Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | Yeast Protein Interactome Collection - DHFR F[1,2] and DHFR F[3] strains, BY4741 and BY4742 (MATa and MATα) | GE Healthcare Dharmacon Inc, Tarassov et al., 2008 | Cat. #YSC5849 | See Supplementary file 2 Tables S9 and S10 for the complete list of strains |
| Strain, strain background (Saccharomyces cerevisiae) | DHFR F[1,2] strains, BY4741 (MATa) | Diss et al., 2017 and this paper | See Supplementary file 2 Tables S9 and S10 for the complete list of strains | |
| Strain, strain background (Saccharomyces cerevisiae) | DHFR F[3] strains, BY4742 (MATα) | Diss et al., 2017 and this paper | See Supplementary file 2 Tables S9 and S10 for the complete list of strains | |
| Strain, strain background (Saccharomyces cerevisiae) | RY1010, PJ69-4A (MATa) | Yachie et al., 2016 | ||
| Strain, strain background (Saccharomyces cerevisiae) | RY1030, PJ69-4alpha (MATα) | Yachie et al., 2016 | ||
| Strain, strain background (Saccharomyces cerevisiae) | YY3094, PJ69-4A (MATa) | This paper – available from Christian Landry upon request | ||
| Strain, strain background (Saccharomyces cerevisiae) | YY3095, PJ69-4alpha (MATα) | This paper – available from Christian Landry upon request | ||
| Strain, strain background (Lachancea kluyveri) | Lachancea kluyveri, CBS 3082 | Kurtzman, 2003 | ||
| Strain, strain background (Zygosaccharomyces rouxii) | Zygosaccharomyces rouxii, CBS 732 | Pribylova et al., 2007 | ||
| Strain, strain background (Escherichia coli) | MC1061 | CGSC | Cat. #6649 | |
| Recombinant DNA reagent | pAG25-linker-F[1,2]-ADHterm (plasmid) | Tarassov et al., 2008 | ||
| Recombinant DNA reagent | pAG32-linker-F[3]-ADHterm (plasmid) | Tarassov et al., 2008 | ||
| Recombinant DNA reagent | pDEST-AD (TRP1) (plasmid) | Rual et al., 2005 | ||
| Recombinant DNA reagent | pDEST-DB (LEU2) (plasmid) | Rual et al., 2005 | ||
| Recombinant DNA reagent | pDN0501 (TRP1) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDN0502 (LEU2) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pHMA1001 (TRP1)(plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pHMA1003 (LEU2) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDEST-DHFR F[1,2] (TRP1) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDEST-DHFR F[1,2] (LEU2) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDEST-DHFR F[3] (TRP1) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDEST-DHFR F[3] (LEU2) (plasmid) | This paper – available from Christian Landry upon request | ||
| Recombinant DNA reagent | pDONR201 (plasmid) | Invitrogen | Cat. #11798–014 | |
| Recombinant DNA reagent | PacI | New England BioLabs Inc | Cat. #R0547S | |
| Recombinant DNA reagent | SacI | New England BioLabs Inc | Cat. #R0156S | |
| Recombinant DNA reagent | SpeI | New England BioLabs Inc | Cat. #R0133S | |
| Recombinant DNA reagent | PI-PspI | New England BioLabs Inc | Cat. #R0695S | |
| Sequence-based reagent | Oligonucleotides | This paper | PCR primers | See Supplementary file 2 Table S12 for the complete list |
| Sequence-based reagent | DEY011 | Integrated DNA Technologies, Inc | gBlock | See Supplementary file 2 Table S12 for the sequence |
| Commercial assay or kit | Presto Mini Plasmid Kit | Geneaid Biotech Ltd | Cat. #PDH300 | |
| Commercial assay or kit | Lexogen Quantseq 3’ mRNA kit | D-Mark Biosciences | Cat. #012.24A | |
| Commercial assay or kit | Gateway BP Clonase II enzyme mix | Thermo Fisher Scientific | Cat. #11789020 | |
| Commercial assay or kit | Gateway LR Clonase II enzyme mix | Thermo Fisher Scientific | Cat. #11791020 | |
| Commercial assay or kit | Gibson Assembly Master Mix | New England BioLabs Inc | Cat. # E2611L | |
| Chemical compound, drug | Kanamycin | BioShop Canada, Inc | Cat. #KAN201.10 | |
| Chemical compound, drug | Ampicillin | BioShop Canada, Inc | Cat. #AMP201 | |
| Chemical compound, drug | Nourseothricin (NAT) | WERNER BioAgents GmbH | Cat. #5.010.000 | |
