title: Genome-wide expression analyses of the stationary phase model of ageing in yeast.
abstract: Ageing processes involved in replicative lifespan (RLS) and chronological lifespan (CLS) have been found to be conserved among many organisms, including in unicellular Eukarya such as yeast Saccharomyces cerevisiae. Here we performed an integrated approach of genome wide expression profiles of yeast at different time points, during growth and starvation. The aim of the study was to identify transcriptional changes in those conditions by using several different computational analyses in order to propose transcription factors, biological networks and metabolic pathways that seem to be relevant during the process of chronological ageing in yeast. Specifically, we performed differential gene expression analysis, gene-set enrichment analysis and network-based analysis, and we identified pathways affected in the stationary phase and specific transcription factors driving transcriptional adaptations. The results indicate signal propagation from G protein-coupled receptors through signaling pathway components and other stress and nutrient-induced transcription factors resulting in adaptation of yeast cells to the lack of nutrients by activating metabolism associated with aerobic metabolism of carbon sources such as ethanol, glycerol and fatty acids. In addition, we found STE12, XBP1 and TOS8 as highly connected nodes in the subnetworks of ageing yeast.
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
authors.forename: Kwanjeera
authors.initials: K
authors.lastname: Wanichthanarak
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology, Göteborg, Sweden.
authors.forename: Nutvadee
authors.initials: N
authors.lastname: Wongtosrad
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden. Electronic address: dina.petranovic@chalmers.se.
authors.forename: Dina
authors.initials: D
authors.lastname: Petranovic
mesh_terms: D019069:Cell Respiration; D019295:Computational Biology; D005227:Fatty Acids / Q000737:chemistry; D015966:Gene Expression Regulation, Fungal; D056726:Genetic Association Studies; D016681:Genome, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D010100:Oxygen / Q000378:metabolism; D012097:Repressor Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D005227:Fatty Acids; D012097:Repressor Proteins; C489241:STE12 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C108767:XBP1 protein, S cerevisiae; D010100:Oxygen
keywords: Gene expression analyses; Integrated analyses; Nutritional starvation; Yeast chronological lifespan