During differentiation of SH-SY5Y neuroblastoma cells to mature neuron-like cells, transcriptome-wide alternative splicing events occur in multiple local splice variant programs. These events are driven by RNA-binding proteins (RBPs). Here, we utilize sequencing analysis to explore these events as well as identifying their potential RBP regulators via motif analysis. We focused on 2 RBPs, PTB and HuR, revealing their role in regulating neuronal differentiation solely by driving alternative splicing.

A major complication of organ transplantation is primary graft dysfunction, which represents the leading cause of early post-transplantation morbidity and mortality. Pre-operative depletion of neutrophil serine proteases in circulating neutrophils by pretreatment with a cathepsin C inhibitor in recipients could prevent early post-operative complications and the development of primary graft dysfunction.

In osteosarcoma, a malignant bone cancer, we observe an overexpression of the enzyme transketolase (TKT). TKT directly binds at residues 201–228 of Yin Yang 1 (YY1). This interaction activates YY1, enabling it to bind to the promoter of P21 activated kinase 4 (PAK4), leading to the expression of PAK4. The increased expression of PAK4 activates the phosphoinositide 3-kinase-Akt signaling pathway, which is a key mechanism in the progression of osteosarcoma. This information suggests potential targets for therapy in osteosarcoma.

The stress response and circadian rhythms are essential to maintain appropriate responses to the environment and are known to be impacted by the gut microbiota. Due to the interconnected nature of these important components of physiology, in this review we explore how the gut microbiota may play a role in regulating the integration of stress and circadian signals in mammals and the consequences for brain health and disease.

SUCNR1, activated by succinate, is a G_i- and G_q-coupled receptor present at the plasma membrane and in endosomes. There are conflicting reports about the pro-/anti-inflammatory effects of the succinate-SUCNR1 signaling axis, and these are likely due to localization-dependent signaling. Here, we show that SUCNR1 signaling, localization, and metabolism are mutually dependent, and that M2-like macrophages express SUCNR1. SUCNR1-mediated G_i protein-coupling stimulates oxidative phosphorylation and glycolytic rate and activates ERK and Akt phosphorylation. Conversely, Akt phosphorylation and glycolytic rate (extracellular acidification rate) are inhibited by SUCNR1 through G_q protein activation. Created with Biorender.com.

Intracellular Ca²⁺ levels are dynamic during mouse terminal erythropoiesis. Low Ca²⁺ levels are required for the expansion of early erythroid progenitors, but levels are increased and then gradually decreased, which is coupled with the erythroid differentiation. Although elevated Ca²⁺ levels induced by ionomycin promotes terminal enucleation via CaM/CaMKK1/AMPK signaling, a decreasing Ca²⁺ concentration is required for the nuclear condensation and polarisation at the late stage of erythroid differentiation.

In the presence of TRIC-B, cytosolic Ca²⁺ activates protein kinase C, which phosphorylates the actin-binding proteins fascin and MARCKS, leading to proper cytoskeletal organization. This allows an appropriate β-catenin distribution inside the cell and its translocation into the nucleus, where it stimulates the transcription of osteoblastogenic genes. Lack of TRIC-B causes impaired intracellular Ca²⁺ handling, compromising the organization of the cytoskeleton, which traps β-catenin and prevents it from translocating into the nucleus, with a negative impact on osteoblastogenesis. Created with BioRender.com.

TNFAIP3-interacting protein 1 (TNIP1; also known as ABIN-1) deficiency drives pyroptosis in the presence of poly(I:C) + 5Z-7-oxozeaenol, a setting mimicking pathogen blockade of TAK1. Upon poly(I:C) + 5Z-7-oxozeaenol stimulation, ABIN-1 deficiency facilitates FAS-associated death domain protein (FADD) recruitment to caspase-8, triggering gasdermin-E (GSDME)-mediated pyroptosis in mouse peritoneal macrophage (MEFs) and gasdermin-D (GSDMD)-mediated pyroptosis in macrophages in a caspase-8/FADD-dependent manner. Thus, ABIN-1 functions as a suppressor of pyroptosis when TAK1, a host kinase responsible for sensing pathogen infection, is inhibited.

Developing inhibitors is like climbing a steep, challenging mountain. PI5P4K inhibitors hold significant promise for the treatment of cancer, immune disorders, and neurological diseases. However, the path to success is fraught with hurdles, and researchers are therefore required to apply their expertise to overcome critical “checkpoints.” While some checkpoints are common to drug discovery, others are unique, reflecting PI5P4K's function as GTP-sensing lipid kinases.

In this study, we identified a novel LDHA isoform transcript, which produced a new protein 3 kDa larger than LDHA, which we named LDHAα. LDHAα is differentially expressed in multiple cancer cell lines and can promote cancer cell growth and glycolysis. LDHAα is transcriptionally activated by c-MYC and FOXM1, and a small molecule inhibitor targeting LDHA could also inhibit LDHAα activity. Our findings reveal a previously undescribed signaling factor in tumor metabolism, which could be leveraged for treatment.

Enhancing endocannabinoid signaling by targeting FAAH effectively mitigates cognitive deficits, reduces amyloid pathology, and modulates neuroinflammatory responses in a preclinical model of Alzheimer's disease. This effect is potentially mediated by attenuating the Aβ-induced overexpression of the Bace1 gene through CB₁-dependent hypermethylation of its promoter region.

Three skeletal muscle diseases are linked to HMGCR, a key enzyme in cholesterol synthesis. These diseases include a muscular dystrophy associated with pathogenic variants in the HMGCR gene, statin-associated myopathy, and autoimmune anti-HMGCR myopathy. We modeled three pathogenic variants in HMGCR and showed that reference HMGCR rescued Hmgcr deficiency in myoblasts, whereas variant forms of HMGCR were not able to do so. We conclude that HMGCR is important for healthy skeletal muscle development.

The Janus kinase–signal transducer and activator of transcription (JAK–STAT) signalling pathway is crucial for animal development and physiology, with its outcomes shaped by spatiotemporal activation and crosstalk with other pathways. Drosophila serves as an ideal model to study these interactions. This review highlights how JAK–STAT integrates with epidermal growth factor receptor (EGFR), c-Jun N-terminal kinase (JNK), Notch, Hippo and other pathways, influencing diverse biological processes. Insights from Drosophila research may help understand JAK–STAT dysregulation in human diseases, with implications for clinical research.

