Genetic Basis of Hidden Phenotypic Variation Revealed by Increased Translational Readthrough in Yeast
Eukaryotic release factors 1 and 3, encoded by SUP45 and SUP35, respectively, in Saccharomyces cerevisiae, are required for translation termination. Recent studies have shown that, besides these two key factors, several genetic and epigenetic mechanisms modulate the efficiency of translation termination. These mechanisms, through modifying translation termination fidelity, were shown to affect various cellular processes, such as mRNA degradation, and in some cases could confer a beneficial phenotype to the cell. The most studied example of such a mechanism is [PSI+], the prion conformation of Sup35p, which can have pleiotropic effects on growth that vary among different yeast strains. However, genetic loci underlying such readthrough-dependent, background-specific phenotypes have yet to be identified. Here, we used sup35C653R, a partial loss-of-function allele of the SUP35 previously shown to increase readthrough of stop codons and recapitulate some [PSI+]-dependent phenotypes, to study the genetic basis of phenotypes revealed by increased translational readthrough in two divergent yeast strains: BY4724 (a laboratory strain) and RM11_1a (a wine strain). We first identified growth conditions in which increased readthrough of stop codons by sup35C653R resulted in different growth responses between these two strains. We then used a recently developed linkage mapping technique, extreme QTL mapping (X-QTL), to identify readthrough-dependent loci for the observed growth differences. We further showed that variation in SKY1, an SR protein kinase, underlies a readthrough-dependent locus observed for growth on diamide and hydrogen peroxide. We found that the allelic state of SKY1 interacts with readthrough level and the genetic background to determine growth rate in these two conditions.
Vyšlo v časopise:
Genetic Basis of Hidden Phenotypic Variation Revealed by Increased Translational Readthrough in Yeast. PLoS Genet 8(3): e32767. doi:10.1371/journal.pgen.1002546
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002546
Souhrn
Eukaryotic release factors 1 and 3, encoded by SUP45 and SUP35, respectively, in Saccharomyces cerevisiae, are required for translation termination. Recent studies have shown that, besides these two key factors, several genetic and epigenetic mechanisms modulate the efficiency of translation termination. These mechanisms, through modifying translation termination fidelity, were shown to affect various cellular processes, such as mRNA degradation, and in some cases could confer a beneficial phenotype to the cell. The most studied example of such a mechanism is [PSI+], the prion conformation of Sup35p, which can have pleiotropic effects on growth that vary among different yeast strains. However, genetic loci underlying such readthrough-dependent, background-specific phenotypes have yet to be identified. Here, we used sup35C653R, a partial loss-of-function allele of the SUP35 previously shown to increase readthrough of stop codons and recapitulate some [PSI+]-dependent phenotypes, to study the genetic basis of phenotypes revealed by increased translational readthrough in two divergent yeast strains: BY4724 (a laboratory strain) and RM11_1a (a wine strain). We first identified growth conditions in which increased readthrough of stop codons by sup35C653R resulted in different growth responses between these two strains. We then used a recently developed linkage mapping technique, extreme QTL mapping (X-QTL), to identify readthrough-dependent loci for the observed growth differences. We further showed that variation in SKY1, an SR protein kinase, underlies a readthrough-dependent locus observed for growth on diamide and hydrogen peroxide. We found that the allelic state of SKY1 interacts with readthrough level and the genetic background to determine growth rate in these two conditions.
