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A high throughput compatible workflow for the biochemical identification and characterisation of molecular glues. 高通量兼容的工作流程,用于分子胶的生化鉴定和表征。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-22 DOI: 10.1016/j.jbc.2025.108526
Ryan Guilbert,Maxime Couturier,Yuanyuan Si,Daniel O' Donovan,David Longmire,Hazel Mak,Paul Clarkson,Argyrides Argyrou
{"title":"A high throughput compatible workflow for the biochemical identification and characterisation of molecular glues.","authors":"Ryan Guilbert,Maxime Couturier,Yuanyuan Si,Daniel O' Donovan,David Longmire,Hazel Mak,Paul Clarkson,Argyrides Argyrou","doi":"10.1016/j.jbc.2025.108526","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108526","url":null,"abstract":"Molecular glues are an emerging modality which induces or enhances an interaction between two proteins. Molecular glues can target proteins via proximity-induced degradation or sequestration and can, therefore, provide opportunities for therapeutic intervention to targets that cannot be modulated by traditional small molecule approaches. Due to their modest molecular weight, molecular glues may not encounter the bioavailability issues associated with PROTACs. Characterisation of molecular glues in hit finding and hit optimisation settings can be challenging, as both the affinity of the glue for the target protein and the resulting improvement in affinity between the proteins of interest need to be assessed in parallel. Here, we propose and validate a workflow to derive both key parameters from a classic concentration response experiment. Furthermore, we provide a method for the rational determination of optimum biochemical assay conditions to identify and characterise molecular glues.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"8 1","pages":"108526"},"PeriodicalIF":4.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143876486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Challenging activity and signaling bias in tachykinin NK1 and NK2 receptors by truncated neuropeptides. 截断神经肽对快激肽NK1和NK2受体的挑战性活性和信号偏倚。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-18 DOI: 10.1016/j.jbc.2025.108522
Jacob E Petersen,Artem Pavlovskyi,Jesper J Madsen,Thue W Schwartz,Thomas M Frimurer,Ole H Olsen
{"title":"Challenging activity and signaling bias in tachykinin NK1 and NK2 receptors by truncated neuropeptides.","authors":"Jacob E Petersen,Artem Pavlovskyi,Jesper J Madsen,Thue W Schwartz,Thomas M Frimurer,Ole H Olsen","doi":"10.1016/j.jbc.2025.108522","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108522","url":null,"abstract":"The tachykinin receptors neurokinin 1 (NK1R) and neurokinin 2 (NK2R) are G protein-coupled receptors that bind preferentially to the natural peptide ligands substance P (SP) and neurokinin A (NKA), respectively. The peptide ligands share a common C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, which contributes to their partial cross-reactivity with each other's non-native receptors. This study examines the impact of truncated tachykinin SP and NKA analogs on signaling activity. SP and NKA were progressively truncated, yielding the shortest versions SP(6-11) and NKA(5-10) with free and acetylated N-terminal. A total of 12 SP and 10 NKA analogs were evaluated for activity in BRET-based cAMP and IP3 accumulation assays targeting both NK1R and NK2R, corresponding to Gs protein and Gq protein activation, respectively. As previously demonstrated, the first three amino acids are dispensable. When activated by SP analogs, NK1R favors activation of Gs over Gq, though this difference diminishes with shorter analogs. In contrast, when NK1R is activated by NKA analogs, the Gq potency exceeds Gs potency by nearly an order of magnitude. For NK2R activation by NKA analogs, there are only minor differences between Gq and Gs potencies, with a slight preference for higher Gq potency. The N-terminal charge status plays a key role, leading to significant differences in analog potency. These findings provide valuable insight into how specific receptor-ligand interactions influence downstream G-protein signaling in GPCRs, which are highly relevant for therapeutic applications. Finally, the proposed \"message-address\" model of neuropeptide signaling is assessed for NK1R and NK2R using truncated SP and NKA analogs.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"34 1","pages":"108522"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 and design principles of far-red-absorbing chlorophyll in the light-harvesting complex. 光吸收复合物中远红吸收叶绿素的鉴定与设计原理。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-18 DOI: 10.1016/j.jbc.2025.108518
