Journal of biochemistry最新文献_第7页

Sequential post-translational modifications regulate damaged DNA-binding protein DDB2 function. 序列翻译后修饰调节受损 DNA 结合蛋白 DDB2 的功能。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-30 DOI: 10.1093/jb/mvae056

Hidenori Kaneoka, Kazuhiko Arakawa, Yusuke Masuda, Daiki Ogawa, Kota Sugimoto, Risako Fukata, Maasa Tsuge-Shoji, Ken-Ichi Nishijima, Shinji Iijima

{"title":"Sequential post-translational modifications regulate damaged DNA-binding protein DDB2 function.","authors":"Hidenori Kaneoka, Kazuhiko Arakawa, Yusuke Masuda, Daiki Ogawa, Kota Sugimoto, Risako Fukata, Maasa Tsuge-Shoji, Ken-Ichi Nishijima, Shinji Iijima","doi":"10.1093/jb/mvae056","DOIUrl":"10.1093/jb/mvae056","url":null,"abstract":"Nucleotide excision repair (NER) is a major DNA repair system and hereditary defects in this system cause critical genetic diseases (e.g. xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy). Various proteins are involved in the eukaryotic NER system and undergo several post-translational modifications. Damaged DNA-binding protein 2 (DDB2) is a DNA damage recognition factor in the NER pathway. We previously demonstrated that DDB2 was SUMOylated in response to UV irradiation; however, its physiological roles remain unclear. We herein analysed several mutants and showed that the N-terminal tail of DDB2 was the target for SUMOylation; however, this region did not contain a consensus SUMOylation sequence. We found a SUMO-interacting motif (SIM) in the N-terminal tail that facilitated SUMOylation. The ubiquitination of a SUMOylation-deficient DDB2 SIM mutant was decreased, and its retention of chromatin was prolonged. The SIM mutant showed impaired NER, possibly due to a decline in the timely handover of the lesion site to XP complementation group C. These results suggest that the SUMOylation of DDB2 facilitates NER through enhancements in ubiquitination.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"325-338"},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792533","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

VP1 of human and murine noroviruses recognizes glycolipid sulfatide via the P domain. 人类和鼠类诺如病毒的 VP1 可通过 P 结构域识别糖脂硫化物。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-30 DOI: 10.1093/jb/mvae051

Bunta Tsukamoto, Yuuki Kurebayashi, Tadanobu Takahashi, Yusuke Abe, Ryohei Ota, Yoshiki Wakabayashi, Anju Nishiie, Akira Minami, Takashi Suzuki, Hideyuki Takeuchi

{"title":"VP1 of human and murine noroviruses recognizes glycolipid sulfatide via the P domain.","authors":"Bunta Tsukamoto, Yuuki Kurebayashi, Tadanobu Takahashi, Yusuke Abe, Ryohei Ota, Yoshiki Wakabayashi, Anju Nishiie, Akira Minami, Takashi Suzuki, Hideyuki Takeuchi","doi":"10.1093/jb/mvae051","DOIUrl":"10.1093/jb/mvae051","url":null,"abstract":"Noroviruses are a prevalent cause of human viral gastroenteritis, yet the precise mechanisms underlying their infection cycle, particularly their interactions with and entry into cells, remain poorly understood. Human norovirus (HuNoV) primarily targets human small intestinal epithelial cells, within which 3-O-sulfogalactosylceramide (sulfatide) ranks among the most abundant glycosphingolipids (GSLs). While sulfatide involvement in the binding and infection mechanism of several viruses has been documented, its interaction with noroviruses remains underexplored. This study investigated whether noroviruses interact with sulfatide. We found that the recombinant viral capsid protein VP1 of HuNoV (genogroups I and II) and murine norovirus (genogroup V) exhibited robust binding to sulfatide compared with other tested GSLs using enzyme-linked immunosorbent assay, thin-layer chromatography binding assay and real-time quantitative reverse transcription polymerase chain reaction binding assay. VP1 also bound 3-O-sulfated lactosylceramide, which shares the 3-O-sulfated galactose moiety with sulfatide. However, both VP1 and its P domain, identified as the sulfatide-binding domain, exhibited limited binding to structural analogues of sulfatide and other sulfated compounds. These findings suggest a specific recognition of the 3-O-sulfated galactose moiety. Notably, we found that sulfatide is a novel binding target for norovirus particles. Overall, our findings reveal a previously unknown norovirus-sulfatide interaction, proposing sulfatide as a potential candidate for norovirus infection receptors.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"299-312"},"PeriodicalIF":2.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620027","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

