Table 1.
Methanol regulated genes of P. pastoris as a source of regulated promoters
| Ranked expression level (methanol)a | Short name | ORF nameb | Co-regulation: 1 = with A/D/F; 2 = with A; 3 = with D/F; 4 = up at glucose limitc | Methanol inductiond |
|---|---|---|---|---|
| 1 | DAS1 | PP7435_Chr3-0352 | 1;4 | Strong |
| 2 | AOX2 | PP7435_Chr4-0863 | 2;4 | Strong |
| 3 | AOX1 | PP7435_Chr4-0130 | 1;4 | Strong |
| 4 | DAS2 | PP7435_Chr3-0350 | 3;4 | Strong |
| 5 | FDH1 | PP7435_Chr3-0238 | 1;4 | Strong |
| 6 | PMP20 | PP7435_Chr1-1351 | Strong | |
| 7 | THI11 | PP7435_Chr4-0952 | Weak | |
| 8 | FLD | PP7435_Chr3-0140 | 3 | Intermediate |
| 9 | FBA1-2 | PP7435_Chr1-0639 | 1 | Strong |
| 10 | SHB17 | PP7435_Chr2-0185 | 3 | Intermediate |
| 11 | FGH1 | PP7435_Chr3-0312 | 1 | Intermediate |
| 12 | DAK2 | PP7435_Chr3-0343 | 3 | Intermediate |
| 13 | CTA1 | PP7435_Chr2-0137 | 3 | Weak |
| 14 | PMP47 | PP7435_Chr3-1139 | 1 | Strong |
| 15 | MPP1 | PP7435_Chr3-0349 | 3 | Weak |
| 16 | FBP1 | PP7435_Chr3-0309 | 3 | Weak |
| 17 | PIM1-2 | PP7435_Chr1-0484 | 2 | Weak |
| 18 | PAS_chr1-1_0037 | PP7435_Chr1-0336 | 1 | Strong |
| 19 | PAS_chr3_1071 | PP7435_Chr3-0094 | 1 | Strong |
| 20 | PEX11 | PP7435_Chr2-0790 | 3;4 | Intermediate |
| 21 | PEX13 | PP7435_Chr2-0217 | 1 | Weak |
| 22 | PAS_chr1-1_0343 | PAS_Chr1-1_0343 | 4 | Intermediate |
| 23 | PEX12 | PP7435_Chr4-0200 | 1 | Weak |
| 24 | INP1 | PP7435_Chr4-0597 | 3 | Weak |
| 25 | PEX6 | PP7435_Chr1-0900 | 1 | Weak |
| 26 | PEX17 | PP7435_Chr4-0347 | 1 | Weak |
| 27 | ATG37 | PP7435_Chr4-0369 | 1 | Weak |
| 28 | TAL1-2 | PP7435_Chr2-0358 | 1 | Intermediate |
| 29 | PEX5 | PP7435_Chr2-0195 | 3 | Intermediate |
| 30 | PEX2 | PP7435_Chr3-1201 | 3 | Weak |
| 31 | PAS_chr3_1020 | PP7435_Chr3-0149 | 3 | Strong |
| 32 | PEX1 | PP7435_Chr3-0122 | 1 | Weak |
| 33 | PEX26 | PP7435_Chr4-0482 | 1 | Weak |
| 34 | PEX10 | PP7435_Chr1-1379 | 3 | Weak |
| 35 | PEX14 | PP7435_Chr4-0157 | 3 | Weak |
| 36 | PAS_chr3_0408 | PP7435_Chr3-0805 | Intermediate | |
| 37 | ARO7 | PP7435_Chr4-0965 | 3 | Weak |
| 38 | PEX8 | PP7435_Chr1-1134 | 1 | Weak |
| 39 | PAS_chr1-4_0459 | PP7435_Chr1-1255 | 1 | Intermediate |
| 40 | FAD1 | PP7435_Chr1-0246 | Intermediate | |
| 41 | YLR177 W | PP7435_Chr1-0659 | 3 | Intermediate |
| 42 | PEX11C | PP7435_Chr1-1331 | 3 | Weak |
| 43 | ACS2 | PP7435_Chr3-0810 | Weak | |
| 44 | PAS_chr3_0439 | PAS_chr3_0439 | 2 | Intermediate |
| 45 | RKI1-2 | PP7435_Chr4-0797 | 3 | Intermediate |
aRelative gene expression levels were derived from signal intensities on DNA microarrays at methanol induction [16, 17] and ordered from highest to lowest
bORF names derived from published P. pastoris genome sequences [19, 20]
cThe gene correlation was calculated using transcriptomic datasets comprising 29 different conditions. The log2 fold change data was used to look for co-regulations in this data set. The data was processed via the DeGNServer to calculate Spearman´s rank correlation using a CLR-based Network and an association cut-off value of 3.8 [21]. Co-regulation was analyzed with three genes involved in methanol utilization: AOX1 (A), DAS1 (D), FBA1-2 (F). Up at glucose limit means that expression is deregulated in glucose limited culture conditions without methanol (data from [12])
dInduction on methanol was classified based on the transcriptional regulation patterns obtained by [16, 17] by comparing expression levels of cells grown on methanol to cells grown on glucose or glycerol