Metabolomics, standards, and metabolic modeling for synthetic biology in plants

Camilla Beate Hill, Tobias Czauderna, Matthias Klapperstueck, Ute Roessner, Falk Schreiber

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions.
    Original languageEnglish
    Article number167
    Number of pages12
    JournalFrontiers in Bioengineering and Biotechnology
    Volume3
    DOIs
    Publication statusPublished - 21 Oct 2015

    Keywords

    • Metabolic engineering
    • Synthetic biology
    • Metabolic modeling
    • Systems biology
    • Metabolomics

    Cite this

    Hill, Camilla Beate ; Czauderna, Tobias ; Klapperstueck, Matthias ; Roessner, Ute ; Schreiber, Falk. / Metabolomics, standards, and metabolic modeling for synthetic biology in plants. In: Frontiers in Bioengineering and Biotechnology. 2015 ; Vol. 3.
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    abstract = "Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions.",
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    Metabolomics, standards, and metabolic modeling for synthetic biology in plants. / Hill, Camilla Beate; Czauderna, Tobias; Klapperstueck, Matthias; Roessner, Ute; Schreiber, Falk.

    In: Frontiers in Bioengineering and Biotechnology, Vol. 3, 167, 21.10.2015.

    Research output: Contribution to journalArticleResearchpeer-review

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    AU - Schreiber, Falk

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