Vesicle trafficking governs the biosynthesis of heparan sulfate (HS) by controlling the positioning of HS-modifying enzymes within Golgi compartments. The proteins Rab1A and Rab2A play dynamic, compensatory roles that affect HS levels by influencing the transport of these enzymes. GOLPH3 facilitates the COPI vesicle-mediated transport of HS-modifying enzymes, revealing new mechanisms and interactions vital for maintaining balanced HS production, which is crucial for cellular functions.

Phytochromes, light-induced reversible photoreceptors in plants, algae, and bacteria, have a Cys residue in either the GAF or ‘PAS-knot’ regions for linear tetrapyrrole linkage. Newly discovered dual-Cys bacteriophytochromes (DCBs) with Cys in both GAF and ‘PAS-knot’ in oxygenic photosynthetic cyanobacteria are plausible intermediates in the evolution of phytobilin-based 'GAF-only' (Cph1) and 'tandem-Cys' (TCCP) cyanobacterial phytochrome families from BV-based 'PAS-only' (cBphP) bacteriophytochromes in cyanobacteria.

Creatine deficiency leads to severe neurodevelopmental disorders. In the brain, creatine is synthesized by oligodendrocytes to supply neighboring neurons. While SLC6A8 mediates neuronal uptake, the creatine release mechanism was unclear. Our results establish SLC22A15 as a key creatine efflux transporter. Inactive by default to prevent loss, it can be triggered by external substrates. SLC22A15 mRNA is predominantly expressed in oligodendrocytes and macrophages, cells rich in intracellular creatine (5–10 mm).

In this study, we uncover the relationship between Pannexin 1 (PANX1) and the Hippo signaling pathway in melanoma. Our data demonstrate a significant positive correlation between PANX1, YAP, TAZ, and IQGAP1 expression in invasive melanoma and breast carcinoma. We reveal that PANX1 regulates YAP protein levels and its transcriptional activity. Pharmacological inhibition of PANX1 reduces YAP expression, highlighting PANX1 as a potential therapeutic target in melanoma. Figure created using BioRender.

Molecular dynamics simulations predicted an exosite in the encounter complex between alpha-1 antitrypsin (AAT) and neutrophil elastase (NE), comprising a patch of acidic residues which interacts with a basic loop on NE. Recombinant AAT variants with mutations of the three acidic residues show reduced association rate compared to wild-type and confirm the role of the exosite in the initial AAT-NE interaction.

β-glucosidase, involved in cellulose degradation, is inhibited by its product, glucose, thereby acting as a bottleneck in industrial saccharification processes. Structure-based rational design improves the glucose tolerance of a β-glucosidase from Acetivibrio thermocellus (WT-AtGH1). The WT-AtGH1 mutants exhibit improved glucose tolerance and catalytic efficiency while maintaining thermal stability. Our study emphasizes the importance of rational design in enhancing the properties of β-glucosidases for industrial applications.

The FEBS Journal editorial team reviews the articles we published in 2024 and reflects on the year's highlights. The articles summarised here broadly cluster in three themes—molecular and cell biology across species, immunology, and cutting-edge methods—whilst still showcasing the diversity of the scientific fields the journal covers. We look forward to many more excellent articles in 2025 and hope these highlights will inspire you to submit your next manuscript to The FEBS Journal. Image created using Wordclouds.com.

Angiotensin-1-converting enzyme (ACE) has two catalytic domains, nACE and cACE. cACE primarily regulates blood pressure, whereas nACE is involved in fibrosis. Current inhibitors lack domain-selectivity, thus there is a need to develop nACE and cACE-selective inhibitors. To better understand domain-selectivity, we determined the structures of nACE and cACE in complex with several diprolyl-derived compounds with variable P2 moieties that utilise differences in residues within the S2 subsite.

In proliferating cells, the YARS tRNA ligase can be detected in the nucleus. Its inactivation induces senescence and the downregulation of LIN9, a member of the Dream complex. When cancer cells escape chemotherapy-mediated senescence, they re-activate this YARS-LIN9 pathway to proliferate.

The growing use of extracellular matrix preparations warrants further research into the environmental impact of their production. This Viewpoint compares the effects of three common preparation protocols on the extracellular matrix's functionality and environmental footprint. The optimal protocol tested demonstrated both enhanced biological properties and the lowest environmental impact.

Mounting evidence suggests that stress granules (SGs), dynamic membraneless compartments involved in cellular stress responses, can transition into pathological condensates upon improper disassembly. This review discusses the evidence supporting this notion. Furthermore, we focus on the regulation of both physiological and pathological condensates by molecular chaperones, highlighting common threads among the two condensate types. This is potentially relevant for early intervention in neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia.

The glucagon-like peptide-1 (GLP-1) receptor is regulated by distinct agonist-induced and constitutive internalization pathways. Upon agonist stimulation, GLP-1 receptor activates Gs and Gi/o, then recruits G protein–coupled receptor kinase 2/3/5/6 to phosphorylate the intracellular loops and C-tail of the receptor. AP2 and clathrin bind directly to the receptor and direct it to clathrin-coated pits. Constitutive internalization occurs via arrestin and Gs-related, clathrin- and caveolae-mediated pathways. The activated receptor can also be internalized via caveolae-mediated signaling. Created with BioRender.com.

The active site of Rhizobium etli Class 3 l-asparaginase ReAV is comprised of two Ser-Lys tandems next to a Zn²⁺ cation coordinated by two cysteines, a lysine, and a water molecule. An exchange of the zinc cation for cadmium, plus mutation in the coordination sphere, slowed the enzyme down, allowing crystallization of its l-Asn substrate complex, which unequivocally indicates Ser48 as the catalytic nucleophile.

