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Bioluminescent Probes for the Detection of Superoxide and Nitric Oxide.
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-16 DOI: 10.1021/acschembio.4c00551
Matthew A Larsen, Mike Valley, Natasha Karassina, Hui Wang, Wenhui Zhou, Jolanta Vidugiriene
{"title":"Bioluminescent Probes for the Detection of Superoxide and Nitric Oxide.","authors":"Matthew A Larsen, Mike Valley, Natasha Karassina, Hui Wang, Wenhui Zhou, Jolanta Vidugiriene","doi":"10.1021/acschembio.4c00551","DOIUrl":"https://doi.org/10.1021/acschembio.4c00551","url":null,"abstract":"<p><p>The regulation of reactive oxygen species (ROS) such as superoxide (SO) and nitric oxide (NO) is crucial in biology, influencing metabolism and signaling pathways. Imbalances in these species lead to oxidative stress and various diseases. Traditional methods for measuring SO and NO face challenges in terms of sensitivity and specificity, particularly in complex biological matrices. This report introduces bioluminescent probes that leverage the intrinsic sensitivity of bioluminescence for direct and selective detection of SO and NO. These probes release analogs of d-luciferin upon reaction with their target ROS. Following addition of luciferase, luminescence is generated proportional to the amount of accumulated luciferin, allowing for quantitation of SO or NO. Both probes exhibit high specificity, confirmed through cell-free assays and cell-based studies in macrophages, demonstrating their utility in measuring cellular SO and NO production. These assays offer a robust, high-throughput platform for studying ROS, providing direct insights into oxidative stress-related mechanisms.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833151","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
Fluorescent d-amino Acid-Based Approach Enabling Fast and Reliable Measure of Antibiotic Susceptibility in Bacterial Cells.
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-12 DOI: 10.1021/acschembio.4c00639
Barbara Walenkiewicz, Michael S VanNieuwenhze
{"title":"Fluorescent d-amino Acid-Based Approach Enabling Fast and Reliable Measure of Antibiotic Susceptibility in Bacterial Cells.","authors":"Barbara Walenkiewicz, Michael S VanNieuwenhze","doi":"10.1021/acschembio.4c00639","DOIUrl":"https://doi.org/10.1021/acschembio.4c00639","url":null,"abstract":"<p><p>The threat of multidrug-resistant bacteria has been increasing steadily in the past century, posing a major health risk (Organización Mundial de la Salud. Directrices Sobre Componentes Básicos Para Los Programas de Prevención y Control de Infecciones a Nivel Nacional y de Establecimientos de Atención de Salud Para Pacientes Agudos; Organización Mundial de la Salud: Ginebra, <b>2017</b>). Even though every year, 226 million antibiotics are prescribed in the United States alone, 50% of these prescriptions are inappropriate for the patient's condition (CDC. Get Smart about Antibiotics Week; Centers for Disease Control and Prevention. <b>2016</b>,https://www.cdc.gov/media/dpk/antibiotic-resistance/antibiotics-week-2016/dpk-antibiotics-week-2016.html). The increasing abuse of antibiotics in healthcare as well as agriculture has resulted in the rise of antibiotic resistance at an alarming rate. In a clinical setting, timely and accurate recognition of the pathogen allows for the most effective choice of treatment, highlighting the need for novel, fast, and reliable antibiotic susceptibility testing. Traditional susceptibility testing techniques require costly and complex experimental setups or extended cell incubation periods, delaying a timely treatment response to the infection. Herein, we report that a short-pulse fluorescent d-amino acid (FDAA)-based approach provides insight not only into bacterial antibiotic susceptibility but also into the mechanism of action of the antibiotic. Using the FDAA-labeling signal as a reflection of peptidoglycan (PG) integrity after antibiotic treatment, we observed that drugs targeting PG biosynthesis resulted in a significant decrease in fluorescence, while antimicrobials affecting other cellular targets resulted in no fluorescence changes. Our method was validated and optimized via fluorescence microscopy and spectrofluorometry, shortening the required procedure time to 15 min and providing reliably reproducible results. Significantly, we demonstrate that our protocol can be used to identify β-lactam-resistant bacterial strains, further demonstrating the utility of these valuable molecular tools.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816783","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
