title: Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.
abstract: Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology.
authors.affiliation: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
authors.forename: Petri-Jaan
authors.initials: PJ
authors.lastname: Lahtvee
authors.affiliation: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
authors.forename: Benjamín J
authors.initials: BJ
authors.lastname: Sánchez
authors.affiliation: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden; National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, 171 65 Solna, Sweden.
authors.forename: Agata
authors.initials: A
authors.lastname: Smialowska
authors.affiliation: Institute of Technology, University of Tartu, 50411 Tartu, Estonia.
authors.forename: Sergo
authors.initials: S
authors.lastname: Kasvandik
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark.
authors.forename: Ibrahim E
authors.initials: IE
authors.lastname: Elsemman
authors.affiliation: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
authors.forename: Francesco
authors.initials: F
authors.lastname: Gatto
authors.affiliation: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark. Electronic address: nielsenj@chalmers.se.
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D014176:Protein Biosynthesis / Q000502:physiology*; D011499:Protein Processing, Post-Translational / Q000502:physiology; D059748:Proteolysis; D020543:Proteome / Q000235:genetics; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D020543:Proteome; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins
keywords: absolute proteome; absolute transcriptome; genome-scale metabolic modeling; integrative data analysis; protein degradation rates; protein turnover; translation efficiency; translational control