Neutral selection and clonal expansion during the development of colon cancer metastasis. 结肠癌转移发展过程中的中性选择和克隆扩增。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae044

Xuelian Lei, Daisuke Yamamoto, Hirotaka Kitamura, Kenji Kita, Noriyuki Inaki, Kazuhiro Murakami, Mizuho Nakayama, Hiroko Oshima, Masanobu Oshima

{"title":"Neutral selection and clonal expansion during the development of colon cancer metastasis.","authors":"Xuelian Lei, Daisuke Yamamoto, Hirotaka Kitamura, Kenji Kita, Noriyuki Inaki, Kazuhiro Murakami, Mizuho Nakayama, Hiroko Oshima, Masanobu Oshima","doi":"10.1093/jb/mvae044","DOIUrl":"10.1093/jb/mvae044","url":null,"abstract":"Intratumour heterogeneity has been shown to play a role in the malignant progression of cancer. The clonal evolution in primary cancer has been well studied, however, that in metastatic tumorigenesis is not fully understood. In this study, we established human colon cancer-derived organoids and investigated clonal dynamics during liver metastasis development by tracking barcode-labelled subclones. Long-term subclone co-cultures showed clonal drift, with a single subclone becoming dominant in the cell population. Interestingly, the selected subclones were not always the same, suggesting that clonal selection was not based on cell intrinsic properties. Furthermore, liver tumours developed by co-transplantation of organoid subclones into the immunodeficient mouse spleen showed a progressive drastic reduction in clonal diversity, and only one or two subclones predominated in the majority of large metastatic tumours. Importantly, selections were not limited to particular subclones but appeared to be random. A trend towards a reduction in clonal diversity was also found in liver metastases of multiple colour-labelled organoids of mouse intestinal tumours. Based on these results, we propose a novel mechanism of metastasis development, i.e. a subclone population of the disseminated tumour cells in the liver is selected by neutral selection during colonization and constitutes large metastatic tumours.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"187-195"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419256","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

Onnamide A suppresses the severe acute respiratory syndrome-coronavirus 2 infection without inhibiting 3-chymotrypsin-like cysteine protease. 翁内酰胺 A 可抑制严重急性呼吸系统综合征-冠状病毒 2 感染，而不会抑制 3-糜蛋白酶样半胱氨酸蛋白酶。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae037

Yasuhiro Hayashi, Nanami Higa, Tetsuro Yoshida, Trianda Ayuning Tyas, Kanami Mori-Yasumoto, Mina Yasumoto-Hirose, Hideki Tani, Junichi Tanaka, Takahiro Jomori

{"title":"Onnamide A suppresses the severe acute respiratory syndrome-coronavirus 2 infection without inhibiting 3-chymotrypsin-like cysteine protease.","authors":"Yasuhiro Hayashi, Nanami Higa, Tetsuro Yoshida, Trianda Ayuning Tyas, Kanami Mori-Yasumoto, Mina Yasumoto-Hirose, Hideki Tani, Junichi Tanaka, Takahiro Jomori","doi":"10.1093/jb/mvae037","DOIUrl":"10.1093/jb/mvae037","url":null,"abstract":"Given the continuous emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of new inhibitors is necessary to enhance clinical efficacy and increase the options for combination therapy for the coronavirus disease 2019. Because marine organisms have been a resource for the discovery of numerous bioactive molecules, we constructed an extract library of marine invertebrates collected from the Okinawa Islands. In this study, the extracts were used to identify antiviral molecules against SARS-CoV-2. Using a cytopathic effect (CPE) assay in VeroE6/TMPRSS2 cells, an extract from the marine sponge Theonella swinhoei was found to reduce virus-induced CPE. Eventually, onnamide A was identified as an antiviral compound in the extract using column chromatography and NMR analysis. Onnamide A inhibited several SARS-CoV-2 variant-induced CPEs in VeroE6/TMPRSS2 cells as well as virus production in the supernatant of infected cells. Moreover, this compound blocked the entry of SARS-CoV-2 pseudo-virions. Taken together, these results demonstrate that onnamide A suppresses SARS-CoV-2 infection, which may be partially related to entry inhibition, and is expected to be a candidate lead compound for the development of anti-SARS-CoV-2 drugs.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"197-203"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081400","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

