TABLE 2.
Functional categories that are significantly influenced by inactivation of C. albicans GCN4 or GCN2
| Functional categorya | Gcn4- and Gcn2-dependent genesb (n = 168)
|
Genes dependent on Gcn4 onlyb (n = 160)
|
||
|---|---|---|---|---|
| Fold enhancementc | Genes | Fold enhancementc | Genes | |
| Amino acid metabolism | 5.0 | AGP1, ARG8, ARO1, ARO4, BAT21, ECM42, GAP5, HIP1, HIS1, HIS3, HIS7, HOM3, HYU1, ILV1, ILV6, LEU42, LYS2, LYS4, LYS22, MET8, MXR1, PRO1, PRO2, THR1, TRP2, TRP3, TRP4, IPF8591 | 5.9 | AAT21, ARO3, ARO8, BAT22, CIS2, DIP51, ECM17, GAP6, GAP7, GCH2, GCN4, HIS4, HIS5, HOM6, ILV2, LEU41, LYS9, LYS21, MET2, MET15, SER33, THR4, THR5, TRP5, IPF1162, IPF2837, IPF8048, IPF13176, IPF14203 |
| Nitrogen and sulfur metabolism | 2.7 | MET8, NIT3, IPF8591, IPF10021, IPF11716 | 4.0 | AAT21, ECM12, GDH2, IPF3549, IPF14203, IPF20164 |
| Protein fate | 2.0 | APE3, ARP2, CDC37, CDC48, CPY1, CTM1, ELC1, HSP78, NPL4, PRC1, PRC3, PRE3, PRE6, PRE8, PUP2, RPN1, RPN2, RPN6, RPN7, RPN8, RPN10, RPT1, RPT4, RPT5, RPT6, SHR3, SRA1, UBC3, VPS1, VPS4, IPF56, IPF14031, IPF4866, IPF7556, IPF11713 | NEd | |
| Cell rescue, defense, and virulence | 2.1 | DDR48, GTT1, HAM1, HK1, HSP12, HSP78, MXR1, OSM2, PRE3, PUP2, SRA1, SSU1, TTR1, ZWF1, IPF4055, IPF9188 | NE | |
| Transport facilitation | NE | 2.3 | ARR3, CDR1, CDR11, DIP51, ENA21, FCY23, GAP6, GAP7, PXA2, SEO1, SMF12, IPF4580, IPF9670, IPF11767, IPF12884, IPF13941 | |
Functional categories are based on those of S. cerevisiae homologues as defined by MIPS (http://mips.gsf.de/genre/proj/yeast/searchCatalogFirstAction.do?db=CYGD), and C. albicans functional assignments are from CandidaDB (http://genolist.pasteur.fr/CandidaDB/) (14). Only those functional categories that show more than two fold enhancement and that also contain more than five genes are shown. Note that a gene can belong to more than one functional category.
The 168 genes that displayed significant increases in expression in response to 3AT in wild-type cells only were defined as Gcn4 and Gcn2 dependent (Fig. 6A, gray sector). The 160 genes that displayed increased expression in response to 3AT in wild-type and gcn2 cells were defined as Gcn4 dependent only (Fig. 6A, black sector).
Fold enhancement, which represents the extent to which genes in the functional category of interest were enriched, was calculated by dividing the proportion of genes within the regulatory subset that belong to that functional category by the proportion of genes in the whole genome that belong to that functional category.
NE, no significant enhancement for this functional category in this regulatory subset, whereas the other regulatory subset does show significant enhancement for this functional category.