Histone H3 N-terminal mutations allow hyperactivation of the yeast GAL1 gene in vivo (original) (raw)

Abstract

Recent work has shown that the yeast histone H4 N-terminus, while not essential for viability, is required for repression of the silent mating loci and activation of GAL1 and PHO5 promoters. Because histone H3 shares many structural features with histone H4 and is intimately associated with H4 in the assembled nucleosome, we asked whether H3 has similar functions. While the basic N-terminal domain of H3 is found to be non-essential (deletion of residues 4-40 of this 135 amino acid protein allows viability), its removal has only a minor effect on mating. Surprisingly, both deletions (of residues 4-15) and acetylation site substitutions (at residues 9, 14 and 18) within the N-terminus of H3 allow hyperactivation of the GAL1 promoter as well as a number of other GAL4-regulated genes including GAL2, GAL7 and GAL10. To a limited extent glucose repression is also alleviated by H3 N-terminal deletions. Expression of another inducible promoter, PHO5, is shown to be relatively unaffected. We conclude that the H3 and H4 N-termini have different functions in both the repression of the silent mating loci and in the regulation of GAL1.

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  1. Arents G., Burlingame R. W., Wang B. C., Love W. E., Moudrianakis E. N. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10148–10152. doi: 10.1073/pnas.88.22.10148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bachmair A., Finley D., Varshavsky A. In vivo half-life of a protein is a function of its amino-terminal residue. Science. 1986 Oct 10;234(4773):179–186. doi: 10.1126/science.3018930. [DOI] [PubMed] [Google Scholar]
  3. Bavykin S. G., Usachenko S. I., Lishanskaya A. I., Shick V. V., Belyavsky A. V., Undritsov I. M., Strokov A. A., Zalenskaya I. A., Mirzabekov A. D. Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells. Nucleic Acids Res. 1985 May 24;13(10):3439–3459. doi: 10.1093/nar/13.10.3439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Belyavsky A. V., Bavykin S. G., Goguadze E. G., Mirzabekov A. D. Primary organization of nucleosomes containing all five histones and DNA 175 and 165 base-pairs long. J Mol Biol. 1980 May 25;139(3):519–536. doi: 10.1016/0022-2836(80)90144-8. [DOI] [PubMed] [Google Scholar]
  5. Chahal S. S., Matthews H. R., Bradbury E. M. Acetylation of histone H4 and its role in chromatin structure and function. Nature. 1980 Sep 4;287(5777):76–79. doi: 10.1038/287076a0. [DOI] [PubMed] [Google Scholar]
  6. Clark-Adams C. D., Norris D., Osley M. A., Fassler J. S., Winston F. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 1988 Feb;2(2):150–159. doi: 10.1101/gad.2.2.150. [DOI] [PubMed] [Google Scholar]
  7. Cross S. L., Smith M. M. Comparison of the structure and cell cycle expression of mRNAs encoded by two histone H3-H4 loci in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Feb;8(2):945–954. doi: 10.1128/mcb.8.2.945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dong F., van Holde K. E. Nucleosome positioning is determined by the (H3-H4)2 tetramer. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10596–10600. doi: 10.1073/pnas.88.23.10596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Durrin L. K., Mann R. K., Grunstein M. Nucleosome loss activates CUP1 and HIS3 promoters to fully induced levels in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1992 Apr;12(4):1621–1629. doi: 10.1128/mcb.12.4.1621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Durrin L. K., Mann R. K., Kayne P. S., Grunstein M. Yeast histone H4 N-terminal sequence is required for promoter activation in vivo. Cell. 1991 Jun 14;65(6):1023–1031. doi: 10.1016/0092-8674(91)90554-c. [DOI] [PubMed] [Google Scholar]
