title: Strategy of transcription regulation in the budding yeast.
abstract: Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirements. First, characters of the internal physiological state, such as growth rate, metabolite levels, or energy availability, could be feedback to tune gene expression. Second, internal needs could be inferred from the external environment, using evolutionary-tuned signaling pathways. Coordination of ribosomal biogenesis with the requirement for protein synthesis is of particular importance, since cells devote a large fraction of their biosynthetic capacity for ribosomal biogenesis. To define the relative contribution of internal vs. external sensing to the regulation of ribosomal biogenesis gene expression in yeast, we subjected S. cerevisiae cells to conditions which decoupled the actual vs. environmentally-expected growth rate. Gene expression followed the environmental signal according to the expected, but not the actual, growth rate. Simultaneous monitoring of gene expression and growth rate in continuous cultures further confirmed that ribosome biogenesis genes responded rapidly to changes in the environments but were oblivious to longer-term changes in growth rate. Our results suggest that the capacity to anticipate and prepare for environmentally-mediated changes in cell growth presented a major selection force during yeast evolution.
authors.affiliation: Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Sagi
authors.initials: S
authors.lastname: Levy
authors.forename: Jan
authors.initials: J
authors.lastname: Ihmels
authors.forename: Miri
authors.initials: M
authors.lastname: Carmi
authors.forename: Adina
authors.initials: A
authors.lastname: Weinberger
authors.forename: Gilgi
authors.initials: G
authors.lastname: Friedlander
authors.forename: Naama
authors.initials: N
authors.lastname: Barkai
mesh_terms: D000426:Alcohol Dehydrogenase / Q000096:biosynthesis / Q000235:genetics; D003470:Culture Media / Q000494:pharmacology; D025461:Feedback, Physiological; D005285:Fermentation / Q000235:genetics; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects / Q000502:physiology; D005800:Genes, Fungal; D018816:Genes, cdc; D009172:Mycology / Q000379:methods; D009711:Nucleotides / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012331:RNA, Fungal / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D012335:RNA, Ribosomal / Q000096:biosynthesis / Q000235:genetics; D012343:RNA, Transfer / Q000096:biosynthesis / Q000235:genetics; D012100:Reproduction, Asexual; D012270:Ribosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000096:biosynthesis / Q000235:genetics; D014158:Transcription, Genetic / Q000187:drug effects / Q000502:physiology
chemical_list: D003470:Culture Media; D009711:Nucleotides; D012331:RNA, Fungal; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D029701:Saccharomyces cerevisiae Proteins; D012343:RNA, Transfer; C516801:ADH1 protein, S cerevisiae; D000426:Alcohol Dehydrogenase