Zdroje
1. JanzenDMGeballeAP 2001 Modulation of translation termination mechanisms by cis- and trans-acting factors. Cold Spring Harbor symposia on quantitative biology 66 459 467
2. RospertSRakwalskaMDubaquieY 2005 Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. Rev Physiol Biochem Pharmacol 155 1 30
3. BidouLRoussetJPNamyO 2010 Translational errors: from yeast to new therapeutic targets. Fems Yeast Research 10 1070 1082
4. von der HaarTTuiteMF 2007 Regulated translational bypass of stop codons in yeast. Trends Microbiol 15 78 86
5. CoxB 1994 Cytoplasmic inheritance. Prion-like factors in yeast. Current biology : CB 4 744 748
6. TuiteMFCoxBS 2006 The [PSI+] prion of yeast: a problem of inheritance. Methods 39 9 22
7. BidouLStahlGHatinINamyORoussetJP 2000 Nonsense-mediated decay mutants do not affect programmed −1 frameshifting. RNA 6 952 961
8. FiroozanMGrantCMDuarteJATuiteMF 1991 Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay. Yeast 7 173 183
9. TrueHLBerlinILindquistSL 2004 Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 431 184 187
10. NamyOGalopierAMartiniCMatsufujiSFabretC 2008 Epigenetic control of polyamines by the prion [PSI+]. Nature cell biology 10 1069 1075
11. ShorterJLindquistS 2005 Prions as adaptive conduits of memory and inheritance. Nat Rev Genet 6 435 450
12. KeelingKMLanierJDuMSalas-MarcoJGaoL 2004 Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. RNA 10 691 703
13. BradleyMEBagriantsevSVishveshwaraNLiebmanSW 2003 Guanidine reduces stop codon read-through caused by missense mutations in SUP35 or SUP45. Yeast 20 625 632
14. EhrenreichIMTorabiNJiaYKentJMartisS 2010 Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464 1039 1042
15. TorabiNKruglyakL 2011 Variants in SUP45 and TRM10 Underlie Natural Variation in Translation Termination Efficiency in Saccharomyces cerevisiae. PLoS Genet 7 e1002211 doi:10.1371/journal.pgen.1002211
16. TrueHLLindquistSL 2000 A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407 477 483
17. PerlsteinEORuderferDMRobertsDCSchreiberSLKruglyakL 2007 Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat Genet 39 496 502
18. GaschAPSpellmanPTKaoCMCarmel-HarelOEisenMB 2000 Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11 4241 4257
19. SmithENKruglyakL 2008 Gene-environment interaction in yeast gene expression. PLoS Biol 6 e83 doi:10.1371/journal.pbio.0060083
20. ShermanMYGoldbergAL 2001 Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29 15 32
21. FrischmeyerPAvan HoofAO'DonnellKGuerrerioALParkerR 2002 An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295 2258 2261
22. ChangYFImamJSWilkinsonMF 2007 The nonsense-mediated decay RNA surveillance pathway. Annual review of biochemistry 76 51 74
23. SiebelCWFengLGuthrieCFuXD 1999 Conservation in budding yeast of a kinase specific for SR splicing factors. Proceedings of the National Academy of Sciences of the United States of America 96 5440 5445
24. ValcarcelJGreenMR 1996 The SR protein family: pleiotropic functions in pre-mRNA splicing. Trends in biochemical sciences 21 296 301
25. YunCYFuXD 2000 Conserved SR protein kinase functions in nuclear import and its action is counteracted by arginine methylation in Saccharomyces cerevisiae. The Journal of cell biology 150 707 718
26. EstrellaLAWilkinsonMFGonzalezCI 2009 The shuttling protein Npl3 promotes translation termination accuracy in Saccharomyces cerevisiae. Journal of molecular biology 394 410 422
27. FormentJMuletJMVicenteOSerranoR 2002 The yeast SR protein kinase Sky1p modulates salt tolerance, membrane potential and the Trk1,2 potassium transporter. Biochimica et biophysica acta 1565 36 40
28. SchenkPWBoersmaAWBrokMBurgerHStoterG 2002 Inactivation of the Saccharomyces cerevisiae SKY1 gene induces a specific modification of the yeast anticancer drug sensitivity profile accompanied by a mutator phenotype. Molecular pharmacology 61 659 666
29. ErezOKahanaC 2001 Screening for modulators of spermine tolerance identifies Sky1, the SR protein kinase of Saccharomyces cerevisiae, as a regulator of polyamine transport and ion homeostasis. Molecular and cellular biology 21 175 184
30. WilmesGMBergkesselMBandyopadhyaySShalesMBrabergH 2008 A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Molecular cell 32 735 746
31. BurkeDDawsonDStearnsT Cold Spring Harbor Laboratory. 2000 Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual Plainview, N.Y. Cold Spring Harbor Laboratory Press xvii 205
32. GrayMPiccirilloSHonigbergSM 2005 Two-step method for constructing unmarked insertions, deletions and allele substitutions in the yeast genome. FEMS microbiology letters 248 31 36
33. BrachmannCBDaviesACostGJCaputoELiJ 1998 Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14 115 132
34. SikorskiRSHieterP 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122 19 27
35. StoriciFLewisLKResnickMA 2001 In vivo site-directed mutagenesis using oligonucleotides. Nature biotechnology 19 773 776
36. StoreyJD 2002 A direct approach to false discovery rates. Journal of the Royal Statistical Society Series B-Statistical Methodology 64 479 498
37. EdgarRDomrachevMLashAE 2002 Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic acids research 30 207 210
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 3
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- PIF4–Mediated Activation of Expression Integrates Temperature into the Auxin Pathway in Regulating Hypocotyl Growth
- Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations
- A Splice Site Variant in the Bovine Gene Compromises Growth and Regulation of the Inflammatory Response
- Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database