Intracellular Photocatalytic Proximity Labeling (iPPL) for Dynamic Analysis of Chromatin-Binding Proteins Targeting Histone H3
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-09 DOI: 10.1021/acschembio.4c0068010.1021/acschembio.4c00680
Kazuki Miura, Hikaru Niimi, Tatsuya Niwa, Hideki Taguchi and Hiroyuki Nakamura*, 
{"title":"Intracellular Photocatalytic Proximity Labeling (iPPL) for Dynamic Analysis of Chromatin-Binding Proteins Targeting Histone H3","authors":"Kazuki Miura,&nbsp;Hikaru Niimi,&nbsp;Tatsuya Niwa,&nbsp;Hideki Taguchi and Hiroyuki Nakamura*,&nbsp;","doi":"10.1021/acschembio.4c0068010.1021/acschembio.4c00680","DOIUrl":"https://doi.org/10.1021/acschembio.4c00680https://doi.org/10.1021/acschembio.4c00680","url":null,"abstract":"<p >We demonstrated a novel approach for protein–protein interaction (PPI) profiling of histone H3 using intracellular photocatalytic-proximity labeling (iPPL). This approach identified that the combination of acriflavine as a photocatalyst and 1-methyl-4-arylurazol (MAUra) as a protein labeling agent was the most efficient strategy to proceed the protein proximity labeling reaction. Furthermore, the identification of the labeled amino acids in histone H3 interacting proteins, histone lysine <i>N</i>-methyltransferase EZH2, showed that the amino acid in EZH2 within a few nanometers from histone H3 is labeled by iPPL. This restricted labeling radius allows for more-focused PPI profiling, compared to conventional proximity labeling methods.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2412–2417 2412–2417"},"PeriodicalIF":3.5,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858683","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
Bioorthogonal Cyclopropenones for Investigating RNA Structure
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-06 DOI: 10.1021/acschembio.4c0063310.1021/acschembio.4c00633
Sharon Chen, Christopher D. Sibley, Brandon Latifi, Sumirtha Balaratnam, Robert S. Dorn, Andrej Lupták, John S. Schneekloth Jr.* and Jennifer A. Prescher*, 
{"title":"Bioorthogonal Cyclopropenones for Investigating RNA Structure","authors":"Sharon Chen,&nbsp;Christopher D. Sibley,&nbsp;Brandon Latifi,&nbsp;Sumirtha Balaratnam,&nbsp;Robert S. Dorn,&nbsp;Andrej Lupták,&nbsp;John S. Schneekloth Jr.* and Jennifer A. Prescher*,&nbsp;","doi":"10.1021/acschembio.4c0063310.1021/acschembio.4c00633","DOIUrl":"https://doi.org/10.1021/acschembio.4c00633https://doi.org/10.1021/acschembio.4c00633","url":null,"abstract":"<p >RNA sequences encode structures that impact protein production and other cellular processes. Misfolded RNAs can also potentiate disease, but a complete picture is lacking. To establish more comprehensive and accurate RNA structure–function relationships, new methods are needed to interrogate RNA in native environments. Existing tools rely primarily on electrophiles that are constitutively “on” or triggered by UV light, often resulting in high background. Here we describe an alternative, chemically triggered approach to cross-link RNAs using bioorthogonal cyclopropenones (CpOs). These reagents selectively react with phosphines to provide ketenes─electrophiles that can trap neighboring nucleophiles to forge covalent cross-links. As a proof-of-concept, we conjugated a CpO motif to thiazole orange (TO-1). TO-1–CpO bound selectively to a model RNA aptamer (Mango) with nanomolar affinity, as confirmed by fluorescence turn-on. After phosphine administration, covalent cross-links were formed between the CpO and RNA. Cross-linking was both time and dose dependent. We further applied the chemically triggered tools to model RNAs under biologically relevant conditions. Collectively, this work expands the toolkit of probes for studying RNA and its native conformations.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2406–2411 2406–2411"},"PeriodicalIF":3.5,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00633","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Molecular Targeted Engagement of DPP9 in Rat Tissue Using CETSA, SP3 Processing, and Absolute Quantitation Mass Spectrometry
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-06 DOI: 10.1021/acschembio.4c0056310.1021/acschembio.4c00563
Matthew T. Mazur*, Baojen Shyong, Qian Huang, Stacey L. Polsky-Fisher, Carl J. Balibar and Weixun Wang, 
