Journal of Molecular Biology最新文献

Microbiota-derived metabolites serve as key messengers mediating host-microbe and microbe-microbe interactions, often through specialized primary metabolic pathways. gutSMASH was initially developed to systematically identify the metabolic gene clusters (MGCs) that encode these pathways in anaerobic gut microbial genomes. Here, we present gutSMASH 2.0, a major update that significantly expands its functionality. This version introduces 14 new detection rules covering 12 additional types of MGCs. The comparative genomics framework was enhanced with 26 experimentally validated MGCs and 15,024 gene clusters from the Cultivated Genome Reference 2 (CGR2) collection. Furthermore, gutSMASH 2.0 integrates transcription factor binding site prediction using LogoMotif's methodology, enabling investigation of MGC regulatory elements. Together, these improvements make gutSMASH a more powerful tool for automated discovery and analysis of niche-determining metabolic pathways in the gut microbiome. gutSMASH 2.0 is freely available at https://gutsmash.bioinformatics.nl/.

Understanding RNA structures - essential for uncovering their biological functions, interactions, and therapeutic potential - relies on both experimental techniques and computational approaches increasingly driven by artificial intelligence. The latter are transforming RNA structural research but depend on large, reliable datasets, which remain limited, particularly for RNA-protein and RNA-DNA complexes. To address this gap, we present RNAsolo 2.0 (https://rnasolo.cs.put.poznan.pl/), an open-access database integrating cleaned, non-redundant RNA 3D structures with detailed information on their intermolecular interactions. Building on the original RNAsolo, which has attracted over 16,000 page views from ∼5,600 users, this release adds Rfam-based family classification, >2,500 precompiled benchmark sets, and multimodal representations encompassing sequence, secondary and tertiary structure, as well as torsion angle data. RNAsolo 2.0 enables searches for RNAs that interact with specific proteins, ligands, or ions, and provides an interactive view of their binding interfaces. The tool offers a robust, user-friendly platform for RNA structural biology and next-generation AI-driven modeling.

This review focuses on a fundamental problem faced by hyperthermophiles that grow at temperatures above 95 °C. At such high temperatures, both linear and open circular DNA denature, leading to strand separation and loss of the double-helical structure. One strategy to prevent denaturation is to maintain DNA in a closed circular form, where the topological constraint on DNA conformations increases the melting temperature by 30-40 °C. However, this conformational restriction is lost when a single-stranded break occurs - a common type of DNA lesion. In hyperthermophiles, circular DNA containing a single-stranded nick begins to unwind and partially denature. Although DNA-bound proteins can slow this process, they protect only a fraction of the double helix. As a result, repairing such damage requires not only restoration of the strand integrity but also restoration of the original linking number between complementary strands. Reverse gyrase, a thermophile-specific enzyme that catalyzes positive supercoiling in closed circular DNA, fulfills this essential role in the DNA repair pathway.