Journal of biochemistry最新文献_第8页

The action of coenzyme B12-dependent diol dehydratase on 3,3,3-trifluoro-1,2-propanediol results in elimination of all the fluorides with formation of acetaldehyde. 辅酶 B12 依赖性二元醇脱水酶对 3,3,3-三氟-1,2-丙二醇的作用会消除所有氟化物并形成乙醛。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-09-03 DOI: 10.1093/jb/mvae047

Koichi Mori, Bernard T Golding, Tetsuo Toraya

{"title":"The action of coenzyme B12-dependent diol dehydratase on 3,3,3-trifluoro-1,2-propanediol results in elimination of all the fluorides with formation of acetaldehyde.","authors":"Koichi Mori, Bernard T Golding, Tetsuo Toraya","doi":"10.1093/jb/mvae047","DOIUrl":"10.1093/jb/mvae047","url":null,"abstract":"3,3,3-Trifluoro-1,2-propanediol undergoes complete defluorination in two distinct steps: first, the conversion into 3,3,3-trifluoropropionaldehyde catalyzed by adenosylcobalamin (coenzyme B12)-dependent diol dehydratase; second, non-enzymatic elimination of all three fluorides from this aldehyde to afford malonic semialdehyde (3-oxopropanoic acid), which is decarboxylated to acetaldehyde. Diol dehydratase accepts 3,3,3-trifluoro-1,2-propanediol as a relatively poor substrate, albeit without significant mechanism-based inactivation of the enzyme during catalysis. Optical and electron paramagnetic resonance (EPR) spectra revealed the steady-state formation of cob(II)alamin and a substrate-derived intermediate organic radical (3,3,3-trifluoro-1,2-dihydroxyprop-1-yl). The coenzyme undergoes Co-C bond homolysis initiating a sequence of reaction by the generally accepted pathway via intermediate radicals. However, the greater steric size of trifluoromethyl and especially its negative impact on the stability of an adjacent radical centre compared to a methyl group has implications for the mechanism of the diol dehydratase reaction. Nevertheless, 3,3,3-trifluoropropionaldehyde is formed by the normal diol dehydratase pathway, but then undergoes non-enzymatic conversion into acetaldehyde, probably via 3,3-difluoropropenal and malonic semialdehyde.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"245-254"},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579802","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

Sex chromosome cycle as a mechanism of stable sex determination. 作为稳定性别决定机制的性染色体周期。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae045

Shun Hayashi, Takuya Abe, Takeshi Igawa, Yukako Katsura, Yusuke Kazama, Masafumi Nozawa

{"title":"Sex chromosome cycle as a mechanism of stable sex determination.","authors":"Shun Hayashi, Takuya Abe, Takeshi Igawa, Yukako Katsura, Yusuke Kazama, Masafumi Nozawa","doi":"10.1093/jb/mvae045","DOIUrl":"10.1093/jb/mvae045","url":null,"abstract":"Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"81-95"},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11289310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563498","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

Identification of two critical amino acid residues in short-chain aldehyde-responsive odorant receptors. 鉴定短链醛反应气味受体中的两个关键氨基酸残基。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2024-07-31 DOI: 10.1093/jb/mvae033

Reina Kanemaki, Toshiya Hayakawa, Haruto Kudo, Masafumi Yohda, Yosuke Fukutani

{"title":"Identification of two critical amino acid residues in short-chain aldehyde-responsive odorant receptors.","authors":"Reina Kanemaki, Toshiya Hayakawa, Haruto Kudo, Masafumi Yohda, Yosuke Fukutani","doi":"10.1093/jb/mvae033","DOIUrl":"10.1093/jb/mvae033","url":null,"abstract":"Mammalian odorant receptors (ORs) are crucial for detecting a broad spectrum of odorants, yet their functional expression poses a significant challenge, often requiring Receptor-transporting proteins (RTPs). This study examines mouse Olfr733 and Olfr732, which, despite high homology, show different functional expression profiles in heterologous cell systems. Our research aimed to identify key amino acids impacting Olfr733's functional expression. We discovered that G112FBW3.40 and L148PBW4.49 (Ballesteros-Weinstein numbering in superscript) substitutions in Olfr732 markedly enhance its RTP-independent expression and ligand responsiveness, mirroring Olfr733. These substitutions, particularly Phe112 and Leu148, are crucial for aldehyde recognition and membrane localization in Olfr733, respectively. While Olfr732-type ORs are conserved across species, Olfr733-types, unique to specific rodents, appear to have evolved from Olfr732, with Pro148 enhancing membrane expression and aldehyde sensitivity. Mouse ORs with ProBW4.49 tend to exhibit improved membrane expression compared to their paralogs, especially when co-expressed with RTP1S. This study concludes that the Pro residue in the fourth transmembrane domain significantly contributes to the structural stability of certain olfactory receptors, highlighting the intricate molecular mechanisms underlying OR functionality and evolution.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"119-130"},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335732","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

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