Genome-wide identification and characterization of 3- Dehydroquinate Dehydratase/ Shikimate Dehydrogenases (DHD/SDH) family genes in Rubus chingii Hu

Objective In the plant shikimate pathway, the dual-function enzyme 3-Dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SDH) stands alone as the sole catalyst responsible for generating both shikimate and gallic acid. This enzyme is instrumental in secondary metabolism, with particular significance in the metabolic route leading to gallic acid production. Methods This work pinpointed members of the DHD/SDH gene family in Rubus chingii Hu through bioinformatic methods and then undertook a thorough examination of their physicochemical properties, predicted subcellular localization, chromosomal distribution, phylogenetic relationships, and promoter cis-acting elements. Additionally, quantitative real-time PCR was used to map the expression patterns of these genes across different tissues, at various fruit developmental stages, and in response to external hormone treatments. In parallel, high-performance liquid chromatography (HPLC) quantified gallic acid and ellagic acid levels in multiple tissues and developmental stages of fruit, offering a comprehensive view of the DHD/SDH gene family’s characteristics and expression dynamics in Rubus chingii Hu. Results Results revealed four DHD/SDH family members in Rubus palmatus, evenly distributed across two chromosomes, encoding protein sequences ranging from 440 to 1325 amino acids. Phylogenetic analysis indicated that RcDHD/SDH proteins belong to the fourth subfamily. Subcellular localization predictions showed these proteins reside in the cell nucleus and all contain the conserved DHD/SDH functional domains. Promoter analysis revealed that RcDHD/SDH genes contain multiple cis-acting elements, including hormone-responsive, light-responsive, and cold-responsive elements. Expression pattern analysis demonstrated significant differences in the expression of the RcDHD/SDH gene family across various tissues and organs in Rubus palmatus. Specifically, RcDHD/SDH1 to RcDHD/SDH4 exhibit relatively similar expression levels in roots, while RcDHD/SDH4 shows high abundance in stems and leaves. During fruit development, the overall expression level of the RcDHD/SDH gene family peaks during the early fruit stage and subsequently declines. This suggests that this gene family may play a crucial role in the early regulation of fruit growth and development. Conclusion This research marks the first in-depth analysis of the DHD/SDH gene family in R. chingii , offering paving the way for subsequent functional investigations and insights into their involvement in shikimate and gallic acid biosynthesis pathway.