ACS Publications最新文献_第4页

Multiomics Analysis of Liver Molecular Dysregulation Leading to Nonviral-Related Hepatocellular Carcinoma Development.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-21 DOI: 10.1021/acs.jproteome.4c00729

Hikaru Nakahara, Atsushi Ono, C Nelson Hayes, Yuki Shirane, Ryoichi Miura, Yasutoshi Fujii, Yosuke Tamura, Shinsuke Uchikawa, Hatsue Fujino, Takashi Nakahara, Eisuke Murakami, Masami Yamauchi, Tomokazu Kawaoka, Daiki Miki, Masataka Tsuge, Tsuyoshi Kobayashi, Hideki Ohdan, Koji Arihiro, Shiro Oka

{"title":"Multiomics Analysis of Liver Molecular Dysregulation Leading to Nonviral-Related Hepatocellular Carcinoma Development.","authors":"Hikaru Nakahara, Atsushi Ono, C Nelson Hayes, Yuki Shirane, Ryoichi Miura, Yasutoshi Fujii, Yosuke Tamura, Shinsuke Uchikawa, Hatsue Fujino, Takashi Nakahara, Eisuke Murakami, Masami Yamauchi, Tomokazu Kawaoka, Daiki Miki, Masataka Tsuge, Tsuyoshi Kobayashi, Hideki Ohdan, Koji Arihiro, Shiro Oka","doi":"10.1021/acs.jproteome.4c00729","DOIUrl":"10.1021/acs.jproteome.4c00729","url":null,"abstract":"Chronic liver diseases exhibit diverse backgrounds, and it is believed that numerous factors contribute to progression to cancer. To achieve effective prevention of nonviral hepatocellular carcinoma, it is imperative to identify fundamental molecular abnormalities at the patient level. Utilizing cancer-adjacent liver tissues obtained from hepatocellular carcinoma patients (chronic liver disease), we conducted RNA-Seq and metabolome analyses. In the chronic liver disease cohort, upregulation of inflammation-associated signals was observed, concomitant with accumulation of acylcarnitine and fatty acid and depletion of NADP+, gamma-tocopherol, and dehydroisoandrosterone-3-sulfate-1 (DHEAS). To minimize heterogeneity, we performed multiomics clustering, successfully categorizing the chronic liver disease cases into two distinct subtypes. Subtype 1 demonstrated elevated inflammatory levels, whereas Subtype 2 included a disproportionately high proportion of elderly cases. Furthermore, RNA-Seq analysis revealed upregulation of inflammatory signals in Subtype 1, while both subtypes exhibited downregulation of fatty acid metabolism. Metabolome analysis indicated a tendency of increased acylcarnitine levels in Subtype 1 and augmented fatty acid accumulation in Subtype 2. Validation of differentially expressed genes using the Gene Expression Omnibus (GEO) data set revealed the potential for amelioration through supplementation with antioxidants such as epigallocatechin gallate (EGCG).","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1102-1117"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466570","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

Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis. 加强蛋白质组学质量控制：可视化工具 QCeltis 的启示。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-24 DOI: 10.1021/acs.jproteome.4c00777

Manasa Vegesna, Niveda Sundararaman, Ajay Bharadwaj, Kirstin Washington, Rakhi Pandey, Ali Haghani, Blandine Chazarin, Aleksandra Binek, Qin Fu, Susan Cheng, David Herrington, Jennifer E Van Eyk

