Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

As sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both ‘β-trefoil bridging themes’ (evolutionarily-related sequence segments) and ‘β-trefoil-like motifs’ (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself–namely, that it is a derived fold formed by ‘budding’ from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the evolution of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature’s sewing table.Author summary: Judged by sequence and structure, about 2,500 different protein evolutionary lineages have been identified to date. Since proteins are central to life, understanding where they came from and how they continue to change is a key challenge in biology. We probed the origins of a relatively recent protein lineage, the β-trefoil, looking at patterns of sequence or structure that are shared between β-trefoils and other protein lineages. On the basis of these shared patterns, we argue that a peptide fragment from the ancient IgG-like β-sandwich evolutionary lineage gave rise to β-trefoils via a process we call “peptide budding”. Revealing and understanding cryptic associations between seemingly distinct protein families can shed light on the mechanisms by which new proteins emerge, and contributes to the growing appreciation that the protein universe is highly connected.