Biochimie最新文献

{"title":"Inside front cover-EDB","authors":"","doi":"10.1016/S0300-9084(25)00131-2","DOIUrl":"10.1016/S0300-9084(25)00131-2","url":null,"abstract":"","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Page IFC"},"PeriodicalIF":3.3,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144571990","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":"Quantitative detection of 2′-O-methylated residues in non-coding RNAs using DNAzymes and quantitative RT-PCR","authors":"Valentyne Lebret-Kogey ,&nbsp;Lilia Ayadi ,&nbsp;Sylvain Maenner ,&nbsp;Yuri Motorin ,&nbsp;Isabelle Behm-Ansmant ,&nbsp;Christelle Aigueperse","doi":"10.1016/j.biochi.2025.07.006","DOIUrl":"10.1016/j.biochi.2025.07.006","url":null,"abstract":"<div><div>In recent decades, post-transcriptional RNA modifications have emerged as a critical regulatory network in cellular processes. The emergence of advanced technologies, including next-generation sequencing (e.g., Illumina) and third-generation sequencing (e.g., Nanopore and PacBio), has significantly improved the detection of RNA modifications in both coding (mRNAs) and non-coding RNAs (ncRNAs). However, these powerful and transcriptome-wide approaches often generate a significant number of false positive hits, highlighting the need for complementary methods allowing validation of the RNA modification profile as well as more precise quantification. In this study, we present further optimization of a straightforward and sensitive protocol using RNA-cleaving deoxyribozymes (DNAzymes) to validate 2′-O-methylations. The validity of this protocol was demonstrated by the analysis of two well-characterized 2′-O-methylated adenines in human U1 and U2 small nuclear RNAs (snRNAs). Using siRNA targeting NOP58 and antisense oligonucleotides targeting scaRNA7, we showcased the sensitivity and specificity of our approach in detecting variations in 2′-O-methylation levels. The DAMP-RNA (DNAzyme-Assisted Methylation Profiling of RNA) method, combining the DNAzyme cleavage with RT-qPCR provides a robust and efficient way to investigate known 2′-O-methylation in any cellular RNA regardless of its abundance, yielding valuable insights into the dynamics of RNA modifications. Despite its limitations, this method represents a significant advancement, enhancing clarity and reproducibility in the epitranscriptomics field, paving the way for further exploration in the RNA biology.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"237 ","pages":"Pages 26-39"},"PeriodicalIF":3.3,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602461","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":"Exploring mitochondrial phototoxicity: Mechanisms, measurement, and mitigation","authors":"Bowen Liu ,&nbsp;Kai Chen ,&nbsp;Yubing Han","doi":"10.1016/j.biochi.2025.07.008","DOIUrl":"10.1016/j.biochi.2025.07.008","url":null,"abstract":"<div><div>Phototoxicity, induced by light exposure, presents a major challenge in fluorescence microscopy, particularly when studying mitochondria. These organelles are sensitive to damage from reactive oxygen species (ROS) generated during imaging. This review discusses the basic principles of phototoxicity, focusing primarily on the effects of phototoxicity on mitochondrial function and structure. It also explores strategies to mitigate damage, including optimized imaging techniques and specialized probes, and considers cases where phototoxicity is utilized for therapeutic purposes. The need for advanced imaging methods to balance damage prevention and mitochondrial research is emphasized.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"237 ","pages":"Pages 16-25"},"PeriodicalIF":3.3,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602460","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":"Venom versatility: Dynamic anticoagulant and procoagulant variations between and within Bothrocophias (toad-head) and basal Bothrops (lance-head) pit vipers","authors":"Lachlan A. Bourke ,&nbsp;David Salazar-Valenzuela ,&nbsp;Marco Mancuso ,&nbsp;Diego R. Quirola ,&nbsp;Amaru Loaiza-Lange ,&nbsp;Christina N. Zdenek ,&nbsp;Matthew R. Lewin ,&nbsp;Ernesto Arbeláez-Ortiz ,&nbsp;Bryan G. Fry","doi":"10.1016/j.biochi.2025.07.001","DOIUrl":"10.1016/j.biochi.2025.07.001","url":null,"abstract":"<div><div>Pinpointing the emergence of toxicological evolutionary novelties can be challenging. In American pit vipers, anticoagulant venoms are the paradigm, with a notable exception being the genus <em>Bothrops</em>, which are typically procoagulant. A recent study found that the basal <em>Bothrops</em> (<em>B. pictus</em>) is anticoagulant, raising two competing