Yeast strains used
| Yeast strain | Description | Use | Source |
| BY4742 | MATα his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Throughout | Brachmann et al., 1998 |
| SF838-9D | MATα leu2-3,112 ura3-52 his4-519 ade6 pep4-3 | Fig. S2 D | Raymond et al., 1992 |
| SEY6210 | MATα leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Throughout | Banta et al., 1988 |
| PLY3909 | MATα hse1Δ::TRP1 vps27Δ::LEU2 ura3-52 his3-Δ200 lys2-801 suc2-Δ9 pep4 | Fig. 1 D | This study |
| PLY1776 | MATα vps27Δ::LEU2 leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Fig. S1 B | This study |
| PLY2858 | MATα vps27Δ::LEU2 ura3-52 his3-Δ200 lys2-801 suc2-Δ9 pep4 | Fig. S1 B | This study |
| GW004 | MATα rsp5Δ::LEU2, pRS416-RSP5 leu2-3112,ade2-,his3-11,trp1-1,can1-100; derived from W303 | Fig. 2 D | Wang et al., 1999 |
| PLY441 vpl23-5 (vps27Δ) | MATα leu2-3,112, ura3-52, his4, ade6 vpl23-5 (vps27Δ) pep4-3 | Fig. S2 D | Raymond et al., 1992 |
| BY4742 YOR124C | MATα ubp2Δ:: Kanr his3Δ0, leu2ΔO, lys2ΔO, uraΔO | Fig. 1 C | Winzeler et al., 1999 |
| PLY3827 | MATα ubp2Δ:: Kanr vps27Δ::HIS3 leu2ΔO, lys2ΔO, uraΔO | Fig. 1 D | This study |
| RH1800 | MATa leu2 his4 ura3 bar1 | Fig. 2 A | Munn et al., 1999 |
| LHY23 | MATa rsp5-1 leu2 ura3 his3 trp1 lys2 bar1 GAL | Fig. 2, A and C | Dunn and Hicke, 2001 |
| KLY201 | MATα end3Δ::Kanr his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Figs. 3 D and S2 F | Liu et al., 2007 |
| BY4742 YJL204C | MATα rcy1Δ::Kanr his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 3 E | Winzeler et al., 1999 |
| vpl4-21 | MATα vps4Δ leu2-3,112, ura3-52, his4, ade6 (SF838-9D) | Fig. 3 E | Raymond et al., 1992 |
| PLY3623 | MATα mvb12Δ vps36-ΔNZF::TRP1::vps36Δ::HIS vps23-ΔUb (F52Q117W125) leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Fig. 5 A | Shields et al., 2009 |
| BY4742 YCL008C | MATα vps23Δ:: KanR his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 5 C | Winzeler et al., 1999 |
| BY4742 YHL002W | MATα hse1Δ::KanR his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 5 B | Winzeler et al., 1999 |
| EN67 | MATa ecm21::G418 csr2::G418 bsd2 rog3::natMX rod1 ygr068c aly2 aly1 ldb19 ylr392c bul1 bul2::HIS his3 ura3 leu2 | Figs. 2 B and S1C | Nikko and Pelham, 2009 |
| SUB492 | MATa lys2-801 leu2-3, 112 ura3-52 his3-200 trp1-1[am] ubi1-1::TRP1 ubi2-2::ura3 ubi3-Δ ubi4-Δ::LEU2 [pUB39][pUB100]; pUB39 is 2µ plasmid with CUP1-Ub (wild type); pUB100 the is plasmid that expresses RPL40A tail | Fig. 2 E | Spence et al., 1995 |
| SUB493 | Isogenic to SUB492 except pUB197 replaces pUB39; pUB197 is 2µ plasmid with CUP1-Ub (K63R) | Fig. 2 E | Spence et al., 1995 |
| PLY3378 | MATα end3::KANR gga1Δ::TRP1 gga2Δ::HIS3 | Fig. S2 F | Bilodeau et al., 2004 |
