Nature Structural & Molecular Biology

Ribosome composition can vary through differences in associated proteins, post-transcriptional and post-translational modifications. Such heterogeneity enables ribosomes to respond to environmental1 or pathological2,3 conditions, and modulate localized translation4. A long-standing observation has also been the differential expression of variant ribosomal RNA (rRNA) alleles across developmental5-7 or cellular states8-14. Yet how exchanging the catalytic ribosome core could regulate translational outcomes remains unknown. Here, we report the functional characterization of a genomically-encoded, divergent rRNA that serves as a dominant-negative repressor of translation during host-to-vector transmission in the human malaria parasite. This allele only encodes for large subunit rRNAs, lacks ITS2 splicing, yet retains conserved rRNA modification and folding patterns alongside vast expansion segments. The resulting large subunit engages mRNA at translation start sites but appears to elongate inefficiently, likely due to divergences in the peptidyl transferase center obstructing the exit tunnel. Through its precisely timed transcription immediately after transmission, this rRNA represses mRNAs that were highly translated in the human, facilitating the transition of the translational program for mosquito-stage development. Our data identify a repressive ribosome population whose antagonistic function is encoded by an independently evolved, variant rRNA allele, defining the conceptual foundation for an additional layer of inherent translational regulation.

OLD, an abortive immunity protein from prophage P2, consists of an ABC ATPase sensor and a TO-PRIM nuclease effector - a core architecture shared by a large protein family, including components of anti-phage systems Gabija, PARIS, Septu, and Lamassu. OLD was originally identified for its lethality in recB-deficient cells and inhibition of bacteriophage {lambda} infection, but the mechanisms governing its activation have remained elusive. Here, we present the cryo-EM structure of an inactive OLD tetramer and show that destabilization into dimeric form opens the TOPRIM catalytic site, stimulating tRNA cleavage. This activity arrests translation, a phenotype rescued by phage-encoded tRNAs. We demonstrate that OLD activation is not strictly RecBCD-dependent: OLD binds aberrant DNA structures in recB-deficient cells, but activation during infection requires recognition of single-stranded DNA hairpins at the phage replication origin. Collectively, our findings reveal how host and phage DNA processing factors create a complex landscape controlling OLD-mediated immunity.

Lamina-associated domains (LADs) are large genomic regions that interact with the nuclear lamina (NL). Much of the underlying "grammar" governing their positioning at the nuclear periphery remains unclear. LADs are composed of heterochromatin and typically harbor repressed genes, and their association with the NL is generally incompatible with strong transcriptional activity. The extent to which transcription globally shapes chromatin-NL interactions is not fully understood. Here, we combined acute transcription inhibition using Flavopiridol or Triptolide with genome-wide mapping of chromatin-NL contacts. We found that chromatin-NL interactions are rapidly rewired upon transcription inhibition. Changes in chromatin-NL contacts upon transcription shutdown are predictable based on transcriptional activity and the presence of H3K9me3-marked heterochromatin. This rewiring is reversible, as genome-NL interactions quickly return to baseline levels following drug wash-off. Notably, gain and loss of chromatin-NL interactions upon transcription shutdown reflect two distinct tethering mechanisms. Inter-LADs genomic regions (iLADs) enriched in highly active genes and located near stable LADs, which are tethered by Lamin A (LMNA/C), become re-attached to the NL following transcription inhibition. In parallel, H3K9-methylated regions tethered to the nuclear envelope by the Lamin B receptor (LBR) undergo extensive detachment from the NL. Strikingly, LMNA/C and LBR oppositely regulate transcription-sensitive LADs and are required for transcriptional control of chromatin-NL contacts. Together, our findings highlight the plasticity and dynamic nature of chromatin-NL interactions and provide the first evidence that LMNA/C- and LBR-mediated tethering mechanisms exhibit distinct sensitivities to transcription inhibition. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/738400v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1c35abborg.highwire.dtl.DTLVardef@79c483org.highwire.dtl.DTLVardef@547ce8org.highwire.dtl.DTLVardef@d4790e_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LITranscription inhibition alters chromatin-NL contacts rapidly and reversibly C_LIO_LIActive transcription prevents inter-LADs located near LMNA/C-tethered LADs from associating with the nuclear lamina. C_LIO_LILBR-tethered heterochromatin is repositioned away from the NL C_LIO_LITranscription-dependent modulation of chromatin-NL contacts is dependent on LMNA/C and partially on LBR C_LI

