Quiescence is a cellular state defined by reversible cell-cycle arrest and diminished biosynthesis, particularly of nucleic acids and proteins. These features protect stem cells from proliferation-induced mutations, self...Quiescence is a cellular state defined by reversible cell-cycle arrest and diminished biosynthesis, particularly of nucleic acids and proteins. These features protect stem cells from proliferation-induced mutations, self-renewal exhaustion, and environmental insults. Despite relevance to development, tissue homeostasis and cancer, we lack understanding about many aspects of quiescence regulation and unique molecular markers for this state. Here, we employ Drosophila and mammalian neural stem cells to reveal that a mechanism for inhibiting translation in quiescence is selective nuclear enrichment of transcripts from more than 2000 genes, resulting in uncoupling between transcriptome and proteome. Three-quarters of these transcripts become increasingly nuclear as quiescence deepens, and nuclear bias predicts protein downregulation for the large majority of targets. We find that a large fraction of nuclear-biased transcripts present GA-rich multivalency and relocalise to nuclear speckles with increased SR-protein enrichment, which we propose promotes their nuclear retention. Finally, our evidence for differing degrees of transcript processing in steady-state quiescence suggests regulated sequential deployment of factors towards cell-cycle reentry. In brief, we present a previously unappreciated layer of post-transcriptional control of quiescence.
Blebs are membrane protrusions formed when localized regions of the plasma membrane detach from the actin cortex, enabling outward expansion driven by intracellular pressure. These structures play critical roles in cell...Blebs are membrane protrusions formed when localized regions of the plasma membrane detach from the actin cortex, enabling outward expansion driven by intracellular pressure. These structures play critical roles in cell migration and proliferation. While cortical actin contraction has been proposed as the primary driver of cytoplasmic fluid influx during bleb expansion, our prior observations revealed compartmentalization of Ca²⁺ ions and specific proteins (e.g., Mena) within expanding blebs. The functional significance of these components remained unresolved. In this study, we demonstrate that elevated Ca²⁺ levels during bleb expansion induce the assembly of a protein superstructure built around the CaMKII holoenzyme, incorporating Mena and other regulatory proteins. This complex exhibits intrinsic osmotic activity, facilitating water influx and directly contributing to bleb expansion. These findings elucidate a novel mechanism underlying bleb expansion and provide new insights into the dynamic regulation of physicochemical properties of the cytoplasm.
The distribution of N-methyladenosine (mA) controls its substrate RNA fate, playing key roles in various biological processes. However, the mechanism underlying site-selective mA deposition of RNAs, especially in the sta...The distribution of N-methyladenosine (mA) controls its substrate RNA fate, playing key roles in various biological processes. However, the mechanism underlying site-selective mA deposition of RNAs, especially in the start codon regions, and the role in epigenetic information transduction connecting tumorigenesis remain largely unknown. Here, we identified RBM15B mainly modulates mA modifications in the 5'untranslated regions (UTRs) and around the start codons of mRNAs transcribed. This process is guided by H3K79me2 histone methylation, a critical epigenetic modification in mixed lineage leukemia. We show that the H47 of RBM15B is a key residue for the recognition of H3K79me2. The selective mA modification orchestrated by the H3K79me2-RBM15B axis enhances translation efficiency of oncogenic transcripts, and promotes self-renewal of leukemic stem cells and leukemia maintenance. We further demonstrate that blockade of the H3K79me2-RBM15B-mA axis inhibits the survival of leukemia cells and promotes cell differentiation, and impairs hematological malignancies. This study uncovers a novel selective mA deposition mechanism mediated by H3K79me2 and RBM15B, highlighting promising therapeutic targets for hematological malignancies.
