Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

Tohge, Takayuki; Scossa, Federico; Fernie, Alisdair R.

doi:10.1104/pp.15.01006

Cited by 35 publications

(22 citation statements)

References 149 publications

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“…It can thus be anticipated that deep probing of further profiling studies will facilitate the elucidation of the genetic complexity of maize flavonoid biosynthesis. Indeed, integrative approaches are increasingly applied to enhance our understanding of metabolic pathway structure and regulation and how these affect the end-phenotypes of plants [46]. …”

Section: Introductionmentioning

confidence: 99%

Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis

et al. 2017

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BackgroundFlavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway.ResultsWe repeatedly detected 25 QTL corresponding to 23 distinct flavonoids across different environments or populations. In addition, a total of 39 genes were revealed both by an expression based network analysis and genetic mapping. Finally, the function of three candidate genes, including two UDP-glycosyltransferases (UGT) and an oxygenase which belongs to the flavone synthase super family, was revealed via preliminary molecular functional characterization.ConclusionWe explored the genetic influences on the flavonoid biosynthesis based on integrating the genomic, transcriptomic and metabolomic information which provided a rich source of potential candidate genes. The integrated genomics based genetic mapping strategy is highly efficient for defining the complexity of functional genetic variants and their respective regulatory networks as well as in helping to select candidate genes and allelic variance before embarking on laborious transgenic validations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0972-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis

et al. 2017

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“…This is particularly relevant given the promiscuity of enzymes in secondary plant metabolism, which has led to exceptional chemodiversity in plants (Weng et al, 2012). This challenge can be tackled by modern developments in plant systems biology that integrate genomics, transcriptomics, proteomics, and metabolomics data (Kliebenstein, 2014;Tohge et al, 2015). Revealing novel promiscuous enzyme functions in plants and other organisms will provide the possibility for engineering enzymes through directed evolution (Tracewell and Arnold, 2009;Chakraborty et al, 2013), which can then be used for the execution of pathway designs.…”

Section: Challenges and Opportunities For Plant Synthetic Biologymentioning

confidence: 99%

Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways

Küken

Nikoloski

2019

Plant Physiol.

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Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.

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“…Here, data of floral secondary metabolite abundance measured in a population of 64 Arabidopsis thaliana (Arabidopsis) natural accessions are presented (Data Citation 1)(Data Citation 2). Sixty-eight secondary metabolites were measured via LC-MS, ions acquired in positive and negative ion detection mode, and compounds annotated through a combination of chemical confirmation with analytical standards and comparative analysis with flavonoids knockout and over-expresser Arabidopsis lines 12 , 13 . The list of the Arabidopsis accessions used in this study, and raw and normalized metabolomics data are provided (Data Citation 1)(Data Citation 2), respectively.…”

Section: Background and Summarymentioning

confidence: 99%

The natural variance of the Arabidopsis floral secondary metabolites

2018

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Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as transcripts, proteins and growth and flowering related phenotypes.

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Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

Cited by 35 publications

References 149 publications

Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis

Integrated genomics-based mapping reveals the genetics underlying maize flavonoid biosynthesis

Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways

The natural variance of the Arabidopsis floral secondary metabolites

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