Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
J Mol Evol. 2024 Aug;92(4):505-524. doi: 10.1007/s00239-024-10191-y. Epub 2024 Jul 18.
Gene duplication followed by nucleotide differentiation is one of the simplest mechanisms to develop new functions for genes. However, the evolutionary processes underlying the divergence of multigene families remain controversial. We used multigene families found within the diversity of toxic proteins in centipede venom to test two hypotheses related to venom evolution: the two-speed mode of venom evolution and the rapid accumulation of variation in exposed residues (RAVER) model. The two-speed mode of venom evolution proposes that different types of selection impact ancient and younger venomous lineages with negative selection being the predominant form in ancient lineages and positive selection being the dominant form in younger lineages. The RAVER hypothesis proposes that, instead of different types of selection acting on different ages of venomous lineages, the different types of selection will selectively contribute to amino acid variation based on whether the residue is exposed to the solvent where it can potentially interact directly with toxin targets. This hypothesis parallels the longstanding understanding of protein evolution that suggests that residues found within the structural or active regions of the protein will be under negative or purifying selection, and residues that do not form part of these areas will be more prone to positive selection. To test these two hypotheses, we compared the venom of 26 centipedes from the order Scolopendromorpha from six currently recognized species from across North America using both transcriptomics and proteomics. We first estimated their phylogenetic relationships and uncovered paraphyly among the genus Scolopendra and evidence for cryptic diversity among currently recognized species. Using our phylogeny, we then characterized the diverse venom components from across the identified clades using a combination of transcriptomics and proteomics. We conducted selection-based analyses in the context of predicted three-dimensional properties of the venom proteins and found support for both hypotheses. Consistent with the two-speed hypothesis, we found a prevalence of negative selection across all proteins. Consistent with the RAVER hypothesis, we found evidence of positive selection on solvent-exposed residues, with structural and less-exposed residues showing stronger signal for negative selection. Through the use of phylogenetics, transcriptomics, proteomics, and selection-based analyses, we were able to describe the evolution of venom from an ancient venomous lineage and support principles of protein evolution that directly relate to multigene family evolution.
基因复制后核苷酸分化是为基因开发新功能的最简单机制之一。然而，多基因家族进化背后的进化过程仍存在争议。我们使用蜈蚣毒液中多样性的毒性蛋白所发现的多基因家族来检验与毒液进化相关的两个假设：毒液进化的双速模式和暴露残基快速变异（RAVER）模型。毒液进化的双速模式提出，不同类型的选择会对古老和年轻的毒液谱系产生影响，负选择是古老谱系的主要形式，正选择是年轻谱系的主要形式。RAVER 假说提出，不同类型的选择不是作用于不同年龄的毒液谱系，而是不同类型的选择将根据残基是否暴露于溶剂中来选择性地导致氨基酸变异，在溶剂中它可以与毒素靶标直接相互作用。这个假说与长期以来对蛋白质进化的理解相平行，即蛋白质的结构或活性区域内的残基将受到负或净化选择，而不形成这些区域一部分的残基将更容易受到正选择。为了检验这两个假设，我们使用转录组学和蛋白质组学比较了来自北美六个目前公认的物种的 26 种蜈蚣的毒液。我们首先估计了它们的系统发育关系，并发现了 Scolopendromorpha 目中的属 Scolopendra 的并系现象和目前公认物种中的隐种多样性的证据。利用我们的系统发育，我们然后使用转录组学和蛋白质组学相结合的方法，对跨识别进化枝的多样化毒液成分进行了特征描述。我们在毒液蛋白的预测三维特性的背景下进行了基于选择的分析，为这两个假设提供了支持。与双速假说一致，我们发现所有蛋白质都普遍存在负选择。与 RAVER 假说一致，我们发现溶剂暴露残基上存在正选择的证据，结构和较少暴露的残基对负选择的信号更强。通过使用系统发生学、转录组学、蛋白质组学和基于选择的分析，我们能够描述古老毒液谱系的毒液进化，并支持与多基因家族进化直接相关的蛋白质进化原则。
