Table 1 |
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Subnetwork organization of gene products whose disruption specifically affects nickel or cadmium tolerance |
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Subnetworksa |
Nickel |
Cadmium |
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Interacting gene products |
Functionally linked gene productsb |
Interacting gene products3 |
Functionally linked gene productsb,c |
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V-ATPase assembly/regulation (sn. 1) |
Rav1, Vma16, Vph1 |
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Proteasome (sn. 3) |
Cue1 |
Bre5, Cdc26, Doa1, Hlj1, Sel1, Ubi4, Ubp6, Ump1 |
Dia2 |
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Chromatin assembly/remodelling (sn. 4) |
SAGA complex (Ada2, Chd1, Gcn5, Hfi1, Ngg1, Spt7*, Spt20); Ino80 complex (Arp5, Arp8, Taf14); COMPASS complex (Bre2, Sdc1); Asf1, Ard1, Eaf7*, Esc2, Hda1*, Hmo1, Ioc2 |
Hmo1 |
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Cell wall integrity pathway (sn. 5) |
Whi3 |
Bem2, Dom34, Ecm33, Kcs1, Pin4, Pog1, Rvs161, Rvs167, Sic1, Sit4*, Sur7, Swi4, Swi6, Whi2 |
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CCR4 and other mRNA processing enzymes (sn. 6) |
Dhh1 |
Paf1 |
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Nuclear pore complex (sn. 7) |
Nup84, Sac3, Thp1 |
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Essential ion homeostasis (sn. 9) |
Pho88 |
Ccc2, Zap1 |
Smf3 |
Gef1, Pho89 |
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AP-3 complex (sn. 10) |
Apl5, Apl6, Apm3, Aps3 |
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General transcription (sn. 11) |
Mft1, Rpb9, Rtt103, Thp2 |
Mediator complexes (Gal11, Med2, Pgd1, Spt21, Srb8*, Srb10); Cad1, Elp4, Tup1, Yap1 |
Mss11 |
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DNA repair (sn. 12) |
Ctf4, Him1, Met18, Mms22, Mre11, Pol32, Rad6, Rad27, Xrs2 |
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Antioxidant defense (sn. 13) |
Atx2, Ccs1, Sod1, Sod2 |
Cad1, Glr1, Gsh1, Gsh2, Yap1, Zwf1 |
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Hog1 pathway (sn. 14) |
Fps1, Hog1, Pbs2, Rck2, Ste11 |
Gre2 |
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Vesicle targeting to, from or within Golgi (sn. 15) |
Erv41, Erv46, Get2, Sac1, Sec22, Sec66; Vps13; Cog5, Cog8; Pep7, Tlg2, Vps3, Vps9, Vps21, Vps45; Arl1, Arl3, Ent3, Gga2, Nhx1*, Rgp1, Ric1, Sys1, Yil039w*, Vps51, Vps54, Ypt6; Vam10*, Vps1*, Vps8*; Pep8*, Vps5*, Vps17*, Vps29*, Vps30*, Vps35*, Vps38* |
Apm2, Snx3* |
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Ubiquitin-dependent sorting to the multivesicular body pathway (sn. 16) |
Vps27*; ESCRT I complex (Vps28*, Mvb12*, Srn2*, Stp22*); ESCRT II complex (Snf8*, Vps25*, Vps36*); ESCRT-III complex (Did4*, Snf7*, Vps20*, Vps24*); Bro1*, Did2*, Doa4*, Vps4* |
Bsd2*, Bul1*, Nhx1*, Tre1* |
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aSubnetworks 1 to 9 are the same as those described in Figure 2 but include deletion mutants specifically sensitive to nickel or cadmium (no nickel or cadmium specific mutants were identified for subnetworks 2 and 8); subnetworks 10 to 16 are newly identified interaction networks comprised of gene products causing nickel-specific or cadmium-specific sensitivity when disrupted (also see Additional data files 3 and 4). bGene products for which no physical or genetic interaction is documented in the BioGRID database [22] but for which a functional relationship with the indicated subnetworks has been reported. cGene mutations causing cadmium sensitivity but nickel resistance are marked with an asterisk. AP-3, Adaptor Protein-3; CCR, Carbon Catabolite Repression; ESCRT, endosomal sorting complexes required for transport; sn., subnetwork. |
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Ruotolo et al. Genome Biology 2008 9:R67 doi:10.1186/gb-2008-9-4-r67 |
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