Bioscience Reports最新文献

RNase H-sensitive accumulation of APOBEC3B in a nucleolus after DNA damage. DNA损伤后核仁中APOBEC3B的rna酶h敏感积累。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-10-06 DOI: 10.1042/BSR20253880

Yohei Saito, Yumi Yamamoto, Fumihiko Yamamoto

{"title":"RNase H-sensitive accumulation of APOBEC3B in a nucleolus after DNA damage.","authors":"Yohei Saito, Yumi Yamamoto, Fumihiko Yamamoto","doi":"10.1042/BSR20253880","DOIUrl":"https://doi.org/10.1042/BSR20253880","url":null,"abstract":"Apolipoprotein B mRNA editing catalytic subunit 3B (A3B), a nuclear enzyme that catalyzes cytidine-to-uridine (C-to-U) editing in single-stranded DNA (ssDNA), contributes to genetic diversity in many cancers. A3B is induced or activated by DNA damage owing to a variety of factors; however, the mechanisms by which A3B accesses ssDNA within the genome remain unclear. In this study, we showed that in unstimulated cells, A3B is retained in the nucleoplasm in an RNA-dependent manner. Upon DNA damage induced by camptothecin or actinomycin D (Act D), both targeting topoisomerase I, or by 1-methyl-3-nitro-1-nitrosoguanidine (MNNG), an alkylating agent that generates apurinic/apyrimidinic sites, A3B accumulates at the nucleolar rim and interior. Using confocal microscopy, we assessed the colocalization of A3B with drug-induced R-loops. A3B accumulation was abolished by RNase treatment, implicating R-loops in its localization. However, the S9.6 antibody, commonly used to detect DNA/RNA hybrids, did not identify R-loop-specific signals in the nucleolus, leaving the direct involvement of R-loops in A3B accumulation unresolved. Conversely, immunoprecipitation-mass spectrometry with data-independent acquisition (IP-MS DIA) revealed increased interactions between A3B and RNA helicases such as DDX17 and DDX21, which are known R-loop-binding proteins, following MNNG or Act D treatment. Our results demonstrate that A3B-induced secondary DNA damage occurs in the nucleolus after DNA damage, providing new insights into the acquisition of cancer diversity involving A3B and the DNA damage response in the nucleolus.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Paratope mapping of tilvestamab, an anti-AXL function-blocking antibody, using high-throughput bacterial expression of secreted scFv-ompY fusion proteins. 利用高通量细菌表达分泌的scFv-ompY融合蛋白，对抗axl功能阻断抗体tilvestamab进行旁位定位。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-25 DOI: 10.1042/BSR20253747

Eleni Christakou, Petri Kursula, David Micklem

{"title":"Paratope mapping of tilvestamab, an anti-AXL function-blocking antibody, using high-throughput bacterial expression of secreted scFv-ompY fusion proteins.","authors":"Eleni Christakou, Petri Kursula, David Micklem","doi":"10.1042/BSR20253747","DOIUrl":"https://doi.org/10.1042/BSR20253747","url":null,"abstract":"Targeting AXL with a highly selective antibody presents a promising approach for inhibiting AXL and potentially improving cancer treatment. An essential step in antibody optimisation is the mapping of paratope residues to epitope residues. In this study, we identify the residues of tilvestamab, a function-blocking anti-AXL monoclonal antibody (mAb), that are essential for its binding to the extracellular domain of AXL. A single-chain variable fragment (scFv) fused to osmotically inducible protein Y (osmY) was designed to enable the secretion of soluble scFv-osmY mutants, which could be directly subjected to high-throughput biolayer interferometry (BLI) screening for binding to the AXL Ig1 domain. Each CDR residue of scFv was mutated to Ala, while additional mutations were made on the basis of predicted contribution to binding. We generated AlphaFold3 predictions for the scFv(tilvestamab)-AXL Ig1 complex to gain insights into the molecular interactions of the essential residues, as determined by the experimental data. Our study reveals that tilvestamab binds to the Ig1 domain of AXL, with twelve residues on scFv (tilvestamab) contributing most to binding, likely being situated at the binding interface. Glu2 near the N terminus of AXL is essential for binding. The data give a structural view into the AXL-tilvestamab complex and allow for further optimisation of the binding interface.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Human polynucleotide phosphorylase in mitochondrial RNA metabolism. 人线粒体RNA代谢中的多核苷酸磷酸化酶。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-25 DOI: 10.1042/BSR20240504

