R2R3 MYB Transcription Factors – Functions outside the DNA-Binding Domain

Millard, Peter S.; Kragelund, Birthe B.; Burow, Meike

doi:10.1016/j.tplants.2019.07.003

Cited by 115 publications

(115 citation statements)

References 84 publications

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“…We also compared the subgroups of Arabidopsis. The clustering pattern of Arabidopsis MYBs is highly consistent with the previous classification [2], indicating the reliability of this phylogenetic approach.…”

Section: Resultssupporting

confidence: 86%

“…Within the MYB TFs family, the 2-domain MYB type, i.e., R2R3-MYB, accounts for a large proportion and has been the main focus in previous studies. Phylogenetic analyses of R2R3-MYBs have been systematically studied in Arabidopsis [1,2] and many other species [7–9], which indicated that its members perform diverse functions in plantspecific processes. However, knowledge of R2R3-MYBs in wheat are had been limited for a long time due to its complex genome composition and lack of reference genome data [19].…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we divided R2R3-MYBs into 15 subgroups (WS1-WS15), while 25 subgroups (S1-S25) were identified in Arabidopsis [2]. The unique subgroup of wheat and Arabidopsis reflecting the species-specific evolutionary history of the MYB family or could also be due to the domain-based phylogeny analyses in this study.…”

Section: Discussionmentioning

confidence: 99%

“…The myeloblastosis (MYB) transcription factors (TFs) constitute one of the most prominent TFs families in plants. Gene expression regulation by MYBs plays a critical role in plant development and environmental adaption [1,2]. MYBs typically feature the presence of 1~4 repeats of the DNA-binding domain at the N-terminal [3].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat

Xiao

Jia

Watt

et al. 2020

Preprint

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MYB transcription factors (TFs) represents one of the largest TF families in plants. In this study, we performed genome-wide MYB-domain screening and identified a total of 997 MYBs in wheat (Triticum aestivum), among which 445 were 2-domain MYBs (R2R3-MYBs) that were clustered into 15 subgroups with varied conservation profiles. Homologous genes were highly conserved across the three subgenomes, with minor variations contributed by segmental duplications. Tandem and proximal gene duplications have contributed significantly to the expansion of the wheat Myb gene family. Furthermore, comprehensive transcriptome profiling of R2R3-Myb genes in 61 different tissue and time point samples revealed a clear pattern of temporal and spatial variations within six expression groups. The comprehensive genomic and transcriptional analyses provided valuable insights into the evolution and biological functions of R2R3-Myb genes in wheat. They would serve as a useful guide to further investigate the potential agronomic traits controlled by this large TF family.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat

Xiao

Jia

Watt

et al. 2020

Preprint

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“…Numerous studies have indicated that the members of a group in large families of plant TFs generally possess similar conserved amino acid motifs or domains, such as MYB, WAKY, and NAC [55][56][57]. In most cases, similar amino acid motifs are likely to share a similar function.…”

Section: Discussionmentioning

confidence: 99%

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

Song

Chen

Zhang

et al. 2020

Preprint

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Abstract Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

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IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

et al. 2019

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Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence‐based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder‐promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA‐binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA‐binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.

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R2R3 MYB Transcription Factors – Functions outside the DNA-Binding Domain

Cited by 115 publications

References 84 publications

Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat

Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

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