Journal ArticleDOI
Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures.
Daniela Delneri,David C. Hoyle,Konstantinos Gkargkas,Konstantinos Gkargkas,Emma Julie Marie Cross,Bharat M. Rash,Leo A. H. Zeef,Hui-Sun Leong,Hazel M. Davey,Andrew Hayes,Douglas B. Kell,Gareth W. Griffith,Stephen G. Oliver,Stephen G. Oliver +13 more
TLDR
Using competition experiments in continuous cultures grown in different nutrient environments, genes that show haploinsufficiency phenotypes or haploproficient phenotypes are identified and this chromosome determines a yeast's mating type, and the concentration of haplOinsufficient genes there may be a mechanism to prevent its loss.Abstract:
Using competition experiments in continuous cultures grown in different nutrient environments (glucose limited, ammonium limited, phosphate limited and white grape juice), we identified genes that show haploinsufficiency phenotypes (reduced growth rate when hemizygous) or haploproficiency phenotypes (increased growth rate when hemizygous). Haploproficient genes (815, 1,194, 733 and 654 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) frequently show that phenotype in a specific environmental context. For instance, genes encoding components of the ubiquitination pathway or the proteasome show haploproficiency in nitrogen-limited conditions where protein conservation may be beneficial. Haploinsufficiency is more likely to be observed in all environments, as is the case with genes determining polar growth of the cell. Haploproficient genes seem randomly distributed in the genome, whereas haploinsufficient genes (685, 765, 1,277 and 217 in glucose-limited, ammonium-limited, phosphate-limited and white grape juice environments, respectively) are over-represented on chromosome III. This chromosome determines a yeast's mating type, and the concentration of haploinsufficient genes there may be a mechanism to prevent its loss.read more
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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Markus J. Herrgård,Neil Swainston,Paul D. Dobson,Warwick B. Dunn,K.Yalçın Arga,Mikko Arvas,Nils Blüthgen,Simon Borger,Roeland Costenoble,Matthias Heinemann,Michael Hucka,Nicolas Le Novère,Peter Li,Wolfram Liebermeister,Monica L. Mo,Ana Paula Oliveira,Dina Petranovic,Stephen Pettifer,Evangelos Simeonidis,Kieran Smallbone,Irena Spasic,Dieter Weichart,Roger Brent,David S. Broomhead,Hans V. Westerhoff,Betul Kirdar,Merja Penttilä,Edda Klipp,Bernhard O. Palsson,Uwe Sauer,Stephen G. Oliver,Pedro Mendes,Jens Nielsen,Douglas B. Kell +33 more
TL;DR: This work describes how it has produced a consensus metabolic network reconstruction for S. cerevisiae, and places special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning.
Journal ArticleDOI
Phenotypic impact of genomic structural variation: insights from and for human disease
TL;DR: This Review describes how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease, and presents advances in delineating disease-causing elements that are affected by structural variants.
Journal ArticleDOI
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.
David Gresham,Michael M. Desai,Cheryl M. Tucker,Harry T. Jenq,Dave A. Pai,Alexandra Ward,Christopher G. DeSevo,David Botstein,Maitreya J. Dunham,Maitreya J. Dunham +9 more
TL;DR: This work describes genetic changes that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats and suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways.
Journal ArticleDOI
The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato
TL;DR: It is reported that heterozygosity for tomato loss-of-function alleles of SINGLE FLOWER TRUSS (SFT), which is the genetic originator of the flowering hormone florigen, increases yield by up to 60%.
Journal ArticleDOI
Progress Toward Understanding Heterosis in Crop Plants
TL;DR: Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids, so multigene models are likely to prove most informative for understanding heterosis.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Functional profiling of the Saccharomyces cerevisiae genome.
Guri Giaever,Angela M. Chu,Li Ni,Carla Connelly,Linda Riles,Steeve Veronneau,Sally Dow,Ankuta Lucau-Danila,Keith Anderson,Bruno André,Adam P. Arkin,Anna Astromoff,Mohamed El Bakkoury,Rhonda Bangham,Rocío Benito,Sophie Brachat,Stefano Campanaro,Matt Curtiss,Karen Davis,Adam M. Deutschbauer,K. D. Entian,Patrick Flaherty,Françoise Foury,David J. Garfinkel,Mark Gerstein,Deanna Gotte,Ulrich Güldener,Johannes H. Hegemann,Svenja Hempel,Zelek S. Herman,Daniel F. Jaramillo,Diane E. Kelly,Steven L. Kelly,Peter Kötter,Darlene LaBonte,David C. Lamb,Ning Lan,Hong Liang,Hong Liao,Lucy Y. Liu,Chuanyun Luo,Marc Lussier,Rong Mao,Patrice Menard,Siew Loon Ooi,José L. Revuelta,Christopher J. Roberts,Matthias Rose,Petra Ross-Macdonald,Bart Scherens,Greg Schimmack,Brenda Shafer,Daniel D. Shoemaker,Sharon Sookhai-Mahadeo,Reginald 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 M. Youngman,Kexin Yu,Howard Bussey,Jef D. Boeke,Michael Snyder,Peter Philippsen,Ronald W. Davis,Mark Johnston +72 more
TL;DR: It is shown that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment, and less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal Growth in four of the tested conditions.
Journal ArticleDOI
Life with 6000 Genes
André Goffeau,Bart Barrell,Howard Bussey,Ronald W. Davis,Bernard Dujon,Horst Feldmann,Francis Galibert,J D Hoheisel,Claude Jacq,Mark Johnston,Edward J. Louis,Hans-Werner Mewes,Yasufumi Murakami,Peter Philippsen,Hervé Tettelin,Stephen G. Oliver +15 more
TL;DR: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration and provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history.
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