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Table 1 Major features of type-1 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

Binding motif for cleavage

Subcellular localization

Conserved residues

Tree

Expression

AA

Kda

pI

BM1

BM2

positions

sp

tm

WolF PSORT

Plant-mPLoc

as

st

cr

Group

oe

fl

uf

ev

en

rs

rsa

1

333

34.9

8.82

RKLL

RKLL

203-223

+

-

ch, m

cw

6

2

3

D

+

+

   

S3

+

3

320

34.4

9.77

 

RRLL

235

+

+

ch, v, ex

cw

6

2

3

D

+

+

    

+

5

319

34.6

9.53

 

RRLL

234

-

+

pl, g_pl, er, g

cw

6

2

3

D

+

+

1

S, SP, F

5

All

+

6

322

35.5

7.18

RKLL

RRVL

202-217

+

-

ch, n, pl

cw

5

2

3

C

+

-

    

+

7

322

35

6.6

RKVA

RRLL

235-259

+

-

ch, v, n

cw

6

2

3

D

+

+

1

S

2

All

+

8

364

40.1

8.66

RKLL

RRLL

263-286

-

+

n, cy, v, er, m, pl

cw

6

2

3

B

+

+

1

S

2

S3 and 4

+

9

322

35.6

9.6

RRLL

RKLL

224-242

+

+

ex, er, v, g, ch, n, cy

cw

5

2

3

C

+

+

 

F

34

 

+

11

593

64.1

8.46

   

-

+

ch, m

cw

6

2

3

A

+

+

1

ES, HE, TE,GS

4

All

+

13

323

35.3

10

 

RRLL

137

-

-

ch

cw

6

2

3

D

-

-

     

14

321

35.3

9.47

RRLL

RKLL

226-248

-

+

er, pe, ex, g, ch

cw

5

2

3

C

+

+

 

F

1

SA

+

17

322

35.4

8.89

RRLW

RRLL

197-221

+

+

v, ch, ex, er, g

cw

6

2

3

D

+

+

   

S3 and 4

+

18

393

43.1

8.39

RKLR

 

207

+

-

ch, ex, g, n, cy, pl, v, er

cw

5

2

3

D

+

+

   

S3 and 4

+

19

331

36.4

8.33

RKLL

RKLL

163-187

-

-

cy, n

cw

6

2

3

D

+

+

     

22

324

35.8

8.8

 

RRKL

613

-

-

n, cy, v

cw

6

2

3

D

+

+

2

GE

1

all

+

23

334

36.8

7.06

   

+

+

ch, n, ex, m, pl, v

cw

6

2

3

D

-

-

     

30

291

32

9

RRLW

RRLL

232-258

-

+

v, ch, g, n, pl

cw

5

1

2

D

+

-

  

4

All

+

31

323

35.6

8.21

RKLK

 

195

+

+

ch, ex, n, pl, v, er

cw

6

2

3

D

+

+

1

  

S3 and 4

 

32

386

41.2

9.51

   

-

+

m, ch

cw

1

0

0

A

+

+

   

S3 and 4

+

36

534

58.9

8.97

   

+

-

v, ch, n, g

cw

6

2

3

D

+

-

   

SA

+

37

398

45.2

5.93

RRLL

RRLL

246-283

-

+

ch, n, ex, v, er, g

cw

6

2

3

C

+

+

     

38

473

52.2

6.41

   

+

-

ex, ch, v, n, cy, pl

cw

6

2

3

D

+

-

1

CE,ME

3

  

43

297

32.6

9.49

RRML

RKLL

241-273

-

+

er, ch, cy, v, ex

cw

6

2

3

C

+

+

     

44

414

46

7.74

 

RKLL

103

-

-

n, cy

cw

6

2

3

D

+

+

 

TS

1

all

+

45

318

33.5

8.6

 

RELL

195

+

+

ch, cy, v, pe

cw

5

2

3

D

+

+

 

TS

2

S3 and 4

+

46

324

35.8

9.67

RRLL

RRLL

263-292

-

+

n, er, cy, ct, ch, m, v

cw

6

2

3

D

+

+

   

all

+

47

326

35.6

9.17

RRML

RKLL

241-273

-

+

v, g, ch

cw

6

2

3

C

+

+

     

49

525

58.4

9.29

   

+

-

ex, ch, v, er

cw

6

2

3

D

+

-

2

  

all

+

50

427

46

9.47

   

+

-

ch, n

cw

4

1

1

D

+

+

1

  

SA and S3

+

51

359

39.8

5.21

RRLL

 

406

-

-

cy, ch, n, pl

cw

2

1

0

C

-

-

     

