PDF(Pubmed)
Abstract：
Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.
摘要：
组蛋白变体是替代核小体中的经典组蛋白的旁系同源物，经常赋予新的功能。然而,组蛋白变体是如何产生和进化的，人们知之甚少。由于基因谱系和位点之间的进化率差异很大，组蛋白进化的重建具有挑战性。在这里，我们使用来自108个线虫基因组的内含子位置数据与氨基酸序列数据相结合，以找到在秀丽隐杆线虫中发现的三种H2A变体的不同进化史：古代H2A。ZHTZ-1，精子特异性HTAS-1和HIS-35，其与规范的S期H2A的不同之处在于单个甘氨酸到丙氨酸的C末端变化。虽然H2A。ZHTZ-1蛋白序列高度保守,它的基因表现出反复的内含子得失。这种模式表明特定的内含子序列或位置对H2A可能不重要。Z功能。对于HTAS-1和HIS-35,我们发现跨物种保守的变体特异性内含子位置。内含子位置保守的模式表明，精子特异性变异HTAS-1最近出现在一部分秀丽隐杆线虫的祖先中，而HIS-35出现在秀丽隐杆线虫的祖先和它的姐妹群,包括Diploscapter属。HIS-35在一些后代谱系中表现出基因保留，但在另一些谱系中表现出基因丢失，表明组蛋白变体的使用或功能可以是高度灵活的。令人惊讶的是,我们发现将HIS-35与核心H2A区分开的单个氨基酸是祖先的，并且在经典的秀丽隐杆线虫H2A序列中很常见。因此，我们推测HIS-35的作用不在于编码功能不同的蛋白质，而是在整个细胞周期或不同组织中实现H2A表达。这项工作说明了编码这种部分冗余功能的基因如何在进化时间尺度上是有利的，但相对可替换的。与这两个基因的保留和丢失的拼凑模式一致。我们的研究表明内含子位置在重建基因家族进化史中的实用性，特别是那些经历特殊序列进化的人。
