1
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Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024; 300:107679. [PMID: 39154912 DOI: 10.1016/j.jbc.2024.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Transfer RNAs (tRNA) are essential small non-coding RNAs that enable the translation of genomic information into proteins in all life forms. The principal function of tRNAs is to bring amino acid building blocks to the ribosomes for protein synthesis. In the ribosome, tRNAs interact with messenger RNA (mRNA) to mediate the incorporation of amino acids into a growing polypeptide chain following the rules of the genetic code. Accurate interpretation of the genetic code requires tRNAs to carry amino acids matching their anticodon identity and decode the correct codon on mRNAs. Errors in these steps cause the translation of codons with the wrong amino acids (mistranslation), compromising the accurate flow of information from DNA to proteins. Accumulation of mutant proteins due to mistranslation jeopardizes proteostasis and cellular viability. However, the concept of mistranslation is evolving, with increasing evidence indicating that mistranslation can be used as a mechanism for survival and acclimatization to environmental conditions. In this review, we discuss the central role of tRNAs in modulating translational fidelity through their dynamic and complex interplay with translation factors. We summarize recent discoveries of mistranslating tRNAs and describe the underlying molecular mechanisms and the specific conditions and environments that enable and promote mistranslation.
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Affiliation(s)
- Dominik B Schuntermann
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Noah M Reynolds
- School of Integrated Sciences, Sustainability, and Public Health, University of Illinois Springfield, Springfield, Illinois, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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2
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Kalita B, Martinez-Cebrian G, McEvoy J, Allensworth M, Knight M, Magli A, Perlingeiro RCR, Dyer MA, Stewart E, Dynlacht BD. PAX fusion proteins deregulate gene networks controlling mitochondrial translation in pediatric rhabdomyosarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606039. [PMID: 39211084 PMCID: PMC11360909 DOI: 10.1101/2024.07.31.606039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Alveolar rhabdomyosarcoma (ARMS) patients harboring PAX3-FOXO1 and PAX7-FOXO1 fusion proteins exhibit a greater incidence of tumor relapse, metastasis, and poor survival outcome, thereby underscoring the urgent need to develop effective therapies to treat this subtype of childhood cancer. To uncover mechanisms that contribute to tumor initiation, we developed a novel muscle progenitor model and used epigenomic approaches to unravel genome re-wiring events mediated by PAX3/7 fusion proteins. Importantly, these regulatory mechanisms are conserved across established ARMS cell lines, primary tumors, and orthotopic-patient derived xenografts. Among the key targets of PAX3- and PAX7-fusion proteins, we identified a cohort of oncogenes, FGF receptors, and genes essential for mitochondrial metabolism and protein translation, which we successfully targeted in preclinical trials. Our data suggest an explanation for the relative paucity of recurring mutations in this tumor, provide a compelling list of actionable targets, and suggest promising new strategies to treat this tumor.
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3
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Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024; 300:107488. [PMID: 38908752 PMCID: PMC11301382 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
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4
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Schultz SK, Katanski CD, Halucha M, Peña N, Fahlman RP, Pan T, Kothe U. Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness. Proc Natl Acad Sci U S A 2024; 121:e2401154121. [PMID: 38889150 PMCID: PMC11214086 DOI: 10.1073/pnas.2401154121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Almost all elongator tRNAs (Transfer RNAs) harbor 5-methyluridine 54 and pseudouridine 55 in the T arm, generated by the enzymes TrmA and TruB, respectively, in Escherichia coli. TrmA and TruB both act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wild type. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modifications such as acp3U47. While overall protein synthesis is not affected in ΔtrmA and ΔtruB strains, the translation of a subset of codons is significantly impaired. As a consequence, we observe translationally reduced expression of many specific proteins, that are either encoded with a high frequency of these codons or that are large proteins. The resulting proteome changes are not related to a specific growth phenotype, but overall cellular fitness is impaired upon deleting trmA and truB in accordance with a general protein synthesis impact. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing tRNA maturation, tRNA aminoacylation, and translation, thereby improving cellular fitness irrespective of the growth conditions which explains the conservation of trmA and truB.
