Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins

Abstract

Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs—consisting of 2–3 tandem double-stranded RNA binding motifs (dsrms)—arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1–β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications.

Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms

“…The addition of new sequence data, alignments and tree inference strategies in the current analysis further reinforced the major features of our previously inferred phylogeny, arguing in favor of its general robustness. Our previous studies suggest that Argonaute (AGO) and double-stranded RNA-binding protein (DRB) phylogenies exhibit similar patterns of duplications and losses as our Dicer tree ( Mukherjee et al 2013 ; Dias et al 2017 ), suggesting a general model in which major components of the RNA interference pathway may have duplicated in early animals, with the duplicate pathway being retained only in the arthropod lineage. Of course, new sequence data or major advances in phylogenetic methods could alter our current view of Dicer evolutionary history.…”

Testing the Hypothesis That the Nylonase NylB Protein Arose De Novo via a Frameshift Mutation

“…Ever since that time it has been widely accepted that this was the correct explanation for the origin of the NylB enzyme. 12,13,14,15,16,17 It has been widely assumed that this happened in an extremely short timeframe, soon after the invention of nylon in 1935. Some people, by extension, have assumed that Ohno's frameshift claim might help explain other nylonases such as NylA and NylC.…”

Functional characterization of a “plant-like” HYL1 homolog in the cnidarianNematostella vectensisindicates a conserved involvement in microRNA biogenesis

“…Further, various fungal groups also exhibit the presence of Dicer and plant-like DSRM proteins and lack animal-like accessory proteins, such as Drosha and Pasha (Dang et al, 2011;Dias et al, 2017).…”

“…Additionally, we also could not find any homologs in bilaterian animals and in unicellular organism like Fungi and Ichthyosporea. However, deep phylogenetic study of DSRM proteins showed that the protozoans and fungi are phylogenetically closer to the DSRM protein of plants (Dias et al, 2017).…”