Journal of biochemistry最新文献

Histone H2B isoform H2bc27 is expressed in the developing brain of mouse embryos. 组蛋白H2B异构体H2bc27在小鼠胚胎发育中的大脑中表达。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-14 DOI: 10.1093/jb/mvaf026

Saki Egashira, Kazumitsu Maehara, Kaori Tanaka, Mako Nakamura, Tatsuya Takemoto, Yasuyuki Ohkawa, Akihito Harada

引用次数: 0

Valosin-containing protein mediates DNA-dependent protein kinase activation in response to DNA topoisomerase II-associated DNA double-strand breaks. 在DNA拓扑异构酶ii相关DNA双链断裂的反应中，含缬草苷蛋白介导DNA依赖性蛋白激酶激活。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-14 DOI: 10.1093/jb/mvaf025

Ryo Sakasai, Yumi Sunatani, Tadashi Matsui, Kuniyoshi Iwabuchi

{"title":"Valosin-containing protein mediates DNA-dependent protein kinase activation in response to DNA topoisomerase II-associated DNA double-strand breaks.","authors":"Ryo Sakasai, Yumi Sunatani, Tadashi Matsui, Kuniyoshi Iwabuchi","doi":"10.1093/jb/mvaf025","DOIUrl":"https://doi.org/10.1093/jb/mvaf025","url":null,"abstract":"DNA topoisomerase II (Top2) induces DNA double-strand breaks (DSBs) to relieve the torsional stress associated with DNA replication and transcription. Etoposide (ETP), a Top2 poison in clinical use as an anticancer drug, traps Top2 reactive intermediates, resulting in the accumulation of DSBs, coupled with the formation of Top2-DNA protein crosslinks (Top2-DPC) at the ends of DSBs. Proteasome-dependent processing of trapped Top2 is necessary for some cellular responses to ETP-induced DSBs; however, the effect of suppressing Top2 removal on DSB repair is not well understood. In this study, we focused on valosin-containing protein (VCP), a proteasome mediator, to analyze the effect of the suppression of Top2-DPC resolution on the repair of ETP-induced DSBs. ETP-induced activation of DNA-dependent protein kinase (DNA-PK), a non-homologous end-joining (NHEJ) factor, was suppressed by VCP inhibitors, similar to the effects observed in proteasome-inhibited cells. Consistent with this finding, VCP inhibition suppressed repair activity in response to ETP-induced DSBs. Additionally, VCP inhibition delayed the resolution of ETP-induced Top2-DPC. These results suggest that the processing of trapped Top2 via the VCP-proteasome pathway is important for efficient DNA-PK activation and subsequent repair in response to ETP-induced DSBs.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063977","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

Improvement of a FRET-based redox probe Redoxfluor through circular permutation and effects of substitution of cysteine residues on its redox properties. 基于fret的氧化还原探针Redoxfluor的循环置换改进及半胱氨酸残基取代对其氧化还原性能的影响。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-14 DOI: 10.1093/jb/mvaf023

Kosuke Shiraishi, Banri Kitamura, Kaho Aramaki, Yasuyoshi Sakai, Jun Hoseki

{"title":"Improvement of a FRET-based redox probe Redoxfluor through circular permutation and effects of substitution of cysteine residues on its redox properties.","authors":"Kosuke Shiraishi, Banri Kitamura, Kaho Aramaki, Yasuyoshi Sakai, Jun Hoseki","doi":"10.1093/jb/mvaf023","DOIUrl":"https://doi.org/10.1093/jb/mvaf023","url":null,"abstract":"The properties of a FRET-based redox probe Redoxfluor have been improved for its sensitivity and dynamic range. Substitution of the Citrine portion of Redoxfluor with circular permutated (cp) Citrine improved the dynamic range without affecting the redox potential. The cp158 mutant, referred to as Redoxfluor 2, possessed the most extended dynamic range and detected intracellular redox changes in yeast and bacteria, while the original did not. Investigation of the glutathione-redox dependency of the FRET ratio of various cysteine-substituted mutants revealed that Cys230 in the linker between Cerulean and the C-terminal cysteine-rich domain (CRD) and Cys385 in Citrine are essential for glutathione redox sensing. Although neither cysteine residues in CRD is essential for glutathione redox sensing, substitution of the CRD cysteine residues prominently affected the dynamic range of redox sensing and the redox potential titrated with glutathione. One of the CRD cysteine-substituted mutants (C259A) showed a greatly extended dynamic range and a substantially reducing redox potential compared to the original Redoxfluor. Redoxfluor 2 and the C259A mutant are suitable for versatile uses including sensitive detection of aberrant redox states, redox visualization in the more reducing intracellular compartments, and high-throughput screening of redox modulators active against pathologically abnormal redox states.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078323","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

Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells. Atg7敲低抑制自噬增强吉西他滨/紫杉醇耐药胰腺癌MIAPaCa2细胞的化疗敏感性。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-07 DOI: 10.1093/jb/mvaf022

Yudai Kudo, Kotaro Hirota, Honoka Tsuzuki, Shinya Kawano, Tomofumi Saka, Riri Hayashi, Yuta Yoshino, Akira Ikari, Satoshi Endo

{"title":"Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells.","authors":"Yudai Kudo, Kotaro Hirota, Honoka Tsuzuki, Shinya Kawano, Tomofumi Saka, Riri Hayashi, Yuta Yoshino, Akira Ikari, Satoshi Endo","doi":"10.1093/jb/mvaf022","DOIUrl":"https://doi.org/10.1093/jb/mvaf022","url":null,"abstract":"The 5-year survival rate for pancreatic cancer is extremely low, at approximately 12%, primarily because most patients present with advanced and unresectable tumors. Chemotherapy regimens, such as gemcitabine (GEM) plus paclitaxel (PTX) and FOLFIRINOX, are standard treatments; however, resistance to these therapies remains a major challenge. Autophagy has been implicated in this resistance. Both the Atg8 and Atg12 conjugation systems are essential for autophagosome maturation, and the ubiquitin-like protein activator Atg7 plays an essential role in these systems. This study investigated the effects of Atg7 knockdown on GEM/PTX sensitivity in GEM/PTX-resistant pancreatic cancer MIAPaCa2 (GP-R) cells. GP-R cells exhibited reduced sensitivity to GEM/PTX, increased expression of autophagy-related factors, and elevated basal autophagy compared to parental cells. Atg7 knockdown in GP-R cells effectively inhibited both basal and GEM/PTX-induced autophagy, significantly increased total and mitochondrial reactive oxygen species (ROS), and led to the induction of apoptotic cell death. These findings suggest that autophagy inhibition via Atg7 knockdown enhances GEM/PTX sensitivity in GP-R cells. In conclusion, targeting Atg7 to inhibit autophagy may be a promising approach to improving the efficacy of GEM/PTX therapy in pancreatic cancer.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019870","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

ZNRF1-dependent regulation of AKT activity modulates Nav subcellular localization and AIS position in neurons to regulate fear-related behavior. 依赖znrf1的AKT活性调节神经元中Nav亚细胞定位和AIS位置，从而调节恐惧相关行为。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-07 DOI: 10.1093/jb/mvaf024

Moeka Ohno, Shuji Wakatsuki, Hiroshi Kuniishi, Masayuki Sekiguchi, Eri Takeuchi, Keizo Takao, Megumi Watase, Takaya Abe, Toshiyuki Araki

引用次数: 0

A refined method for high-purity isolation of uterine glandular epithelial cells in mouse. 一种高纯度分离小鼠子宫腺上皮细胞的改进方法。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-29 DOI: 10.1093/jb/mvaf006

Asmaa M Youssef, Ahmed M Moustafa, Motoharu Hamada, Mayumi Sugiura-Ogasawara, Hisashi Oishi

