title: Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen.
abstract: Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. InSaccharomyces cerevisiae(budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate-controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source-specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR-regulated permease genesGAP1,MEP2,DAL5,PUT4, andDIP5 Our results reveal novel aspects of nitrogen-regulated gene expression and highlight the need for a quantitative approach to study how the cell coordinates protein translation and nitrogen assimilation to optimize cell growth in different environments.
authors.affiliation: Department of Statistics, Harvard University, Cambridge, MA 02138 Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142 airoldi@fas.harvard.edu dgresham@nyu.edu.
authors.forename: Edoardo M
authors.initials: EM
authors.lastname: Airoldi
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Darach
authors.initials: D
authors.lastname: Miller
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Rodoniki
authors.initials: R
authors.lastname: Athanasiadou
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Nathan
authors.initials: N
authors.lastname: Brandt
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Farah
authors.initials: F
authors.lastname: Abdul-Rahman
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Neymotin
authors.affiliation: Department of Statistics, Harvard University, Cambridge, MA 02138.
authors.forename: Tatsu
authors.initials: T
authors.lastname: Hashimoto
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003.
authors.forename: Tayebeh
authors.initials: T
authors.lastname: Bahmani
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003 airoldi@fas.harvard.edu dgresham@nyu.edu.
authors.forename: David
authors.initials: D
authors.lastname: Gresham
mesh_terms: D000641:Ammonia / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D059647:Gene-Environment Interaction; D009584:Nitrogen / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D018085:Regulon; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D000641:Ammonia; D009584:Nitrogen