Cryptococcus neoformans Database in Synthetic Biology Open Language

Abstract

Cryptococcus neoformans is the etiologic agent of cryptococcosis, a lethal worldwide disease. Synthetic biology could contribute to its better understanding through engineering genetic networks. However, its major challenge is the requirement of accessible genetic parts. The database presented here provides 23 biological parts for this organism in Synthetic Biology Open Language.

FIG 1

Schematic representation of the strategy followed for Cryptococcus neoformans database assembly. At first a comprehensive evaluation of the literature for genetic biological parts from C. neoformans was performed in different bibliographic databases, such as PubMed and Google Scholar, with the following terms: promoters, coding sequences, terminators, and the target organism. In addition, the Addgene database was searched with the same terms. Only the genetic biological parts that met specific criteria such as the sequence being complete, being expressed, and being used in the target organism were selected for the following step. BLAST alignments were performed to confirm the genetic part sequence, followed by a search on FungiDB, UniProt, or Ensembl Fungi. Twenty-three parts from 12 articles were included in the database, and four genetic parts were excluded for not complying with the required criteria. The data were compiled in a table (https://doi.org/10.6084/m9.figshare.19990838.v2). The synthetic biology design tool, SBOLDesigner3.1, was used to create and to provide standardized visualizations of these individual genetic parts in the Synthetic Biology Open Language (SBOL), which were then deposited in the SynBioHub repository.