FEBS Letters最新文献

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.

The mechanisms supporting progression of metastatic prostate cancer (PCa) in adipocyte-rich bone marrow remain unclear. We hypothesized that stearoyl-coenzyme A desaturase (SCD) promotes PCa survival in bone by modulating stress responses and regulating lipid peroxidation. We show that SCD-high PCa cells are sensitive to SCD loss, showing smaller spheroids, reduced mTOR signaling, and elevated endoplasmic reticulum (ER) stress. SCD expression is further augmented by adipocytes, and SCD loss induces DNA damage and repair activation only with adipocyte exposure. In vivo, pharmacological SCD inhibition reduces tumor size and increases ER stress and DNA damage in SCD-high-expressing bone tumors. These findings suggest SCD plays a role in redox regulation and DNA repair sensitivity, with therapeutic potential for targeting DNA repair pathways in combination with SCD inhibition. Impact statement This study reveals that stearoyl-CoA desaturase (SCD) supports prostate cancer growth in adipocyte-rich bone by regulating redox balance and DNA repair responses, uncovering a metabolic mechanism linking lipid metabolism to genomic stability and suggesting therapeutic potential for combining SCD and DNA repair pathway inhibition.

Universal stress proteins (USPs) have remained an enigma since their first description by Nystrom and Neidhardt in 1992. Despite being upregulated under diverse stresses and found across a range of bacterial species, decades of studies suggested only general and potentially redundant protective functions for USPs. Recent studies have uncovered that USPs are critical regulators of bacterial survival processes in Actinobacteria, most notably in Mycobacterium tuberculosis, one of the most prolific and lethal of human pathogens. This brief review places these recent studies in the context of earlier publications and discusses their importance for future USP research, our understanding of these regulatory proteins, and novel therapeutic options that these proteins present in Mycobacterium tuberculosis, related Actinobacteria, and across diverse bacterial species.

Circadian regulation in peripheral cells depends on calcium dynamics, but the upstream mechanisms remain unclear. We identify endoplasmic reticulum lipid raft-associated protein 2 (ERLIN2) as a regulator of the peripheral clock. Knockdown and overexpression of ERLIN2 in C2C12 skeletal muscle cells show that ERLIN2 positively regulates cryptochrome circadian regulator 1/2 (CRY1/2) transcription and maintains rhythmicity. ERLIN2 regulates inositol 1,4,5-trisphosphate receptor (IP₃R)-mediated Ca²⁺ release and activates the calcium/calmodulin-dependent protein kinase II (CaMKII)-mitogen-activated protein kinase (MAPK)-cAMP response element-binding protein (CREB) pathway. ATP induced IP₃R-dependent Ca²⁺ transients, CREB phosphorylation, and Per1 expression, reshaping circadian rhythm, effects blocked by IP₃R, Ca²⁺, or CaMKII inhibition. CRY1 enhances and CRY2 suppresses CREB signaling, establishing a feedback loop with ERLIN2. This ERLIN2-Ca²⁺-CREB-CRY1/2 axis couples membrane contact sites to circadian regulation. Impact statement This study reveals ERLIN2 as a key regulator linking calcium signaling to circadian rhythms, establishing an ERLIN2-Ca²⁺-CREB-CRY1/2 axis that advances understanding of cellular clock control.

Recently, we showed that the Per-ARNT-Sim (PAS) domain-containing phosphoglycerate kinase from Leishmania major (LmPAS-PGK) is imported into both the glycosome and the lysosome; however, the mechanism underlying its dual targeting has remained unclear. LmPAS-PGK contains a C-terminal tripeptide sequence and two dileucine base motifs. To investigate the roles of these sorting signals, we generated different complement cell lines from null mutants by transfecting constructs encoding the wild-type protein, an L230A/L231A mutant, the C-terminal tripeptide deleted variant (∆^525-527), a dileucine motif deleted variant (∆^504-508), and a double-deletion mutant (∆^525-527/∆^504-508). Our results demonstrate that the dileucine motif governs the lysosomal targeting of LmPAS-PGK, whereas the C-terminal tripeptide is required for glycosomal localization. Deletion of both motifs abolished trafficking to either organelle, leading to cytosolic redistribution. Notably, ∆^525-527, ∆^504-508, and ∆^525-527/∆^504-508 cells displayed lower virulence compared with control cells in infected macrophages, underscoring the importance of proper LmPAS-PGK localization in Leishmania pathogenicity. Impact statement Here, we show the dileucine motif of PAS-PGK of Leishmania major governs its lysosomal targeting, whereas its C-terminal tripeptide is required for glycosomal localization. Cells lacking these domains displayed lower virulence compared with control cells in infected macrophages. These results increase our understanding of intracellular trafficking, as well as host-parasite interactions.