The three helical Histone Fold Motif (HFM) of core histone proteins provides an evolutionarily favored site for the protein–DNA interface. Despite significant variation in sequence, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families. In this work, we explore the ancestry of non-histone HFM containing families in the plant kingdom. A sequence search algorithm was developed using iterative profile Hidden Markov Models to identify remote homologs of core-histone proteins. The resulting hits were functionally annotated, classified into families, and subjected to comprehensive phylogenetic analyses via Maximum likelihood and Bayesian methods. We have identified 4390 HFM containing proteins in the plant kingdom that are not histones, mostly existing as diverse transcription factor families, distributed widely within and across taxonomic groups. Patterns of homology suggest that core histone subunit H2A has evolved into newer families like NF-YC and DRAP1, whereas the H2B subunit of core histones shares a common ancestry with NF-YB and DR1 class of TFs. Core histone subunits H3 and H4 were found to have evolved into DPE and TAF proteins, respectively. Taken together these results provide insights into diversification events during the evolution of the HFM, including sub-functionalization and neo-functionalization of the HFM.

中文翻译：

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核心组蛋白亚基和含有组蛋白折叠基序 (HFM) 的非组蛋白植物蛋白的共同祖先

核心组蛋白的三个螺旋组蛋白折叠基序 (HFM) 为蛋白质-DNA 界面提供了进化上有利的位点。尽管序列存在显着差异，但 HFM 保留了独特的结构折叠，该折叠已多样化为几个非组蛋白家族。在这项工作中，我们探索了植物界中含有非组蛋白 HFM 的家族的祖先。使用迭代轮廓隐马尔可夫模型开发了一种序列搜索算法，以识别核心组蛋白的远程同源物。对所得命中进行功能注释，分类为家族，并通过最大似然法和贝叶斯方法进行全面的系统发育分析。我们已经在植物界鉴定了 4390 个含有 HFM 的蛋白质，它们不是组蛋白，主要作为不同的转录因子家族存在，广泛分布于分类群内部和跨分类群。同源性模式表明核心组蛋白亚基 H2A 已经进化成新的家族，如 NF-YC 和 DRAP1，而核心组蛋白的 H2B 亚基与 NF-YB 和 DR1 类 TF 具有共同的祖先。发现核心组蛋白亚基 H3 和 H4 已分别进化为 DPE 和 TAF 蛋白。综上所述，这些结果提供了对 HFM 演变过程中多样化事件的见解，包括 HFM 的亚功能化和新功能化。发现核心组蛋白亚基 H3 和 H4 已分别进化为 DPE 和 TAF 蛋白。综上所述，这些结果提供了对 HFM 演变过程中多样化事件的见解，包括 HFM 的亚功能化和新功能化。发现核心组蛋白亚基 H3 和 H4 已分别进化为 DPE 和 TAF 蛋白。综上所述，这些结果提供了对 HFM 演变过程中多样化事件的见解，包括 HFM 的亚功能化和新功能化。