FEBS Letters最新文献

Mitochondrial ribosomal proteins are involved in many cellular processes and not only protein synthesis from mitochondrial DNA. We previously showed that zebrafish mitochondrial ribosomal protein L4 (Mrpl4) is highly expressed in larval intestine. However, the physiological significance of this expression pattern remains unclear. Here, we observed significant defects in intestinal growth and maturation in mrpl4 knockout fish; this was accompanied by disruption of intestinal epithelial integrity leading to inflammatory responses, demonstrating that Mrpl4 plays an essential role in regulating zebrafish intestinal development. Moreover, we found that Notch signaling was downregulated in these mutants, and reactivation of Notch signaling can partially rescue their intestinal defects, suggesting involvement of Notch signaling in the effects of Mrpl4 on intestinal development.

Hepatic stellate cell (HSC) activation is a central mechanism in liver fibrosis, with histone acetyltransferase p300 acting as a pivotal transcriptional cofactor. To define upstream regulators of p300 stability during HSC activation, we performed a deubiquitinase inhibitor screen in activated HSCs and identified ubiquitin carboxyl-terminal hydrolase 2 (USP2) as a p300 deubiquitinase. Single-cell RNA sequencing of fibrotic human liver tissues revealed USP2 as the most specifically expressed USP family member in stromal populations, including HSCs, with marked upregulation in chronic liver disease and advanced metabolic dysfunction-associated steatotic liver disease (MASLD). Moreover, we demonstrated that USP2 stabilizes p300 and promotes HSC activation, whereas USP2 knockdown or pharmacological inhibition suppresses p300 accumulation and fibrogenic responses. These findings identify USP2 as a key regulator of p300 stability and HSC activation in liver fibrosis. Impact statement Our study identifies USP2 as a novel regulator of p300 stability and hepatic stellate cell activation, revealing a previously unrecognized mechanism driving liver fibrosis. These findings provide new insight into fibrogenesis and highlight USP2 as a potential therapeutic target, impacting both fundamental biology and translational fibrosis research.

Spinal muscular atrophy (SMA) is caused by a deficiency in survival motor neuron (SMN) protein; redox imbalance and oxidative stress are also implicated. Protein S-glutathionylation (PSSG) is a reversible redox modification that protects cysteines from irreversible oxidation and regulates protein function. Here, we report stage- and tissue-dependent defects in PSSG levels, accompanied by tissue-specific alterations in the expression of glutathione-related enzymes in Taiwanese SMA mice at early and late symptomatic stages. Importantly, we also provide evidence linking glutathione homeostasis defects with ferroptosis. Finally, partial restoration of SMN by antisense oligonucleotides selectively modulates these abnormalities in a tissue-dependent manner. Our findings suggest S-glutathionylation dysregulation as a novel SMA hallmark and highlight persistent redox imbalance as a therapeutic target beyond SMN restoration. Impact statement This study provides a multi-organ analysis of redox imbalance in spinal muscular atrophy, revealing systemic loss of protein S-glutathionylation in a stage- and tissue-dependent manner. By identifying the heart as particularly redox-vulnerable, this work refines understanding of oxidative stress beyond motor neurons and informs tissue-aware therapeutic evaluation.

Despite evolving independently in diverse organisms, circadian clocks ubiquitously employ period-ARNT-single minded (PAS) and cryptochrome (CRY) proteins as key regulators coupling environmental variables into circadian regulation. In these systems, we often observe complex gene duplication events and evolution of specialized function despite retaining high-sequence identity. These specialized functions often have evolved from ancestral photoactive proteins (LOV/CRY) where upon the ancestral photoactive ligand-binding pockets have been co-opted as protein-protein interaction motifs and targets for drug discovery. In this review, we dissect structural, biochemical, and computational studies of the PAS and CRY superfamilies within circadian clocks to highlight their molecular mechanisms and factors that position them as drug targets for diverse disease phenotypes. Particular focus is placed on discussing how photoactive members of the protein families can inform on allosteric mechanisms that couple cofactor-binding sites to regulation of flexible signaling motifs relevant to circadian regulation and drug discovery.

Circadian clocks are conserved timekeeping systems present across the tree of life. Despite sequence divergence, their negative elements share biophysical traits such as intrinsic disorder, phosphorylation clusters, and charged low-complexity regions, suggesting a shared functional logic beyond primary sequence. Using the fungal protein FREQUENCY (FRQ) as a proxy, we review how intrinsic disorder enables temporal regulation. Using computational analysis, we explore the hypothesis that multisite phosphorylation may incrementally reshape FRQ conformational ensemble, with potential consequences for partner engagement over the circadian day. Thus, in this review we consider how, despite poor sequence conservation, circadian negative elements maintain a conserved mechanism rooted in the physical principles of disorder and post-translational modulation, positioning these properties at the very heart of the molecular chronosome.

