Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats    

Abstract

The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.

A Proteolytic Regulator Controlling Chalcone Synthase Stability and Flavonoid Biosynthesis in Arabidopsis

“…As one of the large subfamilies of F-box proteins and as the critical structural component of SCF-type E3 ubiquitin-protein ligase complex, KFBs are responsible for recruiting the target proteins into the ligase complex for ubiquitination, thus marking them for subsequent degradation (Schumann et al, 2011). Although the Arabidopsis genome codes for more than 100 KFBs, only a small set of these have been functionally characterized so far.…”

“…Since KFB CHS is an annotated structural component of the SCF type ubiquitin-ligase complex (Xu et al, 2009;Schumann et al, 2011), its physical interaction with CHS indicates that CHS might be ubiquitinated and degraded through the ubiquitin/26S proteasome pathway in planta. To test this hypothesis, HA-tagged CHS was transiently expressed in tobacco leaves and examined for potential ubiquitination.…”

“…The peptide sequences of KFBs were retrieved from TAIR based on previous publications (Xu et al, 2009;Schumann et al, 2011). The fulllength amino acid sequences were aligned with the ClustalW program, and phylogenetic analysis was conducted using MEGA6 (Molecular Evolutionary Genetics Analysis Version 6.0) software with the neighbor-joining method.…”

“…They are classified into different subfamilies according to the presence of additional protein-protein interaction domains near their C terminus. One subfamily was designated as the Kelch domain (repeat)-containing F-box (KFB) proteins (Bork and Doolittle, 1994), which is composed of ;103 members in Arabidopsis with only a few that have been characterized (Xu et al, 2009;Schumann et al, 2011). Among them, we recently demonstrated that Arabidopsis KFB01, 20, 39, and 50 (collectively named KFB PALs ) interact with phenylalanine ammonia-lyase (PAL), the first rate-limiting enzyme of phenylpropanoid biosynthetic pathway, and mediate its ubiquitination and subsequent degradation, by which the FKB PALs act as negative regulators controlling the synthesis of the entire class of phenylpropanoid metabolites (Zhang et al, 2013(Zhang et al, , 2015.…”

A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in Cucumis melo L.

“…genomes contain only 68 and 33 F-box genes, respectively (Ou et al, 2003;Jin et al, 2004), the Arabidopsis (Arabidopsis thaliana) genome contains approximately 700 members of this superfamily (Gagne et al, 2002). One subgroup of this family, the KFB, found as a single ortholog in the human genome is highly represented in the Arabidopsis genome, comprising at least 103 KFB sequences, most of them still uncharacterized (Schumann et al, 2011). A rice (Oryza sativa) KFB homolog was found to negatively regulate flavonoid accumulation (Shao et al, 2012).…”