Table 2.
Differentially phosphorylated proteins during intestine regeneration in sea cucumbers.
| Protein accession | Amino acid | Protein description (Nr database) | Modified sequence | Modified ratio | P-value | Protein expression | |
|---|---|---|---|---|---|---|---|
| Mean | SD | ||||||
| CYTOSKELETAL PROTEINS | |||||||
| Unigene13550_All | S | Tubulin alpha-1B chain-like | S(0.999)IQFVDWCPT(0.001)GFK | 0.517 | 2.43E-02 | 0.756 | 0.007 |
| CL128.Contig5_All | S | Tubulin beta chain-like | AVLVDLEPGTMDS(1)VR | 2.224 | 8.71E-03 | 1.280 | 0.140 |
| S | IMNTY(0.004)S(0.002)VVPS(0.994)PK | 2.199 | 4.27E-02 | ||||
| S | MS(1)MKEVDEQMLNVQNK | 1.512 | 3.23E-03 | ||||
| CL2542.Contig6_All | S | Neural alfa2 tubulin | SFNTFFS(0.001)ET(0.092)GS(0.907)GK | 2.228 | 4.14E-03 | 1.456 | 0.263 |
| CL2946.Contig3_All | S | Unconventional myosin-XVI, partial | KGS(1)IAPSIR | 1.675 | 4.98E-03 | 1.024 | 0.424 |
| CL9013.Contig2_All | T | Plastin 3-like | AFVT(1)PNDIVK | 1.505 | 1.49E-02 | 1.558 | 0.193 |
| Unigene27095_All | S | Myosin-IIIb-like | TGT(0.001)LALQNRIS(0.999)QK | 1.657 | 1.15E-02 | 1.187 | 0.462 |
| Unigene638_All | S | Microtubule-associated protein RP/EB family member 1 | TQIS(1)ELSGELTTAR | 1.612 | 4.29E-02 | 0.549 | 0.256 |
| CL1337.Contig7_All | S | Lethal giant larvae homolog 1-like | S(0.965)S(0.035)SENMISLVR | 1.564 | 4.35E-02 | 0.933 | 0.280 |
| PROTEIN SYNTHESIS AND MODIFICATION | |||||||
| Transcription, RNA processing, and modification | |||||||
| CL9265.Contig2_All | S | CASP-like transcription factor | LDPFNS(1)FSR | 2.454 | 5.63E-03 | 0.919 | 0.180 |
| CL859.Contig2_All | S | Pre-mRNA-processing-splicing factor 8 | AIS(0.995)AT(0.005)NLHLR | 1.724 | 1.59E-02 | 1.243 | 0.170 |
| CL5050.Contig1_All | S | Neuroblast differentiation-associated protein AHNAK-like | GPS(1)LKGGADVEIPSGK | 2.257 | 3.06E-03 | 0.634 | 0.036 |
| Translation, ribosomal structure, and biogenesis | |||||||
| CL1510.Contig1_All | Y | Golgi integral membrane protein 4 | AENELGQQY(1)FLQLR | 3.55 | 6.98E-04 | 1.971 | 0.264 |
| CL11778.Contig2_All | T | Golgi reassembly-stacking protein 2-like | S(0.021)FPET(0.953)PVDLS(0.026)QHMK | 1.683 | 1.51E-02 | 1.706 | 0.117 |
| CL11977.Contig3_All | S | Eukaryotic translation initiation factor 4E binding protein | HEY(0.027)S(0.066)T(0.338)T(0.338)PGGT (0.372)MFS(0.546)T(0.156)T(0.156)PGGT (0.001)R | 0.659 | 9.92E-03 | 0.877 | 0.270 |
| Unigene26560_All | Y | Ribosomal protein S10-like | GPSGPVDSQRDS(0.118)Y(0.882)R | 0.637 | 3.21E-02 | 0.520 | 0.203 |
| CL4911.Contig2_All | S | Methyltransferase fibrillarin-like | VYVEPHRLS(1)GVFIAR | 1.794 | 2.80E-02 | 0.750 | 0.293 |