Intestinal mucus is produced by goblet cells and forms a protective layer on the epithelium. Mucus is composed of several different proteins, of which FCGBP is one of the more abundantly present. We now reveal the core structure of FCGBP showing a disulphide-stabilised dimer involving its most C-terminal von Willebrand D domain. This dimer is one of the building blocks in the organisation of the mucus layer.

Rapidly emerging technologies, such as generative AI tools, have already had a reverberating impact on science and society. The notion that such tools could be entrusted with “mapping” the trajectory of scientific discovery toward immediate measurable applications, however, is problematic. I instead argue that curiosity-driven fundamental research should remain the base upon which scientific progress is built. Image courtesy of Edward Padgett.

A manually curated in silico library was screened for potential inhibitors against SARS-CoV-2 PL^pro. Of the 13 hits, Psoralidin and Corylifol-A exhibited notable dual inhibitory activities against SARS-CoV-2 PL^pro and M^pro in functional assays and promising antiviral activities against HCoV-229E and SARS-CoV-2 in cell-based assays. Further in silico analyses suggested stable interaction of Psoralidin with the catalytic core of PL^pro, while Corylifol-A had stronger affinity for its allosteric site. With regard to M^pro, both Psoralidin and Corylifol-A showed stronger affinity for the enzymatic core. Accordingly, we propose Psoralidin, a component of Psoralea corylifolia, as a promising candidate for further development.

Critical limb ischemia (CLI) enhances sphingomyelin synthase 2 (SMS2) production, which increases sphingomyelin concentrations in ischemic skeletal muscles, promoting inflammation via the NFκB pathway. Hypoxia induces this process, which hampers muscle inflammation post-CLI. SMS2 deficiency can counteract these effects, suggesting that sphingomyelin could be a potential therapeutic target for CLI and hypoxia-related inflammatory diseases.

Stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) is a major co-chaperone to both Hsp90 and Hsp70. We find that misbalanced expression of Sti1 in yeast and mammalian cells causes severe growth defects. Deletion of STI1 causes an accumulation of soluble misfolded ubiquitinated proteins and a strong activation of the heat shock response. During proteostatic stress, Sti1 associates with and sequesters soluble misfolded proteins in yeast and mammalian cells, scaffolding the proteostasis network.

The silencing of transposable elements is mediated by piRNAs through post-transcriptional and transcriptional regulation. In Drosophila, piRNAs are processed within unique non-membrane structures: nuage in germline cells and Yb bodies in somatic gonadal cells. These structures serve as a hub for piRNA biogenesis, driven by interactions among PIWI proteins, RNA precursors, and proteins with conserved motifs. This ensures genome integrity and underscores their crucial roles in RNA regulation and cellular function.

Here, we developed a previously undescribed method to increase recombinant protein production in E. coli by modifying DNA sequences coding for the N terminus of produced proteins. Using directed evolution and fluorescent activated cell sorting (FACS) with GFP tagging, we screened diverse N-terminal sequences derived from DNA libraries. This approach improved the yield of soluble recombinant proteins by up to 30-fold.

Cathepsin D (CTSD), primarily intracellular, is crucial for normal cellular processes but can be secreted extracellularly in diseases like metabolic dysfunction-associated steatohepatitis (MASH), associated with liver fat accumulation. Our study investigated how inhibiting CTSD inside and outside of cells influences lipid levels in a mouse model that closely resembles human MASH. Our findings revealed that inhibiting the external activity of CTSD might offer a more effective and protective approach for MASH.

The microglial receptor TREM2 is required for microglia responses in neurodegeneration, and the loss-of-function mutation R47H results in functional deficits linked to metabolism. Using human TREM2^R47H or TREM2^−/− microglia we show that supplementation with either citrate or succinate ameliorates microglia deficiencies due to TREM2 deficiency, including oxidative phosphorylation (OXPHOS), phagocytosis or lipid metabolism, and restores neuronal OXPHOS via secretome products. These findings provide insights into the metabolic pathways that underlie TREM2-related metabolic disturbances in microglia.

This study provides a detailed mechanism for the transmethylation catalyzed by COMT using enzyme kinetic assays and computational simulation. The inclusion of ultrasensitive response measurements of 3-BTMD and SAH helps obtain reliable kinetic data. These results demonstrate an ordered sequential mechanism, where SAM binds first, followed by Mg²⁺ and 3-BTD. The presence of Mg²⁺ reshapes the conformation of the active pocket, facilitating methyl transfer.

RNA molecules, whose structures are often overlooked by researchers, can be targeted for both basic and applied purposes. With the rapid discovery of numerous coding and noncoding RNAs, this guide offers an overview of current strategies for determining the secondary and tertiary structures of RNA and highlights various techniques available for studying RNA modulation and degradation.

This study investigates the putative roles of impaired NIX-mediated mitophagy in cellular senescence of experimental periodontitis under hyperglycemia conditions. Hyperglycemia and a persistent inflammatory micro-environment induced intracellular mtROS accumulation and led to a significant decrease in the expression of NIX, a key protein in the outer mitochondrial membrane, and impaired mitophagy. The periodontal ligament cells exhibited cell cycle arrest, upregulation of SASP expression and senescent cell accumulation, resulting in enhanced periodontal tissue destruction.

The authors show the utility of their computational tool, available at https://enzymeevolver.com, for the identification of novel photoreceptors. Signature residues for the binding of the green-light-sensitive cofactor adenosylcobalamin were determined. The light-sensitive reactions of exemplar proteins containing the proposed signature were confirmed experimentally through biochemical, spectroscopic and crystallographic techniques. Additional green- and red-light-induced photoreceptors are proposed.

Transglutaminase 2 (TG2) is a unique multifunctional protein. It has various transglutaminase and other catalytic and non-catalytic properties that are conformation-dependent. This study characterises the previously undescribed, open conformation-related RNA-binding ability of TG2.

We assessed the effects of gut microbiota on memory impairment in hypoxic mice. Our results showed that memory impairment in hypoxic mice was associated with gut microbiota dysbiosis accompanied by increased gut barrier and blood–brain barrier permeability. Moreover, we found that Ligilactobacillus and Muribaculum were the key microbiota affecting memory function, with the intestinal and blood–brain barriers serving as the primary pathways.Created with BioRender.com.

