title: Rewiring of the yeast transcriptional network through the evolution of motif usage.
abstract: Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about the genetic basis underlying the evolution of gene expression and its contribution to phenotypic diversity. Here we describe a large-scale modulation of the yeast transcription program that is connected to the emergence of the capacity for rapid anaerobic growth. Genes coding for mitochondrial and cytoplasmic ribosomal proteins display a strongly correlated expression pattern in Candida albicans, but this correlation is lost in the fermentative yeast Saccharomyces cerevisiae. We provide evidence that this change in gene expression is connected to the loss of a specific cis-regulatory element from dozens of genes following the apparent whole-genome duplication event. Our results shed new light on the genetic mechanisms underlying the large-scale evolution of transcriptional networks.
authors.affiliation: Department of Molecular Genetics and Department of Physics of Complex systems, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Jan
authors.initials: J
authors.lastname: Ihmels
authors.forename: Sven
authors.initials: S
authors.lastname: Bergmann
authors.forename: Maryam
authors.initials: M
authors.lastname: Gerami-Nejad
authors.forename: Itai
authors.initials: I
authors.lastname: Yanai
authors.forename: Mark
authors.initials: M
authors.lastname: McClellan
authors.forename: Judith
authors.initials: J
authors.lastname: Berman
authors.forename: Naama
authors.initials: N
authors.lastname: Barkai
mesh_terms: D000332:Aerobiosis; D001483:Base Sequence; D002176:Candida albicans / Q000235:genetics; D003593:Cytoplasm / Q000235:genetics; D004271:DNA, Fungal; D019143:Evolution, Molecular; D005285:Fermentation; D005656:Fungal Proteins / Q000235:genetics*; D020440:Gene Duplication; D015966:Gene Expression Regulation, Fungal; D024101:Mitochondrial Proteins / Q000235:genetics; D010100:Oxygen / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012269:Ribosomal Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics; D015003:Yeasts / Q000235:genetics* / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins; D024101:Mitochondrial Proteins; D012269:Ribosomal Proteins; D010100:Oxygen