hypotheses: ancestral <em>Bothrops</em> were anticoagulant with procoagulant venom evolving later, or ancestral <em>Bothrops</em> were procoagulant with anticoagulant venom in <em>B. pictus</em> being a derived trait. To help resolve this, we tested venoms of the sister genus <em>Bothrocophias</em> for pathophysiological actions upon blood clotting. The Ecuadorian <em>Bothrocophias</em> venoms (<em>B. campbelli, B. lojanus,</em> and <em>B. microphthalmus</em>) were compared to <em>Bothrops pictus</em>. Both <em>Bothrocophias lojanus</em> and <em>B. pictus</em> inhibited various blood clotting enzymes, but <em>B. pictus</em> was more potently anticoagulant. Intriguingly, <em>B. campbelli</em> and <em>B. microphthalmus</em> were procoagulant. Both <em>B. microphthalmus</em> populations activated prothrombin, but Zamora Chinchipe locality also activated Factors X and VII. <em>Bothrocophias campbelli</em> showed a novel activity, using Factor Va in a calcium-dependent manner as a cofactor to activate prothrombin, the first time this has been shown for any viperid venom. Organismal phylogenetics failed to resolve the relative positions of <em>B. campbelli</em> and <em>B. lojanus</em>, thus we were unable to ascertain the ancestral trait. To resolve this, more phylogenetic research and venom testing with other <em>Bothrocophias</em> species is needed. Neutralisation tests revealed differential efficacy of PoliVal-ICP (Instituto Clodomiro Picado) and Soro Antibotrópico (Instituto Butantan) antivenoms. Together, these findings aid in designing evidence-based clinical-management strategies and provide foundational data for reconstructing venom evolution.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"237 ","pages":"Pages 1-15"},"PeriodicalIF":3.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565552","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":"Advances in cell cycle regulation to enhance recombinant protein production in CHO cells","authors":"Qi Zhao ,&nbsp;Hui-Jie Zhang ,&nbsp;Ming-Ming Han ,&nbsp;Jumai Abiti ,&nbsp;Jia-Ning Wang ,&nbsp;Xi Zhang ,&nbsp;Wen Wang ,&nbsp;Xiao-Yin Wang ,&nbsp;Tian-Yun Wang ,&nbsp;Yan-Long Jia","doi":"10.1016/j.biochi.2025.06.017","DOIUrl":"10.1016/j.biochi.2025.06.017","url":null,"abstract":"<div><div>Chinese hamster ovary (CHO) cells have become the predominant host system in biopharmaceutical production due to their unique capacity to generate recombinant proteins with complex structures and human-like post-translational modifications. However, low expression levels and product heterogeneity remain critical bottlenecks requiring urgent resolution in CHO cell applications. Current strategies encompass culture condition optimization, vector design improvements, and cell engineering approaches targeting expression regulation mechanisms. Among these approaches, cell cycle regulation has garnered significant attention due to its intrinsic connection to transcriptional activity and biosynthetic processes. Each phase of the cell cycle is tightly regulated and exerts phase-specific influences on gene expression patterns, including temporal control of transcriptional activity, functional specialization, and modulation of cellular processes. Consequently, cell cycle engineering strategies targeting key regulatory nodes – such as cyclin-dependent kinases (CDKs), cyclin family proteins, and E2F transcription factors – have emerged as promising approaches to control cell cycle progression/arrest and thereby enhance recombinant protein yields. This review systematically examines the distinct phases and characteristic features of the cell cycle, while comprehensively analyzing the impact of cell cycle regulation on recombinant protein yield in CHO cells and recent research advancements in this field.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 117-126"},"PeriodicalIF":3.3,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144549918","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":"Neuromesodermal progenitor derived mesenchymal stem cells: A new source for osteogenesis and adipogenesis in vitro","authors":"Ayşegül Doğan,&nbsp;Selinay Şenkal-Turhan,&nbsp;Ezgi Bulut-Okumuş","doi":"10.1016/j.biochi.2025.06.016","DOIUrl":"10.1016/j.biochi.2025.06.016","url":null,"abstract":"<div><div>Derivation of adult mesenchymal stem cells (MSCs) from induced pluripotent stem cells (iPSCs) in culture might be an important approach to generate unlimited cell source for clinical therapies. Identification of appropriate progenitor populations during development is of interest in recent years to establish accurate steps in cell differentiation protocols. In