{"title":"Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis.","authors":"Manasa Vegesna, Niveda Sundararaman, Ajay Bharadwaj, Kirstin Washington, Rakhi Pandey, Ali Haghani, Blandine Chazarin, Aleksandra Binek, Qin Fu, Susan Cheng, David Herrington, Jennifer E Van Eyk","doi":"10.1021/acs.jproteome.4c00777","DOIUrl":"10.1021/acs.jproteome.4c00777","url":null,"abstract":"Large-scale mass-spectrometry-based proteomics experiments are complex and prone to analytical variability, requiring rigorous quality checks across each step in the workflow: sample preparation, chromatography, mass spectrometry, and the bioinformatics stages. This includes quality control (QC) measures that address biological and technical variation. Most QC approaches involve detecting sample outliers and monitoring parameters related to sample preparation and mass spectrometer performance. Evaluating these parameters regularly is essential for reliable downstream analysis and proteomics research. Here, we introduce \"QCeltis\", a Python package designed to facilitate automated QC analysis across the proteomics workflow, aiding in the identification of technical biases and consistency verification. QCeltis is a versatile tool for detecting QC issues in large-scale data-independent acquisition proteomics experiments by not only identifying sample preparation and acquisition issues but also aiding in differentiating between QC issues vs batch effects. QCeltis is available for command-line use in Windows and Linux environments. We present three case studies showcasing QCeltis's capabilities across different data sets, including depleted plasma, whole blood vs plasma, and dried blood spot samples, emphasizing its potential impact on large-scale proteomics projects. This package can be used to enhance data reliability and enable nuanced downstream analysis and interpretation for proteomics studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1148-1160"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481731","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

Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-24 DOI: 10.1021/acs.jproteome.4c00655

Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu, Jie Zhu

{"title":"Heterogeneities of Site-Specific N-Glycosylation in the Hippocampus of Depression-like Behavior Models in Mice Induced by Acute Stress and Chronic Stress.","authors":"Pengyu Ren, Longhui Fu, Xiaojuan Gong, Li Jia, Boqiang Lyu, Mengke Wang, Siyuan Zhang, Shisheng Sun, Na Zhao, Zongben Xu, Jie Zhu","doi":"10.1021/acs.jproteome.4c00655","DOIUrl":"10.1021/acs.jproteome.4c00655","url":null,"abstract":"It is well established that acute and chronic stress contributes to the onset and progression of depression, but the underlying mechanisms have not been elucidated. Here an integrated N-glycoproteomic and proteomic analysis was performed to investigate heterogeneities of glycoprotein and site-specific glycosylation between the hippocampi of control, acute stress-affected (AS), and chronic mild stress-affected (CMS) mice. 1063 unique intact N-glycopeptides, 116 N-glycan compositions, and 512 glycosylation sites were identified. CMS and AS had significant effects on glycosylation. CMS reduced multiantenna glycosylation (N8H8 and N6H5F1S1) more strongly, while AS reduced multiantenna glycosylation (N5H3F1) more strongly. CMS inhibited high-mannose synthesis with high polymerization (N2H9 and N2H8), while AS inhibited high-mannose synthesis with low polymerization (N2H6, H2H5). Furthermore, 26 and 39 glycosylation-related genes (GRGs) were identified in the AS and CMS groups, separately. Functional enrichment analysis for GRGs in the AS and CMS groups exhibited that the up-regulated functions were leading edge membrane and cell adhesion molecule binding; meanwhile, the down-regulated functions were cAMP signaling pathways. Finally, tSNE analysis based on ScRNA-seq revealed that core GRGs were highly expressed in astrocytes. All of these findings improve our understanding of glycosylation in stress-related depression, providing valuable data resources for depression pathogenesis exploration and novel therapeutic target discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1039-1052"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490331","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

Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-25 DOI: 10.1021/acs.jproteome.4c00946

Emma B Timmins-Schiffman, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X MacLean, Miranda C Mudge, Samuel J White, Carly D Kenkel, Lisa J Rodrigues, Brook L Nunn, Jacqueline L Padilla-Gamiño

