Structural insights into partner selection for MYB and bHLH transcription factor complexes

Wang, Baihui; Luo, Qiang; Li, Yingping; Du, Kangxi; Wu, Zhen; Li, Tianyang; Shen, Wen‐Hui; Huang, Chien-Hua; Gan, Jianhua; Ao, Dong

doi:10.1038/s41477-022-01223-w

Cited by 31 publications

(19 citation statements)

References 46 publications

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“…S9b ). Some of these proteins lack certain domains when compared to AtGL3, while the remaining ones shared conserved J az-Interacting D omain (JID), T ranscription A ctivation D omain (TAD), bHLH domain, and C -terminal D omain (CD), as well as the residues required for R2R3 MYB interaction (Wang et al ., 2021) ( Figs. S11,S12 ).…”

Section: Resultsmentioning

confidence: 99%

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A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

Zhu

Schiefelbein

2023

Preprint

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In superrosid species, root epidermal cells differentiate into root hair cells and non-hair cells. In some superrosids, the root hair cells and non-hair cells are distributed randomly (Type I pattern) and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved. In this study, we analyzed superrosid speciesRhodiola rosea,Boehmeria nivea, andCucumis sativusfor their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species. We identifiedR.roseaandB.niveaas Type III species andC.sativusas Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs inR.roseaandB.nivea, and major changes inC.sativus. We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.

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Section: Resultsmentioning

confidence: 99%

“…S13 ). The alignment also revealed conservation of key residues previously shown to be required for bHLH protein interaction and DNA sequence specific recognition (Wang et al ., 2019; Wang et al ., 2021) among the WRLs ( Fig. S13 ).…”

Section: Resultsmentioning

confidence: 99%

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

Zhu

Schiefelbein

2023

Preprint

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“…S14). The alignment also revealed conservation of key residues previously shown to be required for bHLH protein interaction and DNA sequence-specific recognition (Wang et al, 2019(Wang et al, , 2021 among the WRLs (Fig. S14).…”

Section: Identification and Functional Analysis Of Wer Homologsmentioning

confidence: 99%

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

Zhu

Schiefelbein

2023

New Phytologist

View full text Add to dashboard Cite

In superrosid species, root epidermal cells differentiate into root hair cells and nonhair cells. In some superrosids, the root hair cells and nonhair cells are distributed randomly (Type I pattern), and in others, they are arranged in a position-dependent manner (Type III pattern). The model plant Arabidopsis (Arabidopsis thaliana) adopts the Type III pattern, and the gene regulatory network (GRN) that controls this pattern has been defined. However, it is unclear whether the Type III pattern in other species is controlled by a similar GRN as in Arabidopsis, and it is not known how the different patterns evolved.In this study, we analyzed superrosid species Rhodiola rosea, Boehmeria nivea, and Cucumis sativus for their root epidermal cell patterns. Combining phylogenetics, transcriptomics, and cross-species complementation, we analyzed homologs of the Arabidopsis patterning genes from these species.We identified R. rosea and B. nivea as Type III species and C. sativus as Type I species. We discovered substantial similarities in structure, expression, and function of Arabidopsis patterning gene homologs in R. rosea and B. nivea, and major changes in C. sativus.We propose that in superrosids, diverse Type III species inherited the patterning GRN from a common ancestor, whereas Type I species arose by mutations in multiple lineages.

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“…The Z MYB and P bHLH interact with different regions of T WDR in bean, soybean, and Arabidopsis complexes. Finally, Z MYB and P bHLH interact in the same regions of each protein as predicted from crystal structure analysis of Arabidopsis WER and EGL3 (Wang et al 2022). Structures were also predicted for the bean MBW complex containing mutant t EW WDR or z EW MYB proteins.…”

Section: Discussionmentioning

confidence: 90%

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

McClean,

Roy,

Colbert

et al. 2023

Preprint

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Flavonoids are secondary metabolites associated with seed and flower color. A ternary MBW protein complex consisting of interfacingMYB,beta-helix-loop-helix (bHLH), andWD40 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 vulgarisL.) was recently determined to encode a bHLH protein. Two other genes,TandZ, 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 determinedTencoded a seven-bladed β-propeller WDR protein, whileZencoded 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.HighlightThe MBW complex of bean comprised of the classicZ,P, andTgenes associated with seed coat patterning defines critical proteins interactions for flavonoid gene expression.

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Structural insights into partner selection for MYB and bHLH transcription factor complexes

Cited by 31 publications

References 46 publications

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

TandZ, 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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