RMH

RNA-derived 2′,3′-cyclophosphate-terminated nucleotides act as immune signalling molecules in prokaryotes and eukaryotes, but how plants perceive them remains unknown. Sucking insects inject digestive enzymes including RNases into the host plant to acquire nutrients. Here we demonstrate that NIB1, a glycine-rich RNA-binding protein in rice, senses 2′,3′-cyclic nucleotide monophosphates (2′,3′-cNMPs; 2′,3′-cAMP and 2′,3′-cGMP) and adenylyl-(3′→5′)-guanosine 2′,3′-cyclic phosphate (ApG>p) produced by a salivary T2 ribonuclease of green stink bug during feeding. Binding of the RNase products promotes formation of nuclear condensates containing NIB1, which recruit the core immune regulator Enhanced Disease Susceptibility 1 (EDS1) and activate defence, potentially contributing to the immune signalling of Toll/interleukin-1 receptor (TIR) proteins that also produce the nuclease products. Exogenous application of 2′,3′-cAMP, 2′,3′-cGMP or ApG>p elicits NIB1 and EDS1-mediated immune responses. Our findings unveil a conserved pathway in plants, in which glycine-rich RNA-binding proteins perceive the nuclease-generated second messengers to launch defence and point to a potential link between plant TIR nuclease activity and EDS1 signalling. The rice RNA-binding protein NIB1 detects 2′,3′-cyclic nucleotide products from insect saliva RNase, forming nuclear condensates that recruit EDS1 to activate defence, revealing a conserved messenger-based immune pathway in plants.

A key parameter in the experimental design of RNA-seq projects is the choice of sequencing depth. Considering a limited budget, one needs to find a trade-off between the number of samples and the sensitivity of the analysis, particularly concerning lowly expressed genes. While previous studies have proposed a lower bound for the comprehensive analysis of differential gene expression, for the analysis of alternative splicing, it has only been proposed for human adipose tissue. However, alternative splicing differs across tissues and conditions. We analyzed publicly available and newly generated deep-sequenced paired-end RNA-seq samples (between 150 and >500 million reads, read length 50–150 bp) from human buffy coat cells and diverse sets of tissues, including gluteal subcutaneous fat, heart, and hypothalamus. Our results show that the sequencing depth typically used in published cohorts is not sufficient to comprehensively capture the landscape of alternative splicing. This motivates the use of deeper sequencing or long-read technologies in future studies. Toward this goal, we offer guidelines and a website (https://sequencing-depth4splicing.com/) for choosing a suitable sequencing depth.

Proteins often assemble as higher order complexes, underlying a diversity of molecular structures and biological functions. The emergence of protein-protein interactions between binding partners is generally considered to be the primary driver of oligomerization. However, ligand binding has also been demonstrated to affect higher-order assembly, though this phenomenon is not widely considered as a primary driver of oligomerization. Here, we describe the mechanism by which different rubisco oligomeric states are induced via ligand binding. By expanding the phylogenetic sampling of a unique clade of rubisco, we discover a range of oligomeric responses to ligand binding across the phylogeny and identify the structural features responsible for shifts in the oligomeric state that ultimately provide a path to evolving new quaternary structures. Here, we identify a ligand-dependent mechanism giving rise to new protein assemblies, in contrast with the typical process of evolving new protein-protein interfaces directly. Our findings describe a means by which binding and entrenchment of a ligand enables an increase in structural complexity. Proteins often assemble into complexes, and while binding partners typically drive this, ligand binding can too. Here the authors show ligand binding drives distinct rubisco assemblies, revealing an evolutionary path to greater structural complexity.

Bacterial pangenomes provide a shared reservoir of antiphage defenses, yet the ecological and functional constraints shaping this reservoir remain unclear. Here, we combine comparative genomics of 206 Xanthomonas oryzae pv. oryzae (Xoo) genomes with cross-infection assays of 50 strains against 36 phages and heterologous expression of 24 defense systems in a phage-sensitive Xoo chassis. The Xoo pan-defensome comprises a conserved core of 9 subtypes and a variable layer of 35 accessory and cloud subtypes structured by host phylogeography. Phages are more infectious on sympatric than allopatric hosts, consistent with local adaptation. Variable systems show stronger apparent activity than core systems, whereas resistance breadth is not predicted by defense system number. Co-expression of representative co-occurring and mutually exclusive system pairs reveals synergistic and antagonistic interactions underlying non-random repertoire assembly. Together, these findings extend the pan-immunity framework by showing that population-level immune reservoirs are shaped by both ecological structure and functional compatibility. In this study, the authors use comparative genomics and cross-infection assays to show a spatially and evolutionarily structured bacterial immune reservoir in which interactions among defense systems can reinforce or undermine phage resistance, refining the pan-immunity framework.