This study characterizes a translin-like protein from Chlamydomonas reinhardtii, a unicellular alga. The efficient binding of the Crtranslin protein to both single-stranded DNA and RNA aligns it with the nucleic acid-binding properties of the translin protein family, known for its roles in DNA repair, RNA metabolism, and mRNA transport. We report for the first time the presence of a translin-like protein that forms octameric rings, is more closely related to rice translin, and is localized to an organelle not yet known to harbor such a family of proteins, viz., in the basal body and flagella of C. reinhardtii. This study lays the groundwork for future investigations into the molecular functions of Crtranslin and its potential regulatory roles in flagellar dynamics. Impact statement This is the first report of the presence of a nucleic acid-binding protein, Translin, in the basal body and cilia.

Ferritin is a ubiquitous and evolutionarily conserved iron-storage protein that plays a fundamental role in cellular iron homeostasis. By catalyzing the oxidation of ferrous iron and sequestering it as a ferric mineral within a protein nanocage, ferritin prevents toxic accumulation of labile iron and reactive oxygen species that damage proteins, lipids, and DNA. In humans, ferritin assembles into a 24-subunit nearly spherical shell enclosing a central cavity that safely stores thousands of iron atoms. This organized architecture enables ferritin to act as both an efficient iron detoxification system and a dynamic intracellular iron reservoir. Recent advances in cryo-electron microscopy (cryo-EM) have transformed ferritin research by revealing its structural organization, molecular interactions, and functional states at high resolution. Additionally, beyond protein-protein interactions, cryo-EM now enables direct visualization of ferritin-mediated biomineralization, allowing in situ observation of iron nucleation, mineral growth, and core organization within intact nanocages. Together, these advances establish cryo-EM as a transformative tool for elucidating ferritin structure, dynamics, and function - reshaping our understanding of iron metabolism and guiding the rational design of ferritin-based nanomaterials for biomedical applications.

AlphaFold models provide static structural predictions, limiting their use in interpreting flexible regions in low-resolution cryo-EM maps. Here, we assess whether AlphaFold-generated distograms can instead reveal conformational flexibility, focusing on binding-induced hinge motions. For this, we examined the key metabolic AK2/AIFM1 complex, where molecular dynamics and cryo-EM confirm a hinge motion in AK2 upon binding. Notably, this motion is captured in the AlphaFold2/3 distograms of apo AK2, even though it is absent in the predicted structures. By extending our analysis to other systems, we demonstrate that distograms may offer a valuable, model-independent method for interpreting ambiguous hinge regions in cryo-EM maps. Impact statement We reveal that AlphaFold distograms can successfully predict binding-induced hinge motions. This establishes distograms as a valuable, structure-free metric for identifying alternative conformational states, aiding the interpretation of ambiguous densities in cryo-EM maps.

Glycogen is the principal carbon reserve in Synechocystis sp. PCC 6803. We reconstituted its biosynthetic pathway in vitro-GlgC (glucose-1-phosphate adenylyltransferase), two glycogen synthase isoenzymes (GlgA1, GlgA2) and the branching enzyme GlgB-to define how supply, polymerization and branching set flux and product structure. GlgA2 shows higher specific activity and cooperates with GlgB-generated branched primers, whereas GlgA1 has higher substrate affinity and responds more to primer concentration. Product profiling links mechanism to architecture: GlgA1 produces more-branched glycogen, while GlgA2 yields longer, less-branched polymers, with GlgB biasing utilization toward GlgA2. The complementary behaviors of GlgA1 and GlgA2 provide capacity for rapid accumulation versus steady-state maintenance and offer dynamic metabolic levers to tune glycogen content and architecture in cyanobacteria.

Phosphodiesterase 5 (PDE5) regulates several physiological processes, including cardiovascular function. A familial PDE5A variant resulting in an N-terminal truncation (∆M1-Q91) in PDE5A2 has been linked to premature ischemic heart disease, but its functional impact is unclear. Using computational analysis and BRET-based biosensors, we show that ∆M1-Q91 deletion alters structural dynamics and reduces the efficacy of cGMP-induced conformational change in PDE5. Molecular dynamics simulations and normal mode analysis using structural models revealed altered dynamics and correlated motions in the mutant. BRET assays showed a higher EC₅₀ for cGMP-induced, but not sildenafil-induced, conformational change in the ∆M1-Q91 mutant PDE5A2. These findings suggest that M1-Q91 deletion impairs cGMP-mediated allosteric regulation in PDE5A2 without altering inhibitor sensitivity, offering insights into potential precision therapies targeting this variant.