Wei-Ven Tee, Raechell, Enrico Guarnera, Igor N Berezovsky
{"title":"Sequence and Structure at Play in Designing Allosteric Drugs and Alleviating the Drug Resistance.","authors":"Wei-Ven Tee, Raechell, Enrico Guarnera, Igor N Berezovsky","doi":"10.1016/j.jmb.2025.169206","DOIUrl":"10.1016/j.jmb.2025.169206","url":null,"abstract":"<p><p>The advantages of allosteric drugs in targeting selected members of highly conserved protein families are well established. However, the discovery of allosteric effectors remains largely serendipitous, calling for a rational approach to account for their unique mechanisms and specificity towards protein targets. We show that the high-throughput quantification of allosteric signalling on a single-residue resolution allows one to delineate structural and sequence determinants of allosteric communication that are specific to individual members of a structurally conserved protein family. We demonstrate work of the approach using the matrix metalloproteinases (MMPs), a family of proteases also known to be \"undruggable\" because of their sequence/structural traits. Specifically, latent allosteric sites and effectors were identified and fine-tuned for precise functional modulation of MMP-7, MMP-12 and MMP-13. We also explored the allosteric effects of mutations in driving pathogenesis and emergence of the drug resistance, arguing that they should be considered in diagnostics and drug design frameworks. The multiplicity of allosteric sites and alternative effectors allow, for example, to rescue the therapeutic actions of orthosteric or allosteric drugs in cases of emerged resistance, because of mutations at the drug binding sites or other distal locations. To conclude, using the matrix metalloproteinases as an example of undruggable targets, we highlighted here advantages of the allosteric paradigm in drug design and illuminated a utility of our directed design protocol for the rational design of allosteric drugs.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169206"},"PeriodicalIF":4.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085580","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}
Yulia Kremlyakova, Elizaveta K Vlasova, Daniil Luppov, Mikhail Shugay
{"title":"TCREMP: A Bioinformatic Pipeline for Efficient Embedding of T-cell Receptor Sequences from Immune Repertoire and Single-cell Sequencing Data.","authors":"Yulia Kremlyakova, Elizaveta K Vlasova, Daniil Luppov, Mikhail Shugay","doi":"10.1016/j.jmb.2025.169205","DOIUrl":"10.1016/j.jmb.2025.169205","url":null,"abstract":"<p><p>T-cell receptors (TCRs) expressed by T-lymphocytes can recognize antigens presented on the surface of our cells to tell normal cells from infected and malignant ones. An extremely diverse set of TCRs is generated during T-lymphocyte formation and can be surveyed using high-throughput sequencing to tell the story of past and ongoing immune responses. Proper handling of TCR sequencing data and using it to trace antigen specificities is a challenging bioinformatic task. Here we present TCREMP (TCR embedding via Prototypes), a pipeline to digitize TCR amino acid sequences based on their similarity to commonly observed sequences that can provide a reference point for comparative analysis and aid in decoding antigen specificity prediction across TCR repertoire samples that one may find useful for adaptive immunity studies. Our results show that TCREMP embeddings can efficiently distinguish distinct antigen-specific T-cell populations based on single-cell and Major Histocompatibility Complex (MHCs)-multimer-sorted repertoire sequencing data. TCREMP is freely available at https://github.com/antigenomics/tcremp.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169205"},"PeriodicalIF":4.7,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075242","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":"Exploring the central dogma through the lens of gene expression noise.","authors":"Pieter G A Verhagen, Maike M K Hansen","doi":"10.1016/j.jmb.2025.169202","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169202","url":null,"abstract":"<p><p>Over the past two decades, cell-to-cell heterogeneity has garnered increasing attention due to its critical role in both developmental and pathological processes. This growing interest has been driven, in part, by the advancements in live-cell and single-molecule imaging techniques. These techniques have provided mechanistic insights into how processes, transcription in particular, contribute to gene expression noise and, ultimately, cell-to-cell heterogeneity. More recently, however, research has expanded to explore how downstream steps in the central dogma influence gene expression noise. In this review, we mostly examine the impact of transcriptional processes on the generation of gene expression noise but also discuss how post-transcriptional mechanisms modulate noise and its propagation to the protein level. This evaluation emphasizes the need for further investigation into how processes beyond transcription shape gene expression noise, highlighting unanswered questions that remain in the field.