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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