Journal of biochemistry最新文献_第10页

Cytotoxic stress caused by azalamellarin D (AzaD) interferes with cellular protein translation by targeting the nutrient-sensing kinase mTOR. 氮杂霉素 D（AzaD）引起的细胞毒性压力通过靶向营养感应激酶 mTOR 干扰细胞蛋白质翻译。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae038

Tirawit Meerod, Rapeepat Sangsuwan, Kanawut Klumthong, Bunkuea Chantrathonkul, Nadgrita Phutubtim, Piyarat Govitrapong, Somsak Ruchirawat, Poonsakdi Ploypradith, Pattarawut Sopha

{"title":"Cytotoxic stress caused by azalamellarin D (AzaD) interferes with cellular protein translation by targeting the nutrient-sensing kinase mTOR.","authors":"Tirawit Meerod, Rapeepat Sangsuwan, Kanawut Klumthong, Bunkuea Chantrathonkul, Nadgrita Phutubtim, Piyarat Govitrapong, Somsak Ruchirawat, Poonsakdi Ploypradith, Pattarawut Sopha","doi":"10.1093/jb/mvae038","DOIUrl":"10.1093/jb/mvae038","url":null,"abstract":"Analogs of pyrrole alkaloid lamellarins exhibit anticancer activity by modulating multiple cellular events. Lethal doses of several lamellarins were found to enhance autophagy flux in HeLa cells, suggesting that lamellarins may modulate protein homeostasis through the interference of proteins or kinases controlling energy and nutrient metabolism. To further delineate molecular mechanisms and their targets, our results herein show that azalamellarin D (AzaD) cytotoxicity could cause translational attenuation, as indicated by a change in eIF2α phosphorylation. Intriguingly, acute AzaD treatment promoted the phosphorylation of GCN2, a kinase that transduces the integrated stress response (ISR), and prolonged exposure to AzaD could increase the levels of the phosphorylated forms of eIF2α and the other ISR kinase protein kinase R (PKR). However, the effects of AzaD on ISR signalling were marginally abrogated in cells with genetic deletion of GCN2 and PKR, and evaluation of protein target engagement by cellular thermal shift assay (CETSA) revealed no significant interaction between AzaD and ISR kinases. Further investigation revealed that acute AzaD treatment negatively affected mechanistic target of rapamycin (mTOR) phosphorylation and signalling. The analyses by CETSA and computational modelling indicated that mTOR may be a possible protein target for AzaD. These findings indicate the potential for developing lamellarins as novel agents for cancer treatment.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"139-153"},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854934","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

Effects of eyestalk ablation and seawater temperature on d-glutamate levels in the reproductive tissues of male kuruma prawn Marsupenaeus japonicus. 眼柄消融和海水温度对雄性日本对虾生殖组织中 D-谷氨酸水平的影响

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae036

Naoko Yoshikawa, Natsuki Yoshitomi, Kazuki Nakada

引用次数: 0

Intracellular acidification and glycolysis modulate inflammatory pathway in senescent cells. 细胞内酸化和糖酵解调节衰老细胞的炎症途径

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae032

Satoshi Kawakami, Yoshikazu Johmura, Makoto Nakanishi

{"title":"Intracellular acidification and glycolysis modulate inflammatory pathway in senescent cells.","authors":"Satoshi Kawakami, Yoshikazu Johmura, Makoto Nakanishi","doi":"10.1093/jb/mvae032","DOIUrl":"10.1093/jb/mvae032","url":null,"abstract":"Senescent cells accumulate in various organs with ageing, and its accumulation induces chronic inflammation and age-related physiological dysfunctions. Several remodelling of intracellular environments have been identified in senescent cells, including enlargement of cell/nuclear size and intracellular acidification. Although these alterations of intracellular environments were reported to be involved in the unique characteristics of senescent cells, the contribution of intracellular acidification to senescence-associated cellular phenotypes is poorly understood. Here, we identified that the upregulation of TXNIP and its paralog ARRDC4 as a hallmark of intracellular acidification in addition to KGA-type GLS1. These genes were also upregulated in response to senescence-associated intracellular acidification. Neutralization of the intracellular acidic environment ameliorated not only senescence-related upregulation of TXNIP, ARRDC4 and KGA but also inflammation-related genes, possibly through suppression of PDK-dependent anaerobic glycolysis. Furthermore, we found that expression of the intracellular acidification-induced genes, TXNIP and ARRDC4, correlated with inflammatory gene expression in heterogeneous senescent cell population in vitro and even in vivo, implying that the contribution of intracellular pH to senescence-associated cellular features, such as SASP.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"97-108"},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11289320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335733","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

