Journal of biochemistry最新文献_第5页

Suicide substrate reaction-like modification of mouse serine racemase with L-serine. l -丝氨酸修饰小鼠丝氨酸消旋酶的自杀底物样反应。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf019

Akari Hata, Tomokazu Ito, Hitoshi Mori, Takuya Ogawa, Tatsuo Kurihara, Hisashi Hemmi, Tohru Yoshimura

{"title":"Suicide substrate reaction-like modification of mouse serine racemase with L-serine.","authors":"Akari Hata, Tomokazu Ito, Hitoshi Mori, Takuya Ogawa, Tatsuo Kurihara, Hisashi Hemmi, Tohru Yoshimura","doi":"10.1093/jb/mvaf019","DOIUrl":"10.1093/jb/mvaf019","url":null,"abstract":"A pyridoxal 5'-phosphate-dependent fold-type II serine racemase (SR) is responsible for the synthesis of D-Ser, which serves as a co-agonist of N-methyl-D-aspartate glutamate receptor. In addition to racemization, SR catalyzes the dehydration of D- and L-Ser. SR is suggested to be involved in the D-Ser degradation in vivo, but this has not been confirmed. In this study, we found that mouse SR (mSR) underwent a suicide substrate reaction-like modification with its substrate, resulting in a remarkable change in its reaction specificity. mSR gradually lost its activity by the incubation with L- and D-Ser, but not completely. mSR was labelled with [14C]-L-Ser. ESI-MS analysis revealed that the molecular mass of SR increased by 84 Da by the incubation with L-Ser. Taken together with the results of previous crystallographic studies of fission yeast SR, we concluded that the active site lysine residue of mSR was modified with an α-aminoacrylate intermediate generated from L-Ser and converted to a lysinoalanine residue. The modification significantly decreased the racemization and L-Ser dehydration activities, while dramatically increased the D-Ser dehydration activity by the ~100 times reduction of the Km value. This is probably advantageous for the D-Ser degradation by mSR under physiological conditions.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"437-445"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998817","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 potential of erythrocyte α-synuclein to differentiate dementia with Lewy bodies from Parkinson's and Alzheimer's diseases. 红细胞α-突触核蛋白鉴别路易体痴呆与帕金森病和阿尔茨海默病的潜力。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf017

Ryosuke Amagai, Ryunosuke Hosoi, Sakura Yoshioka, Taiki Maruyama, Takayuki Kawai, Soroku Yagihashi, Hitoshi Nukada, Ryuji Sakakibara, Ayako Okado-Matsumoto

{"title":"The potential of erythrocyte α-synuclein to differentiate dementia with Lewy bodies from Parkinson's and Alzheimer's diseases.","authors":"Ryosuke Amagai, Ryunosuke Hosoi, Sakura Yoshioka, Taiki Maruyama, Takayuki Kawai, Soroku Yagihashi, Hitoshi Nukada, Ryuji Sakakibara, Ayako Okado-Matsumoto","doi":"10.1093/jb/mvaf017","DOIUrl":"10.1093/jb/mvaf017","url":null,"abstract":"Dementia with Lewy bodies (DLB) is the second most common neurodegenerative dementia after Alzheimer's disease (AD). Early differentiation of these disorders is crucial for managing core symptoms; however, existing biomarkers remain insufficient. DLB shares motor and cognitive symptoms with Parkinson's disease (PD), and both are classified as synucleinopathies due to abnormal α-synuclein aggregation. Although α-synuclein is predominantly expressed in the central nervous system, it is also abundant in erythrocytes. Recent studies suggest a potential link between erythrocyte-derived α-synuclein and synucleinopathy pathology. Additionally, we previously reported that both erythrocytes and circulating medium and large extracellular vesicles (m/lEVs) in plasma from healthy subjects contain full-length and C-terminally truncated α-synuclein. In this study, we found that erythrocyte α-synuclein levels were significantly lower in DLB compared to AD, PD and healthy controls. Furthermore, α-synuclein levels in circulating m/lEVs were elevated in patients with neurodegenerative diseases. These findings provide new insights into the role of peripheral α-synuclein and suggest its potential utility as a diagnostic marker for DLB. While further validation is needed, erythrocyte-derived α-synuclein may complement nuclear medicine assessments in distinguishing DLB from other neurodegenerative disorders.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"415-424"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007450","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

YTHDF1 promotes pancreatic cancer cell progression by enhancing SF3B2 translation though m6A modification. YTHDF1通过m6A修饰增强SF3B2翻译促进胰腺癌细胞进展。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf018

Chunyang Wang, Kai Huang, Jie Yang, Qingchun Xu, Jiagao Kuai, Guangxian Zhang, Xiaoming Wang

