Evidence for Stabilizing Selection Driving Mutational Turnover of Short Motifs in the Eukaryotic Complementary Sex Determiner (Csd) Protein

Abstract

Short linear motifs (SLiMs) can play pivotal functional roles in proteins, such as targeting proteins to specific subcellular localizations, modulating the efficiency of translation and tagging proteins for degradation. Until recently we had little knowledge about SLiM evolution. Only a few amino acids in these motifs are functionally important, making them likely to evolve ex nihilo and suggesting that they can play key roles in protein evolution. Several reports now suggest that these motifs can appear and disappear while their function in the protein is preserved, a process sometimes referred to as “turnover”. However, there has been a lack of specific experiments to determine whether independently evolved motifs do indeed have the same function, which would conclusively determine whether the process of turnover actually occurs. In this study, we experimentally detected evidence for such a mutational turnover process for nuclear localization signals (NLS) during the post-duplication divergence of the Complementary sex determiner (Csd) and Feminizer (Fem) proteins in the honeybee (Apis mellifera) lineage. Experiments on the nuclear transport activity of protein segments and those of the most recent common ancestor (MRCA) sequences revealed that three new NLS motifs evolved in the Csd protein during the post-duplication divergence while other NLS motifs were lost that existed before duplication. A screen for essential and newly evolved amino acids revealed that new motifs in the Csd protein evolved by one or two missense mutations coding for lysine. Amino acids that were predating the duplication were also essential in the acquisition of the C1 motif suggesting that the ex nihilo origin was constrained by preexisting amino acids in the physical proximity. Our data support a model in which stabilizing selection maintains the constancy of nuclear transport function but allowed mutational turnover of the encoding NLS motifs.

Dual targeting ofSaccharomyces cerevisiaePso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks

“…1D). These results are consistent with different protein families that possess non-canonical NLS motifs, including the recently discovered class of functional bipartite NLS motifs (Koch et al, 2018; Makkerh et al, 1996). Thus, the conserved features of Pso2 MTS and NLS motifs prompted us to investigate their ability to function as organelle targeting signals in vivo .…”

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

“…Although current models for the evolution of short linear motifs (well-characterized functional elements in IDRs) also implicate stabilizing selection (Koch et al, 2018; Landry et al, 2014), these motifs represent only a minority of the residues in disordered regions (Nguyen Ba et al, 2012). Our observation of shared evolutionary signatures associated with specific functions in highly diverged IDRs suggests that this evolutionary mechanism is shaping the proteome on a much wider scale than currently appreciated.…”

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

“…Although current models for the evolution of short linear motifs (well-characterized functional elements in IDRs) also implicate stabilizing selection (Koch et al, 2018;Landry et al, 2014), these motifs represent only a minority of the residues in disordered regions . Our observation of shared evolutionary signatures associated with specific functions in highly diverged IDRs suggests that this evolutionary mechanism is shaping the proteome on a much wider scale than currently appreciated.…”