Genome-wide analysis, classification, expression and interaction of Physcomitrella patens SKP1-like ( PpSKP ) and F-box ( FBX ) genes

Skp1-Cullin-F-box (SCF) E3 ligases are essential to post-translational protein turnover and important to regulation in various developmental and environmental response pathways. The non-seed plant Physcomitrella patens is a powerful tool for functional genomics and provides insights into the evolution of plant gene structures and functions. Here we investigated SKP1-like (PpSKP) and F-box (PpFBX) gene families in Physcomitrella patens. FBX proteins are large family in eukaryotes and act as receptors for recruiting specific substrates for ubiquitylation. A database search identified 228 potential FBX-coding genes in the moss Physcomitrella patens. Several functional domains in the FBX proteins, including kelch repeats, leucine-rich repeats, WD40 repeats, F-box associated (FBA) domain, tubby domain, phloem protein 2 and an unknown functional domain were identified in silico. We classified the FBX-coding genes into 8 subfamilies based on domain composition. SKP1-like are small proteins of approximately 160 amino acids. They are a core component of the SCF complex and some of them interact directly with FBX proteins. Homology search identified 4 PpSKP-like genes in the Physcomitrella patens genome. Our analyses indicated that these 4 PpSKPs belong to a class of SKP1 genes that contains one intron at a conserved position. In addition, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) screens revealed that PpSKP proteins show varying ability to interact with PpFBX proteins. However, PpSKP1-4 are overly expressed and appeared to interact with most of the PpFBX proteins tested. We posit that moss PpSKP1-4 are likely to have functions similar to ASK1 and ASK2 in Arabidopsis and OSK1 and OSK20 in rice. This is the first study to assess the SKP1 and FBX families in Physcomitrella patens, providing a starting point for further research to dissect the functions of PpSKP.