School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania.
Mkwawa University College of Education, University of Dar es Salaam, P.O. Box 2513, Iringa, Tanzania.
BMC Evol Biol. 2017 Feb 16;17(1):54. doi: 10.1186/s12862-017-0901-7.
Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed.
Sequence analysis shows that giraffe has 94-99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity.
There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans.
Toll 样受体 (TLRs) 是对各种病原体固有免疫反应的第一线，预计将成为适应具有不同病原体负担的栖息地的物种中自然选择的目标。长颈鹿和霍加狓基因组序列的最近公布，为在复杂的栖息地多样化过程中检查广泛的陆生有蹄类动物和鲸目动物中选定的 TLR 进化提供了机会。通过直接序列比较和标准进化方法，确定了长颈鹿和密切相关物种之间七种 Toll 样受体 (TLR2、TLR3、TLR4、TLR5、TLR7、TLR9 和 TLR10) 的核苷酸和蛋白质序列多样性程度。此外，还比较了长颈鹿和相关物种之间关键 TLR 基序和结构域的模式。还对陆生有蹄类动物和鲸目动物中 TLR 上的选择压力和分化进行了定量。
序列分析表明，长颈鹿与霍加狓和牛的所有 TLR 分析均具有 94-99%的核苷酸同一性。在一些 TLR 中，长颈鹿、霍加狓和牛之间观察到富含亮氨酸重复序列的数量发生变化。关键 TLR 结构域的模式没有显示长颈鹿、霍加狓和牛之间结构域结构有任何显著差异。选择压力的分子进化分析确定了所有 TLR 检查中的关键位点的正选择，这表明在陆生有蹄类动物和鲸目动物的进化过程中发生了普遍的进化压力。阳性选择位点的分析表明，一些位点是富含亮氨酸基序的一部分，这表明在物种特异性识别病原体相关分子模式方面具有功能相关性。值得注意的是，分支分析显示，在病毒感应 TLR3 中，陆生有蹄类动物和鲸目动物之间存在显著的选择分化。将长颈鹿 TLR3 关键取代映射到受体结构上表明，至少有一个长颈鹿改变的位点与已知在受体信号转导活性中起关键作用的 TLR3 残基重合。
在长颈鹿、霍加狓和牛之间 TLR 结构总体上具有保守性，这表明利用 TLR 途径的固有免疫反应机制在这些物种的进化过程中并没有发生很大变化。然而，更广泛的系统发育分析显示，陆生有蹄类动物和鲸目动物中存在适应性进化的迹象，包括 TLR3 观察到的选择分化。这表明，长期的生态动态导致了介导陆生有蹄类动物和鲸目动物固有免疫的机制的物种特异性创新和功能变异。