Glutamate dehydrogenase (GDH) is a highly regulated key enzyme that catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate, positioning it at a critical hub linking amino acid catabolism to energy production while supplying ammonia for urea synthesis and other nitrogen pathways. Early investigations have shown that bovine GDH (bGDH), which shares 98% sequence identity with its human homolog, assembles into polymeric filaments with altered allosteric responses. Filamentation has only relatively recently been appreciated as a widespread mechanism of enzyme regulation, prompting a reevaluation of these early observations in GDH. Here, we use high resolution cryogenic electron microscopy (cryo EM) to show that bGDH hexamers assemble via reciprocal antenna interactions that oppose the conformational changes associated with GTP inhibition, revealing how filamentation reshapes GDH allostery and with implications for the treatment of human disease.

Co-transcriptional splicing is a conserved feature of eukaryotic gene expression. However, establishing the functional nature of this process has been difficult. Here using high throughput CRISPR/Cas9 screens we surprisingly find that SF3B3, the third largest subunit of the U2 snRNP complex, is a major regulator of RNA Pol II pause release and processivity. Remarkably, the absence of SF3B3 dramatically perturbs transcription but U2 snRNP assembly and RNA splicing remains unaffected. Mechanistically, SF3B3 coordinates the chromatin occupancy of transcriptional kinases (CDK9/12/13) alongside the PAF1c and Integrator complexes to regulate Pol II. Structure / function analyses of SF3B3 revealed that a metazoan specific 18aa sequence within its disordered tail phenocopies its loss and mediates the physical association and stability of SF3B5. We show that loss of SF3B5 mirrors SF3B3 deficiency suggesting this submodule, although resident within the U2 snRNP complex, evolved to primarily coordinate RNA Pol II in a splicing-independent manner.

PIWI proteins are members of the Argonaute family and together with piRNAs protect metazoan germlines from transposons. PIWI proteins adopt a bi-lobed architecture with a central RNA-binding channel. HSP90 function has been linked to piRNA biogenesis, but the precise molecular mechanism is unresolved. Using the mammalian embryonic piRNA pathway as a model system, we find compelling evidence for the existence of PIWIL2- (MILI-) and PIWIL4- (MIWI2-) HSP90 complexes in foetal testis. We purify apo-PIWIL4-HSP90 from cells and determine its structure by cryo-electron microscopy. Distinct from piRNA-bound PIWI, apo-PIWIL4 adopts a unique and open conformation. The HSP90 dimer binds and unfolds PIWIs linker 1 domain. PIWIL4s N domain and the RNA-binding PAZ-MID-PIWI module are placed on opposite sides of the HSP90 dimers lumen. We further demonstrate that PIWI-HSP90 complexes, the open apo-PIWI conformation, and the HSP90 lumen-binding peptide are conserved features of PIWI proteins.

DNA methylation is an essential epigenetic mark that silences transposable elements (TEs) in mammalian genomes1,2. Following DNA replication, methylation patterns must be faithfully restored3,4, yet how the two processes are coordinated remains unclear. Here, using strand-specific, genome-wide analyses5-7 in mouse embryonic stem cells, we show that DNA methylation maintenance is coupled to the lagging-strand synthesis in TE-rich regions. Paradoxically, despite this targeting, the lagging strand is more permissive for TE integration than the leading strand. Notably, insertions of full-length LINE-1s, SINEs, and satellite repeats are all enriched on the lagging strand over evolutionary time. Consequently, most TEs, particularly young elements, are oriented head-on relative to replication forks in the mouse genome, creating an unfavorable genomic configuration8 that is preferentially targeted by DNA methylation maintenance. Mechanistically, DNA methylation maintenance is coupled to the lagging-strand replication via UHRF1-LIG19 and PCNA-PAF1510 interactions, and the interference in this mechanism slows Okazaki fragment maturation, and thereby potentially may facilitate TE retention. Together, we show a mechanism of TE control during DNA replication with an unexpected evolutionary interplay in which DNA methylation may facilitate, rather than solely prevent, TE expansion.

