Cited by 307Gene Regulatory Network AnalysisEvolution and Genetic DynamicsBacterial Genetics and Biotechnology

Evolvability and hierarchy in rewired bacterial gene networks

Open access
Isalan, Mark, Lemerle, Caroline, Michalodimitrakis, Konstantinos, Horn, Carsten, Beltrao, Pedro, Raineri, Emanuele, Garriga-Canut, Mireia, Serrano, Luis·2008·Nature

Abstract

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).

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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
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
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

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