Amphibian Segmentation Clock Models Suggest How Large Genome and Cell Sizes Slow Developmental Rate.

IF 2.2 4区 生物学 Q2 BIOLOGY
Integrative Organismal Biology Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI:10.1093/iob/obae021
A Taylor, A Prasad, R Lockridge Mueller
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Abstract

Evolutionary increases in genome size, cell volume, and nuclear volume have been observed across the tree of life, with positive correlations documented between all three traits. Developmental tempo slows as genomes, nuclei, and cells increase in size, yet the driving mechanisms are poorly understood. To bridge this gap, we use a mathematical model of the somitogenesis clock to link slowed developmental tempo with changes in intra-cellular gene expression kinetics induced by increasing genome size and nuclear volume. We adapt a well-known somitogenesis clock model to two model amphibian species that vary 10-fold in genome size: Xenopus laevis (3.1 Gb) and Ambystoma mexicanum (32 Gb). Based on simulations and backed by analytical derivations, we identify parameter changes originating from increased genome and nuclear size that slow gene expression kinetics. We simulate biological scenarios for which these parameter changes mathematically recapitulate slowed gene expression in A. mexicanum relative to X. laevis, and we consider scenarios for which additional alterations in gene product stability and chromatin packing are necessary. Results suggest that slowed degradation rates as well as changes induced by increasing nuclear volume and intron length, which remain relatively unexplored, are significant drivers of slowed developmental tempo.

两栖动物分段时钟模型揭示大基因组和大细胞如何减缓发育速度
在整个生命树中,我们观察到基因组大小、细胞体积和核体积的进化增长,所有这三个特征之间都存在正相关关系。随着基因组、细胞核和细胞体积的增大,发育节奏也随之减慢,但对其驱动机制却知之甚少。为了弥合这一差距,我们利用体细胞发生时钟数学模型,将发育节奏减慢与基因组大小和核体积增加引起的细胞内基因表达动力学变化联系起来。我们将一个著名的体细胞发生时钟模型应用于两个基因组大小相差 10 倍的两栖动物模型:这两种两栖动物的基因组大小相差 10 倍:章鱼(Xenopus laevis,3.1 Gb)和墨西哥伏两栖动物(Ambystoma mexicanum,32 Gb)。根据模拟和分析推导,我们确定了基因组和核大小增加导致的参数变化,这些变化减缓了基因表达动力学。我们模拟了这些参数变化在数学上再现了墨西哥蟾蜍相对于 X. laevis 的基因表达变慢的生物学情景,并考虑了基因产物稳定性和染色质包装需要额外改变的情景。研究结果表明,降解速度减慢以及核体积和内含子长度增加所引起的变化是导致发育速度减慢的重要原因。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
3.70
自引率
6.70%
发文量
48
审稿时长
20 weeks
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