The histone H3K9 methyltransferase Clr4 is essential for heterochromatin formation in Schizosaccharomyces pombe, yet how it searches for and engages chromatin in vivo remains unclear. Using live-cell single-molecule tracking of PAmCherry-Clr4, we quantified how perturbations to Clr4 alter its diffusion, search behavior, and residence times. Chromodomain and SET-domain Clr4 mutants move faster and more isotropically and have reduced residence times at heterochromatin, reflecting impaired substrate recognition. In contrast, deleting Swi6, which has been proposed to sequester Clr4, does not reduce the slow-state fraction or alter Clr4 diffusion, indicating that chromatin engagement is intrinsic to Clr4 rather than HP1-dependent. Anisotropy analysis at short and intermediate displacements indicates that Clr4 does not explore chromatin by simple three-dimensional diffusion but through a guided, distance-dependent search in which it repeatedly samples nearby nucleosomes before disengaging. Across all other perturbations we examined, such as deletion of the CLRC component Rik1, impaired Clr4 ubiquitination, and using cells with an unmethylatable H3K9R substrate, Clr4 dynamics were only modestly affected, and a chromatin-associated population persisted in every background. This robustness indicates that the chromodomain and SET domains are the primary determinants of how Clr4 engages chromatin in vivo, allowing it to continuously sample the genome while maintaining a stable bound population. Our results suggest how the promiscuous sampling of chromatin may also enable Clr4 to establish novel sites of heterochromatin during adaptation.

Insulin is an essential regulator of glucose homeostasis in vertebrates, and impairment of its synthesis or action leads to diabetes with severe health complications in humans. It is therefore essential to understand how beta cells control insulin synthesis and secretion, including the transcription, translation and decay of its messenger RNA. Using sequencing-based poly(A) tail length profiling from human tissue, genetic evidence for type 2 diabetes, bulk and single-cell transcriptomics and perturbation experiments, here we find that the insulin mRNA is stabilized by the activity of noncanonical poly(A) polymerases of the Tent5 family. We show that Tent5 activity is specific, promoted by both localization at the endoplasmic reticulum and regulatory sequences within the insulin mRNA and regulated by glucose. Overall, our findings provide a mechanistic link between the dynamic control of insulin production by beta cells and the direct regulation of insulin mRNA metabolism.

De novo protein design is advancing rapidly1,2. This is being driven by AI to generate protein backbones, sequences, and structural models3-7. As a result, de novo designed proteins are becoming larger and more complex8-10, and increasingly explore new protein structures11,12. By contrast, natural proteins have evolved structural and functional complexity by modular combination of recurring protein domains13. Approximately 25% of these natural domains are mostly -helical structures14. Here we show how these can be expanded using rational computational design. Following the domain classification scheme CATH15, we build complex all- de novo proteins hierarchically using sequence-to-structure relationships for helix-helix interactions, systematic rules to connect helices, computational tools to design loops, and in silico evaluation. The pipeline starts with a target architecture of free-standing helices. These are connected into a topology by considering local arrangements of helical bundles using understood sequence-to-structure relationships for helix packing. Single-chain sequences are completed using template- and AI-based methods. Finally, AlphaFold models are assessed to give small numbers of designs for experimental validation. We test 31 designs for 14 different architectures and 25 topologies. 75% of these express as stable, monomeric, water-soluble proteins; and >30% yield X-ray crystal structures matching the designs to atomic accuracy and with new-to-nature structures. Finally, several of the scaffolds are functionalised through one-shot designs to deliver ion, small-molecule and protein binders.

