ArticlemSystems2022
Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.ACS synthetic biology · 2024Pooled it
- Transcriptional regulatory network differences between six industrialMetabolic engineering communications · 2026Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- Genome and transcriptomic analysis of the adaptation ofComputational and structural biotechnology journal · 2024Review
- Article
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.mSystems · 2024Article
- A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic acids research · 2023Article
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell reports · 2023Article
- Epistasis and evolution: recent advances and an outlook for prediction.BMC biology · 2023Review
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.Research square · 2023Article
- Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications.Cell reports · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Genotype-fitness maps of evolution have been well characterized for biological components, such as RNA and proteins, but remain less clear for systems-level properties, such as those of metabolic and transcriptional regulatory networks. Here, we take multi-omics measurements of 6 different E. coli strains throughout adaptive laboratory evolution (ALE) to maximal growth fitness. The results show the following: (i) convergence in most overall phenotypic measures across all strains, with the notable exception of divergence in NADPH production mechanisms; (ii) conserved transcriptomic adaptations, describing increased expression of growth promoting genes but decreased expression of stress response and structural components; (iii) four groups of regulatory trade-offs underlying the adjustment of transcriptome composition; and (iv) correlates that link causal mutations to systems-level adaptations, including mutation-pathway flux correlates and mutation-transcriptome composition correlates. We thus show that fitness landscapes for ALE can be described with two layers of causation: one based on system-level properties (continuous variables) and the other based on mutations (discrete variables).
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Registered trials
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.