Gal4 transcription factor

The Gal4 transcription factor is a positive regulator of gene expression of galactose-induced genes.[1]

The Gal4 protein represents a large fungal family of transcription factors, Gal4 family, which includes over 50 members in the yeast Saccharomyces cerevisiae e.g. Oaf1, Pip2, Pdr1, Pdr3, Leu3.[2]

Gal4 domains

Two executive domains, DNA binding and activation domains, provide key function of the Gal4 protein conforming to most of the transcription factors.

DNA binding domain

Localised to the N-terminus, belongs to the Zn(2)-C6 fungal family, which forms a Zn – cysteines thiolate cluster.[3][4] The Gal4 DNA Binding domain recognised specifically response element in GAL1 promoter. [5][6]

Gal4 activation domain

Localised to the C-terminus, belongs to the nine amino acids TransActivation Domain family, 9aaTAD, together with Oaf1, Pip2, Pdr1, Pdr3, but also p53, E2A, MLL.[7][8][9][10][11]

Regulation

Galactose induces Gal4 mediated transcription albeit Glucose causes severe repression.[12][13]

As a part of the Gal4 regulation, inhibitory protein Gal80 recognises and binds to the Gal4 region (853-874 aa)[14][15][16] encompassing the Gal4 activation domain 9aaTAD.[17][18][19]

The inhibitory protein Gal80 is sequestered by regulatory protein Gal3 in Galactose dependent manner.[20][21][22][23]

Mutants

The Gal4 loss-of-function mutant gal4-64 (1-852 aa, deletion of the Gal4 C-terminal 29 aa) lost both interaction with Gal80 and activation function.[24][25][26]

In the Gal4 reverted mutant Gal4C-62 mutant,[27] a sequence (QTAY N AFMN) with the 9aaTAD pattern emerged and restored activation function of the Gal4 protein.(doi: https://doi.org/10.1101/110882)

Inactive constructs

The activation domain Gal4 is inhibited by C-terminal domain in some Gal4 constructs.[28][29] (doi: https://doi.org/10.1101/110882)

Proteosome

A subunit of the 26 S proteasome Sug2 regulatory protein has a molecular and functional interaction with Gal4 function.[30][31]

Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo.[32]

The native Gal4 monoubiquitination protects from 19S-mediated destabilizing under inducing conditions.[33]

Mediators of transcription

The Gal4 activation function is mediated by MED15 (Gal11).[34][35][36][37][38][39][40][41]

The Gal4 protein interacts also with other mediators of transcription as are Tra1,[42][43][44][45][46] TAF9,[47] and SAGA/MED15 complex.[48][49] (http://mcb.asm.org/content/25/1/114/F8.large.jpg)

Application

The broad use of the Gal4 is in yeast two hybrid system to screen or to assay protein-protein interactions in eukaryotic cells from yeast to human.

In the GAL4/UAS system, the Gal4 protein and Gal4 upstream activating region (UAS) are used to study the gene expression and function in organisms such as the fruit fly.

The Gal4 and inhibitory protein Gal80 have found application in a genetics technique for creating individually labeled homozygous cells called Mosaic analysis with a repressible cell marker MARCM.

