Biochimie最新文献_第2页

Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells. 利用超高分辨率质谱法直接分析鲍曼不动杆菌细胞中的脂质 A 和磷脂。

Biochimie Pub Date : 2024-09-24 DOI: 10.1016/j.biochi.2024.09.012

Delphine Vergoz, Annick Schaumann, Isabelle Schmitz, Maria van Agthoven, Sara Martí, Jordi Vila, Carlos Afonso, Emmanuelle Dé, Corinne Loutelier-Bourhis, Stéphane Alexandre

{"title":"Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells.","authors":"Delphine Vergoz, Annick Schaumann, Isabelle Schmitz, Maria van Agthoven, Sara Martí, Jordi Vila, Carlos Afonso, Emmanuelle Dé, Corinne Loutelier-Bourhis, Stéphane Alexandre","doi":"10.1016/j.biochi.2024.09.012","DOIUrl":"10.1016/j.biochi.2024.09.012","url":null,"abstract":"Acinetobacter baumannii, classified as priority number one by the World Health Organization (WHO), is an opportunistic pathogen responsible for infection and is able to develop antibiotic resistance easily. Membranes are bacteria's first line of defense against external aggression, such as antibiotics. A chemical modification of a lipid family or a change in lipid composition can lead to resistance to antibiotics. In this work, we analyzed different A. baumannii strains from various environments with different antibiotic resistance profiles, using matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS). This study shows that it is possible to describe the main lipidome (phospholipids and lipid A) from the simple preparation of lysed cells, and that despite the complexity of the mixture. This ultra-high resolution mass spectrometry technique enables the separation of isobaric ion, to report a new class of lipids. Given its performance, this technique can be used to quickly and reliably characterize the lipidome of clinical strains from different environments.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334286","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}

引用次数: 0

Orchestra of ligand-activated transcription factors in the molecular symphony of SERPINE 1 / PAI-1 gene regulation. 配体激活的转录因子在 SERPINE 1 / PAI-1 基因调控的分子交响乐中的乐队。

Biochimie Pub Date : 2024-09-23 DOI: 10.1016/j.biochi.2024.09.010

Aneta Vrzalova, Radim Vrzal

引用次数: 0

Extracellular vesicles as a potential source of biomarkers for endocrine disruptors in MASLD: A short review on the case of DEHP. 细胞外囊泡作为 MASLD 中内分泌干扰物生物标志物的潜在来源：DEHP 案例简评。

Biochimie Pub Date : 2024-09-21 DOI: 10.1016/j.biochi.2024.09.009

Pierre-Etienne Merret, Lydie Sparfel, Catherine Lavau, Dominique Lagadic-Gossmann, Corinne Martin-Chouly

引用次数: 0

The Barnase-Barstar-based pre-targeting strategy for enhanced antitumor therapy in vivo. 基于 Barnase-Barstar 的预靶向策略用于增强体内抗肿瘤治疗。

Biochimie Pub Date : 2024-09-21 DOI: 10.1016/j.biochi.2024.09.011

G M Proshkina, E I Shramova, A B Mirkasyimov, O Yu Griaznova, E V Konovalova, A A Schulga, S M Deyev

{"title":"The Barnase-Barstar-based pre-targeting strategy for enhanced antitumor therapy in vivo.","authors":"G M Proshkina, E I Shramova, A B Mirkasyimov, O Yu Griaznova, E V Konovalova, A A Schulga, S M Deyev","doi":"10.1016/j.biochi.2024.09.011","DOIUrl":"10.1016/j.biochi.2024.09.011","url":null,"abstract":"There is a great need for novel approaches to the treatment of epithelial ovarian carcinoma, which is the leading cause of mortality from gynecological malignancies. In this study, the pre-targeting technology was used to enhance the in vivo targeting of cytotoxic module composed of nanoliposomes loaded with a truncated form of Pseudomonas aeruginosa exotoxin A (PE40) to cancer cells. Pre-targeting system used in this study is composed of bacterial ribonuclease Barnase and its natural antitoxin Barstar. Barstar, genetically fused to various engineered scaffold proteins specific to tumor-associated antigens (HER2, EpCAM) serves as a primary module for precise cancer cell recognition. Barnase conjugated to a therapeutic agent serves as a cytotoxic or secondary module for malignant cell elimination. Due to strong non-covalent interaction (KD10-14 M) of Barstar and Barnase, the primary and secondary modules efficiently interact with each other on the cell surface, which has been proven by confocal microscopy and flow cytometry. Using mice with SKOV-3 ovarian cancer xenografts, we have shown that regardless of the targeting module, the pre-targeting approach is much more effective than a single-step active targeting.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303198","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}