Essential dextrin structure as donor substrate for 4-α-glucanotransferase in glycogen debranching enzyme. 作为糖原去支链酶中 4-α-葡聚糖转移酶供体底物的重要糊精结构

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae030

Rentaro Uno, Yasushi Makino, Hiroshi Matsubara

{"title":"Essential dextrin structure as donor substrate for 4-α-glucanotransferase in glycogen debranching enzyme.","authors":"Rentaro Uno, Yasushi Makino, Hiroshi Matsubara","doi":"10.1093/jb/mvae030","DOIUrl":"10.1093/jb/mvae030","url":null,"abstract":"Glycogen debranching enzyme is a single polypeptide with distinct catalytic sites for 4-α-glucanotransferase and amylo-α-1,6-glucosidase. To allow phosphorylase to degrade the inner tiers of highly branched glycogen, 4-α-glucanotransferase converts the phosphorylase-limit biantennary branch G-G-G-G-(G-G-G-G↔)G-G- (G: d-glucose, hyphens: α-1,4-linkages; double-headed arrow: α-1,6-linkage) into the G-G-G-G-(G↔)G-G- residue, which is then subjected to amylo-α-1,6-glucosidase to release the remaining G↔ residue. However, while the essential side-chain structure of the 4-α-glucanotransferase donor substrate has been determined to be the G-G-G-G↔ residue (Watanabe, Y., et al. (2008) J. Biochem.143, 435-440), its essential main-chain structure remains to be investigated. In this study, we probed the 4-α-glucanotransferase donor-binding region using novel fluorogenic dextrins Gm-(G4↔)G-Gn-F (F: 1-deoxy-1-[(2-pyridyl)amino]-d-glucitol) and maltohexaose (G6) as the donor and acceptor substrates, respectively. 4-α-Glucanotransferase exhibited maximum activity towards G4-(G4↔)G-F and G4-(G4↔)G-G-F, indicating that recognition of the G4-(G4↔)G-moiety was essential for full enzyme function. Notably, when the 4-α-glucanotransferase activity towards G4-(G4↔)G-G-F was taken as unity, those towards nonbranching dextrins were < 0.001. This indicated that the disproportionation activities towards maltooligosaccharides (Gm) are abnormal behaviours of 4-α-glucanotransferase. Notably, however, these activities have been traditionally measured to identify the 4-α-glucanotransferase mutations causing glycogen storage disease type III. This study provides a basis for more accurate identification.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"109-117"},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140158225","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

Structure-based design, biophysical characterization, and biochemical application of the heterodimeric affinity purification tag based on the Schistosoma japonicum glutathione-S-transferase (SjGST) homodimer. 基于日本血吸虫谷胱甘肽-S-转移酶（SjGST）同源二聚体的异源二聚体亲和纯化标签的结构设计、生物物理特征和生化应用。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae028

Yan Du, Yoshihiro Kobashigawa, Kyo Okazaki, Mizuki Ogawa, Tomoyuki Kawaguchi, Takashi Sato, Hiroshi Morioka

