IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-14 DOI: 10.1016/j.biochi.2025.06.005

Nicolas Mathas , Emmanuelle Braud , Erwan Galardon , Lucie Larigot , Mélanie Etheve-Quelquejeu , Marie-Agnès Sari , Beatrice Le Grand , Etienne B. Blanc , Xavier Coumoul , Julien Dairou

{"title":"Park7 (DJ-1), a Parkinson-associated glyoxalase/deglycase: characterization of enzymatic activity in biological samples using fluorescence-based liquid chromatography","authors":"Nicolas Mathas , Emmanuelle Braud , Erwan Galardon , Lucie Larigot , Mélanie Etheve-Quelquejeu , Marie-Agnès Sari , Beatrice Le Grand , Etienne B. Blanc , Xavier Coumoul , Julien Dairou","doi":"10.1016/j.biochi.2025.06.005","DOIUrl":"10.1016/j.biochi.2025.06.005","url":null,"abstract":"<div><div>Glycation is an inevitable nonenzymatic covalent reaction between nucleophilic groups in proteins and nucleotides, and endogenous reducing sugars or dicarbonyls (e.g., methylglyoxal) leading to protein and/or nucleotide covalent modifications. This process initiates a series of dehydrations, oxidations and rearrangements that lead to a myriad of products called advanced glycation end products (AGEs). Previously, we showed that Park7 (or DJ-1) is a protein deglycase that repairs methylglyoxal-glycated biomolecules by acting on early glycation intermediates and releasing the repaired biomolecule and lactate. Moreover, the <em>PARK7</em> gene is associated with recessive and sporadic forms of Parkinson's disease (PD). Thus, over the last few years, the function of Park7 has become an important research topic for understanding the etiology of PD. In this context, the development of sensitive enzymatic assays is crucial to quantify the activity of Park7 and develop specific modulators. Here, we describe a new method for measuring Park7 activity based on the separation and quantification of glycated and unglycated fluorescent nucleotides by Liquid Chromatography (LC). Kinetic and mechanistic analyses using human recombinant Park7 confirmed the reliability of this approach. In addition, this assay was further validated using cellular lysates. Our results indicate that this novel Park7 assay is simple, sensitive, and specific.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 113-121"},"PeriodicalIF":3.3,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310962","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}

引用次数: 0

Lipidomic analysis of MDCK-parental cells and MDCK-MDR1 cells exposed to GF120918 and clarithromycin highlights the role of P-glycoprotein in sphingolipid transport 对暴露于GF120918和克拉霉素的mdck亲本细胞和MDCK-MDR1细胞的脂质组学分析强调了p -糖蛋白在鞘脂转运中的作用。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-14 DOI: 10.1016/j.biochi.2025.06.007

Théodore Decaix , Romain Magny , David Hozain , Elodie Olivier , Sylvie Gillet , Xavier Declèves , Olivier Laprévote

{"title":"Lipidomic analysis of MDCK-parental cells and MDCK-MDR1 cells exposed to GF120918 and clarithromycin highlights the role of P-glycoprotein in sphingolipid transport","authors":"Théodore Decaix , Romain Magny , David Hozain , Elodie Olivier , Sylvie Gillet , Xavier Declèves , Olivier Laprévote","doi":"10.1016/j.biochi.2025.06.007","DOIUrl":"10.1016/j.biochi.2025.06.007","url":null,"abstract":"<div><div>P-glycoprotein (P-gp) is one of the most studied drug transporters, as it enables the cellular efflux of 50 % of marketed drugs and plays a key role in many drug-drug interactions. While a high number of studies has investigated the use of drug probes to phenotype P-gp activity, identifying endogenous markers remain a not fulfilled challenge. A previous untargeted lipidomic study in healthy volunteers highlighted some sphingolipid species as putative endogenous substrates of P-gp. Based on an untargeted lipidomic analysis of Madin-darby canine kidney parental cells (MDCK-parental cells) and MDCK cells transfected with the MDR1 gene (MDCK-MDR1), the present study aimed to investigate the role of P-gp in intracellular sphingolipid transport and, more generally, to demonstrate the interest of metabolomics strategy in the study of <em>in vitro</em> drug transporters. Using an untargeted lipidomic approach based on liquid chromatography high resolution mass spectrometry, allowed us to detect 131 sphingolipid species within MDCK-parental cells and MDCK-MDR1. Among them, modifications of this sphingolipidome were observed because of MDR1 transfection, mainly involving glucosylceramides. Exposure to two P-gp inhibitors, GF120918 and clarithromycin, increased glucosylceramides, particularly in MDCK-parental cells, probably due to expression of endogenous canine P-gp in this cell line. These results support the hypotheses of a role for P-gp as well as glucosylceramide flippase within the Golgi apparatus of cells. It also provides a proof of concept for understanding pharmaco-metabolomic results in the study of drug transporters in humans.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 21-29"},"PeriodicalIF":3.3,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310961","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}

