The FEBS journal最新文献

{"title":"A CRISPR-Cas9-based system for the dose-dependent study of DNA double-strand break sensing and repair.","authors":"Morgane Auboiron, Jocelyn Coiffard, Sylvain Kumanski, Olivier Santt, Benjamin Pardo, María Moriel-Carretero","doi":"10.1111/febs.70143","DOIUrl":"https://doi.org/10.1111/febs.70143","url":null,"abstract":"<p><p>The integrity of DNA is put at risk by different lesions, among which double-strand breaks (DSBs) occur at a lower frequency but have the most life-threatening consequences. The study of DSB repair requires tools that can induce the accumulation of these breaks and includes the use of chemical genotoxins, ionizing radiation, or the expression of sequence-specific nucleases. While genotoxins and irradiation allow for dose-dependent studies, nuclease expression permits assessments at precise locations. In this work, we have leveraged the repetitive nature of the Ty transposon elements in the genome of Saccharomyces cerevisiae and the cutting activity of the RNA-guided Cas9 nuclease to create a tool that combines sequence specificity and dose-dependency. In particular, we can achieve the controlled induction of 0, 1, 15, or 59 DSBs in cells with an otherwise identical genetic background. We make the first application of this tool to better understand the behavior of the apical kinase of the DNA damage response Tel1 in the nuclear space. We found that Tel1 is capable of forming nuclear foci, which are clustered by condensin when DSBs occur in Ty elements. In striking contrast with other DSB-related protein foci, Tel1 foci are in tight contact with the nuclear periphery, therefore suggesting a role for the nuclear membrane in their congregation.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A somatic multiple myeloma mutation unravels a mechanism of oligomerization-mediated product inhibition in GGPPS.","authors":"Ruba Yehia, Jasmína Mária Portašiková, Rut Mor Yosef, Benny Da'adoosh, Alan Kádek, Petr Man, Moshe Giladi, Yoni Haitin","doi":"10.1111/febs.70181","DOIUrl":"https://doi.org/10.1111/febs.70181","url":null,"abstract":"<p><p>Protein prenylation plays a critical role in regulating the cellular localization of small GTPases and is essential for multiple myeloma (MM) pathology. Geranylgeranyl diphosphate synthase (GGPPS), producing a key prenylation moiety, exists in a dimeric or hexameric form, depending on the species. However, the functional significance of this oligomerization remains unclear. Using crystallography, mass spectrometry, and fluorescence spectroscopy, we show that the GGPPS^R235C mutant-found in the widely studied MM cell line RPMI-8226-exhibits weakened inter-dimer interactions, reduced hexamer stability, and increased apparent substrate affinity and product release kinetics. These effects are even more pronounced in a dimeric mutant, GGPPS^Y246D, demonstrating that interdimer interactions within the hexamer help stabilize a lid region over the active site, thereby stabilizing product binding in an inhibitory conformation. Together, these findings reveal that hexamerization regulates GGPPS activity through product inhibition and underscore the importance of cell line selection and characterization in drug discovery efforts.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the plasticity of substrate recognition by Staphylococcus aureus lysyl-tRNA synthetase and its implications for misacylation.","authors":"Jaykumar Jani, Jigneshkumar Mochi, Smit Shah, Apurba Das, Dhaval Patel, Gayathri Pananghat, Anju Pappachan","doi":"10.1111/febs.70185","DOIUrl":"https://doi.org/10.1111/febs.70185","url":null,"abstract":"<p><p>Transfer RNA (tRNA) misacylation is a widespread phenomenon that affects translational fidelity due to the incorporation of non-cognate amino acids into proteins. We investigated the structural basis for the misacylation of tRNA^Lys by Staphylococcus aureus lysyl-tRNA synthetase (SaLysRS). Activity studies showed that SaLysRS misacylated tRNA^Lys with methionine and arginine. In vivo studies and MALDI-TOF analysis revealed the utilisation of these mischarged tRNAs in protein translation, as deciphered from the incorporation of non-cognate methionine and arginine into proteins. The misincorporation was also detrimental to cell growth. The three-dimensional structure of SaLysRS with its cognate substrate lysine was resolved at 2.3 Å resolution, which revealed key residues and conserved motifs needed for substrate recognition. Structural and mutational analysis and molecular dynamics simulations identified Glu233, Tyr273 and Glu420 as crucial residues for both cognate and non-cognate ligand binding. These insights, well-supported by structural, biochemical and computational data, enhance our knowledge of the mechanisms underlying misacylation in tRNA synthetases and its implications for cell growth.