The Evolutionary History of the F-Box Gene Superfamily Across 34 Viridiplantae Species

The F-box gene superfamily in 34 species across the plant kingdom was analyzed in order to understand its evolutionary history. For F-box domain detection, a protein crystal structure-based protein alignment strategy was used to construct a profile HMM. Using a sensitive HMM-HMM comparison tool (HHblits), and profile HMMs for the F-box, we identified 18790 F-box protein isoforms encoded by 18645 unique non-overlapping genomic loci annotated as protein genes.  In addition, analysis of intergenic regions revealed the presence of a few thousand loci with the potential to code for the F-box domain. Previously annotated genes versus newly identified intergenic F-box coding regions differed in the length of both their F-box domain per se and the length of the full protein. Analysis of the protein architecture of these F-box domain containing proteins from the proteome and from intergenic regions revealed statistically significant over-representation of co-domains such as Kelch and F-box associated, and selective loss or gain of certain F-box protein architectures in these 34 species.

Currently, we are testing the hypothesis that the most common protein architecture across these 34 species - the F-box domain devoid of a protein-protein interaction co-domain such as the WD40 or LRR, is found in combination with Intrinsically Disordered Regions or Disordered Binding Regions, suggesting that post-translation modification(s) of F-box proteins with or without a co-domain(s), may aid in the biological function of E3 Ub-ligase complexes. Work is also underway to detect whether F-box loci birth was a consequence of tandem, segmental, or whole genome duplication(s).