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Cited by 13Plant Gene Expression AnalysisPlant Molecular Biology ResearchGenetic Mapping and Diversity in Plants and Animals

The DOI matches its Crossref record; 74 of the 74 references it cites were found in a registry or an index.

T and Z , partial seed coat patterning genes in common bean, provide insight into the structure and protein interactions of a plant MBW complex

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McClean, Phillip E, Roy, Jayanta, Colbert, Christopher L, Osborne, Caroline, Lee, Rian, Miklas, Phillip N, Osorno, Juan M·2024·G3: Genes, Genomes, Genetics
DOI 10.1093/g3journal/jkae184PMC PMC11457125

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Abstract

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing MYB, beta-helix–loop–helix (bHLH), and WD40 Repeat (WDR) proteins. P, the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of 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 the expression of genes in the flavonoid pathway.

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Figures

Fig. 1. Germplasm used to map the T and Z genes of common bean. The T and Z alleles for each genotype are in parenthesis. a) 5-593 (T Z). b) Earliwax (tEWzEW). c) 65–73 (t65–73Z). d) V0869 (T zEW). e) V0919 (T zEW).
Fig. 1. Germplasm used to map the T and Z genes of common bean. The T and Z alleles for each genotype are in parenthesis. a) 5-593 (T Z). b) Earliwax (tEWzEW). c) 65–73 (t65–73Z). d) V0869 (T zEW). e) V0919 (T zEW).CC BY · PubMed Central
Fig. 2. Genetic maps of T and Z developed using PACE SNP markers bordering the position of RAPD markers linked to each gene. a) The T gene was mapped in population 4–68 (Brady et al. 1998). b) The Z gene was mapped in three populations (4–76, 6–273, and 6–160.161). For both a) and b), the physical position of the polymorphic SNP follows the chromosome designation, and the genetic position is located in parenthesis.
Fig. 2. Genetic maps of T and Z developed using PACE SNP markers bordering the position of RAPD markers linked to each gene. a) The T gene was mapped in population 4–68 (Brady et al. 1998). b) The Z gene was mapped in three populations (4–76, 6–273, and 6–160.161). For both a) and b), the physical position of the polymorphic SNP follows the chromosome designation, and the genetic position is located in parenthesis.CC BY · PubMed Central
Fig. 3. Neighboring joining trees of WDR homologs of common bean a) angiosperm WDR proteins and b) MYB proteins experimentally to act as repressors or activators of flavonoid biosynthesis. Common bean gene models are shown in red.
Fig. 3. Neighboring joining trees of WDR homologs of common bean a) angiosperm WDR proteins and b) MYB proteins experimentally to act as repressors or activators of flavonoid biosynthesis. Common bean gene models are shown in red.CC BY · PubMed Central
Fig. 4. Structural details of the AlphaFold2 protein models of the a) T WDR, b) Z MYB, and c) P bHLH genes. For each protein, the left model is the pLDDT values across the protein. High pLDDT values for a residue suggest a good structural fit. Blue represents high confidence; yellow is moderate confidence; and red and orange are poor confidence. The central figures show the location of the domains in the proteins. For the T WDR protein a), the four WD40 domains are depicted. The R2 and R3 MYB domains are shown for the Z MYB protein b). The MYB-interacting region, helix–loop–helix, and activation domains are highlighted for P bHLH protein. Note that these domains were modeled with high confidence based on their pLDDT values. The right most image for each protein is the disorder score. The green represents the DISOPRED3 score, and the blue represents the IUPred3 score. Regions with disorder scores >0.5 are considered to be disordered. Note that the disorder regions also have low pLDDT values.
Fig. 4. Structural details of the AlphaFold2 protein models of the a) T WDR, b) Z MYB, and c) P bHLH genes. For each protein, the left model is the pLDDT values across the protein. High pLDDT values for a residue suggest a good structural fit. Blue represents high confidence; yellow is moderate confidence; and red and orange are poor confidence. The central figures show the location of the domains in the proteins. For the T WDR protein a), the four WD40 domains are depicted. The R2 and R3 MYB domains are shown for the Z MYB protein b). The MYB-interacting region, helix–loop–helix, and activation domains are highlighted for P bHLH protein. Note that these domains were modeled with high confidence based on their pLDDT values. The right most image for each protein is the disorder score. The green represents the DISOPRED3 score, and the blue represents the IUPred3 score. Regions with disorder scores >0.5 are considered to be disordered. Note that the disorder regions also have low pLDDT values.CC BY · PubMed Central
Fig. 5. Interfaces between components of an AlphaFold-Multimer predicted model of a MBW complex of common bean. a) Interfaces between the T WDR protein (tan) and its interfacing regions with the Z MYB (red) and P bHLH (blue) proteins. To the right is a WebLogo representation of the sequences within the interface region that are highly conserved in other orthologs of the Z and P proteins. b) Interface between the MIR region of the P bHLH protein (green) and the Z MYB R3 domain (red). To the right is a WebLogo representation of the sequence within the interface region that is highly conserved among homologs of the Z protein. The vertical axis for sequences in A and B provides the WebLogo bit score (Crooks et al. 2004). The horizontal axis provides the amino acid positions of the domain in the full protein sequence.
Fig. 5. Interfaces between components of an AlphaFold-Multimer predicted model of a MBW complex of common bean. a) Interfaces between the T WDR protein (tan) and its interfacing regions with the Z MYB (red) and P bHLH (blue) proteins. To the right is a WebLogo representation of the sequences within the interface region that are highly conserved in other orthologs of the Z and P proteins. b) Interface between the MIR region of the P bHLH protein (green) and the Z MYB R3 domain (red). To the right is a WebLogo representation of the sequence within the interface region that is highly conserved among homologs of the Z protein. The vertical axis for sequences in A and B provides the WebLogo bit score (Crooks et al. 2004). The horizontal axis provides the amino acid positions of the domain in the full protein sequence.CC BY · PubMed Central

