Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA 95343, USA.
Department of Molecular and Cell Biology, University of California Merced, Merced, CA 95343, USA.
Nucleic Acids Res. 2023 Nov 10;51(20):10884-10908. doi: 10.1093/nar/gkad797.
Spliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second 'minor' spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes' greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing's persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.
剪接体内含子是通过称为剪接体的核糖核蛋白机器从 RNA 转录本中切除的基因片段。在一些真核生物中，第二个“次要”剪接体负责处理极少数内含子。尽管其作用似乎微不足道，但次要剪接在大约 15 亿年的真核生物进化中一直存在。我们在 3000 多个真核生物基因组中鉴定了次要内含子，报告了多样化的进化历史，包括在一些真菌和绿藻中令人惊讶的高数量、重复丢失以及它们在位置和基因分布上的普遍偏向。我们估计，祖先次要内含子的密度与脊椎动物相当，表明存在长期稳定的趋势。最后，有三个发现表明中性过程在次要内含子进化中起主要作用。首先，次要和主要内含子进化的高度相似模式与功能主义和有害模型的预测形成对比。其次，在包含次要内含子的基因中观察到的功能偏向在很大程度上可以用这些基因的更老年龄来解释。第三，在一个富含次要内含子的真菌中，内含子剪接与细胞增殖没有关联表明，调节作用是谱系特异性的，因此不能为次要剪接的持续存在提供一般解释。这些数据构成了迄今为止对次要内含子及其进化历史的最全面的观察结果，并为未来对这些非凡遗传元件的研究提供了基础。