引用次数: 0

Specificity of lipid transfer proteins: An in vitro story. 脂质转移蛋白的特异性：一个体外故事。

Biochimie Pub Date : 2024-09-19 DOI: 10.1016/j.biochi.2024.09.007

Amazigh Hamaï, Guillaume Drin

{"title":"Specificity of lipid transfer proteins: An in vitro story.","authors":"Amazigh Hamaï, Guillaume Drin","doi":"10.1016/j.biochi.2024.09.007","DOIUrl":"10.1016/j.biochi.2024.09.007","url":null,"abstract":"Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303197","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}

引用次数: 0

Mutations in the N-domain of aryl hydrocarbon receptor interacting protein affect interactions with heat shock protein 90β and phosphodiesterase 4A5. 芳基烃受体相互作用蛋白 N-域的突变会影响与热休克蛋白 90β 和磷酸二酯酶 4A5 的相互作用。

Biochimie Pub Date : 2024-09-18 DOI: 10.1016/j.biochi.2024.09.005

Marita Vella, Iain W Manfield, Brandon C Seychell, Chi H Trinh, Robert Rambo, G Nasir Khan, Josanne Vassallo, Thérèse Hunter, Gary J Hunter

{"title":"Mutations in the N-domain of aryl hydrocarbon receptor interacting protein affect interactions with heat shock protein 90β and phosphodiesterase 4A5.","authors":"Marita Vella, Iain W Manfield, Brandon C Seychell, Chi H Trinh, Robert Rambo, G Nasir Khan, Josanne Vassallo, Thérèse Hunter, Gary J Hunter","doi":"10.1016/j.biochi.2024.09.005","DOIUrl":"10.1016/j.biochi.2024.09.005","url":null,"abstract":"The aryl hydrocarbon receptor interacting protein (AIP) is a cytoplasmic molecular co-chaperone and tumour suppressor that assists in protein stability and complex formation involving the aryl hydrocarbon receptor. Germline mutations in the AIP gene predispose to pituitary tumourigenesis with patients exhibiting an aggressive clinical phenotype. Full length AIP proteins harbouring N-domain mutations (R9Q, R16H, V49 M and K103R) were purified from E.coli utilizing a methodology that maintained structural integrity and monomeric stability. Mutations did not significantly affect the thermal stability of the protein and caused no overall disruptive effect in the protein structure. The mutations studied lowered the binding affinity of AIP towards two of its binding partners; heat shock protein 90β and phosphodiesterase 4A5 (PDE4A5). The inhibition of phosphodiesterase activity by AIP was also greatly reduced by all mutants. While previously published data has mainly concentrated on the tetratricopeptide repeats of the C-domain of AIP, we present clear evidence that AIP N-domain mutations play a significant role in two protein:protein interactions with partner proteins. The complex interactome of AIP suggests that any observable change in one or more of its binding partners cannot be disregarded as it may have repercussions on other biochemical pathways.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303296","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}

引用次数: 0

Established and emerging players in phospholipid scrambling: A structural perspective. 磷脂争夺中的成熟和新兴参与者：结构视角。

Biochimie Pub Date : 2024-09-18 DOI: 10.1016/j.biochi.2024.09.008

Heitor Gobbi Sebinelli, Camille Syska, Alenka Čopič, Guillaume Lenoir

{"title":"Established and emerging players in phospholipid scrambling: A structural perspective.","authors":"Heitor Gobbi Sebinelli, Camille Syska, Alenka Čopič, Guillaume Lenoir","doi":"10.1016/j.biochi.2024.09.008","DOIUrl":"10.1016/j.biochi.2024.09.008","url":null,"abstract":"The maintenance of a diverse and non-homogeneous lipid composition in cell membranes is crucial for a multitude of cellular processes. One important example is transbilayer lipid asymmetry, which refers to a difference in lipid composition between the two leaflets of a cellular membrane. Transbilayer asymmetry is especially pronounced at the plasma membrane, where at resting state, negatively-charged phospholipids such as phosphatidylserine (PS) are almost exclusively restricted to the cytosolic leaflet, whereas sphingolipids are mostly found in the exoplasmic leaflet. Transbilayer movement of lipids is inherently slow, and for a fast cellular response, for example during apoptosis, transmembrane proteins termed scramblases facilitate the movement of polar/charged lipid headgroups through the membrane interior. In recent years, an expanding number of proteins from diverse families have been suggested to possess a lipid scramblase activity. Members of TMEM16 and XKR proteins have been implicated in blood clotting and apoptosis, whereas the scrambling activity of ATG9 and TMEM41B/VMP1 proteins contributes to the synthesis of autophagosomal membrane during autophagy. Structural studies, in vitro reconstitution of lipid scrambling, and molecular dynamics simulations have significantly advanced our understanding of the molecular mechanisms of lipid scrambling and helped delineate potential lipid transport pathways through the membrane. A number of examples also suggest that lipid scrambling activity can be combined with another activity, as is the case for TMEM16 proteins, which also function as ion channels, rhodopsin in the photoreceptor membrane, and possibly other G-protein coupled receptors.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303292","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}