Transcription factors (TFs) bind specific DNA sequences to control gene expression. Modulating TF activity is of considerable therapeutic interest but very few TFs have been drugged successfully. TF DNA-binding interfaces are large and most TFs have no known allosteric ligands or allosteric sites. Here we introduce TF-MAPs, a scalable and general platform to chart complete functional maps of sequence-specific DNA-binding proteins. We apply TF-MAPS to three human disease TFs: HNF1A, FOXG1 and FOXP1. Allostery in all three proteins is distance-dependent, anisotropic and couples the DNA-binding interface to the protein surface. The allosteric surfaces of FOXG1 and FOXP1 are quite diverged, revealing a potential for protein-specific regulation in protein families. All three TFs have potentially druggable small pockets where mutations affect DNA binding, either within the binding interface or distant from it. Application of TF-MAPS will potentially lead to charting functional and allosteric maps for hundreds of human TFs and other DNA-binding proteins to understand DNA recognition and TF regulation, to interpret clinical variants mechanistically and to guide the development of TF-modulating therapeutics. Li and Lehner present TF-MAPS, a scalable platform to chart functional maps of sequence-specific DNA-binding proteins. The authors map allostery in three transcription factors implicated in human disease and reveal potentially druggable small pockets.

Although antimicrobial resistance (AMR) is traditionally viewed as a consequence of antibiotic selection, growing evidence indicates that bacterial immune systems regulate which mobile genetic elements (MGEs) successfully enter, establish, and persist within bacterial populations. Here, we argue that bacterial immunity helps determine access to the mobile resistome and, consequently, shapes the evolutionary opportunities upon which antibiotic selection acts. This review synthesizes current evidence on the interplay between bacterial immunity, counter-defense mechanisms, and MGE-MGE conflict, highlighting how these interactions collectively influence the entry, survival, expression, persistence, and transmission of foreign DNA. We further discuss recent discoveries revealing a far greater diversity of bacterial defence and MGE counter-defence strategies than previously recognized, including conflicts extending beyond genome protection to the regulation of gene expression, and consider how this expanding molecular repertoire influences MGE accessibility and the mobile genetic variation available for AMR evolution. By integrating concepts that are typically discussed separately, we propose that immunity, counter-defense, and MGE competition collectively regulate access to the vast and largely uncatalogued mobile gene pool from which resistance determinants are acquired. Viewed through this framework, AMR emerges not only from antibiotic selection, but also from the evolutionary processes that determine which genetic variants become available for selection, providing a broader perspective on resistance emergence and the uneven distribution of high-risk resistant lineages.

Pathogen-mediated induced resistance (IR) and beneficial microbe-mediated IR are key for plant survival during pathogen attack, yet how these two forms of IR interact remain unclear. Here, we demonstrate that foliar pathogen-triggered induced resistance (IR) orchestrates the assembly of a specific phyllosphere microbiota that can activate IR. Pathogen-triggered IR caused plant flavonol accumulation, which in turn enriched Aureimonas spp., especially the native A. phyllosphaerae Leaf1, in the phyllosphere endophytic microbiota near infection sites. Genetically impairing the capacity of Leaf1 to utilize flavonols reduced its proliferation during pathogen infection. Moreover, Leaf1 protected plants against leaf disease by activating IR and extended the protective range of pathogen-mediated IR. Importantly, pathogen-mediated IR-induced mobilization of native microbiota represented a common yet underrated component of plant resistance to foliar disease. These findings reveal a plant defense “relay” mechanism, whereby pathogen-mediated IR reassembles a specific microbiota that in turn activates IR to jointly combat further pathogen infection.

MobiDB (https://mobidb.org) integrates structural and functional annotations for intrinsically disordered proteins and regions across UniProtKB. The 2027 release strengthens semantic consistency, programmatic access, and reproducible reuse. A refined controlled vocabulary groups features in a hierarchical way and distinguishes evidence classes and types annotation sources as providers, methods, or aggregation rules. A new versioned REST API, along with a developed MCP server, enables scripts, workflows, and tool-using artificial intelligence systems to retrieve and combine evidence-bearing records through documented operations. The redesigned website applies the same vocabulary to protein entries, documentation, and cross-proteome statistics. Additional developments include standardized Nextflow production workflows, updated RING Protein Data Bank interaction processing, integration of Motif Map of the Proteome and Linear Motif mediated Protein–Protein Interaction Database annotations, and a release-aware catalogue of static datasets for large-scale analysis. Following the recent increase in reference proteomes in UniProtKB, MobiDB now provides a more representative estimate of long-disorder with a median residue coverage of 12.3% in eukaryotes, 1.9% in archaea, 1.7% in bacteria, and 3.4% in viruses; and protein prevalence of 48.7%, 11.9%, 11.2%, and 25.0%, respectively. Together, these developments make disorder knowledge easier to discover, relate to function, and reuse with explicit provenance.