Keisuke Saito,Makiko Kosugi,Linhao Qiu,Jun Minagawa,Hiroshi Ishikita
{"title":"Identification and design principles of far-red-absorbing chlorophyll in the light-harvesting complex.","authors":"Keisuke Saito,Makiko Kosugi,Linhao Qiu,Jun Minagawa,Hiroshi Ishikita","doi":"10.1016/j.jbc.2025.108518","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108518","url":null,"abstract":"Photosystem II (PSII) from Prasiola crispa employs a unique ring-shape undecameric light-harvesting complex (Pc-frLHC) in addition to the commonly observed minor monomeric and major trimeric LHCIIs. Each monomer of Pc-frLHC contains four transmembrane helices. In contrast to the typical three-helix LHCIIs that constitute for the peripheral light-harvesting antennas for PSII, Pc-frLHC carries chlorophylls capable of far-red absorption. Combining spectroscopic analyses with a quantum mechanical/molecular mechanical approach, we identified the far-red absorbing chlorophyll(s) in Pc-frLHC, as well as its counterpart in another Trebouxiophyceae alga Coccomyxa sp. Obi (Co-frLHC). Spectroscopic analysis reveals that both complexes exhibit far-red-shifted absorption of chlorophylls at ∼710 nm. In the Pc-frLHC structure, the Chla 603-609 dimer exhibits the strongest excitonic coupling among all apparent chlorophyll dimers. This dimer also exhibits the largest excitation-induced permanent dipole moment along the axis connecting the two chlorophylls, reflecting the most pronounced charge-transfer character. Furthermore, Chla 609 forms the second strongest excitonically coupled dimer with Chla 708, further extending the absorption into the far-red region. The conserved spatial arrangement and orientation of the chlorophyll trimer in Co-frLHC suggest that the Chla 603-609-708 trimer, located in the same frLHC monomer unit, which is predominantly characterized by the Chla 603-609 dimer, provides the structural basis for the far-red absorption in frLHCs.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"7 1","pages":"108518"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Potent activity of prostaglandin J2 on prostanoid DP receptors. 前列腺素J2对前列腺素DP受体的有效活性。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-18 DOI: 10.1016/j.jbc.2025.108523
Kanaho Senoo,Keijo Fukushima,Hitomi Yamamoto,Ayaka Hamaguchi,Akiko Suganami,Harumi Takano,Mayu Yamashita,John W Regan,Yutaka Tamura,Hiromichi Fujino
{"title":"Potent activity of prostaglandin J2 on prostanoid DP receptors.","authors":"Kanaho Senoo,Keijo Fukushima,Hitomi Yamamoto,Ayaka Hamaguchi,Akiko Suganami,Harumi Takano,Mayu Yamashita,John W Regan,Yutaka Tamura,Hiromichi Fujino","doi":"10.1016/j.jbc.2025.108523","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108523","url":null,"abstract":"Prostaglandin D2 (PGD2), an anti-inflammatory mediator, is acting through Gs-protein coupled D-type prostanoid (DP) receptors. DP receptors are not extensively distributed; in tissues, they are the least abundant among members of the prostanoid receptor family, whereas their primary ligand PGD2 is the main prostanoid in most tissues. PGD2 is dehydrated or isomerized to a number of metabolites enzymatically or non-enzymatically. To understand why many metabolites of PGD2 are produced via different pathways, regular cell-based experiments, Black/Leff operational model calculations, and in silico simulations were utilized. Here we show, among the 5 metabolites of PGD2, prostaglandin J2 (PGJ2) was the most potent metabolite for DP receptors, particularly in the cAMP signaling pathway. This result was attributed to PGJ2 forming an extra, and/or stronger hydrogen bond by more negatively charged carbonyl in the cyclopentene ring with DP receptors than PGD2. Therefore, when PGD2 is released into the blood, it would activate DP receptors, which are then continuously activated by PGJ2 to sustain the DP receptor/cAMP-mediated signaling pathway. Thus, the anti-inflammatory effects of PGD2 may be taken over/out competed and/or even enhanced by PGJ2. Here, PGJ2 was found to be a standout mediator of cAMP-mediated signaling pathway, that induces more potent and prolonged DP receptor-activities as a biased ligand, possibly for resolving the inflammatory reaction. Moreover, since each metabolite showed different property, these results provide insight into why many metabolites of PGD2 are produced, and the miscellaneous physiological roles induced by the main prostanoid in most tissues through the least abundant DP receptors.