Gil J, Navarrete E, Hockens C
… +10 more, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Banigan EJ, Rosin LF, Mirny LA, Muller H, Drinnenberg IA
Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in model organisms, and...Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. In polymer simulations, this contact pattern can only be explained by high loop extrusion activity within compartment S, combined with low extrusion elsewhere throughout the genome. This proposed targeting of loop extrusion is a novel phenomenon, not observed in vertebrate models, but we speculate may extend to more organisms, such as other insects. Overall, our study underscores how evolutionarily conserved mechanisms-compartmentalization and loop extrusion-can be repurposed to create new 3D genome architectures.
Seed germination is orchestrated by antagonistic gibberellin (GA) and abscisic acid (ABA) signals converging on the master germination repressor RGL2. Here, we unveil a receptor-competition paradigm where ABA receptors (...Seed germination is orchestrated by antagonistic gibberellin (GA) and abscisic acid (ABA) signals converging on the master germination repressor RGL2. Here, we unveil a receptor-competition paradigm where ABA receptors (PYLs) stabilize RGL2, both through direct physical interaction and through functional sequestration of DWA1, the CUL4-DDB1 E3 ligase substrate adapter mediating RGL2 ubiquitination. GA receptors (GID1s) counteract this stabilization by competitively displacing PYLs from RGL2, leveraging their superior binding capacity to license DWA1-mediated degradation. Crucially, this competition is defined by the concentration of abscisic acid and gibberellin as they regulate PYL and GID1 expression. Genetic epistasis confirms that PYLs act upstream of DWA1, competing directly with GID1 at RGL2. This receptor-occupied switch converts environmental fluctuations into proteolytic decisions: transient stress imposes a reversible "pause state" through PYL dominance, while sustained GA biosynthesis permits germination via GID1-mediated degradation. Our work establishes direct receptor competition as a complementary layer to hormone crosstalk, providing a universal framework for signal-driven developmental transitions.
The histone H3 variant CENP-A is considered an epigenetic landmark of centromeres. Its deposition reflects cell-cycle-regulated assembly of M18BP1, HJURP, and PLK1 on a divalent MIS18α/β scaffold. The localization determ...The histone H3 variant CENP-A is considered an epigenetic landmark of centromeres. Its deposition reflects cell-cycle-regulated assembly of M18BP1, HJURP, and PLK1 on a divalent MIS18α/β scaffold. The localization determinants of this machinery remain poorly characterized. Here, we report that in human cells, artificial M18BP1 dimerization bypasses MIS18α/β, allowing the identification of at least four determinants of M18BP1 centromere localization. These include the SANTA domain, of which we report the first structure, as well as linear motifs in disordered neighboring regions, of which we characterize the interaction footprint on the CENP-A-associated 16-subunit constitutive centromere-associated network (CCAN). Our observations imply that M18BP1, after dimerization, is necessary and sufficient for centromere localization. Its cell-cycle-dependent dimerization on MIS18α/β promotes initial recognition of a multivalent centromeric assembly of old CENP-A and associated proteins, followed by cooption of PLK1 and HJURP and new CENP-A deposition. Our results shed new light on the determinants of centromere epigenetic inheritance in humans.
Crop quality arises from the interplay of genetics and environment. While moderate salt stress is known to enhance fruit sweetness, the underlying molecular mechanisms remain unclear. Using tomato (Solanum lycopersicum)...Crop quality arises from the interplay of genetics and environment. While moderate salt stress is known to enhance fruit sweetness, the underlying molecular mechanisms remain unclear. Using tomato (Solanum lycopersicum) as a model, this study investigates how salt stress promotes fruit sugar accumulation. Root-derived abscisic acid (ABA) transport to fruit acts as the key signal under salt stress. Elevated fruit-ABA activates the kinase SlSnRK2.6, which phosphorylates the SlZHD8 transcription factor. This phosphorylation inhibits SlZHD8 function by reducing its protein stability and DNA-binding, thereby relieving its repression of SlSUS3 and SlSWEET12 to enhance fruit-sugar accumulation. Furthermore, the SlSnRK2.6-SlZHD8-SlSWEET12 module also regulates root-sugar accumulation and confers salt tolerance. Evolutionary analysis revealed a beneficial ZHD8 haplotype, whose reduced promoter-binding affinity promotes fruit-sugar accumulation under normal conditions and enhances salt tolerance. These findings explain how stress enhances quality and highlight the potential of key mutations of ZHD8, particularly the beneficial haplotype, for breeding tomatoes with improved sugar content and salt tolerance.
