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T H E J O U R N A L O F C E L L B I O L O G Y Supplemental material Stelter et al., http://www.jcb.org/cgi/content/full/jcb.201105042/dc1 S1

Figure S1. Dyn2 recruitment to edid-labeled FG domain Nups. (A) Schematic drawing of a Nsp1-eDID construct. Insertion of engineered dynein light chain interacting domain (edid) followed by the Flag epitope (tag) and a LoxP site (for recombination) into the Nsp1 FG repeat nucleoporin. edid is composed of six dynein light chain QT binding motifs in a row derived from the dynein intermediate chain Pac11(previously called DID1; Flemming et al., 2010). The amino acid position within the 823-residue-long Nsp1 is indicated, at which edid, Flag, and loxp were inserted. The different domains of Nsp1 are further indicated. (B) Expression of the Nup-eDID constructs and Dyn2 (pgal-dyn2) after 3-h galactose induction. Whole-cell lysates were separated by SDS-PAGE, blotted onto nitrocellulose, and incubated with anti-flag, anti-dyn2, and anti-arc1 (loading control) antibodies. Wild-type cells revealing endogenous Dyn2 expression (lane 1), dyn2 cells + pgal-dyn2 (lane 2), NSP1-eDID + pgal-dyn2 (lane 3), NSP1-eDID(2) + pgal-dyn2 (lane 4), NUP159 DID-eDID + pgal-dyn2 (lane 5), NUP49-eDID + pgal-dyn2 (lane 6), NUP57-eDID + pgal-dyn2 (lane 7), NUP2-eDID+ pgal-dyn2 (lane 8), NUP1-eDID + pgal-dyn2 (lane 9), and NUP116-eDID + pgal-dyn2 (lane 10). (C) Coenrichment of Dyn2 with the indicated Nup-eDID constructs. NUP-eDID dyn2 strains expressing pgal-dyn2 were lysed after 3-h galactose induction before the indicated TAP constructs were affinity purified. NUP49- TAP expressing NSP1-eDID (lane 1) and NUP1-eDID-TAP (lane 2), NUP60-TAP expressing NUP2-eDID (lane 3), NUP82-TAP expressing NUP159 DID-eDID- FG Nsp1 (lane 4), NUP82-TAP expressing NUP159 DID-eDID (lane 5), NUP116-eDID-TAP NUP159 DID (lane 6), and NUP116-eDID-TAP (lane 7). (D) Dyn2-dependent dimerization of modified edid Nups. Affinity purification from strain lysates NIC96-TAP NUP49-eDID (lanes 1 and 2) and NUP82-TAP NUP159-eDID (lanes 3 and 4) in the presence (lanes 2 and 4) or absence of Dyn2 (lanes 1 and 3), which coexpress GFP-Nup82 and GFP-Nic96, respectively. Eluates and homogenates (HOM) were analyzed by SDS-PAGE and Coomassie blue staining or Western blotting (E) Expression levels of NUP159 DIDeDID-FG Nsp1 and NUP159 DID-eDID-FG Nup1 + pgal::dyn2 after 3-h galactose induction. Wild-type cells showing endogenous Dyn2 expression (lane 1), dyn2 cells + pgal::dyn2 (lane 2), dyn2 NUP159 DID cells + pgal::dyn2 (lane 3), dyn2 NUP159 DID-eDID-FG Nsp1 + pgal::dyn2 (lane 4), and dyn2 NUP159 DID-eDID-FG Nup1 + pgal::dyn2 (lane 5). Whole-cell lysates were boiled in SDS sample buffer and analyzed by SDS-PAGE and Western blotting using anti-dyn2, anti-flag, and anti-arc1 (equal loading) antibodies. CBP, calmodulin-binding peptide S2

Figure S2. Analysis of 60S and 40S ribosome export in edid-labeled FG Nups. (A) Nuclear export of the 60S ribosomal subunit. Indicated strains were transferred to YPR medium for 4 h, and Dyn2 expression was induced by the addition of galactose (t 0 ; uninduced) and further incubated for 4 h (induced). Localization of Rpl25-GFP and mrfp-nop1 (nucleolar marker) was analyzed under the fluorescence microscope. (B) Localization of 20S prerna and larger precursors. Indicated strains were transferred to YPR medium for 4 h (uninduced), and Dyn2 expression was induced for additional 2 h by addition of galactose (induced). In situ hybridization using a Cy3 fluorescently labeled oligonucleotide probe complementary to the ITS1 region was performed. DNA was stained with DAPI. Bars, 2 µm. S3

Figure S3. Analysis of growth and nucleocytoplasmic transport of NUP-eDID + pgal-dyn2 strains transformed with the respective wild-type Nups. (A) NUP49-eDID, NUP57-eDID, NSP1-eDID, and NUP1-eDID were either transformed with pgal-dyn2 or pgal-dyn2 + NUP wild type or NUP wild type alone and spotted on SGC-Leu/-Ura and SDC-Leu/-Ura plates. (B) Poly(A) + RNA was analyzed by in situ hybridization with a Cy3-labeled oligo d(t) probe, and DNA was stained with DAPI. Bar, 5 µm. S4

