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Table 1 Major proteins (≥ 0.2% of total in at least two fractions) of the Haliotis laevigata shell

From: In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix

Protein

Accession

Abundance (% of total)a

Predicted domainsb and other features

Refc

  

NAS

NBS

NCS

NAI

NBI

NCI

PAS

PBS

PAI

PBI

 

Actin(s)

Tri_131427,

Comp103470_c1_ seq20_6

0.05

0.14

0.03

0.1

0.26

0.34

0.01

0.10

0.17

0.32

  

Similar to tyramine beta-hydroxylase/temptin

idb_10968,

Comp112534_c0_seq1_2

0.26

0.17

0.22

0.09

0.06

0.05

–

–

–

–

SSP, IDR (C-term); R/G

 

Uncharacterized

Comp128817_c0_seq1_3, idb_42198

–

0.01

0.02

–

–

–

0.01

–

0.48

0.30

hirudin_antistatin, IDR; P

 

Uncharacterized

Comp49273_c0_seq1_2, idb_46434

0.01

0.02

0.11

–

0.01

0.05

0.45

0.09

1.03

0.49

SSP, IDR; N/Q/S

 

Uncharacterized/similar to putative ferric-chelate reductase 1-like

Tri_28544,

Comp59223_c0_seq1_2

0.29

0.22

0.01

2.42

1.63

1.25

–

–

0.03

0.02

SSP, reelin, DOMON, IDR

 

Uncharacterized

Tri_111928,

Comp64272_c0_seq1_3

0.02

0.03

0.01

0.01

0.05

0.13

0.04

–

3.84

4.43

SSP

 

Similar to perlustrin

Comp70759_c0_seq1_2

0.31

0.40

1.39

–

–

0.30

1.18

0.53

6.04

8.71

SSP, Growth_fac _rcpt/IGFBP; IDR

 

BPTI/Kunitz domain-containing protein (KCP)

CLC_148, CLC_77,

Comp84928_c0_seq1_4

0.41

0.54

0.45

2.05

2.82

3.65

–

–

0.72

0.60

SSP, Kunitz_ BPTI; R/C/G/L

[21]

Similar to aragonite protein AP24

CLC_1642,

Comp85674_c0_seq1_1, Comp85674_c0_ seq2_1

0.23

0.17

0.19

0.41

0.25

0.34

–

–

0.09

0.10

TM; IDR

[17]

Similar to endochitinase

CLC_4146,

Comp87152_c0_seq1_4

0.03

0.06

0.03

–

0.05

0.06

0.01

–

1.96

1.45

SSP, VWA, chitin-bd_II (2×)

 

Uncharacterized

Comp88250_c0_seq2_2

0.06

0.11

0.04

6.10

2.35

1.68

0.01

–

0.03

0.02

TM; IDR

 

Uncharacterized

CLC_12027, idb_54497

5.30

6.70

11.7

0.21

0.59

0.75

–

–

0.40

0.09

SSP,TM; IDR, G/M/P; repeats (Additional file 27: Figure S2A)

 

Similar to tyrosinase

CLC_123, idb_32947

0.05

0.02

0.02

0.81

0.79

0.68

0.03

–

0.14

0.13

SSP; tyrosinase_ Cu-bd, IDR; G; repeats (Additional file 27: Figure S2B)

 

Lustrin A (in several fragments)

CLC_1320 etc

0.15

0.41

0.26

0.61

1.19

0.77

0.09

0.01

0.04

0.01

SSP, Cys_repeats, IDR; C/P; repeats (PPA)7

[13]

Similar to ependymin-related protein 1

CLC_160

–

–

–

–

–

–

–

–

0.73

3.13

SSP, ependymin

[21]

Similar to ependymin-related protein 1

CLC_1876

–

–

–

–

–

–

–

–

0.33

0.58

Ependymin; L/S

[21]

Similar to glycine-, alanine- and asparagine-rich protein (GAAP)

Tri_107535, CLC_21

0.08

0.07

0.03

0.78

0.47

2.72

0.74

0.26

0.53

0.51

IDR; A/G/S; repeats (Additional file 27: Figure S2C)

[21]

Similar to glutamine-rich protein (QRP)

CLC_253

–

–

–

0.80

0.46

0.28

–

–

–

–

IDR; Q; repeats (Additional file 27: Figure S2D)

[21]