| CL609.Contig1_All | S | Heterogeneous nuclear ribonucleoprotein U-like protein 1-like | NY(0.019)S(0.002)GRFDS(0.979)LIEK | 1.892 | 8.20E-03 | 0.857 | 0.244 |
| CL7370.Contig4_All | S | Ribosome-binding protein 1-like isoform 2 | EKPGKS(1)PR | 1.91 | 4.75E-03 | 0.385 | 0.131 |
| CL10446.Contig2_All | S | Nucleic acid-associated protein 36 | KRPS(0.886)S(0.057)T(0.057)NDGPAK | 1.933 | 1.70E-02 | 0.428 | 0.216 |
| Unigene8144_All | S | polyA-binding protein | LFS(1)IIQQSHGDVAGK | 1.653 | 4.22E-03 | 0.719 | 0.229 |
| CL6103.Contig1_All | S | Eukaryotic peptide chain release factor GTP-binding subunit ERF3B isoform 2 | T(0.009)VEVGRAS(0.986)FET(0.004)DKK | 1.575 | 4.16E-03 | 1.097 | 0.045 |
| CL9576.Contig3_All | S | mRNA turnover protein 4 homolog | DKKVS(0.933)LT(0.063)ET(0.004)K | 1.547 | 3.37E-02 | 0.637 | 0.286 |
| CL9627.Contig2_All | S | Eukaryotic translation initiation factor 4B-like | RKDNVVS(1)PR | 1.757 | 2.55E-02 | 0.962 | 0.127 |
| Unigene1047_All | S | Putative 60S ribosomal protein RPL15 | QAMS(1)LRR | 1.712 | 4.10E-02 | 1.296 | 0.428 |
| Unigene33503_All | T | 60S ribosomal protein L27-like isoform 1 | DVFREPT(1)LKK | 2.68 | 1.35E-02 | 1.124 | 0.252 |
| Unigene3874_All | S | 40S ribosomal protein S13 | S(1)VPNWLK | 1.695 | 3.23E-03 | 0.659 | 0.171 |
| Unigene46531_All | S | 40S ribosomal protein S27-like isoform 3 | LTEGCS(1)FR | 1.788 | 2.66E-03 | 0.661 | 0.103 |
| Unigene5010_All | S | Nucleosome assembly protein homolog | LDS(1)LVGQR | 1.726 | 8.53E-03 | 0.823 | 0.221 |
| Unigene53143_All | T | Translation initiation factor 2 subunit alpha (AeIF-2a) | KVHQT(1)VR | 1.513 | 2.63E-02 | 0.870 | 0.123 |
| Unigene7928_All | S | Heterogeneous nuclear ribonucleoprotein A1-like | FGS(0.999)VS(0.001)AVK | 1.761 | 2.30E-05 | 0.908 | 0.250 |
| Unigene26544_All | S | Histone H1.0-like | KLS(0.991)ES(0.009)QVK | 1.597 | 9.24E-04 | 0.901 | 0.259 |
| Unigene29854_All | Y | High mobility group protein 1 homolog | NLSAFFLY(1)SNDER | 1.717 | 1.34E-02 | 0.638 | 0.194 |
| Unigene32660_All | S | Heterogeneous nuclear ribonucleoprotein K-like | DLAGS(1)IIGTR | 1.778 | 4.63E-02 | 0.524 | 0.173 |
| Posttranslational modification, protein turnover, chaperones | |||||||
| CL5303.Contig3_All | S | Peroxiredoxin 6-like | AGGDCMVLPS(1)VKAEDIPALFPK | 2.157 | 3.09E-02 | 0.751 | 0.263 |
| Unigene22155_All | S | E3 ubiquitin-protein ligase UBR4, partial | TQATIS(0.002)LAS(0.975)PT(0.019)ERPQS (0.002)S(0.002)QK | 1.563 | 1.80E-02 | 1.059 | 0.495 |
| Unigene25579_All | S | Heat shock protein 75 kDa, mitochondrial-like | LHS(1)FMEK | 1.639 | 1.05E-02 | 0.994 | 0.148 |
