Literature DB >> 20129976

Experimental genomics of fitness in yeast.

Graham Bell1.   

Abstract

The set of single-gene deletions in yeast can be used to evaluate the effect of mutation on fitness over the whole genome. The measurement of growth in pure culture or relative growth in mixtures has confirmed that most deletions have little effect in laboratory culture. Moreover, there is a sharp distinction between lethality and a very mild impairment of growth, with very few intermediate cases. Different components of fitness, such as growth rate and yield, are positively correlated. Growth is also positively correlated across environments, although new conditions of growth usually identify a few conditionally impaired strains. Double mutants on average show alleviating epistasis, although a few per cent of combinations are synthetic lethal. The properties of the yeast deletion set provide us with the first genome-wide account of fitness, although transferring these conclusions to the field is a task for the future.

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Year:  2010        PMID: 20129976      PMCID: PMC2871833          DOI: 10.1098/rspb.2009.2099

Source DB:  PubMed          Journal:  Proc Biol Sci        ISSN: 0962-8452            Impact factor:   5.349


  20 in total

1.  Global mapping of the yeast genetic interaction network.

Authors:  Amy Hin Yan Tong; Guillaume Lesage; Gary D Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F Berriz; Renee L Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L Wong; Lan V Zhang; Hongwei Zhu; Christopher G Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P Roth; Grant W Brown; Brenda Andrews; Howard Bussey; Charles Boone
Journal:  Science       Date:  2004-02-06       Impact factor: 47.728

2.  Low frequency of mutations with strongly deleterious but nonlethal fitness effects.

Authors:  Angelina Fudala; Ryszard Korona
Journal:  Evolution       Date:  2009-04-13       Impact factor: 3.694

3.  Interactions between stressful environment and gene deletions alleviate the expected average loss of fitness in yeast.

Authors:  Lukasz Jasnos; Katarzyna Tomala; Dorota Paczesniak; Ryszard Korona
Journal:  Genetics       Date:  2008-04       Impact factor: 4.562

4.  The chemical genomic portrait of yeast: uncovering a phenotype for all genes.

Authors:  Maureen E Hillenmeyer; Eula Fung; Jan Wildenhain; Sarah E Pierce; Shawn Hoon; William Lee; Michael Proctor; Robert P St Onge; Mike Tyers; Daphne Koller; Russ B Altman; Ronald W Davis; Corey Nislow; Guri Giaever
Journal:  Science       Date:  2008-04-18       Impact factor: 47.728

5.  Functional profiling of the Saccharomyces cerevisiae genome.

Authors:  Guri Giaever; Angela M Chu; Li Ni; Carla Connelly; Linda Riles; Steeve Véronneau; Sally Dow; Ankuta Lucau-Danila; Keith Anderson; Bruno André; Adam P Arkin; Anna Astromoff; Mohamed El-Bakkoury; Rhonda Bangham; Rocio Benito; Sophie Brachat; Stefano Campanaro; Matt Curtiss; Karen Davis; Adam Deutschbauer; Karl-Dieter Entian; Patrick Flaherty; Francoise Foury; David J Garfinkel; Mark Gerstein; Deanna Gotte; Ulrich Güldener; Johannes H Hegemann; Svenja Hempel; Zelek Herman; Daniel F Jaramillo; Diane E Kelly; Steven L Kelly; Peter Kötter; Darlene LaBonte; David C Lamb; Ning Lan; Hong Liang; Hong Liao; Lucy Liu; Chuanyun Luo; Marc Lussier; Rong Mao; Patrice Menard; Siew Loon Ooi; Jose L Revuelta; Christopher J Roberts; Matthias Rose; Petra Ross-Macdonald; Bart Scherens; Greg Schimmack; Brenda Shafer; Daniel D Shoemaker; Sharon Sookhai-Mahadeo; Reginald K Storms; Jeffrey N Strathern; Giorgio Valle; Marleen Voet; Guido Volckaert; Ching-yun Wang; Teresa R Ward; Julie Wilhelmy; Elizabeth A Winzeler; Yonghong Yang; Grace Yen; Elaine Youngman; Kexin Yu; Howard Bussey; Jef D Boeke; Michael Snyder; Peter Philippsen; Ronald W Davis; Mark Johnston
Journal:  Nature       Date:  2002-07-25       Impact factor: 49.962

6.  Systematic screen for human disease genes in yeast.

Authors:  Lars M Steinmetz; Curt Scharfe; Adam M Deutschbauer; Dejana Mokranjac; Zelek S Herman; Ted Jones; Angela M Chu; Guri Giaever; Holger Prokisch; Peter J Oefner; Ronald W Davis
Journal:  Nat Genet       Date:  2002-07-22       Impact factor: 38.330

Review 7.  Saccharomyces sensu stricto as a model system for evolution and ecology.

