Opportunities in plant synthetic biology

Cook, Charis; Martin, Lisa; Bastow, Ruth

doi:10.1093/jxb/eru013

Cited by 23 publications

(16 citation statements)

References 40 publications

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“…At John Innes centre, different pathways have been characterized for plants capable of fixing nitrogen through bacteria (Oldroyd et al, 2011; Xie et al, 2012). The researchers are now attempting to introduce these pathways in wheat for developing ‘self-fertilizing’ cereal (Cook et al, 2014). By doing so, there will be clear cut reduction in dependency upon inorganic fertilizers because plants will be able to fix atmospheric nitrogen.…”

Section: Applications Of Crispr-cas9 In Plant Biology and Biotechnologymentioning

confidence: 99%

CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing

Noman

Aqeel

2016

Front. Plant Sci.

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Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described.

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Section: Applications Of Crispr-cas9 In Plant Biology and Biotechnologymentioning

confidence: 99%

CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing

Noman

Aqeel

2016

Front. Plant Sci.

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“…More recently, targeted genome editing has emerged as a versatile approach to introduce specific mutations and to introduce one or more transgenes at particular loci [43][44][45][46]. Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can be used to introduce mutations at specific loci, although both methods require two different DNA binding proteins flanking a sequence of interest [47,48].…”

Section: Box 2 Targeted Intervention Strategies For Metabolic Engineementioning

confidence: 99%

Knowledge-driven approaches for engineering complex metabolic pathways in plants

Farré¹,

Twyman²,

Christou³

et al. 2015

Current Opinion in Biotechnology

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“…Most importantly, by sampling various tissues under different environmental conditions, omics data can also be incorporated into the simulation of growth and resource production in metabolic reconstructions; this type of approach has proved to be very valuable in the analysis of metabolism under stress (Williams et al, 2010;Nagele and Weckwerth, 2012). Finally, the reconstruction and simulation of plant metabolism is central in the emerging field of plant synthetic biology (Cook et al, 2014;Fernandez-Castane et al, 2014;Hill et al, 2015;Liu and Stewart, 2015;Shih et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

et al. 2018

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Genome-scale metabolic reconstructions help us to understand and engineer metabolism. Next-generation sequencing technologies are delivering genomes and transcriptomes for an ever-widening range of plants. While such omic data can, in principle, be used to compare metabolic reconstructions in different species, organs and environmental conditions, these comparisons require a standardized framework for the reconstruction of metabolic networks from transcript data. We previously introduced PlantSEED as a framework covering primary metabolism for 10 species. We have now expanded PlantSEED to include 39 species and provide tools that enable automated annotation and metabolic reconstruction from transcriptome data. The algorithm for automated annotation in PlantSEED propagates annotations using a set of signature k-mers (short amino acid sequences characteristic of particular proteins) that identify metabolic enzymes with an accuracy of about 97%. PlantSEED reconstructions are built from a curated template that includes consistent compartmentalization for more than 100 primary metabolic subsystems. Together, the annotation and reconstruction algorithms produce reconstructions without gaps and with more accurate compartmentalization than existing resources. These tools are available via the PlantSEED web interface at http://modelseed.org, which enables users to upload, annotate and reconstruct from private transcript data and simulate metabolic activity under various conditions using flux balance analysis. We demonstrate the ability to compare these metabolic reconstructions with a case study involving growth on several nitrogen sources in roots of four species.

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Opportunities in plant synthetic biology

Cited by 23 publications

References 40 publications

CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing

CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing

Knowledge-driven approaches for engineering complex metabolic pathways in plants

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

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