Uncharacterized/hasina

P0014F12_631

CLC_303

0.09

0.07

0.04

0.64

0.62

1.14

0.01

–

0.09

0.08

Chitin-bd_II (3×), ConA-like; IDR, repeats (Additional file 27: Figure S2E)

[22]

Uncharacterized protein 3 (UP3)

CLC_39

21.98

17.96

20.86

10.19

17.96

4.78

0.13

0.06

0.66

0.75

SSP, IDR; A/L/P; repeats: aa26–52 (GPPPGA[A,V]LR)3

[21]

Similar to cartilage matrix protein/ML7A11

CLC_4, Tri_11338

5.54

6.25

8.68

5.38

6.25

10.33

–

–

1.06

1.03

SSP; IDR, N/D/G; repeats (Additional file 27: Figure S2F)

[22]

Uncharacterized

Tri_33510, CLC_62

0.85

0.87

1.24

4.51

5.63

6.13

0.16

0.23

0.04

0.02

SSP; IDP, Q/G/P; repeats (Additional file 27: Figure S2G)

 

Uncharacterized

CLC_73, idb_17035,

Tri_121458

6.21

7.00

6.33

0.51

0.69

0.66

0.06

0.02

0.41

0.38

IDR; G/P/S; repeats (Additional file 27: Figure S2H)

 

Uncharacterized

idb_16318

0.45

0.09

0.28

0.17

0.04

0.08

–

–

–

–

P/V

 

Uncharacterized/similar to mucin

idb_18725

0.03

0.07

0.12

–

–

0.03

2.26

0.67

0.84

1.38

IDP; A/Q/S/T; repeats (Additional file 27: Figure S2I)

 

Uncharacterized protein 5 (UP5)

idb_50884, idb_18,771, idb_18,767

0.57

0.61

0.12

0.86

3.79

2.69

0.05

–

0.63

0.34

SSP,

methyltransf_FA

[21]

Ependymin-related protein (1)

idb_19681

0.01

0.01

–

–

–

–

0.02

–

5.30

4.89

SSP, ependymin,

[21]

Uncharacterized

idb_20008

0.16

0.17

0.45

0.04

0.05

0.15

0.63

0.21

1.57

1.18

SSP; IDP; Q/G/P; repeats (Additional file 27: Figure S2J)

 

Similar to shell protein 4/aplysianin-A

idb_20988

0.01

0.01

0.01

0.22

0.32

0.42

–

–

0.81

0.71

amine_oxidase

[21]

Similar to ependymin-related protein 1

idb_22001

0.10

0.06

0.10

0.02

0.01

0.16

–

–

0.48

2.80

Ependymin; T

[21]

Uncharacterized

idb_22086, idb_ 22,087, idb_42421

0.06

–

0.04

1.12

1.14

1.68

0.01

0.01

0.09

0.06

pI 3.3, IDP, D; repeats (Additional file 27: Figure S2K)

 

Uncharacterized

Tri_117880, idb_23862

0.01

0.03

0.14

–

0.03

0.06

10.15

9.94

0.48

1.19

pI 3.9; IDP, A/S/T; repeats (Additional file 27: Figure S2L)

 

Ependymin-related protein (1)

Tri_31898, idb_24481

0.05

0.06

0.05

–

–

–

0.20

0.03

7.76

3.13

SSP, ependymin, V

[21]

Uncharacterized

idb_25730

0.05

0.10

0.02

0.21

0.41

0.13

–

–

–

–

VWA, TSP1, chitin-bd_II (2×), ConA_like; G/T; repeats (Additional file 27: Figure S2M)

 

Similar to peroxidase-like

idb_25746

0.11

0.19

0.14

0.84

1.60

2.07

0.02

0.02

2.81

2.93

SSP, peroxidase_ 3; IDR

 

Uncharacterized/similar to zinc transporter

idb_26030

0.35

0.25

0.05

1.10

0.60

0.32

–

–

–

–

SSP, TM, zinc/iron_per-mease, IDR

 

Uncharacterized

idb_26568, idb_26567

0.01

0.03

0.07

–

–

0.01

0.44

0.07

0.39

0.25

SSP, IDP, N/Q/P/S; repeats (Additional file 27: Figure S2N)

 

Uncharacterized

idb_26836

–

–

0.10

–

–

–

0.94

0.34

0.23

0.33

IDP; S/T; repeats (Additional file 27: Figure S2O)

 

Uncharacterized

idb_27355

0.05

0.11

0.39

0.01

0.01

0.07

1.93

1.81

2.91

5.54

SSP, IDP; A/Q/S/T; repeats (Additional file 27: Figure S2P)

