1887

Abstract

is unique among yeasts in its ability to grow rapidly in the complete absence of oxygen. is therefore an ideal eukaryotic model to study physiological adaptation to anaerobiosis. Recent transcriptome analyses have identified hundreds of genes that are transcriptionally regulated by oxygen availability but the relevance of this cellular response has not been systematically investigated at the key control level of the proteome. Therefore, the proteomic response of to anaerobiosis was investigated using metabolic stable-isotope labelling in aerobic and anaerobic glucose-limited chemostat cultures, followed by relative quantification of protein expression. Using independent replicate cultures and stringent statistical filtering, a robust dataset of 474 quantified proteins was generated, of which 249 showed differential expression levels. While some of these changes were consistent with previous transcriptome studies, many of the responses of to oxygen availability were, to our knowledge, previously unreported. Comparison of transcriptomes and proteomes from identical cultivations yielded strong evidence for post-transcriptional regulation of key cellular processes, including glycolysis, amino-acyl-tRNA synthesis, purine nucleotide synthesis and amino acid biosynthesis. The use of chemostat cultures provided well-controlled and reproducible culture conditions, which are essential for generating robust datasets at different cellular information levels. Integration of transcriptome and proteome data led to new insights into the physiology of anaerobically growing yeast that would not have been apparent from differential analyses at either the mRNA or protein level alone, thus illustrating the power of multi-level studies in yeast systems biology.

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2007-11-01
2019-11-13
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Localization and functional category distributions of the identified proteins according to MIPS. The groups and categories having a significant bias are indicated in the pie-charts, their percentages and their -values according to the hypergeometric distribution test are given. (A) Distribution of the identified proteins according to the MIPS localization database. (B) Functional categories of the quantified proteins compared to the MIPS database. [ PDF] (319 kb) Data for the quantified proteins. All quantified proteins are sorted by gene name, including protein and mRNA ratios, their respective standard deviations (SD) and protein identification data. Symbols and abbreviations: AN, detected anaerobically; AE, detected aerobically; NA, no available value; discarded by PCA; * included after PCA. [Excel file](342 kb) MIPS categories having five or more members with a significant mode of protein- and mRNA-expression. A permutation-based test was performed to assess whether the points corresponding to a functional category occupy a specific place in the distribution of all data points. This provided 17 functional categories characterized by the strong homogeneity of their regulatory patterns. [ PDF] (39 kb)

PDF

Localization and functional category distributions of the identified proteins according to MIPS. The groups and categories having a significant bias are indicated in the pie-charts, their percentages and their -values according to the hypergeometric distribution test are given. (A) Distribution of the identified proteins according to the MIPS localization database. (B) Functional categories of the quantified proteins compared to the MIPS database. [ PDF] (319 kb) Data for the quantified proteins. All quantified proteins are sorted by gene name, including protein and mRNA ratios, their respective standard deviations (SD) and protein identification data. Symbols and abbreviations: AN, detected anaerobically; AE, detected aerobically; NA, no available value; discarded by PCA; * included after PCA. [Excel file](342 kb) MIPS categories having five or more members with a significant mode of protein- and mRNA-expression. A permutation-based test was performed to assess whether the points corresponding to a functional category occupy a specific place in the distribution of all data points. This provided 17 functional categories characterized by the strong homogeneity of their regulatory patterns. [ PDF] (39 kb)

EXCEL

Localization and functional category distributions of the identified proteins according to MIPS. The groups and categories having a significant bias are indicated in the pie-charts, their percentages and their -values according to the hypergeometric distribution test are given. (A) Distribution of the identified proteins according to the MIPS localization database. (B) Functional categories of the quantified proteins compared to the MIPS database. [ PDF] (319 kb) Data for the quantified proteins. All quantified proteins are sorted by gene name, including protein and mRNA ratios, their respective standard deviations (SD) and protein identification data. Symbols and abbreviations: AN, detected anaerobically; AE, detected aerobically; NA, no available value; discarded by PCA; * included after PCA. [Excel file](342 kb) MIPS categories having five or more members with a significant mode of protein- and mRNA-expression. A permutation-based test was performed to assess whether the points corresponding to a functional category occupy a specific place in the distribution of all data points. This provided 17 functional categories characterized by the strong homogeneity of their regulatory patterns. [ PDF] (39 kb)

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