引用次数: 0

Role of the FhlA transcriptional activator in metabolic changes in Escherichia coli during fermentation of mixed carbon sources at acidic pH FhlA转录激活因子在酸性混合碳源发酵过程中大肠杆菌代谢变化中的作用。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-12 DOI: 10.1016/j.biochi.2025.06.008

Heghine Gevorgyan , Marine Parsadanyan , Anait Vassilian , Anna Poladyan , Karen Trchounian

引用次数: 0

Utilization of glucose and fructose in bovine embryos assessed by metabolic flux analysis 利用代谢通量分析法评价牛胚胎对葡萄糖和果糖的利用。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-12 DOI: 10.1016/j.biochi.2025.06.004

Daniel J. Lugar , Jaewook Chung , Robert I. Clifford , Halli S. Weiner , Carol L. Keefer , Ganesh Sriram

{"title":"Utilization of glucose and fructose in bovine embryos assessed by metabolic flux analysis","authors":"Daniel J. Lugar , Jaewook Chung , Robert I. Clifford , Halli S. Weiner , Carol L. Keefer , Ganesh Sriram","doi":"10.1016/j.biochi.2025.06.004","DOIUrl":"10.1016/j.biochi.2025.06.004","url":null,"abstract":"<div><div><sup>13</sup>C Metabolic flux analysis (<sup>13</sup>C MFA) is a non-invasive methodology for the measurement of fluxes (rates of carbon flow) throughout a metabolic network and can be used to determine nutrient contributions to central metabolic pathways. <sup>13</sup>C MFA was used in a systemic metabolic investigation of the nutritional physiology of preimplantation bovine blastocysts. Bovine blastocysts were cultured either singly or in groups of five in 40 μl of medium containing <sup>13</sup>C labeled glucose and/or fructose, and the metabolites expelled into the spent media were identified through <sup>13</sup>C MFA of heavy isotope labeling. Similarly, the metabolites in spent media following culture of a bovine trophectoderm cell line (CT-1) were monitored. Flux maps generated using <sup>13</sup>C MFA suggest that less than 10 % of metabolites from the glycolytic pathway were diverted to the pentose phosphate pathway or the tricarboxylic acid cycle in either bovine blastocysts or CT-1 cells with the majority of the hexose (70–80 %) resulting in pyruvate and lactate production.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"236 ","pages":"Pages 10-20"},"PeriodicalIF":3.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295501","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}

引用次数: 0

Lambda exonuclease assisted helicase-dependent amplification CRISPR/Cas12a detection of Listeria monocytogenes Lambda外切酶辅助解旋酶依赖扩增CRISPR/Cas12a检测单核增生李斯特菌。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-09 DOI: 10.1016/j.biochi.2025.06.002

Chen Wang , Qingshuang Wang , Yushi Jin , Chenxi Li , Meiyan Xin , Xue Jiang , Jiayu Wan

