Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

Edoardo M. Airoldi, Darach Miller, Rodoniki Athanasiadou, Nathan Brandt, Farah Abdul-Rahman, Benjamin Neymotin, Tatsu Hashimoto, Tayebeh Bahmani, David Gresham

Research output: Contribution to journalArticle

Abstract

Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces 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 genes GAP1, MEP2, DAL5, PUT4, and DIP5. 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.

Original languageEnglish (US)
Pages (from-to)1383-1396
Number of pages14
JournalMolecular Biology of the Cell
Volume27
Issue number8
DOIs
StatePublished - Apr 15 2016

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Saccharomyces cerevisiae
Nitrogen
Gene Expression
Catabolite Repression
Growth
Regulon
Protein Biosynthesis
Glutamine
Proline
Saccharomycetales
Batch Cell Culture Techniques
Membrane Transport Proteins
RNA Stability

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen. / Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David.

In: Molecular Biology of the Cell, Vol. 27, No. 8, 15.04.2016, p. 1383-1396.

Research output: Contribution to journalArticle

Airoldi, EM, Miller, D, Athanasiadou, R, Brandt, N, Abdul-Rahman, F, Neymotin, B, Hashimoto, T, Bahmani, T & Gresham, D 2016, 'Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen', Molecular Biology of the Cell, vol. 27, no. 8, pp. 1383-1396. https://doi.org/10.1091/mbc.E14-05-1013
Airoldi, Edoardo M. ; Miller, Darach ; Athanasiadou, Rodoniki ; Brandt, Nathan ; Abdul-Rahman, Farah ; Neymotin, Benjamin ; Hashimoto, Tatsu ; Bahmani, Tayebeh ; Gresham, David. / Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen. In: Molecular Biology of the Cell. 2016 ; Vol. 27, No. 8. pp. 1383-1396.
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