T and Z, Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex

Abstract

Flavonoids are secondary metabolites associated with seed and flower color. A ternary MBW protein complex consisting of interfacing MYB, beta-helix-loop-helix (bHLH), and WD40 repeat (WDR) proteins controls the expression of late biosynthetic genes in the flavonoid pathway. P, the master regulator gene of flavonoid expression in common bean (Phaseolus vulgaris L.) was recently determined to encode a bHLH protein. Two other genes, T and Z, are also historically considered regulators since they determine the distribution of color in seeds and flowers. These two genes were cloned using reverse genetics based on genetic mapping, candidate gene selection, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined T encoded a seven-bladed {beta}-propeller WDR protein, while Z encoded a R2R3 MYB protein. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motif in all three genes that are conserved in dicots. One Z MYB motif is a possible {beta}-MoRF that only appears in a structured state when Z MYB is modeled in a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating expression of genes in the flavonoid pathway. HighlightThe MBW complex of bean comprised of the classic Z, P, and T genes associated with seed coat patterning defines critical proteins interactions for flavonoid gene expression.