{"title":"Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching.","authors":"Emma B Timmins-Schiffman, Rayhan Khanna, Tanya Brown, Jenna Dilworth, Brendan X MacLean, Miranda C Mudge, Samuel J White, Carly D Kenkel, Lisa J Rodrigues, Brook L Nunn, Jacqueline L Padilla-Gamiño","doi":"10.1021/acs.jproteome.4c00946","DOIUrl":"10.1021/acs.jproteome.4c00946","url":null,"abstract":"Coral reefs are vital to marine biodiversity and human livelihoods, but they face significant threats from climate change. Increased ocean temperatures drive massive \"bleaching\" events, during which corals lose their symbiotic algae and the important metabolic resources those algae provide. Proteomics is a crucial tool for understanding coral function and tolerance to thermal stress, as proteins drive physiological processes and accurately represent cell functional phenotypes. We examined the physiological condition of coral (Montipora capitata) gametes from parents that either experienced thermal bleaching or were nonbleached controls by comparing data dependent (DDA) and data independent (DIA) acquisition methods and peptide quantification (spectral counting and area-under-the-curve, AUC) strategies. For DDA, AUC captured a broader dynamic range than spectral counting. DIA yielded better coverage of low abundance proteins than DDA and a higher number of proteins, making it the more suitable method for detecting subtle, yet biologically significant, shifts in protein abundance in gamete bundles. Gametes from bleached corals showed a broadscale decrease in metabolic proteins involved in carbohydrate metabolism, citric acid cycle, and protein translation. This metabolic plasticity could reveal how organisms and their offspring acclimatize and adapt to future environmental stress, ultimately shaping the resilience and dynamics of coral populations.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1317-1328"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490332","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

Triangesinenolides A-C: Trimeric Phthalides with Anti-Renal Fibrosis Potential from Angelica sinensis.

IF 4.9 1区化学

Organic Letters Pub Date : 2025-03-07 Epub Date: 2025-02-26 DOI: 10.1021/acs.orglett.5c00317

Hang Lv, Yu Mu, Bixuan Cao, Ping Yi, Nuerbiye Aobulikasimu, Zhongyuan Liu, Xueshi Huang, Li Han

引用次数: 0

Serum N-Glycomics with Nano-LC-QToF LC-MS/MS Reveals N-Glycan Biomarkers for Glioblastoma, Meningioma, and High-Grade Meningioma.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-05 DOI: 10.1021/acs.jproteome.4c01090

Atit Silsirivanit, Michael Russelle S Alvarez, Sheryl Joyce Grijaldo-Alvarez, Riya Gogte, Amnat Kitkhuandee, Nontaphon Piyawattanametha, Wunchana Seubwai, Sukanya Luang, Orasa Panawan, Panupong Mahalapbutr, Kulthida Vaeteewoottacharn, Kanlayanee Sawanyawisuth, Worachart Let-Itthiporn, Charupong Saengboonmee, Pichayen Duangthongphon, Kritsakorn Jingjit, Anuchit Pankongsap, Sakda Waraasawapati, Chaiwat Aphivatanasiri, Carlito B Lebrilla

{"title":"Serum N-Glycomics with Nano-LC-QToF LC-MS/MS Reveals N-Glycan Biomarkers for Glioblastoma, Meningioma, and High-Grade Meningioma.","authors":"Atit Silsirivanit, Michael Russelle S Alvarez, Sheryl Joyce Grijaldo-Alvarez, Riya Gogte, Amnat Kitkhuandee, Nontaphon Piyawattanametha, Wunchana Seubwai, Sukanya Luang, Orasa Panawan, Panupong Mahalapbutr, Kulthida Vaeteewoottacharn, Kanlayanee Sawanyawisuth, Worachart Let-Itthiporn, Charupong Saengboonmee, Pichayen Duangthongphon, Kritsakorn Jingjit, Anuchit Pankongsap, Sakda Waraasawapati, Chaiwat Aphivatanasiri, Carlito B Lebrilla","doi":"10.1021/acs.jproteome.4c01090","DOIUrl":"10.1021/acs.jproteome.4c01090","url":null,"abstract":"Alteration of glycosylation in cancer cells leads to the expression of tumor-associated glycans, which can be used as biomarkers for diagnosis and prognostic prediction of diseases. In this study, we used nano-LC-QToF to identify serum N-glycan biomarkers for the detection of brain tumors. We observed an increase in sialylated N-glycans and a decrease in fucosylated N-glycans in the serum of patients with glioblastoma (GBM) and meningioma (MG) compared to healthy individuals. In GBM, a combination of increased serum sialylated N-glycan (6_4_0_2 compound) and decreased fucosylated N-glycan (4_4_1_0 compound) was identified as the most appropriate panel, with an area under the curve (AUC) of 0.8660, 78.95% sensitivity, 84.21% specificity, and 82.89% accuracy. For MG, a combination of decreased 6_6_2_0 and 5_5_2_0 compounds and increased 4_4_1_1 compound achieved an AUC of 0.9260, 82.35% sensitivity, 78.57% specificity, and 80.26% accuracy for diagnosis of MG. Additionally, an increase in 5_5_1_0 and 4_3_0_0 compounds combined with a decrease in 7_7_4_3 was associated with high-grade MG (WHO grades II-III). In conclusion, we identified serum N-glycan profiles associated with brain tumors, highlighting their potential as biomarkers for the diagnosis and prognosis of these diseases.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1402-1413"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187504","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