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169202"},"PeriodicalIF":4.7,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954736","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":"GTFKAN: A Novel Microbe-drug Association Prediction Model Based on Graph Transformer and Fourier Kolmogorov-Arnold Networks","authors":"Jiacheng Lai, Zhen Zhang, Bin Zeng, Lei Wang","doi":"10.1016/j.jmb.2025.169201","DOIUrl":"10.1016/j.jmb.2025.169201","url":null,"abstract":"<div><div>Microbes have been shown to be closely related to human health. In recent years, lots of computational methods for predicting microbial-drug association have been proposed. In this manuscript, we introduced a novel predictive model, called GTFKAN, to identify potential microbe-drug associations by combining Graph Transformation Networks (GTN) with Fourier Kolmogorov-Arnold Networks (FKAN). In GTFKAN, we would first compute the Gaussian kernel and functional similarity of microbes and drugs respectively, and then adopt random walk and restart (RWR) methods to enhance these similar features to construct a new microbe-drug heterogeneous network HN. At the same time, we would further calculate the cosine similarity of microbes and diseases to construct another microbe-drug heterogeneous network LDIM. Next, we would input HN into GTN to derive the location and structural features of microorganisms and drugs, and input LDIM into FKAN to extract the hidden higher-order features of microorganisms and drugs, respectively. Finally, we would integrate these two features extracted by GTN and FKAN and feed the integrated features into the MLP classifier to infer potential microbial-drug associations. Moreover, to evaluate the performance of GTFKAN, we compared it with state-of-the-art methods based on well-known public datasets, and the experimental results show that GTFKAN can achieve satisfactory predictive performance. In addition, the results of ablation experiments and case studies also demonstrated the superiority of GTFKAN, which means that GTFKAN may be a useful microbial-drug association prediction tool in the future.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169201"},"PeriodicalIF":4.7,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955189","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":"Allosteric Modulation of SERCA Pumps in Health and Disease: Structural Dynamics, Posttranslational Modifications, and Therapeutic Potential.","authors":"Jana Viskupicova, L Michel Espinoza-Fonseca","doi":"10.1016/j.jmb.2025.169200","DOIUrl":"10.1016/j.jmb.2025.169200","url":null,"abstract":"<p><p>Sarco/endoplasmic reticulum (SR/ER) Ca<sup>2+</sup>-ATPase (SERCA) pumps are ubiquitous membrane proteins in all eukaryotic cells, playing a central role in maintaining intracellular calcium homeostasis by re-sequestering Ca<sup>2+</sup> ions from the cytosol into the SR/ER at the expense of ATP hydrolysis. SERCA pumps are well-characterized components of the calcium transport machinery in the cell, playing a role in various physiological processes, including muscle contraction, energy metabolism, secretion exocytosis, gene expression, synaptic transmission, cell survival, and fertilization. Allosteric regulation of SERCA pumps plays a key role in health and disease, and modulation of the SERCA pumps has emerged as a therapeutic approach for the treatment of cardiovascular, muscular, metabolic, and neurodegenerative disorders. In this review, we provide a comprehensive overview of the structural dynamics underlying allosteric modulation of SERCA, focusing on the effects of endogenous regulatory proteins, Ca<sup>2+</sup> ions, ATP, and small molecules. We also examine in detail the role of posttranslational modifications as allosteric modulators of SERCA function, focusing on the oxidative modifications S-glutathionylation, S-nitrosylation, tyrosine nitration, and carbonylation, and non-oxidative modifications that include SUMOylation, acetylation, O-GlcNAcylation, phosphorylation, and ubiquitination. Finally, we discuss the therapeutic potential and challenges of allosteric modulation of SERCA pumps, including the design of small-molecule effectors, microRNA-based interventions, and targeted strategies that modulate SERCA posttranslational regulation. Overall, this review aims to bridge the gap between the mechanisms underlying allosteric modulation of SERCA and the translation of basic science discoveries into effective therapies targeting SERCA pumps.