{"title":"Lambda exonuclease assisted helicase-dependent amplification CRISPR/Cas12a detection of Listeria monocytogenes","authors":"Chen Wang , Qingshuang Wang , Yushi Jin , Chenxi Li , Meiyan Xin , Xue Jiang , Jiayu Wan","doi":"10.1016/j.biochi.2025.06.002","DOIUrl":"10.1016/j.biochi.2025.06.002","url":null,"abstract":"<div><div>We describe the construction of a protospacer adjacent motif-free CRISPR/Cas12a fluorescent biosensor based on lambda exonuclease (λ-exo) and helicase-dependent amplification (HDA) to detect <em>Listeria monocytogenes</em>(<em>L. monocytogenes</em>). The <em>hlyA</em> gene of <em>L. monocytogenes</em> was amplified by HDA. After λ-exo catalyzed cleavage of 5′ phosphorylated single-stranded DNA of amplification product double-stranded DNA, the double-stranded DNA formed single-stranded DNA (ssDNA). The ssDNA as a substrate activated the <em>trans</em>-cleavage capability of CRISPR/Cas12a to cleave the reporter gene to produce fluorescence signals. Under optimized experimental conditions, the lower limit of <em>L. monocytogenes</em> detection by the fluorescent biosensor was 11.5 CFU/mL, with a linear range of detection from 10<sup>1</sup> to 10<sup>7</sup> CFU/mL. The fluorescent biosensor permits simple and sensitive detection of <em>L. monocytogenes</em> and provides a promising analysis platform for clinical diagnosis and biomedical research without protospacer adjacent motif sequence ssDNA.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 106-112"},"PeriodicalIF":3.3,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277038","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}

引用次数: 0

Assessment of venom variation and phylogenetic relationships of Micrurus dumerilii from three different regions of Colombia 哥伦比亚3个不同地区小圆尾鼠毒液变异及系统发育关系的评估。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-09 DOI: 10.1016/j.biochi.2025.06.003

Paola Rey-Suárez , Jeisson Gómez-Robles , Julián Fernández , Bruno Lomonte , Mahmood Sasa , Mónica Saldarriaga-Cordoba , Jaime Andrés Pereañez , Omayra Aguilera , Vitelbina Núñez-Rangel

{"title":"Assessment of venom variation and phylogenetic relationships of Micrurus dumerilii from three different regions of Colombia","authors":"Paola Rey-Suárez , Jeisson Gómez-Robles , Julián Fernández , Bruno Lomonte , Mahmood Sasa , Mónica Saldarriaga-Cordoba , Jaime Andrés Pereañez , Omayra Aguilera , Vitelbina Núñez-Rangel","doi":"10.1016/j.biochi.2025.06.003","DOIUrl":"10.1016/j.biochi.2025.06.003","url":null,"abstract":"<div><div>In the Americas, the genus <em>Micrurus</em> (coral snakes) includes the highest number of snake species, and Colombia is the second country with the greatest species diversity. <em>Micrurus dumerilii</em> has wide distribution and clinical importance in the country. The variability of its venom has not been extensively studied, and this could have implications for the neutralization by antivenoms. In this study, we explored the phylogenetic relationships between specimens from three regions of Colombia (Antioquia, Chocó, and Santander) and the variation in their venoms using proteomics, <em>in vitro</em> and <em>in vivo</em> assays, and assessment of antigenic recognition by the anticoral-INS antivenom. Phylogenetic analyses using <em>nd4</em>, <em>Cyt b</em>, and 16S rRNA gene fragments showed a close relationship between <em>M. dumerilii</em> from Ecuador and Chocó (Colombia), and within the <em>M. dumerilii</em> clade, a particularly close relationship between specimens from Antioquia and Santander. The venoms of <em>M. dumerilii</em> showed high overall similarity in their chromatographic profiles, with peaks corresponding to the three-finger toxin (3FTx) and phospholipase A<sub>2</sub> (PLA<sub>2</sub>) protein families being predominant. Some differences were observed in the number of protein families identified in each venom, but the main fraction responsible for lethality in the venoms from Antioquia, Chocó, and Santander was preserved. The commercial antivenom available in Colombia recognizes venom from all three regions. These general antigenic similarities between samples suggest that it may not be necessary to include <em>M. dumerilii</em> venoms from different geographic areas as immunogens for the production of antivenom against this species.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 93-105"},"PeriodicalIF":3.3,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277037","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}

