The FEBS journal最新文献

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.

Biomolecular condensates are dynamic membraneless compartments that regulate a myriad of cellular functions. A particular type of physiological condensate called stress granules (SGs) has gained increasing interest due to its role in the cellular stress response and various diseases. SGs, composed of several hundred RNA-binding proteins, form transiently in response to stress to protect mRNAs from translation and disassemble when the stress subsides. Interestingly, SGs contain several aggregation-prone proteins, such as TDP-43, FUS, hnRNPA1, and others, which are typically found in pathological inclusions seen in autopsy tissues from amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients. Moreover, mutations in these genes lead to the familial form of ALS and FTD. This has led researchers to propose that pathological aggregation is seeded by aberrant SGs: SGs that fail to properly disassemble, lose their dynamic properties, and become pathological condensates which finally 'mature' into aggregates. Here, we discuss the evidence supporting this model for various ALS/FTD-associated proteins. We further continue to focus on molecular chaperone-mediated regulation of ALS/FTD-associated physiological condensates on one hand, and pathological condensates on the other. In addition to SGs, we review ALS/FTD-relevant nuclear condensates, namely paraspeckles, anisosomes, and nucleolar amyloid bodies, and discuss their emerging regulation by chaperones. As the majority of chaperoning mechanisms regulate physiological condensate disassembly, we highlight parallel themes of physiological and pathological condensation regulation across different chaperone families, underscoring the potential for early disease intervention.

The extracellular matrix (ECM) is a network of proteins and other molecules that encase and support cells and tissues in the body. As clinical and biotechnological uses of ECM are expanding, it is essential to assess the environmental impact associated with its production. Due to high levels of customization, various laboratories employ distinct methods; therefore, this study evaluates three common protocols. Life cycle assessment (LCA) methodology has been developed to evaluate the environmental impacts of products produced through diverse processes. Despite its widespread application in the pharmaceutical industry, LCA has seldom been utilized to estimate the environmental effects of laboratory protocols. This Viewpoint applies LCA to assess the functionality and environmental impacts of ECM produced via P1, P2, and P3. The results of this assessment indicate that the protocol with the highest impact generates approximately 43 times more CO₂-equivalent emissions (CO₂ eq) than that with the lowest impact, while the ECM produced using the least impactful protocol demonstrates the highest biocompatibility. Additional environmental indicators such as eutrophication, photochemical oxidation, and acidification also vary among the tested protocols. This work underscores the need to factor environmental impact in the development of novel biomedical materials.

The glucagon-like peptide-1 receptor (GLP-1R) plays an important role in regulating insulin secretion and reducing body weight, making it a prominent target in the treatment of type 2 diabetes and obesity. Extensive research on GLP-1R signaling has provided insights into the connection between receptor function and physiological outcomes, such as the correlation between Gs signaling and insulin secretion, yet the exact mechanisms regulating signaling remain unclear. Here, we explore the internalization pathway of GLP-1R, which is crucial for controlling insulin release and maintaining pancreatic beta-cell function. Utilizing a reliable and sensitive time-resolved fluorescence resonance energy transfer (TR-FRET) internalization assay, combined with HEK293-derived knockout cell lines, we were able to directly compare the involvement of different endocytic machinery in GLP-1R internalization. Our findings indicate that the receptor internalizes independently of arrestin and is dependent on Gs and Gi/o activation and G protein-coupled receptor kinase phosphorylation. Mechanistically, we observed that the receptor undergoes distinct clathrin- and caveolae-mediated internalization in HEK293 cells. This study also investigated the role of arrestins in GLP-1R function and regulation. These insights into key endocytic components that are involved in the GLP-1R internalization pathway could enhance the rational design of GLP-1R therapeutics for type 2 diabetes and other GLP-1R-related diseases.

Senescence is a tumor suppressor mechanism triggered by oncogene expression and chemotherapy treatment. It orchestrates a definitive cessation of cell proliferation through the activation of the p53-p21 and p16-Rb pathways, coupled with the compaction of proliferative genes within heterochromatin regions. Some cancer cells have the ability to elude this proliferative arrest but the signaling pathways involved in circumventing senescence remain to be characterized. We have recently described that malignant cells capable of evading senescence have an increased expression of specific tRNAs, such as tRNA-Leu-CAA and tRNA-Tyr-GTA, alongside the activation of their corresponding tRNA ligases, namely LARS and YARS. We have previously shown that YARS promotes senescence escape by activating proliferation and cell cycle genes but its functions during this proliferative arrest remain largely unknown. In this study, we have continued to characterize the functions of YARS, describing non-canonical transcriptional functions of the ligase. Our results show that YARS is present in the nucleus of proliferating and senescent cells and interacts with the Trim28 transcriptional regulator. Importantly, YARS binds to the LIN9 promoter, a critical member of the Dream complex responsible for regulating cell cycle gene transcription. The ligase facilitates the binding and the phosphorylation of the type II RNA polymerase and promotes the deposition of activating epigenetic marks on the LIN9 promoter. Consequently, during senescence escape, YARS activates LIN9 expression and both proteins are necessary to induce the proliferation of emergent cells. These results underscore unconventional transcriptional functions of YARS in activating LIN9 expression in proliferating cells and during senescence escape.

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 to build progress.

