EMBO Journal最新文献

The piRNA pathway protects animal germlines from active transposons. Mammals employ a cytoplasmic pathway to destroy transposon transcripts during germline reprogramming. This post-transcriptional mechanism is ancient and found throughout the animal kingdom. A nuclear piRNA pathway mediates transposon DNA re-methylation, which is believed to be bespoke to mammals. However, when exactly piRNA-directed DNA methylation evolved remains unknown. We found that a mammalian-like piRNA pathway evolved early in tetrapod evolution and is found and expressed in its current configuration in the axolotl salamander. Analysis of axolotl testes and oocytes revealed diverse repertoires of piRNAs and pervasive post-transcriptional targeting of young transposons. We identified high levels of genome methylation in axolotl spermatozoa, with full-length transposons being heavily methylated. Our findings reveal that the mammalian nuclear piRNA pathway has ancient vertebrate origins, and it has likely been safeguarding the germline throughout most of tetrapod evolution. Thus, the emergence of piRNA-directed DNA methylation is a pivotal epigenetic evolutionary event that may have laid the foundation for germline reprogramming and genomic imprinting.

The mammalian protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. While the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for LIN-42's function in timing rhythmic development, reflected in C. elegans molting cycles. We observed arrhythmic molts upon combined deletion of a region comprising two distinct sequence elements previously termed SYQ and LT. This region functions as a casein kinase I (CK1)-binding domain (CK1BD) mediating stable binding to KIN-20, the C. elegans CK1δ/ε orthologue. CK1 phosphorylates LIN-42, and the CK1BD sub-domains SYQ/CKBD-A and LT/CKBD-B play distinct roles in controlling CK1-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molt timing in vivo, and loss of LIN-42 binding or of the phosphorylated LIN-42 tail impairs nuclear accumulation of KIN-20. These findings indicate that LIN-42/PER and KIN-20/CK1 form a functionally conserved signaling module of two distinct chronobiological systems.

The Asgard phylum has emerged as a model to study eukaryogenesis because of their close relatedness with the eukaryotes. In this study, we use FtsZ proteins from a member of the class Odinarchaeia as representatives to investigate the probable origin, evolution, and assembly of the FtsZ/tubulin protein superfamily in Asgard archaea. We performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the anchor OdinSepF via OdinFtsZ2's C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting. Our findings highlight the diversity of FtsZ proteins in the archaeal phylum Asgardarchaeota, providing valuable insights into the evolution and differentiation of tubulin-family proteins.

Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the protein's inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphorylation in health and disease.

T cells are critical effector cells counteracting infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-γ and TNF. Cytokine production is a tightly regulated process, but the relative contribution of transcriptional and post-transcriptional regulation to mRNA expression remains unknown. We optimized single-molecule FISH for primary human T cells (T-cell smFISH) to simultaneously quantify nascent RNA, levels of mature mRNA, and its localization with single-cell resolution. T-cell smFISH uncovered heterogeneous cytokine mRNA levels, with high cytokine producers displaying biallelic IFNG/TNF RNA transcription activity. Throughout activation, nuclear cytokine mRNAs accumulated, whereas cytoplasmic cytokine mRNA was degraded through translation-dependent decay. Lastly, T-cell smFISH uncovered cytokine-specific regulation by the RNA-binding protein HuR. Thus, T-cell smFISH provides novel insights in the intricate (post)-transcriptional processes in T cells.

N-glycine myristoylation allows for reversible association of newly synthesized proteins with membranes to regulate essential functions such as cellular signaling and stress responses. This process can be catalyzed during protein synthesis by N-myristoyltransferases (NMTs), and its dysregulation has been implicated both in cancer and heart disease. Although the nascent polypeptide-associated complex (NAC) orchestrates the binding of several co-translational processing factors on ribosomes, its role in facilitating nascent protein myristoylation by NMT2 remains unclear. Here, we show that NAC mediates binding of NMT2 to translating ribosomes, which together form an extended channel that guides the nascent chain as it emerges from the polypeptide exit tunnel to the catalytic site of NMT2. Furthermore, the ternary ribosome:NMT2:NAC complex is stabilized by a ribosomal RNA clamp that, together with NAC, orients NMT2 on the ribosomal surface for co-translational myristoylation of nascent chains. Our work uncovers the molecular mechanism coupling protein synthesis to nascent protein myristoylation and underscores the role of NAC as a master regulator of protein biogenesis on the ribosome.

