SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards
Summary Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors a...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2020-11-01
|
| Series: | Microbial Biotechnology |
| Online Access: | https://doi.org/10.1111/1751-7915.13609 |
| _version_ | 1818162074597982208 |
|---|---|
| author | Stamatios G. Damalas Christos Batianis Maria Martin‐Pascual Victor deLorenzo Vitor A. P. Martins dos Santos |
| author_facet | Stamatios G. Damalas Christos Batianis Maria Martin‐Pascual Victor deLorenzo Vitor A. P. Martins dos Santos |
| author_sort | Stamatios G. Damalas |
| collection | DOAJ |
| description | Summary Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors and methods. We hereby introduce the SEVA 3.1 platform consisting of the SEVA 3.1 vectors and the Golden Gate‐based ‘SevaBrick Assembly’. This platform enables the convergence of standard processes between the SEVA platform, the BioBricks and the Type IIs‐mediated DNA assemblies to reduce complexity and optimize compatibility between parts and methods. It features a wide library of cloning vectors along with a core set of standard SevaBrick primers that allow multipart assembly and exchange of short functional genetic elements (promoters, RBSs) with minimal cloning and design effort. As proof of concept, we constructed, among others, multiple sfGFP expression vectors under the control of eight RBSs, eight promoters and four origins of replication as well as an inducible four‐gene operon expressing the biosynthetic genes for the black pigment proviolacein. To demonstrate the interoperability of the SEVA 3.1 vectors, all constructs were characterized in both Pseudomonas putida and Escherichia coli. In summary, the SEVA 3.1 platform optimizes compatibility and modularity of inserts and backbones with a cost‐ and time‐friendly DNA assembly method, substantially expanding the toolbox for successful synthetic biology applications in Gram‐negative bacteria. |
| first_indexed | 2024-12-11T16:27:53Z |
| format | Article |
| id | doaj.art-5748065e788943498a2c31f69221222f |
| institution | Directory Open Access Journal |
| issn | 1751-7915 |
| language | English |
| last_indexed | 2024-12-11T16:27:53Z |
| publishDate | 2020-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Microbial Biotechnology |
| spelling | doaj.art-5748065e788943498a2c31f69221222f2022-12-22T00:58:40ZengWileyMicrobial Biotechnology1751-79152020-11-011361793180610.1111/1751-7915.13609SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standardsStamatios G. Damalas0Christos Batianis1Maria Martin‐Pascual2Victor deLorenzo3Vitor A. P. Martins dos Santos4Laboratory of Systems and Synthetic Biology Wageningen & Research University Stippeneng 4 Wageningen 6708 WE The NetherlandsLaboratory of Systems and Synthetic Biology Wageningen & Research University Stippeneng 4 Wageningen 6708 WE The NetherlandsLaboratory of Systems and Synthetic Biology Wageningen & Research University Stippeneng 4 Wageningen 6708 WE The NetherlandsSystems Biology Program National Center of Biotechnology − CSIC Madrid 28049 SpainLaboratory of Systems and Synthetic Biology Wageningen & Research University Stippeneng 4 Wageningen 6708 WE The NetherlandsSummary Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors and methods. We hereby introduce the SEVA 3.1 platform consisting of the SEVA 3.1 vectors and the Golden Gate‐based ‘SevaBrick Assembly’. This platform enables the convergence of standard processes between the SEVA platform, the BioBricks and the Type IIs‐mediated DNA assemblies to reduce complexity and optimize compatibility between parts and methods. It features a wide library of cloning vectors along with a core set of standard SevaBrick primers that allow multipart assembly and exchange of short functional genetic elements (promoters, RBSs) with minimal cloning and design effort. As proof of concept, we constructed, among others, multiple sfGFP expression vectors under the control of eight RBSs, eight promoters and four origins of replication as well as an inducible four‐gene operon expressing the biosynthetic genes for the black pigment proviolacein. To demonstrate the interoperability of the SEVA 3.1 vectors, all constructs were characterized in both Pseudomonas putida and Escherichia coli. In summary, the SEVA 3.1 platform optimizes compatibility and modularity of inserts and backbones with a cost‐ and time‐friendly DNA assembly method, substantially expanding the toolbox for successful synthetic biology applications in Gram‐negative bacteria.https://doi.org/10.1111/1751-7915.13609 |
| spellingShingle | Stamatios G. Damalas Christos Batianis Maria Martin‐Pascual Victor deLorenzo Vitor A. P. Martins dos Santos SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards Microbial Biotechnology |
| title | SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards |
| title_full | SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards |
| title_fullStr | SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards |
| title_full_unstemmed | SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards |
| title_short | SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards |
| title_sort | seva 3 1 enabling interoperability of dna assembly among the seva biobricks and type iis restriction enzyme standards |
| url | https://doi.org/10.1111/1751-7915.13609 |
| work_keys_str_mv | AT stamatiosgdamalas seva31enablinginteroperabilityofdnaassemblyamongthesevabiobricksandtypeiisrestrictionenzymestandards AT christosbatianis seva31enablinginteroperabilityofdnaassemblyamongthesevabiobricksandtypeiisrestrictionenzymestandards AT mariamartinpascual seva31enablinginteroperabilityofdnaassemblyamongthesevabiobricksandtypeiisrestrictionenzymestandards AT victordelorenzo seva31enablinginteroperabilityofdnaassemblyamongthesevabiobricksandtypeiisrestrictionenzymestandards AT vitorapmartinsdossantos seva31enablinginteroperabilityofdnaassemblyamongthesevabiobricksandtypeiisrestrictionenzymestandards |