References

  1. ↑ Klar AJ, Halvorson HO (1974). "Studies on the positive regulatory gene, GAL4, in regulation of galactose catabolic enzymes in Saccharomyces cerevisiae". Mol. Gen. Genet. 135 (3): 203–12. PMID 4376212.
  2. ↑ Schjerling P, Holmberg S (1996). "Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators". Nucleic Acids Res. 24 (23): 4599–607. PMC 146297. PMID 8967907.
  3. ↑ Marmorstein R, Carey M, Ptashne M, Harrison SC (1992). "DNA recognition by GAL4: structure of a protein-DNA complex". Nature. 356 (6368): 408–14. Bibcode:1992Natur.356..408M. doi:10.1038/356408a0. PMID 1557122.
  4. ↑ Pan T, Coleman JE (1990). "The DNA binding domain of GAL4 forms a binuclear metal ion complex". Biochemistry. 29 (12): 2023–9. PMID 2186803.
  5. ↑ Liam, Keegan; G., Gill; M., Ptashne (February 1986). "Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein". Science. 231, (4739). doi:10.1126/science.3080805.
  6. ↑ Edward, Giniger; Susan M.Varnum, Varnum; Mark, Ptashne (April 1985). "Specific DNA binding of GAL4, a positive regulatory protein of yeast". Cell. 40 (4). doi:10.1016/0092-8674(85)90336-8.
  7. ↑ Ding WV, Johnston SA (1997). "The DNA binding and activation domains of Gal4p are sufficient for conveying its regulatory signals". Mol. Cell. Biol. 17 (5): 2538–49. PMC 232103. PMID 9111323.
  8. ↑ Melcher K, Johnston SA (1995). "GAL4 interacts with TATA-binding protein and coactivators". Mol. Cell. Biol. 15 (5): 2839–48. PMC 230515. PMID 7739564.
  9. ↑ Piskacek S, Gregor M, Nemethova M, Grabner M, Kovarik P, Piskacek M (2007). "Nine-amino-acid transactivation domain: establishment and prediction utilities". Genomics. 89 (6): 756–68. doi:10.1016/j.ygeno.2007.02.003. PMID 17467953.
  10. ↑ Piskacek M, Havelka M, Rezacova M, Knight A (2016). "The 9aaTAD Transactivation Domains: From Gal4 to p53". PLoS ONE. 11 (9): e0162842. Bibcode:2016PLoSO..1162842P. doi:10.1371/journal.pone.0162842. PMC 5019370. PMID 27618436.
  11. ↑ Piskacek M, Havelka M, Rezacova M, Knight A (2017). "The 9aaTAD Is Exclusive Activation Domain in Gal4". PLoS ONE. 12 (1): e0169261. Bibcode:2017PLoSO..1269261P. doi:10.1371/journal.pone.0169261. PMC 5215927. PMID 28056036.
  12. ↑ Klar AJ, Halvorson HO (1974). "Studies on the positive regulatory gene, GAL4, in regulation of galactose catabolic enzymes in Saccharomyces cerevisiae". Mol. Gen. Genet. 135 (3): 203–12. PMID 4376212.
  13. ↑ Griggs DW, Johnston M (1991). "Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression". Proc. Natl. Acad. Sci. U.S.A. 88 (19): 8597–601. Bibcode:1991PNAS...88.8597G. PMC 52556. PMID 1924319.
  14. ↑ Kumar PR, Yu Y, Sternglanz R, Johnston SA, Joshua-Tor L (2008). "NADP regulates the yeast GAL induction system". Science. 319 (5866): 1090–2. Bibcode:2008Sci...319.1090K. doi:10.1126/science.1151903. PMC 2726985. PMID 18292341.
  15. ↑ Thoden JB, Ryan LA, Reece RJ, Holden HM (2008). "The interaction between an acidic transcriptional activator and its inhibitor. The molecular basis of Gal4p recognition by Gal80p". J. Biol. Chem. 283 (44): 30266–72. doi:10.1074/jbc.M805200200. PMC 2573081. PMID 18701455.
  16. ↑ Johnston SA, Salmeron JM, Dincher SS (1987). "Interaction of positive and negative regulatory proteins in the galactose regulon of yeast". Cell. 50 (1): 143–6. PMID 3297350. , which includes the 9aaTAD domain (862-871 aa)
  17. ↑ Piskacek S, Gregor M, Nemethova M, Grabner M, Kovarik P, Piskacek M (2007). "Nine-amino-acid transactivation domain: establishment and prediction utilities". Genomics. 89 (6): 756–68. doi:10.1016/j.ygeno.2007.02.003. PMID 17467953.
  18. ↑ Piskacek M, Havelka M, Rezacova M, Knight A (2016). "The 9aaTAD Transactivation Domains: From Gal4 to p53". PLoS ONE. 11 (9): e0162842. Bibcode:2016PLoSO..1162842P. doi:10.1371/journal.pone.0162842. PMC 5019370. PMID 27618436.