the current study, iPSC derived MSCs (iMSC) via neuromesodermal progenitors (NMP) were generated using an established in vitro differentiation protocol. Osteogenic and adipogenic differentiation potential of iMSCs were evaluated by in vitro cell culture assays, gene and protein expression analysis. Protein expression profile of iMSCs and secretome of iMSCs were determined by membrane array and LC-MS/MS analysis. Conditioned medium derived from iMSCs was used in differentiation protocol of preadipocytes and preosteoblast cells. Adipogenic and osteogenic cells were derived from iMSCs in vitro. Protein profile of iMSCs were different compared to dental pulp and adipose stem cells. iMSC secretome has a more prominent role to promote adipogenesis in cultured preadipocytes. In conclusion, MSCs with an adipogenic and osteogenic differentiation capacity can be obtained from iPSC derived NMPs in vitro. Secretome of iMSCs have adiponenic potential on preadipocytes and can be a promising option for future studies.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 104-116"},"PeriodicalIF":3.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531628","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":"Regulation of ferroptosis by transcription factor E2F1","authors":"Nishanth Kuganesan ,&nbsp;Samkeliso Dlamini ,&nbsp;Safiyyah Hasan ,&nbsp;L.M. Viranga Tillekeratne ,&nbsp;William R. Taylor","doi":"10.1016/j.biochi.2025.06.013","DOIUrl":"10.1016/j.biochi.2025.06.013","url":null,"abstract":"<div><div>The E2F family of transcription factors plays multiple roles in cell cycle regulation. E2F can be inhibited by binding to RB proteins, an interaction that is regulated by CDK phosphorylation of RB. We previously observed that CDKs, RB, and E2F regulate ferroptosis, a type of programmed cell death characterized by catastrophic peroxidation of membrane lipids. Here we investigate the impact of E2F on ferroptosis. E2F1 regulates both pro and anti-ferroptotic proteins including ALOX5, MYC, SLC7A11, ATF4, and GPX4 and finally renders a net inhibitory role in ferroptosis. Interestingly, we also obtained evidence for a cell type dependent compensatory effect of E2F3 upon E2F1 depletion. Specifically, downregulation of ferroptotic genes upon E2F1 knockdown fails to occur in an osteosarcoma cell line which upregulates E2F3 under these conditions. Taken together, our study identifies a number of E2F targets with the potential to affect ferroptotic sensitivity.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 127-137"},"PeriodicalIF":3.3,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512924","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":"Ornithine decarboxylase 1 and solute carrier transporters: Coordinated gene expression in response to glucotoxicity, an in vitro investigation","authors":"Manpreet Kaur,&nbsp;Neha Dahiya,&nbsp;Varsha Singh","doi":"10.1016/j.biochi.2025.06.014","DOIUrl":"10.1016/j.biochi.2025.06.014","url":null,"abstract":"<div><div>Solute carrier (SLC) transporters have been linked to type 2 diabetes (T2D) and play a crucial role in cellular metabolism. Growth and metabolism depend on ornithine decarboxylase 1 (ODC1), a crucial regulator of polyamine production, especially in the pancreas. This study examines the interaction between ODC1 and SLC gene expressions under glucotoxicity conditions, which simulate hyperglycemia. <em>In silico</em> analysis of human pancreatic β-islet tissue datasets from T2D patients identified differentially expressed SLC genes. <em>In vitro</em> studies were conducted using HEK293T cells and COS-7 cell lines. Overexpression and knockdown of <em>ODC1</em> in HEK293T cells revealed ODC1's influence on the mRNA expression profiles of SLC. <em>In vitro</em> overexpression with and without high glucose also revealed <em>ODC1</em>'s influence on SLC genes. Specifically, <em>ODC1</em> modulated the expression of <em>SLC11A2, SLC30A1, SLC39A6,</em> and other SLCs, including <em>SLC17A6, SLC25A12, SLC26A2, SLC35A5, SLC38A2, SLC9A6, SLC6A8,</em> and <em>SLC20A1</em>. Glucotoxicity mostly suppressed SLC gene expression; however, <em>ODC1</em> overexpression partially reversed this effect for certain SLCs. This work highlights an unrecognized regulatory network involving <em>ODC1</em> and SLCs, suggesting a potential role for polyamine pathway modulation in controlling transport dynamics. These findings suggest a novel regulatory network where ODC1 influences SLC gene expression, impacting metabolic pathways and nutrient transport. This study provides preliminary evidence that ODC1 may be a potential regulator of SLC transporters, offering new insights into the metabolic dysregulation of T2D and potential therapeutic targets.