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Evolvability and hierarchy in rewired bacterial gene networks
Open accessAbstract
Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or sigma-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that approximately 95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage.
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“Microbial cells have an intrinsic capacity to balance self preservation (stress protection) and nutritional competence (SPANC).”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [158]
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“This SPANC balance was intensively studied in E. coli and is governed by strict control of processes such as stress and stringent response [158,159].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [158]
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Metadata
- Authors
- Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., & Serrano, L.
- Affiliations
- European Molecular Biology Laboratory (ES)
- European Molecular Biology Laboratory (DE)
- Centre for Genomic Regulation (ES)
- Corresponding author
- Isalan, Mark
- Venue
- Nature
- Published
- 2008-04
- Volume
- 452
- Issue
- 7189
- Pages
- 840-845
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2666274
- OpenAlex
- W2159993062
- Cited by
- 307
- References
- 46
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 9 · 2023: 8 · 2022: 11 · 2021: 7 · 2020: 8 · 2019: 12 · 2018: 13 · 2017: 9 · 2016: 13 · 2015: 19 · 2014: 18 · 2013: 29 · 2012: 27
- FWCI
- 16.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust (066543, WT066543)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- gene regulatory network rewiring, Escherichia coli, transcription factors, sigma factor, network hierarchy, synthetic gene networks, genome rearrangement, bacterial fitness
- MeSH terms
- Escherichia coli, Genes, Bacterial, Genetic Engineering, Promoter Regions, Genetic, Selection, Genetic, Serial Passage, Sigma Factor, Transcription Factors, Gene Expression Regulation, Bacterial, Open Reading Frames, Heat-Shock Response, Evolution, Molecular, Oligonucleotide Array Sequence Analysis, Escherichia coli Proteins, Gene Regulatory Networks
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 ›
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