引用次数: 0

Inside front cover-EDB 内部前盖- edb

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-07 DOI: 10.1016/S0300-9084(25)00104-X

引用次数: 0

Biochemical and proteomic profiling reveals potent proteolytic activity in the venom of Erythrolamprus melanotus (Shaw's dark ground snake, Xenodontini) 生化和蛋白质组学分析显示，黑腹蛇（肖氏黑地蛇，Xenodontini）的毒液具有强大的蛋白水解活性。

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-04 DOI: 10.1016/j.biochi.2025.05.012

Kristian A. Torres-Bonilla , Juan D. Bayona-Serrano , Paula A. Sáenz-Suarez , Duván F. Zambrano , Manuel H. Bernal-Bautista , Inácio L.M. Junqueira-de-Azevedo , Stephen Hyslop

{"title":"Biochemical and proteomic profiling reveals potent proteolytic activity in the venom of Erythrolamprus melanotus (Shaw's dark ground snake, Xenodontini)","authors":"Kristian A. Torres-Bonilla , Juan D. Bayona-Serrano , Paula A. Sáenz-Suarez , Duván F. Zambrano , Manuel H. Bernal-Bautista , Inácio L.M. Junqueira-de-Azevedo , Stephen Hyslop","doi":"10.1016/j.biochi.2025.05.012","DOIUrl":"10.1016/j.biochi.2025.05.012","url":null,"abstract":"<div><div>We describe here the Duvernoy's venom gland organization and biochemical and proteomic analyses of venom from the Colombian colubrid snake <em>Erythrolamprus melanotus</em>. Histological analysis indicated a serous venom gland distinct from the mucous supralabial gland. SDS-PAGE of the venom revealed >15 bands (∼15 kDa–∼200 kDa) and gelatin zymography revealed potent proteolytic activity; zymographic activity towards casein was considerably less. RP-HPLC yielded 16 peaks, several of which contained proteases, as assessed by gelatin zymography. Enzymatic assays using azocasein, azocoll and hide powder azure confirmed the proteolytic activity. The venom selectively degraded the Aα-chain of fibrinogen without affecting the Bβ and γ-chains (assessed by SDS-PAGE). All proteolytic activity was inhibited by EDTA (metalloproteinase inhibitor) but not by AEBSF (serine proteinase inhibitor). The venom had no <span>l</span>-amino acid oxidase, esterase, and PLA<sub>2</sub> activities. Proteomic analysis indicated the presence primarily of snake venom metalloproteinases (SVMP), snake venom matrix metalloproteinases (svMMP) and cysteine-rich secretory proteins (CRiSP). SVMP and svMMP were the major components, indicating that this venom is rich in proteases, in agreement with the findings for zymography and enzymatic assays. This study provides the first characterization of Colombian <em>E. melanotus</em> venom and highlights its rich content of metalloproteinases and potent proteolytic activity.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 122-133"},"PeriodicalIF":3.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251291","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}

引用次数: 0

Dietary advanced glycation end products (AGEs): A modifiable risk factor in the prevention of chronic diseases associated with aging? 饮食晚期糖基化终产物（AGEs）：预防与衰老相关的慢性疾病的可改变的危险因素？

IF 3.3 3区生物学

Biochimie Pub Date : 2025-06-03 DOI: 10.1016/j.biochi.2025.06.001

Felipe Ávila , Nadia Cruz , Ma Angélica González , Eduardo Fuentes , Sergio Wehinger , Mariane Lutz

