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Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome Nature Precedings
Michael D. Barton; Balazs Papp; Daniel Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/1841/version/1
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Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome Nature Precedings
Michael D. Barton; Balazs Papp; Daniela Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Background: Every protein has a variable atomic and energetic cost to the cell based on the synthesis of its constituent amino acids. Quantifying the cost of amino acid synthesis is challenging, however natural selection is expected to favour the use of proteins whose constituents are cheaper to produce in terms of energetic and atomic cost.

Results: We develop a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models, and directly investigate the effects of the cost of amino acid synthesis on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We used our two new and six previously reported measures of amino acid cost in conjunction with codon...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/1841/version/2
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Population genomics of domestic and wild yeasts Nature Precedings
David M. Carter; Gianni Liti; Alan M. Moses; Leopold Parts; Stephen A. James; Robert P. Davey; Ian N. Roberts; Anders Blomberg; Jonas Warringer; 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; Matthew Jones; Michael A. Quail; Ian Goodhead; Sarah Sims; Frances Smith; Richard Durbin; Edward Louis.
The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide...
Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1988/version/1
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