A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation

Abstract

R2R3-MYB transcription factors (TFs) belong to a large and functionally diverse protein superfamily in plants. In this study, we explore the evolution and function of this family in grapevine (Vitis vinifera L.), a high-value fruit crop. We identified and manually curated 134 genes using RNA-Seq data, and named them systematically according to the Super-Nomenclature Committee. We identified novel genes, splicing variants and grapevine/woody-specific duplicated subgroups, suggesting possible neo- and sub-functionalization events. Regulatory network analysis ascribed biological functions to uncharacterized genes and validated those of known genes (e.g. secondary cell wall biogenesis and flavonoid biosynthesis). A comprehensive analysis of different MYB binding motifs in the promoters of co-expressed genes predicted grape R2R3-MYB binding preferences and supported evidence for putative downstream targets. Enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators. Analysis of the network of Subgroup 2 showed that the resveratrol-related VviMYB14 and VviMYB15 share common co-expressed STILBENE SYNTHASE genes with the uncharacterized VviMYB13. These regulators have distinct expression patterns within organs and in response to biotic and abiotic stresses, suggesting a pivotal role of VviMYB13 in regulating stilbene accumulation in vegetative tissues and under biotic stress conditions.

Activator‐type R2R3‐MYB genes induce a repressor‐type R2R3‐MYB gene to balance anthocyanin and proanthocyanidin accumulation

“…This suggests that the C1 motif also is required for activity functional repressor. However, it is worth noting that the C1 motif also is found in the AtMYB5 homologs which have an activation role and belong to the MAV clade (Wong et al, 2016).…”

Regulation of stilbene biosynthesis in plants

“…influx, a MAPK cascade, and JA signaling but not SA were involved in the MYB14 transcriptional activation. A systems-oriented analysis performed by Wong et al (2016) revealed that the V. vinifera VvMYB14 and VvMYB15 genes share common co-expressed STS genes with the VvMYB13 gene, which is the uncharacterized closest homologue of VvMYB15. In a recent study, the MYB1 gene of V. amurensis (99% homology to VvMYB15 at the protein level) has been cloned and overexpressed in t-resveratrol-producing callus cell cultures of V. amurensis .…”

Transcriptomic and Metabolomic Networks in the Grape Berry Illustrate That it Takes More Than Flavonoids to Fight Against Ultraviolet Radiation

“…Representation analysis of the MapMan BIN terms for their TOP100 co-expressed genes showed that several MYB genes were highly associated with terpenes (Wong et al, 2016). Thus, it is expected that some of these may directly regulate TPS or other genes of the isoprenoid pathway, as occurs with flavonoids or stilbenoids.…”