Table 1. PIP3-binding proteins identified in at least two experiments, based on affinity-binding capture ratios (Experiments 1 and 2) or genetic evidence (Experiment 3B).
| Proteins | Genes | MW (kDa) | Expt. 1 Bound to | Expt. 2 Memb. Prot. Bound to N2 | Expt. 3A Membranes | Expt. 3B, PIP3-Binding, from 3A | Description | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PIP3 | PIP2 | PIP3 | PIP2 | N2 | mg44 | mg+P | N2 | mg44 | mg+P | ||||
| AKT-1, Ser/Thr protein kinase | akt-1* | 62 | 14 | 0 | 11 | 0 | 0 | 0 | 0 | 2 | 1 | 2 | Pleckstrin Homol. Domain for PIP3 |
| Muscle M-line assembly protein | unc-89 | 894 | 5 | 2 | 1 | 0 | 36 | 20 | 27 | 3 | 0 | 0 | Pleckstrin Homol. Domain, PIP2/3 |
| 14-3-3 proteins | par-5**, ftt-2** | 28 | 8 | 0 | 35 | 16 | 87 | 72 | 89 | 2 | 0 | 5 | Likely PHDs binding PIP2 or PIP3 |
| Disorganized muscle protein 1 | dim-1 | 72 | 3 | 1 | 2 | 2 | 17 | 13 | 14 | 6 | 0 | 0 | Associates with a PHD protein |
| Vitellogenins 2, 3, 5, 6 | vit-2*,-3*,-5*,-6* | 186+ | 76 | 8 | 661 | 398 | 4054 | 4512 | 6333 | 233 | 69 | 159 | LDLs related to ApoB100 |
| HSP chaperones: HSP70C, HSP70D, HSP60; DAF21/HSP90 | hsp-3+, -4+, -60+; daf-21+ | 73,72, 60,80 | 26 | 0 | 41 | 18 | 248 | 142 | 183 | 9 | 0 | 1 | Chaperonins req'd for misfolded proteins; HSP-60 is mitochondrial |
| HSP70A | hsp-1 | 70 | 18 | 12 | 38 | 27 | 69 | 51 | 58 | 5 | 0 | 1 | |
| V-type proton ATPase s.u.’s+ | vha-12+, -13+, -15 | 55-66 | 19 | 0 | 26 | 13 | 124 | 90 | 97 | 11 | 2 | 4 | Vacuole H+-translocating ATPase |
| Fatty-acid binding proteins | far-1, −2; lbp-6* | 16-20 | 5 | 0 | 3 | 3 | 30 | 22 | 47 | 0 | 0 | 0 | Lipid transporters; lbp-6 KD is LL |
| Tubulin alpha-2, beta-2 chains | tba-2+, tbb-2+ | 50 | 15 | 3 | 38 | 35 | 104 | 88 | 95 | 1 | 0 | 0 | Structural protein |
| Protein disulfide isomerase 2 | pdi-2+ | 55 | 4 | 0 | 5 | 1 | 86 | 73 | 75 | 3 | 0 | 0 | Role in ER folding oxidized-prots |
| rRNA 2′-O-methyltransferase | fib-1 | 36 | 3 | 0 | 3 | 3 | 35 | 6 | 13 | 0 | 0 | 0 | Fibrillarin, part of U3 SnoRNP |
| Lamin-1 | lmn-1** | 64 | 2 | 0 | 4 | 0 | 6 | 1 | 5 | 0 | 0 | 0 | Nuclear envelope structural prot |
| T-complex protein 1 s.u. ϵ | cct-5+ | 59 | 1 | 0 | 15 | 4 | 20 | 1 | 6 | 0 | 0 | 0 | Chaperonin complex |
| Alpha Enolase | enol-1+,*,** | 47 | 1 | 0 | 9 | 3 | 50 | 29 | 43 | 0 | 0 | 0 | RNAi alters LS, reduces aggreg'n |
| Adenosylhomocysteinase | ahcy-1+ | 48 | 11 | 1 | 23 | 15 | 72 | 24 | 48 | 2 | 0 | 0 | Interacts w. CCT, UBA-1, UBQ-2 |
| Pyruvate carboxylase 1 | pyc-1** | 129 | 35 | 10 | 32 | 28 | 46 | 39 | 57 | 39 | 37 | 43 | Reg. enz. for gluc & lipid metab. |
| Methylcrotonoyl-CoA carbox.β | F02A9.4 | 67 | 54 | 25 | 59 | 52 | 12 | 7 | 11 | 32 | 17 | 22 | Function predicted, not proven |