Table S1. Yeast strains used in this study Strains Genotype References RS453 a MATa or ade2 his3-11 15 leu2-3 112 trp1 ura3-52 Grandi et al., 1995 Ds1-2b c MAT leu2-1 trp1-63 his3-200 ura3-52 Baßler et al., 2001 dyn2 b MAT leu2-1 trp1-63 his3-200 ura3-52 dyn2::loxp Nsp1-eDID dyn2 b edid-loxp at position 275 aa dyn2::loxp Nsp1-eDID(2) dyn2 b edid-loxp at position 2 aa dyn2::loxp Nup1-eDID dyn2 b edid-loxp at position 717 aa dyn2::loxp Nup2-eDID dyn2 b edid-loxp at position 407 aa dyn2::loxp Nup57-eDID dyn2 b edid-loxp at position 71 aa dyn2::loxp Nup49-eDID dyn2 b edid-loxp at position 81 aa dyn2::loxp Nup159 DID-eDID dyn2 a edid-loxp at position 624 aa nup159::kanmx4 dyn2::kanmx4 -edid Nup159 DID-eDID(2) dyn2 a edid-loxp at position 904 aa nup159::kanmx4 dyn2::kanmx4 2 -edid Nup116-eDID dyn2 b edid-loxp at position 197 aa dyn2::loxp Nup159 DID Nsp1-eDID dyn2 a nup159::kanmx4 dyn2::kanmx4, DID-LoxP in NSP1 at position 275 Nsp1-eDID dyn2 Nup159 DID b edid-loxp at position 275 aa dyn2::loxp nup159::hismx6 Nup1-eDID dyn2 Nup159 DID b edid-loxp at position 717 aa dyn2::loxp nup159::hismx6 Nup2-eDID dyn2 Nup159 DID b edid-loxp at position 407 aa dyn2::loxp nup159::hismx6 Nup49-eDID dyn2 Nup159 DID b edid-loxp at position 81 aa dyn2::loxp nup159::hismx6 Nup116-eDID dyn2 Nup159 DID b edid-loxp at position 197 aa dyn2::loxp nup159::hismx6 Nup116-eDID-TAP dyn2 b edid-loxp at position 197 aa dyn2::loxp NUP116-TAP::URA3 Nup116-eDID-TAP dyn2 Nup159 DID b edid-loxp at position 197 aa dyn2::loxp NUP116-TAP:: URA3 nup159::hismx6 Nup1-eDID-TAP dyn2 b edid-loxp at position 717 aa dyn2::loxp NUP1-TAP::URA3 Nup2-eDID Nup60-TAP dyn2 b edid-loxp at position 407 aa dyn2::loxp NUP60-TAP::URA3 Nsp1-eDID dyn2 Nup49-TAP b edid-loxp at position 275 aa dyn2::loxp NUP49-TAP::URA3 Nup159 DID-eDID Nup82-TAP dyn2 a edid-loxp at position 624 aa nup159::kanmx4 dyn2::kanmx4 -edid NUP82-TAP::URA3 Nup49-eDID Nic96-TAP dyn2 b edid-loxp at position 81 aa dyn2::loxp NIC96-TAP::URA3 Nup159 DID dyn2 a nup159::kanmx4 dyn2::kanmx4 Stelter et al., 2007 Nup159 dyn2 a nup159::kanmx4 dyn2::kanmx4 prs414-nup159 Stelter et al., 2007 dyn2 GAL::Dyn2 b GAL-DYN2::HISMX6 dyn2::loxp Nsp1-eDID dyn2 GAL::DYN2 b GAL-DYN2:: HISMX6 dyn2::loxp dyn2 Pho4-GFP GAL::DYN2 b PHO4-GFP::natNT2 GAL-DYN2::HISMX6 dyn2::loxp Nsp1-eDID dyn2 Pho4-GFP b PHO4-GFP::natNT2 dyn2::loxp Nsp1-eDID dyn2 Pho4-GFP GAL:: PHO4-GFP::natNT2 GAL-DYN2::HISMX6 dyn2::loxp DYN2 b Nup57-TAP GAL::DYN2 c NUP57-TAP::TRP1 GAL-DYN2::HISMX6 Nup57-TAP Nsp1-eDID dyn2 b NUP57-TAP::TRP1 dyn2::loxp Nup57-TAP Nsp1-eDID dyn2 GAL:: NUP57-TAP::TRP1 GAL-DYN2::HISMX6 dyn2::loxp DYN2 b nup159 /dyn2 shuffle a nup159::kanmx4 dyn2::kanmx4 plg4 Stelter et al., 2007 nup159 /dyn2 GAL::DYN2 shuffle a nup159::kanmx4 dyn2::kanmx4 GAL-DYN2::HISMX6 plg4 nsp1 /nup57 dyn2 shuffle a nsp1::his3 nup57::his3 dyn2::kanmx4 pch1122-nsp1 prs314-gfp-nup57 Nup159 DID-FG Nsp1 dyn2 a nup159::kanmx4 dyn2::kanmx4 -edid-fg NSP1 Nup159 DID-FG Nup1 dyn2 a nup159::kanmx4 dyn2::kanmx4 -edid-fg NUP1 Nup159 dyn2 a nup159::kanmx4 dyn2::kanmx4 prs414-nup159 Nup159 DID dyn2 a nup159::kanmx4 dyn2::kanmx4 Nup159 DID-FG Nsp1 dyn2 a nup159::kanmx4 dyn2::kanmx4 -FG NSP1 Nup159 DID-eDID-FG Nsp1 dyn2 a nup159::kanmx4 dyn2::kanmx4 -edid-fg Nsp1 Nup82-TAP Nup159 DID dyn2 a S5

