许多蛋白质存在于所谓的序列比对的“暮光地带”中,其中低的成对序列同一性使得很难确定同源性和系统发育。1,2由于蛋白质三级结构通常更保守,3从头算蛋白质折叠的最新进展使推定同源物的基于结构的鉴定成为可能。4,5,6我们提出了鉴定和表征远处同源物的管道,并将其应用于7跨膜结构域离子通道(7TMIC),由昆虫气味剂和味觉受体建立的蛋白质组。先前的序列和有限的基于结构的搜索确定了推定相关的蛋白质,主要在其他动物和植物中。7,8,9,10然而,在非动物中很少发现7TMIC,非植物类群。此外,这些蛋白质显著的序列差异使得不确定是否不同的7TMIC类型(Gr/Or,Grl,GRL,DUF3537,PHTF,和GrlHz)是同源的或会聚的,让他们的进化史悬而未决。我们的管道在古细菌中发现了数千个新的7TMIC,细菌,和单细胞真核生物。使用基于图形的分析和蛋白质语言模型来提取全家族特征,我们证明了7TMIC具有结构和序列相似性,支持同源性。通过基于序列和结构的系统发育学,我们将真核生物7TMIC分为两个家族(A类和B类),这是一个基因复制的结果,在分裂之前导致了Amorpha(动物,真菌,和盟友)和Diaphoretickes(植物和盟友)。我们的工作揭示了7TMIC作为一个神秘的超家族,起源接近细胞生命的进化。更一般地说,这项研究是鉴定极远蛋白质同源物的方法学原理证明。
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.1,2 As protein tertiary structure is often more conserved,3 recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible.4,5,6 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.7,8,9,10 However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins\' remarkable sequence dissimilarity made it uncertain whether disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF, and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria, and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence- and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi, and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily, with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.