NAR’s Breakthrough Articles present high-impact studies answering long-standing questions in the field of nucleic acids research and/or opening up new areas and mechanistic hypotheses for investigation. These articles are chosen by the Editors on the recommendation of Editorial Board Members and Referees. Articles are accompanied by a brief synopsis explaining the findings of the paper and where they fit in the broader context of nucleic acids research. They represent the very best papers published at NAR.
Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis
This study reports the structure of the WhiB1 bacterial transcription factor bound to the C-terminal domain of the primary sigma factor σA (σA CTD) from M. tuberculosis. This protein, like others in the Wbl protein family, contains a [4Fe-4S] cluster and is widely distributed in actinobacteria. WhiB proteins play versatile roles in diverse biological processes. WhiB1 is of particular interest because it is essential for cell growth, and it is suggested to have a role in the initiation of dormancy in response to nitric oxide (NO). NO is a potent antimicrobial chemical produced by the host to combat tuberculosis infection. Consequently, the transcription factors in the defense system of M. tuberculosis that swiftly sense and respond to NO are critical for the survival and pathogenesis of the bacterium. The reactivity of the [4Fe-4S] cluster in WhiB1 is highly selective for NO over O2, making it a specific NO sensor in aerobic bacteria.
Alliance is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing an integrated and comprehensive platform enabling researchers to leverage the extensive body of genetic and genomic studies in these organisms. The Alliance is building a central portal for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance have common data models and workflows for curation. All data are open and freely available. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease.
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures
The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.