  19. ↑ Piskacek M, Havelka M, Rezacova M, Knight A (2017). "The 9aaTAD Is Exclusive Activation Domain in Gal4". PLoS ONE. 12 (1): e0169261. Bibcode:2017PLoSO..1269261P. doi:10.1371/journal.pone.0169261. PMC 5215927. PMID 28056036.
  20. ↑ Egriboz O, Jiang F, Hopper JE (2011). "Rapid GAL gene switch of Saccharomyces cerevisiae depends on nuclear Gal3, not nucleocytoplasmic trafficking of Gal3 and Gal80". Genetics. 189 (3): 825–36. doi:10.1534/genetics.111.131839. PMC 3213366. PMID 21890741.
  21. ↑ Jiang F, Frey BR, Evans ML, Friel JC, Hopper JE (2009). "Gene activation by dissociation of an inhibitor from a transcriptional activation domain". Mol. Cell. Biol. 29 (20): 5604–10. doi:10.1128/MCB.00632-09. PMC 2756894. PMID 19651897.
  22. ↑ Peng G, Hopper JE (2002). "Gene activation by interaction of an inhibitor with a cytoplasmic signaling protein". Proc. Natl. Acad. Sci. U.S.A. 99 (13): 8548–53. Bibcode:2002PNAS...99.8548P. doi:10.1073/pnas.142100099. PMC 124307. PMID 12084916.
  23. ↑ Tsuyumu S, Adams BG (1974). "Dilution kinetic studies of yeast populations: in vivo aggregation of galactose utilizing enzymes and positive regulator molecules". Genetics. 77 (3): 491–505. PMC 1213142. PMID 4369925.
  24. ↑ DOUGLAS HC, CONDIE F (1954). "The genetic control of galactose utilization in Saccharomyces". J. Bacteriol. 68 (6): 662–70. PMC 386212. PMID 13221541.
  25. ↑ DOUGLAS HC, HAWTHORNE DC (1964). "ENZYMATIC EXPRESSION AND GENETIC LINKAGE OF GENES CONTROLLING GALACTOSE UTILIZATION IN SACCHAROMYCES". Genetics. 49: 837–44. PMC 1210618. PMID 14158615.
  26. ↑ Matsumoto K, Adachi Y, Toh-e A, Oshima Y (1980). "Function of positive regulatory gene gal4 in the synthesis of galactose pathway enzymes in Saccharomyces cerevisiae: evidence that the GAL81 region codes for part of the gal4 protein". J. Bacteriol. 141 (2): 508–27. PMC 293654. PMID 6988385.
  27. ↑ Johnston SA, Salmeron JM, Dincher SS (1987). "Interaction of positive and negative regulatory proteins in the galactose regulon of yeast". Cell. 50 (1): 143–6. PMID 3297350.
  28. ↑ Ma J, Ptashne M (1987). "Deletion analysis of GAL4 defines two transcriptional activating segments". Cell. 48 (5): 847–53. PMID 3028647.
  29. ↑ Warfield L, Tuttle LM, Pacheco D, Klevit RE, Hahn S (2014). "A sequence-specific transcription activator motif and powerful synthetic variants that bind Mediator using a fuzzy protein interface". Proc. Natl. Acad. Sci. U.S.A. 111 (34): E3506–13. Bibcode:2014PNAS..111E3506W. doi:10.1073/pnas.1412088111. PMC 4151740. PMID 25122681.
  30. ↑ Chang C, Gonzalez F, Rothermel B, Sun L, Johnston SA, Kodadek T (2001). "The Gal4 activation domain binds Sug2 protein, a proteasome component, in vivo and in vitro". J. Biol. Chem. 276 (33): 30956–63. doi:10.1074/jbc.M102254200. PMID 11418596.
  31. ↑ Russell SJ, Johnston SA (2001). "Evidence that proteolysis of Gal4 cannot explain the transcriptional effects of proteasome ATPase mutations". J. Biol. Chem. 276 (13): 9825–31. doi:10.1074/jbc.M010889200. PMID 11152478.
  32. ↑ Nalley K, Johnston SA, Kodadek T (2006). "Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo". Nature. 442 (7106): 1054–7. doi:10.1038/nature05067. PMID 16929306.
  33. ↑ Ferdous A, Sikder D, Gillette T, Nalley K, Kodadek T, Johnston SA (2007). "The role of the proteasomal ATPases and activator monoubiquitylation in regulating Gal4 binding to promoters". Genes Dev. 21 (1): 112–23. doi:10.1101/gad.1493207. PMC 1759896. PMID 17167105.
  34. ↑ Fassler JS, Winston F (1989). "The Saccharomyces cerevisiae SPT13/GAL11 gene has both positive and negative regulatory roles in transcription". Mol. Cell. Biol. 9 (12): 5602–9. PMC 363730. PMID 2685570.
