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Table 4 Transcriptional regulation of transcriptional regulators

From: Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Short name Pp Description G-D logFC G-D adjPV M-D logFC M-D adjPV X-D logFC X-D adjPV
PAS_chr4_0340 Fungal specific transcription factor domain; Zn2/Cys6 DNA-binding domain 0.35 * 0.72 *** 1.50 ***
CAT8-2 Zinc cluster transcriptional activator; necessary for derepression of a variety of genes under non-fermentative growth conditions in S. cerevisiae −0.07   2.72 *** 5.27 ***
YAP1 Basic leucine zipper (bZIP) transcription factor; required for oxidative stress tolerance 0.27   1.13 *** 1.64 ***
PAS_chr1-4_0516 Putative transcription factor 0.94   7.81 *** 7.86 ***
MPP1 Fungal Zn2/Cys6 DNA-binding domain; homolog to Hansenula polymorpha transcription factor involved in peroxisome biogenesis/degradation 0.90 *** 6.34 *** 6.99 ***
AFT1 Transcription factor, possibly involved in carbohydrate metabolism 2.17 *** 3.68 *** 5.16 ***
YPR022C-3 Putative transcription factor 1.57 *** 2.33 *** 4.55 ***
PAS_chr3_0348 Helix-loop-helix DNA-binding domain 0.06   0.29   3.69 ***
ADR1/MXR1 Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization 1.34 *** 1.61 *** 2.16 ***
RSF2/ROP Zinc-finger protein; involved in transcriptional control of both nuclear and mitochondrial genes in S. cerevisiae −0.10   1.85 *** −0.24  
PpTRM1 Zn(II)2Cys6-type transcription factor involved in the positive regulation of methanol utilization genes in P. pastoris and C. boidinii -0.14   0.74 *** 0.34 *
SNF1 AMP-activated serine/threonine protein kinase; found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis in S. cerevisiae 0.39 ** 0.61 ** 1.42 ***
SNF2 Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; contains DNA-stimulated ATPase activity 0.13   0.40 ** −0.37 **
SNF4 Activating gamma subunit of the AMP-activated Snf1p kinase complex 0.19   0.35   0.76 ***
MIG1-1 Transcription factor involved in glucose repression in S. cerevisiae; regulated by the Snf1p kinase and the Glc7p phosphatase; 0.57 * 1.09 ** 3.09 ***
MIG1-2 Transcription factor involved in glucose repression in S. cerevisiae; regulated by the Snf1p kinase and the Glc7p phosphatase; −0.76 ** −1.23 *** −0.56 ***
SIP2 One of three beta subunits of the Snf1 kinase complex in S. cerevisae 0.00   −0.14   0.65 ***
RDS2 Transcription factor involved in regulating gluconeogenesis and glyoxylate cycle genes; member of the zinc cluster family of proteins; confers resistance to ketoconazole in S. cerevisiae −0.07   0.20   0.83 ***
PAS_chr1-3_0274 Fungal specific transcription factor; Zn2/Cys6 DNA-binding domain 0.11   0.29   0.90 ***
PAS_chr4_0324 Fungal specific transcription factor; Zn2/Cys6 DNA-binding domain −3.07 *** −2.99 *** −3.47 ***
CTH1 Member of the CCCH zinc finger family −2.54 *** −2.81 *** −2.92 ***
PAS_chr1-1_0422 Myb/SANT-like DNA-binding domain −0.13   −0.57   −2.56 ***
PAS_chr3_1209 Helix-loop-helix DNA-binding domain 0.16   −0.21   −2.56 ***
PAS_chr1-1_0122 Helix-loop-helix DNA-binding domain −0.93   −0.57   −2.33 ***
  1. Log2 fold changes and adjusted P-values (* adjPV < 0.1; ** adjPV < 0.05; *** adjPV < 0.01) are shown (see Additional file 1: Table S1 for detailed data). Up-regulated genes are in bold letters, down-regulated genes in bold and italics.