Active Site Assembly by SMG5 as a Mechanism for SMG6 Endonuclease Licencing in Nonsense-mediated mRNA Decay

Enes S Arpa  ¹ , Michael Taschner  ² , Mara De Matos  ³ , Stefanie Jonas  ⁴ , David Gatfield  ⁵

Affiliations

• PMID: 41763597
• DOI: 10.1016/j.jmb.2026.169734

Free article

Abstract

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway that eliminates transcripts containing premature termination codons (PTCs). Substantial progress has been made in defining the transcript features that mark aberrant translation termination for NMD activation, yet key mechanistic steps remain incompletely understood – including how recruitment of the central NMD factor UPF1 is coupled to the downstream effector phase in which targeted mRNAs are nucleolytically degraded. In metazoans, NMD employs an endonucleolytic route mediated by SMG6, a PIN-domain nuclease, alongside SMG5 and SMG7, which act downstream of PTC recognition. SMG5 has recently been proposed to licence SMG6 activity, yet the molecular basis of this licencing has remained elusive. Here, we combine AlphaFold structural predictions with biochemical assays to investigate interactions among human SMG5, SMG6, and SMG7. Structural models predict a high-confidence interface between SMG5 and SMG6 PIN domains that forms a composite active site: a conserved SMG5 aspartate (D893) complements the SMG6 acidic triad to reinstate the canonical tetrad required for PIN-domain catalysis. In vitro, SMG6 alone exhibits weak endonucleolytic activity, which is enhanced ∼10-fold by the SMG5 PIN domain. Mutational analyses confirm that conserved residues from both proteins are essential for this composite configuration. Our findings reveal that the SMG5 PIN domain, previously considered catalytically inert, plays a critical role in activating SMG6 by completing its active site. This work provides mechanistic insight into the SMG5-dependent licencing step and uncovers a composite PIN nuclease architecture at the heart of the metazoan NMD effector phase.

Genome-wide association studies identify new candidate genes and tissues underlying resistance to a natural toxin in drosophilids.

Michele Marconcini  ¹ , Caroline Fragnière  ¹ , Ambra Masuzzo  ¹ , Richard Benton  ¹

• PMID: 41692494
• DOI: 10.1093/g3journal/jkag032

Abstract

Many insects can rapidly evolve resistance to artificial insecticides through changes in toxin target proteins. Over longer timescales, insects also evolve resistance to naturally occurring toxins to exploit new ecological niches, but the underlying mechanisms often remain poorly understood. A classic example is Drosophila sechellia, an extreme specialist for the ripe noni fruit of Morinda citrifolia. Noni is toxic for other insects – including D. sechellia’s close relatives D. simulans and D. melanogaster – due to this fruit’s high content of octanoic acid (OA). However, the mechanistic bases of OA susceptibility and resistance across species remain unclear. Here, we first show that the species-specific tolerance of OA is independent of these drosophilids’ distinct microbiomes. Screening large, genetically-diverse panels of D. melanogaster and D. simulans strains revealed broad variation in OA resistance, with some lines surviving as well as D. sechellia. Resistance to OA does not correlate with resistance of these lines to other insecticides, implying a distinct toxicity mode-of-action. Genome-wide association and transcriptome-to-phenotype analyses identified multiple genes linked to OA resistance, with diverse expression patterns and functions, including epithelial septate junction formation, and lipid transport. Loss-of-function analysis in D. melanogaster confirmed that at least two of these – Bez, a CD36-family fatty acid transporter, and CG13003, a putative extracellular matrix component – positively contribute to OA resistance. Integration of our findings with those from previous complementary genetic approaches supports a model in which OA has no singular target, and that resistance is defined by multigenic and multi-tissue defense mechanisms.

Ancient co-option of LTR retrotransposons as yeast centromeres.

Max A B Haase  ^{1   2} , Luciana Lazar-Stefanita  ³ , Lyam Baudry  ⁴ , Aleksandra Wudzinska  ³ , Xiaofan Zhou  ⁵ , Antonis Rokas  ⁶ , Chris Todd Hittinger  ⁷ , Boris Pfander  ⁸ , Andrea Musacchio  ^{9   10} , Jef D Boeke  ^{11   12   13}

• PMID: 41708848
• DOI: 10.1038/s41586-025-10092-0

Abstract

Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear^1-4. The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres^1,5. How this transition occurred has remained unresolved⁶. Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis-elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

• Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion
• Meltem Weger  ¹ , Daniel Mauvoisin  ^{2   3} , Dominic Hoyle  ¹ , Jingkui Wang  ^{4   5} , Eva Martin  ^{2   4} , James Rae  ¹ , Charles Ferguson  ¹ , Glynis Klinke  ⁶ , Michelle Cielesh  ⁷ , Kyle L Macauslane  ⁸ , Mark Larance  ⁷ , Manfredo Quadroni  ⁹ , Iain Templeman  ¹⁰ , Jean-Philippe Walhin  ¹⁰ , Leonidas G Karagounis  ^{2   11   12} , James A Betts  ¹⁰ , Jonathan D Johnston  ¹³ , Fanny Durussel  ¹⁴ , Dmitri Firsov  ¹⁴ , Stephane Fournier  ^{15   16} , Olivier Müller  ^{15   16} , Benjamin L Schulz  ⁸ , Robert G Parton  ^{1   17} , Benjamin D Weger  ^{18   19} , Frédéric Gachon  ^{20   21   22   23}
• Affiliations
• PMID: 41644694
• DOI: 10.1038/s42255-026-01453-8
• Abstract
• The liver has a key role in inter-organ communication by secreting most circulating plasma proteins. However, the mechanisms governing hepatic protein secretion remain unclear. Here we show that hepatic protein secretion follows a diurnal rhythm regulated by food intake in humans and mice. Using liver microsomal proteomics, we find that proteins implicated in the early secretory pathway, such as protein glycosylation and folding in the endoplasmic reticulum (ER) and Golgi apparatus, exhibit a rhythmic expression profile, which is abolished in Bmal1-knockout mice. Mechanistically, we show that hepatic glycogenolysis provides substrates for protein N-glycosylation. In mice, perturbing hepatic glycogenolysis with pharmacological or nutritional interventions leads to ER stress and attenuates diurnal protein secretion. We confirm these results in humans, as genetic variants associated with glycogen storage disease and congenital disorders of glycosylation also alter hepatic protein secretion. Overall, our work uncovers hepatic glycogen metabolism as a circadian regulator of protein secretion.

Mendelian randomization linking metabolites with enzymes reveals pathway regulation and therapeutic avenues

Adriaan van der Graaf  ¹ , Sadegh Rizi  ² , Chiara Auwerx  ³ , Zoltán Kutalik  ⁴

Affiliations

• PMID: 41650937
• DOI: 10.1016/j.ajhg.2025.12.013

Abstract

Reactions between metabolites are catalyzed by enzymes. These biochemical reactions form complex metabolic networks, which are only partially characterized in humans and whose regulation remains poorly understood. Here, we assess human biochemical reactions and regulation using Mendelian randomization (MR), a genetic observational causal inference technique, to understand the methods’ strengths and weaknesses in identifying metabolic reactions and regulation. We combine four metabolite and two protein quantitative trait locus (QTL) studies to determine how well MR recovers 945 curated canonical enzyme-substrate/product relationships. Using genetic variants from an enzyme’s transcribed (cis) region as instrumental variables, MR-inferred estimates have high precision (35%-47%) but low recall (3.2%-4.6%) for identifying the substrates and products of an enzyme. Testing reverse causality from metabolites to enzymes using genome-wide instruments yields lower precision (1.8%-8.5%) and recall (1.0%-1.9%) due to an increased multiple-testing burden. Literature review of 106 Bonferroni-significant results identifies 45 links (43%) confirmed by different degrees of evidence, including bidirectional links between linoleate and cytochrome P450 3A4 (CYP3A4) levels (p = 8.6 × 10^-32). Eleven enzymes in the 106 links involve drug targets, allowing for an interpretation between N-acetyl putrescine and IL1RAP (p = 2.7 × 10^-7), as IL1RAP is a target of the psoriasis drug spesolimab, and putrescine levels are elevated in psoriatic tissues. This work highlights how MR can be leveraged to explore human metabolic regulation and identify both canonical reactions and previously unknown regulation.

The HCF-1:OGT axis regulates neuronal proliferation and differentiation

Ayushma  ¹ , Priyanka Prakash Srivastava  ¹ , Shruti Kaushal  ² , Jaspreet K Dhanjal  ² , Vaibhav Kapuria  ³ , Shilpi Minocha  ⁴

Affiliations

• PMID: 41651253
• DOI: 10.1016/j.nbd.2026.107308

Free article

Abstract

Neuronal differentiation requires precise coordination of progenitor proliferation, lineage commitment, and chromatin regulation to establish functional brain architecture. Host Cell Factor-1 (HCF-1), an X-linked transcriptional co-regulator linked to human intellectual disability, is essential for early development, yet its lineage-specific roles during mammalian neurogenesis remain incompletely defined. Here, we investigate the function of the HCF-1-OGT axis during neuronal differentiation and forebrain development. Early embryonic loss of HCF-1 resulted in developmental arrest due to gastrulation defects, while conditional deletion in Nkx2.1-derived neuronal lineages caused pronounced cortical disorganization, reduced GABAergic interneuron survival, and severe defects in forebrain commissures, including the corpus callosum and anterior commissure. These abnormalities were not observed following glial-restricted deletion, indicating a neuron-specific requirement for HCF-1. Neuronal ablation alone did not phenocopy these defects; however, combined neuronal ablation and HCF-1 loss exacerbated cortical and commissural abnormalities, revealing increased neuronal vulnerability. Transcriptomic profiling following HCF-1 depletion identified widespread dysregulation of gene networks associated with neuronal differentiation, synaptic organization, chromatin regulation, and axon guidance. Consistently, HCF-1 directly occupied promoters of key neuronal genes, including Elavl3 and NeuroD1, and its loss reduced activating chromatin marks at these loci. In vitro, depletion of HCF-1 or inhibition of OGT impaired neuronal proliferation, differentiation, and neurite outgrowth. Glycoproteomic analysis further revealed disruption of OGT-dependent protein networks involved in neuronal structure and maturation. Together, these findings identify HCF-1 as a central regulator of neuronal differentiation and forebrain organization and provide mechanistic insight into how disruption of the HCF-1-OGT axis contributes to neurodevelopmental disorders.