National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894.
Proc Natl Acad Sci U S A. 2023 Apr 18;120(16):e2300154120. doi: 10.1073/pnas.2300154120. Epub 2023 Apr 10.
The evolution of genomes in all life forms involves two distinct, dynamic types of genomic changes: gene duplication (and loss) that shape families of paralogous genes and extension (and contraction) of low-complexity regions (LCR), which occurs through dynamics of short repeats in protein-coding genes. Although the roles of each of these types of events in genome evolution have been studied, their co-evolutionary dynamics is not thoroughly understood. Here, by analyzing a wide range of genomes from diverse bacteria and archaea, we show that LCR and paralogy represent two distinct routes of evolution that are inversely correlated. The emergence of LCR is a prominent evolutionary mechanism in fast evolving, young protein families, whereas paralogy dominates the comparatively slow evolution of old protein families. The analysis of multiple prokaryotic genomes shows that the formation of LCR is likely a widespread, transient evolutionary mechanism that temporally and locally affects also ancestral functions, but apparently, fades away with time, under mutational and selective pressures, yielding to gene paralogy. We propose that compensatory relationships between short-term and longer-term evolutionary mechanisms are universal in the evolution of life.
在所有生命形式的基因组进化中，涉及两种截然不同的、动态的基因组变化类型：基因复制（和丢失），这塑造了同源基因家族；以及低复杂度区域（LCR）的扩展（和收缩），这是通过蛋白质编码基因中的短重复动态发生的。尽管已经研究了这两种类型的事件在基因组进化中的作用，但它们的共同进化动态尚未得到充分理解。在这里，通过分析来自不同细菌和古菌的广泛基因组，我们表明 LCR 和同源性代表了两种相反相关的进化途径。LCR 的出现是快速进化的年轻蛋白质家族的一个突出的进化机制，而同源性则主导着相对较慢进化的旧蛋白质家族。对多个原核基因组的分析表明，LCR 的形成可能是一种广泛存在的、短暂的进化机制，它会在时间和空间上影响甚至是祖先的功能，但显然，随着时间的推移，在突变和选择压力下，LCR 会逐渐消失，从而产生基因同源性。我们提出，短期和长期进化机制之间的补偿关系在生命进化中是普遍存在的。
