£3	¥	P55	OE	FL	UF	EV	EN	RS	RSA
1	155	16.1	6.8	+	-	ex, m, v, ch	pl	10	4	4	1	0	4	N	+	+		EP	1
2	174	18.9	8.6	-	-	ch, cy, m, n	pl, ch	8	2	2	0	2	2	A	-	-			0
3	162	17.9	6.1	+	-	ex, ch	pl	6	3	2	1	2	4	G	+	+			0		+
4	113	12.6	4.9	-	-	ch, n, m, pl, g_pl	pl, n	2	1	4	1	2	2	-	-	-			0
5	159	17	4.9	+	-	ex, ch, m	pl	9	5	4	3	1	4	P	+	-		HE	1
6	177	18.7	8.8	+	+	v, pl, ex	pl	11	5	4	2	1	4	A	+	-		GS	1
7	155	16.8	5.6	+	+	ex, v, ch, n	pl	11	4	3	1	3	4	A	-	-			0
8	167	17.8	5.3	-	+	ex, ch, v	pl	7	2	3	2	1	4	T	-	-			0
9	192	21.5	10	+	+	ch	pl	5	4	4	1	1	4	T	-	-			0
10	199	21.2	5.1	+	-	ex, ch, m, v	pl	7	2	4	0	0	4	P	-	-			0
11	296	33.7	4.7	-	-	n	n	6	3	4	1	2	4	H	-	-			0
12	155	16.7	8.4	+	-	ex, ch	pl	8	4	2	1	0	3	A	+	+		ES	1		+
13	160	16.8	8.3	+	-	ex, ch, v	pl	11	4	2	1	0	4	S	+	-			0	S4	+
14	159	17.4	5.1	+	-	ch, v, ex	pl	11	3	4	2	1	4	S	+	+			0
15	159	17.3	5.1	+	-	pl, ch, er, ex	pl	11	3	4	2	1	4	S	+	+			0
16	198	21.3	5.1	+	-	ex	pl	7	5	4	3	1	4	I	+	+		GS	1	SA and S3	+
17	187	20.3	4.5	+	+	ch	pl, n	8	4	3	1	2	4	A	+	+		HE, F	2	S4	+
18	181	19.5	8.3	+	-	ch, m, v	pl	8	3	3	3	1	4	A	+	+		TS	1	SA	+
19	159	17	5	+	-	ex, ch, m	pl	9	5	4	3	1	4	P	+	+		GE, F	4
20	239	26	5.6	-	+	ch, ch_m, n, m, cy	pl	9	4	4	2	1	4	S	+	-			0	S3 and 4	+
21	161	17.2	7.9	+	-	ch, ex, cy	pl	11	3	4	1	2	4	A	-	-			0
22	483	55.4	4.6	+	-	ex, v, g, n	n	5	3	4	1	2	4	P	+	+			0		+
23	198	20.8	4.9	+	-	ch, ex, cy	pl	6	3	3	1	1	4	P	+	+		F	5
24	180	19.6	8.9	+	-	v, ch, ex	pl	9	3	3	0	0	4	P	+	+		F	3
25	172	18.6	4.9	+	-	ex, ch	pl	11	5	3	3	1	4	K	+	+			0
26	154	16.2	5.5	+	-	ex, m, ch	pl	10	4	2	1	1	4	A	+	+		L	1	SA and S3	+
27	149	16.4	4.7	+	-	ex, v, ch	pl	10	3	4	1	2	4	N	+	+			0
28	166	17.1	8.3	+	-	ex, pl, ch, m, v	pl	11	4	2	1	0	4	S	+	+			0	SA	+
29	149	16.7	4.8	+	-	v, ch, ex, er	pl	10	2	4	1	1	4	N	+	+		EP, HE	3
30	149	16.4	4.6	+	+	ex, v, cy, m	pl	10	2	4	1	0	4	T	+	+		EP,GS	24
31	165	17.8	5.5	+	-	pl, g, ex, er	pl	11	4	2	1	1	3	K	-	-			0
32	155	16.5	8.4	+	+	ch, v, cy, n, m	pl	10	4	3	1	0	4	T	+	+			0
33	152	15.9	5.1	+	-	ex, ch	pl	9	4	3	1	2	4	A	+	-		GS	1
34	152	16.2	4.7	+	+	v, pl	pl	11	4	4	2	2	4	A	+	+			0
35	154	16.1	4.6	+	-	ex, ch, n	pl	10	4	4	2	2	4	A	+	-			0		+
36	152	16.3	4.7	+	-	ex, ch, cy, m	pl	11	5	4	3	2	4	A	+	+			0
37	167	17.9	5.4	-	-	ch, cy, n, ct_n	pl	8	4	4	2	1	4	P	+	+			0		+
38	163	17.8	7.8	+	-	ex, ch, pl	pl	9	5	3	1	2	4	P	+	+			0	S3	+
39	158	17.4	4.5	-	-	ch, ex, n	pl	10	5	2	3	1	4	K	+	-			0		+
40	164	17.6	5.7	+	+	v, ex, pl, m, er_pl, n	pl	9	5	3	2	2	4	A	+	+	1	HE	1		+
41	151	16.1	5.3	+	-	ch, v, n, m, ex	pl	11	5	2	1	2	4	M	+	+		HE, GS	2
42	159	17.2	6.1	+	-	ex, ch, v, m	pl	10	3	4	1	1	4	S	+	+			0
