YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis

Journal Article · 08 November 2022 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkac1041 · OSTI ID:1897545

Teixeira, Miguel Cacho ; Viana, Romeu; Palma, Margarida; Oliveira, Jorge; Galocha, Mónica; Mota, Marta Neves; Couceiro, Diogo; Pereira, Maria Galhardas; Antunes, Miguel; Costa, Inês V.; Pais, Pedro; Parada, Carolina; Chaouiya, Claudine; Sá-Correia, Isabel; Monteiro, Pedro Tiago

Abstract YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users’ choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.

• Sponsoring Organization: USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain
• OSTI ID: 1897545
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 51; ISSN 0305-1048
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United Kingdom
• Language: English