FEBS Letters最新文献

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.

Understanding how environmental changes affect the health of organisms and ecosystems is complex, but recent interdisciplinary advances and the recognition of immune function as a dynamic mediator offer exciting progress. Environmental immunotoxicology in teleost fishes is evolving beyond cataloguing stressors towards a mechanistic, integrative framework that leverages omics, in vivo tracking and cross-disciplinary modelling. However, knowledge gaps in immune mechanisms, toxicokinetics and multi-stressor interactions remain. The present work highlights these gaps, advocating for immune function as both a mechanistic lens and an integrative health indicator. Such a framework can improve predictive risk assessments, management strategies and our understanding of contaminant effects on resilience, disease susceptibility and population viability. While challenges remain, the field is poised for significant growth through collaborative innovation and advancing technology.

Mycobacterium tuberculosis (Mtb) employs multiple strategies to evade host immunity, including disruption of antigen presentation. Dendritic cells (DCs) are crucial for effective antigen presentation and T-cell activation. In this study, we show that the mycobacterial protein ESAT-6 impairs monocyte to DC differentiation, with reduced expression of the DC markers CD209 and CD1a. ESAT-6 treatment elevated IL-6 and IL-10 levels, but blocking the biological activity of these cytokines failed to restore DC differentiation. Mechanistically, ESAT-6 suppressed phosphorylation of p65, establishing that ESAT-6 impairs DC differentiation by inhibiting NF-κB activation, a function dependent on the last six amino acids of its C-terminal domain. This mechanism may represent a novel immune evasion strategy employed by Mtb to subvert host adaptive immune responses during infection.

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.

DNA double-strand break (DSB) repair is critical for genome stability and requires chromatin remodeling for efficient processing. Fun30, an ATP-dependent chromatin remodeler, promotes long-range DNA end resection to generate 3' overhangs, a key step in homologous recombination. Persistent DSBs relocate to the nuclear periphery, particularly through interactions with the inner nuclear membrane protein Mps3 and the nuclear pore complex component Nup84. By tracking a single irreparable break, we show that Fun30 facilitates this relocation. In fun30Δ cells, Mps3 and Nup84 enrichment at DSBs was reduced, indicating impaired tethering. We further demonstrate that Fun30 promotes deposition of the histone variant H2A.Z at DSBs. Thus, Fun30 favors relocation of persistent DSBs to the nuclear periphery by supporting resection and H2A.Z incorporation.

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.