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Article Dans Une Revue Nucleic Acids Research Année : 2023

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

Miguel Cacho Teixeira
Romeu Viana
  • Fonction : Auteur
Margarida Palma
  • Fonction : Auteur
Jorge Oliveira
  • Fonction : Auteur
Mónica Galocha
  • Fonction : Auteur
Marta Neves Mota
  • Fonction : Auteur
Diogo Couceiro
  • Fonction : Auteur
Maria Galhardas Pereira
  • Fonction : Auteur
Miguel Antunes
  • Fonction : Auteur
Inês Costa
  • Fonction : Auteur
Pedro Pais
  • Fonction : Auteur
Carolina Parada
  • Fonction : Auteur
Claudine Chaouiya
  • Fonction : Auteur
  • PersonId : 1103549
Isabel Sá-Correia
  • Fonction : Auteur
Pedro Tiago Monteiro

Résumé

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.

Dates et versions

hal-04052724 , version 1 (30-03-2023)

Identifiants

Citer

Miguel Cacho Teixeira, Romeu Viana, Margarida Palma, Jorge Oliveira, Mónica Galocha, et al.. YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Research, 2023, 51 (D1), pp.D785-D791. ⟨10.1093/nar/gkac1041⟩. ⟨hal-04052724⟩
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