Japanese encephalitis is the leading cause of viral encephalitis in India and contributes to a significant disease burden in South Asian countries. However, there is a lack of effective treatments, highlighting the urgent need for novel therapeutic approaches. Here, we utilized a combined strategy of proteomics studies and connectivity map-based analysis to identify promising inhibitors for treating Japanese encephalitis viral infection.

Polysome profile analysis indicates that the translation of most mRNAs is suppressed during hypoxia. However, the collagen-modifying enzymes PLOD2 and P4HA1 remain to be efficiently translated under these conditions. The hypoxia-induced translation of PLOD2 and P4HA1 mRNAs relies on RBM4 and eIF4E2 in human colon cancer HCT116 cells. Both PLOD2 and P4HA1 are essential for collagen hydroxylation, which is critical for extracellular matrix (ECM) remodeling and metastasis.

Cobalamin biosynthesis can be traced back to the last universal common ancestor. After a stage of chemical evolution of the acetyl-CoA pathway, the enzymatic synthesis of cobalamin evolved, allowing life to be independent of the insoluble solid-state catalysts that tethered primordial CO₂ assimilation to the Earth's crust, suggesting a role for corrin synthesis in the origin of free-living cells, acetogens and methanogens.

To investigate the impact of dietary components on animal growth, an Escherichia coli single-gene deletion library was screened using the Caenorhabditis elegans growth model. Thirty-four E. coli mutants were identified to delay worm development. Notably, E. coli purE gene is a critical genetic factor that promotes host development in a dose-dependent manner. Certain intermediates from bacterial purine metabolism act as cues to modulate development and activate the DAF-16-mediated stress response in C. elegans.

Shh, expressed in epithelial cells, is an early key signaling molecule in palate development. We found that ISL1 regulates Shh expression in palatal epithelial cells, suggesting a critical role for ISL1 in epithelial–mesenchymal interactions during palatal development. Hedgehog signaling mediates the effect of ISL1 on palate development by regulating the expression of Sox2, Foxe1, Foxd2, and Msx1. The ISL1 mutant provides a disease model for understanding the pathogenesis of cleft palate and developing potential therapies.

Recent studies show that Ni⁰ catalyzes amino acid synthesis from 2-oxoacids via reductive amination. We show that the cofactor pyridoxal is reductively aminated to pyridoxamine, the NH₂-transferring intermediate of transaminations, with NH₃ (~ 5 mm) and H₂ (5 bar) on Ni⁰ catalysts within hours in water under serpentinizing hydrothermal vent conditions (pH 11 and 80 °C). At metabolic origin, this hybrid catalytic shuttle connects solid-state catalysts to aqueous phase pyridoxamine-dependent transaminations.

Aminoacyl-tRNA synthetases catalyze the ligation of a specific amino acid to a cognate tRNA—a reaction that lays the foundations for deciphering the genetic code. Pathogenic alleles in these synthetases can lead to dominant or recessive disorders, for which little or no disease-specific treatments exist. We review pathogenic human synthetase alleles, the molecular and cellular mechanisms of disease, and approaches to allele-specific treatment.

Inflammation contributes to male infertility primarily due to the activation and recruitment of immune cells to the reproductive organs and the further abundant release of different pro-inflammatory mediators. Prolonged inflammation injures testicular cells, which sustain spermatogenesis and steroidogenesis, and can result in morphologically abnormal dysfunctional sperm. Here, we discuss the ways in which inflammation can impair male reproductive function and outline the most common inflammatory factors that negatively impact male fertility.

This study investigated the Cryo-EM structures of full-length human contactin-2 (CNTN2). We found that full-length human CNTN2 exhibits concentration-dependent homodimerization. Notably, our results indicate that the Ig1-6 domains, rather than the previously proposed Ig1-4 domains, are crucial for facilitating CNTN2-dependent cell adhesion and clustering. Additionally, structure-guided mutagenesis analyses further confirmed that the homodimerization of CNTN2, as observed in our structural data, is essential for effective cell adhesion.

The presence of a resident or transient microbiome in the blood has been explored and debated for over a decade. Here, we evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples using specific negative controls. Our results strongly suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people.

Porphyromonas gingivalis (Pg), a periodontal bacterium implicated in systemic diseases, release outer membrane vesicles (OMVs). Here, we show that Pg OMVs induce stress fiber formation and degrade vascular endothelial cadherin (VEc) via lysosomes and endosomes in endothelial cells, leading to hyper-permeability. The inhibition of Rho kinases impairs this. These findings provide new insights into the pathogenesis of systemic diseases associated with periodontal diseases.

Calcium/calmodulin-dependent serine protein kinase interaction protein 1/2 (Caskin1/2) is essential neuronal scaffold protein with tandem SAM domains that form homopolymers. We identified SASH1 as a novel binding partner of Caskin1/2 and found that it could disassemble Caskin1-SAMs homopolymers through heterogeneous SAM-SAM interactions. Specifically, the mid-loop (ML) of SASH1-SAM1 binds the end-helix (EH) of Caskin1-SAM1 via electrostatic interactions, disrupting polymers. The new interaction and depolymerization mechanisms underpin Caskin1's neuronal role.

Problem-based learning (PBL) has become a widely used pedagogy across medical schools. Central to the success of any PBL program are the cases, each of which is a narrative of a patient's experience of disease. We provide guidance to case authors to optimize the value of cases to learners, while avoiding key pitfalls. Our approach is a methodical stepwise process that can be easily followed by the novice writer.

Here, we report KTX207, a previously undescribed cereblon-based PDE4 PROTAC that can specifically target PDE4D shortform for degradation. We showed that KTX207 could improve selectivity, potency and enable a long-lasting effect when used at a sub-nanomolar concentration. A significant decline in cell growth and TNF-α inhibition pinpointed the anti-proliferative and anti-inflammatory effects of KTX207. Our work highlights the advantages of targeted degradation to establish isoform specificity, which represents an evolution in the development of PDE4 inhibitors.