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"64 1","pages":"108523"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics. 蛋白酶体底物受体hRpn13的PROTAC连接区域的优化使分子动力学结构建模合理化。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-18 DOI: 10.1016/j.jbc.2025.108520
Xiuxiu Lu,Venkata R Sabbasani,Bakar Hassan,Rolf E Swenson,Kylie J Walters
{"title":"Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics.","authors":"Xiuxiu Lu,Venkata R Sabbasani,Bakar Hassan,Rolf E Swenson,Kylie J Walters","doi":"10.1016/j.jbc.2025.108520","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108520","url":null,"abstract":"Proteasome substrate receptor hRpn13 is a promising target for cancer therapy. hRpn13 PROTACs induce apoptosis by targeting the hRpn13 proteolytic product hRpn13Pru, which contains an intact ubiquitin- and proteasome-binding Pru domain. We generated a PROTAC series based on hRpn13Pru-targeting XL5 by varying the linker that connects it to a warhead against the VHL-based ubiquitin E3 ligase machinery. Among eight tested derivatives, XL5-VHL-7 with a -(CH2)5- alkyl linker promoted hRpn13Pru degradation and induced cellular apoptosis with 2-fold improved potency compared to the original PROTAC. By using this PROTAC series with slight chemical modifications in the linker region, we were able to evaluate the efficacy of structural modeling with molecular dynamics for refining PROTACs. Overall, we found that the experimental data correlated with efficacy predictions based on molecular dynamics and structural modeling. Moreover, we could observe hRpn13:PROTAC:VHL complexes by 2D NMR that support the structural modeling and stronger affinity of XL5-VHL-7 compared to the original hRpn13 PROTAC. Our NMR data further indicate that hRpn13 Pru affinity for XL5-VHL-7 is higher within the VHL complex present than with XL5-VHL-7 alone. Altogether, we develop an hRpn13 PROTAC with 2-fold increased potency by optimizing the linker and demonstrate the current benefit and limitations for including modeling with molecular dynamics to aid PROTAC optimization.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"43 1","pages":"108520"},"PeriodicalIF":4.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
MitoSNO inhibits mitochondrial hydrogen peroxide (mtH2O2) generation by α-ketoglutarate dehydrogenase (KGDH). MitoSNO抑制α-酮戊二酸脱氢酶(KGDH)产生线粒体过氧化氢(mtH2O2)。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-16 DOI: 10.1016/j.jbc.2025.108510
Olivia Chalifoux,Samantha Sterman,Ben Faerman,Meijing Li,Stephanie Trezza,Marek Michalak,Luis B Agellon,Ryan J Mailloux
{"title":"MitoSNO inhibits mitochondrial hydrogen peroxide (mtH2O2) generation by α-ketoglutarate dehydrogenase (KGDH).","authors":"Olivia Chalifoux,Samantha Sterman,Ben Faerman,Meijing Li,Stephanie Trezza,Marek Michalak,Luis B Agellon,Ryan J Mailloux","doi":"10.1016/j.jbc.2025.108510","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108510","url":null,"abstract":"Here, we demonstrate mitochondrial hydrogen peroxide (mtH2O2) production by α-ketoglutarate dehydrogenase (KGDH) can be inhibited by MitoSNO, alleviating lipotoxicity. MitoSNO in the nanomolar range inhibits mtH2O2 by ∼50% in isolated liver mitochondria without disrupting respiration, whereas the mitochondria-selective derivative used to synthesize MitoSNO, mitochondria-selective N-acetyl-penicillamine (MitoNAP), had no effect on either mtH2O2 generation or oxidative phosphorylation (OxPhos). Additionally, mtH2O2 generation in isolated liver mitochondria was almost abolished when MitoSNO was administered in the low micromolar range. The potent inhibitory effect of MitoSNO was comparable to 2-keto-3-methyl-valeric acid (KMV) and valproic acid (VA), selective inhibitors for KGDH-mediate mH2O2 production. S1QEL 1.1 (S1) and S3QEL (S3), which are known to selectively suppress mtH2O2 genesis through inhibition of complex I and complex III respectively, without disrupting respiration, had