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Citations

Cites

Research works printed but not linked: 3

  1. Bassett, 2001, Inheritance of the Fib gene from 5-593 for fibula arcs pattern of partly colored seed coat in the background genotype t P [C r] Z J G B V Rk, Annu Rep Bean Improv Coop, 44, 171
  2. Bassett, 2011, The genetics of the color pattern of seed coats in G19833, a Liborino class common bean, Annu Rep Bean Improv Coop, 54, 50
  3. Prakken, 1974, Meded. Landbouwhogeschool Wageningen, 1

Metadata

Authors
McClean, P. E., Roy, J., Colbert, C. L., Osborne, C., Lee, R., Miklas, P. N., & Osorno, J. M.
Affiliations
  • North Dakota State University (US)
  • Agricultural Research Service (US)
Corresponding author
McClean, Phillip E
ORCID
Venue
G3: Genes, Genomes, Genetics
Publisher
Oxford University Press (OUP)
Published
2024-08-21
Volume
14
Issue
10
ISSN
2160-1836 (ISSN-L)
DOI
10.1093/g3journal/jkae184
PMC
PMC11457125
OpenAlex
W4401782765
Cited by
13
References
74
Citations by year
2026: 7 · 2025: 6
FWCI
1.77
Type
journal article
Language
en
Open access
Licence
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
USDA
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant Gene Expression Analysis
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
T gene, flavonoid biosynthesis, MBW complex, MYB, bHLH, WD40 repeats, Phaseolus vulgaris, protein-protein interaction, protein structure, flower color, seed color
MeSH terms
Flavonoids, Models, Molecular, Mutation, Phylogeny, Plant Proteins, Protein Binding, Seeds, Genes, Plant, Gene Expression Regulation, Plant, Phaseolus, Basic Helix-Loop-Helix Transcription Factors, Basic Helix-Loop-Helix Proteins

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