Horizontal gene transfer (HGT) is an important source of gene innovation in prokaryotic and eukaryotic organisms. Several genes acquired by hosts of parasitoid wasps via HGT have been reported to protect hosts from paras...Horizontal gene transfer (HGT) is an important source of gene innovation in prokaryotic and eukaryotic organisms. Several genes acquired by hosts of parasitoid wasps via HGT have been reported to protect hosts from parasitoid wasps. In contrast, little is known about whether HGT-acquired genes in parasitoid wasps are involved in attacking their hosts. Here, we report a prokaryote-type CDP-diacylglycerol synthase (PTCDS) gene that was horizontally transferred into the last common ancestor of two parasitoid wasps, Leptopilina heterotoma and L. syphax, from the bacterial family Rickettsiaceae. We experimentally demonstrated that PTCDS is linked to ensure the appropriate storage amount of venom in the venom reservoir of parasitoid wasps. PTCDS knockdown downregulated the expression of certain vesicle-mediated transport genes, thereby reducing the secretion of venom into venom reservoir without altering its composition. This resulted in a significant increase in the proportion of encapsulated wasp eggs in parasitized hosts, ultimately leading to host immune-mediated killing. We conclude that parasitoid wasps use the foreign gene PTCDS to influence venom amounts against host defence, providing new insight into the arms race between parasitoid wasps and hosts.
Activation of PLK1, a master mitotic kinase, requires phosphorylation of its activation segment on Thr210, within a basic consensus sequence for Aurora kinases. Aurora B-dependent phosphorylation of Thr210 has been repor...Activation of PLK1, a master mitotic kinase, requires phosphorylation of its activation segment on Thr210, within a basic consensus sequence for Aurora kinases. Aurora B-dependent phosphorylation of Thr210 has been reported, but other evidence identified a strict requirement for the Aurora A partner Bora for Thr210 phosphorylation. Here, we investigate the elusive mechanistic basis for this requirement. We show that Aurora A:Bora phosphorylates Thr210 of PLK1 in vitro. On the contrary, T210 was not phosphorylated by isolated Aurora A, additional Aurora A:activator complexes, or Aurora B:INCENP, even when used at high kinase/substrate ratios. A transient interaction of Bora and PLK1, identified by structural modeling and probed mutationally, is uniquely required for Thr210 phosphorylation. Dependency on Bora for Thr210 phosphorylation is eliminated after mutating Lys208, in the Aurora consensus, into arginine. This conservative mutation turns PLK1 into a substrate of nearly all tested active Aurora kinases, including Aurora B. Collectively, these results shine a new light on the specificity of the PLK1 activation mechanism.
The evolutionarily conserved, intrinsically disordered protein Bora is critical for initiating the activation of mitotic kinases. Once phosphorylated at Ser112 by Cyclin A-Cdk1 kinase, phospho-Bora activates unphosphoryl...The evolutionarily conserved, intrinsically disordered protein Bora is critical for initiating the activation of mitotic kinases. Once phosphorylated at Ser112 by Cyclin A-Cdk1 kinase, phospho-Bora activates unphosphorylated Aurora A kinase (AURKA), directing it towards Polo-like kinase 1 (Plk1), thus promoting Cyclin B-Cdk1 activation and mitotic entry. Here, by combining structural modeling and in vitro assays, we provide evidence that Bora wraps around the N-terminal lobe of AURKA to position its phospho-Ser112 near AURKA's T-loop, mimicking T-loop phosphorylation. Additionally, Bora transiently interacts with the αC helix of the Plk1 kinase domain through a conserved motif, guiding AURKA activity towards the Plk1 T-loop, which is otherwise impervious to phosphorylation by AURKA. We highlight the importance of this motif for Bora function in vitro and during mitotic entry in Xenopus laevis egg extracts. Our results reveal critical molecular details of mitotic kinase activation, which could lead to the development of pathway-specific inhibitors.