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Affiliation(s)
- Sarah K. Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, ABT1K 3M4, Canada
| | | | - Mateusz Halucha
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL60637
| | - Noah Peña
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL60637
| | - Richard P. Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, ABT6G 2H7, Canada
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL60637
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, ABT1K 3M4, Canada
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5
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Masuda I, Hou YM. A tRNA modification pattern that facilitates interpretation of the genetic code. Front Microbiol 2024; 15:1415100. [PMID: 38933027 PMCID: PMC11199890 DOI: 10.3389/fmicb.2024.1415100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Interpretation of the genetic code from triplets of nucleotides to amino acids is fundamental to life. This interpretation is achieved by cellular tRNAs, each reading a triplet codon through its complementary anticodon (positions 34-36) while delivering the amino acid charged to its 3'-end. This amino acid is then incorporated into the growing polypeptide chain during protein synthesis on the ribosome. The quality and versatility of the interpretation is ensured not only by the codon-anticodon pairing, but also by the post-transcriptional modifications at positions 34 and 37 of each tRNA, corresponding to the wobble nucleotide at the first position of the anticodon and the nucleotide on the 3'-side of the anticodon, respectively. How each codon is read by the matching anticodon, and which modifications are required, cannot be readily predicted from the codon-anticodon pairing alone. Here we provide an easily accessible modification pattern that is integrated into the genetic code table. We focus on the Gram-negative bacterium Escherichia coli as a model, which is one of the few organisms whose entire set of tRNA modifications and modification genes is identified and mapped. This work provides an important reference tool that will facilitate research in protein synthesis, which is at the core of the cellular life.
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6
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Shao B, Yan J, Zhang J, Liu L, Chen Y, Buskirk AR. Riboformer: a deep learning framework for predicting context-dependent translation dynamics. Nat Commun 2024; 15:2011. [PMID: 38443396 PMCID: PMC10915169 DOI: 10.1038/s41467-024-46241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts in these data and identify sequence determinants of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. When trained on an unbiased dataset, Riboformer corrects experimental artifacts in previously unseen datasets, which reveals subtle differences in synonymous codon translation and uncovers a bottleneck in translation elongation. Further, we show that Riboformer can be combined with in silico mutagenesis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Lili Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ye Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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7
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Smith TJ, Giles RN, Koutmou KS. Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation. Semin Cell Dev Biol 2024; 154:105-113. [PMID: 37385829 DOI: 10.1016/j.semcdb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
RNAs are central to protein synthesis, with ribosomal RNA, transfer RNAs and messenger RNAs comprising the core components of the translation machinery. In addition to the four canonical bases (uracil, cytosine, adenine, and guanine) these RNAs contain an array of enzymatically incorporated chemical modifications. Transfer RNAs (tRNAs) are responsible for ferrying amino acids to the ribosome, and are among the most abundant and highly modified RNAs in the cell across all domains of life. On average, tRNA molecules contain 13 post-transcriptionally modified nucleosides that stabilize their structure and enhance function. There is an extensive chemical diversity of tRNA modifications, with over 90 distinct varieties of modifications reported within tRNA sequences. Some modifications are crucial for tRNAs to adopt their L-shaped tertiary structure, while others promote tRNA interactions with components of the protein synthesis machinery. In particular, modifications in the anticodon stem-loop (ASL), located near the site of tRNA:mRNA interaction, can play key roles in ensuring protein homeostasis and accurate translation. There is an abundance of evidence indicating the importance of ASL modifications for cellular health, and in vitro biochemical and biophysical studies suggest that individual ASL modifications can differentially influence discrete steps in the translation pathway. This review examines the molecular level consequences of tRNA ASL modifications in mRNA codon recognition and reading frame maintenance to ensure the rapid and accurate translation of proteins.
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Affiliation(s)
- Tyler J Smith
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Rachel N Giles
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA.
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8
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Maharjan S, Gamper H, Yamaki Y, Henley RY, Li NS, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou YM. Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569632. [PMID: 38106193 PMCID: PMC10723379 DOI: 10.1101/2023.12.09.569632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.
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9
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Nakano Y, Gamper H, McGuigan H, Maharjan S, Sun Z, Krishnan K, Yigit E, Li NS, Piccirilli JA, Kleiner R, Nichols N, Hou YM. Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569604. [PMID: 38106225 PMCID: PMC10723452 DOI: 10.1101/2023.12.09.569604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.
