The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

Abstract

The ‘Standard European Vector Architecture’ database (SEVA-DB, http://seva.cnb.csic.es) was conceived as a user-friendly, web-based resource and a material clone repository to assist in the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes. The SEVA-DB adopts simple design concepts that facilitate the swapping of functional modules and the extension of genome engineering options to microorganisms beyond typical laboratory strains. Under the SEVA standard, every DNA portion of the plasmid vectors is minimized, edited for flaws in their sequence and/or functionality, and endowed with physical connectivity through three inter-segment insulators that are flanked by fixed, rare restriction sites. Such a scaffold enables the exchangeability of multiple origins of replication and diverse antibiotic selection markers to shape a frame for their further combination with a large variety of cargo modules that can be used for varied end-applications. The core collection of constructs that are available at the SEVA-DB has been produced as a starting point for the further expansion of the formatted vector platform. We argue that 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.

Bricks and blueprints: methods and standards for DNA assembly

“…New standard plasmid formats have thus been developed to facilitate swapping of parts between constructs. For rapid prototyping of Escherichia coli gene network constructs the Breadboard standard has been developed 17 .For working across a broad range of bacterial species, Standard European Vector Architecture (SEVA) plasmids are a standard that gives plasmids a modular structure with unique restriction sites that flank fundamental parts such as selection markers and origins of replication, which often need to be exchanged in order to efficiently operate in different organisms 18,19 .…”

“…New standard plasmid formats have thus been developed to facilitate swapping of parts between constructs. For rapid prototyping of Escherichia coli gene network constructs the Breadboard standard has been developed 17 .For working across a broad range of bacterial species, Standard European Vector Architecture (SEVA) plasmids are a standard that gives plasmids a modular structure with unique restriction sites that flank fundamental parts such as selection markers and origins of replication, which often need to be exchanged in order to efficiently operate in different organisms 18,19 .The drawback of all digestion and ligation methods is the need to remove forbidden digestion sites within DNA parts prior to cloning them. Homing endonucleases such as I-SceI have been proposed as a way to overcome this as they are equivalent to restriction endonucleases but only cut at long recognition sequences, which are unlikely to be found in cloning parts 20 .…”

Anodic respiration of Pseudomonas putida KT2440 in a stirred-tank bioreactor

“…The gene ubiC was inserted into EcoR I/ Hind III of the vector pSEVA234 [28], resulting in the plasmid pSEVA234-ubiC.…”

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

“…First, the efficiency of P. putida EM383 as a receiver of plasmids through electroporation was tested. As an example, pSEVA251 [65], an standard, kanamycin resistant, broadhost-range cloning vector endowed with a promiscuous multi-copy RSF1010 origin of replication, was used. As shown in Table 3, the multi-deleted strain maintained its transformation capacity within the same order of magnitude known for the wild-type bacterium.…”