Dominant constraints on the evolution of rhythmic gene expression

Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown...

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Bibliographic Details
Published in:Computational and structural biotechnology journal 2023-01, Vol.21, p.4301-4311
Main Authors: Cheng, Yang, Chi, Yuhao, Sun, Linying, Wang, Guang-Zhong
Format: Article
Language:English
Subjects:
Circadian evolution
Circadian rhythms
Energy expenditure
Rhythmic gene expression
Transcription-translation feedback loop (TTFL)
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Summary:Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown whether analogous design principles govern the gene expression output of circadian clocks. In this study, we performed a comparative analysis of rhythmic gene expression in eight diverse species and identified four common distribution patterns of cycling gene expression across these species. We hypothesized that the maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the peaks of rhythmic expression have been subjected to this type of selective pressure. The results suggest that selective pressure from circadian regulation efficiently removes unnecessary gene products from the transcriptome, thereby significantly impacting its evolutionary path. [Display omitted] •Comparing cycling transcriptomes across eight species revealed four conserved patterns of cycling genes•High expression levels and large relative amplitude can predict cycling genes.•Peaks of rhythmic expression have undergone selection.•Large-scale computational simulations based on energetic cost optimization can reproduce conserved patterns of cycling genes.
ISSN:2001-0370
2001-0370
DOI:10.1016/j.csbj.2023.08.035