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169200"},"PeriodicalIF":4.7,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955262","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}
Michele Bonus, Julian Greb, Jaimeen D Majmudar, Markus Boehm, Magdalena Korczynska, Azadeh Nazemi, Alan M Mathiowetz, Holger Gohlke
{"title":"TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction.","authors":"Michele Bonus, Julian Greb, Jaimeen D Majmudar, Markus Boehm, Magdalena Korczynska, Azadeh Nazemi, Alan M Mathiowetz, Holger Gohlke","doi":"10.1016/j.jmb.2025.169196","DOIUrl":"10.1016/j.jmb.2025.169196","url":null,"abstract":"<p><p>Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology and chemoproteomics approaches have generated extensive data on cysteine ligandability, these complementary data types remain largely disconnected. Here, we present TopCysteineDB, a comprehensive resource integrating structural information from the PDB with chemoproteomics data from activity-based protein profiling experiments. Analysis of the complete PDB yielded 264,234 unique cysteines, while the proteomics dataset encompasses 41,898 detectable cysteines across the human proteome. Using TopCovPDB, an automated classification pipeline complemented by manual curation, we identified 787 covalent cysteines and systematically categorized other functional roles, including metal-binding, cofactor-binding, and disulfide bonds. Mapping residue-wise structural information to sequence space enabled cross-referencing between structural and proteomics data, creating a unified view of cysteine ligandability. For TopCySPAL, a machine learning model was developed, integrating structural features and proteomics data, achieving strong predictive performance (AUROC: 0.964, AUPRC: 0.914) and robust generalization to novel cases. TopCysteineDB and TopCySPAL are freely accessible through a webinterface, TopCysteineDBApp (https://topcysteinedb.hhu.de/), designed to facilitate exploration of cysteine sites across the human proteome. The interface provides an interactive visualization featuring a color-coded mapping of chemoproteomics data onto cysteine site structures and the highlighting of identified peptide sequences. It offers customizable dataset downloads and ligandability predictions for user-provided structures. This resource advances targeted covalent inhibitor design by providing integrated access to previously dispersed data types and enabling systematic analysis and prediction of cysteine ligandability.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169196"},"PeriodicalIF":4.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954853","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}
Ainan Geng , Rohit Roy , Stephanie Gu , Serafima Guseva , Supriya Pratihar , Yeongjoon Lee , Linshu Li , Isaac J. Kimsey , Mark A. Wilson , Hashim M. Al-Hashimi
{"title":"Insight into the Conformational Ensembles Formed by U–U and T–T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations","authors":"Ainan Geng , Rohit Roy , Stephanie Gu , Serafima Guseva , Supriya Pratihar , Yeongjoon Lee , Linshu Li , Isaac J. Kimsey , Mark A. Wilson , Hashim M. Al-Hashimi","doi":"10.1016/j.jmb.2025.169197","DOIUrl":"10.1016/j.jmb.2025.169197","url":null,"abstract":"<div><div>Nucleic acid base pairs interconvert between alternative conformations on a free energy landscape, and these dynamics play critical roles in recognition, folding, and catalysis. U–U and T–T mismatches can adopt two nearly isoenergetic wobble conformations, distinguished by their relative shearing displacements. Experimental NMR evidence suggests that these conformations dynamically interconvert in RNA motifs containing tandem U–U mismatches. However, whether such motions occur ubiquitously across U–U and T–T mismatches