Historically, cytokines belonging to the gp130 family bind to specific ligand-binding receptors that stimulate cell signaling through a receptor complex comprising gp130, or gp130 together with another structurally related signaling receptor. However, recent findings increasingly dispel these stereotypes and suggest that the receptor specificity of gp130-activating cytokines is less strict than originally assumed. Weitz et al. now provide the latest example of this pleiotropy and report that human interleukin-6 can bind and stimulate signaling via the interleukin-11 receptor.

Comment on: https://doi.org/10.1111/febs.17309.

Kinetics, pH-temperature optima, and substrate preference for CNP-α-l-Fuc and 2′FL in hydrolysis were determined for three novel (EaGH29, SeGH29, and PmGH29) and two previously identified GH29A α-l-fucosidases (BF3242 and TfFuc1). All five enzymes also catalyzed transglycosylation, which was favored at high neutral to alkaline pH. New crystal structures of TfFuc1 and BF3242 presented an unconventional Asn residue located between the two catalytic residues in the active site.

The acquisition of bacterial endosymbionts by ancient host cells followed by massive adaptation of the partners gave rise to mitochondria and plastids. Today, various systems with younger and less integrated endosymbionts provide insights into the initial steps in the endosymbiont to organelle transition. In this review, we summarize the current evidence for protein import into diverse bacterial endosymbionts which represents a hallmark in this transition process.

Colorectal cancer (CRC) is a significant global health concern. Villin-1 (VIL1) is significantly upregulated in CRC at both the mRNA and protein levels as confirmed by transcriptomics and western blot analysis. VIL1 promotes proliferation and migration while inhibiting apoptosis. Conversely, knockout of VIL1 suppresses these effects and activates ferroptosis. VIL1 binds to NF-κB, controlling its expression. Overexpression of VIL1 inhibits ferroptosis and promotes tumor growth. The VIL1/NF-κB axis regulates CRC progression, making the VIL1 a potential therapeutic target in CRC.

Alexander Wlodawer is a structural biologist who has made seminal contributions to our understanding of protein structure–function relationships. He obtained his PhD from the University of California, Los Angeles, and has spent the majority of his career at the National Cancer Institute in Frederick, Maryland, where he currently holds a Senior Investigator position at the NCI's Center for Structural Biology. He has been a member of the Editorial Board of The FEBS Journal since 2007. In this interview, Alex talks about carving his own scientific path, the era of ‘big things’ in structural biology, and the most challenging editorial task.

This editorial highlights and celebrates the winner of the 2024 Richard Perham prize. This was selected from shortlisted original articles that were published in The FEBS Journal in 2023 and received prize nominations from the Editorial Board. The winning paper, by Matteo Brindisi, Luca Frattaruolo, Federica Sotgia, Michael P Lisanti, Anna Rita Cappello and colleagues, shows how high cholesterol levels promote breast cancer aggressiveness. Image created using Wordclouds.com.

This paper reviews a decade of research on FAHD1, an important yet underappreciated enzyme in mitochondrial metabolism. FAHD1 plays a crucial role in energy production, oxidative stress regulation, and processes related to aging and overall health. Here, we highlight FAHD1's potential as a therapeutic target due to its influence on key metabolic pathways essential for cellular function. The research advocates for broader recognition of FAHD1 in metabolic science, especially regarding its relevance to aging and metabolic health. The mitochondrial schematic in the background of the Graphical Abstract was generated using DALL-E, an AI-based image generation tool.

ADP-glucose pyrophosphorylase (GlgC) catalyses the rate-limiting step in glycogen synthesis, converting glucose-1-phosphate to ADP-glucose. Here, GlgC activity was coupled to glycogen synthase (GlgA), whereby ADP-release causes NADH oxidation through pyruvate kinase (PK) and lactate dehyrdogenase (LDH) reactions, recorded at 340 nm. Reassessment of GlgC catalytic properties revealed a complex interplay between activator molecules (3-PGA) and inhibitors (inorganic phosphate), showing how glycogen formation responds to carbon and energy fluctuations in cyanobacteria.

A carbonic anhydrase, PhyCA, from the hydrothermal vent bacterium Persephonella hydrogeniphila, was investigated by introducing various single mutations to its proton shuttling residues. Enzymatic activity and thermostability was assessed for each mutant, revealing functional differences. Molecular dynamics simulations were conducted to observe conformational changes caused by the mutations. This study highlights how specific mutations in the carbonic anhydrase active site can impact proton shuttle efficiency and protein stability, contributing to a better understanding of carbonic anhydrase function.

Depletion of regulatory T cells (Tregs) from CD4⁺ CAR-T cells enhances the antitumor effects of CD8⁺ CAR-T cells in CD19-targeted immunotherapy against CD19-expressing B-cell lymphoma or leukemia. CD4⁺ CD25- helper T cells promote CD8⁺ cytotoxicity through IL-2 signaling, while CD4⁺ CD25⁺ Tregs suppress CD8⁺ killing by reducing IL-2 availability. Removing Tregs from the CD4⁺ CAR-T cell population augments the tumoricidal activity of CD8⁺ CAR-T cells in vitro and in in vivo xenograft models.

Mutations in lysyl oxidase (LOX), a predominantly extracellular matrix-modifying enzyme, are highly associated with aortic aneurysms in humans and mice. Using a conditional knockout strategy, here we show that LOX-specific deletion in smooth muscle cells leads to cytoskeletal defects and abnormalities in calcium homeostasis, which are processes also associated with aneurysms. Our results suggest that LOX serves as a coordinator of multiple cellular events that safeguard the aortic media from such vascular diseases.

The electrospray ionization mass spectrometric experiments reported in this study describe the resistance to the oxidation of the cysteines of metallothionein-3 to form disulfide bonds by the presence of differing stoichiometries of cadmium and zinc. The rate of oxidation of the cysteines in metallothionein-3 was determined following addition of a single aliquot of the oxidant. The mass of the protein decreased by 2 Da for every disulfide bond formed.

Adaptive transcription via molecules such as CREB, MEF2, SRF, AP1, Nr4a1, and Egr1 constitutes a universal mechanism for directed cell state transitions in health and disease. These molecules are involved in physiological adaptation processes, pathological maladaptations, curative adaptations, and development of resistance to treatment. Decoding the logic behind adaptive transcription programs will uncover fundamental organizational principles of biological systems and facilitate the development of novel therapeutic concepts for a variety of diseases.