Amino acid residues responsible for the different pH dependency of cell-specific ferredoxins in the electron transfer reaction with ferredoxin-NADP+ reductase from maize leaves. 在与玉米叶片中的铁氧还蛋白-NADP+还原酶进行电子转移反应时，细胞特异性铁氧还蛋白对 pH 值的依赖性不同的氨基酸残基。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae043

Yoko Kimata-Ariga, Hikaru Tanaka, Shunsuke Kuwano

{"title":"Amino acid residues responsible for the different pH dependency of cell-specific ferredoxins in the electron transfer reaction with ferredoxin-NADP+ reductase from maize leaves.","authors":"Yoko Kimata-Ariga, Hikaru Tanaka, Shunsuke Kuwano","doi":"10.1093/jb/mvae043","DOIUrl":"10.1093/jb/mvae043","url":null,"abstract":"In the chloroplast stroma, dynamic pH changes occur from acidic to alkaline in response to fluctuating light conditions. We investigated the pH dependency of the electron transfer reaction of ferredoxin-NADP+ reductase (FNR) with ferredoxin (Fd) isoproteins, Fd1 and Fd2, which are localized in mesophyll cells and bundle sheath cells, respectively, in the leaves of C4 plant maize. The pH-dependent profile of the electron transfer activity with FNR was quite different between Fd1 and Fd2, which was mainly explained by the opposite pH dependency of the Km value of these Fds for FNR. Replacement of the amino acid residue at position of 65 (D65N) and 78 (H78A) between the two Fds conferred different effect on their pH dependency of the Km value. Double mutations of the two residues between Fd1 and Fd2 (Fd1D65N/H78A and Fd2N65D/A78H) led to the mutual exchange of the pH dependency of the electron transfer activity. This exchange was mainly explained by the changes in the pH-dependent profile of the Km values. Therefore, the differences in Asp/Asn at position 65 and His/Ala at position 78 between Fd1 and Fd2 were shown to be the major determinants for their different pH dependency in the electron transfer reaction with FNR.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"237-244"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305995","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

Comprehensive analysis of non-selective and selective autophagy in yeast atg mutants and characterization of autophagic activity in the absence of the Atg8 conjugation system. 全面分析酵母 atg 突变体的非选择性和选择性自噬，以及 Atg8 连接系统缺失时自噬活性的特征。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae042

Tamara Ginevskaia, Aleksei Innokentev, Kentaro Furukawa, Tomoyuki Fukuda, Manabu Hayatsu, Shun-Ichi Yamashita, Keiichi Inoue, Shinsuke Shibata, Tomotake Kanki

{"title":"Comprehensive analysis of non-selective and selective autophagy in yeast atg mutants and characterization of autophagic activity in the absence of the Atg8 conjugation system.","authors":"Tamara Ginevskaia, Aleksei Innokentev, Kentaro Furukawa, Tomoyuki Fukuda, Manabu Hayatsu, Shun-Ichi Yamashita, Keiichi Inoue, Shinsuke Shibata, Tomotake Kanki","doi":"10.1093/jb/mvae042","DOIUrl":"10.1093/jb/mvae042","url":null,"abstract":"Most autophagy-related genes, or ATG genes, have been identified through studies using budding yeast. Although the functions of the ATG genes are well understood, the contributions of individual genes to non-selective and various types of selective autophagy remain to be fully elucidated. In this study, we quantified the activity of non-selective autophagy, the cytoplasm-to-vacuole targeting (Cvt) pathway, mitophagy, endoplasmic reticulum (ER)-phagy and pexophagy in all Saccharomyces cerevisiae atg mutants. Among the mutants of the core autophagy genes considered essential for autophagy, the atg13 mutant and mutants of the genes involved in the two ubiquitin-like conjugation systems retained residual autophagic functionality. In particular, mutants of the Atg8 ubiquitin-like conjugation system (the Atg8 system) exhibited substantial levels of non-selective autophagy, the Cvt pathway and pexophagy, although mitophagy and ER-phagy were undetectable. Atg8-system mutants also displayed intravacuolar vesicles resembling autophagic bodies, albeit at significantly reduced size and frequency. Thus, our data suggest that membranous sequestration and vacuolar delivery of autophagic cargo can occur in the absence of the Atg8 system. Alongside these findings, the comprehensive analysis conducted here provides valuable datasets for future autophagy research.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"217-227"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141283834","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

Chondroitin sulfate liposome: clustering toward high functional efficiency. 硫酸软骨素脂质体：向高功能效率集聚。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae041

