Do yeast cells dream of metabolic sheep?

⟵

References and Data Sources

⟶

Rainer Machné

The YRO Literature DAG

A few specific paths through the vast directed acyclic graph of scientific progress1. Is it a linear and logical process (Karl Popper) or a historical development, shaped by traditions, big egos and vanity (Ludwik Fleck (1935))?

In firefox, I recomment to install the PubPeer app that notifies you of pubpeer entries for any cited paper on any webpage.

TODO: the following lists exist mainly to include all refs here; todo: expand, and/or collect all refs from all markdown source files, and draw a citation DAG.

Yeast Respiratory Oscillations

Pulse Width Modulation and Yeast Growth

PCA/SVD Analysis

FM=PWM in Other Contexts

Philosophy

Chromatin as a Metabolic Sensor

PWM Model Parameters

TODO: load/add the param table

Omic Data Sources

ID Reference experiment measurement strains units platform source
klevecz04 Klevecz et al. (2004) oscillation transcriptome IFO 0233 fluor./a.u. Affymetrix Yeast Genome S98 SGD
li06 Li and Klevecz (2006) oscillation transcriptome IFO 0233 fluor./a.u. Affymetrix Yeast Genome 2.0 Dataset S1 of Machné and Murray (2012)
tu05 Tu et al. (2005) oscillation transcriptome CEN.PK122 fluor./a.u. Affymetrix Yeast Genome 2.0 Dataset S1 of Machné and Murray (2012)
slavov11 Slavov et al. (2011) oscillation transcriptome DBY12007 fluor./log2(sample/ref.) custom Agilent array supporting website
nocetti16 Nocetti and Whitehouse (2016) oscillation transcriptome CEN.PK read counts/RPKM Illumina n.a. GEO:GSE77631
chin12 Chin et al. (2012) oscillation transcriptome CEN.PK113-7D fluor./a.u. Affymetrix Yeast Genome 2.0 GEO:GSE30053
wang15 Wang et al. (2015) oscillation transcriptome CEN.PK122 read counts/RPKM Illumina HiSeq 2500 Supplementary Table S1
kuang14 Kuang et al. (2014) oscillation transcriptome CEN.PK122 read counts/FPKM Illumina HiSeq 2000 Supplementary Table S1
oneill20 O' Neill et al. (2020) oscillation proteome CEN.PK113-7D fold change/(max/min) Supplementary Data 1
machne22pre Machné et al. (2021) oscillation transcriptome IFO 0233 normalized read counts Illumina 1G E-MTAB-11901; Supplementary Data 2
orlando08 Orlando et al. (2008) cell cycle transcriptome BF264-15Dau fluor./a.u. Affymetrix Yeast Genome 2.0 GEO:GSE8799
bristow14 Bristow et al. (2014) cell cycle transcriptome BF264-15Dau fluor./a.u. Affymetrix Yeast Genome 2.0 GEO:GSE49650
cho17 Cho et al. (2017) cell cycle transcriptome BF264-15D fluor./a.u. Affymetrix Yeast Genome 2.0 GEO:GSE96997
simm.12 Simmons Kovacs et al. (2012) cell cycle transcriptome BF264-15DU fluor./a.u. Affymetrix Yeast Genome 2.0 GEO:GSE32974
camp.20_mRNA Campbell et al. (2020) cell cycle transcriptome CEN.PK113-7D mRNA/pg NextSeq 500, nCounter Dataset S01
camp.20_protein Campbell et al. (2020) cell cycle proteome CEN.PK113-7D protein/pg Ultimate 3000 RSLC nano Dataset S01
slavov11b Slavov and Botstein (2011) growth rate transcriptome DBY11369 fluor./log2(sample/ref.) custom Agilent array supporting website
brauer08 Brauer et al. (2008) growth rate transcriptome DBY10085,DBY9492,DBY9497 fluor./log2(sample/ref.) custom Agilent array supporting website
xia22_transcripts Xia et al. (2022) growth rate transcriptome CEN.PK113-7D mRNA/(n/cell) NextSeq 500, Affymetrix QuantiGene Supplementary Data 3
xia22_proteins Xia et al. (2022) growth rate proteome CEN.PK113-7D protein/(n/cell) Ultimate 3000 RSLC nano Supplementary Data 1
paulo16 Paulo et al. (2016) growth rate proteome BY4742 TNT intensity/a.u. Orbitrap Fusion Lumos, SPS-MS3 Supplemental Table 1
hackett16 Hackett et al. (2016) growth rate proteome FY-derivative protein/log2(sample/ref.) Agilent 6538 Q-TOF and 6550 Q-TOF Table S9
jackson20 Jackson et al. (2020) growth rate transcriptome FY4/FY5 mRNA/(n/cell) single cell sequencing GEO:GSE125162
slavov14_protein Slavov et al. (2014) batch culture proteome DBY12007 TMT/(sample/mean) Orbitrap Velos Pro Document S2
slavov14_mRNA Slavov et al. (2014) batch culture transcriptome DBY12007 fluor./log2(sample/mean) custom Agilent array Document S2
gasch17 Gasch et al. (2017) stress transcriptome BY4741 normalized read counts HiSeq-2500 1T v4 GEO:GSE102475
oduibhir14 O'Duibhir et al. (2014) mutant collection transcriptome BY4742 (Haploid MATalpha) normalized fluorescence Biorobotics MicroGridII spotter E‐MTAB‐1383, E‐MTAB‐1384; GSE42526, GSE42527