43	181	19.6	9.5	+	-	ch, v	pl	7	4	4	1	1	4	I	+	+			0	SA and S3	+
44	187	19.9	6.8	+	+	ex, v	pl	7	5	4	2	1	4	I	+	+			0	All	+
45	159	17.3	6.5	+	-	ex, ch, n, cy	pl	7	3	4	3	1	4	I	+	+			0	SA	+
46	389	45	5.1	-	-	n	n	5	3	4	1	2	4	P	+	+			0		+
47	188	20.2	8.4	+	-	ex, v, ch, m	pl, n	7	3	4	0	1	4	P	+	+			0
48	193	21.2	7.7	+	+	n, ex, ch, cy, v	pl, n	7	3	4	1	0	4	P	+	+		F	2
49	197	21.5	6.9	+	+	ex, ch, n, m, v	pl, n	8	3	4	1	0	4	P	-	NA			0
50	467	50.6	6.5	-	-	n, ch, pl, m	pl, n	7	4	3	1	3	4	A	+	+			0
51	368	37.4	4.3	+	+	ex, ch, v, n	n	8	4	2	1	2	4	P	+	+			0		+
52	65	7.3	4.5	-	-	cy, n, ch, pl, ex	pl, n	5	1	1	0	1	1	-	+	+			0
53	161	17.8	9	+	+	ch, ex	pl	7	5	4	3	1	4	I	+	-		S	1		+
54	175	18.7	6.1	+	-	ch, m, ex	pl	7	5	4	3	1	4	I	+	+			0	All	+
55	141	15.3	5.9	-	-	ch, m	cw	4	1	4	2	1	3	-	+	+			0
56	167	18.8	8.3	+	-	ch, ex, cy, m, pl	pl, n	7	4	3	1	2	4	D	+	+			0		+
57	154	16	6.4	+	+	ex, ch, cy, m	pl	9	4	4	2	0	4	N	+	+		GE	1
58	195	21.1	5.2	+	-	ex, ch	pl	7	5	4	3	1	4	I	+	-			0	all
59	173	18.9	4.5	+	-	ex, ch, n	pl	10	5	2	3	1	4	K	+	+			0
60	195	21.7	9.9	+	-	ch	pl	6	4	4	1	1	4	T	+	-			0		+
61	468	51.7	8.7	-	-	n, ch, cy	pl, n	7	4	3	3	1	3	G	+	-			0	All	+
62	118	13.2	6.9	-	+	ch, cy, n, ex	pl	4	1	3	2	3	2	-	-	-			0
63	170	18.3	5.9	+	-	ch, v, ex, m	pl	7	5	4	2	2	4	V	+	+		TE	1		+
64	177	19.1	10	+	-	ch	pl	7	4	4	3	1	4	I	+	+			0	SA	+
65	180	19.1	5.3	+	-	ch, m	pl	6	5	4	3	1	4	I	+	+	1		0	all	+
66	160	17.8	7.8	+	-	ex, ch, n, cy	pl	7	3	4	0	2	4	T	+	+		TS, EP	4	SA
67	174	18.8	4.6	+	-	ex, ch	pl	11	5	4	3	1	4	K	+	+			0
68	177	19	5.5	+	-	ch, ex, v, m	pl	7	5	4	3	2	4	V	+	+			0		+
69	179	19.3	9.2	+	-	ch	pl	7	5	4	3	2	4	I	+	-			0		+
70	177	19.2	10.1	+	-	ch	pl	7	4	4	3	1	4	I	+	-			0	All	+
71	183	19.6	5.7	+	-	ch, m	pl	6	5	4	3	1	4	I	+	+			0		+
72	183	20	9.4	+	-	ch, n	pl	7	5	4	1	1	4	I	+	+			0		+
73	212	22.6	7.7	+	-	ex, m, v	pl	7	5	4	2	1	4	I	+	+			0	SA and S4	+
74	159	17.4	5.5	+	-	ch, ex, n, cy, m	pl	6	3	4	3	1	3	I	+	+			0	S3 and 4	+
75	170	19.1	9	+	-	ch, pl	pl, n	7	5	3	1	2	4	D	+	+			0	S4	+
76	228	25	9	+	-	ch, v, ex	n	9	3	2	0	0	4	P	+	+		F	1
77	220	23	4.6	-	-	ch, n	pl	9	3	3	1	1	4	P	+	+			0
78	163	17.7	5.7	+	-	pl, g, ex, ch	pl	11	4	2	1	1	4	K	+	-			0	SA and S3
79	155	16.6	6.9	+	+	er, ex, er_pl, ch, m, pl, cy	pl	10	4	3	1	0	4	T	+	-			0	S3 and 4
80	229	24.9	5.7	+	-	ch, ex	pl, n	7	4	3	2	2	4	A	-	-			0
81	184	19.3	4.8	-	-	ch, m, n	pl	5	2	4	2	1	3	P	+	-	1		0	S3	+
82	334	34.4	4.4	+	+	ex, ch, v, n	n	8	4	2	1	2	4	P	+	+			0
83	249	26.9	4.7	+	-	ch, ex, v	pl, n	7	4	3	1	2	4	A	+	+			0
84	193	20.5	4.7	+	-	ex, ch, v	pl	7	5	4	2	1	4	V	+	+			0	S3	+
85	156	16.9	8.4	+	-	ex, v, pl	pl	8	3	3	0	0	4	R	+	+			0	All	+