Unraveling the Impact of TLR4 and Sex on Chronic Alcohol Consumption-Induced Lipidome Dysregulation in Extracellular Vesicles.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-05 DOI: 10.1021/acs.jproteome.4c00786

Carla Perpiñá-Clérigues, Susana Mellado, Cristina Galiana-Roselló, Francisco García-García, María Pascual

{"title":"Unraveling the Impact of TLR4 and Sex on Chronic Alcohol Consumption-Induced Lipidome Dysregulation in Extracellular Vesicles.","authors":"Carla Perpiñá-Clérigues, Susana Mellado, Cristina Galiana-Roselló, Francisco García-García, María Pascual","doi":"10.1021/acs.jproteome.4c00786","DOIUrl":"10.1021/acs.jproteome.4c00786","url":null,"abstract":"The lipids that form extracellular vesicles (EVs) play critical structural and regulatory roles, and cutting-edge bioinformatics strategies have shown the ability to decipher lipid metabolism and related molecular mechanisms. We previously demonstrated that alcohol abuse induces an inflammatory immune response through Toll-like receptor 4 (TLR4), leading to structural and cognitive dysfunction. This study evaluated how TLR4 and sex as variables (male/female) impact the lipidome of plasma-resident EVs after chronic alcohol exposure. Using a mouse model of chronic ethanol exposure in wild-type and TLR4-deficient mice, enrichment networks generated by LINEX2 highlighted significant ethanol-induced changes in the EV lipid substrate-product of enzyme reactions associated with glycerophospholipid metabolism. We also demonstrated ethanol-induced differences in Lipid Ontology enrichment analysis in EVs, focusing on terms related to lipid bilayer properties. A lipid abundance analysis revealed higher amounts of significant lipid subclasses in all experimental comparisons associated with inflammatory responses and EV biogenesis/secretion. These findings suggest that interrogating EV lipid abundance with a sensitive lipidomic-based strategy can provide deep insight into the molecular mechanisms underlying biological processes associated with sex, alcohol consumption, and TLR4 immune responses and open new avenues for biomarker identification and therapeutic development.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1197-1208"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143187512","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

A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-21 DOI: 10.1021/acs.jproteome.4c00871

Markus Schneider, Daniel P Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt, Martin Frejno

{"title":"A Scalable, Web-Based Platform for Proteomics Data Processing, Result Storage and Analysis.","authors":"Markus Schneider, Daniel P Zolg, Patroklos Samaras, Samia Ben Fredj, Dulguun Bold, Agnes Guevende, Alexander Hogrebe, Michelle T Berger, Michael Graber, Vishal Sukumar, Lizi Mamisashvili, Igor Bronsthein, Layla Eljagh, Siegfried Gessulat, Florian Seefried, Tobias Schmidt, Martin Frejno","doi":"10.1021/acs.jproteome.4c00871","DOIUrl":"10.1021/acs.jproteome.4c00871","url":null,"abstract":"The exponential increase in proteomics data presents critical challenges for conventional processing workflows. These pipelines often consist of fragmented software packages, glued together using complex in-house scripts or error-prone manual workflows running on local hardware, which are costly to maintain and scale. The MSAID Platform offers a fully automated, managed proteomics data pipeline, consolidating formerly disjointed functions into unified, API-driven services that cover the entire process from raw data to biological insights. Backed by the cloud-native search algorithm CHIMERYS, as well as scalable cloud compute instances and data lakes, the platform facilitates efficient processing of large data sets, automation of processing via the command line, systematic result storage, analysis, and visualization. The data lake supports elastically growing storage and unified query capabilities, facilitating large-scale analyses and efficient reuse of previously processed data, such as aggregating longitudinally acquired studies. Users interact with the platform via a web interface, CLI client, or API, providing flexible, automated access. Readily available tools for accessing result data include browser-based interrogation and one-click visualizations for statistical analysis. The platform streamlines research processes, making advanced and automated proteomic workflows accessible to a broader range of scientists. The MSAID Platform is globally available via https://platform.msaid.io.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1241-1249"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471994","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

