Home LiteratureArticle Details
PMID: 8082184 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III.

Current genetics ·Vol. 25 ·No. 5 ·1994-05-00 ·Pages 396-406

Fondrat C, Kalogeropoulos A

Abstract

The systematic sequencing of the yeast genome reveals the presence of many potential genes of unknown function. One way to approach their function is to define which regulatory system controls their transcription. This can also be accomplished by the detection of an upstream activation sequence (UAS). Such a detection can be done by computer, provided that the definition of a UAS includes sufficient and precise rules. We have established such rules for the UASs of the GAL4, RAP1 (RPG box), GCN4, and the HAP2/HAP3/HAP4 regulatory proteins, as well as for a motif (PAC) frequently found upstream of the genes of the RNA polymerase A and C subunits. These rules were applied to the chromosome III DNA sequence, and gave precise predictions.

MeSH Terms
Base Sequence CCAAT-Binding Factor Chromosomes, Fungal Consensus Sequence DNA, Fungal/genetics DNA-Binding Proteins Fungal Proteins/genetics Gene Expression Regulation, Fungal Genes, Fungal Molecular Sequence Data Open Reading Frames Protein Kinases/genetics Ribosomal Proteins/genetics Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins Transcription Factors/genetics
Chemicals
CCAAT-Binding Factor DNA, Fungal DNA-Binding Proteins Fungal Proteins GAL4 protein, S cerevisiae HAP4 protein, S cerevisiae Ribosomal Proteins Saccharomyces cerevisiae Proteins Transcription Factors Protein Kinases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Fondrat C
Institut de Génétique et Microbiologie, Centre Universitaire d'Orsay, France.
Kalogeropoulos A
References (35)
35 references, click to expand
  1. Control of ribosome biogenesis in yeast.
    Trends Genet. 1988 Mar;4(3):64-8 PMID: 3076293
  2. Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984.
    Eur J Biochem. 1985 Jul 1;150(1):1-5 PMID: 2410266
  3. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
    Protein Sci. 1992 Dec;1(12):1677-90 PMID: 1304897
  4. Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements.
    Cell. 1987 Dec 4;51(5):721-32 PMID: 3315231
  5. Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8 PMID: 3162770
  6. Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein.
    Mol Cell Biol. 1988 Dec;8(12):5086-99 PMID: 3072472
  7. RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III).
    J Biol Chem. 1991 Aug 15;266(23 ):15300-7 PMID: 1869554
  8. Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner.
    Cell. 1987 Dec 24;51(6):953-61 PMID: 2826015
  9. Consensus patterns in DNA.
    Methods Enzymol. 1990;183:211-21 PMID: 2179676
  10. Structure and regulation of KGD1, the structural gene for yeast alpha-ketoglutarate dehydrogenase.
    Mol Cell Biol. 1989 Jun;9(6):2695-705 PMID: 2503710
  11. Principle of codification for quick comparisons with the entire biomolecule databanks and associated programs in FORTRAN 77.
    Nucleic Acids Res. 1986 Jan 10;14(1):197-204 PMID: 3753764
  12. The yeast H+-ATPase gene is controlled by the promoter binding factor TUF.
    J Biol Chem. 1989 May 5;264(13):7437-46 PMID: 2523395
  13. From data banks to data bases.
    Res Microbiol. 1991 Sep-Oct;142(7-8):913-6 PMID: 1784830
  14. Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2-HAP3-responsive site.
    Mol Cell Biol. 1988 Feb;8(2):647-54 PMID: 2832731
  15. A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription.
    EMBO J. 1986 Mar;5(3):603-8 PMID: 3011415
  16. Contacts between the factor TUF and RPG sequences.
    J Biol Chem. 1990 Aug 25;265(24):14669-74 PMID: 2201690
  17. DNA recognition by GAL4: structure of a protein-DNA complex.
    Nature. 1992 Apr 2;356(6368):408-14 PMID: 1557122
  18. BISANCE: a French service for access to biomolecular sequence databases.
    Comput Appl Biosci. 1990 Oct;6(4):355-6 PMID: 2257496
  19. GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast.
    Cell. 1985 Nov;43(1):177-88 PMID: 3907851
  20. Nucleotide sequence of yeast gene CP A1 encoding the small subunit of arginine-pathway carbamoyl-phosphate synthetase. Homology of the deduced amino acid sequence to other glutamine amidotransferases.
    Eur J Biochem. 1985 Jan 15;146(2):371-81 PMID: 3881260
  21. Tripartite upstream promoter element essential for expression of Saccharomyces cerevisiae ribosomal protein genes.
    Mol Cell Biol. 1986 Feb;6(2):674-87 PMID: 3023862
  22. Correlation between observed transcripts and sequenced ORFs of chromosome III of Saccharomyces cerevisiae.
    Nucleic Acids Res. 1993 Mar 11;21(5):1149-53 PMID: 8464699
  23. Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein.
    Science. 1986 Oct 24;234(4775):451-7 PMID: 3532321
  24. A knowledge base for predicting protein localization sites in eukaryotic cells.
    Genomics. 1992 Dec;14(4):897-911 PMID: 1478671
  25. Chromosome III of Saccharomyces cerevisiae: an ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes.
    Yeast. 1990 Sep-Oct;6(5):383-401 PMID: 2220074
  26. Conserved sequences upstream of yeast ribosomal protein genes.
    Curr Genet. 1985;9(4):273-7 PMID: 3916723
  27. Analysis of upstream activation sites of yeast ribosomal protein genes.
    Nucleic Acids Res. 1987 Aug 11;15(15):6037-48 PMID: 3627978
  28. Identification of an upstream activation sequence and other cis-acting elements required for transcription of COX6 from Saccharomyces cerevisiae.
    Mol Cell Biol. 1989 Dec;9(12):5350-8 PMID: 2555697
  29. Positive regulation of the LPD1 gene of Saccharomyces cerevisiae by the HAP2/HAP3/HAP4 activation system.
    Mol Gen Genet. 1992 Jan;231(2):296-303 PMID: 1310523
  30. The complete DNA sequence of yeast chromosome III.
    Nature. 1992 May 7;357(6373):38-46 PMID: 1574125
  31. Nucleotide sequence of the yeast ILV2 gene which encodes acetolactate synthase.
    Nucleic Acids Res. 1985 Jun 11;13(11):4011-27 PMID: 2989783
  32. Specific DNA binding of GAL4, a positive regulatory protein of yeast.
    Cell. 1985 Apr;40(4):767-74 PMID: 3886158
  33. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.
    J Mol Biol. 1990 Apr 20;212(4):563-78 PMID: 2329577
  34. Structure and regulation of KGD2, the structural gene for yeast dihydrolipoyl transsuccinylase.
    Mol Cell Biol. 1990 Aug;10(8):4221-32 PMID: 2115121
  35. Expression of yeast cytochrome c1 is controlled at the transcriptional level by glucose, oxygen and haem.
    Mol Gen Genet. 1992 Apr;232(3):447-59 PMID: 1316998
Article Info
Journal
Current genetics
Abbr.
Curr Genet
ISSN
0172-8083
DOI
10.1007/BF00351777
Published
1994-05-00
Pages
396-406
Language
English
Region
United States
NLM ID
8004904
Subset
IM
External Links
PubMed source DOI: 10.1007/BF00351777 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2