Journal of biochemistry最新文献_第9页

Photocontrol of small GTPase Ras fused with a photoresponsive protein. 与光响应蛋白融合的小 GTPase Ras 的光控。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae017

Nobuyuki Nishibe, Shinsaku Maruta

引用次数: 0

G protein-coupled receptor 84 gene expression is regulated by the ER stress response in the liver. 肝脏中的 G 蛋白偶联受体 84 基因表达受 ER 应激反应调控。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae027

Soshi Kanemoto

{"title":"G protein-coupled receptor 84 gene expression is regulated by the ER stress response in the liver.","authors":"Soshi Kanemoto","doi":"10.1093/jb/mvae027","DOIUrl":"10.1093/jb/mvae027","url":null,"abstract":"G protein-coupled receptor 84 (Gpr84) is reportedly activated by medium-chain fatty acids and is involved in the pathology of liver fibrosis. Inflammatory stimulants, such as lipopolysaccharide and tumor necrosis factor-α, upregulate Gpr84 expression. However, the detailed molecular mechanism by which Gpr84 is induced remains unknown. Inflammatory stimulation also evokes endoplasmic reticulum (ER) stress, but there has been no direct evidence to link Gpr84 expression and the ER stress response. Administration of tunicamycin (Tm) provokes ER stress and acute steatosis in the liver tissue of mice. Here, in situ hybridization analysis revealed that induction of Gpr84 expression occurred in parenchymal cells in the liver tissue following Tm administration. Gene expression analysis using a reporter assay showed that the intron 1 region of Gpr84 was involved in induction of the gene under ER stress conditions. Furthermore, Tm-dependent upregulation of Gpr84 was blocked by the small chemical compound AEBSF, an inhibitor of ER stress transducers, in vitro and in vivo. In conclusion, the current study marks the discovery that the ER stress agent Tm induces the expression of Gpr84.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"55-68"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Cryo-EM advances in GPCR structure determination. 冷冻电镜在确定 GPCR 结构方面的进展。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae029

Wataru Shihoya, Aika Iwama, Fumiya K Sano, Osamu Nureki

引用次数: 0

Production of CA125 with Tn antigens using a glycosylphosphatidylinositol anchoring system. 利用糖基磷脂酰肌醇锚定系统生产带有 Tn 抗原的 CA125。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae019

Yu-He Tang, Ji-Xiong Leng, Ganglong Yang, Xiao-Dong Gao, Yi-Shi Liu, Morihisa Fujita

{"title":"Production of CA125 with Tn antigens using a glycosylphosphatidylinositol anchoring system.","authors":"Yu-He Tang, Ji-Xiong Leng, Ganglong Yang, Xiao-Dong Gao, Yi-Shi Liu, Morihisa Fujita","doi":"10.1093/jb/mvae019","DOIUrl":"10.1093/jb/mvae019","url":null,"abstract":"Cancer antigen 125 (CA125) is a serum marker associated with ovarian cancer. Despite its widespread use, CA125 levels can also be elevated in benign conditions. Recent reports suggest that detecting serum CA125 that carries the Tn antigen, a truncated O-glycan containing only N-acetylgalactosamine on serine or threonine residues, can improve the specificity of ovarian cancer diagnosis. In this study, we engineered cells to express CA125 with a Tn antigen. To achieve this, we knocked out C1GALT1 and SLC35A1, genes encoding Core1 synthase and a transporter for cytidine-5'-monophospho-sialic acid respectively, in human embryonic kidney 293 (HEK293) cells. In ClGALT1-SLC35A1-knockout (KO) cells, the expression of the Tn antigen showed a significant increase, whereas the expression of the T antigen (galactose-β1,3-N-acetylgalactosamine on serine or threonine residues) was decreased. Due to the inefficient secretion of soluble CA125, we employed a glycosylphosphatidylinositol (GPI) anchoring system. This allowed for the expression of GPI-anchored CA125 on the cell surface of ClGALT1-SLC35A1-KO cells. Cells expressing high levels of GPI-anchored CA125 were then enriched through cell sorting. By knocking out the PGAP2 gene, the GPI-anchored form of CA125 was converted to a secretory form. Through the engineering of O-glycans and the use of a GPI-anchoring system, we successfully produced CA125 with Tn antigen modification.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"23-34"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139931354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. NLRP3 炎性体的形成通过多种机制抑制应激颗粒的组装。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae009