| Chemical compound, drug | Hygromycin B (HygB) | BioShop Canada, Inc | Cat. #HYG003 | |
| Chemical compound, drug | Methotrexate (MTX) | BioShop Canada, Inc | Cat. #MTX440 | |
| Software, algorithm | MUSCLE v 3.8.31 | Edgar, 2004 | RRID:SCR_011812 | |
| Software, algorithm | gitter (R package version 1.1.1) | Wagih and Parts, 2014 | ||
| Software, algorithm | normalmixEM function (R mixtools package) | Benaglia et al., 2009 | ||
| Software, algorithm | FastQC | Andrews, 2010 | RRID:SCR_014583 | |
| Software, algorithm | cutadapt | Martin, 2011 | RRID:SCR_011841 | |
| Software, algorithm | bwa | Li and Durbin, 2009 | RRID:SCR_010910 | |
| Software, algorithm | HTSeq (Python package) | Anders et al., 2015 | RRID:SCR_005514 | |
| Software, algorithm | BLASTP (version 2.6.0+) | Camacho et al., 2009 | RRID:SCR_001010 | |
| Software, algorithm | FoldX suite version 4 | Guerois et al., 2002 and Schymkowitz et al., 2005 | RRID:SCR_008522 | |
| Software, algorithm | FreeSASA | Mitternacht, 2016 | ||
| Software, algorithm | Biopython | Cock et al., 2009 | RRID:SCR_007173 | |
| Other, database | IntAct | Orchard et al., 2014 | RRID:SCR_006944 | https://www.ebi.ac.uk/intact/ |
| Other, database | Yeast Gene Order Browser (YGOB) | Byrne and Wolfe, 2005 | http://ygob.ucd.ie/ | |
| Other, database | PhylomeDB | Huerta-Cepas et al., 2008 | RRID:SCR_007850 | http://phylomedb.org/ |
| Other, database | Protein Data Bank (PDB) | Berman et al., 2000 | RRID:SCR_012820 | https://www.rcsb.org/ |
| Other, database | Ensembl | Zerbino et al., 2018 | RRID:SCR_002344 | http://useast.ensembl.org/info/data/ftp/index.html |
| Other, database | TheCellMap (version of March 2016) | Usaj et al., 2017 | http://thecellmap.org/ | |
| Other, database | Saccharomyces Genome Database (SGD) | Cherry et al., 2012 | RRID:SCR_004694 | https://www.yeastgenome.org/ |
| Other, database | Complex Portal | Meldal et al., 2015 | RRID:SCR_015038 | https://www.ebi.ac.uk/complexportal/ |
| Other, database | CYC2008 catalog | Pu et al., 2009,Pu et al., 2007 | http://wodaklab.org/cyc2008/ | |
| Other, database | YEASTRACT | Teixeira et al., 2018, Teixeira et al., 2006 | RRID:SCR_006076 | http://www.yeastract.com/ |
| Other, database | Yeast GFP Fusion Localization Database (YeastGFP) | Huh et al., 2003 | https://yeastgfp.yeastgenome.org/ | |
| Other, database | The Protein Families Database (Pfam) | El-Gebali et al., 2019 | RRID:SCR_004726 | https://pfam.xfam.org/ |
| Other, database | UniprotKB database | The UniProt Consortium, 2019 | RRID:SCR_004426 | https://www.uniprot.org/ |
| Other, database | BIOGRID-3.5.166 | Chatr-Aryamontri et al., 2017, Chatr-Aryamontri et al., 2013 | RRID:SCR_007393 | https://thebiogrid.org/ |
| Other, database | Ohnologs | Singh et al., 2015 | http://ohnologs.curie.fr/ | |
| Other, dataset | Supplementary materials of Benschop et al. (2010) | Benschop et al., 2010 | https://doi.org/10.1016/j.molcel.2010.06.002 | |
| Other, dataset | Supplementary materials of Kim et al. (2019) | Kim et al., 2019 | https://doi.org/10.1101/gr.231860.117 | |
| Other, dataset | Supplementary materials of Ihmels et al. (2004) | Ihmels et al., 2004 | https://doi.org/10.1093/bioinformatics/bth166 | |
| Other, dataset | Supplementary materials of Gasch et al. (2017) | Gasch et al., 2017 | https://doi.org/10.1371/journal.pbio.2004050 | |
| Other, dataset | Supplementary materials of Guan et al. (2007) | Guan et al., 2007 | https://doi.org/10.1534/genetics.106.064329 | |
| Other, dataset | Supplementary materials of Tarassov et al. (2008) | Tarassov et al., 2008 | https://doi.org/10.1126/science.1153878 | |
| Other, dataset | Supplementary materials of Stynen et al. (2018) | Stynen et al., 2018 | https://doi.org/10.1016/j.cell.2018.09.050 | |
| Other, dataset | Supplementary materials of Lan and Pritchard (2016) | Lan and Pritchard, 2016 | https://doi.org/10.1126/science.aad8411 |