FEBS Letters最新文献

RNA sequences with the potential to form G-quadruplexes (rGQs) are widespread but largely unfolded in cells by unknown mechanisms. rGQ folding status is a critical regulator of RNA splicing and translation. We show that rGQs can be unfolded by SR proteins, SR-related proteins, and other Arg-rich proteins, including SRSF1, SRSF3, SRSF9, U1-70K, and U2AF1. The length and composition of Arg-rich regions are key determinants of this activity: Arg residues are the primary drivers, while acidic residues attenuate the unfolding activity. To unfold ARPC2 rGQ, at least 13 Arg residues are required. Our findings identify Arg-rich proteins as previously unrecognized, helicase-independent regulators of rGQ structures, with potential broad impacts on RNA processing that merit further investigation.

The Dot/Icm type IV secretion system (T4SS) is essential for Legionella pneumophila infection, but its in situ architecture and mechanism remain incompletely understood. Using cryo-electron tomography, we performed subtomogram averaging and 3D classification to resolve structural heterogeneity within the complex. We identified multiple assembly states of the inner membrane complex, including a fully assembled form with a hexamer-of-dimers DotO ATPase and symmetry mismatches between subcomplexes. A composite in situ model revealed a central channel above the inner membrane, likely used for substrate secretion. Imaging of infected macrophages showed T4SSs tethered to host vacuoles and extracellular vesicle release, suggesting additional effector delivery routes. These findings provide insight into Dot/Icm T4SS structure and infection-related dynamics.

Mitochondrial protein Slm35 is linked to TOR1 signaling, mitophagy, and stress response in Saccharomyces cerevisiae. Nonetheless, little is known about its regulation or how it affects stress adaptation. In this work, we identified stress-related transcription factor binding sites and two upstream open reading frames (uORFs) in the 5'-UTR of SLM35. Using transcriptional reporters, we showed that the transcription factor Gis1 represses SLM35 transcription; however, Slm35 protein levels increased under oxidative stress and in early stationary phase, suggesting post-transcriptional regulation. Site-directed mutagenesis revealed that one uORF negatively regulates translation, with its disruption leading to altered Slm35 levels and a reproducible increase in mitophagy flux. These findings reveal multilayered control of SLM35 expression and underscore the role of uORF-mediated translation in mitochondrial stress responses. Impact statement This study shows that SLM35, encoding a mitochondrial protein, is controlled through multiple regulatory layers, combining transcriptional repression by stress-responsive factors with uORF-mediated translational regulation. By linking these mechanisms to mitophagy, the work provides new insight into mitochondrial quality control under stress.

Phosphoinositides, comprising less than 10% of membrane lipids, function as 'lipid codes' within cellular compartments through seven species formed by myo-inositol headgroup phosphorylation. This review examines their diverse roles in endocytic transport, encompassing endocytosis, endosomal sorting, degradation, and recycling, as well as specialized mechanisms, such as caveolin-mediated endocytosis. The review also investigates the involvement of specific kinases and phosphatases in these processes. Additionally, it discusses the impact of technological advancements, such as fluorescent biosensors, super-resolution microscopy, optogenetics, and synthetic biology, on elucidating phosphoinositide dynamics during endocytic trafficking. Perturbations in phosphoinositide metabolism have been associated with human diseases, including cancer and neurodegenerative disorders. Exploring these pathways may unveil potential therapeutic targets, with subsequent research focusing on their spatiotemporal regulation, tissue-specific metabolism, the synergistic effects of phosphoinositides with other lipids, and the incorporation of systems biology to bridge basic cell biology with translational medicine.

Inositol phosphates (InsPs) represent a conserved class of water-soluble signaling molecules found in all eukaryotes. Their biosynthesis involves a tightly regulated enzymatic network, with inositol polyphosphate multikinase (IPMK) functioning as a pivotal catalytic hub. IPMK exhibits broad substrate specificity, phosphorylating various InsPs and phosphatidylinositol 4,5-bisphosphate. Beyond its enzymatic activity, IPMK also modulates key signaling pathways through noncatalytic mechanisms, including direct interactions with protein partners. This review highlights the functional attributes of IPMK, its diverse roles in cellular physiology and disease, and outlines current challenges and future directions in IPMK research.

