title: Impact of high pH stress on yeast gene expression: A comprehensive analysis of mRNA turnover during stress responses.
abstract: Environmental alkalinisation represents a stress condition for yeast Saccharomyces cerevisiae, to which this organism responds with extensive gene expression remodelling. We show here that alkaline pH causes an overall decrease in the transcription rate (TR) and a fast destabilisation of mRNAs, followed by a more prolonged stabilisation phase. In many cases, augmented mRNA levels occur without the TR increasing, which can be attributed to mRNA stabilisation. In contrast, the reduced amount of mRNAs is contributed by both a drop in the TR and mRNA stability. A comparative analysis with other forms of stress shows that, unlike high pH stress, heat-shock, osmotic and oxidative stresses present a common transient increase in the TR. An analysis of environmentally-responsive (ESR) genes for the four above stresses suggests that up-regulated genes are governed mostly by TR changes and complex transient bidirectional changes in mRNA stability, whereas the down-regulated ESR gene set is driven by mRNA destabilisation and a lowered TR. In all the studied forms of stress, mRNA stability plays an important role in ESR. Overall, changes in mRNA levels do not closely reflect the rapid changes in the TR and stability upon exposure to stress, which highlights the existence of compensatory mechanisms.
authors.affiliation: Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Canadell
authors.affiliation: Departamento de Genética, Universitat de València, Burjassot, València 46100, Spain; ERI Biotecmed, Universitat de València, Burjassot, València 46100, Spain.
authors.forename: José
authors.initials: J
authors.lastname: García-Martínez
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, València 46100, Spain; ERI Biotecmed, Universitat de València, Burjassot, València 46100, Spain.
authors.forename: Paula
authors.initials: P
authors.lastname: Alepuz
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, València 46100, Spain; ERI Biotecmed, Universitat de València, Burjassot, València 46100, Spain. Electronic address: Jose.E.Perez@uv.es.
authors.forename: José E
authors.initials: JE
authors.lastname: Pérez-Ortín
authors.affiliation: Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain. Electronic address: Joaquin.Arino@uab.es.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Ariño
mesh_terms: D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D059647:Gene-Environment Interaction; D006863:Hydrogen-Ion Concentration; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000096:biosynthesis* / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins
keywords: Alkaline stress; Environmental stress response; Genomic Run-On; Saccharomyces cerevisiae; mRNA stability