| Yeast strain | Description | Use | Source |
| BY4742 | MATα his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Throughout | Brachmann et al., 1998 |
| SF838-9D | MATα leu2-3,112 ura3-52 his4-519 ade6 pep4-3 | Fig. S2 D | Raymond et al., 1992 |
| SEY6210 | MATα leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Throughout | Banta et al., 1988 |
| PLY3909 | MATα hse1Δ::TRP1 vps27Δ::LEU2 ura3-52 his3-Δ200 lys2-801 suc2-Δ9 pep4 | Fig. 1 D | This study |
| PLY1776 | MATα vps27Δ::LEU2 leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Fig. S1 B | This study |
| PLY2858 | MATα vps27Δ::LEU2 ura3-52 his3-Δ200 lys2-801 suc2-Δ9 pep4 | Fig. S1 B | This study |
| GW004 | MATα rsp5Δ::LEU2, pRS416-RSP5 leu2-3112,ade2-,his3-11,trp1-1,can1-100; derived from W303 | Fig. 2 D | Wang et al., 1999 |
| PLY441 vpl23-5 (vps27Δ) | MATα leu2-3,112, ura3-52, his4, ade6 vpl23-5 (vps27Δ) pep4-3 | Fig. S2 D | Raymond et al., 1992 |
| BY4742 YOR124C | MATα ubp2Δ:: Kanr his3Δ0, leu2ΔO, lys2ΔO, uraΔO | Fig. 1 C | Winzeler et al., 1999 |
| PLY3827 | MATα ubp2Δ:: Kanr vps27Δ::HIS3 leu2ΔO, lys2ΔO, uraΔO | Fig. 1 D | This study |
| RH1800 | MATa leu2 his4 ura3 bar1 | Fig. 2 A | Munn et al., 1999 |
| LHY23 | MATa rsp5-1 leu2 ura3 his3 trp1 lys2 bar1 GAL | Fig. 2, A and C | Dunn and Hicke, 2001 |
| KLY201 | MATα end3Δ::Kanr his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Figs. 3 D and S2 F | Liu et al., 2007 |
| BY4742 YJL204C | MATα rcy1Δ::Kanr his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 3 E | Winzeler et al., 1999 |
| vpl4-21 | MATα vps4Δ leu2-3,112, ura3-52, his4, ade6 (SF838-9D) | Fig. 3 E | Raymond et al., 1992 |
| PLY3623 | MATα mvb12Δ vps36-ΔNZF::TRP1::vps36Δ::HIS vps23-ΔUb (F52Q117W125) leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 mel | Fig. 5 A | Shields et al., 2009 |
| BY4742 YCL008C | MATα vps23Δ:: KanR his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 5 C | Winzeler et al., 1999 |
| BY4742 YHL002W | MATα hse1Δ::KanR his3Δ0 leu2Δ0 lys2Δ0 ura3Δ0 | Fig. 5 B | Winzeler et al., 1999 |
| EN67 | MATa ecm21::G418 csr2::G418 bsd2 rog3::natMX rod1 ygr068c aly2 aly1 ldb19 ylr392c bul1 bul2::HIS his3 ura3 leu2 | Figs. 2 B and S1C | Nikko and Pelham, 2009 |
| SUB492 | MATa lys2-801 leu2-3, 112 ura3-52 his3-200 trp1-1[am] ubi1-1::TRP1 ubi2-2::ura3 ubi3-Δ ubi4-Δ::LEU2 [pUB39][pUB100]; pUB39 is 2µ plasmid with CUP1-Ub (wild type); pUB100 the is plasmid that expresses RPL40A tail | Fig. 2 E | Spence et al., 1995 |
| SUB493 | Isogenic to SUB492 except pUB197 replaces pUB39; pUB197 is 2µ plasmid with CUP1-Ub (K63R) | Fig. 2 E | Spence et al., 1995 |
| PLY3378 | MATα end3::KANR gga1Δ::TRP1 gga2Δ::HIS3 | Fig. S2 F | Bilodeau et al., 2004 |