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A guide to characterizing the dynamic mitochondria-endoplasmic reticulum contact sites.","authors":"Antigoni Diokmetzidou, Luca Scorrano","doi":"10.1111/febs.70184","DOIUrl":"https://doi.org/10.1111/febs.70184","url":null,"abstract":"<p><p>Organelles were once regarded as discrete entities, but it is now established that they interact through specialized membrane contacts maintained by protein tethers and lipid interactions. Among these, mitochondria-endoplasmic reticulum contact sites (MERCS) emerged as hubs for calcium signaling, lipid metabolism, and mitochondrial dynamics. Here, we critically appraise current methodologies for MERC visualization and quantification, survey the molecular toolbox for their selective perturbation, and highlight common experimental pitfalls. We also discuss key conceptual issues-defining MERCs on structural and functional grounds, addressing redundancy among tethering factors, and distinguishing primary MERC-mediated effects from secondary cellular responses. Finally, we propose that an integrative strategy combining imaging, precise biochemical isolation, proteomics, and functional assays will be essential to resolve outstanding questions about MERC dynamics in physiology and pathology.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Helicobacter pylori infection promotes the formation of the β-catenin/HIF-1α complex, enabling adaptive responses in gastric cancer cells.","authors":"Héctor A Tapia, Camila García-Navarrete, Patricio Silva, Joaquín Lizana, Carla Fonfach, Ignacio Pezoa-Soto, Tania Flores, Nadia Hernández, Daniel Peña-Oyarzún, Jorge Toledo, Safka Hernández-Gutiérrez, Daniela Herrera, Manuel Varas-Godoy, Denisse Bravo, Vicente A Torres","doi":"10.1111/febs.70179","DOIUrl":"https://doi.org/10.1111/febs.70179","url":null,"abstract":"<p><p>Helicobacter pylori is a gastric pathogen associated with the development of gastric cancer. By attaching to the gastric epithelium, it triggers signaling pathways that lead to effects ranging from apoptosis to cell proliferation. H. pylori has been shown to promote nuclear translocation of β-catenin, inducing gene expression related to the cell cycle. However, recent studies indicate it also causes cell cycle arrest by stabilizing hypoxia-inducible factor 1-alpha (HIF-1α). The mechanisms underlying these opposing effects remain unknown. Here, we explored the effects of H. pylori infection on β-catenin and transcription factor 7-like 2 (TCF7L2, also known as TCF-4) interaction, as well as downstream transcriptional activity. We observed that, despite maintaining total and nuclear levels of β-catenin and TCF-4, bacterial infection disassembled the β-catenin/TCF-4 complex, as shown by co-localization and co-immunoprecipitation assays. These changes were followed by decreased TCF/lymphoid enhancer-binding factor (Lef)-dependent transcription and reduced cell proliferative capacity. Conversely, H. pylori promoted the association of β-catenin and HIF-1α in a protein complex that enhanced transcription of hypoxia response elements. Inhibition of HIF-1α prevented this association and preserved β-catenin/TCF-4 interaction, restoring TCF/Lef-dependent activity. The requirement of HIF-1α was further confirmed by short hairpin RNA (shRNA) and by using a urease mutant strain unable to stabilize HIF-1α. Interestingly, infection was associated with upregulation of HIF-1α target genes involved in migration and invasion. Consequently, H. pylori increased cell invasion while decreasing cell proliferative capacity in a HIF-1α-dependent manner. Thus, our results demonstrate that H. pylori decreases cell proliferation by reducing β-catenin/TCF-4 interaction, while increasing β-catenin/HIF-1α complex formation, which is associated with cell invasion as an adaptive mechanism.