{"title":"A refined method for high-purity isolation of uterine glandular epithelial cells in mouse.","authors":"Asmaa M Youssef, Ahmed M Moustafa, Motoharu Hamada, Mayumi Sugiura-Ogasawara, Hisashi Oishi","doi":"10.1093/jb/mvaf006","DOIUrl":"10.1093/jb/mvaf006","url":null,"abstract":"The uterine endometrium consists of luminal epithelium, glandular epithelium and stromal cells, with uterine glands playing a pivotal role in pregnancy success among mammals. Uterine glands secrete essential factors that regulate embryo development and implantation; however, their cellular biology remains poorly understood. This study presents a refined method for isolating three distinct endometrial cell types with high purity, with a specific emphasis on glandular epithelial (GE) cells. The method combines mechanical dissociation, enzymatic digestion and immunomagnetic separation. The isolated GE cells were maintained in culture and exhibited proliferation in response to steroid hormones. Furthermore, oestrogen responsiveness was abrogated by Estrogen Receptor 1 (Esr1) knockdown mediated by siRNA. Here, we present an efficient and reproducible method for isolating uterine GE cells with high purity, enabling their in vitro maintenance, hormone responsiveness assessment and functional gene knockdown. These findings establish a robust platform for advancing our understanding of uterine gland biology, facilitating detailed investigations into molecular mechanisms underlying glandular function and their critical roles in establishing pregnancy success. Future research could explore the contribution of these isolated cells to endometrial receptivity and embryo implantation.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"329-337"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143005237","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

Various methods to detect small GTPase activation: from radioisotope-based methods to the Small GTPase ActIvitY ANalysing (SAIYAN) system. 检测小GTPase活性的各种方法：从基于放射性同位素的方法到小GTPase活性分析（SAIYAN）系统。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-29 DOI: 10.1093/jb/mvaf012

Miharu Maeda, Kota Saito

{"title":"Various methods to detect small GTPase activation: from radioisotope-based methods to the Small GTPase ActIvitY ANalysing (SAIYAN) system.","authors":"Miharu Maeda, Kota Saito","doi":"10.1093/jb/mvaf012","DOIUrl":"10.1093/jb/mvaf012","url":null,"abstract":"Small GTPases act as molecular switches regulating various cellular processes by cycling between the GDP- and GTP-bound states. Several methods, including radioisotope-based nucleotide exchange assays, effector-binding pull-down assays and fluorescence-based biosensor methods, have been developed to assess the activation of small GTPases. In vitro techniques mainly provide quantitative insights, whereas live-cell imaging approaches facilitate the real-time monitoring of the activation dynamics of small GTPases. Recent advances, such as the development of fluorescence resonance energy transfer-based probes and membrane-localization sensors, have improved the spatial and temporal resolution of small GTPase activation dynamics. Specifically, the small GTPase activity analysing system using a split fluorescent protein to detect membrane recruitment upon activation provides a novel approach to study small GTPases in living cells. This review comprehensively discusses various conventional and emerging small GTPase activation analysis techniques, highlighting their advantages and disadvantages in studying small GTPase activation dynamics under different cellular conditions.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"321-327"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12036015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557027","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

Mitochondria-targeting siRNA screening identifies mitochondrial calcium uniporter as a factor involved in nucleoid morphology. 线粒体靶向siRNA筛选鉴定线粒体钙单转运蛋白是参与类核形态的一个因素。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-29 DOI: 10.1093/jb/mvaf008

Hirotaka Kanon, Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Tatsuki Yasuda, Aoi Ichikawa, Ruo Ueyama, Taiki Baba, Kohsuke Takeda, Emi Ogasawara, Naotada Ishihara