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 87-103"},"PeriodicalIF":3.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509937","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":"Recombinant expression and purification of wheat aminoacyl-tRNA synthetases and IRES-dependent polypeptide synthesis with homogeneously derived purified factors","authors":"Haruyuki Furukawa,&nbsp;Ryota Yamagami,&nbsp;Yuto Nagashio,&nbsp;Kensuke Tsutsumi,&nbsp;Kazuki Goto,&nbsp;Takumi Nishioka,&nbsp;Takumi Kondo,&nbsp;Keigo Hisamatsu,&nbsp;Takeru Aga,&nbsp;Ryunosuke Watanabe,&nbsp;Hiroyuki Hori,&nbsp;Chie Tomikawa,&nbsp;Kazuyuki Takai","doi":"10.1016/j.biochi.2025.06.010","DOIUrl":"10.1016/j.biochi.2025.06.010","url":null,"abstract":"<div><div>Reconstitution of the translation system including the full set of aminoacyl-tRNA synthetases (ARSs) has been achieved with the components from <em>Escherichia coli</em> and human. We are trying to reconstitute the plant translation system because plants are also essential targets of biotechnology. Some eukaryotic ARSs form multi-synthetase complexes (MSCs), while plant MSCs have not been fully characterized by the conventional top-down approaches isolating them from plant tissues. To reveal more about the plant MSCs by bottom-up approaches and to reconstitute the plant translation system, we attempted here to prepare individual wheat ARSs by <em>E. coli</em> expression methods and sequenced tRNAs expressed in wheat germs. The 16 ARSs other than CysRS, IleRS, LysRS and ThrRS were synthesized in <em>E. coli</em> and were purified to near homogeneity. Fourteen of them other than ValRS and AsnRS had their aminoacylation activity. Then, the 6 ARSs that were not prepared successfully in <em>E. coli</em> (ValRS, AsnRS, IleRS, ThrRS, LysRS, and CysRS) were synthesized in a wheat-germ cell-free translation system and purified. As a result, ThrRS and ValRS, but not the other four, could aminoacylate wheat germ tRNA. Some of the unsuccessful ARSs might require unidentified co-translational interactions for formation of their active forms. Finally, a reconstituted wheat translation system containing 8 ARSs, eEFs, eRFs, ribosome, and total tRNA was constructed. The system successfully translated an mRNA encoding a hemagglutinin-tag and a randomly generated sequence of 5 amino acids downstream of a cricket paralysis virus internal ribosome entry site, which enables translation independent of initiation factors.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 30-44"},"PeriodicalIF":3.3,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478234","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":"Repurposing of propafenone, an FDA approved anti-arrhythmic drug for antileishmanial therapy","authors":"Anindita Paul,&nbsp;Pradyot Kumar Roy,&nbsp;Sandra Lalchhuanawmi,&nbsp;Neerupudi Kishore Babu,&nbsp;Mohd Faiz Khan,&nbsp;Sushma Singh","doi":"10.1016/j.biochi.2025.06.012","DOIUrl":"10.1016/j.biochi.2025.06.012","url":null,"abstract":"<div><div>Elimination of the Neglected Tropical Disease Visceral Leishmaniasis (VL) is a Sustainable Development Goal. It is caused by <em>Leishmania donovani.</em> The therapeutic options for the treatment of VL are limited due to problems such as drug resistance and toxicities. Drug repurposing can be a promising alternative in this case. In this work, the antileishmanial potential of FDA approved anti-arrhythmic drug propafenone has been evaluated for repurposing. It reduced the viability of <em>L. donovani</em> promastigotes and intracellular amastigotes with an IC₅₀ of 8.25 ± 2.48 μM and 11.19 ± 0.01 μM respectively. In the macrophages, the IC₅₀ was 32 ± 7.07 μM. Propafenone treatment altered morphology of parasites and induced damage to the body and flagellum. The cell membrane became damaged and more permeable when the promastigotes were treated with this drug. However, no change in the cell membrane potential was detected. Treatment with propafenone was detrimental to mitochondrial health of <em>L. donovani</em>. It significantly depolarized the mitochondrial membrane and decreased the ATP levels in the promastigotes. Propafenone also induced oxidative stress in the parasites. Cell cycle arrest was detected at the G₂/M stage. The data suggests that propafenone has antileishmanial potential and can be evaluated further in an experimental VL model.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 64-73"},"PeriodicalIF":3.3,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478235","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}