Copper is essential, yet toxic. High levels of copper are removed from the cells by proteins called P_1B-ATPases that have poorly understood metal-binding domains (MBDs). Here, we present MBD structures from the P_1B-ATPase LpCopA, where a metal-binding core senses copper conditions, enabling a flexible tail to block copper export at low concentrations and to allow export at higher copper levels. Thus, these ‘vacuum cleaners’ tune their own activity and balance cellular copper levels.

Ruminococcus gnavus (R. gnavus) can degrade mucin, modify bile acids, and secrete metabolites into circulation via the portal vein to the liver for further processing and subsequent systemic circulation. R. gnavus is associated with metabolic syndrome and inflammatory bowel disease severity. It is suspected that R. gnavus may play a role in liver function, as its increased presence is associated with excessive steatosis and delayed clearance of the hepatitis virus in both clinical and preclinical studies.

Aberrant activation of Wnt signalling leads to human diseases such as cancer. At steady state, the levels of β-catenin, a key mediator of Wnt signalling output, are tightly controlled by a cytosolic “destruction” complex or degradasome, which consists of APC, AXIN, and the kinases CK1α and GSK3β. By performing quantitative analysis of cellular AXIN protein levels at steady state, in AXIN2 knockout cells and upon tankyrase inhibition (TNKSi), Schmidt et al. revealed a unique role of AXIN2 in regulating the total AXIN pool (TAP) and Wnt/β-catenin signalling activity, which has important clinical ramifications.

Comment on: https://doi.org/10.1111/febs.17226.

Some enzymes are able to catalyse the same reaction despite possessing different structures. Here, we used a combined strategy of analysing published literature and knowledge-based computational resources to explore this. We conclude that multiple varieties of convergent functional evolution exist to date, but that it is necessary to investigate sequence, structural features, active site geometry and enzyme mechanisms to accurately identify cases with such convergence.

Solid-state NMR has emerged as an important technique for studying membrane fusion. In this review, we summarize recent advancements in solid-state NMR for investigating membrane fusion proteins and their applications in elucidating the mechanisms of membrane fusion. Created using WPS software.

The genome of the marine bacterium Halomonas titanicae KHS3 codes for a chemotaxis-related signal transduction pathway that controls the activity of an associated diguanylate cyclase, and shares similarities with the Wsp pathway from Pseudomonas. In this work, we identify guanine and hypoxanthine as specific ligands for its receptor, Htc10. We further demonstrate that Htc10 heterologously activates the Wsp pathway in Pseudomonas putida and responds to the discovered ligands.

This study explores how fluid viscosity influences cell behavior and ECM remodeling. Elevated extracellular fluid viscosity induces collagen substrate remodeling and enhances cell spreading. We identify cytoskeletal regulators of this process. Further, we show that high osmotic pressure overrides viscosity-induced cell spreading. Our findings illuminate viscosity's role in both physiological and pathological conditions, shedding light on potential therapeutic targets.

White adipose tissue (WAT) is essential for energy balance and hormone regulation. In obesity, WAT becomes dysfunctional, leading to inflammation and other changes that promote different stages of carcinogenesis. This review explores how unhealthy WAT under obese conditions supports carcinoma growth through both systemic effects and modulation of the local tumor microenvironment. We discuss the bidirectional interaction between tumors and WAT, highlighting promising targets for cancer treatment. Figure created with Biorender.com.

In Drosophila, daily rhythms have been identified in the fly visual structures, in terms of gene expression, morphology, and behavior. A functional circadian clock in the retina is important not just for the fine-tuning of visual sensitivity, but also for the proper maintenance of neuronal integrity.

The D5 helicase–primase enzyme is a crucial component of the viral replication machinery associated with the Mpox virus. Here, we describe the structural features of the D5 protein and discuss the implications of its role in the genome uncoating process and Mpox viral replication.

The major pro-inflammatory cytokine IL-6 signals via the IL-6 α-receptor in complex with the gp130 β-receptor. Here, we show that IL-6 also binds to the IL-11 α receptor and induces signaling via gp130 homodimers, albeit with a lower affinity compared to IL-11. These findings provide new insights into IL-6 signaling and therefore offer new potential therapeutic intervention options in the future.

ZO-2 acts as a scaffold for LATS1 and YAP, thus bringing them together and facilitating their interactions. Increasing ZO-2 levels can promote the interaction between LATS1 and YAP until ZO-2 exceeds the concentrations of LATS1 and YAP. High levels of ZO-2 titrate LATS1 and YAP into separate complexes, thus inhibiting their interactions.

The cytokine IL-11 binds to the cell surface receptors IL-11Rα and gp130 to form a hexameric signalling complex. Variants of IL-11Rα and gp130 are associated with craniosynostosis, resulting in an altered skull shape and bone metabolism. In this structural snapshot, we use our recent structure of the IL-11 signalling complex to examine the positions and environment of craniosynostosis-associated receptor variants, revealing amino acid types and locations that are highly represented.

Autophagy is a key regulator of macrophage function, influencing critical processes like polarization, cytokine secretion, and phagocytosis. Its impact on macrophage behavior varies across different tissues and disease contexts, where it can either promote protective responses or contribute to detrimental outcomes, depending on the physiological or pathological conditions.

Traditionally, adipocytes have been viewed as energy storage units, which upregulate inflammatory factors in response to obesity. However, emerging evidence demonstrates that adipocytes are highly responsive to systemic infection, and upregulate cytokines and antimicrobial compounds in response. Here, we propose that adipocytes form immune hubs that are able to integrate local immune signals and, in turn, disseminate their own signals to control the local immune response and pathogen burden.

α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) allow calcium influx into the cell through their interactions with various auxiliary proteins. Excessive calcium influx leads to overexcitation, causing seizures, mood disorders and confusion. Auxiliary subunit regulators which promote Stargazin inhibition, cornichon homolog (CNIH)-3 upregulation and γ8 dual modulation can alter AMPAR gating mechanisms and kinetics to decrease the calcium influx, as well as subsequently attenuate overexcitation.

