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Rule-Based Design of Plant Expression Vectors Using GenoCAD.

Coll A, Wilson ML, Gruden K, Peccoud J - PLoS ONE (2015)

Bottom Line: It 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.Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments.The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.

ABSTRACT
Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It 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. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

No MeSH data available.


Example of two different designs for promoter analysis studies.A. The expression cassette includes a FTG under the control of a NPRO and fused with an ETG by means of a LNK. B. The expression cassette has reverse orientation and double TER.
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pone.0132502.g002: Example of two different designs for promoter analysis studies.A. The expression cassette includes a FTG under the control of a NPRO and fused with an ETG by means of a LNK. B. The expression cassette has reverse orientation and double TER.

Mentions: The main requirement of promoter-reporter systems is that the sequence of the promoter of interest (native promoter) has to be fused to a reporter protein. To that end, the rule npct breaks down the expression cassette into a NPRO followed by a FTG and TER12. The rule rnpct allows the user to clone the expression cassette in reverse orientation. Moreover, using the same rules mentioned above a single or double terminator can be added to the cassette, and epitope tags and/or linker domains can be included at both sides of the FTG. As an example, Fig 2 shows 2 different designs suitable for promoter analysis studies.


Rule-Based Design of Plant Expression Vectors Using GenoCAD.

Coll A, Wilson ML, Gruden K, Peccoud J - PLoS ONE (2015)

Example of two different designs for promoter analysis studies.A. The expression cassette includes a FTG under the control of a NPRO and fused with an ETG by means of a LNK. B. The expression cassette has reverse orientation and double TER.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492961&req=5

pone.0132502.g002: Example of two different designs for promoter analysis studies.A. The expression cassette includes a FTG under the control of a NPRO and fused with an ETG by means of a LNK. B. The expression cassette has reverse orientation and double TER.
Mentions: The main requirement of promoter-reporter systems is that the sequence of the promoter of interest (native promoter) has to be fused to a reporter protein. To that end, the rule npct breaks down the expression cassette into a NPRO followed by a FTG and TER12. The rule rnpct allows the user to clone the expression cassette in reverse orientation. Moreover, using the same rules mentioned above a single or double terminator can be added to the cassette, and epitope tags and/or linker domains can be included at both sides of the FTG. As an example, Fig 2 shows 2 different designs suitable for promoter analysis studies.

Bottom Line: It 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.Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments.The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.

ABSTRACT
Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It 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. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

No MeSH data available.