 

Uncharacterized

idb_27864

–

–

–

–

–

–

9.47

16.53

0.57

0.26

pI 4.1, IDP, A/Q/S/T; repeats (Additional file 27: Figure S2Q)

 

Uncharacterized

idb_27866

0.02

0.10

0.11

–

–

–

19.70

22.06

0.80

0.84

pI 4.5, IDP,A/G/S/T; repeats (Additional file 27: Figure S2R)

 

Uncharacterized

idb_32603, idb_32602

0.02

0.08

0.14

–

–

0.06

6.05

3.21

1.81

2.05

SSP; IDP; Q/P/S; repeats (Additional file 27: Figure S2S)

 

Uncharacterized protein 2 (UP2)

idb_34528

0.74

0.82

1.18

0.09

0.21

0.40

–

–

0.07

0.4

SSP/TM; IDP, A/L/P; repeats

[21]

Uncharacterized

idb_3591

0.59

0.62

0.90

0.23

0.32

0.35

0.01

0.01

0.03

0.01

SSP; IDP, G/S

 

Uncharacterized

idb_36583

0.01

0.04

0.17

–

0.01

0.05

4.32

4.03

0.99

0.74

IDP, G/S/T; repeats (Additional file 27: Figure S2T)

 

Similar to ependymin-1/2

idb_40080

–

–

–

–

–

–

–

–

0.56

0.59

Ependymin; T/V

[21]

Uncharacterized/similar to basic proline-rich protein/methionine-rich protein (MRP; aa162–270)

idb_4071

0.60

0.44

0.50

0.09

0.17

0.18

0.01

–

0.09

0.13

pI 5.1; IDP; Q/P; repeats (Additional file 27: Figure S2U)

 

Uncharacterized

idb_43368

0.01

0.02

–

0.40

0.44

1.53

0.51

0.23

0.05

0.05

pI 3.3, IDP, A/Q/G/S; repeats (Additional file 27: Figure S2V)

 

Uncharacterized

idb_44689

0.01

0.03

0.12

0.01

0.03

0.09

7.57

5.40

0.99

1.36

IDP, G/S/T; repeats

(Additional file 27: Figure S2W)

 

Uncharacterized

idb_47306

0.71

0.86

3.25

0.71

0.86

1.22

0.24

0.12

0.24

0.18

SSP; IDP, 46 AQ-repeats in C-term, A/Q/G; pI 4.8 (Additional file 27: Figure S2X)

 

Uncharacterized

idb_51205

–

–

–

–

–

–

17.70

21.70

0.77

0.49

pI 4.0, IDP, repeats; A/Q/S/T (Additional file 27: Figure S2Y)

 

Uncharacterized

idb_5218

0.98

1.38

0.97

0.33

0.46

0.32

–

–

0.02

0.01

  

Similar to ependymin-related protein (2)

idb_52687

0.01

0.02

–

–

0.02

–

0.05

0.02

3.06

3.94

Ependymin; T

[21]

Uncharacterized

idb_66139

0.14

0.03

–

1.06

0.82

0.34

–

–

0.02

0.06

Repeats: [HQVXL]2 in aa56–65

 

Uncharacterized

Tri_108584

8.64

7.60

8.24

3.32

2.35

2.00

0.09

0.07

0.48

0.45

SSP; IDP, P/S; repeats (Additional file 27: Figure S2Z)

 

Uncharacterized protein 4 (UP4)

Tri_119193

5.84

5.43

5.58

9.74

4.28

3.58

1.62

0.52

0.22

0.19

TM; A/L

[21]

Uncharacterized

Tri_127820

0.45

0.12

0.16

2.00

0.82

0.87

1.26

0.32

–

–

SSP; IDR, G/L/P

 

Similar to carbonic anhydrase

Tri_130845, idb_813

–

–

–

0.02

0.02

0.01

–

–

0.40

0.50

SSP, αCA_2; Q/G

 

Uncharacterized protein 1 (UP1)

Tri_1743

0.13

0.68

0.92

0.03

0.13

0.33

1.02

1.78

12.27

16.68

SSP, IDR; A/Q/L

[21]

Glycin-rich boundary protein

Tri_17455, Tri_2746

3.43

3.42

1.03

0.83

3.51

2.69

0.01

–

0.25

0.18

SSP/TM; IDR, A/Q; aa176–203 similar to [G-MGA] 7, aa96–123 [QQQA]7

 