Daisuke Yoshioka, Takanori Nakamura, Yuji Kubota, Mutsuhiro Takekawa

{"title":"Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms.","authors":"Daisuke Yoshioka, Takanori Nakamura, Yuji Kubota, Mutsuhiro Takekawa","doi":"10.1093/jb/mvae009","DOIUrl":"10.1093/jb/mvae009","url":null,"abstract":"Proper regulation of cellular response to environmental stress is crucial for maintaining biological homeostasis and is achieved by the balance between cell death processes, such as the formation of the pyroptosis-inducing NLRP3 inflammasome, and pro-survival processes, such as stress granule (SG) assembly. However, the functional interplay between these two stress-responsive organelles remains elusive. Here, we identified DHX33, a viral RNA sensor for the NLRP3 inflammasome, as a SG component, and the SG-nucleating protein G3BP as an NLRP3 inflammasome component. We also found that a decrease in intracellular potassium (K+) concentration, a key 'common' step in NLRP3 inflammasome activation, markedly inhibited SG assembly. Therefore, when macrophages are exposed to stress stimuli with the potential to induce both SGs and the NLRP3 inflammasome, such as cytoplasmic poly(I:C) stimulation, they preferentially form the NLRP3 inflammasome but avoid SG assembly by sequestering G3BP into the inflammasome and by inducing a reduction in intracellular K+ levels. Thus, under such conditions, DHX33 is primarily utilized as a viral RNA sensor for the inflammasome. Our data reveal the functional crosstalk between NLRP3 inflammasome-mediated pyroptosis and SG-mediated cell survival pathways and delineate a molecular mechanism that regulates cell-fate decisions and anti-viral innate immunity under stress.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"629-641"},"PeriodicalIF":2.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of cytotoxic amyloid oligomers generated during disaggregation. 分解过程中产生的细胞毒性淀粉样蛋白寡聚体的结构。

IF 2.7 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae023

Toshisuke Kaku, Kazunori Ikebukuro, Kaori Tsukakoshi

{"title":"Structure of cytotoxic amyloid oligomers generated during disaggregation.","authors":"Toshisuke Kaku, Kazunori Ikebukuro, Kaori Tsukakoshi","doi":"10.1093/jb/mvae023","DOIUrl":"10.1093/jb/mvae023","url":null,"abstract":"Amyloidosis is characterized by the abnormal accumulation of amyloid proteins. The causative proteins aggregate from monomers to oligomers and fibrils, among which some intermediate oligomers are considered as major toxins. Cytotoxic oligomers are generated not only by aggregation but also via fibril disaggregation. However, little is known about the structural characteristics and generation conditions of cytotoxic oligomers produced during disaggregation. Herein, we summarized the structural commonalities of cytotoxic oligomers formed under various disaggregation conditions, including the addition of heat shock proteins or small compounds. In vitro experimental data demonstrated the presence of high-molecular-weight oligomers (protofibrils or protofilaments) that exhibited a fibrous morphology and β-sheet structure. Molecular dynamics simulations indicated that the distorted β-sheet structure contributed to their metastability. The tendency of these cytotoxic oligomers to appear under mild disaggregation conditions, implied formation during the early stages of disaggregation. This review will aid researchers in exploring the characteristics of highly cytotoxic oligomers and developing drugs that target amyloid aggregates.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"575-585"},"PeriodicalIF":2.7,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals. 对日本人进行全血转录组分析，绘制年龄和性别特异性基因表达图谱。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae008

Yu-Ichi Aoki, Keiko Taguchi, Hayato Anzawa, Junko Kawashima, Noriko Ishida, Akihito Otsuki, Atsushi Hasegawa, Liam Baird, Takafumi Suzuki, Ikuko N Motoike, Kinuko Ohneda, Kazuki Kumada, Fumiki Katsuoka, Kengo Kinoshita, Masayuki Yamamoto

{"title":"Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals.","authors":"Yu-Ichi Aoki, Keiko Taguchi, Hayato Anzawa, Junko Kawashima, Noriko Ishida, Akihito Otsuki, Atsushi Hasegawa, Liam Baird, Takafumi Suzuki, Ikuko N Motoike, Kinuko Ohneda, Kazuki Kumada, Fumiki Katsuoka, Kengo Kinoshita, Masayuki Yamamoto","doi":"10.1093/jb/mvae008","DOIUrl":"10.1093/jb/mvae008","url":null,"abstract":"Whole blood transcriptome analysis is a valuable approachin medical research, primarily due to the ease of sample collection and the richness of the information obtained. Since the expression profile of individual genes in the analysis is influenced by medical traits and demographic attributes such as age and gender, there has been a growing demand for a comprehensive database for blood transcriptome analysis. Here, we performed whole blood RNA sequencing (RNA-seq) analysis on 576 participants stratified by age (20-30s and 60-70s) and gender from cohorts of the Tohoku Medical Megabank (TMM). A part of female segment included pregnant women. We did not exclude the globin gene family in our RNA-seq study, which enabled us to identify instances of hereditary persistence of fetal hemoglobin based on the HBG1 and HBG2 expression information. Comparing stratified populations allowed us to identify groups of genes associated with age-related changes and gender differences. We also found that the immune response status, particularly measured by neutrophil-to-lymphocyte ratio (NLR), strongly influences the diversity of individual gene expression profiles in whole blood transcriptome analysis. This stratification has resulted in a data set that will be highly beneficial for future whole blood transcriptome analysis in the Japanese population.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"611-627"},"PeriodicalIF":2.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139546411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The ATPase activity of ABCA1 is increased by cholesterol in the presence of anionic lipids. 在阴离子脂质存在的情况下，胆固醇会增加 ABCA1 的 ATP 酶活性。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae003

