ACS Chemical Biology最新文献

{"title":"PhOxi-seq Detects Enzyme-Dependent m2G in Multiple RNA Types","authors":"Marie Klimontova,&nbsp;Kimberley Chung Kim Chung,&nbsp;Han Zhang,&nbsp;Tony Kouzarides,&nbsp;Andrew J. Bannister* and Ryan Hili*,&nbsp;","doi":"10.1021/acschembio.4c0054810.1021/acschembio.4c00548","DOIUrl":"https://doi.org/10.1021/acschembio.4c00548https://doi.org/10.1021/acschembio.4c00548","url":null,"abstract":"<p >In recent years, RNA-modifying enzymes have gained significant attention due to their impact on critical RNA-based processes and, consequently, human pathology. However, identifying sites of modifications throughout the transcriptome remains challenging largely due to the lack of accurate and sensitive detection technologies. Recently, we described PhOxi-seq as a method capable of confirming known sites of m²G within abundant classes of RNA, namely, purified rRNA and purified tRNA. Here, we further explore the selectivity of PhOxi-seq and describe an optimized PhOxi-seq workflow, coupled to a novel bioinformatic pipeline, that is capable of detecting enzyme-dependent m²G sites throughout the transcriptome. In this way, we generated a database of potential THUMPD3-dependent m²G sites in multiple RNA classes within a human cancer cell line and further identify potential non-THUMPD3 controlled m²G sites. These potential sites should serve as the basis for further confirmation studies for m²G within the human transcriptome.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2399–2405 2399–2405"},"PeriodicalIF":3.5,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858570","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}

{"title":"Correction to “Targeting the Early Step of Building Block Organization in Viral Capsid Assembly”","authors":"Ayala Lampel,&nbsp;Yaron Bram,&nbsp;Anat Ezer,&nbsp;Ronit Shaltiel-Karyo,&nbsp;Jamil S. Saad,&nbsp;Eran Bacharach and Ehud Gazit*,&nbsp;","doi":"10.1021/acschembio.4c0077810.1021/acschembio.4c00778","DOIUrl":"https://doi.org/10.1021/acschembio.4c00778https://doi.org/10.1021/acschembio.4c00778","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2594 2594"},"PeriodicalIF":3.5,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858861","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}

{"title":"Correction to “Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from Marine Cyanobacterium Moorena producens JHB Discovered via Coculture with Candida albicans”","authors":"Thuan-Ethan Ngo,&nbsp;Andrew Ecker,&nbsp;Byeol Ryu,&nbsp;Aurora Guild,&nbsp;Ariana Remmel,&nbsp;Paul D. Boudreau,&nbsp;Kelsey L. Alexander,&nbsp;C. Benjamin Naman,&nbsp;Evgenia Glukhov,&nbsp;Nicole E. Avalon,&nbsp;Vikram V. Shende,&nbsp;Lamar Thomas,&nbsp;Samira Dahesh,&nbsp;Victor Nizet,&nbsp;Lena Gerwick and William H. Gerwick*,&nbsp;","doi":"10.1021/acschembio.4c0073910.1021/acschembio.4c00739","DOIUrl":"https://doi.org/10.1021/acschembio.4c00739https://doi.org/10.1021/acschembio.4c00739","url":null,"abstract":"","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2593 2593"},"PeriodicalIF":3.5,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00739","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858841","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}

{"title":"A Stable Dehydratase Complex Catalyzes the Formation of Dehydrated Amino Acids in a Class V Lanthipeptide","authors":"George T. Randall,&nbsp;Emily S. Grant-Mackie,&nbsp;Shayhan Chunkath,&nbsp;Elyse T. Williams,&nbsp;Martin J. Middleditch,&nbsp;Meifeng Tao,&nbsp;Paul W. R. Harris,&nbsp;Margaret A. Brimble and Ghader Bashiri*,&nbsp;","doi":"10.1021/acschembio.4c0063710.1021/acschembio.4c00637","DOIUrl":"https://doi.org/10.1021/acschembio.4c00637https://doi.org/10.1021/acschembio.4c00637","url":null,"abstract":"<p >Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that bear the characteristic lanthionine (Lan) or methyllanthionine (MeLan) thioether linkages. (Me)Lan moieties bestow lanthipeptides with robust stability and diverse antimicrobial, anticancer, and antiallodynic activities. Installation of (Me)Lan requires dehydration of serine and threonine residues to 2,3-dehydroalanine (Dha) and (<i>Z</i>)-2,3-dehydrobutyrine (Dhb), respectively. LxmK and LxmY enzymes comprise the biosynthetic machinery of a newly discovered class V lanthipeptide, lexapeptide, and are proposed to catalyze the dehydration of serine and threonine residues in the precursor peptide. We demonstrate that LxmK and LxmY form a stable dehydratase complex to dehydrate precursor peptides. In addition, we present crystal structures of the LxmKY heterodimer, revealing structural and mechanistic features that enable iterative phosphorylation and elimination by the LxmKY complex. These findings provide molecular insights into class V lanthionine synthetases and lay the foundation for their applications as enzymatic tools in the biosynthesis of exquisitely modified peptides.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2548–2556 2548–2556"},"PeriodicalIF":3.5,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867872","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}