References

Albeck, J. G., G. B. Mills, and J. S. Brugge. 2013. "Frequency-Modulated Pulses of ERK Activity Transmit Quantitative Proliferation Signals." Mol Cell 49 (2): 249-61. https://doi.org/10.1016/j.molcel.2012.11.002.
Alter, O., P. O. Brown, and D. Botstein. 2000. "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling." Proc Natl Acad Sci U S A 97 (18): 10101-6. https://doi.org/10.1073/pnas.97.18.10101.
Amariei, C., R. Machné, V. Stolc, T. Soga, M. Tomita, and D. B. Murray. 2014. "Time Resolved DNA Occupancy Dynamics During the Respiratory Oscillation Uncover a Global Reset Point in the Yeast Growth Program." Microb Cell 1 (9): 279-88. https://doi.org/10.15698/mic2014.09.166.
Brauer, M. J., C. Huttenhower, E. M. Airoldi, R. Rosenstein, J. C. Matese, D. Gresham, V. M. Boer, O. G. Troyanskaya, and D. Botstein. 2008. "Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast." Mol Biol Cell 19 (1): 352-67. https://doi.org/10.1091/mbc.E07-08-0779.
Brauer, M. J., A. J. Saldanha, K. Dolinski, and D. Botstein. 2005. "Homeostatic Adjustment and Metabolic Remodeling in Glucose-Limited Yeast Cultures." Mol Biol Cell 16 (5): 2503-17. https://doi.org/10.1091/mbc.E04-11-0968.
Bristow, S. L., A. R. Leman, L. A. Simmons Kovacs, A. Deckard, J. Harer, and S. B. Haase. 2014. "Checkpoints Couple Transcription Network Oscillator Dynamics to Cell-Cycle Progression." Genome Biol 15 (9): 446. https://doi.org/10.1186/s13059-014-0446-7.
Burnetti, A. J., M. Aydin, and N. E. Buchler. 2016. "Cell Cycle Start Is Coupled to Entry into the Yeast Metabolic Cycle Across Diverse Strains and Growth Rates." Mol Biol Cell 27 (1): 64-74. https://doi.org/10.1091/mbc.E15-07-0454.
Cai, L., C. K. Dalal, and M. B. Elowitz. 2008. "Frequency-Modulated Nuclear Localization Bursts Coordinate Gene Regulation." Nature 455 (7212): 485-90. https://doi.org/10.1038/nature07292.
Campbell, K., J. Westholm, S. Kasvandik, F. Di Bartolomeo, M. Mormino, and J. Nielsen. 2020. "Building Blocks Are Synthesized on Demand During the Yeast Cell Cycle." Proc Natl Acad Sci U S A 117 (14): 7575-83. https://doi.org/10.1073/pnas.1919535117.
Chin, S. L., I. M. Marcus, R. R. Klevecz, and C. M. Li. 2012. "Dynamics of Oscillatory Phenotypes in Saccharomyces Cerevisiae Reveal a Network of Genome-Wide Transcriptional Oscillators." FEBS J 279 (6): 1119-30. https://doi.org/10.1111/j.1742-4658.2012.08508.x.
Cho, C. Y., F. C. Motta, C. M. Kelliher, A. Deckard, and S. B. Haase. 2017. "Reconciling Conflicting Models for Global Control of Cell-Cycle Transcription." Cell Cycle 16 (20): 1965-78. https://doi.org/10.1080/15384101.2017.1367073.
Dalal, C. K., L. Cai, Y. Lin, K. Rahbar, and M. B. Elowitz. 2014. "Pulsatile Dynamics in the Yeast Proteome." Curr Biol 24 (18): 2189-94.
Finn, R. K., and R. E. Wilson. 1954. "Population Dynamics of a Continuous Propagator for Microorganisms." J. Agric. Food Chem. 2 (2): 66-69. https://doi.org/10.1021/jf60022a609.
Fleck, Ludwig. 1935. Entstehung Und Entwicklung Einer Wissenschaftlichen Tatsache: Einführung in Die Lehre Vom Denkstil Und Denkkollektiv. Basel: Benno Schwabe & Co.
Fox Keller, Evelyn. 1996. Refiguring Life: Metaphors of Twentieth-Century Biology. Columbia University Press.
Gagliardi, P. A., and O. Pertz. 2024. "The Mitogen-Activated Protein Kinase Network, Wired to Dynamically Function at Multiple Scales." Curr Opin Cell Biol 88 (June): 102368. https://doi.org/10.1016/j.ceb.2024.102368.
Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. "Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes." Mol Biol Cell 11 (12): 4241-57.
