ArticleGenetics2021
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 9 citations in OpenAlex.
- Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.PLoS computational biology · 2024Article
- Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts.Life (Basel, Switzerland) · 2023Article
- On the incongruence of genotype-phenotype and fitness landscapes.PLoS computational biology · 2022Article
- Mutation bias shapes the spectrum of adaptive substitutions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional regulatory networks (TRNs) are enriched for certain "motifs." Motif usage is commonly interpreted in adaptationist terms, i.e., that the optimal motif evolves. But certain motifs can also evolve more easily than others. Here, we computationally evolved TRNs to produce a pulse of an effector protein. Two well-known motifs, type 1 incoherent feed-forward loops (I1FFLs) and negative feedback loops (NFBLs), evolved as the primary solutions. The relative rates at which these two motifs evolve depend on selection conditions, but under all conditions, either motif achieves similar performance. I1FFLs generally evolve more often than NFBLs. Selection for a tall pulse favors NFBLs, while selection for a fast response favors I1FFLs. I1FFLs are more evolutionarily accessible early on, before the effector protein evolves high expression; when NFBLs subsequently evolve, they tend to do so from a conjugated I1FFL-NFBL genotype. In the empirical S. cerevisiae TRN, output genes of NFBLs had higher expression levels than those of I1FFLs. These results suggest that evolutionary accessibility, and not relative functionality, shapes which motifs evolve in TRNs, and does so as a function of the expression levels of particular genes.
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