Table 1

Subnetwork organization of gene products whose disruption specifically affects nickel or cadmium tolerance

Subnetworksa

Nickel

Cadmium


Interacting gene products

Functionally linked gene productsb

Interacting gene products3

Functionally linked gene productsb,c


V-ATPase assembly/regulation (sn. 1)

Rav1, Vma16, Vph1

Proteasome (sn. 3)

Cue1

Bre5, Cdc26, Doa1, Hlj1, Sel1, Ubi4, Ubp6, Ump1

Dia2

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

Cell wall integrity pathway (sn. 5)

Whi3

Bem2, Dom34, Ecm33, Kcs1, Pin4, Pog1, Rvs161, Rvs167, Sic1, Sit4*, Sur7, Swi4, Swi6, Whi2

CCR4 and other mRNA processing enzymes (sn. 6)

Dhh1

Paf1

Nuclear pore complex (sn. 7)

Nup84, Sac3, Thp1

Essential ion homeostasis (sn. 9)

Pho88

Ccc2, Zap1

Smf3

Gef1, Pho89

AP-3 complex (sn. 10)

Apl5, Apl6, Apm3, Aps3

General transcription (sn. 11)

Mft1, Rpb9, Rtt103, Thp2

Mediator complexes (Gal11, Med2, Pgd1, Spt21, Srb8*, Srb10); Cad1, Elp4, Tup1, Yap1

Mss11

DNA repair (sn. 12)

Ctf4, Him1, Met18, Mms22, Mre11, Pol32, Rad6, Rad27, Xrs2

Antioxidant defense (sn. 13)

Atx2, Ccs1, Sod1, Sod2

Cad1, Glr1, Gsh1, Gsh2, Yap1, Zwf1

Hog1 pathway (sn. 14)

Fps1, Hog1, Pbs2, Rck2, Ste11

Gre2

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*

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*


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.

Ruotolo et al. Genome Biology 2008 9:R67   doi:10.1186/gb-2008-9-4-r67

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