| Unigene15415_All | S | Polypeptide N-acetylgalactosaminyltransferase 10-like | AT(0.002)DPVRS(0.998)PIMAGGLFAIDR | 1.871 | 2.79E-02 | 1.205 | 0.058 |
| SIGNAL RECOGNITION AND TRANSDUCTION | |||||||
| CL11595.Contig1_All | S | Tyrosine kinase receptor Cad96Ca-like | IEAISIQS(0.958)S(0.042)K | 0.581 | 4.36E-03 | 0.641 | 0.185 |
| Unigene32568_All | S | TBC1 domain family member 1-like | KHY(0.006)S(0.994)CEDQLDR | 0.591 | 2.15E-02 | 1.870 | 0.883 |
| Unigene9348_All | S | Sterile alpha and TIR motif-containing protein 1-like | VFDS(0.948)PT(0.052)RPK | 0.615 | 4.59E-02 | 1.686 | 0.929 |
| CL6832.Contig3_All | S | Epidermal growth factor receptor substrate 15-like 1-like | DDPFAS(0.911)FS(0.075)S(0.01)S(0.003) S(0.001)K | 1.615 | 1.37E-02 | 1.127 | 0.342 |
| CL7251.Contig2_All | S | TBC1 domain family member 24-like | S(0.26)S(0.737)PQS(0.002)LS(0.001)VPIA | 1.668 | 1.48E-02 | 0.932 | 0.113 |
| Unigene12365_All | S | Putative calcium-binding protein p22 | FIS(0.994)LDKS(0.006)EAGK | 2.775 | 1.95E-02 | 0.833 | 0.144 |
| CL2850.Contig5_All | S | Ras-related GTP binding protein D | MSPNETLFLES(0.955)T(0.045)NK | 1.968 | 1.89E-02 | 1.075 | 0.436 |
| CL3382.Contig2_All | Y | tyrosine-protein kinase HTK16-like | ATGANNDY(0.004)Y(0.996)R | 0.502 | 6.36E-03 | 0.802 | 0.038 |
| CL6145.Contig1_All | Y | Low quality protein: tyrosine-protein kinase Tec-like | YVLDDQY(1)TSSGAR | 0.561 | 3.19E-02 | 1.021 | 0.438 |
| CL12103.Contig1_All | S | Rho guanine nucleotide exchange factor 7-like isoform 1 | ELS(0.001)PNT(0.069)LS(0.931)PR | 1.514 | 1.20E-02 | 1.041 | 0.234 |
| CL5733.Contig2_All | T | Calcium/calmodulin-dependent protein kinase (CaM kinase) II delta-like isoform 1 | QET(1)VDCLKK | 1.802 | 3.72E-02 | 0.557 | 0.101 |
| Unigene15296_All | S | FERM domain-containing protein 5-like | RS(1)GS(1)FILK | 1.511 | 1.53E-03 | 0.768 | 0.051 |
| Unigene3880_All | T | Oryzias latipes 14-3-3 protein beta/alpha-1-like | ADT(1)PKVELNPDELAK | 1.517 | 3.04E-02 | 0.688 | 0.262 |
| Unigene21911_All | T | Spectrin alpha chain, brain-like isoform 2 | QET(1)FDAGLQSFEK | 2.176 | 4.36E-02 | 1.059 | 0.123 |
| CL8872.Contig1_All | Y | Proto-oncogene tyrosine-protein kinase Src | LVKDDHY(1)LAR | 0.467 | 1.58E-02 | 0.825 | 0.007 |
| CL9595.Contig1_All | S | Titin-like | SYPDS(0.009)S(0.008)NVRQS(0.965)PS (0.013)S(0.003)HTR | 0.553 | 5.51E-04 | 1.097 | 0.176 |
| S | RGPADS(1)PIGR | 0.561 | 2.33E-04 | ||||
| Y | RTES(0.002)PS(0.003)Y(0.995)R | 0.627 | 8.89E-03 | ||||
| S | Y(0.007)HDDDRS(0.986)Y(0.007)DR | 0.599 | 3.79E-03 | ||||
| CL5942.Contig1_All | S | PKG | S(0.002)S(0.042)S(0.955)DS(0.001)VEST | 2.483 | 1.29E-03 | 1.416 | 0.418 |