{"title":"YTHDF1 promotes pancreatic cancer cell progression by enhancing SF3B2 translation though m6A modification.","authors":"Chunyang Wang, Kai Huang, Jie Yang, Qingchun Xu, Jiagao Kuai, Guangxian Zhang, Xiaoming Wang","doi":"10.1093/jb/mvaf018","DOIUrl":"10.1093/jb/mvaf018","url":null,"abstract":"N6-Methyladenosine (m6A), a pivotal RNA modification, plays a critical role in carcinogenesis across multiple cancer types. YT521-B homology domain family protein 1 (YTHDF1), a binding protein of m6A, facilitates the translation of downstream targets via m6A recognition. However, the involvement of YTHDF1 in pancreatic cancer progression and its mechanistic underpinnings remain poorly understood. In this study, we observed significant upregulation of YTHDF1 in pancreatic cancer cell lines (SW1990 and PANC-1) compared to the normal human pancreatic cell line hTERT-HPNE. Functional assays revealed that YTHDF1 knockdown markedly suppressed cell proliferation and invasion, whereas its overexpression enhanced these malignant phenotypes in both SW1990 and PANC-1 cells. Mechanistically, YTHDF1 interacted with coding sequence (CDS) region of splicing factor 3B subunit 2 (SF3B2), whereas YTHDF1 downregulation reduced SF3B2 protein levels without altering its mRNA expression, suggesting post-transcriptional regulation via m6A modification. Importantly, SF3B2 overexpression rescued the suppressed proliferation and invasion caused by YTHDF1 knockdown in SW1990 and PANC-1 cells. Collectively, our findings demonstrate that YTHDF1 drives pancreatic cancer progression by enhancing SF3B2 translation through m6A modification, thereby providing novel mechanistic insights and a potential therapeutic target for pancreatic cancer.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"425-435"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002305","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

Suppression of ATP-dependent (S)-NAD(P)H-hydrate dehydratase expression inhibits adipocyte differentiation of 3T3-L1 preadipocytes by increasing excessive accumulation of NADHX. 抑制atp依赖性(S)-NAD(P)H-hydrate dehydratase表达通过增加NADHX的过度积累抑制3T3-L1前脂肪细胞的脂肪细胞分化。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf015

Kazuki Nakajima, Kodai Takahashi, Masako Tanaka, Mina Kawashima, Koshi Machida, Yoichi Nakao, Keiyo Takubo, Nobuhito Goda

{"title":"Suppression of ATP-dependent (S)-NAD(P)H-hydrate dehydratase expression inhibits adipocyte differentiation of 3T3-L1 preadipocytes by increasing excessive accumulation of NADHX.","authors":"Kazuki Nakajima, Kodai Takahashi, Masako Tanaka, Mina Kawashima, Koshi Machida, Yoichi Nakao, Keiyo Takubo, Nobuhito Goda","doi":"10.1093/jb/mvaf015","DOIUrl":"10.1093/jb/mvaf015","url":null,"abstract":"ATP-dependent (S)-NAD(P)H-hydrate dehydratase (NAXD) is a crucial enzyme in the nicotinamide adenine dinucleotide repair system that regenerates NAD(P)H, an essential electron donor in metabolic redox reactions. NAD+-related metabolic pathways connect cellular metabolism and the expression of genes responsible for adipogenesis; however, the biological significance of the NAXD-mediated repair pathway remains unclear. Herein, we showed that NAXD is essential for normal adipocyte differentiation of 3T3-L1 murine preadipocytes. Silencing of the Naxd gene attenuated differentiation-induced lipid accumulation with excessive accumulation of hydrated NADH (NADHX) without altering NAD+ levels. FK866, a specific inhibitor of NAMPT, further reduced lipid accumulation even in Naxd-silenced cells with substantial decrease in NAD+. Supplementation with nicotinamide mononucleotide, a precursor of NAD+, restored NAD+ levels comparably in Naxd- and LacZ-silenced cells treated with FK866, but failed to recover adipocyte differentiation of Naxd-silenced cells to the level of LacZ-silenced cells. In contrast, exposure of wild-type 3T3-L1 cells to NADHX recapitulated the Naxd deficiency-elicited inhibitory effects on adipocyte differentiation with reduced expression of master transcriptional regulators of adipogenesis, peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α. These results suggest that NAXD supports normal adipogenesis, in part, by inhibiting excessive accumulation of NADHX.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"403-414"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12136578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143670015","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

Effect of N1-methyladenosine in the quantification of RNA. n1 -甲基腺苷在RNA定量中的作用。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf014

Fangran Liu

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