Biochimica et biophysica acta. General subjects最新文献

{"title":"Diffusion properties of transfer RNAs in the yeast cytoplasm under normal and osmotic stress conditions","authors":"Vijay Phanindra Srikanth Kompella ,&nbsp;Maria Carmen Romano ,&nbsp;Ian Stansfield ,&nbsp;Ricardo L. Mancera","doi":"10.1016/j.bbagen.2025.130798","DOIUrl":"10.1016/j.bbagen.2025.130798","url":null,"abstract":"<div><div>The mechanism by which aminoacyl-tRNAs are supplied to translating ribosomes for protein synthesis is likely to involve a process of diffusion within the cellular environment, which is inevitably impacted by macromolecular crowding. Osmotic stress leading to cell shrinkage increases the concentration of macromolecules in the cytoplasm, reducing protein diffusion. The impact of macromolecular crowding on the translation machinery in eukaryotes remains uncharacterised. In this study Brownian dynamics simulation were used for the first time to study the effect of macromolecular crowding on the microsecond-time scale diffusion properties of tRNAs and their ternary complexes within a model yeast cytoplasmic environment. Under normal cell-like conditions, the diffusion of tRNAs and ternary complexes was predicted to be reduced by up to 8-fold (compared with dilute conditions), whilst diffusion under severe osmotic stress conditions decreased by up to a remarkable 80-fold. All molecules exhibited sub-diffusive behaviour, which was stronger under osmotic stress. These findings may be readily used to predict protein translation dynamics, including the crucial process of tRNA delivery to the ribosome, under a variety of conditions.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130798"},"PeriodicalIF":2.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of tumor-associated fibroblast-derived exosomes in chemotherapy resistance of colorectal cancer and its application prospect","authors":"Meichen Liu ,&nbsp;Teng-zheng Li ,&nbsp;Congcong Xu","doi":"10.1016/j.bbagen.2025.130796","DOIUrl":"10.1016/j.bbagen.2025.130796","url":null,"abstract":"<div><div>Colorectal cancer (CRC) is the second most common malignant tumor in the world. With its increasing incidence and younger age trend, its impact on human health has been paid more and more attention. Currently, we have a variety of chemotherapy drugs that can be used to treat colorectal cancer. However, the drug resistance of colorectal cancer has become a significant factor affecting its cure rate. Some studies have reported that exosomes are related to the occurrence of drug resistance. However, the exact mechanism is not precise. Therefore, we focused on the role of cancer associated-fibroblast-derived (CAFs-derived) exosomes in colorectal progression. It was found that cancer cells transmit information through exosome interaction and induce chemotherapy resistance by promoting epithelial-mesenchymal transition (EMT), up-regulating the Wnt/β-catenin signaling pathway, transforming growth factor-β1 (TGF-β1) pathway, promoting angiogenesis and other possible molecular mechanisms. In addition, in terms of clinical significance and therapeutic strategies, we explore the clinical relevance of CAFs-derived exosomes in colorectal cancer patients and their potential as potential biomarkers for predicting chemotherapy response. We also provide a new possible direction for overcoming chemotherapy resistance in colorectal cancer by targeting CAFs-derived exosomes.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130796"},"PeriodicalIF":2.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A role in intracellular K+ in protecting pathogenic dimorphic fungi against induced cell death by bioinspired antimicrobial peptides","authors":"Filipe Zaniratti Damica ,&nbsp;Douglas Ribeiro Lucas ,&nbsp;Estefany Bras Toledo ,&nbsp;Marilúcia de Carvalho Ribeiro ,&nbsp;Anna Lvovna Okorokova Façanha ,&nbsp;Ana Eliza Zeraik ,&nbsp;Sérgio Henrique Seabra ,&nbsp;Juliana Azevedo da Silva ,&nbsp;Valdirene Moreira Gomes ,&nbsp;André de Oliveira Carvalho","doi":"10.1016/j.bbagen.2025.130795","DOIUrl":"10.1016/j.bbagen.2025.130795","url":null,"abstract":"<div><div>Antimicrobial peptides (AMPs) are promising drugs, though their fungal combat mechanisms remain partly unclear. We designed three AMPs (dAMPs) based on the γ-core of the <em>Vu</em>-Def₁ seed defensin from <em>Vigna unguiculata</em> L. Walp. named RR, D-RR, and WR, and assessed their actions on <em>Candida tropicalis</em> and <em>Candida albicans</em>. Amidst their actions are cell shrinkage caused by K⁺ efflux from fungal cells. K⁺ involvement in fungal death by these peptides was explored. We assessed cell shrinkage, oxidative stress, mitochondria hyperpolarization, membrane permeabilization, medium acidification, antimicrobial activity under hypoosmotic conditions, and cellular degradation. Viability assays were performed with channel blockers and K⁺ addition at various times. The interactions of dAMPs with salts and fungal cells were analyzed using circular dichroism and microscopy. K⁺ and Cl⁻ channels were not directly involved in dAMPs-induced death. Supplementation with K⁺ protected fungal cells from death. In tests, cations often deactivated them through charge neutralization. Peptides maintained their conformation with K⁺ and were found in cell cytoplasm indicating K⁺ did not neutralize charges. K⁺ did not prevent oxidative stress, but protected from cell shrinkage and mitochondria hyperpolarization. dAMPs rapidly stimulated medium acidification, followed by inhibition after 1 min, and K⁺ prevented acidification. Membrane permeabilization occurred after 20 min, faster with WR, explaining lack of protection from blockers. Fungal death was accelerated under hypoosmotic conditions. Electrophoresis revealed protein degradation, while ultrastructural analysis of the cells showed vacuolization, indicative of cytoplasmic degradation. Thus, K⁺ prevented cell death by maintaining internal levels, averting activation of cell degradation process.