ArticleProceedings of the National Academy of Sciences of the United States of America2005
Circuit topology and the evolution of robustness in two-gene circadian oscillators.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Deduction of signaling mechanisms from cellular responses to multiple cues.NPJ systems biology and applications · 2022Article
- Model-Based Design of a Synthetic Oscillator Based on an Epigenetic Methylation Memory System.ACS synthetic biology · 2022Article
- A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis.Nature chemical biology · 2022Article
- Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses.STAR protocols · 2021Article
- Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa.Scientific reports · 2020Article
- It's not magic - Hsp90 and its effects on genetic and epigenetic variation.Seminars in cell & developmental biology · 2019Review
- Constructing network topologies for multiple signal-encoding functions.BMC systems biology · 2019Article
- Modeling Reveals a Key Mechanism for Light-Dependent Phase Shifts of Neurospora Circadian Rhythms.Biophysical journal · 2018Article
- Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution.Molecular systems biology · 2018Article
- Systems and synthetic biology approaches in understanding biological oscillators.Quantitative biology (Beijing, China) · 2018Article
- Computing with biological switches and clocks.Natural computing · 2018Article
- Incoherent Inputs Enhance the Robustness of Biological Oscillators.Cell systems · 2017Article
- Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines.BMC systems biology · 2017Article
- Robust network topologies for generating oscillations with temperature-independent periods.PloS one · 2017Article
- Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations.PLoS computational biology · 2016Article
- Evolution of robust circadian clocks in Drosophila melanogaster populations reared in constant dark for over 330 generations.Die Naturwissenschaften · 2016Article
- A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators.ACS synthetic biology · 2016Article
- Dynamic information routing in complex networks.Nature communications · 2016Article
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Abstract
Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.