SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

Abstract

The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.

Figure 1.

General organization of the SEVA plasmids and access statistics. (A) General organization of SEVA vectors as shown in the SEVA 4.0 homepage. All plasmids contain three basic modules (antibiotic marker, replication origin and cargo), the boundaries between being punctuated by unusual restriction sites. These are accompanied by a primary gadget site (additional sites are available also to this end). Clicking each of the segments enables users to visualize all choices and copy the cognate DNA sequence. The colored arrows above the cargo and Ab^R modules represent the directionality of the transcription flow of that element. (B) Visits to https://seva-plasmids.com during the period July 2021–June 2022. (C) Plasmids distributed since the onset of the SEVA platform.

Figure 2.

Updated nomenclature of SEVA vectors. The figure sketches the expanded rules for naming each of the four positions available for composing a complete SEVA code. The first position identifies the antibiotic resistance. The second position is the origin of replication (a sole numeric code 1 to 9 and then a capital letter is added). In case of either variants or addition(s) of either the antibiotic marker or a second replication origin, a lower-case letter is then inserted next. The third position is the cargo, which can be mono-function (named 1 to n) or variants/multi-function thereof (number followed by a capital letter). Finally, the fourth position is for the gadgets, which are designated by lowercase Greek letters (α to ω). For instance; pSEVA237M means a Km^R plasmid with a pBBR1 origin of replication and a promoterless msfGFP reporter (mono-function). pSEVA2313R means Km^R, pBBR1 origin and a P_EM7→mCherry cargo (bi-function). pSEVA2a2b8Rα means Km^R plasmid selectable in Gram-positive hosts with a double RK2-SCP2* replication origin, a bi-functional cargo xylS-P_m→ mCherry and a hok-sok gadget (see text for explanation)

Figure 3.

Details and utilities of the Find you plasmid section. The core of the database embodies the three subsections listed on top. Clicking each of them leads users to a different utility, the most useful of them being the Find your canonical plasmid, which can be composed according to necessities and then searched through the plasmid collection. The same section also leads to the resource named SEVA Golden Standard, which guides users through a complete roadmap for assembling complex constructs with Type IIS restriction technology. Separate Tables with the lists of canonical and non-canonical (SEVAsib) vectors can be accessed as well.

Figure 4.

Mapping the community of SEVA users. The upper panel shows the steady increase of followers of the SEVA Twitter account https://twitter.com/SEVAplasmids in the first part of 2022. The profiles of all followers were downloaded through the Twitter API (application programming interface) and the resulting network of users visualized using Gephi software (https://gephi.org/) for complex node analysis. Each square represents a community of followers (nodes) with shared interests, language or geographic location (C1–C7), labelled with the percentage share of followers in that group. Denser clusters in the visualisation (such as C3 or C4) indicate closely-knit communities, wherein many users follow each other. Note predominance of synthetic biologists and biotechnology companies.