The three-dimensional (3D) genome architecture is highly elastic, adapting to nuclear processes such as transcription and the DNA damage response (Dekker & Mirny 2016; Carre-Simon & Fabre 2021). Nucleotide excision repair (NER) acts within this chromatin context to detect and repair mutagenic lesions induced by ultraviolet (UV) irradiation (Sancar 2016). UV irradiation has been shown to induce restructuring of the 3D genome across multiple scales, including chromatin compartments, domains, and loops. However, the extent to which NER activity contributes to this remodelling is unresolved, as the only prior study tracking such UV-induced changes was limited to repair-proficient cells (Kaya & Adebali 2025). Here, by combining genome-wide chromatin profiling of repair-deficient human cells with loop extrusion simulations, we show that lesion-stalled RNA polymerase II (RNAPII) and repair-associated barriers constrain loop extrusion. These events counter the loop-lengthening effects of UV-induced transcriptional shutdown, leading to shorter chromatin loops and reinforced chromatin domains that facilitate efficient lesion recognition and repair. The contribution by NER machinery underscores 3D genome reorganisation as an active mechanism both initiated and harnessed by DNA repair, rather than a passive consequence of DNA damage. The contribution by RNAPII extends its role beyond activating transcription-coupled repair to promoting a genome-wide repair-permissive state. Together, these findings advance our understanding of how nuclear processes coordinate on a shared chromatin substrate to preserve genome integrity.

Mammalian sperm chromatin carries epigenetic information with the potential to influence offspring phenotype, making its faithful characterization essential. It has been suggested that cauda sperm preparations are contaminated by somatic chromatin, that this contamination dominates genome-wide profiles, and that valid results require pretreatment with somatic cell lysis buffer, DNase I, and dithiothreitol. Here we show that properly purified cauda sperm contain no detectable somatic cells or cell-free DNA and that this pretreatment disrupts sperm chromatin organization. SCLB permeabilizes the sperm nucleus, allowing DNase I to fragment the sperm genome in situ, while DTT treatment causes chromatin to leak out of the nucleus. Using ATAC-see, we further demonstrate that Tn5 transposase can access intact protamine-condensed sperm chromatin without DTT, refuting the premise that profiles from untreated sperm reflect contamination. Pretreatment therefore damages the chromatin it claims to purify, and published profiles of untreated cauda sperm are valid and require no systematic re-examination.

Molecular glue degrader EM12-FS covalently modifies cereblon (CRBN) His353, enabling selective recruitment of the neosubstrate NTAQ1 to the CRL4CRBN ubiquitin ligase. We determined the cryo-EM structure of the NTAQ1-EM12-FS-CRBN-DDB1 complex, revealing a non-canonical neosubstrate interface created by covalent remodeling of the CRBN sensor loop. Imidazylation repositions His353 to eliminate the steric clash that prevents NTAQ1 engagement by reversible IMiDs, and the engineered interface is stabilized by a distinctive T-shaped C-H/{pi} interaction between sulfated His353 and NTAQ1 Phe126. Biochemical and mutational analyses define the determinants of ternary complex formation and ubiquitination. These findings show that site-specific synthetic modification of CRBN can reprogram induced-proximity pharmacology, expanding specificity beyond the G-loop degron and establishing a framework for covalent engineering of new degrader modalities.

