General description

What is the SEVA Platform?

The Standard European Vector Architecture (SEVA) platform is a web-based resource and a material clone repository to assist the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes.

The SEVA database (SEVA-DB) is a resource for implementation of a standard for physical assembly of vector plasmids and for their non-ambiguous nomenclature as well as the index for a repository of functional sequences and actual constructs available to the community. The database was designed to simplify the choice of a given vector for the sake of specific applications, in such a way the user can easily decide the best configuration of replication origins, antibiotic resistance and business segments.

The SEVA-DB adopts simple design concepts imported from Systems Engineering into vector architecture and development to facilitate the swapping of functional modules and the extension genome engineering options to microorganisms beyond typical Laboratory strains. This platform has been implemented in the Molecular Environmental Microbiology Laboratory of the Centro Nacional de Biotecnología (CSIC).

What is the SEVA format?

The SEVA format involves a set of rules for the physical assembly of the three basic components of plasmid vectors (origin of replication, selection marker and the business cargo) as well as a fixed nomenclature for the designation of the corresponding constructs.

Each of the naturally-occurring sequences destined for the various constructs are minimized to the shortest DNA sequence that retains functionality. Furthermore, the sequences are erased of any of the following restriction sites: HindIII, PstI, XbaI, BamHI, SmaI, KpnI, SacI, SalI, EcoRI, SfiI, SphI, AatII, AvrII, PshAI, SwaI, AscI, FseI, PacI, SpeI, SanDI and NotI. Finally each of the modules is flanked by fixed, rare restriction sites: origin of replication by FseI and AscI; antibiotic marker by SwaI and PshA; and the cargo by PacI and SpeI.

For the nomenclature of vectors that follow the SEVA standard, see the section below.

(MARTÍNEZ-GARCÍA E. et al, SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. Nucleic Acids Res) Article

What is the added value of adopting the SEVA format and SEVA vectors?

The adoption of the SEVA format can become a shortcut to fill the phenomenal gap between the existing power of DNA synthesis and the actual engineering of predictable and efficacious bacteria. Such a scaffold enables the exchangeability of multiple origins of replication with diverse antibiotic selection markers to shape a frame for their further combination with a large variety of cargo modules for varied end-applications. The core collection of constructs available at the SEVA-DB has been produced as the starting point for the further expansion of the formatted vector platform.


The nomenclature of SEVA constructs | + |

Besides the standardized layout of constructs the SEVA format calls for the unequivocal designation for each of the vectors with the nomenclature explained in detail in that section and the code summarized in the plasmid list section. All vectors are called pSEVA followed by a digit cipher with four positions. The first one reflects the antibiotic resistance marker. The second position of the code is for the origin of replication. The third spot goes for the cargo module. In cases where there is a variant of the same cargo type we then add a capital letter to the numeral. And finally the fourth position is for the gadgets, which are designated by lower cases greek letters.


Ordering SEVA plasmids | + |

Plasmid already available in SEVA-DB and those that will enrich the collection in the future are distributed world-wide to researchers at any academic or non-profit laboratory. No MTAs will be requested prior to shipping the constructs to potential users of such categories. The SEVA-DB will distribute petitions of a small number of clones at no cost for the user, but may charge handling, maintenance and shipping fees for large requests.


Contributing new SEVA constructs to the plasmid repository

If you wish to contribute with your favourite module please follow these simple rules:

1- Remove, if any, the following restriction sites from your sequence: HindIII, PstI, XbaI, BamHI, SmaI, KpnI, SacI, SalI, EcoRI, SfiI, SphI, AvrII, PshAI, SwaI, AscI, FseI, PacI, SpeI, SanDI and NotI.

2- Flank your module with the appropriate restriction sites:

– Origin of replication by FseI and AscI.
– Antibiotic marker: SwaI and PshA.
– Cargoes: PacI and SpeI. The major transcriptional flow encoded in this segment must follow the
direction PacI ➔ SpeI.

3- Adhere to Open Access policy and send your new construct (plasmid and strain) to us for inclusion in the SEVA database, where we will assign a code according the SEVA rules.

Contributors to the collection of SEVA vectors must be accredited by the curators of the platform to follow the standards specified above, stored in the SEVA repository and assigned a definitive code prior to public release. Users are discouraged to assign SEVA codes that are not explicitly endorsed by the SEVA-DB managers.


+ Reporting problems

For any suggestions, comments or problems with the database or vectors please contact the collection curator (seva at cnb.csic.es).


+ Disclaimer

In case of utilization for commercial or industrial purposes, solicitors should be aware that some of the DNA sequences employed in the SEVA plasmids could be subjected to intellectual property restrictions, for which SEVA platform disclaims any carrier liability.


+ Acknowledgements

The SEVA-DB platform is supported by the BIO and FEDER CONSOLIDER-INGENIO programmes of the Spanish Ministry of Economy and Competitiveness, the European Research Council (ERC), The Korea Research Institute of Bioscience and Biotechnlogy (KRIBB)  and ST-FLOW Contracts of the EU, the ERANET Program for Industrial Biotechnology and the PROMPT Project of the Autonomous Community of Madrid.