Predictive Behavior Within Microbial Genetic Networks
Open accessAbstract
The homeostatic framework has dominated our understanding of cellular physiology. We question whether homeostasis alone adequately explains microbial responses to environmental stimuli, and explore the capacity of intracellular networks for predictive behavior in a fashion similar to metazoan nervous systems. We show that in silico biochemical networks, evolving randomly under precisely defined complex habitats, capture the dynamical, multidimensional structure of diverse environments by forming internal representations that allow prediction of environmental change. We provide evidence for such anticipatory behavior by revealing striking correlations of Escherichia coli transcriptional responses to temperature and oxygen perturbations—precisely mirroring the covariation of these parameters upon transitions between the outside world and the mammalian gastrointestinal tract. We further show that these internal correlations reflect a true associative learning paradigm, because they show rapid decoupling upon exposure to novel environments.
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Changes in DNA topology contributed to global transcriptional changes by altered DNA superhelicity, mediated by mutations found in genes such as fis, topAB, gyrAB and dusB.
“Furthermore, changes in DNA topology contributed to global transcriptional changes by altered DNA superhelicity, mediated by mutations found in genes such as fis, topAB, gyrAB and dusB[150].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [150]
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- Authors
- Tagkopoulos, I., Liu, Y.-C., & Tavazoie, S.
- Affiliations
- Princeton University (US)
- Corresponding author
- Tagkopoulos, Ilias
- Liu, Yir-Chung
- Tavazoie, Saeed
- Venue
- Science
- Published
- 2008-06-06
- Volume
- 320
- Issue
- 5881
- Pages
- 1313-1317
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2931280
- OpenAlex
- W2153685804
- Cited by
- 519
- References
- 27
- Citations by year
- 2026: 15 · 2025: 22 · 2024: 16 · 2023: 37 · 2022: 31 · 2021: 28 · 2020: 50 · 2019: 33 · 2018: 33 · 2017: 22 · 2016: 17 · 2015: 26 · 2014: 28 · 2013: 23 · 2012: 21
- FWCI
- 16.06
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (DP1OD003787)
- National Institute of General Medical Sciences (P50GM071508)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- anticipatory behavior, homeostasis, internal representations, environmental forecasting, Escherichia coli, transcriptional response, temperature perturbation, associative learning, gastrointestinal tract
- MeSH terms
- Adaptation, Physiological, Aerobiosis, Anaerobiosis, Computer Simulation, Escherichia coli, Homeostasis, Kinetics, Models, Biological, Mutation, Oxygen, Temperature, Transcription, Genetic, Models, Statistical, Ecosystem, Directed Molecular Evolution, Oligonucleotide Array Sequence Analysis, Gene Regulatory Networks, Metabolic Networks and Pathways
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