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human tissue kallikrein 14 induces the expression of IL-6, IL-8, and CXCL1 in skin fibroblasts through protease-activated receptor 1 signaling.","authors":"Laura Sasiadek, Ewa Bielecka, Katherine Falkowski, Magdalena Kulczycka, Grzegorz Bereta, Anna Maksylewicz, Natalia Zubrzycka, Ewelina Dobosz, Joanna Kozieł, Justyna Drukała, Maciej Lech, Natalia Horbach, Marcin Poręba, Klaudia Brix, Grzegorz Dubin, Jan Potempa, Tomasz Kantyka","doi":"10.1111/febs.70170","DOIUrl":"https://doi.org/10.1111/febs.70170","url":null,"abstract":"<p><p>Human tissue kallikrein 14 (KLK14) is protease with trypsin/chymotrypsin specificity that is abundant in the skin. It is involved in skin desquamation and wound healing by cleaving cell-cell adhesion molecules and extracellular matrix components. In the process of wound healing, a paracrine communication between the epithelium, human skin fibroblasts (HSFs), and immune cells is essential for proper regulation. Previous reports highlighted stimulation of interleukin-6 (IL-6), interleukin-8 (IL-8), and growth-regulated alpha protein (CXCL1) production by keratinocyte-conditioned medium in fibroblast cells and implicated these cytokines in cancer. Here, we hypothesize that KLK14 may be a paracrine mediator released by keratinocytes that activates fibroblasts via proteinase-activated receptor (PAR) pathway, affecting the HSF secretome. Semiquantitative real-time PCR and ELISA demonstrated that proteolytically active KLK14 induced the expression of IL-6, IL-8, and CXCL1 by 15-, 847-, and 50-fold, respectively, and resulted in the release of the proteins in ng/ml quantities from stimulated HSFs to the culture medium. Through the implementation of the PAR-1 antagonist RWJ 56110, we demonstrated that the KLK14-mediated release of IL-6 and IL-8 is dependent on PAR-1 activation. Contrarily, PAR-1 activation was shown to function as a limiting factor in the KLK14-mediated CXCL1-releasing pathway. Furthermore, human recombinant IL-6, IL-8, and CXCL1 enhanced closure of a cell-free gap in an HaCaT cell monolayer, mimicking wound healing of keratinocytes in the skin. KLK14-stimulated HSF conditioned media also induced wound healing in the HaCaT model in an IL-6-dependent manner, as a cytokine-neutralizing antibody significantly decreased this activity. Thus, KLK14 in the skin may participate in paracrine signaling between fibroblasts and keratinocytes, in that keratinocyte-secreted KLK14 initiates the release of IL-6, IL-8, and CXCL1 from fibroblasts, which in turn act on proximal keratinocytes to trigger their migration for wound closure. Our findings add to the understanding of the role of KLK14 in the related processes of wound healing and tumor development.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omic analysis identifies biological processes underlying progressive interstitial lung disease in systemic sclerosis.","authors":"Selena Bouffette, Perrine Soret, Alice Cole, Emmanuel Nony, Pierre Barbier Saint Hilaire, Grégory Leclerc, Lamine Alaoui, Audrey Aussy, Isabelle Wehrle, Aude Le Gall, Mark Coulon, Marc Pallardy, Voon Ong, Jeanne Allinne, Philippe Moingeon, David Abraham, Christopher P Denton","doi":"10.1111/febs.70177","DOIUrl":"https://doi.org/10.1111/febs.70177","url":null,"abstract":"<p><p>Systemic sclerosis (SSc) is a rare autoimmune connective tissue disorder, and its primary cause of mortality is interstitial lung disease (ILD). This study aimed to identify markers in patients with SSc that are associated with ILD progression. In total, 52 SSc patients and five healthy volunteers (HVs) were included. Patient plasma samples were available for measurement of soluble mediators by metabolomics, proteomics, and cytokine quantification. Gene expression profiling was performed on patients' whole blood and skin biopsies, and immunophenotyping was carried out on peripheral blood mononuclear cells. Comparisons were made between patients with progressive ILD, those with no ILD, and HVs. Our results confirm the involvement of pro-inflammatory mechanisms in SSc-related ILD, with elevated type 1 interferon (IFN1), fractalkine (CX3CL1), and C-C motif chemokine 2 (CCL2), as well as the profibrotic markers C-X-C motif chemokine 17 (CXCL17), thrombospondin (THBS), and latent transforming growth factor beta-binding protein 1 (LTBP1). At the cellular level, lower inflammatory activity was observed in SSc-ILD patients, which may be due to ongoing immunosuppressive therapies. ILD progression is associated with a significant increase in plasma levels of cytoskeletal proteins and lipids, notably triglycerides. To our knowledge, this is the first study using an innovative approach to compare SSc patients with ILD to those without ILD. Our study was performed on well-characterized patients, from which we gathered insightful comparative data offering a multi-level biological picture of SSc-related ILD. A novel finding of our study is the correlation between elevated triglyceride levels and ILD progression, possibly linked to fibrogenesis through the role of triglycerides in endoplasmic reticulum stress.