Table 1.
Phosphopeptides of Arabidopsis RNA metabolism proteins
| Gene IDa | Protein name | Peptide sequence | Sites | Xcorrb | Confirmed by MS3 | Process involved |
|---|---|---|---|---|---|---|
| SR proteins | ||||||
| At3g49430 | SRp34a | pSRSPpSKpSPPK | 3 | 2.47 | Pre-mRNA splicing | |
| At3g61860 | RSp31 | ARpSPEYDRc | 1 | 2.31 | Yes | Pre-mRNA splicing |
| RpSLpSPVYRc | 2 | 2.50 | ||||
| At4g25500 | RSp40/SRp35 | SRpSPRpSPPADEd | 2 | 2.32 | Pre-mRNA splicing | |
| At5g52040 | RSp41 | ARLpSPDYK | 1 | 2.61 | Pre-mRNA splicing | |
| GEpSRpSPPPYEK | 2 | 2.72 | ||||
| GEpSRpSPPPYEKR | 2 | 2.84 | ||||
| pSKSSPENGQVEpSPGQIMEVEAGR | 2 | 3.25 | ||||
| At5g52040.1 | RSp41 splice variant 1 | GYDGADpSPIREpSPSRpSPPAEE3 | 3 | 3.83 | Yes | |
| At4g31580 and/or At2g24590 | SRZ22/RSZ22 and/or RSZ22a | ARpSPPPPR | 1 | 2.27 | Pre-mRNA splicing | |
| At3g53500 | RSZ32 | KVIDApSPK | 1 | 2.23 | Yes | Pre-mRNA splicing |
| DQSLpSPDRK | 1 | 2.12 | ||||
| At2g37340 | RSZ33 | NSVVpSPVVGAGGDSSK | 1 | 3.73 | Yes | Pre-mRNA splicing |
| MDDpSLpSPR | 2 | 2.56 | ||||
| IIDGpSPPPSPK | 2 | 2.80 | Yes | |||
| DRpSPVLDDEGpSPK | 2 | 4.04 | Yes | |||
| SPVLDDEGpSPK | 1 | 2.55 | Yes | |||
| At5g64200 | SC35 | KVDAASRpSQpSPYAAEd | 2 | 2.63 | Yes | Pre-mRNA splicing |
| SNERpSPpSPGpSPAPLR | 3 | 3.11 | Yes | |||
| At1g55310 | SR33/SCL33 | SRpSGDYYpSPPPR | 2 | 2.44 | Yes | Pre-mRNA splicing |
| At3g55460 | SCL30 | GRpSPPPPPPR | 1 | 2.56 | Yes | Pre-mRNA splicing |
| SRpSYpSPAPR | 2 | 2.04 | Yes | |||
| SRpSVEVpSPR | 2 | 2.84 | Yes | |||
| RpSYpSPGYEGAAAAAPDR | 2 | 3.64 | Yes | |||
| pSYpSPGYEGAAAAAPDR | 2 | 2.26 | ||||
| RYpSPPYYpSPPR | 2 | 2.62 | Yes | |||
| YpSPPYYpSPPR | 2 | 2.59 | ||||
| At3g13570 | SCL30a | HQpSRpSVpSPQDR | 3 | 2.72 | Pre-mRNA splicing | |
| GYNpSPPAKR | 1 | 2.16 | ||||
| At1g16610 | SR45 | GRpSPPPPPSK | 1 | 3.05 | Yes | Pre-mRNA splicing |
| GRpSPpSSPPPR | 2 | 2.35 | Yes | |||
| VpSSPPKPVSAAPK | 1 | 3.17 | ||||
| RS domain | ||||||
| At1g07350.1 | Tra-2-like protein splice variant 1 | DRpSYpSPYYR | 2 | 2.50 | Pre-mRNA splicing | |
| DRpSPYYMR | 1 | 2.39 | ||||
| DRpSYpSPHYQGR | 2 | 2.09 | ||||
| At3g63400 | CypRS64 | NFpSPGDVSDR | 1 | 2.03 | Pre-mRNA splicing | |
| At3g63400.1 | CypRS64 splice variant 1 | SFRpSPpSPSGVPK | 2 | 2.48 | Yes | |
| At2g29210 | HsSRm160-like | NRpSPpSPLYR | 2 | 2.08 | Pre-mRNA splicing | |
| RpSPpSPLYR | 2 | 2.17 | ||||
| HTpSPSHIKQDGpSMpSPVR | 3 | 2.91 | ||||
| LPpSPPVAQRLPpSPPPR | 2 | 3.11 | ||||
| LPpSPSIEQR | 1 | 2.33 | ||||
| RNA helicases | ||||||
| At1g32490 | DEAH box RNA helicase | SGQpSDEpSDGEVAVR | 2 | 3.27 | Yes | Pre-mRNA splicing |
| At5g08610 | DEAD box RNA helicase (RH26) | GKFTpSDEDNADPEVVR | 1 | 4.10 | Unknown | |
| GKFpTpSDEDNADPEVVR | 2 | 3.52 | Yes | |||
| FTpSDEDNADPEVVR | 1 | 3.56 | ||||
| Other | ||||||
| At1g04080 | Similar to yeast PRP39 splicing factor | SQVDGSTEQpSPK | 1 | 3.18 | Yes | Pre-mRNA splicing |
| At4g17720 | RRM-containing protein | VHLSEpSPK | 1 | 2.17 | Yes | Unknown |
| At5g04430 | NOVA-like RNA-binding protein | RpSPEPHDSSEADSAEKPTHIR | 1 | 5.20 | Pre-mRNA splicing | |
| pSPEPHDpSSEADSAEKPTHIR | 2 | 3.05 | ||||
| At5g48650 | NTF2-containing RNA-binding protein | DKFGVPAVSLPpSPK | 1 | 2.49 | Yes | Nucleocytoplasmic transport |
| At5g51300 | Splicing factor 1 (SF1)-like | MLQSGMPLDDRPEGQR pSPpSPEPVYDNMGIR | 2 | 4.39 | Pre-mRNA splicing | |
aTAIR database entry. Phosphorylation sites are indicated by a lower case ‘p’ preceeding the phosphoamino acid. Unambiguous sites are indicated in boldface, and ambiguous pSer sites are indicated in italics.
bOf the assigned peptide.
cFound to be phosphorylated in vitro by SRPK4 (Figure 6).
dC-terminus of the protein.