Cell division involves the complete reorganization of the cellular architecture, requiring precise coordination of cellular processes in space and time, but how does this control system work at the atomic level? Three ne...Cell division involves the complete reorganization of the cellular architecture, requiring precise coordination of cellular processes in space and time, but how does this control system work at the atomic level? Three new studies offer a glimpse under the hood, revealing structural details of the intricate interactions between Aurora A and PLK1 kinases and the co-factor Bora, and how they act together to trigger timely entry to mitosis.
Proper oogenesis requires a programmed transition from an undifferentiated germ-cell gene expression program to a maternal gene-expression state. While this process depends on the heterochromatin-mediated silencing of ge...Proper oogenesis requires a programmed transition from an undifferentiated germ-cell gene expression program to a maternal gene-expression state. While this process depends on the heterochromatin-mediated silencing of germ-cell genes, the upstream mechanisms that enforce this transcriptional shift remain unclear. Here, we uncover a translation-driven chromatin remodeling program that promotes oocyte fate in Drosophila. Through a loss of function screen, we identify TORC1 activity (Mio, Raptor), ribosome biogenesis (Zfrp8, Bystin, Aramis), and a translation factor (eEF1α1) as essential for silencing the germ-cell program. We show that TORC1 activity increases during oocyte specification, and that disruption of TORC1 activity, translation, or ribosome biogenesis during this window impairs heterochromatin maintenance at germ-cell gene loci. Polysome profiling reveals that Zfrp8 promotes translation of the nuclear pore component Nucleoporin 44A (Nup44A), whose function is independently required for chromatin organization and repression of a cohort of germ-cell genes. Taken together, our findings reveal that a transient increase in translation orchestrates chromatin remodeling to ensure commitment to oocyte fate.
Lysosomes are emerging as important signaling hubs for antiviral defense, yet how they enable type I interferon (IFN-β) production is unclear. Here, we identify an evolutionarily repurposed lysosomal pathway, centered on...Lysosomes are emerging as important signaling hubs for antiviral defense, yet how they enable type I interferon (IFN-β) production is unclear. Here, we identify an evolutionarily repurposed lysosomal pathway, centered on the LAMTOR-Rag GTPase complex, that governs IFN-β production through dual transcriptional and post-transcriptional regulation. Genetic ablation of LAMTOR or Rag GTPases in macrophages abolishes IFN-β responses despite intact pattern recognition receptor (PRR) signaling, uncovering a lysosome-specific checkpoint essential for antiviral immunity. Mechanistically, Rag GTPase activity controls IRF expression to prime IFN transcription, while upon PRR stimulation, the tumor suppressor FLCN recruits p38 MAPK to lysosomes, where Rag-dependent p38 phosphorylation stabilizes Ifnb1 mRNA. Nutrient availability dynamically modulates Rag nucleotide states and thereby its activation, linking IFN production to metabolic capacity. Notably, this checkpoint operates independently of mTORC1, illustrating how an ancient nutrient-sensing module has been co-opted for immune regulation. Disruption of the LAMTOR-Rag-FLCN-p38 axis impairs IFN induction in vitro and antiviral responses in vivo, underscoring its physiological significance. Our findings support the role of the lysosome as a central signaling hub integrating metabolic and immune cues, suggesting future directions for potential therapeutic strategies against viral infections.