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130795"},"PeriodicalIF":2.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The multifaceted role of YSL proteins: Iron transport and emerging functions in plant metal homeostasis","authors":"Anil Kumar ,&nbsp;Riya Joon ,&nbsp;Gourav Singh ,&nbsp;Jagtar Singh ,&nbsp;Ajay Kumar Pandey","doi":"10.1016/j.bbagen.2025.130792","DOIUrl":"10.1016/j.bbagen.2025.130792","url":null,"abstract":"<div><div>Understanding metal transport in plants has always been critical. Several gene families have been identified in the last two decades that have aided in the understanding of channelized metal transport, including their uptake, distribution, and storage in plants. Identifying Yellow Stripe-like (YSL) genes has contributed to an improved understanding of metal homeostasis in plants, especially monocots. Several studies have demonstrated that these genes play a role in transporting metals complexed with phytosiderophores (PS) and/or nicotianamine (NA). In the current review, we have discussed and opinionated the signalling role of YSL protein in maintaining inter and intracellular metal homeostasis in plants. Although the genes are known to have a broader range of metal substrate specificity, these are primary iron (Fe) transporters, and a detailed Fe transport in plants is discussed. Furthermore, based on recent findings, alternative functions of these genes are also discussed. Overall, we provide a broader overview of YSL protein in modulating the Fe mobilization and provides evidence of the expanding functions in plants.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130792"},"PeriodicalIF":2.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating gold nanostars into condensed DNA","authors":"Christopher C. Perry ,&nbsp;Reinhard W. Schulte ,&nbsp;Ryan N. Fuller ,&nbsp;Nathan R. Wall ,&nbsp;Kevin E. Nick ,&nbsp;Magdalena Wegrzyn ,&nbsp;Jamie R. Milligan","doi":"10.1016/j.bbagen.2025.130793","DOIUrl":"10.1016/j.bbagen.2025.130793","url":null,"abstract":"<div><div>X-irradiation has extensive applications in therapy and considerable attention has been devoted to the radiosensitizing properties of nanoparticles composed of high atomic number elements, particularly gold. Low energy electrons and/or heterogenous catalysis are widely suspected to be involved in radiosensitization, but there is uncertainty about their contributions. Because of their greater surface area to volume ratio relative to spherical particles per unit mass of gold, nanostars permit more low energy electrons to escape and possess an increased catalytic activity. Condensed DNA represents a highly useful model for mammalian chromatin, particularly with respect to the types and yields of DNA damage produced by ionizing radiation. Here we describe the incorporation of spherical gold nanoparticles and of gold nanostars into a condensed DNA model system. The resulting self-assembled micron-sized co-aggregates involve an intimate association between gold and DNA, maximizing the opportunity for the production of DNA damage. After increasing the ionic strength, the co-condensate becomes disaggregated and the DNA is available for subsequent assays. This model system provides a previously unavailable tool for examining the mechanisms of radiosensitization of DNA damage by gold nanoparticles with implications for possible applications in radiotherapy.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130793"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein-protein interactions as determinants of operon architecture","authors":"Silky Bedi,&nbsp;S.M. Rose,&nbsp;Simerpreet Kaur ,&nbsp;Preeti Negi ,&nbsp;Sharmistha Sinha","doi":"10.1016/j.bbagen.2025.130794","DOIUrl":"10.1016/j.bbagen.2025.130794","url":null,"abstract":"<div><div>Operons, clusters of genes under a single promoter, often exhibit a specific gene order influencing their physiological function. While functional relatedness is a known factor for clustering, the underlying drivers of gene ordering remain unclear. To investigate this, we analyzed the <em>pdu</em> operon, encoding proteins for 1,2 Pdu bacterial microcompartment. Our bioinformatics revealed no link between the sequence similarity and proximity of the genes in the operon. However quantitative mapping of protein-protein interactions within the operon using a barrage of spectroscopic tools showed a strong correlation between interaction strength and gene proximity. Our data thus indicates that protein-protein interactions play a significant role in determining gene order within the <em>pdu</em> operon, potentially contributing to the efficient assembly and function of these microcompartments.