  35. ↑ Han Y, Kodadek T (2000). "Peptides selected to bind the Gal80 repressor are potent transcriptional activation domains in yeast". J. Biol. Chem. 275 (20): 14979–84. PMID 10809742.
  36. ↑ Hashimoto H, Kikuchi Y, Nogi Y, Fukasawa T (1983). "Regulation of expression of the galactose gene cluster in Saccharomyces cerevisiae. Isolation and characterization of the regulatory gene GAL4". Mol. Gen. Genet. 191 (1): 31–8. PMID 6350827.
  37. ↑ Hashimoto H, Kikuchi Y, Nogi Y, Fukasawa T (1983). "Regulation of expression of the galactose gene cluster in Saccharomyces cerevisiae. Isolation and characterization of the regulatory gene GAL4". Mol. Gen. Genet. 191 (1): 31–8. PMID 6350827.
  38. ↑ Long RM, Mylin LM, Hopper JE (1991). "GAL11 (SPT13), a transcriptional regulator of diverse yeast genes, affects the phosphorylation state of GAL4, a highly specific transcriptional activator". Mol. Cell. Biol. 11 (4): 2311–4. PMC 359938. PMID 2005915.
  39. ↑ Nogi Y, Fukasawa T (1980). "A novel mutation that affects utilization of galactose in Saccharomyces cerevisiae". Curr. Genet. 2 (2): 115–20. doi:10.1007/BF00420623. PMID 24189802.
  40. ↑ Sakurai H, Hiraoka Y, Fukasawa T (1993). "Yeast GAL11 protein is a distinctive type transcription factor that enhances basal transcription in vitro". Proc. Natl. Acad. Sci. U.S.A. 90 (18): 8382–6. PMC 47360. PMID 8378310.
  41. ↑ Suzuki Y, Nogi Y, Abe A, Fukasawa T (1992). "GAL11 protein, an auxiliary transcription activator for genes encoding galactose-metabolizing enzymes in Saccharomyces cerevisiae". Mol. Cell. Biol. 12 (10): 4806. PMC 360407. PMID 1406662.
  42. ↑ Lin L, Chamberlain L, Zhu LJ, Green MR (2012). "Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4". Proc. Natl. Acad. Sci. U.S.A. 109 (6): 1997–2002. Bibcode:2012PNAS..109.1997L. doi:10.1073/pnas.1116340109. PMC 3277556. PMID 22308403.
  43. ↑ Majmudar CY, Labut AE, Mapp AK (2009). "Tra1 as a screening target for transcriptional activation domain discovery". Bioorg. Med. Chem. Lett. 19 (14): 3733–5. doi:10.1016/j.bmcl.2009.05.045. PMC 4322765. PMID 19497740.
  44. ↑ Lin L, Chamberlain L, Zhu LJ, Green MR (2012). "Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4". Proc. Natl. Acad. Sci. U.S.A. 109 (6): 1997–2002. Bibcode:2012PNAS..109.1997L. doi:10.1073/pnas.1116340109. PMC 3277556. PMID 22308403.
  45. ↑ Majmudar CY, Labut AE, Mapp AK (2009). "Tra1 as a screening target for transcriptional activation domain discovery". Bioorg. Med. Chem. Lett. 19 (14): 3733–5. doi:10.1016/j.bmcl.2009.05.045. PMC 4322765. PMID 19497740.
  46. ↑ Reeves WM, Hahn S (2005). "Targets of the Gal4 transcription activator in functional transcription complexes". Mol. Cell. Biol. 25 (20): 9092–102. doi:10.1128/MCB.25.20.9092-9102.2005. PMC 1265783. PMID 16199885.
  47. ↑ Klein J, Nolden M, Sanders SL, Kirchner J, Weil PA, Melcher K (2003). "Use of a genetically introduced cross-linker to identify interaction sites of acidic activators within native transcription factor IID and SAGA". J. Biol. Chem. 278 (9): 6779–86. doi:10.1074/jbc.M212514200. PMID 12501245.
  48. ↑ Larschan E, Winston F (2005). "The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription". Mol. Cell. Biol. 25 (1): 114–23. doi:10.1128/MCB.25.1.114-123.2005. PMC 538787. PMID 15601835.
  49. ↑ Larsson M, Uvell H, Sandström J, Rydén P, Selth LA, Björklund S (2013). "Functional studies of the yeast med5, med15 and med16 mediator tail subunits". PLoS ONE. 8 (8): e73137. Bibcode:2013PLoSO...873137L. doi:10.1371/journal.pone.0073137. PMC 3750046. PMID 23991176.
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