A Systems Biology Approach Identifies a R2R3 MYB Gene Subfamily with Distinct and Overlapping Functions in Regulation of Aliphatic Glucosinolates

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2007 Dec 21

PMID 18094747

Citations 143

Authors

Ida Elken Sonderby

Bjarne Gram Hansen

Nanna Bjarnholt

Carla Ticconi

Barbara Ann Halkier

Daniel J Kliebenstein

Affiliations

Soon will be listed here.

Abstract

Background: Glucosinolates are natural metabolites in the order Brassicales that defend plants against both herbivores and pathogens and can attract specialized insects. Knowledge about the genes controlling glucosinolate regulation is limited. Here, we identify three R2R3 MYB transcription factors regulating aliphatic glucosinolate biosynthesis in Arabidopsis by combining several systems biology tools.

Methodology/principal Findings: MYB28 was identified as a candidate regulator of aliphatic glucosinolates based on its co-localization within a genomic region controlling variation both in aliphatic glucosinolate content (metabolite QTL) and in transcript level for genes involved in the biosynthesis of aliphatic glucosinolates (expression QTL), as well as its co-expression with genes in aliphatic glucosinolate biosynthesis. A phylogenetic analysis with the R2R3 motif of MYB28 showed that it and two homologues, MYB29 and MYB76, were members of an Arabidopsis-specific clade that included three characterized regulators of indole glucosinolates. Over-expression of the individual MYB genes showed that they all had the capacity to increase the production of aliphatic glucosinolates in leaves and seeds and induce gene expression of aliphatic biosynthetic genes within leaves. Analysis of leaves and seeds of single knockout mutants showed that mutants of MYB29 and MYB76 have reductions in only short-chained aliphatic glucosinolates whereas a mutant in MYB28 has reductions in both short- and long-chained aliphatic glucosinolates. Furthermore, analysis of a double knockout in MYB28 and MYB29 identified an emergent property of the system since the absence of aliphatic glucosinolates in these plants could not be predicted by the chemotype of the single knockouts.

Conclusions/significance: It seems that these cruciferous-specific MYB regulatory genes have evolved both overlapping and specific regulatory capacities. This provides a unique system within which to study the evolution of MYB regulatory factors and their downstream targets.

Citing Articles

Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus.

Ricono A, Ludwig E, Casto A, Zorich S, Sumner J, Bird K Plant J. 2025; 121(4):e70011.

PMID: 39993006 PMC: 11849911. DOI: 10.1111/tpj.70011.

Novel Regulators and Their Epistatic Networks in Arabidopsis' Defence Responses to Alternaria alternata Infection.

Zeng Q, Liu X, Yan X, Zhang J, Li C, Yan C Mol Plant Pathol. 2025; 26(2):e70058.

PMID: 39894981 PMC: 11788323. DOI: 10.1111/mpp.70058.

A 2-oxoglutarate-dependent dioxygenase, GLUCORAPHASATIN SYNTHASE 1 (GRS1) is a major determinant for different aliphatic glucosinolates between radish and Chinese cabbage.

Choi P, Nugroho A, Moon H, Kim D Plant Mol Biol. 2024; 115(1):1.

PMID: 39656296 DOI: 10.1007/s11103-024-01537-7.

The RNA-Binding Protein BoRHON1 Positively Regulates the Accumulation of Aliphatic Glucosinolates in Cabbage.

Bai X, Zhang R, Zeng Q, Yang W, Fang F, Sun Q Int J Mol Sci. 2024; 25(10).

PMID: 38791354 PMC: 11120748. DOI: 10.3390/ijms25105314.

Chromosome-scale reference genome of broccoli ( var. Plenck) provides insights into glucosinolate biosynthesis.

Wu Q, Mao S, Huang H, Liu J, Chen X, Hou L Hortic Res. 2024; 11(5):uhae063.

PMID: 38720933 PMC: 11077082. DOI: 10.1093/hr/uhae063.