Tatsumasa Shioiri, Jun Tsuchimoto, Kaori Fukushige, Takao Takeuchi, Munekazu Naito, Hideto Watanabe, Nobuo Sugiura

{"title":"Chondroitin sulfate liposome: clustering toward high functional efficiency.","authors":"Tatsumasa Shioiri, Jun Tsuchimoto, Kaori Fukushige, Takao Takeuchi, Munekazu Naito, Hideto Watanabe, Nobuo Sugiura","doi":"10.1093/jb/mvae041","DOIUrl":"10.1093/jb/mvae041","url":null,"abstract":"Chondroitin sulfate (CS) is a linear polysaccharide chain of alternating residues of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc), modified with sulfate groups. Based on the structure, CS chains bind to bioactive molecules specifically and regulate their functions. For example, CS whose GalNAc is sulfated at the C4 position, termed CSA, and CS whose GalNAc is sulfated at both C4 and C6 positions, termed CSE, bind to a malaria protein VAR2CSA and receptor type of protein tyrosine phosphatase sigma (RPTPσ), respectively, in a specific manner. Here, we modified CSA and CSE chains with phosphatidylethanolamine (PE) at a reducing end, attached them to liposomes containing phospholipids and generated CSA and CSE liposomes. The CS-PE was incorporated into the liposome particles efficiently. Inhibition ELISA revealed specific interaction of CSA and CSE with recombinant VAR2CSA and RPTPσ, respectively, more efficiently than CS chains alone. Furthermore, CSE liposome was specifically incorporated into RPTPσ-expressing HEK293T cells. These results indicate CS liposome as a novel and efficient drug delivery system, especially for CS-binding molecules.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"229-236"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305996","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

Selection and characterization of aptamers targeting the Vif-CBFβ-ELOB-ELOC-CUL5 complex. 以 Vif-CBFβ-ELOB-ELOC-CUL5 复合物为靶标的适配体的筛选和表征。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae040

Kazuyuki Kumagai, Keisuke Kamba, Takuya Suzuki, Yuto Sekikawa, Chisato Yuki, Michiaki Hamada, Kayoko Nagata, Akifumi Takaori-Kondo, Li Wan, Masato Katahira, Takashi Nagata, Taiichi Sakamoto

{"title":"Selection and characterization of aptamers targeting the Vif-CBFβ-ELOB-ELOC-CUL5 complex.","authors":"Kazuyuki Kumagai, Keisuke Kamba, Takuya Suzuki, Yuto Sekikawa, Chisato Yuki, Michiaki Hamada, Kayoko Nagata, Akifumi Takaori-Kondo, Li Wan, Masato Katahira, Takashi Nagata, Taiichi Sakamoto","doi":"10.1093/jb/mvae040","DOIUrl":"10.1093/jb/mvae040","url":null,"abstract":"The viral infectivity factor (Vif) of human immunodeficiency virus 1 forms a complex with host proteins, designated as Vif-CBFβ-ELOB-ELOC-CUL5 (VβBCC), initiating the ubiquitination and subsequent proteasomal degradation of the human antiviral protein APOBEC3G (A3G), thereby negating its antiviral function. Whilst recent cryo-electron microscopy (cryo-EM) studies have implicated RNA molecules in the Vif-A3G interaction that leads to A3G ubiquitination, our findings indicated that the VβBCC complex can also directly impede A3G-mediated DNA deamination, bypassing the proteasomal degradation pathway. Employing the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we have identified RNA aptamers with high affinity for the VβBCC complex. These aptamers not only bind to the VβBCC complex but also reinstate A3G's DNA deamination activity by inhibiting the complex's function. Moreover, we delineated the sequences and secondary structures of these aptamers, providing insights into the mechanistic aspects of A3G inhibition by the VβBCC complex. Analysis using selected aptamers will enhance our understanding of the inhibition of A3G by the VβBCC complex, offering potential avenues for therapeutic intervention.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"205-215"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140915615","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

CDP-DAG synthesis by peripheral membrane-bound Tam41-type enzymes. 外周膜结合的 Tam41 型酶合成 CDP-DAG。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae046

Koji Okamoto

引用次数: 0

Neurodegenerative diseases associated with the disruption of proteostasis and their therapeutic strategies using chemical chaperones. 与蛋白稳态破坏有关的神经退行性疾病及其利用化学伴侣的治疗策略。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae048

Takashi Sugiyama, Hideki Nishitoh

引用次数: 0