Department of Mathematics, University of Bergen, Bergen, Norway.
Computational Biology Unit, University of Bergen, Bergen, Norway.
Proc Biol Sci. 2023 Mar 8;290(1994):20222140. doi: 10.1098/rspb.2022.2140.
Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the reasons for these differences are not completely understood. Here, we use a mathematical model to explore the hypothesis that the energetic demands imposed by an organism's changing environment influence how many oDNA genes it retains. The model couples the physical biology of cell processes of gene expression and transport to a supply-and-demand model for the environmental dynamics to which an organism is exposed. The trade-off between fulfilling metabolic and bioenergetic environmental demands, and retaining genetic integrity, is quantified for a generic gene encoded either in oDNA or in nuclear DNA. Species in environments with high-amplitude, intermediate-frequency oscillations are predicted to retain the most organelle genes, whereas those in less dynamic or noisy environments the fewest. We discuss support for, and insight from, these predictions with oDNA data across eukaryotic taxa, including high oDNA gene counts in sessile organisms exposed to day-night and intertidal oscillations (including plants and algae) and low counts in parasites and fungi.
线粒体和质体依赖于许多核编码基因，但保留了它们在自身细胞器 DNA（oDNA）中发挥功能所需的一小部分基因。不同物种保留的 oDNA 基因数量不同，这些差异的原因尚不完全清楚。在这里，我们使用数学模型来探讨这样一种假设，即生物体不断变化的环境所带来的能量需求会影响其保留的 oDNA 基因数量。该模型将细胞基因表达和运输的物理生物学与生物体所暴露的环境动态的供需模型相结合。对于在 oDNA 或核 DNA 中编码的通用基因，在满足代谢和生物能量环境需求与保留遗传完整性之间进行了权衡。预测具有高幅度、中频振荡的环境中的物种将保留最多的细胞器基因，而那些在动态性或噪声较小的环境中的物种保留的细胞器基因最少。我们将结合真核生物分类群中的 oDNA 数据，讨论这些预测的依据和启示，包括暴露于昼夜和潮间带振荡（包括植物和藻类）的固着生物中的高 oDNA 基因计数和寄生虫和真菌中的低计数。
