Journal of biochemistry最新文献

Innate immune signals triggered on organelle membranes. 先天免疫信号触发细胞器膜。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-08 DOI: 10.1093/jb/mvaf016

Yoshihiko Kuchitsu, Tomohiko Taguchi

{"title":"Innate immune signals triggered on organelle membranes.","authors":"Yoshihiko Kuchitsu, Tomohiko Taguchi","doi":"10.1093/jb/mvaf016","DOIUrl":"https://doi.org/10.1093/jb/mvaf016","url":null,"abstract":"Our body is constantly exposed to pathogens, and equipped with a highly elaborate immune system to fight against invading pathogens. The first line of defense is the innate immune system. It has evolved to detect conserved microbial molecular patterns, dubbed pathogen-associated molecular patterns (PAMPs), through pattern recognition receptors (PRRs). The binding of PRRs to PAMPs activates intracellular signalling cascades that lead to the expression of proinflammatory cytokines, type I interferons, and other antiviral proteins that all coordinate the elimination of pathogens and infected cells. PRRs can be classified as transmembrane receptors, including Toll-like receptors (TLRs) and some C-type lectin receptors (CLRs), and as cytosolic receptors including retinoic acid-inducible gene-I (RIG-I)-like receptors, nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, and cyclic GMP-AMP (cGAMP) synthase (cGAS). Studies have revealed that innate immune signals, including the ones activated by cytosolic PRRs, are triggered on organelle membranes. Here we review the recent insights into how organelle membranes and their associated membrane lipids contribute to PRR-mediated innate immune signals.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803377","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

Identification of a novel Eps 15 homology domain-containing protein 1 (EHD1) and EHD4-binding motif in phostensin. 光导素中新的EHD1和ehd4结合基序的鉴定。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvaf002

Kuang-Yung Huang, Hui-Chun Yu, Ming-Chi Lu, Hsien-Yu Huang Tseng, Jyun-Jie Shen, Chia-Ying Lin, Pin-Chen Chen, Ya-Ting Shen, Pei-Rong Chung, Hsiao-Kuei Tsai, Si-Ru Zhou, Chia-Lin Wang, Ning-Sheng Lai, Ta-Hsien Lin, Hsien-Bin Huang

{"title":"Identification of a novel Eps 15 homology domain-containing protein 1 (EHD1) and EHD4-binding motif in phostensin.","authors":"Kuang-Yung Huang, Hui-Chun Yu, Ming-Chi Lu, Hsien-Yu Huang Tseng, Jyun-Jie Shen, Chia-Ying Lin, Pin-Chen Chen, Ya-Ting Shen, Pei-Rong Chung, Hsiao-Kuei Tsai, Si-Ru Zhou, Chia-Lin Wang, Ning-Sheng Lai, Ta-Hsien Lin, Hsien-Bin Huang","doi":"10.1093/jb/mvaf002","DOIUrl":"10.1093/jb/mvaf002","url":null,"abstract":"Phostensin (PTS) encoded by KIAA1949 binds to protein phosphatase 1, F-actin, Eps 15 homology domain-containing protein 1 (EHD1) and EHD4. Most EHD-binding proteins contain a consensus motif, Asn-Pro-Phe (NPF), which interacts with the C-terminal EH domain of EHD proteins. Nevertheless, the NPF motif is absent in PTS. The binding motif for PTS to interact with EHD1 (or EHD4) remains unknown. Here, we identified that PTS-α binds to EHD1 (or EHD4) through the region of residues 51-80, which contains a consensus motif, 64ILV(X)4(L/V)RL74S. This novel consensus motif is also found in vacuolar protein sorting-35 (vps35). Replacement of 64ILV(X)4(L/V)RL74S with 64AAA(X)4(L/V)RL74S or with 64ILV(X)4AEA74A significantly reduces the binding efficiency of PTS-α to either EHD1 or EHD4 in GST pull-down assay and far western blotting assay. In addition, replacement of 218ILV(X)4VRL228S with 218AAA(X)4AEA228A decreases the binding ability of vps35 to EHD4 in far western blotting assay. Overexpression of the PTS-β in 293 T cells attenuated the endocytic trafficking of transferrin. However, this attenuation of transferrin in endocytic trafficking was disrupted when 293 T cells overexpressed the mutant PTS-β with a defective EHD-binding motif, suggesting that PTS-β can regulate the endocytic recycling via associating with EHD1 or EHD4.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"297-304"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949467","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

Replication across O6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin-remodelling enzyme Smarcad1.

