The yeast metabolic cycle: insights into the life of a eukaryotic cell
Open accessAbstract
The budding yeast Saccharomyces cerevisiae undergoes robust oscillations in oxygen consumption during continuous growth under nutrient-limited conditions. Comprehensive microarray studies reveal that more than half of the yeast genome is expressed periodically as a function of these respiratory oscillations, thereby specifying an extensively orchestrated program responsible for regulating numerous cellular outputs. Here, we summarize the logic of the yeast metabolic cycle (YMC) and highlight additional cellular processes that are predicted to be compartmentalized in time. Certain principles of temporal orchestration as seen during the YMC might be conserved across other biological cycles.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Sleep has been identified in every animal that has been carefully studied.
“Sleep has been recognized in each animal carefully scrutinized.”
From The Biology of General Anesthesia from Paramecium to Primate (2019) · cites this paper as [28]
Behaviorally quiescent or sleep-like states may be as globally widespread as susceptibility to volatile anesthetics.
“behaviorally quiescent or sleep-like states may be as globally penetrant as susceptibility to volatile anesthetics [22–29].”
From The Biology of General Anesthesia from Paramecium to Primate (2019) · cites this paper as [28]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750 · see citing works
Damiola, F., Le Minh, N., Preitner, N., Kornmann, B., Fleury-Olela, F., & Schibler, U. (2000) · Genes & Development · doi:10.1101/gad.183500 · Cited by 2,394 · see citing works
Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock
Panda, S., Antoch, M. P., Miller, B. H., Su, A. I., Schook, A. C., Straume, M., Schultz, P. G., Kay, S. A., Takahashi, J. S., & Hogenesch, J. B. (2002) · Cell · doi:10.1016/s0092-8674(02)00722-5 · Cited by 2,272 · see citing works
Entrainment of the circadian clock in the liver by feeding
Stokkan, K.-A., Yamazaki, S., Tei, H., Sakaki, Y., & Menaker, M. (2001) · Science · doi:10.1126/science.291.5503.490 · Cited by 1,800 · see citing works
Orchestrated Transcription of Key Pathways in <i>Arabidopsis</i> by the Circadian Clock
Harmer, S. L., Hogenesch, J. B., Straume, M., Chang, H.-S., Han, B., Zhu, T., Wang, X., Kreps, J. A., & Kay, S. A. (2000) · Science · doi:10.1126/science.290.5499.2110 · Cited by 1,640 · see citing works
Control Mechanism of the Circadian Clock for Timing of Cell Division in Vivo
Matsuo, T., Yamaguchi, S., Mitsui, S., Emi, A., Shimoda, F., & Okamura, H. (2003) · Science · doi:10.1126/science.1086271 · Cited by 1,132 · see citing works
Regulation of clock and NPAS2 DNA binding by the redox state of NAD cofactors
Rutter, J., Reick, M., Wu, L. C., & McKnight, S. L. (2001) · Science · doi:10.1126/science.1060698 · Cited by 1,059 · see citing works
Self-citationCircadian Gene Expression in Individual Fibroblasts
Nagoshi, E., Saini, C., Bauer, C. R., Laroche, T., Naef, F., & Schibler, U. (2004) · Cell · doi:10.1016/j.cell.2004.11.015 · Cited by 1,003 · see citing works
Mammalian circadian biology: elucidating genome-wide levels of temporal organization
Lowrey, P. L., & Takahashi, J. S. (2004) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.5.061903.175925 · Cited by 976 · see citing works
Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes
Tu, B. P., Kudlicki, A. S., Rowicka, M., & McKnight, S. L. (2005) · Science · doi:10.1126/science.1120499 · Cited by 889 · see citing works
Self-citationNovick, A., & Szilard, L. (1950) · Science · doi:10.1126/science.112.2920.715 · Cited by 766 · see citing works
Microarray Analysis and Organization of Circadian Gene Expression in Drosophila
McDonald, M. J., & Rosbash, M. (2001) · Cell · doi:10.1016/s0092-8674(01)00545-1 · Cited by 606 · see citing works
van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heijnen, J. J., Hoare, M., Lange, H. C., et al. (2000) · Enzyme and Microbial Technology · doi:10.1016/s0141-0229(00)00162-9 · Cited by 598 · cited 1× · see citing works
“PK strain, first adopted by the European yeast community (van Dijken et al. 2000), is our strain of choice for the study of these robust, approximately 4–5-hour metabolic cycles.”
