Actinobacteria TFDB: An integrated view of transcription factors in Actinobacteria

Abstract

Actinobacteria represent a prolific source of bioactive natural products. However, the complex transcriptional regulatory networks in these bacteria, particularly the interplay between transcription factors (TFs) and their regulatory ligands (TF-RLs), remain poorly characterized and lack dedicated resources. In this context, we introduce the Actinobacteria Transcription Factor Database (Actinobacteria TFDB), a comprehensive repository that systematically integrates TF-centric data across 25 representative species. The current version encompasses 629 TFs, classified into 69 families, documents 11,776 TF-target relationships and 28 TF posttranslational modification sites. Uniquely, it features a dedicated collection of 54 experimentally validated TF-RL interactions. Beyond providing standardized annotations, sequence and structural features, and regulatory networks, Actinobacteria TFDB incorporates a specialized TF-RL module that enables interactive exploration and visualization of allosteric regulatory mechanisms. By consolidating multi-dimensional TF data from diverse sources, this resource empowers systems-level analyses and facilitates the rational design of regulatory strategies to activate silent biosynthetic gene clusters and optimize metabolite production. The database is publicly available at http://mingleadgene.com:9315/#/home.

Keywords

Actinobacteria / Transcription factors / Database

Data availability statement

The web interface to the database is available at http://mingleadgene.com:9315/#/home.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

CRediT authorship contribution statement

Yu Fu: Writing – original draft, Investigation, Funding acquisition, Formal analysis. Zhan-Hui Xu: Writing – original draft, Investigation, Formal analysis. Yi-Fan Liang: Writing – original draft, Investigation, Formal analysis. Shi-Qi Yang: Investigation, Formal analysis. Xue-Qin Xie: Investigation, Formal analysis. Bang-Ce Ye: Visualization, Validation, Supervision, Funding acquisition. Di You: Writing – original draft, Visualization, Validation, Supervision, Project administration, Methodology, Investigation, Funding acquisition.

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