MYB5a/NEGAN activates petal anthocyanin pigmentation and shapes the MBW regulatory network in Mimulus luteus var. variegatus

AbstractMuch of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use DNA sequence analysis and spatiotemporal patterns of gene expression to identify MYB5a - homologous to the NEGAN transcriptional activator from M. lewisii - as a likely candidate gene within the pla2 region. Transgenic manipulation of gene expression confirms that MYB5a is both necessary and sufficient for petal lobe anthocyanin pigmentation. The deployment of MYB5a/NEGAN to the petal lobe stands in contrast to its more restricted role as a nectar guide anthocyanin activator in other Mimulus species. Transcriptome sequencing of a MYB5a RNAi line reveals the degree to which other regulators of the anthocyanin pathway - including R3 MYB repressors and bHLH and WD40 co-activators - are responsive to the level of expression of MYB5a. Overall, this work reveals that a genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the genes downstream of MYB5a but also on all of its known partners in the anthocyanin regulatory network.Graphical abstract.Solid black arrows indicate the direction (though not magnitude) of gene expression change, following RNAi knockdown of MYB5a/NEGAN in M. l. variegatus. The number of black arrows corresponds to the number of gene copies identified in the transcriptome. Grey symbols denote positive and negative regulatory interactions. RTO is an R3 MYB protein that inhibits anthocyanin biosynthesis by sequestering bHLH proteins away from the MBW complex.

Download Full-text

The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus

Genetics ◽

10.1093/genetics/iyaa036 ◽

2021 ◽

Vol 217 (2) ◽

Author(s):

Xingyu Zheng ◽

Kuenzang Om ◽

Kimmy A Stanton ◽

Daniel Thomas ◽

Philip A Cheng ◽

...

Keyword(s):

Gene Expression ◽

Regulatory Network ◽

Reaction Diffusion ◽

Genomic Region ◽

Anthocyanin Pigmentation ◽

Genetic Changes ◽

Cascading Effects ◽

Nectar Guides ◽

Rnai Line ◽

Visual Diversity

Abstract Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible for the transition to anthocyanin-pigmented petals in M. l. variegatus. In other monkeyflower taxa, MYB5a/NEGAN is part of a reaction-diffusion network that produces semi-repeating spotting patterns, such as the array of spots in the nectar guides of both M. lewisii and M. guttatus. Its co-option for the evolution of an apparently non-patterned trait—the solid petal lobe pigmentation of M. l. variegatus—illustrates how reaction-diffusion can contribute to evolutionary novelty in non-obvious ways. Transcriptome sequencing of a MYB5a RNAi line of M. l. variegatus reveals that this genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the enzyme-encoding genes traditionally thought of as the targets of MYB5a but also on all of its known partners in the anthocyanin regulatory network.

Download Full-text

Anthocyanin Regulatory/Structural Gene Expression in Phalaenopsis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.134.1.88 ◽

2009 ◽

Vol 134 (1) ◽

pp. 88-96 ◽

Cited By ~ 23

Author(s):

Hongmei Ma ◽

Margaret Pooler ◽

Robert Griesbach

Keyword(s):

Gene Expression ◽

Anthocyanin Biosynthesis ◽

Structural Genes ◽

Wild Type ◽

Anthocyanin Pigmentation ◽

Chain Reaction ◽

Wild Type Phenotype ◽

Coordinated Expression ◽

Polymerase Chain ◽

Low Levels

Anthocyanin biosynthesis requires the coordinated expression of Myc, Wd, Chs, Dfr, and Myb. Chs and Dfr are structural genes, while Myc, Myb, and Wd are regulatory genes. Reverse transcription polymerase chain reaction was used to measure the expression of these genes in Phalaenopsis amabilis and Phalaenopsis schilleriana. P. amabilis expresses an albescent phenotype with petals and sepals that are anthocyanin free, while P. schilleriana has a wild-type phenotype with anthocyanin-containing petals and sepals. As expected, the petals and sepals of P. schilleriana expressed high levels of Chs and Dfr. The petals and sepals of P. amabilis expressed high levels of Chs and very low levels of Dfr. In P. amabilis and P. schilleriana, anthocyanin-specific Myc and Wd were expressed; however, Myb specific for anthocyanin biosynthesis were undetectable in P. amabilis. This suggests that the absence of Myb expression was responsible for the lack of dihydroflavonol 4-reductase and results in the absence of anthocyanin pigmentation in P. amabilis petals and sepals. This was confirmed by particle bombardment of P. amabilis petals with functional Mybs isolated from P. schilleriana. Comparisons of anthocyanin-related Myb gene expression between P. schilleriana and P. amabilis are between genetically different species. Phalaenopsis ‘Everspring Fairy’ expresses a harlequin phenotype with white petals and sepals containing large anthocyanin sectors. Harlequin flowers are ideal to evaluate anthocyanin-related Myb gene expression within genetically identical but differently pigmented tissue. High levels of anthocyanin-specific Myb and Dfr transcripts were present in the purple, but not in the white, sectors of Phalaenopsis ‘Everspring Fairy’ petals and sepals. There was no differential expression of Chs, Wd, and Myc between the purple and white sectors. These results are in agreement with the results from P. amabilis and P. schilleriana.