BackgroundCircadian Regulation of Gene Expression Systems in the Drosophila Head
Claridge‐Chang, A., Wijnen, H., Naef, F., Boothroyd, C. E., Rajewsky, N., & Young, M. W. (2001) · Neuron · doi:10.1016/s0896-6273(01)00515-3 · Cited by 444 · see citing works
NPAS2: A Gas-Responsive Transcription Factor
Dioum, E. M., Rutter, J. P., Tuckerman, J. R., Gonzalez, G., Gilles‐Gonzalez, M., & McKnight, S. L. (2002) · Science · doi:10.1126/science.1078456 · Cited by 432 · see citing works
Self-citationMetabolism and the Control of Circadian Rhythms
Rutter, J. P., Reick, M., & McKnight, S. L. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.090501.142857 · Cited by 401 · see citing works
Self-citationSuprachiasmatic Nucleus: Use of <sup>14</sup> C-Labeled Deoxyglucose Uptake as a Functional Marker
Schwartz, W. J., & Gainer, H. (1977) · Science · doi:10.1126/science.887940 · Cited by 358 · see citing works
Mori, T., Binder, B. J., & Johnson, C. H. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10183 · Cited by 332 · see citing works
A genomewide oscillation in transcription gates DNA replication and cell cycle
Klevecz, R. R., Bolen, J., Forrest, G., & Murray, D. B. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306490101 · Cited by 321 · see citing works
Cyclic changes in metabolic state during the life of a yeast cell
Tu, B. P., Mohler, R. E., Liu, J. C., Dombek, K. M., Young, E. T., Synovec, R. E., & McKnight, S. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708365104 · Cited by 260 · see citing works
Self-citationEnergetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth
von Meyenburg, H. K. (1969) · Archives of Microbiology · doi:10.1007/bf00414585 · Cited by 252 · see citing works
Chen, Z., Odstrcil, E. A., Tu, B. P., & McKnight, S. L. (2007) · Science · doi:10.1126/science.1140958 · Cited by 234 · see citing works
Self-citationMetabolic cycles as an underlying basis of biological oscillations.
Tu, B. P., & McKnight, S. L. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1980 · Cited by 229 · see citing works
Self-citationDAMPED SINUSOIDAL OSCILLATIONS OF CYTOPLASMIC REDUCED PYRIDINE NUCLEOTIDE IN YEAST CELLS
Chance, B., Estabrook, R. W., & Ghosh, A. K. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.51.6.1244 · Cited by 220 · see citing works
Wu, J., Tolstykh, T., Lee, J., Boyd, K., Stock, J. B., & Broach, J. R. (2000) · The EMBO Journal · doi:10.1093/emboj/19.21.5672 · Cited by 186 · see citing works
Oscillatory metabolism ofSaccharomyces cerevisiaein continuous culture
Satroutdinov, A. D., Kuriyama, H., & Kobayashi, H. (1992) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1992.tb05525.x · Cited by 162 · see citing works
Richard, P. (2003) · FEMS Microbiology Reviews · doi:10.1016/s0168-6445(03)00065-2 · Cited by 161 · see citing works
Circadian Rhythms in Rapidly Dividing Cyanobacteria
Kondo, T., Mori, T., Lebedeva, N. V., Aoki, S., Ishiura, M., & Golden, S. S. (1997) · Science · doi:10.1126/science.275.5297.224 · Cited by 159 · see citing works
High-resolution timing of cell cycle-regulated gene expression
Rowicka, M., Kudlicki, A. S., Tu, B. P., & Otwinowski, Z. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706022104 · Cited by 79 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Exploring phylogeny to find the function of sleep
Anafi, R. C., Kayser, M. S., & Raizen, D. M. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-018-0098-9 · Cited by 259 · see citing works
The Biology of General Anesthesia from Paramecium to Primate
Kelz, M. B., & Mashour, G. A. (2019) · Current Biology · doi:10.1016/j.cub.2019.09.071 · Cited by 151 · see citing works
The functional basis of adaptive evolution in chemostats
Gresham, D., & Hong, J. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12082 · Cited by 122 · see citing works
SDH5 mutations and familial paraganglioma: somewhere Warburg is smiling
Kaelin, W. G. (2009) · Cancer Cell · doi:10.1016/j.ccr.2009.08.013 · Cited by 67 · see citing works
- Authors
- Tu, B. P., & McKnight, S. L.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Venue
- Cold Spring Harbor Symposia on Quantitative Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-01
- Volume
- 72
- Issue
- 1
- Pages
- 339-343
- ISSN
- 0091-7451 (ISSN-L)
- OpenAlex
- W2122075848
- Cited by
- 38
- References
- 29
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 4 · 2023: 3 · 2022: 1 · 2021: 2 · 2020: 3 · 2019: 3 · 2018: 1 · 2017: 2 · 2015: 3 · 2014: 1 · 2013: 1 · 2012: 2
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cold Spring Harbor Symposia on Quantitative Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- McKnight Foundation
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- Saccharomyces cerevisiae, respiratory oscillations, periodic gene expression, temporal gene regulation, eukaryotic cell cycle, metabolic oscillations
- MeSH terms
- Activity Cycles, Circadian Rhythm, Genes, Fungal, Oxygen Consumption, Saccharomyces cerevisiae, Transcription, Genetic, Gene Expression Profiling
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
