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Table 2 Important features of type-2 LuPMEs

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

LuPME

Mature protein

Subcellular localization

# of Conserved residues

Tree

Expression

AA

Kda

pI

SP

TM

WolF PSORT

Plant-mPLoc

AS

ST

CR

Group

OE

FL

UF

EV

EN

RS

RSA

2

192

21

4.8

+

-

ch, ex, v

cw

1

1

2

E

-

-

  

0

  

4

305

34.4

6.5

-

-

n, cy, m, ch, ex

cw

5

1

3

E

-

-

  

0

  

10

348

38.2

8.4

+

+

ch, ex, v, m

cw

4

2

3

E

+

+

 

ES, L, GE, HE, TE, ME

12

All

+

12

223

23.1

8.7

-

-

ch, n, m

cw

2

0

2

C

+

-

  

0

 

+

15

267

29.9

5.7

-

-

n, cy, pl

cw

3

1

2

E

+

+

  

0

  

16

329

37.1

9.4

+

-

ch

cw

5

1

3

E

+

-

  

0

 

+

20

252

27.6

8.9

-

-

cy, ch, ex, n, m

cw

5

1

3

D

-

-

  

0

  

21

352

39.1

8.5

-

+

ex, er, ch, cy, m, v

cw

6

2

3

E

+

+

  

0

All

+

24

414

45.4

8.3

-

+

ex, ch, v, er

cw

5

2

3

E

+

+

1

 

0

All

 

25

319

34.7

8.5

+

-

ch, ex, m, v

cw

4

1

3

E

+

-

  

0

 

+

26

322

35.4

9.5

+

-

ch

cw

5

1

3

E

+

NA

  

0

all

+

27

363

39.7

8.9

+

+

ch, v, n, pl

cw

6

2

3

E

+

+

  

0

SA and S4

+

28

74

8.5

11.2

-

-

cy, ch, n, pl

cw, ch

0

0

0

D

+

+

  

0

  

29

356

39.3

9.1

+

+

ch, v, n, pl

cw

6

2

3

E

+

+

 

F

2

all

+

33

219

24.8

4.9

-

-

cy, ch, n, pe

cw

5

0

2

A

-

-

  

0

  

34

317

35.5

7.7

-

-

cy, n, ch

cw

6

2

3

E

+

+

1

 

0

 

+

35

145

15.9

9.1

-

-

n, ch, cy

cw

3

0

1

D

-

-

  

0

  

39

348

38.8

7.8

+

+

v, cy, ch, m

cw

4

2

3

E

+

+

  

0

  

40

316

35.8

9

+

-

ch, n, m

cw

5

1

3

E

+

+

 

TSC

1

  

41

340

37.3

6.3

+

-

ex, v, er, ch, n

cw

3

2

3

E

+

+

  

0

  

42

216

24.4

8.4

-

-

m, ch, v, n

cw, n

1

0

0

E

-

NA

  

0

  

48

379

40.2

8.7

-

-

ch, m, n

cw

3

0

2

C

+

+

  

0

 

+

52

336

37.6

6

-

-

cy, er, n

cw

6

1

3

A

+

-

  

0

 

+

55

330

36.2

9

+

-

ch, v, ex, n

cw

3

1

3

E

+

+

  

0

  

57

260

28.8

6.8

-

-

n, cy, ct, ex

cw

2

1

3

E

-

-

  

0

  

58

123

14.4

9.4

-

-

cy, n

cw

3

0

1

C

+

-

 

F

1

  

59

318

35.6

7.7

-

-

cy, n, ct, ct_pl

cw

6

2

3

E

+

+

  

0

SA

+

60

325

35.2

8.4

+

+

ch, ex

cw

4

1

3

E

-

-

  

0

  

61

302

31.9

9.4

-

-

cy, ch, m, n

cw

6

2

3

D

+

+

1

 

0

S3 and 4

 

67

418

45.9

5.6

-

+

v, g, ex, ch

cw

4

2

3

E

+

+

  

0

All

 

68

316

35.1

9.4

-

-

m, ch, n

cw

6

2

3

E

+

+

 

ES

1

SA

+

69

220

24.5

7.9

-

-

ch, n, cy

cw

5

2

3

D

+

+

  

0

  

77

318

35.2

7.7

+

-

ch, n

cw

5

1

3

E

+

+

  

0

 

+

87

348

38.5

7.3

-

-

cy, ct, n

cw

3

2

3

E

-

-

  

0

  

88

140

15.5

8.9

-

-

cy, ch, m

cw

1

0

0

E

-

-

  

0

  

89

311

33.6

5.2

-

-

n, ch, cy, ex

n

3

2

2

E

+

+

  

0

 

+

90

339

37.1

6.3

+

-

n, er, er_pl, m, pl, ch, cy

cw

3

2

3

E

+

+

  

0

 

+

94

332

37.6

8.5

+

-

ex, v, er, cy

cw

3

1

2

E

+

+

  

0

  

98

354

40.1

8.1

+

-

ch, n, ex, cy

cw

5

1

3

E

-

-

  

0

  

100

289

32.3

7

-

-

cy, n, ct, ch

cw

1

0

2

E

-

NA

  

0

  

101

318

36.2

7.2

+

-

ex, v, er, ch, cy

cw

4

1

2

E

+

+

 

F

3

  

102

317

35.1

5.5

-

-

cy, n, ct

cw

5

2

3

E

+

+

  

0

All

+

103

359

39.8

8.9

+

-

ch, cy, n, m, ex

cw

6

2

3

E

+

+

  

0

all

+

104

349

38.4

9.3

-

-

m, ch_m, ch

cw

4

1

3

E

-

-

  

0

  

105

343

37.6

9.1

-

-

ch, cy

cw

6

2

3

E

+

+

1

 

0

SA

+

  1. LuPME8, LuPME51, LuPME97, and LuPME22 have two PME domains. (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. (AS): Number of conserved residues at active site (out of 6); (ST): Number of conserved stabilizer residues (out of 2). CR: Number of conserved catalytic residues (out of 3). 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 the OneKP 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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BMC Genomics

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