Rhizobium etli is a nitrogen-fixing bacterium that encodes two l-asparaginases. The structure of the inducible R. etli asparaginase ReAV has been recently determined to reveal a protein with no similarity to known enzymes with l-asparaginase activity, but showing a curious resemblance to glutaminases and β-lactamases. The uniqueness of the ReAV sequence and 3D structure make the enzyme an interesting candidate as potential replacement for the immunogenic bacterial-type asparaginases that are currently in use for the treatment of acute lymphoblastic leukemia. The detailed catalytic mechanism of ReAV is still unknown; therefore, the enzyme was subjected to mutagenetic experiments to investigate its catalytic apparatus. In this work, we generated two ReAV variants of the conserved Lys138 residue (K138A and K138H) that is involved in zinc coordination in the wild-type protein and studied them kinetically and structurally. We established that the activity of wild-type ReAV and the generated variants is significantly reduced in the presence of Cd²⁺ cations, which slow down the proteins while improving their apparent substrate affinity. Moreover, the inhibitory effect of Cd²⁺ is enhanced by the substitutions of Lys138, which disrupt the metal coordination sphere. The proteins with impaired activity but increased affinity were cocrystallized with the L-Asn substrate. Here, we present the crystal structures of wild-type ReAV and its K138A and K138H variants, unambiguously revealing bound l-asparagine in the active site. After careful analysis of the stereochemistry of the nucleophilic attack, we assign the role of the primary nucleophile of ReAV to Ser48. Furthermore, we propose that the reaction catalyzed by ReAV proceeds according to a double-displacement mechanism.

Mucus in the colon is crucial for intestinal homeostasis by forming a barrier that separates microbes from the epithelium. This is achieved by the structural arrangement of the major mucus proteins, such as MUC2 and FCGBP, both of which are comprised of several von Willebrand D domains (vWD) and assemblies. Numerous disulfide bonds stabilise these domains, and intermolecular bonds generate multimers of MUC2. The oligomeric nature of FCGBP is not known. Human hFCGBP contains 13 vWD domains whereas mouse mFCGBP consists of only 7. We found unpaired cysteines in the vWD1 (human and mouse) and vWD5 (mouse)/vWD11 (human) assemblies which were not involved in disulfide bonds. However, the most C-terminal vWD domains, vWD7 (mouse)/vWD13 (human), formed disulfide-linked dimers. The intermolecular bond between C₅₂₈₄ and C₅₄₀₃ of human hFCGBP was observed by using mass spectrometry to generate the dimer. Cryo-EM structure analysis of recombinant mouse mFCGBP revealed a compact dimer with two symmetric intermolecular disulfide bonds between C₂₄₆₂ and C₂₅₈₁, corresponding to the dimerising cysteines in the human hFCGBP. This compact conformation involves interactions between the vWD assemblies, but although the domains involved at the interface are the same, the nature of the interactions differ. Mouse mFCGBP was also found to exist in a semi-extended conformation. These different interactions offer insights into the dynamic nature of the FCGBP homodimer.

The emergence of new coronavirus variants and concerns about vaccine effectiveness against these novel variants emphasize the need for broad-spectrum therapeutics targeting conserved coronaviral non-structural proteins. Accordingly, a virtual library of 178 putative inhibitors targeting SARS-CoV-2 Papain-like protease (PL^pro) was compiled through a systematic review of published literature and subsequently screened using molecular docking. Selected hits were analyzed for protease inhibitory activities, binding strength, and antiviral activities against HCoV229E-based surrogate system and subsequently against SARS-CoV-2 for validation. Differences in potential modes of action were investigated using an HCoV229E-based system, combined with in silico and biophysical methods against SARS-CoV-2 system. Of the 178 hits, 13 molecules showed superior docking scores against PL^pro and met the inclusion criteria for further investigations. Of these, seven showed notable inhibitory activities against PL^pro. Particularly, both Psoralidin and Corylifol-A exhibited superior and, importantly, dual activities against SARS-CoV-2 M^pro. Both molecules were found to be biologically active against HCoV229E and SARS-CoV-2; however, Psoralidin exhibited more consistent effects and was relatively well-tolerated. Detailed in silico analyses of their interactions with the two proteases identified differences in their modes of action, primarily due to differences in their binding of PL^pro. Based on these findings, we propose Psoralidin as a potential candidate for further development as a broad-spectrum antiviral and Corylifol-A as an ideal candidate for lead optimization.

Over 400 different types of post-translational modifications (PTMs) have been reported and over 200 various types of PTMs have been discovered using mass spectrometry (MS)-based proteomics. MS-based proteomics has proven to be a powerful method capable of global PTM mapping with the identification of modified proteins/peptides, the localization of PTM sites and PTM quantitation. PTMs play regulatory roles in protein functions, activities and interactions in various heart related diseases, such as ischemia/reperfusion injury, cardiomyopathy and heart failure. The recognition of PTMs that are specific to cardiovascular pathology and the clarification of the mechanisms underlying these PTMs at molecular levels are crucial for discovery of novel biomarkers and application in a clinical setting. With sensitive MS instrumentation and novel biostatistical methods for precise processing of the data, low-abundance PTMs can be successfully detected and the beneficial or unfavorable effects of specific PTMs on cardiac function can be determined. Moreover, computational proteomic strategies that can predict PTM sites based on MS data have gained an increasing interest and can contribute to characterization of PTM profiles in cardiovascular disorders. More recently, machine learning- and deep learning-based methods have been employed to predict the locations of PTMs and explore PTM crosstalk. In this review article, the types of PTMs are briefly overviewed, approaches for PTM identification/quantitation in MS-based proteomics are discussed and recently published proteomic studies on PTMs associated with cardiovascular diseases are included.