  11. Fedor M. J., Kornberg R. D. Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes. Mol Cell Biol. 1989 Apr;9(4):1721–1732. doi: 10.1128/mcb.9.4.1721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fedor M. J., Lue N. F., Kornberg R. D. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol. 1988 Nov 5;204(1):109–127. doi: 10.1016/0022-2836(88)90603-1. [DOI] [PubMed] [Google Scholar]
  13. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  14. Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature. 1992 Jan 16;355(6357):219–224. doi: 10.1038/355219a0. [DOI] [PubMed] [Google Scholar]
  15. Finley R. L., Jr, Chen S., Ma J., Byrne P., West R. W., Jr Opposing regulatory functions of positive and negative elements in UASG control transcription of the yeast GAL genes. Mol Cell Biol. 1990 Nov;10(11):5663–5670. doi: 10.1128/mcb.10.11.5663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Flick J. S., Johnston M. Two systems of glucose repression of the GAL1 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1990 Sep;10(9):4757–4769. doi: 10.1128/mcb.10.9.4757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Griggs D. W., Johnston M. Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8597–8601. doi: 10.1073/pnas.88.19.8597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Grunstein M. Histone function in transcription. Annu Rev Cell Biol. 1990;6:643–678. doi: 10.1146/annurev.cb.06.110190.003235. [DOI] [PubMed] [Google Scholar]
  19. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 1988 Dec 23;55(6):1137–1145. doi: 10.1016/0092-8674(88)90258-9. [DOI] [PubMed] [Google Scholar]
  20. Han M., Kim U. J., Kayne P., Grunstein M. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2221–2228. doi: 10.1002/j.1460-2075.1988.tb03061.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hayes J. J., Clark D. J., Wolffe A. P. Histone contributions to the structure of DNA in the nucleosome. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6829–6833. doi: 10.1073/pnas.88.15.6829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hebbes T. R., Thorne A. W., Crane-Robinson C. A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 1988 May;7(5):1395–1402. doi: 10.1002/j.1460-2075.1988.tb02956.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Hill C. S., Thomas J. O. Core histone-DNA interactions in sea urchin sperm chromatin. The N-terminal tail of H2B interacts with linker DNA. Eur J Biochem. 1990 Jan 12;187(1):145–153. doi: 10.1111/j.1432-1033.1990.tb15288.x. [DOI] [PubMed] [Google Scholar]
  24. Johnson L. M., Fisher-Adams G., Grunstein M. Identification of a non-basic domain in the histone H4 N-terminus required for repression of the yeast silent mating loci. EMBO J. 1992 Jun;11(6):2201–2209. doi: 10.1002/j.1460-2075.1992.tb05279.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Johnson L. M., Kayne P. S., Kahn E. S., Grunstein M. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6286–6290. doi: 10.1073/pnas.87.16.6286. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Johnston M. A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol Rev. 1987 Dec;51(4):458–476. doi: 10.1128/mr.51.4.458-476.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Johnston M., Davis R. W. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Aug;4(8):1440–1448. doi: 10.1128/mcb.4.8.1440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kayne P. S., Kim U. J., Han M., Mullen J. R., Yoshizaki F., Grunstein M. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell. 1988 Oct 7;55(1):27–39. doi: 10.1016/0092-8674(88)90006-2. [DOI] [PubMed] [Google Scholar]
  29. Kim U. J., Han M., Kayne P., Grunstein M. Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2211–2219. doi: 10.1002/j.1460-2075.1988.tb03060.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Knezetic J. A., Luse D. S. The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro. Cell. 1986 Apr 11;45(1):95–104. doi: 10.1016/0092-8674(86)90541-6. [DOI] [PubMed] [Google Scholar]
  31. Kornberg R. D., Lorch Y. Irresistible force meets immovable object: transcription and the nucleosome. Cell. 1991 Nov 29;67(5):833–836. doi: 10.1016/0092-8674(91)90354-2. [DOI] [PubMed] [Google Scholar]