| T | T(0.068)WT(0.924)FCGT(0.008)PEYVAP | 3.490 | 5.03E-03 | ||||
| T | T(0.037)WT(0.349)FCGT(0.614)PEYVAP | 4.720 | 7.11E-03 | ||||
| Unigene270_All | S | Protein kinase, cAMP-dependent, catalytic, beta a-like | IKGPGDTSHFDDYEEEPIRIS(0.905)S(0.073) T(0.022)EK | 2.227 | 1.13E-02 | 0.837 | 0.026 |
| ENERGY PRODUCTION AND CONVERSION | |||||||
| CL2205.Contig3_All | S | ATP-citrate synthase | KPAS(0.998)FMT(0.002)SIVDER | 1.558 | 3.89E-02 | 1.260 | 0.272 |
| Unigene200_All | S | Aldehyde dehydrogenase 3 family, member A2 | PVPS(1)ELVMGIR | 3.812 | 1.89E-02 | 1.289 | 0.257 |
| CL2397.Contig1_All | S | ATP-binding cassette sub-family D member 3-like | RKS(1)T(1)FADLK | 0.463 | 4.36E-02 | 0.708 | 0.103 |
| SUBSTANCE TRANSPORT AND METABOLISM | |||||||
| Amino acid transport and metabolism | |||||||
| CL5840.Contig2_All | S | Glutamine synthetase | GAS(1)IRIPR | 3.302 | 1.54E-03 | 1.128 | 0.212 |
| CL11928.Contig1_All | S | Peroxisomal sarcosine oxidase-like | KNS(1)EPAIIEK | 0.201 | 2.92E-03 | 0.311 | 0.089 |
| CL6111.Contig2_All | S | Protein transport protein Sec31A-like isoform 1 | RPAGAS(1)FGFGGK | 1.749 | 4.75E-03 | 1.710 | 0.400 |
| S | S(0.209)KS(0.79)LEEALS(0.001)QGQFC | 4.286 | 3.36E-02 | ||||
| Unigene32921_All | S | Probable thiopurine S-methyltransferase-like | MFAWCS(0.82)S(0.18)IK | 2.859 | 2.12E-03 | 3.157 | 0.481 |
| Coenzyme transport and metabolism | |||||||
| CL12230.Contig2_All | S | Small ubiquitin-related modifier 3 | VVGS(0.003)EGS(0.947)T(0.05)VQFK | 1.701 | 5.75E-03 | ||
| Unigene29548_All | S | NADH-cytochrome b5 reductase-like | S(0.01)MDY(0.021)T(0.01)S(0.011)CVLDS (0.013)IQAVS(0.645)T(0.645)DT(0.645)F | 0.645 | 2.83E-02 | 1.047 | 0.036 |
| T | S(0.01)MDY(0.021)T(0.01)S(0.011)CVLDS (0.013)IQAVS(0.645)T(0.645)DT(0.645)F | 0.645 | 2.83E-02 | ||||
| T | S(0.01)MDY(0.021)T(0.01)S(0.011)CVLDS (0.013)IQAVS(0.645)T(0.645)DT(0.645)F | 0.645 | 2.83E-02 | ||||
| Lipid transport and metabolism | |||||||
| CL8209.Contig2_All | S | Acetyl-Coenzyme A acyltransferase 2-like | TPFGAFGGS(1)LK | 1.774 | 2.20E-02 | 0.957 | 0.330 |
| CL3144.Contig1_All | S | Oxysterol-binding protein-related protein 11-like | YS(0.012)S(0.976)S(0.011)ESIGGR | 0.635 | 4.01E-02 | 0.802 | 0.072 |
| CL2380.Contig1_All | S | Niemann-Pick type C1 domain-containing protein | HPGS(1)KAQLEDVWEK | 3.795 | 6.02E-04 | 2.317 | 0.276 |
| Inorganic ion transport and metabolism | |||||||
| CL4987.Contig2_All | S | Catalase | LT(0.012)T(0.042)S(0.502)S(0.445)GCPID | 0.624 | 9.00E-03 | 0.881 | 0.100 |
| CL574.Contig3_All | T | Sarco/endoplasmic reticulum calcium transporting ATPase | VGEAT(0.965)ET(0.035)ALTVLVEK | 2.423 | 1.59E-02 | 0.772 | 0.200 |