Table 2.
Phosphoproteins with Different Phosphopeptide Abundance in the Cyp46a1−/− Retina Compared with the Wild-Type Retina
| Protein | Peptide sequence | Phosphorylation site | Peptide ratio, KO/WT |
|---|---|---|---|
| Information transfer (gene transcription and translation, mRNA binding, stability, and processing) | |||
| NOLC1 | ESEEEEEEEETEEK | S2 | 8.4 |
| HTATSF1 | EFEEDSDEKEEEGDDDEEEVVYER | S6 | 7.0 |
| PURA | GPGLGSTQGQTIALPAQGLIEFR | T7 | 6.6 |
| PABPC1L2B | DFDDDSDDEATFR | S6 | 5.1 |
| NUCKS1 | EMoLLEDVGSEEEPEEDDEAPFQEK | S9 | 4.3 |
| SRSF10 | SFDYNYR | S1 | 2.5 |
| SRRM2 | SPVPSAFSDQSR | S1 | 2.4 |
| YTHDC1 | GISPIVFDR | S3 | 2.3 |
| GTF2F1 | GTSRPGTPSAEAASTSSTLR | T2, T7 | 2.2 |
| G3BP1 | STSPAPADVAPAQEDLR | S3 | 0.5 |
| LUC7L2 | SEDRRSSEEREAGEI | S6, S7 | 0.3 |
| Neuritogenesis | |||
| GPRIN1 | VRPGSVLAAALAPQEATEPVR | S5 | KO only |
| PCLO | RFSLNLGGIADAPK | S3 | KO only |
| RTN4 | RGSGSVDETLFALPAASEPVIPSSAEK | S3, S5 | KO only |
| RP1L1 | RPASVECLPSVSVPYQVAQK | S4 | KO only |
| BRSK2 | SISGASSGLSTSPLSSPR | S1 | 6.8 |
| AQP4 | SQVETEDLILKPGVVHVIDIDRGEEK | S1 | 3.2 |
| Cytoskeleton maintenance | |||
| SLC9A1 | IGSDPLAYEPK | S3 | KO only |
| TJP1 (ZO-1) | DDISEIQSLASDHSGR | S11, S14 | KO only |
| MARCKS | ESGEGAEAEGATAEGAK | S2 | 11.1 |
| MAP1B | SPCDSGYSYETIEK | S1 | 6.1 |
| DPYSL3 | GGTPAGSTRGSPTRPNPPVR | T3, S7 S11 |
0.4 |
| Membrane vesicle trafficking | |||
| ARFGAP3 | LTNTSFTEIEK | S5 | KO only |
| SYNRG | QLSLEGAGLAMEEFK | S3 | 13.8 |
| TOM1L2 | GIEFPMoADLDALSPIHTPQR | S13, T17 | 4.5 |
| Signal transduction | |||
| CAMKK1 | SFGNPFEPQAR | S1 | KO only |
| PCP2 | VTVNSLPGFQPIGPK | S5 | KO only |
| PCP2 | AGSPDQEGFFNLLTHVQGDR | S3 | 3.0 |
| RAP1GAP | SSAIGIENIQEVQEK | S2 | KO only |
Involvement in only one biological process is indicated for each protein, although many proteins participate in more than one biological process.
AQP4, aquaporin-4 isoform M23A; ARFGAP3, ADP-ribosylation factor GTPase-activating protein 3; BRSK2, brain-specific serine/threonine-protein kinase 2; CAMKK1, calcium/calmodulin-dependent protein kinase kinase 1; DPYSL3, dihydropyrimidinase-related protein 3; G3BP1, Ras GTPase-activating protein-binding protein 1; GPRIN1, G-protein–regulated inducer of neurite outgrowth 1 isoform X1; GTF2F1, general transcription factor IIF subunit 1 isoform X1; HTATSF1, HIV Tat-specific factor 1 homolog; KO, Cyp46a1−/− retina; LUC7L2, putative RNA-binding protein Luc7-like 2; MAP1B, microtubule-associated protein 1B isoform X1; MARCKS, myristoylated alanine-rich C-kinase substrate; Mo, oxidized methionine; NOLC1, nucleolar and coiled-body phosphoprotein 1 isoform B; NUCKS1, nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 isoform 1; PABPC1L2B, polyadenylate-binding protein 1–like 2; PCLO, protein piccolo isoform X4; PCP2, Purkinje cell protein 2 isoform 1; PURA, transcriptional activator protein Pur-α isoform X1; RAP1GAP, rap1 GTPase-activating protein 1 isoform 3; RP1L1, retinitis pigmentosa 1–like 1 protein; RTN4, reticulon-4 isoform A; SLC9A1, sodium/hydrogen exchanger 1 isoform X2; SRRM2, serine/arginine repetitive matrix protein 2; SRSF10, serine/arginine-rich splicing factor 10 isoform 2; SYNRG, synergin γ; TJP1, tight junction protein ZO-1 isoform 2; TOM1L2, target of Myb protein 1 isoform X1; WT, wild-type retina; YTHDC1, YTH domain-containing protein 1 isoform X6; ZO-1, zonula occludens 1.