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvaf007

Karin Shigenobu-Ueno, Reihi Sakamoto, Eiichiro Kanatsu, Yoshitaka Kawasoe, Tatsuro S Takahashi

{"title":"Replication across O6-methylguanine activates futile cycling of DNA mismatch repair attempts assisted by the chromatin-remodelling enzyme Smarcad1.","authors":"Karin Shigenobu-Ueno, Reihi Sakamoto, Eiichiro Kanatsu, Yoshitaka Kawasoe, Tatsuro S Takahashi","doi":"10.1093/jb/mvaf007","DOIUrl":"10.1093/jb/mvaf007","url":null,"abstract":"SN1-type alkylating reagents generate O6-methylguanine (meG) lesions that activate the mismatch repair (MMR) response. Since post-replicative MMR specifically targets the nascent strand, meG on the template strand is refractory to rectification by MMR and, therefore, can induce non-productive MMR reactions. The cycling of futile MMR attempts is proposed to cause DNA double-strand breaks in the subsequent S phase, leading to ATR-checkpoint-mediated G2 arrest and apoptosis. However, the mechanistic details of futile MMR cycling, especially how this reaction is maintained in chromatin, remain unclear. Using replication-competent Xenopus egg extracts, we herein establish an in vitro system that recapitulates futile MMR cycling in the chromatin context. The meG-T mispair, but not the meG-C pair, is efficiently targeted by MMR in our system. MMR attempts on the meG-strand result in the meG-to-A correction, whilst those on the T-strand induce iterative cycles of strand excision and resynthesis. Likewise, replication across meG generates persistent single-strand breaks on the daughter DNA containing meG. Moreover, the depletion of Smarcad1, a chromatin remodeller previously reported to facilitate MMR, impairs the retention of single-strand breaks. Our study thus provides experimental evidence that chromatin replication across meG induces futile MMR cycling that is assisted by Smarcad1.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"247-258"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065974","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

Production of non-triple-helical collagen polypeptides under hypoxia and the implication for tumour. 缺氧条件下非三螺旋胶原多肽的生成及其对肿瘤的意义。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvae099

Kosuke Sekine, Kazuhiro Tokunaka, Arihiro Tomura, Hidemitsu Sugihara, Yuki Saijo, Yongchol Shin, Toshihiko Hayashi, Makoto Morita, Yasutada Imamura

{"title":"Production of non-triple-helical collagen polypeptides under hypoxia and the implication for tumour.","authors":"Kosuke Sekine, Kazuhiro Tokunaka, Arihiro Tomura, Hidemitsu Sugihara, Yuki Saijo, Yongchol Shin, Toshihiko Hayashi, Makoto Morita, Yasutada Imamura","doi":"10.1093/jb/mvae099","DOIUrl":"10.1093/jb/mvae099","url":null,"abstract":"Non-triple-helical collagen polypeptides (NTHs) are alternative gene products lacking the typical collagen triple-helical structure. This study investigated NTH production in tumour cells and tissues. NTH α1(IV) was detected in various human tumour cell lines and extracted from human lung cancer tissues and tumours in mice. NTH production was significantly affected by serum concentration and occurred under hypoxic or hypoxia-mimetic conditions, even with sufficient ascorbic acid. This suggests NTHs are produced under physiological hypoxia, potentially contributing to tumour angiogenesis. NTH production generally coincided with hypoxia-inducible factor-1α (HIF-1α) accumulation, except with cobalt chloride, indicating HIF-1α is not directly involved in NTH α1(IV) production. NTH electrophoretic mobility on SDS-PAGE was higher under hypoxia or deferoxamine treatment, likely due to suppressed lysyl hydroxylase 3 activity. This study demonstrates NTH production in tumour cells and tissues under hypoxia, suggesting their association with tumour angiogenesis and potential as therapeutic targets.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"287-295"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931804","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

Biochemical characterization and mutational analysis of lysophosphatidic acid acyltransferases of Escherichia coli highlighting their involvement in the generation of membrane phospholipid diversity. 大肠杆菌溶血磷脂酸酰基转移酶的生化特性和突变分析，强调其参与膜磷脂多样性的产生。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvae093

Nittikarn Suwanawat, Takuya Ogawa, Yosuke Toyotake, Jun Kawamoto, Tatsuo Kurihara

{"title":"Biochemical characterization and mutational analysis of lysophosphatidic acid acyltransferases of Escherichia coli highlighting their involvement in the generation of membrane phospholipid diversity.","authors":"Nittikarn Suwanawat, Takuya Ogawa, Yosuke Toyotake, Jun Kawamoto, Tatsuo Kurihara","doi":"10.1093/jb/mvae093","DOIUrl":"10.1093/jb/mvae093","url":null,"abstract":"Lysophosphatidic acid acyltransferase (LPAAT) is an enzyme responsible for the second acylation step of phospholipid biosynthesis and transforms lysophosphatidic acid to phosphatidic acid, a universal precursor of various phospholipids. In addition to the well-studied plsC-encoded LPAAT (EcPlsC), we previously found that Escherichia coli has another LPAAT that is encoded by yihG (EcYihG). EcPlsC and EcYihG are integral membrane proteins and have never been solubilized and purified in their active form. To better understand the difference in their enzymatic functions and how the two paralogs differently contribute to lipid diversity, we established a method to purify both enzymes in their active form and comparatively analysed their biochemical characteristics. Our findings illustrate that EcPlsC possesses the highest activity at pH 8.0 and 37°C with selectivity for unsaturated fatty acyl-CoAs (e.g. palmitoleoyl-CoA), whereas EcYihG works optimally at pH 7.5 and 30°C and prefers saturated fatty acyl-CoAs (e.g. myristoyl-CoA). In addition, we performed a mutational analysis based on AlphaFold2 models and revealed that one residue, which is located at the putative acyl-donor-selectivity tunnel entrance, plays a pivotal role in selecting acyl donor substrates. This provides new insights into how LPAATs recognize specific fatty acyl groups and incorporate them into membrane phospholipids.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"259-272"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894961","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

