Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life

Many proteins exist in the so-called “twilight zone” of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. As protein tertiary structure is often more conserved, recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible. However, structural screening and phylogenetics are in their infancy, particularly for twilight zone proteins. We present a pipeline for the identification and characterization of distant homologs, and apply it to 7-transmembrane domain ion channels (7TMICs), a protein group founded by insect Odorant and Gustatory receptors. Previous sequence and limited structure-based searches identified putatively-related proteins, mainly in other animals and plants. However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins’ remarkable sequence dissimilarity made it uncertain if disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3...诸多蛋白质存在于所谓的序列比对黄昏带（twilight zone of sequence alignment）中，该区域内成对序列一致性较低，使得同源性与系统发育关系的判定颇具难度。由于蛋白质三级结构通常更为保守，近年来从头蛋白质折叠（ab initio protein folding）技术的进步使得基于结构的推定同源蛋白（putative homologs）鉴定成为可行方案。然而，结构筛选与系统发育学仍处于起步阶段，针对序列比对黄昏带蛋白质的相关研究更是如此。本研究提出了一套用于远缘同源蛋白鉴定与表征的分析流程，并将其应用于7跨膜结构域离子通道（7-transmembrane domain ion channels, 7TMICs）——一类由昆虫嗅觉受体与味觉受体所定义的蛋白质家族。此前的序列比对与有限的基于结构的搜索仅在其他动物与植物中鉴定出了推定的同源相关蛋白。然而，在非动物、非植物的类群中，几乎未发现7TMICs。此外，这些蛋白质显著的序列差异使得我们无法确定不同类型的7TMICs（Gr/Or、Grl、GRL、DUF3...）之间是否存在演化关联。