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to \"AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation\".","authors":"","doi":"10.1111/febs.70175","DOIUrl":"https://doi.org/10.1111/febs.70175","url":null,"abstract":"","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the roles of conserved context-dependent cis-regulatory elements (cdCREs) in multicellularity, human health and disease.","authors":"Andrew McEwan, Alexander Rattray, Greg Hutchings, Elizabeth Hay, Chris Murgatroyd, Alasdair MacKenzie","doi":"10.1111/febs.70174","DOIUrl":"https://doi.org/10.1111/febs.70174","url":null,"abstract":"<p><p>Human development and health depend on the precise expression of relevant genes in specific cells, at precise times and in response to appropriate stimuli. This is known as context-dependent gene regulation and relies on the activities of a diverse 'zoo' of DNA elements within the genome that are collectively called context-dependent cis-regulatory elements (cdCREs). cdCREs may comprise as much as 10% of the genome and include better-known sequences such as enhancers, silencers and promoters that form the basis of complex multicellularity. Diverse vertebrate body plans not only share considerable phenotypic similarities but also cell types, the genes they express and, in a growing number of cases, in the function and nucleotide sequence of cdCREs. The current review will critically evaluate current methodologies to identify cdCREs and re-evaluate a place for comparative genomics amongst them. We will also explore the function of cdCREs and discuss methods of analysing their function in disease-associated physiologies and behaviours using in vivo models such as CRISPR-generated GA mouse lines. Finally, we will study the effects of epigenetic mechanisms such as DNA methylation on cdCRE activity and examine how genetics and epigenetics can interact to alter disease susceptibility. Given that genome-wide association studies (GWAS) suggest that 95% of disease-associated genomic variation reside in the 98% of the less understood noncoding genome, the need to understand the role of conserved vertebrate cdCREs in development and health in vivo has never been more pressing.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the family of ankyrin repeat-containing proteins of Plasmodium falciparum: a structural and functional perspective.","authors":"Poonam Kumari, Avinash Kumar Gautam, Md Muzahidul Islam, Iqbal Taliy Junaid, Zainab Khan, Asif Mohmmed, Samudrala Gourinath, Pawan Malhotra","doi":"10.1111/febs.70178","DOIUrl":"https://doi.org/10.1111/febs.70178","url":null,"abstract":"<p><p>The invasion of host erythrocytes by Plasmodium falciparum is a fundamental step in its pathogenesis, relying on precisely regulated, transient interactions between parasite proteins and the host erythrocytes. Approximately 20% of eukaryotic proteins contain tandem repeat regions that majorly facilitate protein-protein interactions, with ankyrin (ANK) repeats being the most frequent, and are associated with various diseases. Despite significant advancements in understanding the importance of ANK repeats across various organisms, their roles within the phylum Apicomplexa, including P. falciparum, remain largely unexplored. This study focuses on the significance of ANK repeat proteins in P. falciparum growth and pathogenesis. Here, using in silico approaches, we deciphered the ANK repeat protein family in P. falciparum and elucidated the crystal structure of one of its members, PfANK_1. Co-immunoprecipitation assays revealed several potential interacting partners of PfANK_1, showing its involvement in the functioning of the PfClag9-PfRhopH complex. The stability and interactions of PfANK_1 within the complex were confirmed through multiple approaches, such as bio-layer interferometry (BLI), co-localization studies, and molecular dynamic simulations. Given the crucial role of the PfClag9-PfRhopH complex in erythrocyte invasion, PfANK_1 presents a promising druggable target. The structural analysis uncovered the binding interface and key interacting residues of PfANK_1 with the components of the PfClag9-PfRhopH complex. The work thus provides the first molecular and structural characterization of an ANK repeat protein in P. falciparum, offering new insights into the role of these proteins in the parasite life cycle and providing a potential platform for structure-function relationship-guided drug discovery.</p>","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}