A family of polyketide synthase genes expressed in ripening Rubus fruits

Quality traits of raspberry fruits such as aroma and color derive in part from the polyketide derivatives, benzalacetone and dihydrochalcone, respectively. The formation of these metabolites during fruit ripening is the result of the activity of polyketide synthases (PKS), benzalcetone synthase and chalcone synthase (CHS), during fruit development. To gain an understanding of the regulation of these multiple PKSs during fruit ripening, we have characterized the repertoire of Rubus PKS genes and studied their expression patterns during fruit ripening. Using a PCR-based homology search, a family of ten PKS genes (Ripks1-10) sharing 82-98% nucleotide sequence identity was identified in the Rubus idaeus genome. Low stringency screening of a ripening fruit-specific cDNA library, identified three groups of PKS cDNAs. Group 1 and 2 cDNAs were also represented in the PCR amplified products, while group 3 represented a new class of Rubus PKS gene. The Rubus PKS gene-family thus consists of at least eleven members. The three cDNAs exhibit distinct tissue-specific and developmentally regulated patterns of expression. RiPKS5 has high constitutive levels of expression in all organs, including developing flowers and fruits, while RiPKS6 and RiPKS11 expression is consistent with developmental and tissue-specific regulation in various organs. The recombinant proteins encoded by the three RiPKS cDNAs showed a typical CHS-type PKS activity. While phylogenetic analysis placed the three Rubus PKSs in one cluster, suggesting a recent duplication event, their distinct expression patterns suggest that their regulation, and thus function(s), has evolved independently of the structural genes themselves.