The innate immune system is known for its ability to recognize cytosolic DNA as evidence of infection, but detailed studies of this process have been mostly limited to mice and cell lines. To investigate inflammasome res...The innate immune system is known for its ability to recognize cytosolic DNA as evidence of infection, but detailed studies of this process have been mostly limited to mice and cell lines. To investigate inflammasome responses in human primary cells, we used engineered viruses encoding the inflammasome reporter caspase-1-EGFP. We show that released genomes of vaccinia virus and monkeypox virus trigger robust inflammasome assembly in human primary cells. To determine the involved inflammasome sensors, we generated nanobodies against AIM2. Three of them inhibit AIM2 inflammasome assembly by blocking the polymerization of the AIM2 Pyrin domain, most potently as bivalent nanobodies. Utilizing an engineered vaccinia virus expressing bivalent AIM2 nanobodies, we demonstrate that inflammasomes in primary human macrophages and keratinocytes are nucleated by AIM2, while CD14 monocytes assemble NLRP3 inflammasomes. This finding resolves the discrepancy between the previously reported activation of AIM2 inflammasomes in mice and NLRP3 inflammasomes in humans, and provides the first evidence for cell-type-specific regulation of DNA-triggered inflammasome activation. The newly developed AIM2-specific nanobodies offer a precise tool to dissect and potentially target AIM2 inflammasome assembly in other disease contexts.
Shi J, Zhang X, Cai C
… +22 more, Liu S, Yu J, James ER, Liu L, Emery BR, McMurray Bires MR, Torres-Arce E, Rawal HC, Ramsay J, Kunisaki J, Zhou C, Milstone DS, Patti ME, Yang X, Jenkins TG, Quinlan A, Cairns BR, Schimmel P, Hotaling JM, Aston KI, Zhou T, Chen Q
Sperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. However, the molecular determinants of sperm fitness during aging remain ill-d...Sperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. However, the molecular determinants of sperm fitness during aging remain ill-defined. Here, we profiled sperm small non-coding RNAs (sncRNAs) using PANDORA-seq, which overcomes RNA modification-induced detection bias to capture previously undetectable sncRNA species associated with mouse and human spermatozoa throughout the lifespan. We identified an "aging cliff" in mouse sperm RNA profiles-a sharp age-specific transition marked by significant shifts in genomic and mitochondrial tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs). Notably, rsRNAs in mouse sperm heads exhibited a transformative length shift, with longer rsRNAs increasing and shorter ones decreasing with age, suggesting altered biogenesis or processing with age. Remarkably, this sperm head-specific shift in rsRNA length was consistently observed in two independent human aging cohorts. Moreover, transfecting a combination of tsRNAs and rsRNAs resembling the RNA species in aged sperm was able to induce transcriptomic changes in mouse embryonic stem cells, impacting metabolism and neurodegeneration pathways, mirroring the phenotypes observed in offspring fathered by aged sperm. These findings provide novel insights into longitudinal dynamics of sncRNAs during sperm aging, highlighting an rsRNA length shift conserved in mice and humans.
Alternative splicing (AS) is a key mechanism for generating regulatory and phenotypic diversity in multicellular eukaryotes. Large-scale comparative transcriptomic studies have revealed that AS leads to lineage-specific...Alternative splicing (AS) is a key mechanism for generating regulatory and phenotypic diversity in multicellular eukaryotes. Large-scale comparative transcriptomic studies have revealed that AS leads to lineage-specific and tissue-specific transcriptomic and proteomic changes, underscoring its contribution to the evolution of gene products and functions. In this review, we highlight the patterns and mechanisms of AS evolution across species, exploring how technological advancements are transforming our understanding of splicing evolution. Furthermore, we discuss mechanistic and functional insights from recent studies, including groundbreaking discoveries on how AS has shaped phenotypic evolution in mammals.
