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

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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.·2023·G3 Genes Genomes Genetics
DOI 10.1101/2023.09.28.560026PMC PMC11457125

Preprint — published as 10.1093/g3journal/jkae184 · Paper page

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Abstract

Flavonoids are secondary metabolites associated with seed and flower color. A ternary MBW protein complex consisting of interfacing M YB, b eta-helix-loop-helix (bHLH), and W D40 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 β-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 β-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. Highlight: The 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.

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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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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
openRxiv
Published
2023-10-01
Volume
14
Issue
10
ISSN
2160-1836 (ISSN-L)
DOI
10.1101/2023.09.28.560026
PMC
PMC11457125
OpenAlex
W4401782765
Cited by
13
References
1
Citations by year
2026: 7 · 2025: 6
FWCI
1.77
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • G3 Genes Genomes Genetics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • U.S. Department of Agriculture
  • National Institutes of Health
  • Agricultural Research Service
  • National Institute of General Medical Sciences (R15GM146232, R01GM126207)
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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CoChat. (2026). Citation check: T and Z , Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex. https://app.cochat.ai/papers/10.1101/2023.09.28.560026
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McClean, P. E., Roy, J., Colbert, C. L., Osborne, C., Lee, R., Miklas, P. N., & Osorno, J. M. (2023). T and Z , Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex. G3 Genes Genomes Genetics. https://doi.org/10.1101/2023.09.28.560026

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