Article thumbnail

Nutrient control of eukaryote cell growth: a systems biology study in yeast

By Alex Gutteridge, Pınar Pir, Juan I Castrillo, Philip D Charles, Kathryn S Lilley and Stephen G Oliver
Topics: Research article
Publisher: BioMed Central
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol
  2. (2006). A cultural divide on the use of chemostats.
  3. A language and environment for statistical computing
  4. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol
  5. (2006). Butow RA: Mitochondrial retrograde signaling. Annu Rev Genet
  6. (2002). CA: Nitrogen regulation in Saccharomyces cerevisiae. Gene
  7. (2006). Cell growth control: little eukaryotes make big contributions. Oncogene
  8. (2004). Characterization of the products of the genes SNO1 and SNZ1 involved in pyridoxine synthesis in Saccharomyces cerevisiae.
  9. (2005). Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol Cell Proteomics
  10. (2005). Continuous culture--making a comeback? Microbiology
  11. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing.
  12. (2007). Daran J-M: Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Mol Biol Cell
  13. (2006). Daran JM: When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol Syst Biol
  14. (2005). Entian KD: A history of research on yeasts 9: regulation of sugar metabolism. Yeast
  15. (1996). Estruch F: The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE).
  16. (1985). F: Differential sensitivities to glucose and galactose repression of gluconeogenic and respiratory enzymes from Saccharomyces cerevisiae. Arch Microbiol
  17. (2004). F: Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature
  18. (1997). Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae.
  19. (2004). Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature
  20. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet
  21. (1997). Genetic regulation of nitrogen metabolism in the fungi. Microbiol Mol Biol Rev
  22. (1999). Glucose repression in yeast.
  23. (2006). Glucose signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev
  24. (2006). GM: Proteomic analysis of experimentally induced azole resistance in Candida glabrata.
  25. (2009). Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol Biol Cell
  26. (2006). Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol
  27. (2003). Hapala I: Terbinafine resistance in a pleiotropic yeast mutant is caused by a single point mutation in the ERG1 gene. Biochem Biophys Res Commun
  28. (2008). How Saccharomyces responds to nutrients. Annu Rev Genet
  29. (2008). I: Collective behavior in gene regulation: post-transcriptional regulation and the temporal compartmentalization of cellular cycles.
  30. (1991). I: Positive and negative elements upstream of the meiosis-specific glucoamylase gene in Saccharomyces cerevisiae. Mol Gen Genet
  31. (2009). Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol
  32. (2004). JR: Sense and sensibility: nutritional response and signal integration in yeast. Current Opinion in Microbiology
  33. (2003). MD: The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur.
  34. (2008). Medvedovic M: LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics
  35. (2007). Metabolic Control in the Eukaryotic Cell, a Systems Biology Perspective. Methods in Microbiology
  36. (2006). Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol
  37. (1999). MN: The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature
  38. (2007). Modification in reverse: the SUMO proteases. Trends Biochem Sci
  39. (1997). Molecular genetics of sulfur assimilation in filamentous fungi and yeast. Annu Rev Microbiol
  40. (2008). New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess.
  41. (2008). Nutritional control via Tor signaling in Saccharomyces cerevisiae. Current Opinion in Microbiology
  42. (2004). O'Shea EK: Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci USA
  43. (2001). Parrou JL: Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev
  44. (2002). Pérez-Ortín JE: Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast
  45. (2006). Persson B: New aspects on phosphate sensing and signalling in Saccharomyces cerevisiae.
  46. (1994). Piérard A: A segment of mRNA encoding the leader peptide of the CPA1 gene confers repression by arginine on a heterologous yeast gene transcript. Mol Cell Biol
  47. (1995). Pronk JT: Regulation of carbon metabolism in chemostat cultures of Saccharomyces cerevisiae grown on mixtures of glucose and ethanol. Yeast
  48. (2004). Pronk JT: Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study.
  49. (2005). Pronk JT: Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae.
  50. (2007). Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.
  51. (1991). RAS genes in Saccharomyces cerevisiae: signal transduction in search of a pathway. Trends Genet
  52. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet
  53. (2004). Role of reserve carbohydrates in the growth dynamics of Saccharomyces cerevisiae.
  54. Sá-Correia I: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.
  55. (2008). Saccharomyces cerevisiae SFP1: at the crossroads of central metabolism and ribosome biogenesis.
  56. (1998). Schüller C: Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity.
  57. (2003). Ser3p (Yer081wp) and Ser33p (Yil074cp) are phosphoglycerate dehydrogenases in Saccharomyces cerevisiae.
  58. (2008). SG: Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae. Yeast
  59. (2004). SG: Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc Natl Acad Sci USA
  60. (2007). SG: Growth control of the eukaryote cell: a systems biology study in yeast.
  61. (2002). SG: Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae. Methods
  62. (2006). SG: Integrative investigation of metabolic and transcriptomic data.
  63. (2004). SG: Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics.
  64. (2009). Systems biology: the elements and principles of life.
  65. (2008). The early steps of glucose signalling in yeast.
  66. (1999). The economics of ribosome biosynthesis in yeast. Trends Biochem Sci
  67. (1991). The gene encoding squalene epoxidase from Saccharomyces cerevisiae: cloning and characterization. Gene
  68. (1998). The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation.
  69. (2006). The TOR signalling network from yeast to man.
  70. (2008). Thiele DJ: Post-transcriptional regulation of gene expression in response to iron deficiency: co-ordinated metabolic reprogramming by yeast mRNA-binding proteins. Biochem Soc Trans
  71. (2003). Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr Genet
  72. (2009). Troyanskaya O: Predicting cellular growth from gene expression signatures. PLoS Comput Biol
  73. (1999). Verrips CT: Function of trehalose and glycogen in cell cycle progression and cell viability in Saccharomyces cerevisiae.
  74. (2009). Wessels LF: Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data. BMC Genomics
  75. Y: KEGG for linking genomes to life and the environment.