The fitness trade-off between growth and stress resistance determines the phenotypic landscape

Bell G. Experimental genomics of fitness in yeast. Proc R Soc B Biol Sci. 2010;277:1459–67.

Article  Google Scholar 

Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science. 2002;296:752–5.

Article  CAS  PubMed  Google Scholar 

Perlstein EO, Ruderfer DM, Roberts DC, Schreiber SL, Kruglyak L. Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat Genet. 2007;39:496–502.

Article  CAS  PubMed  Google Scholar 

Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, et al. Population genomics of domestic and wild yeasts. Nature. 2009;458:337–41.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peter J, De Chiara M, Friedrich A, Yue J-X, Pflieger D, Bergström A, et al. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature. 2018;556:339–44.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kitano H. Biological robustness. Nat Rev Genet. 2004;5:826–37.

Article  CAS  PubMed  Google Scholar 

Bergkessel M, Basta DW, Newman DK. The physiology of growth arrest: uniting molecular and environmental microbiology. Nat Rev Microbiol. 2016;14:549–62.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, et al. Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science. 2012;336:1157–60.

Article  CAS  PubMed  Google Scholar 

Wenger JW, Piotrowski J, Nagarajan S, Chiotti K, Sherlock G, Rosenzweig F. Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. PLOS Genet. 2011;7:e1002202.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zakrzewska A, van Eikenhorst G, Burggraaff JEC, Vis DJ, Hoefsloot H, Delneri D, et al. Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell. 2011;22:4435–46.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Święciło A. Cross-stress resistance in Saccharomyces cerevisiae yeast—new insight into an old phenomenon. Cell Stress Chaperones. 2016;21:187–200.

Article  PubMed  PubMed Central  Google Scholar 

De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, et al. Domestication reprogrammed the budding yeast life cycle. Nat Ecol Evol. 2022;6:448–60.

Article  PubMed  Google Scholar 

Lewis JA, Broman AT, Will J, Gasch AP. Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains. Genetics. 2014;198:369–82.

Article  PubMed  PubMed Central  Google Scholar 

Smith EN, Kruglyak L. Gene–environment interaction in yeast gene expression. PLoS Biol. 2008;6:e83.

Article  PubMed  PubMed Central  Google Scholar 

Landry CR, Oh J, Hartl DL, Cavalieri D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene. 2006;366:343–51.

Article  CAS  PubMed  Google Scholar 

Caudal E, Loegler V, Dutreux F, Vakirlis N, Teyssonnière E, Caradec C, et al. Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast. preprint. Genomics; 2023.

Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, et al. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol. 2007;6:4.

Article  PubMed  PubMed Central  Google Scholar 

Knijnenburg TA, Daran JM, Van Den Broek MA, Daran-Lapujade PA, De Winde JH, Pronk JT, et al. Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data. BMC Genomics. 2009;10:53.

Article  PubMed  PubMed Central  Google Scholar 

Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, et al. Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. BMC Genomics. 2008;9:341.

Article  PubMed  PubMed Central  Google Scholar 

Regenberg B, Grotkjær T, Winther O, Fausbøll A, Åkesson M, Bro C, et al. Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol. 2006;7:R107.

Article  PubMed  PubMed Central  Google Scholar 

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000;11:4241–57.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Slavov N, Botstein D. Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol Biol Cell. 2011;22:1997–2009.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005;310:1152–8.

Article  CAS  PubMed  Google Scholar 

Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021;49:D325–34.

Article  Google Scholar 

Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A. High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci U S A. 2003;100:15724–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Levy SF, Siegal ML. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol. 2008;6:e264.

Article  PubMed  PubMed Central  Google Scholar 

Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006;441:840–6.

Article  CAS  PubMed  Google Scholar 

Choi JK, Kim Y-J. Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet. 2009;41:498–503.

Article  CAS  PubMed  Google Scholar 

Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K. Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell. 2014;156:812–24.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lahtvee P-J, Sánchez BJ, Smialowska A, Kasvandik S, Elsemman IE, Gatto F, et al. Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell Syst. 2017;4:495-504.e5.

Article  CAS  PubMed  Google Scholar 

Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, et al. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature. 2010;464:1039–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe’er D, et al. Learning a prior on regulatory potential from eQTL data. PLoS Genet. 2009;5:e1000358.

Article  PubMed  PubMed Central  Google Scholar 

Chaithanya KV, Sinha H. MKT1 alleles regulate stress responses through post-transcriptional modulation of Puf3 targets in budding yeast. preprint. Genetics; 2023.

Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, et al. Saccharomyces genome database informs human biology. Nucleic Acids Res. 2018;46:D736–42.

Article  CAS  PubMed  Google Scholar 

Deutschbauer AM, Davis RW. Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet. 2005;37:1333–40.

Article  CAS  PubMed  Google Scholar 

Zhang A, Shen Y, Gao W, Dong J. Role of Sch9 in regulating Ras-cAMP signal pathway in Saccharomyces cerevisiae. FEBS Lett. 2011;585:3026–32.

Article  CAS  PubMed  Google Scholar 

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, et al. Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 2013;41(Database issue):D955-961.

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