{"title":"Single-Cell Multiomics Identifies Glycan Epitope LacNAc as a Potential Cell-Surface Effector Marker of Peripheral T Cells in Bladder Cancer Patients","authors":"Xiangyu Wu,&nbsp;Zihan Zhao,&nbsp;Wenhao Yu,&nbsp;Siyang Liu,&nbsp;Meng Zhou,&nbsp;Ning Jiang,&nbsp;Xiang Du,&nbsp;Xin Yang,&nbsp;Jinbang Chen,&nbsp;Hongqian Guo* and Rong Yang*,&nbsp;","doi":"10.1021/acschembio.4c0063510.1021/acschembio.4c00635","DOIUrl":"https://doi.org/10.1021/acschembio.4c00635https://doi.org/10.1021/acschembio.4c00635","url":null,"abstract":"<p >Cancer is a systemic disease continuously monitored and responded to by the human global immune system. Peripheral blood immune cells, integral to this surveillance, exhibit variable phenotypes during tumor progression. Glycosylation, as one of the most prevalent and significant post-translational modifications of proteins, plays a crucial role in immune system recognition and response. Glycan analysis has become a key method for biomarker discovery. LacNAc, a prominent glycosylation modification, regulates immune cell activity and function. Therefore, we applied our previously developed single-cell glycomic multiomics to analyze peripheral blood in cancer patients. This platform utilizes chemoenzymatic labeling with DNA barcodes for detecting and quantifying LacNAc levels at single-cell resolution without altering the transcriptional status of immune cells. For the first time, we systematically integrated single-cell transcriptome, T cell receptor (TCR) repertoire, and glycan epitope LacNAc analyses in tumor-patient-derived peripheral blood. Our integrated analysis reveals that lower-stage bladder cancer patients showed significantly higher levels of LacNAc in peripheral T cells, and peripheral T cells with high levels of cell-surface LacNAc exhibit higher cytotoxicity and TCR clonal expansion. In summary, we identified LacNAc as a potential cell-surface effector marker for peripheral T cells in bladder cancer patients, which enhances our understanding of peripheral immune cells and offers potential advancements in liquid biopsy.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2535–2547 2535–2547"},"PeriodicalIF":3.5,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142867870","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}

{"title":"γ-Secretase Cleaves Bifunctional Fatty Acid-Conjugated Small Molecules with Amide Bonds in Mammalian Cells","authors":"Kai Tahara,&nbsp;Akinobu Nakamura,&nbsp;Xiaotong Wang,&nbsp;Keishi Mitamura,&nbsp;Yuki Ichihashi,&nbsp;Keiko Kano,&nbsp;Emi Mishiro-Sato,&nbsp;Kazuhiro Aoki,&nbsp;Yasuteru Urano,&nbsp;Toru Komatsu and Shinya Tsukiji*,&nbsp;","doi":"10.1021/acschembio.4c0043210.1021/acschembio.4c00432","DOIUrl":"https://doi.org/10.1021/acschembio.4c00432https://doi.org/10.1021/acschembio.4c00432","url":null,"abstract":"<p >Connecting two small molecules, such as ligands, fluorophores, or lipids, together via a linker with amide bonds is a widely used strategy to generate synthetic bifunctional molecules for various biological and biomedical applications. Such bifunctional molecules have been used in live-cell experiments under the assumption that they should be stable in cells. However, we recently found that a membrane-targeting bifunctional molecule, composed of a lipopeptide and the small-molecule ligand trimethoprim, referred to as mgcTMP, underwent amide-bond cleavage in mammalian cells. In this work, we first identified γ-secretase as the major protease degrading mgcTMP in cells. We next investigated the intracellular degradation of several different types of amide-linked bifunctional compounds and found that <i>N</i>-terminally fatty acid-conjugated small molecules are susceptible to γ-secretase-mediated amide-bond cleavage. In contrast, amide-linked bifunctional molecules composed of two small molecules, such as ligands and hydrophobic groups, which lack lipid modification, did not undergo intracellular degradation. These findings highlight a previously overlooked consideration for the development and application of lipid-based bifunctional molecules in chemical biology research.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2438–2450 2438–2450"},"PeriodicalIF":3.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858810","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}