Table S1. Yeast strains used in this study (Continued) Strains Genotype References Nup82-TAP Nup159 DID-eDID-FG Nsp1 dyn2 a Nup82-TAP Nup159 DID-FG Nsp1 dyn2 a Nup82-TAP Nup159 DID Nsp1-eDID dyn2 a Nup82-TAP Nup159 DID-eDID-FG Nsp1 dyn2 a -edid-fg Nsp1 -FG Nsp1 NUP82-TAP::URA3 nup159::kanmx4 dyn2: kanmx4 prs414-nup159 DID -edid-fg Nsp1 GAL::DYN2 dyn2 a GAL-DYN2::HISMX6 dyn2::loxp Nup57-FG Nsp1 Nsp1 FG dyn2 a nsp1::his3 nup57::his3 dyn2::kanmx4 psb32-p ADH1 -NSP1 FG prs314-p NOP1 -NUP57-FG NSP1 Nup57-eDID-FG Nsp1 Nsp1 FG dyn2 a nsp1::his3 nup57::his3 dyn2::kanmx4 psb32-p ADH1 -NSP1 FG prs314-p NOP1 -NUP57-eDID-FG NSP1 a RS453 genetic background. b Ds1-2b genetic background. c dyn2 genetic background. Table S2. Plasmids used in this study Plasmids Comments References prs414-nup159 Stelter et al., 2007 Stelter et al., 2007 prs414-nup159-edid prs414-nup159 DID-eDID 623 edid-flag PCR amplified from pfa6aloxp-edid-flag-loxp-hismx4 and cloned as Bgl2 in the BamH1 cut prs414-nup159 DID - FG NSP1 edid-fg NSP1 edid-fg NUP1 prs314-p NOP1 prs314-p NOP1 -NUP57 FG prs314-p NOP1 -NUP57- FG NSP1 prs314-p NOP1 -NUP57- edid-fg NSP1 pura3 mrfp-nop1 RPL25-EGFP FG NSP1 (1 591 aa) was PCR amplified from genomic DNA from a wild-type strain and cloned as Pst1 Apa1 in prs414-nup159 DID edid-fg NSP1 (1 591 aa + edid-flag-loxp) was PCR amplified from genomic DNA from a NSP1-eDID dyn2 and cloned as Pst1 Apa1 in prs414-nup159 DID edid-fg NUP1 (382 1,076 aa + edid-flag-loxp) was PCR amplified from genomic DNA from a NUP1-eDID dyn2 and cloned as Pst1 Apa1 in prs414-nup159 DID NOP1 Promoter was cloned as BamH1 EcoR1 in prs314 and a Nde1 restriction site was created before the EcoR1 Nup57 FG(224 541 aa) was PCR amplified from genomic DNA and cloned as EcoR1 Xho1 in prs314-p NOP1 FG NSP1 (1 591 aa) was PCR amplified from genomic DNA from a wild-type strain and cloned as Nde1 in prs314-p NOP1 -Nup57 FG edid-fg NSP1 (1 591 aa + edid-flag-loxp) was PCR amplified from genomic DNA from a NSP1-eDID dyn2 and cloned as Nde1 in prs314-p NOP1 -Nup57 FG Ulbrich et al., 2009 YEp351-GAL-DYN2 DYN2 PCR amplified and cloned as BamH1 Hind3 Yep352-GAL-DYN2 DYN2 PCR amplified and cloned as BamH1 Hind3 Yep352-GAL-DYN2-GFP DYN2-GFP was a PCR amplified from DYN2-GFP (Stelter et al., 2007) strain and cloned as BamH1 Hind3 in Yep352-GAL-DYN2 plasmid prs303-gal::dyn2 prs303-gal::dyn2::his3 pfa6a-edid-flag-loxp- HindIII-eDID-BamH1-Flag-Sal1-loxP-HISMX4-loxP HISMX4-loxP pun100-nup49 Subcloned from genomic library plasmid (3.5 kb) prs315-nup57 Subcloned from genomic library plasmid psb32-nsp1 Subcloned from genomic library plasmid pun100-nup1 Subcloned from genomic library plasmid S6

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