Abstract
Mutational specificity analysis can yield valuable insights into processes that generate genetic change or maintain genetic stability. Powerful diagnostic tools for such analysis have been created by combining genetic assays for mutation with DNA sequencing. Here, steps for isolating spontaneous mutations in the yeast (Saccharomyces cerevisiae) suppressor tRNA gene SUP4-o as a prelude to sequence characterization are described (modifications of this protocol can be used to study induction of mutations by various physical or chemical agents). Mutations in SUP4-o are selected on drug-containing medium by virtue of their inactivation of suppressor activity. The small size, detailed knowledge of detectably mutable sites, and other features of the target gene facilitate subsequent analysis of these mutations.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, Ellenberger T (2006) DNA repair and mutagenesis, 2nd edn. ASM, Washington, DC
Sargentini NJ, Smith KC (1985) Spontaneous mutagenesis: the roles of DNA repair, replication and recombination. Mutat Res 154:1–27
Drake JW (1991) Spontaneous mutagenesis. Annu Rev Genet 25:125–146
Pierce MK, Giroux CN, Kunz BA (1987) Development of a yeast system to assay mutational specificity. Mutat Res 182:65–74
Kunz BA, Pierce MK, Mis JRA et al (1987) DNA sequence analysis of the mutational specificity of U.V. light in the SUP4-o gene of yeast. Mutagenesis 2:445–453
Giroux CN, Mis JRA, Pierce MK et al (1988) DNA sequence analysis of spontaneous mutations in the SUP4-o gene of Saccharomyces cerevisiae. Mol Cell Biol 8:978–981
Goodman HM, Olson MV, Hall BD (1977) Nucleotide sequence of a mutant eukaryotic gene: the yeast tyrosine-inserting ochre suppressor SUP4-o. Proc Natl Acad Sci U S A 74:5453–5457
Hall BD, Clarkson SG, Tocchini-Valentini G (1982) Transcription initiation of eukaryotic transfer RNA genes. Cell 29:3–5
Knapp G, Beckwith JS, Johnson PF et al (1978) Transcription and processing of intervening sequences in yeast tRNA genes. Cell 14:221–236
Shaw KJ, Olson MV (1984) Effects of altered 5′-flanking sequences on the in vivo expression of a Saccharomyces cerevisiae tRNAtyr gene. Mol Cell Biol 4:657–665
Allison DS, Hall BD (1985) Effects of alterations in the 3′-flanking sequence on in vivo and in vitro expression of the yeast SUP4-o tRNAtyr gene. EMBO J 4:2657–2664
Newlon CS (1988) Yeast chromosome replication and segregation. Microbiol Rev 52:568–601
Wang SS, Hopper AK (1988) Isolation of a yeast gene involved in species-specific pre-tRNA processing. Mol Cell Biol 8:5140–5149
Kunz BA, Armstrong JD, Glattke M et al (1990) The SUP4-o system for analysis of mutational specificity in yeast. In: Mendelsohn ML, Albertini RJ (eds) Mutation in the environment, part A: basic mechanisms. Alan R. Liss, New York, pp 337–346
Kohalmi SE, Glattke M, McIntosh EM et al (1991) Mutational specificity of DNA precursor pool imbalances in yeast arising from deoxycytidylate deaminase deficiency or treatment with thymidylate. J Mol Biol 220:933–946
Kohalmi L, Kunz BA (1992) In vitro mutagenesis of the yeast SUP4-o gene to identify all sites where substitutions can be detected in vivo with the SUP4-o system. Environ Mol Mutagen 19:282–287
Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for the transformation of Escherichia coli. Gene 57:267–272
Robzyk K, Kassir Y (1992) A simple and highly efficient procedure for rescuing autonomous plasmids from yeast. Nucleic Acids Res 20:3790
Nishimura N, Morita M, Nishimura Y et al (1990) A rapid and highly efficient method for preparation of competent Escherichia coli cells. Nucleic Acids Res 18:6169
Drake JW (1991) A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A 88:7160–7164
Adams WT, Skopek TR (1987) Statistical test for the comparison of samples from mutational spectra. J Mol Biol 194:391–396
Kang X, Yadao F, Gietz RD et al (1992) Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C—T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutagenesis. Genetics 130:285–294
Armstrong JD, Kunz BA (1995) Nucleotide excision repair and gene orientation modulate the strand specificity of ultraviolet mutagenesis in yeast. Environ Mol Mutagen 25:12–22
Karthikeyan R, Vonarx EJ, Straffon AFL et al (2000) Evidence from mutational specificity studies that yeast DNA polymerases δ and ε replicate different DNA strands at an intracellular replication fork. J Mol Biol 299:405–419
Zimmermann FK (1973) A yeast strain for visual screening for the two reciprocal products of mitotic crossing over. Mutat Res 21:263–269
Kunz BA, Ayre BG, Downes AMT et al (1989) Base-pair substitutions alter the site-specific mutagenicity of UV and MNNG in the SUP4-o gene of yeast. Mutat Res 226:273–278
Cariello NF, Cui L, Beroud C et al (1994) Database and software for the analysis of mutations in the human p53 gene. Cancer Res 54:4454–4460
Armstrong JD, Kunz BA (1990) Site and strand specificity of UVB mutagenesis in the SUP4-o gene of yeast. Proc Natl Acad Sci U S A 87:9005–9007
Kohalmi SE, Kunz BA (1988) The role of neighbouring bases and assessment of strand specificity in ethylmethanesulphonate and N-methyl-Nˊ-nitro-N-nitrosoguanidine mutagenesis in the SUP4-o gene of Saccharomyces cerevisiae. J Mol Biol 204:561–568
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Kunz, B.A. (2014). Mutational Specificity Analysis: Assay for Mutations in the Yeast SUP4-o Gene. In: Xiao, W. (eds) Yeast Protocols. Methods in Molecular Biology, vol 1163. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0799-1_15
Download citation
DOI: https://doi.org/10.1007/978-1-4939-0799-1_15
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-0798-4
Online ISBN: 978-1-4939-0799-1
eBook Packages: Springer Protocols