Download Full-text

A Method to Construct Gene Regulatory Networks to Estimate and Calculate Time Delays

Jurnal Teknologi ◽

10.11113/jt.v62.1755 ◽

2013 ◽

Vol 62 (1) ◽

Author(s):

Mohd Saberi Mohamad ◽

Chai Suk Phin

Keyword(s):

Gene Expression ◽

Gene Regulatory Network ◽

Regulatory Network ◽

Time Delays ◽

Time Course ◽

Target Gene ◽

Biological Research ◽

Expression Change ◽

Gene Regulatory ◽

Regulator Genes

In general, the motive of this research is to infer gene regulatory network in order to clarify the basis consequences of biological process at the molecular level. Time course gene expression profiling dataset has been widely used in basic biological research, especially in transcription regulation studies since the microarray dataset is a short time course gene expression dataset and have lots of errors, missing value, and noise. In this research, R library is implemented in this method to construct gene regulatory which aims to estimate and calculate the time delays between genes and transcription factor. Time delay is the parameters of the modeled time delay linear regression models and a time lag during gene expression change of the regulator genes toward target gene expression. The constructed gene regulatory network provided information of time delays between expression change in regulator genes and its target gene which can be applied to investigate important time-related biological process in cells. The result of time delays and regulation patterns in gene regulatory network may contribute into biological research such as cell development, cell cycle, and cell differentiation in any of living cells.

Download Full-text

Integrated analysis of the transcriptome and metabolome of purple and green leaves of Tetrastigma hemsleyanum reveals gene expression patterns involved in anthocyanin biosynthesis

PLoS ONE ◽

10.1371/journal.pone.0230154 ◽

2020 ◽

Vol 15 (3) ◽

pp. e0230154 ◽

Cited By ~ 1

Author(s):

Jianli Yan ◽

Lihua Qian ◽

Weidong Zhu ◽

Jieren Qiu ◽

Qiujun Lu ◽

...

Keyword(s):

Gene Expression ◽

Anthocyanin Biosynthesis ◽

Expression Patterns ◽

Integrated Analysis ◽

Gene Expression Patterns ◽

Tetrastigma Hemsleyanum ◽

Green Leaves

Download Full-text

Study on the Relationship between the miRNA-centered ceRNA Regulatory Network and Fatigue

Journal of Molecular Neuroscience ◽

10.1007/s12031-021-01845-3 ◽

2021 ◽

Author(s):

Xingzhe Yang ◽

Feng Li ◽

Jie Ma ◽

Yan Liu ◽

Xuejiao Wang ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulatory Network ◽

Regulatory Network ◽

Hot Spot ◽

Genetic Research ◽

Noncoding Rnas ◽

Messenger Rnas ◽

Effective Prevention ◽

Gene Regulatory ◽

The Relationship

AbstractIn recent years, the incidence of fatigue has been increasing, and the effective prevention and treatment of fatigue has become an urgent problem. As a result, the genetic research of fatigue has become a hot spot. Transcriptome-level regulation is the key link in the gene regulatory network. The transcriptome includes messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). MRNAs are common research targets in gene expression profiling. Noncoding RNAs, including miRNAs, lncRNAs, circRNAs and so on, have been developed rapidly. Studies have shown that miRNAs are closely related to the occurrence and development of fatigue. MiRNAs can regulate the immune inflammatory reaction in the central nervous system (CNS), regulate the transmission of nerve impulses and gene expression, regulate brain development and brain function, and participate in the occurrence and development of fatigue by regulating mitochondrial function and energy metabolism. LncRNAs can regulate dopaminergic neurons to participate in the occurrence and development of fatigue. This has certain value in the diagnosis of chronic fatigue syndrome (CFS). CircRNAs can participate in the occurrence and development of fatigue by regulating the NF-κB pathway, TNF-α and IL-1β. The ceRNA hypothesis posits that in addition to the function of miRNAs in unidirectional regulation, mRNAs, lncRNAs and circRNAs can regulate gene expression by competitive binding with miRNAs, forming a ceRNA regulatory network with miRNAs. Therefore, we suggest that the miRNA-centered ceRNA regulatory network is closely related to fatigue. At present, there are few studies on fatigue-related ncRNA genes, and most of these limited studies are on miRNAs in ncRNAs. However, there are a few studies on the relationship between lncRNAs, cirRNAs and fatigue. Less research is available on the pathogenesis of fatigue based on the ceRNA regulatory network. Therefore, exploring the complex mechanism of fatigue based on the ceRNA regulatory network is of great significance. In this review, we summarize the relationship between miRNAs, lncRNAs and circRNAs in ncRNAs and fatigue, and focus on exploring the regulatory role of the miRNA-centered ceRNA regulatory network in the occurrence and development of fatigue, in order to gain a comprehensive, in-depth and new understanding of the essence of the fatigue gene regulatory network.

Download Full-text