{"title":"Structure-based design, biophysical characterization, and biochemical application of the heterodimeric affinity purification tag based on the Schistosoma japonicum glutathione-S-transferase (SjGST) homodimer.","authors":"Yan Du, Yoshihiro Kobashigawa, Kyo Okazaki, Mizuki Ogawa, Tomoyuki Kawaguchi, Takashi Sato, Hiroshi Morioka","doi":"10.1093/jb/mvae028","DOIUrl":"10.1093/jb/mvae028","url":null,"abstract":"Schistosoma japonicum glutathione-S-transferase (SjGST), the so-called GST-tag, is one of the most widely used protein tags for the purification of recombinant proteins by affinity chromatography. Attachment of SjGST enables the purification of a protein of interest (POI) using commercially available glutathione-immobilizing resins. Here we produced an SjGST mutant pair that forms heterodimers by adjusting the salt bridge pairs in the homodimer interface of SjGST. An MD study confirmed that the SjGST mutant pair did not disrupt the heterodimer formation. The modified SjGST protein pair coexpressed in Escherichia coli was purified by glutathione-immobilized resin. The stability of the heterodimeric form of the SjGST mutant pair was further confirmed by size exclusion chromatography. Surface plasmon resonance measurements unveiled the selective formation of heterodimers within the pair, accompanied by a significant suppression of homodimerization. The heterodimeric SjGST exhibited enzymatic activity in assays employing a commercially available fluorescent substrate. By fusing one member of the heterodimeric SjGST pair with a fluorescent protein and the other with the POI, we were able to conveniently and sensitively detect protein-protein interactions using fluorescence spectroscopy in the pull-down assays. Thus, utilization of the heterodimeric SjGST would be a useful tag for protein science.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"69-80"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110365","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

SdrR, a LysR-type regulator, responds to the mycobacterial antioxidant defense. SdrR 是一种 LysR 型调节器，能对分枝杆菌的抗氧化防御做出反应。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae026

Chen Zhu, Wen-Ping Wei, Jing-Ning An, Jia-Ling Hu, Chun-Hui Gao, Min Yang

引用次数: 0

Structure-specific DNA endonuclease T7 endonuclease I cleaves DNA containing UV-induced DNA lesions. 结构特异性 DNA 内切酶 T7 内切酶 I 能切割含有紫外线诱导 DNA 病变的 DNA。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-01 DOI: 10.1093/jb/mvae024

Kazuki Matsubara, Shouta Ueda, Junpei Yamamoto, Shigenori Iwai, Narumi Aoki Shioi, Arato Takedachi, Isao Kuraoka

{"title":"Structure-specific DNA endonuclease T7 endonuclease I cleaves DNA containing UV-induced DNA lesions.","authors":"Kazuki Matsubara, Shouta Ueda, Junpei Yamamoto, Shigenori Iwai, Narumi Aoki Shioi, Arato Takedachi, Isao Kuraoka","doi":"10.1093/jb/mvae024","DOIUrl":"10.1093/jb/mvae024","url":null,"abstract":"The T7 gene 3 product, T7 endonuclease I, acts on various substrates with DNA structures, including Holliday junctions, heteroduplex DNAs and single-mismatch DNAs. Genetic analyses have suggested the occurrence of DNA recombination, replication and repair in Escherichia coli. In this study, T7 endonuclease I digested UV-irradiated covalently closed circular plasmid DNA into linear and nicked plasmid DNA, suggesting that the enzyme generates single- and double-strand breaks (SSB and DSB). To further investigate the biochemical functions of T7 endonuclease I, we have analysed endonuclease activity in UV-induced DNA substrates containing a single lesion, cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts (6-4PP). Interestingly, the leading cleavage site for CPD by T7 endonuclease I is at the second and fifth phosphodiester bonds that are 5' to the lesion of CPD on the lesion strand. However, in the case of 6-4PP, the cleavage pattern on the lesion strand resembled that of CPD, and T7 endonuclease I could also cleave the second phosphodiester bond that is 5' to the adenine-adenine residues opposite the lesion, indicating that the enzyme produces DSB in DNA containing 6-4PP. These findings suggest that T7endonuclease I accomplished successful UV damage repair by SSB in CPD and DSB in 6-4PP.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"35-42"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139996327","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

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