Table 2.
Workflow validation: circadian clock protein orthologs from the reference proteomes to the designated bait/reference proteins, found using OrthoFinder
| Reference | Ref. proteome match |
|---|---|
| Arthropod | |
| CLK (Dm O61735) | Dp: CLK (A0A212EGJ4), Mm: NOT FOUND |
| CYC (Dm O61734) | Dp: CYC (A0A212EKE6) |
| Mm: ARNTL (Q9WTL8), ARNTL2 (Q2VPD4) | |
| TIM (Dm P49021) | Dp: TIM (A0A212ETU4) |
| PER (Dm P07663) | Dp: PER (A0A212F9R2) |
| Mm: PER1 (O35973), PER2 (O54943), PER3 (O70361) | |
| CRY1 (Dm O77059) | Dp: CRY1 (A0A212EI23) |
| CRY2 (Dp A0A212FAM3) | Mm: CRY1 (P97784), CRY2 (Q9R194) |
| PDP1e (Dm Q8SZT1) | Mm: DBP (Q60925), HLF (Q8BW74), TEF (Q9JLC6) |
| VRI (Dm Q9VMS4) | Mm: NFIL3 (O08750) |
| Mammalian | |
| REV-ERBa (Mm Q3UV55) | Dm: EIP75B (P13055) |
| RORa (Mm P51448) | Dm: HR3 (P31396) |
Indicated in the left column are the baits, and in the right their counterparts. Alongside the protein name of the bait and the source organism, the sequence’s UniProt identifier is also indicated. The baits are grouped by the phylogenetic clade they originate from: ‘Arthropod’ baits were all from Drosophila melanogaster, except for CRY2 (from Danaus plexippus); ‘Mammalian’ baits were from Mus musculus. Only one ortholog – CLK from M. musculus (O08785) – was not found. Species: Dm - Drosophila melanogaster, Dp - Danaus plexippus, Mm - Mus musculus. Protein names: CLK (Circadian locomotor output cycles kaput), CYC (Cycle), PER (period), TIM (Timeless), CRY1 (Cryptochrome 1), CRY2 (Cryptochrome 2), PDP1e (PAR Domain Protein 1 epsilon), VRI (Vrille), REV-ERBa (NR1D1/Nuclear Receptor Subfamily 1 Group D Member 1), RORa (RAR Related Orphan Receptor A; NR1F1/Nuclear receptor subfamily 1 group F member 1), NPAS2 (Neuronal PAS Domain Protein 2), ARNTL (Aryl hydrocarbon Receptor Nuclear Translocator-Like protein), DBP (D-box Binding Protein), HLF (Hepatic Leukemia Factor), TEF (Thyrotroph Embryonic Factor), NFIL3 (Nuclear Factor, Interleukin 3 Regulated), EIP75B (Ecdysone-induced protein 75B, isoforms C/D; NR1D3), HR3 (Probable nuclear hormone receptor HR3). PER1, PER2, and PER3 are in-paralogs. ARNTL1 and ARNTL2 are in-paralogs. Note: these orthologs were not used as baits themselves (see text for clarification)