| 60S ribosomal proteins | rpl-4, 5, 7–10, 20, 36 | 12-39 | 51 | 1 | 79 | 63 | 624 | 344 | 454 | 75 | 9 | 12 | Other 60S proteins not PIP3-spec. |
| 40S ribosomal proteins | rps-7, 12, 13, 19,23,25 | 13-22 | 16 | 1 | 0 | 0 | 213 | 107 | 149 | 42 | 5 | 7 | Other 40S proteins not PIP3-spec. |
| Cullin-associated, NEDD8-dissociated protein 1 | cand-1* | 70 | 1 | 0 | 0 | 0 | 6 | 0 | 3 | 14 | 10 | 0 | Assembles SCF (SKP1-CUL1-F-box) /E3-ubiquitin ligase complexes |
| Rad-50 | rad-50 | 150 | 1 | 0 | 1 | 0 | 5 | 3 | 3 | 15 | 6 | 13 | HR-directed DNA DS-break repair |
| Translationally-controlled tumor protein homolog | tct-1 | 21 | 1 | 0 | 1 | 0 | 15 | 1 | 2 | 28 | 20 | 14 | ER protein needed in developm't, growth, locomotion, reproduction |
| Dynein heavy chain, cytoplasm | dhc-1 | 522 | 11 | 6 | 0 | 1 | 34 | 3 | 1 | 188 | 77 | 117 | Places microtubule organizing ctr |
| Peroxiredoxin | prdx-3 | 25 | 1 | 0 | 1 | 1 | 5 | 0 | 4 | 15 | 17 | 26 | Oxidative-stress response |
| Acetyl-coA acetyltransferase, mit. | kat-1 | 42 | 0 | 0 | 0 | 0 | 14 | 1 | 0 | 16 | 9 | 13 | Fatty-acid β-oxidation, via Sir2 |
| Proteasome α subunits | pas-1,-3,-5,-6,-7 | 28 | 1 | 0 | 10 | 2 | 17 | 11 | 17 | 7 | 5 | 6 | Proteasome structural/regul. SU's |
| Fatty acid desaturases | fat-1,-2*,-4*,-6,-7 | 39-52 | 0 | 0 | 0 | 0 | 63 | 1 | 3 | 0 | 0 | 0 | These proteins (8 lipid biosynthesis enzymes, 2 MDR proteins, and 1 intermediate filament protein) are found ONLY in membrane preps & have very high N2/mg44 ratios |
| Fatty acid elongases | elo-3, −4, −5 | 32-38 | 0 | 0 | 0 | 0 | 18 | 1 | 0 | 0 | 0 | 0 | |
| Multidrug resistance proteins | pgp-1, pgp-3 | 140+ | 0 | 0 | 0 | 0 | 25 | 1 | 5 | 0 | 0 | 0 | |
| Intermediate filament protein | Ifb-1 | 67 | 0 | 0 | 3 | 4 | 18 | 0 | 7 | 0 | 0 | 0 | |
Related proteins that behaved similarly have been grouped together as indicated. Expt. 1: Worm (N2) proteins, recovered after affinity binding to PIP2- or PIP3-coated beads, were electrophoresed on polyacrylamide/SDS gels, and identified from trypsin-digested gel slices by LC-MS/MS proteomics. Expt. 2: Membrane proteins were isolated from wild-type worms (N2), and associated proteins were recovered using a detergent that dissociates protein complexes (unlike Expts. 1 and 3). Expt. 3A: Membrane proteins were isolated from wild-type worms (N2), a PI3K-null mutant (mg44) or mg44 adults fed PIP3. Expt. 3B: Proteins from 3A were bound to PIP3-beads, eluted, resolved by electrophoresis, and identified from trypsin-digested gel slices by LC-MS/MS proteomics. Spectral counts are shown, indicating the number of significant peptide identifications per protein, a crude measure of relative protein abundance. Deep yellow highlighting indicates ratios of ≥5; lighter yellow indicates suggestive differences. *RNAi knockdown extends lifespan; **RNAi reduces lifespan; †RNAi alters protein aggregation.