  32. Kruger W., Herskowitz I. A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol Cell Biol. 1991 Aug;11(8):4135–4146. doi: 10.1128/mcb.11.8.4135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  34. Köhrer K., Domdey H. Preparation of high molecular weight RNA. Methods Enzymol. 1991;194:398–405. doi: 10.1016/0076-6879(91)94030-g. [DOI] [PubMed] [Google Scholar]
  35. Laybourn P. J., Kadonaga J. T. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science. 1991 Oct 11;254(5029):238–245. doi: 10.1126/science.254.5029.238. [DOI] [PubMed] [Google Scholar]
  36. Lorch Y., LaPointe J. W., Kornberg R. D. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell. 1987 Apr 24;49(2):203–210. doi: 10.1016/0092-8674(87)90561-7. [DOI] [PubMed] [Google Scholar]
  37. Mahadevan L. C., Willis A. C., Barratt M. J. Rapid histone H3 phosphorylation in response to growth factors, phorbol esters, okadaic acid, and protein synthesis inhibitors. Cell. 1991 May 31;65(5):775–783. doi: 10.1016/0092-8674(91)90385-c. [DOI] [PubMed] [Google Scholar]
  38. Marvin K. W., Yau P., Bradbury E. M. Isolation and characterization of acetylated histones H3 and H4 and their assembly into nucleosomes. J Biol Chem. 1990 Nov 15;265(32):19839–19847. [PubMed] [Google Scholar]
  39. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  40. McKerrow J. H. Human fibroblast collagenase contains an amino acid sequence homologous to the zinc-binding site of Serratia protease. J Biol Chem. 1987 May 5;262(13):5943–5943. [PubMed] [Google Scholar]
  41. Megee P. C., Morgan B. A., Mittman B. A., Smith M. M. Genetic analysis of histone H4: essential role of lysines subject to reversible acetylation. Science. 1990 Feb 16;247(4944):841–845. doi: 10.1126/science.2106160. [DOI] [PubMed] [Google Scholar]
  42. Mirzabekov A. D., Shick V. V., Belyavsky A. V., Bavykin S. G. Primary organization of nucleosome core particle of chromatin: sequence of histone arrangement along DNA. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4184–4188. doi: 10.1073/pnas.75.9.4184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Morgan B. A., Mittman B. A., Smith M. M. The highly conserved N-terminal domains of histones H3 and H4 are required for normal cell cycle progression. Mol Cell Biol. 1991 Aug;11(8):4111–4120. doi: 10.1128/mcb.11.8.4111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Nehlin J. O., Carlberg M., Ronne H. Control of yeast GAL genes by MIG1 repressor: a transcriptional cascade in the glucose response. EMBO J. 1991 Nov;10(11):3373–3377. doi: 10.1002/j.1460-2075.1991.tb04901.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Norton V. G., Imai B. S., Yau P., Bradbury E. M. Histone acetylation reduces nucleosome core particle linking number change. Cell. 1989 May 5;57(3):449–457. doi: 10.1016/0092-8674(89)90920-3. [DOI] [PubMed] [Google Scholar]
  46. Norton V. G., Marvin K. W., Yau P., Bradbury E. M. Nucleosome linking number change controlled by acetylation of histones H3 and H4. J Biol Chem. 1990 Nov 15;265(32):19848–19852. [PubMed] [Google Scholar]
  47. Park E. C., Szostak J. W. Point mutations in the yeast histone H4 gene prevent silencing of the silent mating type locus HML. Mol Cell Biol. 1990 Sep;10(9):4932–4934. doi: 10.1128/mcb.10.9.4932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Rothstein R. J. One-step gene disruption in yeast. Methods Enzymol. 1983;101:202–211. doi: 10.1016/0076-6879(83)01015-0. [DOI] [PubMed] [Google Scholar]
  49. Sarkar G., Sommer S. S. The "megaprimer" method of site-directed mutagenesis. Biotechniques. 1990 Apr;8(4):404–407. [PubMed] [Google Scholar]
  50. Schuster T., Han M., Grunstein M. Yeast histone H2A and H2B amino termini have interchangeable functions. Cell. 1986 May 9;45(3):445–451. doi: 10.1016/0092-8674(86)90330-2. [DOI] [PubMed] [Google Scholar]