References

Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U . Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4(2):249-64. DOI: 10.1093/biostatistics/4.2.249. View

Rosso M, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B . An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol. 2004; 53(1-2):247-59. DOI: 10.1023/B:PLAN.0000009297.37235.4a. View

Hirai M, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A . Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci U S A. 2007; 104(15):6478-83. PMC: 1849962. DOI: 10.1073/pnas.0611629104. View

Gigolashvili T, Berger B, Mock H, Muller C, Weisshaar B, Flugge U . The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana. Plant J. 2007; 50(5):886-901. DOI: 10.1111/j.1365-313X.2007.03099.x. View

Doerge R . Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet. 2002; 3(1):43-52. DOI: 10.1038/nrg703. View

Hemm M, Ruegger M, Chapple C . The Arabidopsis ref2 mutant is defective in the gene encoding CYP83A1 and shows both phenylpropanoid and glucosinolate phenotypes. Plant Cell. 2003; 15(1):179-94. PMC: 143490. DOI: 10.1105/tpc.006544. View

Agarwal M, Hao Y, Kapoor A, Dong C, Fujii H, Zheng X . A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem. 2006; 281(49):37636-45. DOI: 10.1074/jbc.M605895200. View

Mewis I, Appel H, Hom A, Raina R, Schultz J . Major signaling pathways modulate Arabidopsis glucosinolate accumulation and response to both phloem-feeding and chewing insects. Plant Physiol. 2005; 138(2):1149-62. PMC: 1150428. DOI: 10.1104/pp.104.053389. View

Zhu J, Verslues P, Zheng X, Lee B, Zhan X, Manabe Y . HOS10 encodes an R2R3-type MYB transcription factor essential for cold acclimation in plants. Proc Natl Acad Sci U S A. 2005; 102(28):9966-71. PMC: 1175003. DOI: 10.1073/pnas.0503960102. View

10.

Tissier A, Marillonnet S, Klimyuk V, Patel K, Torres M, Murphy G . Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: a tool for functional genomics. Plant Cell. 1999; 11(10):1841-52. PMC: 144107. DOI: 10.1105/tpc.11.10.1841. View

11.

Kliebenstein D, Pedersen D, Barker B, Mitchell-Olds T . Comparative analysis of quantitative trait loci controlling glucosinolates, myrosinase and insect resistance in Arabidopsis thaliana. Genetics. 2002; 161(1):325-32. PMC: 1462090. DOI: 10.1093/genetics/161.1.325. View

12.

Stracke R, WERBER M, Weisshaar B . The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001; 4(5):447-56. DOI: 10.1016/s1369-5266(00)00199-0. View

13.

Gray J . Guard cells: transcription factors regulate stomatal movements. Curr Biol. 2005; 15(15):R593-5. DOI: 10.1016/j.cub.2005.07.039. View

14.

Kliebenstein D, Rowe H, Denby K . Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant J. 2005; 44(1):25-36. DOI: 10.1111/j.1365-313X.2005.02508.x. View

15.

Kliebenstein D, Kroymann J, Mitchell-Olds T . The glucosinolate-myrosinase system in an ecological and evolutionary context. Curr Opin Plant Biol. 2005; 8(3):264-71. DOI: 10.1016/j.pbi.2005.03.002. View

16.

Brem R, Yvert G, Clinton R, Kruglyak L . Genetic dissection of transcriptional regulation in budding yeast. Science. 2002; 296(5568):752-5. DOI: 10.1126/science.1069516. View

17.

Bennett R, Wenke T, Freudenberg B, Mellon F, Ludwig-Muller J . The tu8 mutation of Arabidopsis thaliana encoding a heterochromatin protein 1 homolog causes defects in the induction of secondary metabolite biosynthesis. Plant Biol (Stuttg). 2005; 7(4):348-57. DOI: 10.1055/s-2005-837634. View

18.

Clough S, Bent A . Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1999; 16(6):735-43. DOI: 10.1046/j.1365-313x.1998.00343.x. View

19.

Lehfeldt C, Shirley A, Meyer K, Ruegger M, Cusumano J, Viitanen P . Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell. 2000; 12(8):1295-306. PMC: 149103. DOI: 10.1105/tpc.12.8.1295. View

20.

Levy M, Wang Q, Kaspi R, Parrella M, Abel S . Arabidopsis IQD1, a novel calmodulin-binding nuclear protein, stimulates glucosinolate accumulation and plant defense. Plant J. 2005; 43(1):79-96. DOI: 10.1111/j.1365-313X.2005.02435.x. View