Abstract
Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed Arabidopsis Skp1-Like (ASK) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in ASK genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the ASK2 coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of ASK1 yield high levels of expression implied negative expression regulation of ASK1 by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.
Highlights
Proteins play fundamental roles in driving life processes by sensing diverse environmental cues, catalyzing biochemical reactions, monitoring the stability of genetic materials, and combating abiotic and biotic stresses
The size variation among these closely related Arabidopsis species indicates that the S-Phase Kinase-Associated Protein 1 (Skp1) family is, like the F-box gene superfamily, under a rapid birth-and-death evolutionary process
Retroposed Arabidopsis Skp1-Like (ASK) genes originated from one single ancestor locus Instead of cross kingdom long-distant phylogenetic studies (Kong et al, 2004, 2007), we focused on a short evolutionary history within the Arabidopsis genus, so that the orthology relationships and duplication history of individual ASK members could be more clearly illustrated
Summary
Proteins play fundamental roles in driving life processes by sensing diverse environmental cues, catalyzing biochemical reactions, monitoring the stability of genetic materials, and combating abiotic and biotic stresses. They are believed to be the only molecules capable of mechanical movement in any organism. This function has been demonstrated to be important in plants, as evidenced by the extremely large expansion of several gene superfamilies that encode plant UPS members (Vierstra, 2009)
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