Wittouck Stijn, van Noort Vera
Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.
BMC Evol Biol. 2017 Mar 20;17(1):83. doi: 10.1186/s12862-017-0932-0.
Protein post-translational modifications (PTMs) change protein properties. Each PTM type is associated with domain families that apply the modification (writers), remove the modification (erasers) and bind to the modified sites (readers) together called toolkit domains. The evolutionary origin and diversification remains largely understudied, except for tyrosine phosphorylation. Protein palmitoylation entails the addition of a palmitoyl fatty acid to a cysteine residue. This PTM functions as a membrane anchor and is involved in a range of cellular processes. One writer family and two erasers families are known for protein palmitoylation.
In this work we unravel the evolutionary history of these writer and eraser families. We constructed a high-quality profile hidden Markov model (HMM) of each family, searched for protein family members in fully sequenced genomes and subsequently constructed phylogenetic distributions of the families. We constructed Maximum Likelihood phylogenetic trees and using gene tree rearrangement and tree reconciliation inferred their evolutionary histories in terms of duplication and loss events. We identified lineages where the families expanded or contracted and found that the evolutionary histories of the families are correlated. The results show that the erasers were invented first, before the origin of the eukaryotes. The writers first arose in the eukaryotic ancestor. The writers and erasers show co-expansions in several eukaryotic ancestral lineages. These expansions often seem to be followed by contractions in some or all of the lineages further in evolution.
A general pattern of correlated evolution appears between writer and eraser domains. These co-evolution patterns could be used in new methods for interaction prediction based on phylogenies.
蛋白质翻译后修饰（PTM）会改变蛋白质特性。每种PTM类型都与执行修饰（写入器）、去除修饰（擦除器）以及结合修饰位点（读取器）的结构域家族相关，这些结构域家族统称为工具包结构域。除酪氨酸磷酸化外，其进化起源和多样化在很大程度上仍未得到充分研究。蛋白质棕榈酰化是指在半胱氨酸残基上添加棕榈酰脂肪酸。这种PTM起到膜锚定的作用，并参与一系列细胞过程。已知一个写入器家族和两个擦除器家族与蛋白质棕榈酰化有关。
在这项工作中，我们揭示了这些写入器和擦除器家族的进化历史。我们为每个家族构建了高质量的隐马尔可夫模型（HMM），在全基因组测序中搜索蛋白质家族成员，随后构建了这些家族的系统发育分布。我们构建了最大似然系统发育树，并使用基因树重排和树调和方法推断了它们在复制和丢失事件方面的进化历史。我们确定了家族扩张或收缩的谱系，发现这些家族的进化历史是相关的。结果表明，擦除器在真核生物起源之前就已出现。写入器最早出现在真核生物祖先中。写入器和擦除器在几个真核生物祖先谱系中共同扩张。这些扩张在进化过程中似乎常常伴随着某些或所有谱系的收缩。
写入器和擦除器结构域之间出现了相关进化的一般模式。这些共同进化模式可用于基于系统发育的新的相互作用预测方法。
