Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate

Oscillations in patterns of expression of a large fraction of yeast genes are associated with the “metabolic cycle,” usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells. Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations. We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.

[1]  Anders Ståhlberg,et al.  Single-cell gene expression profiling using reverse transcription quantitative real-time PCR. , 2010, Methods.

[2]  Patrick H. Bradley,et al.  Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations , 2010, Molecular biology of the cell.

[3]  S. Letovsky,et al.  Quantification of the yeast transcriptome by single-molecule sequencing , 2009, Nature Biotechnology.

[4]  S. Schreiber,et al.  Amino Acid Metabolic Origin as an Evolutionary Influence on Protein Sequence in Yeast , 2009, Journal of Molecular Evolution.

[5]  Edoardo M. Airoldi,et al.  Predicting Cellular Growth from Gene Expression Signatures , 2009, PLoS Comput. Biol..

[6]  Matthew J. Brauer,et al.  Slow Growth Induces Heat-shock Resistance in Normal and Respiratory-deficient Yeast , 2022 .

[7]  Yoshiyuki Sakaki,et al.  Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs , 2008, BMC Genomics.

[8]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.

[9]  Eran Segal,et al.  Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation , 2008, Molecular systems biology.

[10]  Matthew J. Brauer,et al.  Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. , 2008, Molecular biology of the cell.

[11]  K. Tsurugi,et al.  Destabilization of energy-metabolism oscillation in the absence of trehalose synthesis in the chemostat culture of yeast. , 2007, Archives of biochemistry and biophysics.

[12]  Steven L McKnight,et al.  Restriction of DNA Replication to the Reductive Phase of the Metabolic Cycle Protects Genome Integrity , 2007, Science.

[13]  Andrzej Kudlicki,et al.  SCEPTRANS: an online tool for analyzing periodic transcription in yeast , 2007, Bioinform..

[14]  B. Tu,et al.  Metabolic cycles as an underlying basis of biological oscillations , 2006, Nature Reviews Molecular Cell Biology.

[15]  William Stafford Noble,et al.  The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. , 2006, Genes & development.

[16]  B. Futcher.  Metabolic cycle, cell cycle, and the finishing kick to Start , 2006, Genome Biology.

[17]  A. Kudlicki,et al.  Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes , 2005, Science.

[18]  Letian Kuai,et al.  A nuclear degradation pathway controls the abundance of normal mRNAs in Saccharomyces cerevisiae. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Kara Dolinski,et al.  Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. , 2005, Molecular biology of the cell.

[20]  J. François,et al.  Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose , 2005, The FEBS journal.

[21]  D. Murray,et al.  A genomewide oscillation in transcription gates DNA replication and cell cycle. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Armin Fiechter,et al.  Changes in carbohydrate composition and trehalase-activity during the budding cycle of Saccharomyces cerevisiae , 2004, Archiv für Mikrobiologie.

[23]  David Lloyd,et al.  Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. , 2003, Experimental cell research.

[24]  J. Boonstra,et al.  Trehalose and glycogen accumulation is related to the duration of the G1 phase of Saccharomyces cerevisiae. , 2003, FEMS yeast research.

[25]  W. Webb,et al.  Precise nanometer localization analysis for individual fluorescent probes. , 2002, Biophysical journal.

[26]  Artyom M Grigoryan,et al.  Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization. , 2002, Journal of biomedical optics.

[27]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[28]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[29]  F S Fay,et al.  Visualization of single RNA transcripts in situ. , 1998, Science.

[30]  H. Kuriyama,et al.  Autonomous metabolic oscillation in continuous culture of Saccharomyces cerevisiae grown on ethanol. , 1996, FEMS microbiology letters.

[31]  Fernand Meyer,et al.  Topographic distance and watershed lines , 1994, Signal Process..

[32]  B Chance,et al.  Metabolic coupling and synchronization of NADH oscillations in yeast cell populations. , 1971, Archives of biochemistry and biophysics.

[33]  C. Beck,et al.  Enzyme Pattern and Aerobic Growth of Saccharomyces cerevisiae Under Various Degrees of Glucose Limitation , 1968, Journal of bacteriology.

[34]  A. Ghosh,et al.  DAMPED SINUSOIDAL OSCILLATIONS OF CYTOPLASMIC REDUCED PYRIDINE NUCLEOTIDE IN YEAST CELLS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Yi Liu,et al.  Single-Cell Gene Expression Profiling , 2022 .