little to no effect on mtH2O2 production by liver mitochondria. We also identified it was a major mtH2O2 source as well but MitoSNO and MitoNAP did not affect mtH2O2 production by this ETC-linked enzyme. The MitoSNO also suppressed mtH2O2 production and partially rescued mitochondrial respiration in Huh-7 cells subjected to palmitate (PA) and fructose (Fruc) induced lipotoxicity. MitoSNO also prevented cell death and abrogated intrahepatic lipid accumulation in these Huh-7 cells. MitoSNO nullified mtH2O2 overgeneration and partially rescued OxPhos in liver mitochondria from mice fed a high fat diet (HFD). Our findings demonstrate that MitoSNO interferes with mtH2O2 production through KGDH S-nitrosation and may be useful in alleviating non-alcoholic fatty liver disease (NAFLD).","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"45 1","pages":"108510"},"PeriodicalIF":4.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii. 抗伯纳氏Coxiella burnetii潜在药物靶点甲基异柠檬酸裂解酶的结构与催化机理。
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-16 DOI: 10.1016/j.jbc.2025.108517
William S Stuart, Christopher H Jenkins, Philip M Ireland, Michail N Isupov, Isobel H Norville, Nicholas J Harmer
{"title":"Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii.","authors":"William S Stuart, Christopher H Jenkins, Philip M Ireland, Michail N Isupov, Isobel H Norville, Nicholas J Harmer","doi":"10.1016/j.jbc.2025.108517","DOIUrl":"10.1016/j.jbc.2025.108517","url":null,"abstract":"<p><p>We present a comprehensive investigation into the catalytic mechanism of methylisocitrate lyase, a potential drug target candidate against the zoonotic pathogen Coxiella burnetii, the causative agent of Q fever and a federal select agent. Current treatment regimens are prolonged, often with incomplete clearance of the pathogen. We utilized a structure-based bioinformatics pipeline to identify methylisocitrate lyase as a candidate therapeutic target against C. burnetii from a list of essential genes. WT C. burnetii methylisocitrate lyase has a k<sub>cat</sub> of 13.8 s<sup>-1</sup> (compared to 105 s<sup>-1</sup> for Salmonella enterica), and isocitrate inhibits with a K<sub>I</sub> of 11 mM. We have determined the previously uncharacterized substrate-bound structure of this enzyme family, alongside product and inhibitor-bound structures. These structures of WT enzyme reveal that in the active state the catalytic C118 is positioned 2.98 Å from O5 of methylisocitrate and Arg152 moves toward the substrate relative to the inhibitor bound structure. Analysis of structure-based mutants reveals that Arg152 and Glu110 are both essential for catalysis. We suggest that Arg152 acts as the catalytic base that initiates the methylisocitrate lyase reaction. These results deepen our understanding of the catalytic mechanism of methylisocitrate lyase and could aid the development of new therapeutics against C. burnetii.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"108517"},"PeriodicalIF":4.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 frequency transcription leads to rapid R-loop formation. 高频转录导致r环快速形成。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-16 DOI: 10.1016/j.jbc.2025.108514
Bradleigh Palmer,Chun-Ying Lee,Leya Yang,Tapas Paul,Sua Myong
{"title":"High frequency transcription leads to rapid R-loop formation.","authors":"Bradleigh Palmer,Chun-Ying Lee,Leya Yang,Tapas Paul,Sua Myong","doi":"10.1016/j.jbc.2025.108514","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108514","url":null,"abstract":"R-loops are transcriptionally generated three-stranded nucleic acid structures where the mRNA hybridizes with template DNA, leaving a displaced single-stranded non-template DNA loop. Previously, we demonstrated that R-loop and subsequent G-quadruplex formation upregulate transcription. However, the mechanistic basis of how transcription activity generates R-loop formation is unknown. Here, we investigate the kinetics of transcription and its impact on R-loop formation using single-molecule fluorescence resonance energy transfer (smFRET) and electrophoretic mobility shift assay (EMSA). We show that R-loop formation is tuned by the frequency and the rate of transcription, controlled by the RNAP and NTP concentrations, respectively. We provide a plausible mechanism in which gradually increasing the duration of the promoter opening leads to the R-loop formation. Through stochastic simulation, we demonstrate that the frequency of transcription primarily governs R-loop formation. This work highlights the intricate balance between transcription dynamics and R-loop formation, providing new insights into the structure-function relationship.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"108 1","pages":"108514"},"PeriodicalIF":4.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Impact of an oxidative RNA lesion on in vitro replication catalyzed by SARS-CoV-2 RNA-dependent RNA polymerase. RNA氧化损伤对SARS-CoV-2 RNA依赖性RNA聚合酶催化的体外复制的影响