remains unknown, as high-resolution nucleic acid structures typically report only a single conformation. Here, we used NMR spectroscopy, a structure-based survey of the Protein Data Bank, and molecular dynamics (MD) simulations to investigate wobble dynamics in U–U and T–T mismatches when flanked by canonical Watson-Crick base pairs in RNA and DNA duplexes. The structure-based survey revealed that U–U mismatches have propensities to adopt alternative wobble conformations even when controlling for sequence and identified potential intermediates along the wobble transition. Off-resonance <em>R</em><sub>1ρ</sub> relaxation dispersion experiments detected no micro- to millisecond dynamics for U–U mismatches in duplex RNA and T–T mismatches in duplex DNA. However, alternative conformer refinement of the electron density in X-ray structures, inter-proton NOEs, carbonyl carbon chemical shifts, an RDC-derived conformational ensemble, and MD simulations indicated that U–U and T–T mismatches exist in a dynamic equilibrium between two wobble conformations, with the minor state exceeding 30% and the transitions occurring on the nanosecond timescale. Our findings suggest that U–U and T–T ubiquitously undergo sub-microsecond wobble motions, contributing to the energetic landscape and dynamic plasticity of nucleic acids, with important implications for processes that generate and act on these mismatches.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169197"},"PeriodicalIF":4.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957904","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}
Olivia N P Zbihley, Katherine Johnson, Luke R Frietze, Wen Zhang, Marcus Foo, Hoang Anh V Tran, Nicolas Chevrier, Tao Pan
{"title":"Mammalian Queuosine tRNA Modification Impacts Translation to Enhance Cell Proliferation and MHC-II Expression.","authors":"Olivia N P Zbihley, Katherine Johnson, Luke R Frietze, Wen Zhang, Marcus Foo, Hoang Anh V Tran, Nicolas Chevrier, Tao Pan","doi":"10.1016/j.jmb.2025.169188","DOIUrl":"10.1016/j.jmb.2025.169188","url":null,"abstract":"<p><p>Queuosine (Q) is a conserved tRNA modification in the wobble anticodon position of tRNAs that read codons of Tyr/His/Asn/Asp. Eukaryotic tRNA Q-modification requires the metabolite queuine - derived from diet or catabolism of the gut microbiome - and a host-genome encoded enzyme complex, QTRT1/QTRT2. tRNA Q-modification has been shown to regulate translational efficiency, but the response of the mammalian transcriptome and tRNAome to tRNA Q-modification in the context of cell proliferation has not been thoroughly investigated. Using cells that differ only in their tRNA Q-modification levels, we found that both human HEK293T cultures and the primary, murine bone marrow-derived dendritic cells (BMDCs) proliferate faster when tRNA Q-modification level is high. We carried out tRNA-seq and mRNA-seq to elucidate the molecular mechanisms underlying this phenotype, revealing distinct tRNA modification and transcriptome changes associated with altered proliferation. In both cell types, the m<sup>2</sup><sub>2</sub>G tRNA modification is positively correlated to Q-modification, consistent with its reported role in enhancing translational efficiency. We also find that elevated Q-modification levels result in transcriptome changes, but in a context-dependent manner. In HEK293T cells, upregulated genes are in catabolic processes and signaling pathway activation; whereas in BMDCs, upregulated genes are in immune response mediation, proliferation, and immunoglobulin diversification. Codon usage analysis of differentially expressed transcripts is consistent with Q-modification enhancing the translation of ribosomal proteins, which increases cell proliferation. We also find that tRNA Q-modification increases surface presentation of MHC-II in BMDCs. Our results provide insights into the broader implications of tRNA Q-modifications in regulating diverse biological functions.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169188"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955969","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}
Konstantin M. Petricek , Marieluise Kirchner , Manuela Sommerfeld , Heike Stephanowitz , Marie F. Kiefer , Yueming Meng , Sarah Dittrich , Henriette E. Dähnhardt , Knut Mai , Eberhard Krause , Philipp Mertins , Sylvia J. Wowro , Michael Schupp