Authors:  Taissa Replansky; Vassiliki Koufopanou; Duncan Greig; Graham Bell
Journal:  Trends Ecol Evol       Date:  2008-07-24       Impact factor: 17.712

8.  Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae.

Authors:  Joseph Schacherer; Joshua A Shapiro; Douglas M Ruderfer; Leonid Kruglyak
Journal:  Nature       Date:  2009-02-11       Impact factor: 49.962

9.  Population genomics of domestic and wild yeasts.

Authors:  Gianni Liti; David M Carter; Alan M Moses; Jonas Warringer; Leopold Parts; Stephen A James; Robert P Davey; Ian N Roberts; Austin Burt; Vassiliki Koufopanou; Isheng J Tsai; Casey M Bergman; Douda Bensasson; Michael J T O'Kelly; Alexander van Oudenaarden; David B H Barton; Elizabeth Bailes; Alex N Nguyen; Matthew Jones; Michael A Quail; Ian Goodhead; Sarah Sims; Frances Smith; Anders Blomberg; Richard Durbin; Edward J Louis
Journal:  Nature       Date:  2009-02-11       Impact factor: 49.962

10.  A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.

Authors:  David K Breslow; Dale M Cameron; Sean R Collins; Maya Schuldiner; Jacob Stewart-Ornstein; Heather W Newman; Sigurd Braun; Hiten D Madhani; Nevan J Krogan; Jonathan S Weissman
Journal:  Nat Methods       Date:  2008-07-11       Impact factor: 28.547

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  23 in total

Review 1.  Molecular spandrels: tests of adaptation at the genetic level.

Authors:  Rowan D H Barrett; Hopi E Hoekstra
Journal:  Nat Rev Genet       Date:  2011-10-18       Impact factor: 53.242

2.  Editorial.

Authors:  Michael P Hassell
Journal:  Proc Biol Sci       Date:  2011-01-07       Impact factor: 5.349

3.  Inferences about the distribution of dominance drawn from yeast gene knockout data.

Authors:  Aneil F Agrawal; Michael C Whitlock
Journal:  Genetics       Date:  2010-11-23       Impact factor: 4.562

4.  Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing.

Authors:  Russell Lande; Emmanuelle Porcher
Journal:  Genetics       Date:  2015-05-11       Impact factor: 4.562

Review 5.  Evolutionary rescue and the limits of adaptation.

Authors:  Graham Bell
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2013-01-19       Impact factor: 6.237

Review 6.  Frequent ploidy changes in growing yeast cultures.

Authors:  Yaniv Harari; Yoav Ram; Martin Kupiec
Journal:  Curr Genet       Date:  2018-03-10       Impact factor: 3.886

7.  Accelerating Mutational Load Is Not Due to Synergistic Epistasis or Mutator Alleles in Mutation Accumulation Lines of Yeast.

Authors:  Jean-Nicolas Jasmin; Thomas Lenormand
Journal:  Genetics       Date:  2015-11-23       Impact factor: 4.562

8.  The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations.

Authors:  Evgeni M Frenkel; Benjamin H Good; Michael M Desai
Journal:  Genetics       Date:  2014-02-10       Impact factor: 4.562

9.  Identification of the fitness determinants of budding yeast on a natural substrate.

Authors:  Marie Filteau; Guillaume Charron; Christian R Landry
Journal:  ISME J       Date:  2016-12-09       Impact factor: 10.302

10.  Measuring competitive fitness in dynamic environments.

Authors:  Ivan A Razinkov; Bridget L Baumgartner; Matthew R Bennett; Lev S Tsimring; Jeff Hasty
Journal:  J Phys Chem B       Date:  2013-08-07       Impact factor: 2.991

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