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10
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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11
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Shao B, Yan J, Zhang J, Buskirk AR. Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538053. [PMID: 37163112 PMCID: PMC10168224 DOI: 10.1101/2023.04.24.538053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined with in silico mutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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12
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Masuda I, Hou YM. Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen. STAR Protoc 2023; 4:102196. [PMID: 36995932 PMCID: PMC10074243 DOI: 10.1016/j.xpro.2023.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/31/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).1.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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13
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Abstract
As rapidly growing bacteria begin to exhaust essential nutrients, they enter a state of reduced growth, ultimately leading to stasis or quiescence. Investigation of the response to nutrient limitation has focused largely on the consequences of amino acid starvation, known as the "stringent response." Here, an uncharged tRNA in the A-site of the ribosome stimulates the ribosome-associated protein RelA to synthesize the hyperphosphorylated guanosine nucleotides (p)ppGpp that mediate a global slowdown of growth and biosynthesis. Investigations of the stringent response typically employ experimental methodologies that rapidly stimulate (p)ppGpp synthesis by abruptly increasing the fraction of uncharged tRNAs, either by explicit amino starvation or by inhibition of tRNA charging. Consequently, these methodologies inhibit protein translation, thereby interfering with the cellular pathways that respond to nutrient limitation. Thus, complete and/or rapid starvation is a problematic experimental paradigm for investigating bacterial responses to physiologically relevant nutrient-limited states.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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14
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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15
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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16
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McFeely CAL, Dods KK, Patel SS, Hartman MCT. Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA. Nucleic Acids Res 2022; 50:11374-11386. [PMID: 36300637 PMCID: PMC9638912 DOI: 10.1093/nar/gkac846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Breaking codon degeneracy for the introduction of non-canonical amino acids offers many opportunities in synthetic biology. Yet, despite the existence of 64 codons, the code has only been expanded to 25 amino acids in vitro. A limiting factor could be the over-reliance on synthetic tRNAs which lack the post-transcriptional modifications that improve translational fidelity. To determine whether modified, wild-type tRNA could improve sense codon reassignment, we developed a new fluorous method for tRNA capture and applied it to the isolation of roughly half of the Escherichia coli tRNA isoacceptors. We then performed codon competition experiments between the five captured wild-type leucyl-tRNAs and their synthetic counterparts, revealing a strong preference for wild-type tRNA in an in vitro translation system. Finally, we compared the ability of wild-type and synthetic leucyl-tRNA to break the degeneracy of the leucine codon box, showing that only captured wild-type tRNAs are discriminated with enough fidelity to accurately split the leucine codon box for the encoding of three separate amino acids. Wild-type tRNAs are therefore enabling reagents for maximizing the reassignment potential of the genetic code.
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Affiliation(s)
- Clinton A L McFeely
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Shivam S Patel
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University , Richmond, VA 23220 , USA
- Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220 , USA
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17
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tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Rep 2022; 41:111539. [PMID: 36288695 PMCID: PMC9643105 DOI: 10.1016/j.celrep.2022.111539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/31/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3′-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival. Masuda et al. show that loss of m1G37 from the 3′ side of the tRNA anticodon renders a modified wobble nucleotide of the anticodon insufficient to decode a set of rare codons, providing a functional underpinning for the “modification circuit” between position 37 and the wobble position of the tRNA anticodon.
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18
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Mangano K, Marks J, Klepacki D, Saha CK, Atkinson GC, Vázquez-Laslop N, Mankin AS. Context-based sensing of orthosomycin antibiotics by the translating ribosome. Nat Chem Biol 2022; 18:1277-1286. [PMID: 36138139 DOI: 10.1038/s41589-022-01138-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Orthosomycin antibiotics inhibit protein synthesis by binding to the large ribosomal subunit in the tRNA accommodation corridor, which is traversed by incoming aminoacyl-tRNAs. Structural and biochemical studies suggested that orthosomycins block accommodation of any aminoacyl-tRNAs in the ribosomal A-site. However, the mode of action of orthosomycins in vivo remained unknown. Here, by carrying out genome-wide analysis of antibiotic action in bacterial cells, we discovered that orthosomycins primarily inhibit the ribosomes engaged in translation of specific amino acid sequences. Our results reveal that the predominant sites of orthosomycin-induced translation arrest are defined by the nature of the incoming aminoacyl-tRNA and likely by the identity of the two C-terminal amino acid residues of the nascent protein. We show that nature exploits this antibiotic-sensing mechanism for directing programmed ribosome stalling within the regulatory open reading frame, which may control expression of an orthosomycin-resistance gene in a variety of bacterial species.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Amgen Research, Thousand Oaks, CA, USA
| | - James Marks
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.,National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Chayan Kumar Saha
- Department of Experimental Medicine, Lund University, Lund, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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19
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Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
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20
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Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife 2021; 10:70619. [PMID: 34382933 PMCID: PMC8384417 DOI: 10.7554/elife.70619] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here, we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jae-Yeon Hwang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
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