Navid Bakshi, Madhuri Kanavalli, Karolina Z Nowak, Katarzyna J Bandyra

{"title":"Human polynucleotide phosphorylase in mitochondrial RNA metabolism.","authors":"Navid Bakshi, Madhuri Kanavalli, Karolina Z Nowak, Katarzyna J Bandyra","doi":"10.1042/BSR20240504","DOIUrl":"https://doi.org/10.1042/BSR20240504","url":null,"abstract":"Ever since its discovery more than 70 years ago, the enzyme polynucleotide phosphorylase (PNPase) has been the subject of intensive research that has highlighted its key functional roles. The enzyme was first described in 1955 for its ability to synthesise RNA from nucleoside diphosphates. This discovery led to a Nobel Prize in Physiology or Medicine in 1959 for using PNPase to synthesise artificial RNA. However, it soon became evident that the primary function of this enzyme, conserved across diverse species, is 3'-5' RNA phosphorolysis rather than polymerisation. Remarkably, over 60 years later, it was discovered that PNPase has an even broader range of functions as it was shown to act as a conditional RNA chaperone in bacteria. In humans, PNPase (hPNPase) is located in mitochondria, where it plays a role in mitochondrial RNA (mtRNA) metabolism, thereby regulating mitochondrial function and the overall cell fitness. In this review, we present the current scope of knowledge of hPNPase, including its structure, subcellular localisation, metabolic activity, roles in mtRNA transport, processing and degradation, and its involvement in apoptosis.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":"45 9","pages":"531-546"},"PeriodicalIF":4.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

High expression of Fgr in the left ventricle attenuates myocardial injury in the infarcted region via regulating the phosphorylation level of PI3K/Akt. 左心室Fgr的高表达通过调节PI3K/Akt磷酸化水平减轻梗死区心肌损伤。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-23 DOI: 10.1042/BSR20253737

Dongpu Shao, Zhiguo Zhang, Honglei Ji, Lei Shi

{"title":"High expression of Fgr in the left ventricle attenuates myocardial injury in the infarcted region via regulating the phosphorylation level of PI3K/Akt.","authors":"Dongpu Shao, Zhiguo Zhang, Honglei Ji, Lei Shi","doi":"10.1042/BSR20253737","DOIUrl":"https://doi.org/10.1042/BSR20253737","url":null,"abstract":"FGR proto-oncogene (Fgr), a member of the Src family kinases, has garnered attention for its potential involvement in apoptotic signaling, yet its role in cardiovascular diseases, particularly acute myocardial infarction (AMI), remains unexplored. This study sought to investigate whether elevated left ventricular Fgr expression alleviates myocardial injury in the infarcted area and whether this protective mechanism is mediated by modulating phosphoinositide 3-kinase (PI3K)/Akt phosphorylation. The transcriptome-wide association study was initially utilized to screen for susceptibility genes in the left ventricle, with findings validated using bulk-RNA sequencing data from a rat model of left anterior descending coronary artery (LAD) ligation; subsequently, human spatial transcriptomics combined with single-nucleus RNA sequencing data confirmed differential expression of Fgr and PI3K/Akt in the infarcted region. Fgr knockdown via siRNA in H9C2 cells and pharmacological inhibition with TL02-59 in rats were conducted to assess cellular survival and cardiac function, respectively. Fgr emerged as a common candidate gene identified through multi-omics data analysis, with its up-regulation confirmed both in vivo and in vitro. Fgr silencing in an in vitro oxygen-glucose deprivation model significantly reduced cell survival and suppressed PI3K/Akt phosphorylation, whereas TL02-59 administration in rats subjected to LAD ligation impaired post-infarction cardiac function while concurrently inhibiting PI3K/Akt phosphorylation levels. This study demonstrates that Fgr is markedly up-regulated in AMI and exerts cardioprotective effects, possibly through modulation of PI3K/Akt signaling phosphorylation, thereby underscoring its potential as a therapeutic target.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Anti-tumor and immunomodulatory activity of Ganoderma parvulum-derived polysaccharides. 小灵芝多糖的抗肿瘤和免疫调节活性。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-22 DOI: 10.1042/BSR20240113