Profiling translation in the nervous system. 神经系统的侧写翻译。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvae096

Toshiharu Ichinose, Hiromu Tanimoto

引用次数: 0

Interaction mapping between nucleoporins in the fission yeast Schizosaccharomyces pombe using mass-spectrometry. 裂变酵母裂糖酵母核孔蛋白相互作用质谱图谱研究。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvae095

Haruhiko Asakawa, Koji Nagao, Tatsuo Fukagawa, Chikashi Obuse, Yasushi Hiraoka, Tokuko Haraguchi

{"title":"Interaction mapping between nucleoporins in the fission yeast Schizosaccharomyces pombe using mass-spectrometry.","authors":"Haruhiko Asakawa, Koji Nagao, Tatsuo Fukagawa, Chikashi Obuse, Yasushi Hiraoka, Tokuko Haraguchi","doi":"10.1093/jb/mvae095","DOIUrl":"10.1093/jb/mvae095","url":null,"abstract":"Nuclear pore complexes (NPCs) act as gateways across the nuclear envelope for molecular transport between the nucleus and the cytoplasm in eukaryotes. NPCs consist of several subcomplexes formed by multiple copies of approximately 30 different proteins known as nucleoporins (Nups). In the fission yeast Schizosaccharomyces pombe, the NPC structure is unique, particularly in its outer ring subcomplexes, where the cytoplasmic and nucleoplasmic outer rings are composed of distinct sets of proteins. However, it remains unclear how this unique outer ring structure in S. pombe is supported by interactions between subcomplexes or individual Nups. In this study, we investigated protein-protein interactions between S. pombe Nups using mass spectrometry and identified Nups that interact with each subcomplex or a specific Nup. The cytoplasmic outer ring Nups bind to both the cytoplasmic filament Nups and the inner ring Nups, while the nucleoplasmic outer ring Nups bind to the nuclear basket Nups in addition to the inner ring Nups. Among the inner ring Nups, Nup155 interacts with most of the cytoplasmic and nucleoplasmic outer ring Nups, suggesting that Nup155 may serve as a hub supporting the uniquely asymmetric outer ring structure of the S. pombe NPC.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"273-286"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894964","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

SSB promotes DnaB helicase passage through DnaA complexes at the replication origin oriC for bidirectional replication. SSB促进dna解旋酶通过复制起点处的dna复合体进行双向复制。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-04-02 DOI: 10.1093/jb/mvaf003

Yusuke Akama, Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama

{"title":"SSB promotes DnaB helicase passage through DnaA complexes at the replication origin oriC for bidirectional replication.","authors":"Yusuke Akama, Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama","doi":"10.1093/jb/mvaf003","DOIUrl":"10.1093/jb/mvaf003","url":null,"abstract":"For bidirectional replication in Escherichia coli, higher order complexes are formed at the replication origin oriC by the initiator protein DnaA, which locally unwinds the left edge of oriC to promote the loading of two molecules of DnaB helicases onto the unwound region via dynamic interactions with the helicase-loader DnaC and the oriC-bound DnaA complex. One of the two helicases must translocate rightwards through oriC-bound DnaA complex. Here, we used a synthetic forked oriC DNA, which mimics the unwound state of oriC, to examine DnaB translocation through the oriC-bound DnaA complex. We found that DnaB helicase alone cannot pass through the oriC-bound DnaA complex without the help of single-strand binding protein (SSB). In the presence of SSB, DnaB passed through this complex along with its helicase function, releasing DnaA molecules. In addition, DnaB helicase activity is known to be inhibited by oversupply of DnaC, but this inhibition was relieved by SSB. These results suggest a mechanism that when two DnaB helicases are loaded at oriC, one translocates leftwards to expand the DnaA-unwound region and allows SSB binding to the single-stranded DNA, and such SSB molecules then stimulate translocation of the other helicase rightwards through the oriC-bound DnaA complex.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"305-316"},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949469","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

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 : 2025-03-27 DOI: 10.1093/jb/mvaf005

Hiroaki Tachiwana, Noriko Saitoh

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 : 2025-03-21 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":"https://doi.org/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":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0