Autophagy requires precise regulation of autophagosome-lysosome fusion, yet the molecular details of this process remain incompletely understood. Here, we identify the class V myosin MYO5A as a critical regulator of auto...Autophagy requires precise regulation of autophagosome-lysosome fusion, yet the molecular details of this process remain incompletely understood. Here, we identify the class V myosin MYO5A as a critical regulator of autophagic flux. The genetic or pharmacological inhibition of MYO5A in Saccharomyces cerevisiae, mammalian cells, or Caenorhabditis elegans blocked autophagic flux by preventing autophagosome-lysosome fusion. MYO5A facilitates the maturation of autophagosomes into fusion-competent intermediates as its loss altered the localization of fusion machinery on autophagosomes and reduced the pool of stationary autophagosomes, a step that proved critical for subsequent fusion with lysosomes. Domain mapping and targeted mutagenesis revealed that two LIR motifs (PAYRVL and QAYIGL) within the coiled-coil and globular tail domains of MYO5A mediate its direct interaction with LC3 on autophagosomes. Live imaging in mammalian cells and C. elegans added support for this role, revealing how MYO5A regulates autophagic flux to ensure fusion. Together, these findings establish MYO5A as a regulator of autophagy and highlight its potential as a target for fine-tuning autophagic flux.
How animals evolved from their unicellular ancestor is a fundamental biological question. The fact that all animals are monophyletic-sharing a single common ancestor-implies their origin from unicellular eukaryotes was l...How animals evolved from their unicellular ancestor is a fundamental biological question. The fact that all animals are monophyletic-sharing a single common ancestor-implies their origin from unicellular eukaryotes was likely driven by rare and highly advantageous innovations. While the fossil record and initial genomic comparisons suggested animals originated by the rapid acquisition of many novel genes, new research on animal's closest unicellular relatives reveals most of those genes originated before animals evolved. Here we present a new model for animal origins, which shares similarities with the origin of one of the greatest technological innovations of our time: the smartphone. We show that the origin of both animals and smartphones was due to the integration and repurposing of pre-existing components driven by a novel "operating system", rather than the sudden emergence of many new parts. This model offers testable predictions and a new theoretical framework for understanding complex biological innovation.
Cancer does not simply develop unchecked-it strategically exploits its host with parasitic precision. From immune evasion to tissue remodeling, cancer cells mirror the survival strategies of parasitic helminths. This res...Cancer does not simply develop unchecked-it strategically exploits its host with parasitic precision. From immune evasion to tissue remodeling, cancer cells mirror the survival strategies of parasitic helminths. This resemblance suggests that malignant cells have co-opted deeply conserved, evolutionarily honed tactics used by parasites to persist within their hosts. By mimicking helminths, cancer cells may also engage type-2 immune responses, traditionally associated with anti-parasitic defense, as part of the host's attempt to control their expansion. Such parallels could also help explain why type-2 immunity, once considered tumor-promoting, has recently emerged as a potential source of tumoricidal activity. In this Perspective, we explore mechanistic parallels between cancer and helminth infection. Recognizing the parasitic nature of cancer cells not only challenges established models of oncogenesis but also reveals mechanisms that could be leveraged for therapy.
Pseudomonas putida is a plant-beneficial rhizobacterium that encodes multiple type-VI secretion systems (T6SS) to outcompete phytopathogens in the rhizosphere. Among its antibacterial effectors, Tke5 (a member of the BTH...Pseudomonas putida is a plant-beneficial rhizobacterium that encodes multiple type-VI secretion systems (T6SS) to outcompete phytopathogens in the rhizosphere. Among its antibacterial effectors, Tke5 (a member of the BTH_I2691 protein family) is a potent pore-forming toxin that disrupts ion homeostasis without causing considerable membrane damage. Tke5 harbours an N-terminal MIX domain, which is required for T6SS-dependent secretion in other systems. Many MIX domain-containing effectors require T6SS adaptor proteins (Tap) for secretion, but their molecular mechanisms of adaptor-effector binding remain elusive. Here, we report the 2.8 Å cryo-EM structure of the Tap3-Tke5 complex of P. putida strain KT2440, providing structural and functional insights into how effector Tke5 is recruited by its cognate adaptor protein Tap3. Functional dissection shows that the α-helical region of Tke5 is sufficient to kill intoxicated bacteria, while its β-rich region likely contributes to target membrane specificity. These findings delineate a mechanism of BTH_I2691 proteins for Tap recruitment and toxin activity, contributing to our understanding of a widespread yet understudied toxin family.