Neuroendocrine cells communicate with other cells by releasing neurotransmitters or hormones by exocytosis, which involves SNARE-mediated fusion between secretory vesicles and the plasma membranes of the secreting cells. In neurons two plasma membrane SNARE proteins, Syntaxin-1a and SNAP25, join with the vesicle membrane SNARE protein Synaptobrevin-2 to form a four-helix bundle, which drives membrane fusion. The assembly of these SNAREs, which is highly orchestrated in cells, has been intensely studied in solution using fragments of the SNARE proteins without their transmembrane domains or lipid anchors. However, in cell and model membranes, Syntaxin and SNAP25 are known to oligomerize and cluster, and little is known about how clustering affects their incorporation into SNARE complexes. In cells, the SM protein Munc18 has been implicated in aiding secretory vesicle docking and facilitating SNARE complex assembly through its interactions with Syntaxin. To understand how Munc18 orchestrates SNARE complex assembly on membranes, we employed protein reconstitution in model membranes as well as biochemical and biophysical assays to show that lipid-dependent oligomerization of Syntaxin affects Munc18-Syntaxin binding and SNAP25 insertion into the plasma membrane acceptor SNARE complex. We showcase the consequences of the different modes of Munc18-Syntaxin and SNAP25 interaction on Syntaxins oligomerization and orientation relative to the membrane surface, as well as on docking and fusion of purified insulin granules. We also determined low-resolution structures by cryoEM in nanodiscs and on the surface of proteoliposomes of membrane-bound assembly states of Munc18/Syntaxin and Munc18/Syntaxin/SNAP25 complexes.

Human subtelomeres contain duplicated sequence that is shared among the ends of non-homologous chromosomes and provides a substrate for ectopic exchange [1-6]. However, incomplete reference assemblies and chromosome-by-chromosome analyses have prevented a population-scale view of the extent and organization of subtelomeric exchange [7-9]. Here we apply a reference-free pangenome approach to 465 near-complete human assemblies, comparing every chromosome end against every other, and find that high-identity pseudo-homolog regions occur on 41 of 48 chromosome arms. These regions form structured sequence communities in which previously described exchange systems appear as local peaks within a broader continuum. Human and mouse chromosome-contact maps show preferential proximity between subtelomeres with similar sequences. In mouse meiosis this proximity is strongest at the zygotene bouquet, when telomeres cluster at the nuclear envelope; in human data it persists even in adjacent flanks that lack the shared sequence used to define each pair. In a three-generation telomere-to-telomere pedigree, whole-genome comparison identifies putative recombination between subtelomeric regions on non-homologous chromosomes that matches this community organization, while recovering the obligate Xp/Yp PAR1 recombination in the male germline. These results generalize known subtelomeric exchange systems into a near-ubiquitous architecture and support recurrent ectopic exchange as a genome-wide force in the concerted evolution of human chromosome ends.

Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyanobacterial ancestor. In land plants, PEP has roughly doubled in size, expanding into a [~]1 MDa multisubunit machinery through the acquisition of numerous nuclear-encoded subunits. Based on phylogenetic analyses, this added complexity has been widely attributed to the demands of plant terrestrialization. Contrary to this view, we show that in the unicellular green alga Chlamydomonas reinhardtii, PEP assembles into an even larger [~]2 MDa complex containing twelve previously uncharacterized nuclear-encoded subunits (PEPS1-12), representing an RNA polymerase architecture of unprecedented size. A cryo-EM structure at 2.7 [A] resolution reveals that several of these subunits occupy positions analogous to those in land plant PEP, and that metabolic enzyme folds have been repurposed as structural scaffolds stabilizing the highly expanded plastid-encoded core. Despite this, most of the newly identified PEPS subunits lack detectable sequence or structural similarity to their land plant counterparts. These findings demonstrate that PEP complexity is not a hallmark of land plant evolution and may instead reflect, at least in part, the evolutionary entrenchment of additional subunits around an expanded plastid-encoded core. More broadly, they suggest that essential organellar machines can acquire substantial structural complexity that leaves little trace in sequence-based analyses, a pattern consistent with constructive neutral evolution.

