Rule-Based Design of Plant Expression Vectors Using GenoCAD

Coll, Anna; Wilson, Mandy; Gruden, Kristina; Peccoud, Jean

doi:10.1371/journal.pone.0132502

Cited by 13 publications

(9 citation statements)

References 37 publications

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“…To aid the former, a number of CAD packages for designing complex genetic circuits from standardised parts have been developed. Gene Designer and BioStudio were developed to facilitate the design and construction of synthetic yeast chromosomes (Richardson et al , 2010, 2017); GenoCAD, which has been applied to the design of synthetic genetic constructs for plants, exemplified the use of formal language for enabling biological design (Czar et al , 2009; Coll et al , 2015); j5 provides a drag and drop interface for arranging genetic parts into complex designs (Hillson et al , 2012); and Cello automates design by drawing on libraries of genetic Boolean logic gates, molecular devices that implement a logical function to produce a binary output dependent on one or more binary inputs (Nielsen et al , 2016). Typically, a given design process will result in numerous combinations for which, even aided by automation, testing would be inordinately laborious and expensive.…”

Section: Applying the Principles Of Engineering To Biologymentioning

confidence: 99%

Beyond natural: synthetic expansions of botanical form and function

Patron

2020

New Phytologist

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Summary Powered by developments that enabled genome‐scale investigations, systems biology emerged as a field aiming to understand how phenotypes emerge from network functions. These advances fuelled a new engineering discipline focussed on synthetic reconstructions of complex biological systems with the goal of predictable rational design and control. Initially, progress in the nascent field of synthetic biology was slow due to the ad hoc nature of molecular biology methods such as cloning. The application of engineering principles such as standardisation, together with several key technical advances, enabled a revolution in the speed and accuracy of genetic manipulation. Combined with mathematical and statistical modelling, this has improved the predictability of engineering biological systems of which nonlinearity and stochasticity are intrinsic features leading to remarkable achievements in biotechnology as well as novel insights into biological function. In the past decade, there has been slow but steady progress in establishing foundations for synthetic biology in plant systems. Recently, this has enabled model‐informed rational design to be successfully applied to the engineering of plant gene regulation and metabolism. Synthetic biology is now poised to transform the potential of plant biotechnology. However, reaching full potential will require conscious adjustments to the skillsets and mind sets of plant scientists.

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Section: Applying the Principles Of Engineering To Biologymentioning

confidence: 99%

Beyond natural: synthetic expansions of botanical form and function

Patron

2020

New Phytologist

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“…Further, more precise parts-level function data will enable the use of biological computer-aided design (Bio-CAD) software tools that can fully automate parts selection and circuit construction ( Khalil et al, 2012 ; Chen et al, 2013b ; Nielsen et al, 2016 ). Software tools that have been used for construction of gene circuits in plants include GeneDesigner ( Villalobos et al, 2006 ), CellModeller ( Dupuy et al, 2007 ), BiopartsBuilder ( Yang et al, 2015 ), GenoCAD ( Coll et al, 2015 ), and GoldenBraid ( Vazquez-Vilar et al, 2017 ). These and other tools provide a common syntax that enables modular construction of multiple circuit configurations out of available genetic parts.…”

Section: Considerations For Selecting Partsmentioning

confidence: 99%

Quantitative and Predictive Genetic Parts for Plant Synthetic Biology

McCarthy

Medford

2020

Front. Plant Sci.

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Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.

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“…Recently, we developed a design strategy for plant expression vectors and we implemented it, as a grammar, in the Computer-Aided Design (CAD) software GenoCAD [ 37 ]. This software tool allows the user to quickly design genetic constructs based on the notion of genetic parts, thereby laying a foundation for the set-up of overlap-dependent assembly methods in plants [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

“…This software tool allows the user to quickly design genetic constructs based on the notion of genetic parts, thereby laying a foundation for the set-up of overlap-dependent assembly methods in plants [ 38 ]. The grammar includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs thus minimizing the risk of introducing errors [ 37 ].…”

Section: Introductionmentioning

confidence: 99%

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

Lukan¹,

Machens²,

Coll³

et al. 2018

PLoS ONE

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Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science.

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Rule-Based Design of Plant Expression Vectors Using GenoCAD

Cited by 13 publications

References 37 publications

Beyond natural: synthetic expansions of botanical form and function

Beyond natural: synthetic expansions of botanical form and function

Quantitative and Predictive Genetic Parts for Plant Synthetic Biology

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

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