Increased sugar consumption is a main driver of the increased prevalence of obesity and non-communicable diseases (NCDs). Therefore, understanding host and microbial sugar metabolism and its metabolic effects is crucial. A high-sugar diet can induce gut dysbiosis, and gut microbial sugar fermentation can produce deleterious metabolites, potentially contributing to the development of NCDs. However, the intricate relationship between dietary sugars and the gut microbiota requires further elucidation.

Mitogen-activated protein kinases (MAPKs) regulate various cellular processes, including proliferation, differentiation, and motility. Alterations in these signalling pathways can lead to various diseases, including cancer. The atypical MAPKs ERK3 (MAPK6), ERK4 (MAPK4), ERK7/8 (MAPK15) and NLK have long been neglected in kinomic studies. This review highlights their unique characteristics and important physiological roles, as well as their potential for targeting strategies in cancer therapy. Created with BioRender.com.

The accumulation of senescent cells in the skin contributes to age-related phenotypes including extracellular matrix (ECM) degradation, chronic inflammation, and epidermal thinning. These changes impair the skin's fundamental role as a barrier against insult, injury, and infection. Here we highlight the underappreciated role of mTORC1 signalling and the lysosome in supporting senescence phenotypes in the skin, including the inflammatory senescence-associated secretory phenotype (SASP).

This review explores how changes in nucleotide metabolism affect the tumour microenvironment and immune responses in cancer. Here, we discuss the dual role of nucleotide metabolism in promoting cancer cell growth and shaping immune suppression. We highlight how therapies targeting nucleotide pathways can enhance immunotherapy efficacy, offering new strategies for more effective and personalised cancer treatments. Figure created using Biorender.com.

In this state-of-the-art review, we describe how DNA- and RNA-binding proteins (DRBPs) may bind both DNA and RNA and discuss the putative functional relevance of this dual binding. Furthermore, we perform an exploratory analysis into protein domains that are associated with DRBPs. Importantly, to exemplify the significance of DRBPs in T cell biology, we detail the activity of several established and putative DRBPs during the antigen-induced T cell response.

Breast cancer is a complex disease significantly influenced by estrogen receptors (ERs) and the extracellular matrix (ECM), both of which are critical in shaping tumor behavior. ERα and ERβ modulate cancer progression and therapeutic response with their interactions intricately linked to ECM dynamics. The ECM, integral to the tumor microenvironment, cooperates with ERs to regulate cellular functions. Deciphering the ERs-ECM complex interactions offers the potential for advancing breast cancer therapies.

Disrupted cholesterol homeostasis commonly features in the development of multiple disease pathologies. Here, we explored the role of cholesterol in the development of inflammatory bowel disease (IBD). We found that exposure to high cholesterol inhibits SREBP2, subsequently promoting the endocytic degradation of tight junction proteins (TJPs), resulting in epithelial barrier impairment. Using a UK Biobank cohort, we additionally identified a single nucleotide polymorphism in SREBF2, the gene encoding SREBP2, associated with IBD incidence in humans.

The human β₁-adrenergic receptor (β₁AR) carries common (S49G) and rare (R31Q, A29T) single-nucleotide polymorphisms (SNPs) in its extracellular N-terminal domain. These were found to alter receptor O-glycosylation and/or proteolytic cleavage, resulting in SNP-dependent differences in β₁AR cell surface expression and function that also involved the common C-terminal R389G polymorphism. Thus, GPCR SNPs can modify receptor processing and function even when located outside well-known domains that govern ligand binding and activation.

The W proteins of Nipah and Hendra viruses exhibit fibrillation abilities in vitro, which have been attributed to the intrinsically disordered N-terminal domain (NTD). Our research shows that the C-terminal domain (CTD) of both viruses is intrinsically disordered and non-fibrillogenic. Furthermore, we demonstrate that CTD and NTD interact with each other and that this interaction drives protein compaction and affects the secondary structure content, thereby favoring fibril elongation over nucleation.

An unhealthy diet impairs the symbiotic relationship between the gut microbiota and the host, contributing to obesity. At the intestinal level, identification of host–microbe events essential for proper neuroendocrine/immune signaling is key to the development of microbiome-based strategies to promote metabolic health in obesity (probiotics, biotherapeutic products, and fecal microbiota transplantation). These strategies may help restore food sensing and so, eating behavior, and confer protection against intestinal and systemic inflammation.

Mannose, which is the C-2 epimer of glucose, has the ability to dampen the Warburg effect, resulting in slow-cycling cancer cells that are highly susceptible to chemotherapy. This anticancer effect of mannose appears when its catabolism is compromised in cancer cells. Moreover, de novo synthesis of mannose within cancer cells has also been identified as a potential target for enhancing chemosensitivity through targeting glycosylation pathways. This review summarizes the current state of our knowledge of mannose metabolism and provides insights into its manipulation as a potential anticancer strategy.

Vaccination plays a crucial role in mediating protection against infectious diseases, but immune responses to vaccination are highly variable and frequently sub-optimal in vulnerable populations. Here, we review the latest preclinical and clinical evidence demonstrating that the gut microbiota plays a significant role in regulating immune responses to vaccination, discuss the potential mechanisms involved, and suggest future avenues of research in this field.

Here, we discuss how lung cancer treatment can be transformed by targeting TGF-β for better outcomes. Inhibiting TGF-β signaling halts tumor growth, boosts immune response, and enhances treatment efficacy. By tackling TGF-β's role in epithelial–mesenchymal transition (EMT) and immune evasion, this approach opens new avenues for more effective lung cancer therapies and improved patient outcomes, offering hope for a brighter future in lung cancer treatment and patient care.

The vaginal microbiota is a protective gateway for the urinary and reproductive systems and evidence supports that predominant colonization by lactobacilli, particularly Lactobacillus crispatus, can multimodally protect against urogynecologic pathogens. Here we review emerging insights into host-microbiome interactions that present promising opportunities for future therapies in the management of urogenital diseases, including bacterial vaginosis, urinary tract infections, bladder pain syndrome, urinary incontinence, and more. Created with BioRender.com.

