A Simplified Explanation for the Frameshift Mutation that Created a Novel C-terminal Motif in the APETALA3 Gene Lineage

Abstract

Background: The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the <i>Arabidopsis</i> gene <i>APETALA3</i> (<i>AP3</i>). Previous work has demonstrated that the ancestral paleo<i>AP3</i> lineage was duplicated at some point within the basal eudicots to give rise to the paralogous <i>TM6</i> and eu<i>AP3</i> lineages. This event was followed in eu<i>AP3</i> orthologs by the replacement of the C-terminal paleo<i>AP3</i> motif with the derived eu<i>AP3</i> motif. It has been suggested that the new motif was created by an eight-nucleotide insertion that produced a translational frameshift. Results: The addition of 25 eudicot <i>AP3</i> homologs to the existing dataset has allowed us to clarify the process by which the eu<i>AP3</i> motif evolved. Phylogenetic analysis indicates that the eu<i>AP3</i>/<i>TM6</i> duplication maps very close to the base of the core eudicots, associated with the families Trochodendraceae and Buxaceae. We demonstrate that although the transformation of paleo<i>AP3</i> into eu<i>AP3</i> was due to a frameshift mutation, this was the result of a single nucleotide deletion. The use of ancestral character state reconstructions has allowed us to demonstrate that the frameshift was accompanied by few other nucleotide changes. We further confirm that the sequence is evolving as coding region. Conclusion: This study demonstrates that the simplest of genetic changes can result in the remodeling of protein sequence to produce a kind of molecular 'hopeful monster.' Moreover, such a novel protein motif can become conserved almost immediately on the basis of what appears to be a rapidly generated new function. Given that the existing data on the function of such C-terminal motifs are somewhat disparate and contradictory, we have sought to synthesize previous findings within the context of the current analysis and thereby highlight specific hypotheses that require further investigation before the significance of the eu<i>AP3</i> frameshift event can be fully understood.