Evolutionary relationships between prodomains in the TGF-β family have gone unanalyzed due to a perceived lack of conservation. We developed a novel approach, identified these relationships, and suggest hypotheses for new regulatory mechanisms in TGF-β signaling. First, a quantitative analysis placed each family member from flies, mice, and nematodes into the Activin, BMP, or TGF-β subfamily. Second, we defined the prodomain and ligand via the consensus cleavage site. Third, we generated alignments and trees from the prodomain, ligand, and full-length sequences independently for each subfamily. Prodomain alignments revealed that six structural features of 17 are well conserved: three in the straitjacket and three in the arm. Alignments also revealed unexpected cysteine conservation in the "LTBP-Association region" upstream of the straitjacket and in β8 of the bowtie in 14 proteins from all three subfamilies. In prodomain trees, eight clusters across all three subfamilies were present that were not seen in the ligand or full-length trees, suggesting prodomain-mediated cross-subfamily heterodimerization. Consistency between cysteine conservation and prodomain clustering provides support for heterodimerization predictions. Overall, our analysis suggests that cross-subfamily interactions are more common than currently appreciated and our predictions generate numerous testable hypotheses about TGF-β function and evolution.

中文翻译：

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TGF-β前结构域比对揭示了意外的半胱氨酸保守性，与跨亚科异二聚化的系统发育预测一致。

由于人们认为缺乏保守性，TGF-β 家族中前结构域之间的进化关系尚未得到分析。我们开发了一种新方法，确定了这些关系，并提出了 TGF-β 信号传导新调控机制的假设。首先，定量分析将果蝇、小鼠和线虫的每个家族成员归入激活素、BMP 或 TGF-β 亚家族。其次，我们通过共有切割位点定义了前结构域和配体。第三，我们为每个亚科独立地从前结构域、配体和全长序列生成比对和树。前域比对显示，17 个结构特征中的 6 个结构特征保存完好：3 个在紧身衣中，3 个在手臂中。比对还揭示了来自所有三个亚家族的 14 种蛋白质中紧身衣上游的“LTBP 关联区域”和领结的 β8 中出乎意料的半胱氨酸保守性。在前结构域树中，存在跨越所有三个亚科的八个簇，这些簇在配体或全长树中未见，表明前结构域介导的跨亚科异二聚化。半胱氨酸保守性和前结构域聚类之间的一致性为异二聚化预测提供了支持。总体而言，我们的分析表明，跨亚科相互作用比目前认为的更为常见，并且我们的预测产生了许多关于 TGF-β 功能和进化的可检验假设。