Uncharacterized/similar to AP7

Tri_24151

4.02

2.23

0.24

1.51

1.33

0.87

–

0.02

0.04

0.20

SSP

[17]

Uncharacterized/similar to shell protein 4/

ML3D4

Tri_25106

0.07

0.07

0.04

1.19

3.16

2.44

0.02

0.01

3.35

1.71

SSP

[21]

Uncharacterized

Tri_29101

0.07

0.05

0.05

0.70

1.08

1.59

–

–

0.04

0.02

RmlC-like_jelly_ roll_fold, IDR, A/S/T; repeats (Additional file 27: Figure S2Za)

 

Ependymin-related protein (1)

Tri_31892

Comp22593_c0_seq1_3

0.50

1.10

2.11

0.04

0.11

0.42

0.41

0.10

13.92

9.71

SSP, ependymin,

[21, 103]

Similar to ependymin-related protein (1)

Tri_31897

0.03

0.01

–

–

–

–

–

–

2.76

1.57

SSP, ependymin

[21]

Uncharacterized

Tri_35519

0.18

0.15

0.09

0.13

0.14

0.17

–

–

0.61

0.48

ConA_like, TM

 

Uncharacterized

Tri_45070

0.34

0.40

0.58

0.08

0.12

0.17

0.01

0.01

0.01

0.01

IDP; P/S/T

 

Uncharacterized/similar to molluscan shell protein 1/MSI60-related protein/DGRP/P008C13_381

Tri_57798, CLC_5

0.05

0.14

0.13

8.38

4.38

8.64

–

0.83

1.60

1.55

pI 3.5, IDP; A/D/G; repeats (Additional file 27: Figure S2Zb)

[21, 22]

Uncharacterized/similar to ferric-chelate reductase 1

Tri_61496

0.12

0.12

0.09

0.46

0.29

0.63

–

–

0.17

0.12

Reeler, TM, IDR; S

 

Uncharacterized/

similar to putative ferric-chelate reductase 1-like

/ML7B12

Tri_63049

0.43

0.58

0.24

0.35

0.34

0.55

–

–

0.02

0.02

Reeler, IDR; T

[22]

Uncharacterized

Tri_64952

0.20

0.01

0.22

1.47

0.61

0.68

–

–

0.01

–

IDR; R/G/S

 

Carbonic anhydrase

Tri_72839

0.01

–

0.01

0.40

0.21

0.63

–

–

–

0.01

SSP, carbonic_ anhydrase_a; IDR

 

Uncharacterized

Tri_73035

1.38

1.55

1.42

0.77

1.02

1.15

0.02

–

0.06

0.04

TM; IDP, A/G/P

 

Uncharacterized

Tri_81308

0.26

0.32

0.17

0.13

0.16

0.12

–

–

0.02

0.02

  

Perlustrin

PLS_HALLA

0.14

0.49

–

–

2.00

–

–

–

–

–

IGFBP_N; C

[16]

Perlucin(s)

PLC_HALLA

7.44

8.12

0.05

4.36

28.50

8.57

0.03

0.04

2.40

0.14

CLECT

[14]

Perlwapin

PWAP_HALLA

Comp36269_c0_seq1_4

3.77

4.00

2.85

1.76

2.23

1.84

0.02

–

0.80

0.23

WAP; C/G/P

[19, 21]

  1. For more detailed annotations see Additional file 4: Table S2 and Additional file 5: Table S3. SSP predicted signal sequence peptide, TM predicted transmembrane segment, IDR predicted intrinsically disordered sequence regions, IDP predicted intrinsically disordered protein (predicted disorder < 90%), N nacre, P prismatic layer, S acid-soluble, I acid-insoluble: A, B, C, shell cleaning protocols as detailed in Methods. Amino acids constituting > 10% of the overall amino acid composition are indicated by their standard one-letter abbreviation
  2. acalculated from MaxQuant iBAQ intensities; the values are rounded to the second decimal
  3. bdomain abbreviations are those of InterProScan (http://www.ebi.ac.uk/interpro/)
  4. csimilar protein previously identified in Haliotis shell proteome. A complete list of accepted identifications is contained in tables S2 and S3 (Additional files 4 and 5). The quantitatively most important major proteins (abundance > 1.0 in at least two fractions) and abundance percentages > 1.0 are in bold. Figure S2 is contained in Additional file 27