引用次数: 0

Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview. 从微藻类到哺乳动物的脂滴降解机制比较概述。

Biochimie Pub Date : 2024-09-17 DOI: 10.1016/j.biochi.2024.09.006

Chems Amari, Marta Carletti, Siqi Yan, Morgane Michaud, Juliette Salvaing

{"title":"Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview.","authors":"Chems Amari, Marta Carletti, Siqi Yan, Morgane Michaud, Juliette Salvaing","doi":"10.1016/j.biochi.2024.09.006","DOIUrl":"10.1016/j.biochi.2024.09.006","url":null,"abstract":"Lipid droplets (LDs) are organelles composed of a hydrophobic core (mostly triacylglycerols and steryl esters) delineated by a lipid monolayer and found throughout the tree of life. LDs were seen for a long time as simple energy storage organelles but recent works highlighted their versatile roles in several fundamental cellular processes, particularly during stress response. LDs biogenesis occurs in the ER and their number and size can be dynamically regulated depending on their function, e.g. during development or stress. Understanding their biogenesis and degradation mechanisms is thus essential to better apprehend their roles. LDs degradation can occur in the cytosol by lipolysis or after their internalization into lytic compartments (e.g. vacuoles or lysosomes) using diverse mechanisms that depend on the considered organism, tissue, developmental stage or environmental condition. In this review, we summarize our current knowledge on the different LDs degradation pathways in several main phyla of model organisms, unicellular or pluricellular, photosynthetic or not (budding yeast, mammals, land plants and microalgae). We highlight the conservation of the main degradation pathways throughout evolution, but also the differences between organisms, or inside an organism between different organs. Finally, we discuss how this comparison can help to shed light on relationships between LDs degradation pathways and LDs functions.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303294","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}

引用次数: 0

Lipid remodeling in context of cellular senescence. 细胞衰老背景下的脂质重塑

Biochimie Pub Date : 2024-09-17 DOI: 10.1016/j.biochi.2024.09.003

Khaled Tighanimine

引用次数: 0

Using targeted proteomics-based detection of collagen propeptides to quantify fibrillar collagen biogenesis in vitro. 利用基于蛋白质组学的胶原蛋白肽靶向检测，量化体外纤维胶原蛋白的生物生成。

Biochimie Pub Date : 2024-09-14 DOI: 10.1016/j.biochi.2024.09.004

Matthias Kühle, Joachim Kuhn, Thanh-Diep Ly, Cornelius Knabbe, Bastian Fischer

{"title":"Using targeted proteomics-based detection of collagen propeptides to quantify fibrillar collagen biogenesis in vitro.","authors":"Matthias Kühle, Joachim Kuhn, Thanh-Diep Ly, Cornelius Knabbe, Bastian Fischer","doi":"10.1016/j.biochi.2024.09.004","DOIUrl":"10.1016/j.biochi.2024.09.004","url":null,"abstract":"The collagen superfamily, as the major structural component of the extracellular matrix, encompasses 28 distinct subtypes, with type-I and -III forming fibrils crucial for the matrix scaffold. During collagen biogenesis, trimers of type-I and -III procollagen are secreted into the extracellular matrix. The N- and C-terminal propeptides of these trimers are proteolytically cleaved from procollagen during secretion, initiating collagen fibril formation. The propeptides are released into extracellular space and, therefore, have been used to quantify collagen biogenesis. But high-throughput methods for the quantification of these biomarkers are still lacking. This study presents a state-of-the-art multiplexed approach for the simultaneous quantification of PINP, PICP, PIIINP and PIIICP from cell culture supernatants. The ability of targeted proteomics to quantify these propeptides from cell culture samples was assessed in this study. Using tryptic digestion and solid phase extraction, we were able to accurately quantify precollagen propeptides in a range of 3-1000 ng/mL. The assay showed an average inter-assay variance of 6.86 % with an overall recovery ranging from 92 to 98 %. The assay was validated using recombinant protein standards diluted in surrogate matrix and tested using transforming growth factor β1 mediated induction of normal human dermal fibroblasts. In summary, the assay presented in this paper offers a novel, robust, and precise high-throughput method for measuring human collagen propeptides in cell culture supernatants, empowering researchers to assess collagen biogenesis effectively in in vitro experiments.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303199","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}

引用次数: 0