IF 4 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-16 DOI: 10.1016/j.jbc.2025.108512
Masataka Akagawa, Kaoru Sugasawa, Kiyoe Ura, Akira Sassa
{"title":"Impact of an oxidative RNA lesion on in vitro replication catalyzed by SARS-CoV-2 RNA-dependent RNA polymerase.","authors":"Masataka Akagawa, Kaoru Sugasawa, Kiyoe Ura, Akira Sassa","doi":"10.1016/j.jbc.2025.108512","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108512","url":null,"abstract":"<p><p>The production of reactive oxygen species in response to RNA virus infection results in the oxidation of viral genomic RNA within infected cells. These oxidative RNA lesions undergo replication catalyzed by the viral replisome. G to U transversion mutations are frequently observed in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and may be linked to the replication process catalyzed by RNA-dependent RNA polymerase (RdRp) past the oxidative RNA lesion 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG). To better understand the mechanism of viral RNA mutagenesis, it is crucial to elucidate the role of RdRp in replicating across oxidative lesions. In this study, we investigated the RNA synthesis catalyzed by the reconstituted SARS-CoV-2 RdRp past a single 8-oxo-rG. The RdRp-mediated primer extension was significantly inhibited by 8-oxo-rG on the template RNA. A steady-state multiple-turnover reaction demonstrated that the turnover rate of RdRp was significantly slow when replication was blocked by 8-oxo-rG, reflecting low bypass efficiency even with prolonged reaction time. Once RdRp was able to bypass 8-oxo-rG, it preferentially incorporated rCMP, with a lesser amount of rAMP opposite 8-oxo-rG. In contrast, RdRp demonstrated greater activity in extending from the mutagenic rA:8-oxo-rG terminus compared to the lower efficiency of extension from the rC:8-oxo-rG pair. Based on steady-state kinetic analyses for the incorporation of rNMPs opposite 8-oxo-rG and chain extension from rC:8-oxo-rG or rA:8-oxo-rG, the relative bypass frequency for rA:8-oxo-rG was found to be seven-fold higher than that for rC:8-oxo-rG. Therefore, the properties of RdRp indicated in this study may contribute to the mechanism of mutagenesis of the SARS-CoV-2 genome.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"301 6","pages":"108512"},"PeriodicalIF":4.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Recently Discovered Heteromeric Enzymes in Natural Product Biosynthesis. 天然产物生物合成中新发现的异聚酶。
IF 4.8 2区 生物学
Journal of Biological Chemistry Pub Date : 2025-04-15 DOI: 10.1016/j.jbc.2025.108516
Zhongtian Yu,Ikuro Abe
{"title":"Recently Discovered Heteromeric Enzymes in Natural Product Biosynthesis.","authors":"Zhongtian Yu,Ikuro Abe","doi":"10.1016/j.jbc.2025.108516","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.108516","url":null,"abstract":"The abundant diversity and elegant complexity in the chemical structures of natural products have attracted vigorous investigations of the chemistry and enzymology underlying their biosynthetic processes over the past few decades. Among the biochemical events, the formation of complexes of heteromeric enzymes has been observed in the biosynthesis of several natural products and metabolic pathways. In this review, we aim to consolidate the recently discovered cases of heteromeric enzymes in natural product biosynthesis and metabolism, in order to clarify the genetic and structural bases leading to the formation of these heteromeric complexes and provide insights for the rational redesign of proteins in biosynthetic machineries.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"9 1","pages":"108516"},"PeriodicalIF":4.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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