  51. Shick V. V., Belyavsky A. V., Bavykin S. G., Mirzabekov A. D. Primary organization of the nucleosome core particles. Sequential arrangement of histones along DNA. J Mol Biol. 1980 May 25;139(3):491–517. doi: 10.1016/0022-2836(80)90143-6. [DOI] [PubMed] [Google Scholar]
  52. Shrader T. E., Crothers D. M. Artificial nucleosome positioning sequences. Proc Natl Acad Sci U S A. 1989 Oct;86(19):7418–7422. doi: 10.1073/pnas.86.19.7418. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Smith M. M., Murray K. Yeast H3 and H4 histone messenger RNAs are transcribed from two non-allelic gene sets. J Mol Biol. 1983 Sep 25;169(3):641–661. doi: 10.1016/s0022-2836(83)80163-6. [DOI] [PubMed] [Google Scholar]
  54. Taylor I. C., Workman J. L., Schuetz T. J., Kingston R. E. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 1991 Jul;5(7):1285–1298. doi: 10.1101/gad.5.7.1285. [DOI] [PubMed] [Google Scholar]
  55. Thorne A. W., Kmiciek D., Mitchelson K., Sautiere P., Crane-Robinson C. Patterns of histone acetylation. Eur J Biochem. 1990 Nov 13;193(3):701–713. doi: 10.1111/j.1432-1033.1990.tb19390.x. [DOI] [PubMed] [Google Scholar]
  56. Torchia T. E., Hamilton R. W., Cano C. L., Hopper J. E. Disruption of regulatory gene GAL80 in Saccharomyces cerevisiae: effects on carbon-controlled regulation of the galactose/melibiose pathway genes. Mol Cell Biol. 1984 Aug;4(8):1521–1527. doi: 10.1128/mcb.4.8.1521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Tschopp J. F., Emr S. D., Field C., Schekman R. GAL2 codes for a membrane-bound subunit of the galactose permease in Saccharomyces cerevisiae. J Bacteriol. 1986 Apr;166(1):313–318. doi: 10.1128/jb.166.1.313-318.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wallis J. W., Rykowski M., Grunstein M. Yeast histone H2B containing large amino terminus deletions can function in vivo. Cell. 1983 Dec;35(3 Pt 2):711–719. doi: 10.1016/0092-8674(83)90104-6. [DOI] [PubMed] [Google Scholar]
  59. Waterborg J. H., Matthews H. R. Patterns of histone acetylation in Physarum polycephalum. H2A and H2B acetylation is functionally distinct from H3 and H4 acetylation. Eur J Biochem. 1984 Jul 16;142(2):329–335. doi: 10.1111/j.1432-1033.1984.tb08290.x. [DOI] [PubMed] [Google Scholar]
  60. West R. W., Jr, Chen S. M., Putz H., Butler G., Banerjee M. GAL1-GAL10 divergent promoter region of Saccharomyces cerevisiae contains negative control elements in addition to functionally separate and possibly overlapping upstream activating sequences. Genes Dev. 1987 Dec;1(10):1118–1131. doi: 10.1101/gad.1.10.1118. [DOI] [PubMed] [Google Scholar]
  61. West R. W., Jr, Yocum R. R., Ptashne M. Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: location and function of the upstream activating sequence UASG. Mol Cell Biol. 1984 Nov;4(11):2467–2478. doi: 10.1128/mcb.4.11.2467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Workman J. L., Roeder R. G. Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell. 1987 Nov 20;51(4):613–622. doi: 10.1016/0092-8674(87)90130-9. [DOI] [PubMed] [Google Scholar]
  63. Workman J. L., Roeder R. G., Kingston R. E. An upstream transcription factor, USF (MLTF), facilitates the formation of preinitiation complexes during in vitro chromatin assembly. EMBO J. 1990 Apr;9(4):1299–1308. doi: 10.1002/j.1460-2075.1990.tb08239.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Workman J. L., Taylor I. C., Kingston R. E. Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes. Cell. 1991 Feb 8;64(3):533–544. doi: 10.1016/0092-8674(91)90237-s. [DOI] [PubMed] [Google Scholar]
  65. Xu H. X., Johnson L., Grunstein M. Coding and noncoding sequences at the 3' end of yeast histone H2B mRNA confer cell cycle regulation. Mol Cell Biol. 1990 Jun;10(6):2687–2694. doi: 10.1128/mcb.10.6.2687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Yocum R. R., Hanley S., West R., Jr, Ptashne M. Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Oct;4(10):1985–1998. doi: 10.1128/mcb.4.10.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]