{"title":"Molecular Targeted Engagement of DPP9 in Rat Tissue Using CETSA, SP3 Processing, and Absolute Quantitation Mass Spectrometry","authors":"Matthew T. Mazur*,&nbsp;Baojen Shyong,&nbsp;Qian Huang,&nbsp;Stacey L. Polsky-Fisher,&nbsp;Carl J. Balibar and Weixun Wang,&nbsp;","doi":"10.1021/acschembio.4c0056310.1021/acschembio.4c00563","DOIUrl":"https://doi.org/10.1021/acschembio.4c00563https://doi.org/10.1021/acschembio.4c00563","url":null,"abstract":"<p >The cellular thermal shift assay (CETSA) provides a means of understanding the extent to which a small molecule ligand associates with a protein target of therapeutic interest, thereby inferring target engagement. Better analytical detection methods, including mass spectrometry, are being implemented to improve quantitation within these assays, providing both absolute quantitation and a very high analyte specificity. To understand the target engagement, and hence inhibition, of the protein dipeptidyl peptidase 9 (DPP9) in rat tissue, CETSA experiments, coupled with single-pot, solid-phase-enhanced sample preparation (“SP3”) and absolute quantitation by high-resolution mass spectrometry, demonstrated a temperature-dependent “melting curve” by ex vivo incubation of compound with rat tissue and further demonstrated in vivo engagement by a dose-dependent response to treatment. These experiments illustrate the ability to extend the CETSA to in vivo dosed-animal samples using absolute quantitation of DPP9 by mass spectrometry and demonstrate a viable path for interrogating therapeutic molecules for drug discovery.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2477–2486 2477–2486"},"PeriodicalIF":3.5,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867783","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
Interspecies Crosstalk via LuxI/LuxR-Type Quorum Sensing Pathways Contributes to Decreased Nematode Survival in Coinfections of Pseudomonas aeruginosa and Burkholderia multivorans
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-05 DOI: 10.1021/acschembio.4c0064110.1021/acschembio.4c00641
Betty L. Slinger, Samalee Banerjee, Josephine R. Chandler* and Helen E. Blackwell*, 
{"title":"Interspecies Crosstalk via LuxI/LuxR-Type Quorum Sensing Pathways Contributes to Decreased Nematode Survival in Coinfections of Pseudomonas aeruginosa and Burkholderia multivorans","authors":"Betty L. Slinger,&nbsp;Samalee Banerjee,&nbsp;Josephine R. Chandler* and Helen E. Blackwell*,&nbsp;","doi":"10.1021/acschembio.4c0064110.1021/acschembio.4c00641","DOIUrl":"https://doi.org/10.1021/acschembio.4c00641https://doi.org/10.1021/acschembio.4c00641","url":null,"abstract":"<p >Quorum sensing (QS) is a prominent chemical communication mechanism used by common bacteria to regulate group behaviors at high cell density, including many processes important in pathogenesis. There is growing evidence that certain bacteria can use QS to sense not only themselves but also other species and that this crosstalk could alter collective behaviors. In the current study, we report the results of culture-based and <i>in vivo</i> coinfection experiments that probe interspecies interactions between the opportunistic pathogens <i>Pseudomonas aeruginosa</i> and <i>Burkholderia multivorans</i> involving their LuxI/LuxR-type QS circuits. Using a <i>Caenorhabditis elegans</i> infection model, we show that infections with both species result in poorer host outcomes compared with monoinfections. We use genetic mutants and a transwell infection assay to establish that crosstalk via LuxR-type receptors and signals is important for this coinfection pathogenicity. Using laboratory cocultures with cell-based reporter systems, we show that the RhlR and CepR receptors in <i>P. aeruginosa</i> and <i>B. multivorans</i>, respectively, can each recognize a QS signal produced by the other species. Lastly, we apply chemical biology to complement our genetic approach and demonstrate the potential to regulate interspecies interactions between the wild-type strains of <i>P. aeruginosa</i> and <i>B. multivorans</i> through the application of synthetic compounds that modulate RhlR and CepR activities. Overall, this study reveals that interspecies interaction via QS networks is possible between <i>P. aeruginosa</i> and <i>B. multivorans</i> and that it can contribute to coinfection severity with these two species.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2557–2568 2557–2568"},"PeriodicalIF":3.5,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858846","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
Aptamer and N-Degron Ensemble (AptaGron) as a Target Protein Degradation Strategy
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-04 DOI: 10.1021/acschembio.4c0053610.1021/acschembio.4c00536
