EMBO Journal最新文献

Dimethylsulfoniopropionate (DMSP) catabolism by marine Roseobacters is important for global biogeochemical cycling and the climate. Many Roseobacters contain competing DMSP demethylation and cleavage pathways, but only cleavage produces the climate-cooling gas dimethylsulfide. Here, we identify the "switch" regulator in Roseobacters, DmdR, which transcriptionally represses demethylation (dmdA, encoding DMSP demethylase), cleavage (acuI, encoding acryloyl-CoA reductase) and oxidative stress protection (dmdEF, dinB) genes under low intracellular DMSP levels. Increased DMSP levels lead to DMSP cleavage and accumulation of cytotoxic cleavage product acryloyl-CoA. Acryloyl-CoA binding to DmdR derepresses dmdA-acuI transcription to stimulate acryloyl-CoA catabolism and DMSP demethylation. Upregulation of the newly identified peroxidase DmdF, and possibly also of DmdE and DinB, counteracts oxidative stress associated with DMSP demethylation. Thus, DmdR, along with DmdR-independent regulators of DMSP cleavage, likely maintains cellular DMSP levels to allow its antistress functions, but accelerates demethylation and catabolism of toxic intermediates at higher DMSP levels. Of note, DmdR appears to control acryloyl-CoA catabolism/detoxification even in abundant marine bacteria lacking dmdA, suggesting additional mechanisms. DmdR and DmdEF are widespread in Earth's oceans and important for biogeochemical cycling and climate-active gas production.

Chromatin organization, through the assembly of DNA with histones and the folding of nucleosome chains, regulates DNA accessibility for transcription, DNA replication and repair. Although models derived from in vitro studies have proposed distinct nucleosome chain geometries, the organization of chromatin within the crowded cell nucleus remains elusive. Using cryo-electron tomography of thin vitreous sections, we directly observed the path of nucleosomal and linker DNA in situ from a flash-frozen organism - Drosophila embryos. We quantified linker length and curvature, characterizing an irregular zig-zag chromatin-folding motif, with a low degree of linker bending. Nucleosome conformations could be identified on individual particles in favorable orientations without structure averaging. Additionally, we observed particles that accommodate a number of DNA gyres ranging from less than one to up to three, which resemble previously proposed non-octameric nucleosomal particles with variable DNA wrapping.

Gene drives are engineered alleles that bias their own inheritance in offspring, enabling the spread of specific traits throughout a population. Targeting female fertility genes in a gene drive can be an efficient strategy for population suppression. In this study, we investigated nine female fertility genes in Drosophila melanogaster using CRISPR-based homing gene drives. Employing a multiplexed gRNA approach to prevent the formation of functional resistance alleles, we aimed to maintain high drive-conversion efficiency with low fitness costs in female drive-carriers. Drive efficiency was assessed in individual crosses and had varied performance across different target genes. Notably, drives targeting the octopamine β2 receptor (oct) and stall (stl) genes exhibited the highest drive-conversion rates and were further tested in cages. A drive targeting stl successfully suppressed a cage population with a high release frequency, though suppression failed in another replicate cage with a lower initial release frequency. Fitness costs in female drive carriers were observed in test cages, impacting the overall efficiency of population suppression. Further tests on the fertility of these lines using individual crosses indicated that some fitness costs were due to maternal deposition of Cas9 combined with new gRNA expression, which would only occur in progeny of drive males when testing split drives with separate Cas9 (when mimicking cages with complete drives) but not for complete drive systems. This could enable success in complete drives with higher maternal Cas9 deposition, even if cage experiments in split drives fail. Overall, our findings identify oct and stl as promising fertility targets and demonstrate both the potential and the constraints of fertility-based suppression drives, providing empirical evidence to guide the design and assessment of more efficient population control strategies.

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 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.

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.

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 distribution of N⁶-methyladenosine (m⁶A) controls its substrate RNA fate, playing key roles in various biological processes. However, the mechanism underlying site-selective m⁶A 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 m⁶A 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 m⁶A 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-m⁶A axis inhibits the survival of leukemia cells and promotes cell differentiation, and impairs hematological malignancies. This study uncovers a novel selective m⁶A deposition mechanism mediated by H3K79me2 and RBM15B, highlighting promising therapeutic targets for hematological malignancies.

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.

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.