The size of organelles and cellular structures needs to be tightly regulated and coordinated with overall cell size. A well-studied example is the Cdc42-driven polarization and subsequent septin ring formation in Saccharomyces cerevisiae, where the size of the resulting structures scales with cell size. However, the mechanisms underlying this scaling remain unclear. Here, we combine live-cell imaging, genetic perturbations, and three-dimensional mathematical modeling to investigate how septin ring size is controlled. Our integrative approach reveals that positive feedback in the polarization pathway, together with an increase of the amount of polarity proteins as cell size grows, can explain the scaling of the Cdc42 cluster and, consequently, septin ring diameter. Additionally, we show that in cells lacking the formin Bni1, where F-actin-cable assembly and directed polarization are disrupted, exocytosis becomes diffuse, leading to abnormally large septin rings. By integrating new experimental findings and mathematical modeling of yeast polarization, our study provides insights into the origin of septin ring size control.

Recent studies have identified a family of rod-shaped proteins thought to mediate lipid transfer at intracellular membrane contacts by a bridge-like mechanism. We show that one such protein, bridge-like lipid transfer protein 3A (BLTP3A)/UHRF1BP1 binds VAMP7 vesicles via its C-terminal region, and anchors them to lysosomes via its chorein domain-containing N-terminal region binding to Rab7. Upon lysosome damage, BLTP3A-positive vesicles rapidly (within minutes) dissociate from lysosomes. Lysosome damage is known to activate the CASM (Conjugation of ATG8 to Single Membranes) pathway, leading to lipidation and lysosomal recruitment of mammalian ATG8 (mATG8) proteins. We find that this process drives the reassociation of BLTP3A with damaged lysosomes via an interaction of its LIR motif with mATG8 which coincides with a dissociation from the vesicles. Our findings reveal that BLTP3A is an effector of CASM, potentially as part of a mechanism to help repair or minimize lysosome damage.

The paternal preconception environment has been implicated as a modulator of phenotypic traits and disease risk in F1 offspring. However, the prevalence and mechanisms of such intergenerational epigenetic inheritance (IEI) in mammals remain poorly defined. Moreover, the interplay between paternal exposure, genetics, and age on emergent offspring features is unexplored. Here, we measure the quantitative impact of three paternal environments on early embryogenesis across genetic backgrounds. Using in vitro fertilisation (IVF) at scale, we capture batch-robust transcriptomic signatures of IEI with single-blastocyst resolution. Amongst these, paternal gut microbiota dysbiosis is linked with aberrant expression of (extra-)embryonic lineage regulators in blastocysts. In contrast, a paternal low-protein high-sugar diet associates with subtle preimplantation growth effects. We further identify gene expression variability as a paternally induced F1 phenotype, and highlight confounding issues for IEI, such as batch effects and under-sampling. Finally, while genetic background dominantly modifies the inherited signature of paternal environment, aged fathers universally impact F1 expression programmes across genetic contexts. This study systematically characterises how paternal conditioning programs subtle but detectable molecular responses in early embryos, and proposes guiding principles to dissect intergenerational phenomenology.

Maternal antibodies are transferred transplacentally to fetuses and then through lactation to infants to protect them whilst their own immune system is still immature. However, these maternal antibodies also suppress neonatal B-cell responses, thereby impairing vaccine efficacy and leaving infants potentially vulnerable to life-threatening pathogens, such as rotaviruses. Currently available rotavirus vaccines are composed of live-attenuated viral strains administered to infants orally at 6-8 weeks old. Although high concentrations of maternal antibodies correlate with poor production of antibodies following vaccination (i.e., seroconversion), the immunological basis of this interference is unknown. To investigate the underlying mechanisms, we here developed a mouse model of neonatal oral rotavirus vaccination, in which vaccination only fails to induce seroconversion if maternal antibodies are present. Such antibodies are shown to block vaccine replication, while faster maternal antibody waning is observed in vaccinated compared to unvaccinated pups. FcγRIIB deletion does not overcome interference in pups, although pup IgG levels increase when maternal antibody titers are very low. Our findings show that maternal antibody-mediated vaccine clearance is a key mechanism of interference with oral rotavirus vaccines, with a minor role for FcγRIIB in neonatal IgG responses.