86	150	16.2	9.2	+	+	v, ex, pl	pl	10	2	4	0	1	4	A	+	+			0	All	+
87	162	17.7	9	+	-	ch	pl	7	5	4	3	1	4	I	+	+			0		+
88	172	18.3	5.4	+	+	ch	pl	7	5	4	3	1	4	I	+	+		TS	1	All	+
89	155	16.6	8.8	+	+	ex, pl, v, ch, cy, m	pl	10	2	4	0	1	4	A	+	+			0	S3 and 4	+
90	188	19.9	5.7	-	-	ch, m, cy	pl, cy	6	3	3	2	1	2	P	+	+		F	1		+
91	327	36.6	9.2	-	+	pl, ch, m, er	pl	9	4	3	2	3	4	T	+	+			0
92	162	17.9	7.8	+	-	ex, ch	pl	6	3	2	1	2	4	G	+	+			0	all	+
93	156	16.5	4.4	+	+	n, ex, m, er_pl, pl, er	pl	11	5	4	2	2	4	G	+	-		EP	1
94	331	35.9	6.3	-	+	n, g, pl, er_pl, cy	cy	9	4	4	2	1	4	S	+	+	1	TE	1	SA and S4	+
95	157	17.3	5.3	-	-	cy, ch, n, ex	pl	8	4	3	1	2	3	P	+	+			0		+

(SP): presence of signal peptide; (TM): presence of transmembrane domain. Subcellular localization: ch: chloroplast; cw: cell wall; cy: cytosol; er: endoplasmic reticulum; ex: extracellular/cell wall; g: Golgi apparatus; m: mitochondria; n: nuclear; pl: plasma membrane; v: vacuolar membrane; pe: peroxisome; ct: cytoskeleton. Number of conserved residues at each one of the following: (*) non polar bundle-hairpin interface (out of 12); (§) polar bundle-hairpin interface (out of 5); (□) Polar interacting with PME aromatic residues (out of 5); (£2) acidic patch on α2 helix (out of 3); (£3) acidic patch on α3 helix (out of 3); (¥) disulphide bridge (out of 4). Expression: A gene was reported as positive if the coverage with the EST or assembled RNAseq sequence was higher than 80% and the identity higher than 98%. (OE) Overall expression based on all the methods assessed: (+) expression was detected with at least one of the methods; (-) expression not detected in any of the methods. (FL) Gene expression based on qRT-PCR (Fluidigm): (+) it was expressed in at least one tissue; (-) no expression; (NA) no assay done. (UF): Number of genes aligning with unigenes reported by Fenart et al.[35], 80% coverage and 98% identity. (EV) Venglat et al.[36] ESTs, 80% coverage and 98%identity: (F) flower; (S) stem; (SP) stem peel; (ES) etiolated seedling; (L) leaf; (GE) globular embryo; (HE) heart embryo; (TE) torpedo embryo; (ME) mature embryo; (TS) torpedo seed coat; (GS) globular seed coat; (EP) endosperm pooled. (EN) Number of ESTs from NCBI as of April 2013. (RS): Alignment with RNAseq assembled sequences data (80% coverage and 98%identity) obtained from one kp project at different positions in the stem: (SA) shoot apical meristem; (S3): stem 3; (S4) stem 4. (RSA): RNAseq shoot apical meristem.

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