Poly (ADP-ribose) Polymerase 1 (PARP1) is an abundant nuclear enzyme that dynamically engages chromatin in diverse cellular scenarios. In the context of DNA repair, PARP1 becomes enzymatically activated and subsequently attaches ADP-ribose units onto various proteins, including histones, to signal and coordinate the DNA damage response. In the absence of DNA damage, PARP1 modulates chromatin structure by directly binding to nucleosomes, however, the molecular basis of this interaction is unknown. Here, we define a distinct, enzymatically inactive mode of PARP1 chromatin binding, in which the Zn1, Zn2, Zn3, and BRCT domains cooperatively bind nucleosomal linker DNA and drive compaction of undamaged chromatin. This binding mode does not trigger catalytic activation and therefore is insensitive to PARP inhibitors (PARPi). Together, our results support a model in which PARP1 associates with the genome in an inactive state to compact chromatin and to surveil for DNA lesions. SummaryPARP1 engages undamaged chromatin in a distinct binding mode that results in chromatin compaction but does not lead to enzymatic activation.

Bitterness is a key taste modality mediated in vertebrates by TAS2R G-protein-coupled receptors, which also function in diverse extraoral tissues. Recent cryo-EM structures have revealed a non-classical intracellular pocket in TAS2R14, raising the question of whether ligand pocket choice can be predicted computationally and what sequence features control it. Here we evaluate the Boltz-2 co-folding framework on all currently available agonist-TAS2R cryo-EM complexes and show that it correctly identifies the experimentally observed binding pocket for 12 of 15 pairs, including intracellular binding that docking into predicted receptor models fails to reproduce. Focusing on aristolochic acid, which binds intracellularly to TAS2R14 and extracellularly to TAS2R43, we use a series of in silico morphing experiments to pinpoint transmembrane helices 3 and 7, and specific residues within them, as key determinants of pocket preference. Extending the analysis to [~]1,500 agonist-receptor associations from BitterDB, we find that while most receptors are predicted to bind agonists predominantly in the extracellular pocket, several TAS2Rs may have both extracellularly and intracellularly binding ligands. Finally, by fine-tuning the Boltz-2 affinity module on [~]7,000 positive and negative experimental data points, we obtain a TAS2R-specific classifier that improves AUROC from 0.54 to 0.82 and average precision from 0.24 to 0.58 on a validation set.

The Ser/Thr kinase ATM orchestrates cellular responses to DNA double-strand breaks (DSBs) and promotes DSB repair by homologous recombination. In this process, ATM is activated by DNA and the MRN (MRE11, RAD50, and NBS1) complex. Here we show that mutations of the conserved PIKK regulatory domain (PRD) within ATMs kinase domain can confer a maximally active state that no longer requires MRN/DNA. In ATM-knockout human cells, the PRD mutants display substantially higher phosphorylation of histone H2AX, KAP1, and CHK2 than wild-type ATM, with or without IR-induced DNA damage. Cryo-EM structures of two PRD mutants each revealed basal or activated conformations depending on bound ligands, suggesting that disrupting the ordered portion of the PRD results in an enzyme poised to transition to the active conformation. However, the identity of the active-site nucleotide is a key driver of the conformational switching. We speculate that this plasticity might be exploited to develop small-molecule ATM modulators for therapeutic applications.

Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection1,2. We previously showed that DRT10, a tripartite system comprising an RT, a noncoding RNA (ncRNA), and a SLATT effector protein, catalyzes protein-primed, tandem-repeat DNA synthesis in a mechanism strikingly analogous to eukaryotic telomerase3. However, the structural basis by which the RT-ncRNA complex directs repeat addition processivity and controls repeat length remains unknown. Here we present cryo-EM reconstructions of two evolutionarily diverse DRT10 RT-ncRNA systems that reveal an unanticipated 2:1 architecture, wherein two RT monomers bind opposite sides of a single, pseudo-symmetric ncRNA. Biochemical experiments demonstrate that each RT monomer reverse transcribes the template encoded on its respective side of the ncRNA, but only one generates the long repetitive product, with the template sequence defined by the distance between two flanking stem-loop anchors. Together with earlier studies of DRT2, DRT3, and DRT94-6, our findings identify a conserved mechanistic logic underlying ncRNA-templated tandem-repeat synthesis across Class 2 UG antiviral systems, despite vastly different architectural solutions.