Table 1 Functional classification of genes up-regulated in particular colony phenotypes
From: Global changes in gene expression associated with phenotypic switching of wild yeast
Structured biofilm colony morphotype | Smooth colony morphotype | |
|---|---|---|
Cell wall | SVS1, ASP3-1,-2,-3,-4, BSC1, OSW5 | SPS100, CTS1 , FLO9, PFS1, PSA1, ZPS1 |
Secretory transport & processing | BST1, LST7, PER1, CWH41, MNN9, YOL107W, APM4, GVP36, YIP4 | BTN2, NCE102, GYP7 , KTR4, PEP12, SNC2, TIM17, TIM21 |
Metabolism | JLP1, MLS1, SNZ1, SNZ2, TPI1 — YMR226C, BNA1, ENO1, HPT1, MDH2, RHR2, SOL4 | DSF1, PIG2, STR3, CRS5, CUP1-1, FBP26, FOL2, FRE6, HXK1, MTD1, NFS1, SFA1 |
Amino acids | ARG3, ARG4, BAT1, MET17, MET22, ARG1, GDH3, LAP3 | GCV1, GCV2, GCV3, SHM2 |
Lipids & fatty acids | INO1 — ECI1, POT1, POX1, TES1, VPS66 | YNL144C, ERG3, ERG4, HFD1 — AUR1, CEM1, CSG2, SUR1, SUR4 |
Nucleotides | RNR4 — ADE1, ADE2, ADE8, ADE13, PRS3 | |
Transport | ITR1, PUT4, VHT1, PDR12, VBA3, ATO2, CAN1, GAP1, MEP2, PIC2 | YFL054C HXT15, MUP3, PHO84, THI74, ZRC1, HXT5, HXT17, PHO89, YFL054C, HXT1, HXT2, HXT3, HXT4, HXT6, HXT10, , HXT12, HXT13, MAL11, PHO87, ZRT2 |
Degradation | HSP33, MGR1, NAS2, YSP3 | ATG8, BSD2, CIC1, DFG16, GID8, JID1, UMP1, RPN5, RPN13, RPT2, SNA3, VID24, YPT53 |
Stress response | DDR48, GRX3 — TSA1, YBL036C, CTA1, SOD2, TSA2 | OLA1, HSP42, SPG1, SSA3, SSA4, APJ1, FES1, GPX1, HSP30, HSP78, SSE1, YNL190W, AAD6, CCT5, CPR6, GLO1, GSH1, HSP104 , HSP150, MGE1, OYE3, PST1, RCN2, SED1, STI1, TRX3, YDJ1,YGP1 |
Regulation | ||
Translation & RNA processing | BRR2, MTQ2, SLF1, DUS4, SPP381, IST3, MRS2, RPP1A, RPR2 | PUS2, SLH1, NGL3, RPA135, RSC30, YDR341C, CBF5, SRO9, RPP2A, RPS30B, RPL35B, RRP3, RRP7, SRC1 |
Signal transduction | FAR3 | GPA2, MTH1, MRK1, STD1, LST8, RGS2, YMR291W, GLC8, HRK1, KIC1, MTH1, STE7, YAK1 |
Cell cycle & polarity | SHE1 | PCL9, HBT1, TAH11, CLG1, CDC13, CDC3, DSE1, VHS1 |
Transcription | CUP9, SFG1, TEC1, YAP7, DAL80, RDS1 | YFL052W, HMS1, RLM1, USV1, ZPR1, ALPHA2, CIN5, GIS1, HAP4, OPI1, PHO2, STP2, STP4 |
- chromatin structure | HHF1 | TOS8 , IOC4, HHT1, TMA23,TOD6 |
General transcription | IWR1, RBA50, RPA135, SPT15, SUA7, TAF12, TFA1 | |
Transposons* | 8 genes, 10 genes, 1 genes | |
Unknown* | 7 genes, 5 genes, 17 genes | 8 genes, 4 genes, 11 genes |
Others | YLR164W, DIA1, DIA3, MRH1, MRPS17, IXR1, PIN3 |