{"title":"The TRIM33 Bromodomain Recognizes Histone Lysine Lactylation","authors":"Raymundo Nuñez,&nbsp;Paul F. W. Sidlowski,&nbsp;Erica A. Steen,&nbsp;Sarah L. Wynia-Smith,&nbsp;Daniel J. Sprague,&nbsp;Robert F. Keyes and Brian C. Smith*,&nbsp;","doi":"10.1021/acschembio.4c0024810.1021/acschembio.4c00248","DOIUrl":"https://doi.org/10.1021/acschembio.4c00248https://doi.org/10.1021/acschembio.4c00248","url":null,"abstract":"<p >Histone lysine lactylation (Kla) regulates inflammatory gene expression in activated macrophages and mediates the polarization of inflammatory (M1) to reparative (M2) macrophages. However, the molecular mechanisms and key protein players involved in Kla-mediated transcriptional changes are unknown. As Kla is structurally similar to lysine acetylation (Kac), which is bound by bromodomains, we hypothesized that bromodomain-containing proteins bind histone Kla. Here, we screened 28 recombinantly expressed bromodomains for binding to histone Kla peptides via AlphaScreen assays. TRIM33 was the sole bromodomain tested that bound histone Kla peptides. TRIM33 attenuates inflammatory genes during late-stage macrophage activation; thus, TRIM33 provides a potential link between histone Kla and macrophage polarization. Orthogonal biophysical techniques, including isothermal titration calorimetry and protein-detected nuclear magnetic resonance, confirmed the submicromolar binding affinity of the TRIM33 bromodomain to both Kla and Kac histone post-translational modifications. Sequence alignments of human bromodomains revealed a unique glutamic acid residue within the TRIM33 binding pocket that we found confers TRIM33 specificity for binding Kla compared with other bromodomains. Molecular modeling of interactions of Kla with the TRIM33 bromodomain binding pocket and site-directed mutagenesis of glutamic acid confirmed the critical role of this residue in the selective recognition of Kla by TRIM33. Collectively, our findings implicate TRIM33, a bromodomain-containing protein, as a novel reader of histone Kla, potentially bridging the gap between histone Kla and macrophage polarization. This study enhances our understanding of the regulatory role of histone Kla in macrophage-mediated inflammation and offers insights into the underlying structural and biophysical mechanisms.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2418–2428 2418–2428"},"PeriodicalIF":3.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858800","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}

{"title":"Recruitment to the Proteasome Is Necessary but Not Sufficient for Chemically Induced, Ubiquitin-Independent Degradation of Native Proteins.","authors":"Madeline Balzarini, Joel Tong, Weijun Gui, Isuru M Jayalath, Bin-Bin Schell, Thomas Kodadek","doi":"10.1021/acschembio.4c00422","DOIUrl":"10.1021/acschembio.4c00422","url":null,"abstract":"<p><p>Targeted protein degradation (TPD) is a promising strategy for drug development. Most degraders function by forcing the association of the target protein (TP) with an E3 Ubiquitin (Ub) ligase, which, in favorable cases, results in the polyubiquitylation of the TP and its subsequent degradation by the 26S proteasome. An alternative strategy would be to create chemical dimerizers that bypass the requirement for polyubiquitylation by recruiting the target protein directly to the proteasome. Direct-to-proteasome degraders (DPDs) may exhibit different characteristics than ubiquitin-dependent degraders, but few studies of this type of TPD have been published, largely due to the dearth of suitable proteasome ligands. To facilitate studies of DPDs, we report here a mammalian cell line in which the HaloTag protein is fused to the proteasome via Rpn13, one of the ubiquitin receptors. In these cells, a chloroalkane serves as a covalent proteasome ligand surrogate. We show that chimeric molecules comprised of a chloroalkane linked to a ligand for the BET family of proteins or the Cdk2/7/9 family of kinases result in ubiquitin-independent degradation of some of these target proteins. We use this system, the first that allows facile degradation of native proteins in a ubiquitin-independent fashion, to probe two issues: the effect of varying the length of the linker connecting the chloroalkane and the target ligand and the selectivity of degradation within the protein families engaged by the target ligand.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2323-2335"},"PeriodicalIF":4.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491016","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}