{"title":"An acetylated Lysine Residue of Its Low-glucose Inhibitory Domain Controls Activity and Protein Interactions of ChREBP","authors":"Konstantin M. Petricek , Marieluise Kirchner , Manuela Sommerfeld , Heike Stephanowitz , Marie F. Kiefer , Yueming Meng , Sarah Dittrich , Henriette E. Dähnhardt , Knut Mai , Eberhard Krause , Philipp Mertins , Sylvia J. Wowro , Michael Schupp","doi":"10.1016/j.jmb.2025.169189","DOIUrl":"10.1016/j.jmb.2025.169189","url":null,"abstract":"<div><div>Carbohydrate response element-binding protein (ChREBP) is a transcription factor activated by glucose metabolites that orchestrates the expression of genes involved in glycolysis, <em>de novo</em> lipogenesis, and ATP homeostasis. Inadequate ChREBP activity impairs the cellular adaptations to glucose exposure and in humans associates with dyslipidemia, fatty liver disease, and type 2 diabetes. ChREBP activity is regulated by cytosolic-nuclear translocation involving its low-glucose inhibitory domain (LID). Whether this domain is targeted by post-translational lysine acetylation is unknown. Here we report a novel LID acetylation site that controls activity and protein interactions of ChREBP. Mutation of this residue increased glucose-induced activity and target gene expression of ChREBP. Mechanistically, mutant ChREBP protein showed more nuclear localization and enhanced genomic binding to a target promoter. Interactions with proteins that exhibit differential binding upon glucose exposure were attenuated by the mutation, demonstrating the importance of the LID in the formation of the protein interactome. Particularly interactions with 14-3-3 proteins, factors that regulate cytosolic/nuclear trafficking of ChREBP, were reduced, whereas interactions with proteins of the nucleosome remodeling deacetylase complex (NuRD) were increased. These molecular insights may shape new therapeutic strategies to target ChREBP activity and counteract metabolic diseases.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169189"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951797","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}
Rubayet Elahi, Sebastian Mesones Mancilla, Montana L Sievert, Luciana Ribeiro Dinis, Opeoluwa Adewale-Fasoro, Alexis Mann, Yonatan Zur, Sean T Prigge
{"title":"Decoding the Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance.","authors":"Rubayet Elahi, Sebastian Mesones Mancilla, Montana L Sievert, Luciana Ribeiro Dinis, Opeoluwa Adewale-Fasoro, Alexis Mann, Yonatan Zur, Sean T Prigge","doi":"10.1016/j.jmb.2025.169156","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169156","url":null,"abstract":"<p><p>Post-transcriptional tRNA modifications are essential for accurate and efficient protein translation across all organisms. The apicoplast organelle genome of Plasmodium falciparum contains a minimal set of 25 complete tRNA isotypes, making it an ideal model for studying minimal translational machinery. Efficient decoding of mRNA codons by this limited tRNA set depends on post-transcriptional modifications. In this study, we sought to define the minimal set of tRNA-modifying enzymes. Using comparative genomics and apicoplast protein localization prediction tools, we identified 16 nucleus-encoded tRNA-modifying enzymes predicted to localize to the apicoplast. Experimental studies confirmed apicoplast localization for 14 enzymes, including two with dual localization. Combining an apicoplast metabolic bypass parasite line with gene disruption tools, we disrupted 12 of the 14 apicoplast-localized enzymes. Six of these enzymes were found to be essential for parasite survival, and six were dispensable. All six essential enzymes are thought to catalyze modifications in the anticodon loop of tRNAs, and their deletions resulted in apicoplast disruption. Of the two genes refractory to deletion, one exhibited dual localization, suggesting essential functions outside the apicoplast. The other, which appears to localize solely to the apicoplast, may play an indispensable role that is not circumvented by our metabolic bypass. Our findings suggest the apicoplast translation system relies on a minimal set of tRNA modifications concentrated in the anticodon loop. This work advances our understanding of minimal translational machinery in reduced organelles, such as the apicoplast, with promising applications in synthetic biology.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169156"},"PeriodicalIF":4.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955303","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}