Gasch, A. P., F. B. Yu, J. Hose, L. E. Escalante, M. Place, R. Bacher, J. Kanbar, et al. 2017. "Single-Cell RNA Sequencing Reveals Intrinsic and Extrinsic Regulatory Heterogeneity in Yeast Responding to Stress." PLoS Biol 15 (12): e2004050. https://doi.org/10.1371/journal.pbio.2004050.
Hackett, S. R., V. R. Zanotelli, W. Xu, J. Goya, J. O. Park, D. H. Perlman, P. A. Gibney, D. Botstein, J. D. Storey, and J. D. Rabinowitz. 2016. "Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux." Science 354 (6311). https://doi.org/10.1126/science.aaf2786.
Hartwell, L. H., and M. W. Unger. 1977. "Unequal Division in Saccharomyces Cerevisiae and Its Implications for the Control of Cell Division." J Cell Biol 75 (2 Pt 1): 422-35.
Jackson, C. A., D. M. Castro, G. A. Saldi, R. Bonneau, and D. Gresham. 2020. "Gene Regulatory Network Reconstruction Using Single-Cell RNA Sequencing of Barcoded Genotypes in Diverse Environments." Elife 9 (January). https://doi.org/10.7554/eLife.51254.
Klevecz, R. R., J. Bolen, G. Forrest, and D. B. Murray. 2004. "A Genomewide Oscillation in Transcription Gates DNA Replication and Cell Cycle." Proc Natl Acad Sci U S A 101 (5): 1200-1205. https://doi.org/10.1073/pnas.0306490101.
Klevecz, R. R., C. M. Li, I. Marcus, and P. H. Frankel. 2008. "Collective Behavior in Gene Regulation: The Cell Is an Oscillator, the Cell Cycle a Developmental Process." FEBS J 275 (10): 2372-84. https://doi.org/10.1111/j.1742-4658.2008.06399.x.
Kuang, Z., L. Cai, X. Zhang, H. Ji, B. P. Tu, and J. D. Boeke. 2014. "High-Temporal-Resolution View of Transcription and Chromatin States Across Distinct Metabolic States in Budding Yeast." Nat Struct Mol Biol 21 (10): 854-63. https://doi.org/10.1038/nsmb.2881.
Kubik, S., M. J. Bruzzone, D. Challal, R. Dreos, S. Mattarocci, P. Bucher, D. Libri, and D. Shore. 2019. "Opposing Chromatin Remodelers Control Transcription Initiation Frequency and Start Site Selection." Nat Struct Mol Biol 26 (8): 744-54. https://doi.org/10.1038/s41594-019-0273-3.
Küenzi, M. T., and A. Fiechter. 1969. "Changes in Carbohydrate Composition and Trehalase-Activity During the Budding Cycle of Saccharomyces Cerevisiae." Archives of Microbiology 64 (4): 396-407. https://doi.org/10.1007/BF00417021.
Li, C. M., and R. R. Klevecz. 2006. "A Rapid Genome-Scale Response of the Transcriptional Oscillator to Perturbation Reveals a Period-Doubling Path to Phenotypic Change." Proc Natl Acad Sci U S A 103 (44): 16254-59. https://doi.org/10.1073/pnas.0604860103.
Liu, X., S. Oh, L. Peshkin, and M. W. Kirschner. 2020. "Computationally Enhanced Quantitative Phase Microscopy Reveals Autonomous Oscillations in Mammalian Cell Growth." Proc Natl Acad Sci U S A, October. https://doi.org/10.1073/pnas.2002152117.
Machné, R., S. H. Bernhart, I. M. Axmann, P. F. Stadler, and D. B. Murray. 2021. "Spatio-Temporal Coordination of Transcription During the Cell Growth Cycle in Budding Yeast." bioRxiv. https://doi.org/10.1101/2021.05.26.444658v1.
Machné, R., and D. B. Murray. 2012. "The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System Between Metabolism and Chromatin." PLoS One 7 (6): e37906. https://doi.org/10.1371/journal.pone.0037906.
Macosko, E. Z., A. Basu, R. Satija, J. Nemesh, K. Shekhar, M. Goldman, I. Tirosh, et al. 2015. "Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets." Cell 161 (5): 1202-14. https://doi.org/10.1016/j.cell.2015.05.002.