{"title":"Understanding Polysulfide-Mediated Papain Inhibition and Differentiating between Disulfide vs Persulfide Formation","authors":"Meg Shieh,&nbsp;Anna Y. Chung,&nbsp;Stephen Lindahl,&nbsp;Melany Veliz,&nbsp;Charlotte A. Bain and Ming Xian*,&nbsp;","doi":"10.1021/acschembio.4c0057310.1021/acschembio.4c00573","DOIUrl":"https://doi.org/10.1021/acschembio.4c00573https://doi.org/10.1021/acschembio.4c00573","url":null,"abstract":"<p >Protein cysteine residues are sensitive to redox-regulating molecules, including reactive sulfur species (RSS). As an important member of the RSS family, polysulfides are known to react with protein cysteines to form persulfides and disulfides, both affecting protein functions. In this work, we studied how polysulfides could impact cysteine proteases through careful mechanistic and kinetic studies. The model protein papain was treated with different polysulfides to elucidate the efficacy of polysulfides as inhibitors for this protein. We also explored the effects of different reductants that could regenerate papain activity after polysulfide-mediated inhibition. A triarylphosphine reagent, TXPTS, was found to be efficient in differentiating between papain persulfidation and disulfide formation.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2487–2493 2487–2493"},"PeriodicalIF":3.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858779","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}

{"title":"Mycobacterium tuberculosis Mce3R TetR-like Repressor Forms an Asymmetric Four-Helix Bundle and Binds a Nonpalindrome Sequence†","authors":"Navanjalee T. Panagoda,&nbsp;Gábor Balázsi and Nicole S. Sampson*,&nbsp;","doi":"10.1021/acschembio.4c0068710.1021/acschembio.4c00687","DOIUrl":"https://doi.org/10.1021/acschembio.4c00687https://doi.org/10.1021/acschembio.4c00687","url":null,"abstract":"<p ><i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), the causative agent of tuberculosis, is a major global health concern. TetR family repressors (TFRs) are important for <i>Mtb</i>’s adaptation to the human host environment. Our study focuses on one notable <i>Mtb</i> repressor, Mce3R, composed of an unusual double TFR motif. Mce3R-regulated genes encode enzymes implicated in cholesterol metabolism, resistance against reactive oxygen species, and lipid transport activities important for <i>Mtb</i> survival and persistence in the host and for the cellular activity of a 6-azasteroid derivative. Here, we present the structure of Mce3R bound to its DNA operator, unveiling a unique asymmetric assembly previously unreported. We obtained a candidate DNA-binding motif through MEME motif analysis, comparing intergenic regions of <i>mce3R</i> orthologues and identifying nonpalindromic regions conserved between orthologues. Using an electrophoretic mobility shift assay (EMSA), we confirmed that Mce3R binds to a 123-bp sequence that includes the predicted motif. Using scrambled DNA and DNA oligonucleotides of varying lengths with sequences from the upstream region of the <i>yrbE3A</i> (<i>mce3</i>) operon, we elucidated the operator region to be composed of two Mce3R binding sites, each a 25-bp asymmetric sequence separated by 53 bp. Mce3R binds with a higher affinity to the downstream site with a <i>K</i>_d of 2.4 ± 0.7 nM. The cryo-EM structure of Mce3R bound to the 123-bp sequence was refined to a resolution of 2.51 Å. Each Mce3R monomer comprises 21 α-helices (α1-α21) folded into an asymmetric TFR-like structure with a core asymmetric four-helix bundle. This complex has two nonidentical HTH motifs and a single ligand-binding domain. The two nonidentical HTHs from each TFR bind within the high-affinity, nonpalindromic operator motif, with Arg53 and Lys262 inserted into the major groove. Site-directed mutagenesis of Arg53 to alanine abrogated DNA binding, validating the Mce3R/DNA structure obtained. Among 811,645 particles, 63% were Mce3R homodimer bound to two duplex oligonucleotides. Mce3R homodimerizes primarily through α15, and each monomer binds to an identical site in the DNA duplex oligonucleotide.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"19 12","pages":"2580–2592 2580–2592"},"PeriodicalIF":3.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00687","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142858783","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}