{"title":"Mitochondria-targeting siRNA screening identifies mitochondrial calcium uniporter as a factor involved in nucleoid morphology.","authors":"Hirotaka Kanon, Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Tatsuki Yasuda, Aoi Ichikawa, Ruo Ueyama, Taiki Baba, Kohsuke Takeda, Emi Ogasawara, Naotada Ishihara","doi":"10.1093/jb/mvaf008","DOIUrl":"10.1093/jb/mvaf008","url":null,"abstract":"Mitochondria are believed to have originated from the endosymbiosis of bacteria and they still contain their own genome, which is called mitochondrial DNA (mtDNA). Under fluorescence microscopy of cultured mammalian cells, mtDNA is observed as numerous tiny dot-like structures called mitochondrial nucleoids. In live-imaging, the morphology and distribution of nucleoids are changed dynamically, but the molecular details remain poorly understood. In this study, we constructed a custom siRNA library targeting 1,164 human mitochondria-related genes, and from live-imaging-based screening of HeLa cells, we identified that mitochondrial calcium uniporter (MCU), a pore-forming subunit of the mitochondrial Ca2+ channel, is involved in nucleoid morphology. We found that suppression of MCU by RNAi induced the formation of highly enlarged nucleoids as well as respiratory dysfunction and that the re-introduction of MCU or treatment with Ca2+ ionophore recovered the enlarged nucleoid morphology. These results suggest that mitochondrial Ca2+ uptake via MCU is associated with nucleoid morphology. The constructed siRNA library might be widely applied to analyze the roles of mitochondrial proteins in various cellular events, making it useful to understand the multifaceted functions of mitochondria in human cells.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"339-350"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382595","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

The HP1 hinge region: more than just a linker for heterochromatin. HP1铰链区：不仅仅是异染色质的连接体。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-29 DOI: 10.1093/jb/mvaf005

Hiroaki Tachiwana, Noriko Saitoh

引用次数: 0

Method for isolation and quantification of inositol glycan produced by glycosylinositol phosphoceramide-hydrolysing phospholipase D in plants. 植物中糖基肌醇磷酸神经酰胺水解磷脂酶D产肌醇聚糖的分离与定量方法。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-29 DOI: 10.1093/jb/mvaf013

Majidul Islam, Rumana Yesmin Hasi, Yuta Umemura, Hide-Nori Tanaka, Yudai Kondo, Toshiki Ishikawa, Minoru Nagano, Hanif Ali, Ryushi Kawakami, Mutsumi Aihara, Tamotsu Tanaka

{"title":"Method for isolation and quantification of inositol glycan produced by glycosylinositol phosphoceramide-hydrolysing phospholipase D in plants.","authors":"Majidul Islam, Rumana Yesmin Hasi, Yuta Umemura, Hide-Nori Tanaka, Yudai Kondo, Toshiki Ishikawa, Minoru Nagano, Hanif Ali, Ryushi Kawakami, Mutsumi Aihara, Tamotsu Tanaka","doi":"10.1093/jb/mvaf013","DOIUrl":"10.1093/jb/mvaf013","url":null,"abstract":"Glycosylinositol phosphoceramide (GIPC) is the most abundant sphingolipids in plants. Previously, we found phospholipase D (PLD) activity that hydrolyzes GIPC to phytoceramide 1-phosphate (PCerP) in plants and revealed that GIPC-PLD activity is carried out by an enzyme encoded by non-specific phospholipase C3 (NPC3) gene. In this study, we established a method for isolation and quantification of inositol glycan (InoGly), a counterpart of PCerP produced from GIPC, using TLC imaging. We confirmed that Arabidopsis thaliana NPC3 protein and partially purified GIPC-PLD from cabbage produced InoGly in a similar amount to that of PCerP from purified GIPC. We applied our method to determination of InoGly present in plant tissues and found that it was present at 40-80 nmol/g (wet weight) in cabbage leaves, radish root and broccoli stem and increased to 80-120 nmol/g after homogenization of the tissues. Similar increases in PCerP and decreases in GIPC were observed after homogenization, indicating that InoGly and PCerP were produced from GIPC by GIPC-PLD activity in response to homogenization. We believe our method, which does not require a complicated process or large device, will contribute to a better understanding of GIPC metabolism and signalling in plants.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"387-394"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573085","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