Katherin Contreras-Ramirez, Xiomara López-Legarda, Jorge H Tabares-Guevara, Juan C Hernandez, Freimar Segura-Sánchez, Janny A Villa-Pulgarin

{"title":"Anti-tumor and immunomodulatory activity of Ganoderma parvulum-derived polysaccharides.","authors":"Katherin Contreras-Ramirez, Xiomara López-Legarda, Jorge H Tabares-Guevara, Juan C Hernandez, Freimar Segura-Sánchez, Janny A Villa-Pulgarin","doi":"10.1042/BSR20240113","DOIUrl":"https://doi.org/10.1042/BSR20240113","url":null,"abstract":"Polysaccharides have gained considerable attention recently because of their anti-tumor and immunoregulatory properties. Its activity depends on the type of fungus that produces it, the extraction method, and the molecular weight.Materials and methods: This study evaluated the anti-tumor and immunoregulatory properties of Ganoderma parvulum (GP)-derived polysaccharides.Results: GP crude polysaccharides inhibited mice's lymphoma without cytotoxicity. In vitro studies showed that exopolysaccharides (GEPS) and intrapolysaccharides (GIPS) of G. parvulum inhibited the proliferation of tumor cells, but no cell death was observed. Significantly, GEPS and GIPS increased the production of nitric oxide, TNF-α, MCP-1, and IL-10, and an increase in IL-1β, IL-18, and Caspase-1, while NLRP3 was down-regulated. Also, it decreases the production of IL-10 and IL-6.Conclusion: These observations suggest that GP-derived polysaccharides may exert anti-tumor activity primarily by activating the host's immune system via macrophage stimulation.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Evaluating plasma adipokines and their cognate receptors as biomarkers for non-invasive diagnosis of endometrial cancer. 评估血浆脂肪因子及其同源受体作为子宫内膜癌非侵入性诊断的生物标志物。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-22 DOI: 10.1042/BSR20253508

Rebecca Karkia, Eshwa Zahra, Chaeyeoun Min, Kako Hirai, Evgeny Makarov, Emmanouil Karteris, Jayanta Chatterjee

{"title":"Evaluating plasma adipokines and their cognate receptors as biomarkers for non-invasive diagnosis of endometrial cancer.","authors":"Rebecca Karkia, Eshwa Zahra, Chaeyeoun Min, Kako Hirai, Evgeny Makarov, Emmanouil Karteris, Jayanta Chatterjee","doi":"10.1042/BSR20253508","DOIUrl":"10.1042/BSR20253508","url":null,"abstract":"Endometrial cancer (EC) is the most common gynaecological malignancy in developed countries. Early detection remains challenging, with no established plasma-based biomarkers for clinical use. This study aimed to evaluate plasma adipokines and their receptor expression as diagnostic biomarkers for EC. Plasma levels of leptin, soluble leptin receptor, visfatin and asprosin were quantified in EC and control patients using ELISA. The free leptin index (FLI) was calculated as a ratio of leptin to soluble leptin receptor. Gene expression of corresponding receptors, including leptin receptor (Ob-R), insulin receptor (INSR), glucagon-like peptide-1 receptor [GLP-1 receptor (GLP-1R)], and asprosin-associated receptors, toll-like receptor 4 (TLR4), protein tyrosine phosphatase receptor type D (PTPRD), and olfactory receptor family 4 subfamily M member 1, was assessed by RT-qPCR from total blood. Plasma leptin levels were significantly elevated in EC patients, with the FLI over four times higher than controls (P=0.008). Soluble leptin receptor levels trended lower in EC, though non-significantly. Visfatin and asprosin plasma levels showed non-significant elevations. Gene expression analyses revealed significantly increased levels of GLP-1R, TLR4 and PTPRD in EC patients, suggestive of a diagnostic potential. Notably, plasma biomarker levels were not independently correlated with body mass index (BMI). Elevated FLI and up-regulation of adipokine receptor expression highlight the potential of combining plasma-based and molecular biomarkers for EC diagnosis. However, the lack of independence from BMI and conflicting literature underscores the need for larger, standardised studies to validate these findings and determine clinical applicability.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Kinetic and homology model analysis of diaminopimelate decarboxylase from Cyanothece sp. ATCC 51142: unveiling a key enzyme in lysine biosynthesis. Cyanothece sp. ATCC 51142二氨基酰脱羧酶的动力学和同源性模型分析：揭示赖氨酸生物合成的关键酶。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-18 DOI: 10.1042/BSR20253430

