Limits...
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 three different designs for localization studies purposes as developed with the plant grammar.A. Scheme of the most basic structure we can design, where the expression cassette includes the GEN fused to a FTG by means of a LNK domain on the N terminal. B. Sample design includes an expression cassette with 2 PRO and a GEN fused to a FTG on the N terminal and to an ETG on the C terminal. C. Same as B but with the expression cassette in reverse orientation.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4492961&req=5

pone.0132502.g001: Example of three different designs for localization studies purposes as developed with the plant grammar.A. Scheme of the most basic structure we can design, where the expression cassette includes the GEN fused to a FTG by means of a LNK domain on the N terminal. B. Sample design includes an expression cassette with 2 PRO and a GEN fused to a FTG on the N terminal and to an ETG on the C terminal. C. Same as B but with the expression cassette in reverse orientation.

Mentions: Route loc guides the user through the design of plant expression vectors for localization studies (S2 Table). By means of lcas rule, localization category (LOC) is rewritten into a complete plasmid that includes an expression cassette (CAS) and vector backbone (VEC). The next rule is prct, which breaks the cassette down into PRO12, open reading frame (CDS) and TER12. The orientation of the expression cassette can be reversed by using rcas rule. Rules npro, pro1, pro2, ter1 and ter2 allow the user to design an expression cassette with a native promoter, single or double promoter, and single or double terminator. Afterwards, rule gnftg break the CDS down into an ATG, GFTG, and STOP codon. Therefore, this rule constrains the user to design an expression cassette with a gene fused at least with one fluorescent protein, which is the minimal requirement for plasmids with localization application purposes. Two rules (nftg and cftg) incorporate flexibility into the design, allowing users to add the fluorescent protein on the 5’ or 3’-end of the gene. Moreover, epitope tags and/or linker domains can also be added at both sides of the FTG (rules tftg, ftgt, lftg and ftgl). Lastly, as it was described, GEN category can be rewritten in order to add other open reading frames, epitope tags and/or linkers at the 5’ and/or 3’-end of the gene. To demonstrate the flexibility of this approach, 3 examples of different designs with different degrees of complexity, all of them applicable for protein localization studies, are shown in Fig 1.


Rule-Based Design of Plant Expression Vectors Using GenoCAD.

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

Example of three different designs for localization studies purposes as developed with the plant grammar.A. Scheme of the most basic structure we can design, where the expression cassette includes the GEN fused to a FTG by means of a LNK domain on the N terminal. B. Sample design includes an expression cassette with 2 PRO and a GEN fused to a FTG on the N terminal and to an ETG on the C terminal. C. Same as B but with the expression cassette in reverse orientation.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132502.g001: Example of three different designs for localization studies purposes as developed with the plant grammar.A. Scheme of the most basic structure we can design, where the expression cassette includes the GEN fused to a FTG by means of a LNK domain on the N terminal. B. Sample design includes an expression cassette with 2 PRO and a GEN fused to a FTG on the N terminal and to an ETG on the C terminal. C. Same as B but with the expression cassette in reverse orientation.
Mentions: Route loc guides the user through the design of plant expression vectors for localization studies (S2 Table). By means of lcas rule, localization category (LOC) is rewritten into a complete plasmid that includes an expression cassette (CAS) and vector backbone (VEC). The next rule is prct, which breaks the cassette down into PRO12, open reading frame (CDS) and TER12. The orientation of the expression cassette can be reversed by using rcas rule. Rules npro, pro1, pro2, ter1 and ter2 allow the user to design an expression cassette with a native promoter, single or double promoter, and single or double terminator. Afterwards, rule gnftg break the CDS down into an ATG, GFTG, and STOP codon. Therefore, this rule constrains the user to design an expression cassette with a gene fused at least with one fluorescent protein, which is the minimal requirement for plasmids with localization application purposes. Two rules (nftg and cftg) incorporate flexibility into the design, allowing users to add the fluorescent protein on the 5’ or 3’-end of the gene. Moreover, epitope tags and/or linker domains can also be added at both sides of the FTG (rules tftg, ftgt, lftg and ftgl). Lastly, as it was described, GEN category can be rewritten in order to add other open reading frames, epitope tags and/or linkers at the 5’ and/or 3’-end of the gene. To demonstrate the flexibility of this approach, 3 examples of different designs with different degrees of complexity, all of them applicable for protein localization studies, are shown in Fig 1.

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.