Mohammad Faysal Al Mazid, Olha Shkel, Eunteg Ryu, Jiwon Kim, Kyung Ho Shin, Yun Kyung Kim, Hyun Suk Lim* and Jun-Seok Lee*, 
{"title":"Aptamer and N-Degron Ensemble (AptaGron) as a Target Protein Degradation Strategy","authors":"Mohammad Faysal Al Mazid,&nbsp;Olha Shkel,&nbsp;Eunteg Ryu,&nbsp;Jiwon Kim,&nbsp;Kyung Ho Shin,&nbsp;Yun Kyung Kim,&nbsp;Hyun Suk Lim* and Jun-Seok Lee*,&nbsp;","doi":"10.1021/acschembio.4c0053610.1021/acschembio.4c00536","DOIUrl":"https://doi.org/10.1021/acschembio.4c00536https://doi.org/10.1021/acschembio.4c00536","url":null,"abstract":"<p >Target protein degradation (TPD) is a promising strategy for catalytic downregulation of target proteins through various cellular proteolytic pathways. Despite numerous reports on novel TPD mechanisms, the discovery of target-specific ligands remains a major challenge. Unlike small-molecule ligands, aptamers offer significant advantages, owing to their SELEX-based systematic screening method. To fully utilize aptamers for TPD, we designed an aptamer and N-degron ensemble system (AptaGron) that circumvents the need for synthetic conjugations between aptamers and proteolysis-recruiting units. In our AptaGron system, a peptide nucleic acid containing an N-degron peptide and a sequence complementary to the aptamer was designed. Using this system, we successfully degraded three target proteins, tau, nucleolin, and eukaryotic initiation factor 4E (eIF4E), which lack specific small-molecule ligands. Our results highlight the potential of the AptaGron approach as a robust platform for targeted protein degradation.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2462–2468 2462–2468"},"PeriodicalIF":3.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867763","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
Characterization of a Dual Function Peptide Cyclase in Graspetide Biosynthesis
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-04 DOI: 10.1021/acschembio.4c0062610.1021/acschembio.4c00626
Garret M. Rubin, Krishna P. Patel, Yujia Jiang, Alivia C. Ishee, Gustavo Seabra, Steven D. Bruner* and Yousong Ding*, 
{"title":"Characterization of a Dual Function Peptide Cyclase in Graspetide Biosynthesis","authors":"Garret M. Rubin,&nbsp;Krishna P. Patel,&nbsp;Yujia Jiang,&nbsp;Alivia C. Ishee,&nbsp;Gustavo Seabra,&nbsp;Steven D. Bruner* and Yousong Ding*,&nbsp;","doi":"10.1021/acschembio.4c0062610.1021/acschembio.4c00626","DOIUrl":"https://doi.org/10.1021/acschembio.4c00626https://doi.org/10.1021/acschembio.4c00626","url":null,"abstract":"<p >Graspetides are a diverse family of ribosomally synthesized and post-translationally modified peptides with unique macrocyclic structures formed by ATP-grasp enzymes. Group 11 graspetides, including prunipeptin, feature both macrolactone and macrolactam cross-links. Despite the known involvement of a single ATP-grasp cyclase in the dual macrocyclizations of groups 5, 7, and 11 graspetides, detailed mechanistic insights into these enzymes remain limited. Here, we reconstructed prunipeptin biosynthesis from <i>Streptomyces coelicolor</i> using recombinant PruA and PruB macrocyclase. PruB exhibited kinetic behavior similar to other characterized graspetide cyclases, with a notably higher <i>k</i><sub>cat</sub>, likely due to utilization of an ATP-regeneration system. The X-ray crystal structure of PruB revealed distinct features as compared to groups 1 and 2 enzymes. Site-directed mutagenesis identified critical roles of key residues for the PruB reaction, including the DxR motif conserved in other graspetide cyclases. Additionally, computational modeling of the PruA/PruB cocomplex uncovered substrate interactions and suggested that PruB first catalyzes a macrolactone bond formation on PruA. This study enhances our understanding of ATP-grasp enzyme mechanisms in graspetide biosynthesis and provides insights for engineering these enzymes for future applications.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2525–2534 2525–2534"},"PeriodicalIF":3.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858822","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
Development of a Versatile Plant-Derived Mitochondrial Targeting Sequence Based on a Reporter Protein Sorting Analysis and Biological Information
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-02 DOI: 10.1021/acschembio.4c0062510.1021/acschembio.4c00625
Naoya Abe, Masaki Odahara, Shamitha Rao Morey and Keiji Numata*, 
