Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes

  title={Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes},
  author={Benjamin P. Tu and Andrzej S. Kudlicki and Maga Rowicka and Steven L. McKnight},
  pages={1152 - 1158}
Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential… 

The yeast metabolic cycle: insights into the life of a eukaryotic cell.

  • B. TuS. McKnight
  • Biology
    Cold Spring Harbor symposia on quantitative biology
  • 2007
The logic of the yeast metabolic cycle (YMC) is summarized and additional cellular processes that are predicted to be compartmentalized in time are highlighted, certain principles of temporal orchestration as seen during the YMC might be conserved across other biological cycles.

Genome-wide oscillation of transcription in yeast.

Cyclic changes in metabolic state during the life of a yeast cell

The results reveal the logic of cellular metabolism during different phases of the life of a yeast cell and indicate that oscillation in the abundance of key metabolites might help control the temporal regulation of cellular processes and the establishment of a cycle.

Post-transcriptional Regulation Drives Temporal Compartmentalization of the Yeast Metabolic Cycle

It is shown that an integrated computational analysis of gene expression time series during the metabolic cycle and the mRNA binding specificity of PUF-family proteins allow for a clear demonstration of the very specific role exerted by selective post-transcriptional mRNA degradation in yeast metabolic cycle global regulation.

Ultradian metabolic cycles in yeast.

  • B. Tu
  • Biology
    Methods in enzymology
  • 2010

Systems approaches for the study of metabolic cycles in yeast.

Regulation of the yeast metabolic cycle by transcription factors with periodic activities

Analysis of the phases at which transcription factor activities peak supports previous findings suggesting that the various cellular functions occur during specific phases of the yeast metabolic cycle.

Flavin-based metabolic cycles are integral features of growth and division in single yeast cells

Robust and pervasive metabolic cycles that were synchronized with the cell division cycle (CDC) and oscillated across four different nutrient conditions are uncovered and the response of these metabolic cycles to chemical and genetic perturbations is studied.

Metabolic cycling without cell division cycling in respiring yeast

It is discovered that a prototrophic batch culture of budding yeast, growing in a phosphate-limited ethanol medium, synchronizes spontaneously and goes through multiple metabolic cycles, whereas the fraction of cells in the G1/G0 phase of the CDC increases monotonically from 90 to 99%.

Restriction of DNA Replication to the Reductive Phase of the Metabolic Cycle Protects Genome Integrity

It is shown that cell cycle mutants impeded in metabolic cycle–directed restriction of cell division exhibit substantial increases in spontaneous mutation rate, and circadian, metabolic, and cell division cycles may be coordinated similarly as an evolutionarily conserved means of preserving genome integrity.



A genomewide oscillation in transcription gates DNA replication and cell cycle.

Microarray analysis from a yeast continuous synchrony culture system shows a genomewide oscillation in transcription, which may be an evolutionarily important mechanism for reducing oxidative damage to DNA during replication.

Ammonia pulses and metabolic oscillations guide yeast colony development.

Evidence is presented that the three membrane proteins Ato1p, Ato2p, and Ato3p, members of the YaaH family, are involved in ammonia production in Saccharomyces cerevisiae colonies.

The rhythm of yeast.

Global analysis of protein localization in budding yeast

The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.

Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours.

It is found that populations dividing at rates as rapid as once per 10 h manifest circadian gating of cell division, since phases in which cell division slows or stops recur with a circadian periodicity.

Oscillations in continuous cultures of budding yeast: A segregated parameter analysis

A model is proposed that explains the insurgence of these oscillation as a consequence of changes in cell cycle parameters due to alternate growth in glucose and in ethanol as well as the complex changes of the cell population.

Multiple oscillators regulate circadian gene expression in Neurospora

The predicted or known functions of the clock-controlled genes demonstrate that the clock contributes to a wide range of cellular processes, including cell signaling, development, metabolism, and stress responses.

Global analysis of protein expression in yeast

A Saccharomyces cerevisiae fusion library is created where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location, and it is found that about 80% of the proteome is expressed during normal growth conditions.