Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges

Tiedge, Kira; Muchlinski, Andrew; Zerbe, Philipp

doi:10.1093/synbio/ysaa005

Title: Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges

Abstract

Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production have intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of ‘user-friendly’ biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically importantmore »« less

Authors:

Tiedge, Kira ^[1]; Muchlinski, Andrew ^[1];

^[1]

Univ. of California, Davis, CA (United States)

Publication Date:: Mon Jun 01 00:00:00 EDT 2020

Research Org.:: Univ. of California, Davis, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; German Research Foundation (DFG)

OSTI Identifier:: 1633655

Grant/Contract Number:: SC0019178

Resource Type:: Accepted Manuscript

Journal Name:: Synthetic Biology

Additional Journal Information:: Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2397-7000

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Plant Specialized Metabolism; DNA Synthesis; Terpenoid Metabolism; Gene Discovery; Enzyme Functional Analysis; Functional Genomics, Switchgrass

Citation Formats


                    Tiedge, Kira, Muchlinski, Andrew, and Zerbe, Philipp. Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges.  United States: N. p., 2020. 
Web.  doi:10.1093/synbio/ysaa005.

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                    Tiedge, Kira, Muchlinski, Andrew, & Zerbe, Philipp. Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges.  United States.  https://doi.org/10.1093/synbio/ysaa005

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                    Tiedge, Kira, Muchlinski, Andrew, and Zerbe, Philipp. Mon .  
"Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges".  United States.  https://doi.org/10.1093/synbio/ysaa005.  https://www.osti.gov/servlets/purl/1633655.

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@article{osti_1633655,

  title        = {Genomics-enabled analysis of specialized metabolism in bioenergy crops: Current progress and challenges},

  author       = {Tiedge, Kira and Muchlinski, Andrew and Zerbe, Philipp},

  abstractNote = {Plants produce a staggering diversity of specialized small molecule metabolites that play vital roles in mediating environmental interactions and stress adaptation. This chemical diversity derives from dynamic biosynthetic pathway networks that are often species-specific and operate under tight spatiotemporal and environmental control. A growing divide between demand and environmental challenges in food and bioenergy crop production have intensified research on these complex metabolite networks and their contribution to crop fitness. High-throughput omics technologies provide access to ever-increasing data resources for investigating plant metabolism. However, the efficiency of using such system-wide data to decode the gene and enzyme functions controlling specialized metabolism has remained limited; due largely to the recalcitrance of many plants to genetic approaches and the lack of ‘user-friendly’ biochemical tools for studying the diverse enzyme classes involved in specialized metabolism. With emphasis on terpenoid metabolism in the bioenergy crop switchgrass as an example, this review aims to illustrate current advances and challenges in the application of DNA synthesis and synthetic biology tools for accelerating the functional discovery of genes, enzymes and pathways in plant specialized metabolism. These technologies have accelerated knowledge development on the biosynthesis and physiological roles of diverse metabolite networks across many ecologically and economically important plant species and can provide resources for application to precision breeding and natural product metabolic engineering.},

  doi          = {10.1093/synbio/ysaa005},

  journal      = {Synthetic Biology},

  number       = 1,

  volume       = 5,

  place        = {United States},

  year         = {Mon Jun 01 00:00:00 EDT 2020},

  month        = {Mon Jun 01 00:00:00 EDT 2020}

}

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https://doi.org/10.1093/synbio/ysaa005

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Figures / Tables:

Figure 1: Overview of currently available genome resources for key bioenergy crops.

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