Zhi-Min Li, Suhang Chen, Weikang Luo, Fang Wang, Siqi Wang, Liyang Huang, Xinyue Xiong, Congcong Xie, Zhimin Li

{"title":"Kinetic and homology model analysis of diaminopimelate decarboxylase from Cyanothece sp. ATCC 51142: unveiling a key enzyme in lysine biosynthesis.","authors":"Zhi-Min Li, Suhang Chen, Weikang Luo, Fang Wang, Siqi Wang, Liyang Huang, Xinyue Xiong, Congcong Xie, Zhimin Li","doi":"10.1042/BSR20253430","DOIUrl":"10.1042/BSR20253430","url":null,"abstract":"Diaminopimelate decarboxylase (DAPDC), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the decarboxylation of diaminopimelate (DAP) to yield L-lysine, a key step in lysine biosynthesis. This present study presents a preliminary characterization of DAPDC encoded by the cce1351 gene in Cyanothece sp. ATCC 51142 (CsDAPDC), focusing on its biochemical properties and model structure characteristics. The enzyme exhibited a peak activity at 30°C and pH 8.0, and the catalytic constant (kcat) and substrate binding affinity Michaelis constant (KM) were determined as 1.68 s-1 and 1.20 mM at the above-mentioned condition, respectively. Homology modeling and molecular docking analysis revealed that Gly286, Gly330, Tyr428, and Asp118 interacted with the PLP cofactor, and Ser249, Tyr372, and Tyr428 interacted with the DAP substrate. Additionally, Cys399, Glu400, and Tyr436 from the other monomer were also involved in binding DAP and PLP. Site-directed mutagenesis confirmed the functional roles of these key residues in catalysis. This work provides valuable insights into the catalytic mechanism of CsDAPDC and highlights the enzyme's potential for applications in metabolic engineering of cyanobacteria for enhanced lysine production.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 autochthonous Saccharomyces cerevisiae by rapid laboratory evolution technique of genome shuffling. 利用基因组洗牌快速实验室进化技术改良本土酿酒酵母。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-12 DOI: 10.1042/BSR20253121

Ravichandra Hospet, Devarajan Thangadurai, Jeyabalan Sangeetha, Natália Cruz-Martins

{"title":"Improvement of autochthonous Saccharomyces cerevisiae by rapid laboratory evolution technique of genome shuffling.","authors":"Ravichandra Hospet, Devarajan Thangadurai, Jeyabalan Sangeetha, Natália Cruz-Martins","doi":"10.1042/BSR20253121","DOIUrl":"10.1042/BSR20253121","url":null,"abstract":"The process of selecting indigenous Saccharomyces cerevisiae strains as a starter culture for specific fermentation has several requisites, including the assessment of distinct parameters based on desirable and traditional enological criteria. In most wineries, commercial S. cerevisiae strains are used for wine fermentation. However, it is rare to find indigenous S. cerevisiae strains used in wine production, even though these isolates are better adapted to specific regions and are often preferred for producing local fruit wines. Here, the identification and characterization of indigenous S. cerevisiae were carried out by 28S rRNA sequencing, followed by Fourier transform infrared spectroscopy analysis for further confirmation. The strain improvement technique of genome shuffling was incorporated to ameliorate sugar tolerance and enhance alcohol production in the S. cerevisiae RHTD10 strain. As a result, it was observed that the improved strain from the third round of shuffling tolerated sugar stress of 30% and produced 10.14 ± 0.21% of alcohol, which is higher than the wild strain of 7.11 ± 0.22% alcohol.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Demixing of four simultaneously co-expressed phase-separating proteins in the endoplasmic reticulum lumen. 内质网腔内四种同时共表达的相分离蛋白的分离。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-09-02 DOI: 10.1042/BSR20253165