{"title":"Dietary advanced glycation end products (AGEs): A modifiable risk factor in the prevention of chronic diseases associated with aging?","authors":"Felipe Ávila , Nadia Cruz , Ma Angélica González , Eduardo Fuentes , Sergio Wehinger , Mariane Lutz","doi":"10.1016/j.biochi.2025.06.001","DOIUrl":"10.1016/j.biochi.2025.06.001","url":null,"abstract":"<div><div>Advanced glycation end products (AGEs) are a heterogeneous group of compounds formed during the advanced stages of the Maillard reaction through non-enzymatic reactions, occurring mainly between reducing sugars or their oxidation metabolites and amino groups in proteins, lipids, and nucleic acids. These compounds can be endogenously formed, particularly under hyperglycemic conditions. In addition, AGEs are also produced exogenously during the thermal processing of foods, contributing to the dietary intake of these compounds. The accumulation of AGEs in body tissues has been associated with aging and the pathogenesis of various non-communicable diseases. Dietary intake of AGEs contributes significantly to their systemic burden. Consequently, reducing the intake of dietary AGEs has been proposed as a modifiable risk factor for the prevention of chronic, age-related diseases. This review examines and discusses current evidence on the molecular mechanisms by which dietary and endogenous AGEs contribute to cellular senescence and the progression of prevalent age-associated pathologies, including diabetes, cardiovascular diseases, musculoskeletal disorders, and neurodegeneration.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 80-92"},"PeriodicalIF":3.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236119","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}

引用次数: 0

Integrated physiologic and proteomic analysis of Antarctic yeast Rhodotorula mucilaginosa AN5 in response to Cd stress at low concentration 南极酵母黏胶红酵母AN5对低浓度镉胁迫的生理和蛋白质组学综合分析

IF 3.3 3区生物学

Biochimie Pub Date : 2025-05-30 DOI: 10.1016/j.biochi.2025.05.011

Guangfeng Kan , Yuexin Zhang , huixing Sheng , Ke Song , Yun Ju , Wanli Zong , Yanxiao Jiang , Yingying Wang , Cuijuan Shi

{"title":"Integrated physiologic and proteomic analysis of Antarctic yeast Rhodotorula mucilaginosa AN5 in response to Cd stress at low concentration","authors":"Guangfeng Kan , Yuexin Zhang , huixing Sheng , Ke Song , Yun Ju , Wanli Zong , Yanxiao Jiang , Yingying Wang , Cuijuan Shi","doi":"10.1016/j.biochi.2025.05.011","DOIUrl":"10.1016/j.biochi.2025.05.011","url":null,"abstract":"<div><div>In Antarctica, sea ice microorganisms are subjected to principal abiotic environmental stresses, such as low temperature, strong UV radiation and high salinity, but increasingly serious heavy metal pollution might has more grievous implication there. Herein, morphological, physiological and isobaric tag for relative and absolute quantification (iTRAQ)-based proteomic analyses were performed to anatomize the heavy metal adaptation mechanism of <em>Rhodotorula mucilaginosa</em> AN5, a type of basidiomycetous yeast strain isolated from Antarctic sea ice. Morphological observation showed that yeast AN5 could partly alleviate cadmium stress by the increase of cell size. KEGG functional enrichment along with physiological analysis showed that heavy metal tolerance of sea ice yeast might prominently be related to unsaturated fatty acids biosynthesis regulated by peroxisome proliferators-activated receptor (PPAR) signaling pathway, which is the first report in non-animal field. In addition, redox equilibrium, substances metabolism and energy generation also played key roles for yeast acclimation upon Cd stress. In general, Antarctic yeast could cope with heavy metal mainly by morphological alteration, ROS-scavenging capacity improvement and unsaturated fatty acids biosynthesis. This research provided particular insight into the tolerance mechanisms of Antarctic sea ice yeast in response to heavy metal stress.</div></div>","PeriodicalId":251,"journal":{"name":"Biochimie","volume":"235 ","pages":"Pages 68-79"},"PeriodicalIF":3.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201044","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}

引用次数: 0

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