53

322

35.4

9.05

RRLL

RRLL

213-239

-

-

cy, ch

cw

5

2

3

C

+

+

 

F

5

  

54

533

58.9

9.79

RRLL

RRLL

253-281

-

+

n, cy, er

cw, n

6

2

3

D

+

+

1

ES, S, F

3

all

+

56

322

35.6

9.61

RRLL

RKLL

222-240

+

+

ex, er, v, g, ch, n

cw

5

2

3

C

+

+

 

F

37

  

62

334

36

9.94

 

RRLL

217

+

+

ch, n, ex, v, cy

cw

6

2

3

D

-

-

     

63

518

57.6

9.54

   

+

+

ch, ex, er, n, cy, m

cw

6

2

3

D

-

-

     

64

322

35.9

10.32

 

RKVL

358

-

-

ch, n

cw

6

2

3

D

-

-

     

65

319

34.3

9.01

 

RRLL

187

-

-

n, ch, cy, v

cw

6

2

3

D

-

-

     

66

348

38.9

5.87

RRLL

RRML

265-289

-

+

cy, cy_pe, pe, er, pl

cw

5

2

3

C

+

+

 

F

4

  

70

387

42.7

7.71

RKLR

 

204

+

-

ch, n

cw

6

2

3

D

+

+

   

all

+

71

529

58.6

5.92

   

+

-

ch, n, ex, v, m

cw

6

2

3

D

+

+

    

+

72

407

46.1

5.57

RRLL

RRLL

318-350

-

-

n, cy, ch

cw

6

2

3

C

+

-

 

F

10

 

+

73

223

24.6

9.03

 

RKLL

250

+

-

ch, n

cw

6

2

3

D

+

+

1

  

all

+

74

526

58.6

9.29

   

+

-

ch, ex, v, er, g

cw

6

2

3

D

+

-

   

all

+

75

327

36.1

9.92

 

GRLL

 

+

+

ch, v, n

cw

6

2

3

D

-

-

     

76

335

36.8

8.76

 

RRLL

224

+

-

ex, ch, v

cw

6

1

3

D

-

-

     

78

400

45.4

6.12

RRLL

RRLL

227-258

+

+

ch, ex, v, g, n

cw

6

2

3

C

+

+

     

79

536

59

9.04

   

+

-

v, ch, n

cw

6

2

3

D

+

+

   

all

+

80

327

36.1

9.68

   

+

+

ch, v

cw

6

2

3

D

-

-

     

81

327

36

9.13

 

GRLL

 

+

-

ex, er, ch, v

cw

6

2

3

D

+

+

     

82

334

37.2

9.49

RRLL

REYL

242-253

-

+

cy, cy_n, ch, n

cw

6

2

3

B

-

-

     

83

322

35.4

8.95

RRLL

RKLL

237-260

-

+

er, ex, g, ch, cy, v

cw

5

2

3

C

+

-

 

F

16

  

84

547

60.7

5.25

   

-

+

ch, pl, n

cw

6

2

3

A

+

+

     

85

318

33.4

7.84

 

RKLL

203

+

+

ch, cy, cy_n, v, pe

cw

5

2

3

D

+

+

   

S3 and 4

 

86

330

37

9.52

RRLL

REYL

241-252

-

+

cy, cy_n, n, ch, pl, v

cw

5

2

3

B

-

-

     

91

321

35.2

9

RKLL

RRLL

274-301

-

+

n, cy, cy_pe, v, er, ct

cw

6

2

3

B

+

+

1

F

1

all

+

92

331

36.3

7.82

 

RRLL

267

+

+

pl, er, v, n

cw

6

2

3

D

+

+

 

S

1

all

+

93

347

37.7

5.16

RRLL

RRFL

246-272

-

+

cy, ex, pe

cw

3

2

3

C

+

+

 

F

1

 

+

95

323

34.8

9.47

 

RRLL

214

+

+

ex, v, ch, g, pl

cw

6

2

3

D

-

-

     

96

327

36.6

10.22

 

RKVL

154

-

-

n, cy, pl, ct_pl, ch, ct

cw

6

2

3

D

-

-

     

97

402

45.1

10.48

 

RRVL

228

+

+

v, g, n, pl, ex

cw

6

2

3

D

-

-

     

99

324

36.2

8.24

RRLL

RRML

277-301

-

+

cy, er, ch, pl, v

cw

5

2

3

C

+

-

 

F

10

  
  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 transcript 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 apaical meristem; (S3): stem 3; (S4) stem 4. (RSA): RNAseq shoot apical meristem.
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BMC Genomics

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