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130794"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"STAT3-orchestrated gene expression signatures and tumor microenvironment in esophageal squamous cell carcinoma uncovered by single-cell sequencing","authors":"Shilian Pang ,&nbsp;Yurao Chen ,&nbsp;Zemao Zheng ,&nbsp;Luoshai Wang ,&nbsp;Ronghuai Chen ,&nbsp;Ming He ,&nbsp;Xiang Zhao ,&nbsp;Juan Yao ,&nbsp;Liyan Jin","doi":"10.1016/j.bbagen.2025.130791","DOIUrl":"10.1016/j.bbagen.2025.130791","url":null,"abstract":"<div><h3>Background</h3><div>The progression of Esophageal Squamous Cell Carcinoma (ESCC) can be dissected with greater precision using multi-omics and single-cell RNA sequencing (scRNA-seq) compared to traditional methodologies. These advanced approaches enable a comprehensive understanding of cellular heterogeneity and molecular dynamics, offering higher resolution insights into cancer development. Moreover, analyzing transcription factor regulatory networks provides innovative avenues for identifying cancer biomarkers and therapeutic targets, driving new perspectives in cancer research.</div></div><div><h3>Objective</h3><div>To explore the molecular mechanisms and cellular dynamics of ESCC.</div></div><div><h3>Methods</h3><div>Utilizing bulk-RNA-seq and single-cell transcriptomics, our study identify major cell types, transcriptomic gene and function changes during ESCC progression. Validation experiments in clinical sample tissues and ESCC cell lines to confirm core regulation factor in ESCC.</div></div><div><h3>Results</h3><div>We identified six major cell types in the ESCC scRNA-seq dataset and revealed profound shifts in cellular composition and transcriptional profiles. Notably, STAT3 was found to be a core regulator in ESCC and negatively regulated LHPP expression at promoter sites. Elevated STAT3 and reduced LHPP expression were consistently observed in patient samples, highlighting their inverse relationship in ESCC pathogenesis.</div></div><div><h3>Conclusion</h3><div>This study integrates bulk-seq and scRNA-seq data to reveal the pivotal role of STAT3 in ESCC. STAT3 negatively regulates LHPP expression, driving tumor progression. These findings underscore the therapeutic potential of targeting STAT3 in ESCC. <strong>Key words:</strong> ESCC, single-cell transcriptomics, ESCC microenvironment, STAT3.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130791"},"PeriodicalIF":2.8,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo","authors":"Sayoko Ito-Harashima,&nbsp;Natsuko Miura","doi":"10.1016/j.bbagen.2025.130787","DOIUrl":"10.1016/j.bbagen.2025.130787","url":null,"abstract":"<div><div>Compartmentalization of multiple enzymes <em>in cellulo</em> and <em>in vitro</em> is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid–liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows <em>in vitro</em> and <em>in vivo</em> regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies <em>in vitro</em> and <em>in cellulo</em>. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130787"},"PeriodicalIF":2.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression analysis of glutamate receptor-like genes in three Dendrobium species","authors":"Miao Zhu,&nbsp;Xuying Wang,&nbsp;Xinran Li","doi":"10.1016/j.bbagen.2025.130789","DOIUrl":"10.1016/j.bbagen.2025.130789","url":null,"abstract":"<div><div>Glutamate receptor-like (<em>GLRs</em>) genes play essential roles in plant growth and development, and in coping with environmental stresses; however, information on <em>GLR</em> genes in <em>Dendrobium</em> species is lacking. We identified 25 <em>GLR</em> genes in three <em>Dendrobium</em> species, which were classified into three subfamilies based on their phylogenetic relationships. These genes have been relatively conserved during evolution. Analysis of cis-acting elements and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations revealed the complexity and diversity of <em>GLR</em> gene regulation and functions. Further, gene expression analysis showed that different <em>GLR</em> members exhibited different expression patterns during <em>Dendrobium</em> growth and development, and some were involved in pathogen infection and in response to hormones. These results provide important information on the <em>GLR</em> gene family of <em>Dendrobium,</em> and a foundation for further functional, and trait regulation and improvement studies.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130789"},"PeriodicalIF":2.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional involvement of RNAs and intrinsically disordered proteins in the assembly of heterochromatin","authors":"Chikashi Obuse ,&nbsp;Jun-ichi Nakayama","doi":"10.1016/j.bbagen.2025.130790","DOIUrl":"10.1016/j.bbagen.2025.130790","url":null,"abstract":"<div><div>Heterochromatin is a highly condensed chromatin structure observed in the nuclei of eukaryotic cells. It plays a pivotal role in repressing undesired gene expression and establishing functional chromosomal domains, including centromeres and telomeres. Heterochromatin is characterized by specific histone modifications and the formation of higher-order chromatin structures mediated by proteins, such as HP1 and Polycomb repressive complexes (PRCs), which recognize the specific histone modifications. Recent studies have identified the involvement of non-coding RNAs (ncRNAs) and intrinsically disordered proteins (IDPs) in heterochromatin, leading to the proposal of a new model in which liquid-liquid phase separation (LLPS) contributes to heterochromatin formation and function. This emerging model not only broadens our understanding of heterochromatin's molecular mechanisms but also provides insights into its dynamic regulation depending on cellular context. Such advancements pave the way for exploring heterochromatin's role in genome organization and stability, as well as its implications in development and disease.</div></div>","PeriodicalId":8800,"journal":{"name":"Biochimica et biophysica acta. General subjects","volume":"1869 6","pages":"Article 130790"},"PeriodicalIF":2.8,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}