Cell-Free Expression of Soluble Leafhopper Proteins from Brochosomes.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-03-07 DOI: 10.1021/acssynbio.4c00773

Caleb G Lay, Gabriel R Burks, Zheng Li, Jeffrey E Barrick, Charles M Schroeder, Ashty S Karim, Michael C Jewett

{"title":"Cell-Free Expression of Soluble Leafhopper Proteins from Brochosomes.","authors":"Caleb G Lay, Gabriel R Burks, Zheng Li, Jeffrey E Barrick, Charles M Schroeder, Ashty S Karim, Michael C Jewett","doi":"10.1021/acssynbio.4c00773","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00773","url":null,"abstract":"Brochosomes are proteinaceous nanostructures produced by leafhopper insects with superhydrophobic and antireflective properties. Unfortunately, the production and study of brochosome-based materials has been limited by poor understanding of their major constituent subunit proteins, known as brochosomins, as well as their sensitivity to redox conditions due to essential disulfide bonds. Here, we used cell-free gene expression (CFE) to achieve recombinant production and analysis of brochosomin proteins. Through the optimization of redox environment, reaction temperature, and disulfide bond isomerase concentration, we achieved soluble brochosomin yields of up to 341 ± 30 μg/mL. Analysis using dynamic light scattering and transmission electron microscopy revealed distinct aggregation patterns among cell-free mixtures with different expressed brochosomins. We anticipate that the CFE methods developed here will accelerate the ability to change the geometries and properties of natural and modified brochosomes, as well as facilitate the expression and structural analysis of other poorly understood protein complexes.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571548","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

Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-07 DOI: 10.1021/acs.biochem.5c00038

Shramana Chatterjee, Joel A Rankin, Mark A Farrugia, Simahudeen Bathir J S Rifayee, Christo Z Christov, Jian Hu, Robert P Hausinger

{"title":"Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.","authors":"Shramana Chatterjee, Joel A Rankin, Mark A Farrugia, Simahudeen Bathir J S Rifayee, Christo Z Christov, Jian Hu, Robert P Hausinger","doi":"10.1021/acs.biochem.5c00038","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00038","url":null,"abstract":"The ethylene-forming enzyme (EFE) from the fungus Penicillium digitatum strain Pd1 was heterologously produced in Escherichia coli and its properties were compared to the extensively characterized bacterial enzyme from Pseudomonas savastanoi strain PK2. Both enzymes catalyze four reactions: the conversion of 2-oxoglutarate (2OG) to ethylene and CO2, oxidative decarboxylation of 2OG coupled to l-arginine (l-Arg) hydroxylation, uncoupled oxidative decarboxylation of 2OG, and the production of 3-hydroxypropionate (3-HP) from 2OG. The strain Pd1 enzyme exhibited a greater ratio of ethylene production over l-Arg hydroxylation than the PK2 strain EFE. The uncoupled decarboxylation of 2OG and 3-HP production are minor reactions in both cases, but they occur to a greater extent using the fungal enzyme. Additional distinctions of the fungal versus bacterial enzyme are noted in the absorbance maxima and l-Arg dependence of their anaerobic electronic spectra. The structures of the Pd1 EFE apoprotein and the EFE·Mn(II)·2OG complex resembled the corresponding structures of the PK2 enzyme, but notable structural differences were observed in the computationally predicted Pd1 EFE·Fe(II)·2OG·l-Arg complex versus the PK2 EFE·Mn(II)·2OG·l-Arg crystal structure. These studies extend our biochemical understanding and represent the first structural and conformational characterization of a eukaryotic EFE.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571550","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