Meyenburg, Kaspar von. 1969. "Katabolit-Repression und der Sprossungszyklus von Saccharomyces cerevisiae." Vierteljahrsschrift Der Naturforschenden Gesellschaft in Zürich. PhD thesis, ETH Zürich.
Nocetti, N., and I. Whitehouse. 2016. "Nucleosome Repositioning Underlies Dynamic Gene Expression." Genes Dev 30 (6): 660-72. https://doi.org/10.1101/gad.274910.115.
O'Duibhir, E., P. Lijnzaad, J. J. Benschop, T. L. Lenstra, D. van Leenen, M. J. Groot Koerkamp, T. Margaritis, M. O. Brok, P. Kemmeren, and F. C. Holstege. 2014. "Cell Cycle Population Effects in Perturbation Studies." Mol Syst Biol 10 (June): 732. https://doi.org/10.15252/msb.20145172.
O' Neill, J. S., N. P. Hoyle, J. B. Robertson, R. S. Edgar, A. D. Beale, S. Y. Peak-Chew, J. Day, A. S. H. Costa, C. Frezza, and H. C. Causton. 2020. "Eukaryotic Cell Biology Is Temporally Coordinated to Support the Energetic Demands of Protein Homeostasis." Nat Commun 11 (1): 4706. https://doi.org/10.1038/s41467-020-18330-x.
Omberg, L., G. H. Golub, and O. Alter. 2007. "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data from Different Studies." Proc Natl Acad Sci U S A 104 (47): 18371-76. https://doi.org/10.1073/pnas.0709146104.
Orlando, D. A., C. Y. Lin, A. Bernard, J. Y. Wang, J. E. Socolar, E. S. Iversen, A. J. Hartemink, and S. B. Haase. 2008. "Global Control of Cell-Cycle Transcription by Coupled CDK and Network Oscillators." Nature 453 (7197): 944-47. https://doi.org/10.1038/nature06955.
Paulo, J. A., J. D. O'Connell, R. A. Everley, J. O'Brien, M. A. Gygi, and S. P. Gygi. 2016. "Quantitative Mass Spectrometry-Based Multiplexing Compares the Abundance of 5000 s. Cerevisiae Proteins Across 10 Carbon Sources." J Proteomics 148 (October): 85-93. https://doi.org/10.1016/j.jprot.2016.07.005.
Schwabe, D., S. Formichetti, J. P. Junker, M. Falcke, and N. Rajewsky. 2020. "The Transcriptome Dynamics of Single Cells During the Cell Cycle." Mol Syst Biol 16 (11): e9946. https://doi.org/10.15252/msb.20209946.
Simmons Kovacs, L. A., M. B. Mayhew, D. A. Orlando, Y. Jin, Q. Li, C. Huang, S. I. Reed, S. Mukherjee, and S. B. Haase. 2012. "Cyclin-Dependent Kinases Are Regulators and Effectors of Oscillations Driven by a Transcription Factor Network." Mol Cell 45 (5): 669-79. https://doi.org/10.1016/j.molcel.2011.12.033.
Slavov, N., and D. Botstein. 2011. "Coupling Among Growth Rate Response, Metabolic Cycle, and Cell Division Cycle in Yeast." Mol Biol Cell 22 (12): 1997-2009. https://doi.org/10.1091/mbc.E11-02-0132.
Slavov, N., B. A. Budnik, D. Schwab, E. M. Airoldi, and A. van Oudenaarden. 2014. "Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis." Cell Rep 7 (3): 705-14. https://doi.org/10.1016/j.celrep.2014.03.057.
Slavov, N., J. Macinskas, A. Caudy, and D. Botstein. 2011. "Metabolic Cycling Without Cell Division Cycling in Respiring Yeast." Proc Natl Acad Sci U S A 108 (47): 19090-95. https://doi.org/10.1073/pnas.1116998108.
Tu, B. P., A. Kudlicki, M. Rowicka, and S. L. McKnight. 2005. "Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes." Science 310 (5751): 1152-58.
Wang, G. Z., S. L. Hickey, L. Shi, H. C. Huang, P. Nakashe, N. Koike, B. P. Tu, J. S. Takahashi, and G. Konopka. 2015. "Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale." Cell Rep 13 (9): 1868-80. https://doi.org/10.1016/j.celrep.2015.10.043.
Xia, J., B. J. Sanchez, Y. Chen, K. Campbell, S. Kasvandik, and J. Nielsen. 2022. "Proteome Allocations Change Linearly with the Specific Growth Rate of Saccharomyces Cerevisiae Under Glucose Limitation." Nat Commun 13 (1): 2819. https://doi.org/10.1038/s41467-022-30513-2.