ACS Chemical Biology最新文献

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, 2017). 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. 2016,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.

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 N-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.

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.

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.

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 in vivo coinfection experiments that probe interspecies interactions between the opportunistic pathogens Pseudomonas aeruginosa and Burkholderia multivorans involving their LuxI/LuxR-type QS circuits. Using a Caenorhabditis elegans 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 P. aeruginosa and B. multivorans, 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 P. aeruginosa and B. multivorans 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 P. aeruginosa and B. multivorans and that it can contribute to coinfection severity with these two species.

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.

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 Streptomyces coelicolor using recombinant PruA and PruB macrocyclase. PruB exhibited kinetic behavior similar to other characterized graspetide cyclases, with a notably higher k_cat, 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.

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.

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 Nicotiana tabacum, 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.

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.