Functional diversification of the Tubby-like protein gene families (TULPs) during eukaryotic evolution

The Tubby-like protein (TULP) is ubiquitous among multicellular organisms but has extremely diversified functions. Although functional analyses of certain mammalian and model plant TULPs are available and phylogenies separately based on animal or plant TULPs have been reconstructed, the origin, evolutionary history, and functional divergence of TULPs remain obscure. The existence of TULP in unicellular organisms is also not found yet. In this study, 145 TULP homologs were identified from four eukaryotic supergroups—Excavata, Chromalveolata, Archaeplastida (plants), and Opistokonta (fungi and animals). In addition to the tubby domain, many TULPs also contain different motifs (F-box, WD40 repeat, or SOCS box) in their N-terminus regions, leading to their groupings into three classes, in which TULPs with no N-terminal modifications (class II) locate at the basal positions on the phylogeny. Our comparison data reveals that phosphatidylinositol 4,5-bisphosphate (PIP2) binding sites are conserved in class II TULPs, especially those that are animal derived, but not in TULPs from classes I and III. Differentiation at the three PIP2 binding sites implies that the function of class II TULPs differs from those of other two classes. We further demonstrate that only class II TULPs can be targeted to the plasma membrane, suggesting functional divergence and differentiation of TULPs. Functional divergence and differentiation of TULPs should have occurred after duplications and structural modifications around 1100 MYA as eukaryotic organisms started diversifying.