Transglutaminase 2 (TG2) exhibits various protein-modifying catalytic and protein-protein interaction properties and is highly expressed in endothelial cells. To provide insight into its endothelial functions, the TG2 interactome was identified in HUVECs using biotinylated recombinant TG2 and affinity chromatography. Subsequently, endogenous TG2-silenced and a triple Flag-tagged transgenic TG2-expressing HUVEC line was created, allowing isolation of intracellularly assembled TG2-interacting proteins. Conformation-dependency of TG2's interactome was also determined. RNA-binding proteins associated with TG2 were the most enriched gene ontology terms in all experiments, with a 42% overlap between the TG2 interactome and known RNA-binding proteins in HUVECs. Consistent with TG2's recently described RNA-binding ability, our findings reveal its potential role in post-transcriptional regulation at a central hub within the RNA-binding protein network.

In eukaryotes, nuclear size scales with cell size, maintaining a constant nucleocytoplasmic volume ratio, known as the N/C ratio. Although nucleocytoplasmic transport plays a crucial role in nuclear size control, the underlying mechanisms remain elusive. Here, we investigated the impact of overexpression of a nuclear export signal (NES) fused with GFP (NES-GFP) in fission yeast on nuclear size. The overexpression of NES-GFP disrupts nuclear export, leading to the nuclear accumulation of cargo proteins and the formation of intranuclear microtubule bundles, thereby increasing the nuclear volume to cell volume (N/C) ratio dependent on nuclear import and microtubule nucleation. Enhanced formation of intranuclear microtubule bundles in cells overexpressing NES-GFP further accelerates nuclear expansion. We propose that membrane tension in the nucleus plays an important role in nuclear size control.

Elevated levels of extrachromosomal DNAs (ecDNAs) are associated with poor prognoses of many cancer types. These large circular DNAs typically harbour oncogenes and regulatory elements which, together with high levels of ecDNA transcription, confer a growth advantage to cancer cells. Replication of ecDNAs, followed by their unequal distribution at mitosis, further promotes rapid cancer evolution. In contrast to ecDNAs, the role of circular DNA by-products from V(D)J recombination in cancer development has largely been overlooked. Developing lymphocytes generate millions of excised signal circles (ESCs) each day through gene rearrangement at the immunoglobulin and T-cell receptor loci. Despite their similar size to ecDNAs, ESCs were long assumed to be inert and lost during cell division. However, it is now known that ESCs potently trigger genome instability when complexed with recombinase proteins. Not only this, but new data show that just like ecDNAs, ESCs replicate and persist, with high levels strongly correlating with poor prognosis of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). Despite these striking similarities, the properties of ESCs and ecDNAs are seldom linked. Here, we provide the first comparative review of ecDNAs and ESCs, and highlight the reasons why these molecules are more closely related than once assumed.

The maintenance of protein homeostasis is a fundamental premise for the survival of all life. The synthesis, folding, localization, and degradation of thousands of proteins must be organized according to various conditions. To ensure such a stable and functional proteome, the proteostasis network evolved. Dedicated to this, the fourth School on Proteostasis, a co-funded EMBO|FEBS Lecture Course in memory of Susan Lindquist, took place in Espoo, Finland on 16-19 September 2025, with 59 early career researchers (PhD students or postdoctoral fellows), 18 leading scientists, and two editors attending and discussing the current state of the field. From basic principles to the latest therapeutic developments, this meeting provided a comprehensive overview of proteostasis. This report summarizes the lecture course and highlights selected presentations.

Almost all organisms on earth undergo rhythmic physiological and behavioral changes over the course of day. These rhythms are fundamental in most organisms and are referred to as circadian rhythms. The molecular mechanisms regulating these changes have evolved significantly in different kingdoms of life and they engage in crosstalk with most cellular functions. These molecular mechanisms have been studied for a long time using different model organisms and carefully designed experiments. In the past two decades or so, with advances in high throughput technologies and access to ever increasing computational power, the molecular mechanisms regulating circadian rhythms are being explored at multiple spatial and temporal scales. In this review, we introduce diverse regulatory mechanisms of circadian rhythms. We then focus on the proteins involved in circadian regulation, their structures, complexes and dynamics. This is followed by a review of computational methods such as structural modeling, integrative modeling and molecular simulations as applied to understanding the clock proteins in different organisms and insights obtained from the same. Finally, we highlight the limitations and future prospects of these methods in understanding the circadian regulation.