{"title":"Development of a Versatile Plant-Derived Mitochondrial Targeting Sequence Based on a Reporter Protein Sorting Analysis and Biological Information","authors":"Naoya Abe,&nbsp;Masaki Odahara,&nbsp;Shamitha Rao Morey and Keiji Numata*,&nbsp;","doi":"10.1021/acschembio.4c0062510.1021/acschembio.4c00625","DOIUrl":"https://doi.org/10.1021/acschembio.4c00625https://doi.org/10.1021/acschembio.4c00625","url":null,"abstract":"<p >Methods for the delivery of exogenous substances to specific organelles are important because each organelle functions according to its own role. Specifically, mitochondria play an important role in energy production. Recently, plant mitochondrial transformation via delivery methods to mitochondria has been actively researched. Mitochondrial targeting sequences (MTSs) are essential for transporting bioactive molecules, such as nucleic acids, to mitochondria. However, the selectivity and efficacy of MTSs as carrier molecules in plants are not yet sufficient. In this study, we developed an effective MTS in plants via a quantitative comparison of the targeting functions of several MTSs. The presequence of HSP60 from <i>Nicotiana tabacum</i>, which is highly similar to that of several other model plants, showed high mitochondrial-targeting ability among the MTSs tested. This result suggests the applicability of the HSP60 presequence for MTSs in various plants. We further investigated this HSP60 presequence through stepwise shortening on the basis of secondary structure prediction, aiming to simplify synthesis and increase the solubility of the peptides. As shown by assessment of the mitochondrial targeting ability, the 15 residues from the N-terminus of the HSP60 presequence for the MTS, which is particularly conserved among various model plants, retained a targeting efficacy comparable to that of the full-length HSP60 presequence. This developed sequence from the HSP60 sequence is a promising MTS for transfection into plant mitochondria.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2515–2524 2515–2524"},"PeriodicalIF":3.5,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00625","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains
IF 3.5 2区 生物学
ACS Chemical Biology Pub Date : 2024-12-02 DOI: 10.1021/acschembio.4c0066310.1021/acschembio.4c00663
Fumihiro Ishikawa*, Maya Nohara, Akimasa Miyanaga, Satoki Kuramoto, Natsuki Miyano, Shumpei Asamizu, Fumitaka Kudo, Hiroyasu Onaka, Tadashi Eguchi and Genzoh Tanabe*, 
{"title":"Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains","authors":"Fumihiro Ishikawa*,&nbsp;Maya Nohara,&nbsp;Akimasa Miyanaga,&nbsp;Satoki Kuramoto,&nbsp;Natsuki Miyano,&nbsp;Shumpei Asamizu,&nbsp;Fumitaka Kudo,&nbsp;Hiroyasu Onaka,&nbsp;Tadashi Eguchi and Genzoh Tanabe*,&nbsp;","doi":"10.1021/acschembio.4c0066310.1021/acschembio.4c00663","DOIUrl":"https://doi.org/10.1021/acschembio.4c00663https://doi.org/10.1021/acschembio.4c00663","url":null,"abstract":"<p >Nonribosomal peptides (NRPs), one of the most widespread secondary metabolites in nature, with therapeutically significant activities, are biosynthesized by modular nonribosomal peptide synthetases (NRPSs). Aryl acids contribute to the structural diversity of NRPs as well as nonproteinogenic amino acids and keto acids. We previously confirmed that a single Asn-to-Gly substitution in the 2,3-dihydroxybenzoic acid-activating adenylation (A) domain EntE involved in enterobactin biosynthesis accepts monosubstituted benzoic acid derivatives with nitro, cyano, bromo, and iodo functionalities at the 2 or 3 positions. Here, we showed that the mutant EntE (N235G) accommodates various disubstituted benzoic acid derivatives with halogen, methyl, methoxy, nitro, and cyano functionalities at the 2 and 3 positions and monosubstituted benzoic acid with an alkyne at the 3 position. Structural analysis of the mutant EntE (N235G) with nonhydrolyzable aryl-AMP analogues using 3-chloro-2-methylbenzoic acid and 3-prop-2-ynoxybenzoic acid revealed how bulky 3-chloro-2-methylbenzoic acid and clickable 3-prop-2-ynoxybenzoic acid are recognized by enlarging the substrate-binding pocket of the enzyme. When engineered EntE mutants were coupled with enterobactin and vibriobactin biosynthetic enzymes, 3-hydroxybenzoic acid-, salicylic acid-, and 3-bromo-2-fluorobenzoic acid-containing peptides were produced as early stage intermediates, highlighting the potential of NRP biosynthetic pathway engineering for constructing diverse aryl acid-containing metabolites.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2569–2579 2569–2579"},"PeriodicalIF":3.5,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867757","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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