Kazuki Sakata, Noriyuki Kioka, Kazumitsu Ueda, Yasuhisa Kimura

{"title":"The ATPase activity of ABCA1 is increased by cholesterol in the presence of anionic lipids.","authors":"Kazuki Sakata, Noriyuki Kioka, Kazumitsu Ueda, Yasuhisa Kimura","doi":"10.1093/jb/mvae003","DOIUrl":"10.1093/jb/mvae003","url":null,"abstract":"High-density lipoprotein (HDL) transports excess cholesterol from peripheral tissues back to the liver, and plasma HDL levels are inversely related to cardiovascular disease incidence. ATP-binding cassette A1 (ABCA1) is a member of the ABC protein superfamily, and generates nascent HDL, which consists of several hundreds of phospholipids and cholesterol wrapped by apolipoprotein A-I (apoA-I). However, it remains unclear whether cholesterol is a transport substrate of ABCA1. Since ATP hydrolysis of ABC proteins is typically increased by their transport substrates, we characterized the effects of cholesterol on the ATPase activity of purified ABCA1 using liposomes of various lipid compositions. ABCA1 showed substantial ATPase activity (20-30 nmol$cdot$min-1$cdot$mg-1) only in liposomes containing anionic lipids, including phosphatidylserine. Cholesterol increased the ATPase activity by 1.6- to 3-fold in the presence of anionic lipids. Moreover, phosphatidylserine addition to BHK/ABCA1 cells increased phosphatidylcholine and cholesterol efflux to apoA-I. Next, we investigated the sterol specificity of ABCA1. The ATPase activity of ABCA1 was strongly enhanced by desmosterol and zymosterol, similar to cholesterol. In contrast, 7-dehydrocholesterol and lathosterol weakly increased the ATPase activity, and no increase was observed with stigmasterol or brassicasterol. These findings suggest that ABCA1 transports cholesterol and prefers cholesterol over plant sterols as a transport substrate.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"599-609"},"PeriodicalIF":2.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139432514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus. 暴怒火球菌中用于处理 rRNA 的核糖核酸酶 FAU-1 的同源三聚体结构。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae010

Gota Kawai, Kiyoshi Okada, Seiki Baba, Asako Sato, Taiichi Sakamoto, Akio Kanai

{"title":"Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus.","authors":"Gota Kawai, Kiyoshi Okada, Seiki Baba, Asako Sato, Taiichi Sakamoto, Akio Kanai","doi":"10.1093/jb/mvae010","DOIUrl":"10.1093/jb/mvae010","url":null,"abstract":"Crystal structure of a ribonuclease for ribosomal RNA processing, FAU-1, from Pyrococcus furiosus was determined with the resolution of 2.57 Å in a homo-trimeric form. The monomer structure consists of two domains: N-terminal and C-terminal domains. C-terminal domain forms trimer and each N-terminal domain locates outside of the trimer core. In the obtained crystal, a dinucleotide, pApUp, was bound to the N-terminal domain, indicating that N-terminal domain has the RNA-binding ability. The affinities to RNA of FAU-1 and a fragment corresponding to the N-terminal domain, FAU-ΔC, were confirmed by polyacrylamide gel electrophoresis and nuclear magnetic resonance (NMR). Interestingly, well-dispersed NMR signals were observed at 318K, indicating that the FAU-ΔC-F18 complex form an ordered structure at higher temperature. As predicted in our previous works, FAU-1 and ribonuclease (RNase) E show a structural similarity in their RNA-binding regions. However, structural similarity between RNase E and FAU-1 could be found in the limited regions of the N-terminal domain. On the other hand, structural similarity between C-terminal domain and some proteins including a phosphatase was found. Thus, it is possible that the catalytic site is located in C-terminal domain.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"671-676"},"PeriodicalIF":2.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside. 无细胞系统中核糖体的直接可视化揭示了氨基糖苷的功能演变。

IF 2.7 4区生物学

Journal of biochemistry Pub Date : 2024-05-31 DOI: 10.1093/jb/mvae002

Junta Tomono, Kosuke Asano, Takuma Chiashi, Masato Suzuki, Masayuki Igarashi, Yoshiaki Takahashi, Yoshikazu Tanaka, Takeshi Yokoyama

{"title":"Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.","authors":"Junta Tomono, Kosuke Asano, Takuma Chiashi, Masato Suzuki, Masayuki Igarashi, Yoshiaki Takahashi, Yoshikazu Tanaka, Takeshi Yokoyama","doi":"10.1093/jb/mvae002","DOIUrl":"10.1093/jb/mvae002","url":null,"abstract":"The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"587-598"},"PeriodicalIF":2.7,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139478590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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