Characterisation of the DNA Binding Domain of the Yeast RAP1 Protein

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1990 May 11

PMID 2187178

Citations 36

Authors

Y A Henry

A Chambers

J S Tsang

A J Kingsman

S M Kingsman

Affiliations

Soon will be listed here.

Abstract

The 827 amino acid yeast RAP1 protein interacts with DNA to regulate gene expression at numerous unrelated loci in the yeast genome. By a combination of amino, carboxy and internal deletions, we have defined an internal 235 amino acid fragment of the yeast RAP1 protein that can bind efficiently to the RAP1 binding site of the PGK Upstream Activation Sequence (UAS). This domain spans residues 361 to 596 of the full length protein and lacks any homology to the DNA binding 'zinc finger' or 'helix-turn-helix' structural motifs. All the RAP1 binding sites we have tested bind domain 361-596, arguing that RAP1 binds all its chromosomal sites via this domain. The domain could not be further reduced in size suggesting that it represents the minimal functional DNA binding domain. The relevance of potential regions of secondary structure within the minimal binding domain is discussed.

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References

Melton D, Krieg P, Rebagliati M, Maniatis T, Zinn K, Green M . Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984; 12(18):7035-56. PMC: 320141. DOI: 10.1093/nar/12.18.7035. View

Capieaux E, Vignais M, Sentenac A, Goffeau A . The yeast H+-ATPase gene is controlled by the promoter binding factor TUF. J Biol Chem. 1989; 264(13):7437-46. View

Keegan L, Gill G, Ptashne M . Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science. 1986; 231(4739):699-704. DOI: 10.1126/science.3080805. View

Huet J, Cottrelle P, Cool M, Vignais M, Thiele D, Marck C . A general upstream binding factor for genes of the yeast translational apparatus. EMBO J. 1985; 4(13A):3539-47. PMC: 554694. DOI: 10.1002/j.1460-2075.1985.tb04114.x. View

Buchman A, Lue N, Kornberg R . Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein. Mol Cell Biol. 1988; 8(12):5086-99. PMC: 365610. DOI: 10.1128/mcb.8.12.5086-5099.1988. View

Nishizawa M, Araki R, Teranishi Y . Identification of an upstream activating sequence and an upstream repressible sequence of the pyruvate kinase gene of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1989; 9(2):442-51. PMC: 362619. DOI: 10.1128/mcb.9.2.442-451.1989. View

Raychaudhuri P, Bagchi S, Nevins J . DNA-binding activity of the adenovirus-induced E4F transcription factor is regulated by phosphorylation. Genes Dev. 1989; 3(5):620-7. DOI: 10.1101/gad.3.5.620. View

Thukral S, Tavianini M, BLUMBERG H, Young E . Localization of a minimal binding domain and activation regions in yeast regulatory protein ADR1. Mol Cell Biol. 1989; 9(6):2360-9. PMC: 362309. DOI: 10.1128/mcb.9.6.2360-2369.1989. View

Hurd H, Roberts J . Upstream regulatory sequences of the yeast RNR2 gene include a repression sequence and an activation site that binds the RAP1 protein. Mol Cell Biol. 1989; 9(12):5359-72. PMC: 363704. DOI: 10.1128/mcb.9.12.5359-5372.1989. View

10.

Chambers A, Tsang J, Stanway C, Kingsman A, Kingsman S . Transcriptional control of the Saccharomyces cerevisiae PGK gene by RAP1. Mol Cell Biol. 1989; 9(12):5516-24. PMC: 363722. DOI: 10.1128/mcb.9.12.5516-5524.1989. View

11.

Stanway C, Chambers A, Kingsman A, Kingsman S . Characterization of the transcriptional potency of sub-elements of the UAS of the yeast PGK gene in a PGK mini-promoter. Nucleic Acids Res. 1989; 17(22):9205-18. PMC: 335125. DOI: 10.1093/nar/17.22.9205. View

12.

Diffley J, Stillman B . Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science. 1989; 246(4933):1034-8. DOI: 10.1126/science.2511628. View

13.

Halfter H, Kavety B, Vandekerckhove J, Kiefer F, Gallwitz D . Sequence, expression and mutational analysis of BAF1, a transcriptional activator and ARS1-binding protein of the yeast Saccharomyces cerevisiae. EMBO J. 1989; 8(13):4265-72. PMC: 401629. DOI: 10.1002/j.1460-2075.1989.tb08612.x. View

14.

Rhode P, Sweder K, Oegema K, Campbell J . The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev. 1989; 3(12A):1926-39. DOI: 10.1101/gad.3.12a.1926. View

15.

Longtine M, Wilson N, Petracek M, Berman J . A yeast telomere binding activity binds to two related telomere sequence motifs and is indistinguishable from RAP1. Curr Genet. 1989; 16(4):225-39. DOI: 10.1007/BF00422108. View

16.

Shore D, Stillman D, Brand A, Nasmyth K . Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication. EMBO J. 1987; 6(2):461-7. PMC: 553417. DOI: 10.1002/j.1460-2075.1987.tb04776.x. View

17.

Miller J, McLachlan A, Klug A . Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985; 4(6):1609-14. PMC: 554390. DOI: 10.1002/j.1460-2075.1985.tb03825.x. View

18.

Garnier J, Osguthorpe D, Robson B . Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978; 120(1):97-120. DOI: 10.1016/0022-2836(78)90297-8. View

19.

Garner M, Revzin A . A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981; 9(13):3047-60. PMC: 327330. DOI: 10.1093/nar/9.13.3047. View

20.

Fried M, Crothers D . Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981; 9(23):6505-25. PMC: 327619. DOI: 10.1093/nar/9.23.6505. View