SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Abstract

The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

Figure 1.

The formatted structure of SEVA plasmids. The image show an interactive map with the organization of SEVA vectors as shown in the 3.0 version of the database. All plasmids contain three basic modules: a cargo, a replication origin and an antibiotic marker as indicated. Fixed restriction sites punctuate boundaries between modules in all constructs are indicated. Note the numbering position +1 of the DNA sequence is the first T of the unique PacI site. The preferred site(s) for inserting functional gadgets are indicated. See http://seva.cnb.csic.es for details.

Figure 2.

Interactive maps of SEVA plasmids. By clicking in the corresponding segment of the vector scheme, user gets a roll-down list of choices for each of the available modules as well as their DNA sequence for further analysis or composition with other genetic parts.

Figure 3.

Updated nomenclature of SEVA vectors. The figure sketches the rules for naming each of the 4 positions available for shaping a complete SEVA code. Each of them is assigned to a code of four unequivocal positions in an alphanumeric cipher: The first position is for the antibiotic resistance. For the second position, the first nine origins of replication receive a sole numeric code 1 to 9 beyond which a capital letter will be added to ‘9’, starting with an A (9A) and following with 9B, 9C etc. In case of either variants or addition(s) of a second replication origin, a lower case letter is then added. The third position, each cargo is assigned a sole ordinal numeric code 1 to n (n being unlimited). Finally, the fourth position is for the gadgets, which are designated by lower case Greek letters (α to ω).

Figure 4.

Updated numbering of core SEVA modules. The list of available modules for each position of the code shown in Figure 3 are shown.