AXIN1 and AXIN2 are highly related proteins that inhibit the proto-oncogenic Wnt/β-catenin pathway. Both proteins are degraded through a tankyrase (TNKS)-dependent mechanism. Here, we show that AXIN2 promotes TNKS-mediated degradation of AXIN1. Mechanistically, AXIN2 recruits TNKS into AXIN1 condensates because it interacts with both components. Concordantly, loss of AXIN2 disrupted regulation of AXIN1 expression by TNKS in SW480 colorectal cancer cells, which may have therapeutic implications for colorectal cancer through TNKS inhibitors.

Ensuring the synthesis of full-length, correctly folded proteins is vital for maintaining homeostasis. If a translating ribosome stalls, the trailing ribosomes collide into it, which if left unresolved leads to deleterious effects on the cell due to the accumulation of protein aggregates. Ribosome Quality Control (RQC) detects the collided ribosomes and removes the aberrant mRNA and nascent peptide. Conversely, dysfunctional RQC or excessive ribosome collisions that overwhelm RQC can lead to proteotoxicity and diseases.

Following antigen stimulation, naïve T cells undergo activation and differentiate into effector and memory T cells. These cell fate transitions are accompanied by dynamic reorganization of the 3D genome architecture across multiple levels including compartments, topologically associating domains and loops. Here, we summarize the evidence connecting changes in genome organization to transcriptional remodeling during T cell activation and discuss the diverse mechanisms that collectively reshape genome architecture during this process.

Centrosomes are dominant microtubule-organizing centers in animal cells that are required for efficient mitoses to ensure normal embryonic development. Mammalian cells respond to centrosome loss-of-function by activating the mitotic surveillance pathway, a timing mechanism that leads to 53BP1-, USP28-, and p53-dependent cell death or arrest when a defined threshold is exceeded. Mouse embryos without centrosomes undergo embryonic arrest at mid-gestation (E9) whereas different developing tissues mount graded responses to centrosome loss (≥ E15).

The gut microbiome and its metabolic byproducts play crucial roles as regulators of the bidirectional gut–brain axis. In this review, we describe the mechanisms through which the interaction between gut microbial products and host receptors influences the pathophysiological changes seen in Disorders of Gut–Brain Interaction, specifically their effect on the gastrointestinal transit, visceral sensitivity, intestinal barrier function, secretion, and central nervous system processing. Figure created using BioRender (biorender.com).

This review explores the eukaryotic Nα-terminal acetyltransferases (NAT), a family of key enzymes that co-translationally modify protein N-termini. Aberrant expression and mutant NAT variants are implicated in various human diseases such as cancer, neurodevelopmental disorders and a family of rare developmental syndromes. Highlighting the complex role of Nα-terminal acetylation in protein folding and aggregation, here, we have reviewed its impact on disease-associated proteins including alpha-synuclein and huntingtin.

In cells of the myeloid lineage, NLRP3 stimulation leads to disassembly of the trans-Golgi network (TGN). The resulting dispersed TGN serves as a scaffold for NLRP3 aggregation, leading to cytokine production and pyroptosis. In contrast, it is proposed that the magnitude of interactions between the polybasic motif of NLRP3 and the TGN in adaptive immunity is low, which triggers cytokine production, but does not result in pyroptotic cell death.

During ER stress, an accumulation of misfolded proteins within the ER disrupts proper ER-protein folding. Thus, there is a need for ER quality control mechanisms to decrease ER-protein load until the stress is resolved. In this review, we highlight five mechanisms that aim to decrease ER-protein load and increase ER-protein folding capacity, and we discuss the crosstalk between them. Graphical abstract created with Biorender.com.

This review explores the enigmatic centriolar satellites, which are crucial cellular structures first identified in vertebrate cells. We highlight their roles – from forming cilia to responding to cellular stress. Centering on the scaffolding protein PCM1, we reveal their significance in health and disease, highlighting their connection to developmental and neurodegenerative disorders, and setting the stage for further investigation into their intriguing biology.

The gut-brain axis regulates bidirectional interactions between gut microbiota and the central nervous system (CNS) in multiple sclerosis (MS) and MS experimental models. Here, we summarize the most significant contributions to this emerging field of research. We further highlight the effects of diet on the microbiota and propose cellular and molecular mechanisms that govern these interactions in the context of the disease.

Actin isoforms are abundant cytoskeletal proteins that exhibit high structural and functional conservation yet have different cellular roles. This review discusses the structural and functional roles of actin isoforms, their biochemistries, and interactions with myosin motor proteins. Further, this review discusses the implications of post-translational modifications and disease-causing mutations on actin isoform biochemistry, function, and interactions.

This work investigates the archaeome, an essential segment of the human microbiome, focusing on its relationship with the immune system. Here, we outline the types of archaea across different body areas and underscore possible links to health issues, such as obesity and specific cancers. Additionally, we emphasize recent findings on the role of archaeal molecules and by-products, including methane, in influencing immune reactions and their effects on immune mechanisms.

Germ-free and gnotobiotic mouse technology allows the unraveling of complex host–microbiota interactions within a reductionist framework. The implementation of these methodologies poses significant technical and experimental challenges. This review explores practical insights aimed at enhancing the precision and success of germ-free and gnotobiotic experiments.

Disturbances of the microbiota–gut–brain axis are evident in people with Huntington's disease (HD) and in HD animal models. Here, we provide an overview of how the trillions of microorganisms residing in the gut, their secretory products, and the microbiota–gut–brain axis may contribute to HD pathogenesis. We discuss in depth the currently available therapeutic strategies targeting gut microbes, and their promising potential as non-invasive, safe, and efficacious treatments for HD.

Numerous microbes, including those indigenous to the human microbiome, produce amyloidogenic proteins. These proteins have critical functions in bacterial physiology and their lifestyles. Emerging evidence indicates that microbial amyloids also interact directly or indirectly with host-derived amyloid proteins, such as those which underlie Parkinson's and Alzheimer's diseases. In this review, we discuss these interactions between microbial and host amyloid proteins and their contributions to neurodegenerative, amyloid diseases.