Haruki Hasegawa

{"title":"Demixing of four simultaneously co-expressed phase-separating proteins in the endoplasmic reticulum lumen.","authors":"Haruki Hasegawa","doi":"10.1042/BSR20253165","DOIUrl":"https://doi.org/10.1042/BSR20253165","url":null,"abstract":"Intracellular protein crystallization represents an intriguing form of biomolecular assembly. While the list of intracellularly crystallizing proteins is growing and their physiological roles are being elucidated, the underlying requirements and processes for intracellular crystallogenesis remain largely unknown. To reveal cellular capacity and morphological plasticity to accommodate protein crystals and crystal-like inclusion bodies, this study examines how simultaneously co-expressed phase-separating proteins influence each other's behavior in the endoplasmic reticulum (ER) lumen. To this end, four cargoes were selected based on their ability to produce distinctive inclusion body types and morphologies irrespective of originating species, function, or sequence homology. The co-expressed model proteins independently phase-separated into distinctive inclusions and coexisted in the ER without losing their signature morphologic characteristics. The continued growth of intra-ER protein crystals and droplets suggested that co-expressed cargo proteins were continuously synthesized and folded in the ER, thereby fueling the growth of the corresponding inclusion bodies. Thus, even in the crowded ER environment, each of the four overexpressed cargo proteins can find their mates through self-association and assemble into four unique structures in the ER. This study demonstrates that cells can accommodate up to four distinct types of mesoscale inclusion bodies in the ER lumen simultaneously, and the respective phase-separation events proceed without interfering with each other and without morphological mixing.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":"45 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Structural insights into substrate binding, residue contributions, and catalytic mechanism of phosphopantetheine adenylyltransferase from Helicobacter pylori. 幽门螺杆菌磷酸蜂氨酸腺苷转移酶的底物结合、残基贡献和催化机制的结构见解。

IF 4.7 3区生物学

Bioscience Reports Pub Date : 2025-08-22 DOI: 10.1042/BSR20241405

I-Ting Ko, Yi-Ting Yuan, Cheng-Ju Hsieh, Hui-Ting Hsu, Hsien-Sheng Yin

{"title":"Structural insights into substrate binding, residue contributions, and catalytic mechanism of phosphopantetheine adenylyltransferase from Helicobacter pylori.","authors":"I-Ting Ko, Yi-Ting Yuan, Cheng-Ju Hsieh, Hui-Ting Hsu, Hsien-Sheng Yin","doi":"10.1042/BSR20241405","DOIUrl":"https://doi.org/10.1042/BSR20241405","url":null,"abstract":"Phosphopantetheine adenylyltransferase (PPAT) (PPAT; EC 2.7.3.3) is a key enzyme in coenzyme A (CoA) biosynthesis. It catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant), producing pyrophosphate and 3'-dephospho-CoA (dPCoA). Although the crystal structures of PPATs with various ligands have been studied, the specific contributions of residues to catalytic efficiency remain unclear. Here, we present the crystal structures of Helicobacter pylori PPAT (HpPPAT) in its apo form and complexes with Ppant and ATP. Additionally, we report the structure of the HpPPAT P8A mutant bound to dPCoA, providing the first complete occupancy structure of a PPAT complex across the hexamer. In the HpPPAT:ATP complex structure, critical active site residues Thr10, His18, Arg88, and Arg91, conserved in Escherichia coli PPAT (EcPPAT), are identified. HpPPAT utilizes Pro8, Lys42, and Arg133 for ATP binding. This differs from the binding pattern observed in other bacterial PPATs. Mutations of these residues, except for Thr10 and Lys42, resulted in a complete loss of enzymatic activity. This result highlights their critical roles. Mutating Thr10 and Lys42 to alanine reduced catalytic efficiency compared to WT HpPPAT but retained substantial activity. These residues are expected to orient the nucleophile for an in-line displacement mechanism. Based on structural studies and mutagenesis data with kinetic measurements and insights from other bacterial PPATs, we propose a refined catalytic mechanism for HpPPAT that emphasizes species-specific active-site interactions. This mechanism provides a foundation structure-based drugs H. pylori infections.","PeriodicalId":8926,"journal":{"name":"Bioscience Reports","volume":"0 ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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