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Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough. Nat Commun 2024; 15:4446. [PMID: 38789441 PMCID: PMC11126739 DOI: 10.1038/s41467-024-48387-x] [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: 02/22/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Anastasiia Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Tobias Jumel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
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2
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Girardo B, Schopfer LM, Yue Y, Lockridge O, Larson MA. Polyaminated, acetylated and stop codon readthrough of recombinant Francisella tularensis universal stress protein in Escherichia coli. PLoS One 2024; 19:e0299701. [PMID: 38683788 PMCID: PMC11057771 DOI: 10.1371/journal.pone.0299701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/14/2024] [Indexed: 05/02/2024] Open
Abstract
Recombinant Francisella tularensis universal stress protein with a C-terminal histidine-tag (rUsp/His6) was expressed in Escherichia coli. Endogenous F. tularensis Usp has a predicted molecular mass of 30 kDa, but rUsp/His6 had an apparent molecular weight of 33 kDa based on Western blot analyses. To determine the source of the higher molecular weight for rUsp/His6, post translational modifications were examined. Tryptic peptides of purified rUsp/His6 were subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) and fragmentation spectra were searched for acetylated lysines and polyaminated glutamines. Of the 24 lysines in rUsp/His6, 10 were acetylated (K63, K68, K72, K129, K175, K201, K208, K212, K233, and K238) and three of the four glutamines had putrescine, spermidine and spermine adducts (Q55, Q60 and Q267). The level of post-translational modification was substoichiometric, eliminating the possibility that these modifications were the sole contributor to the 3 kDa extra mass of rUsp/His6. LC-MS/MS revealed that stop codon readthrough had occurred resulting in the unexpected addition of 20 extra amino acids at the C-terminus of rUsp/His6, after the histidine tag. Further, the finding of polyaminated glutamines in rUsp/His6 indicated that E. coli is capable of transglutaminase activity.
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Affiliation(s)
- Benjamin Girardo
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Lawrence M. Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Yinshi Yue
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Marilynn A. Larson
- Pathology and Microbiology Department, University of Nebraska Medical Center, Omaha, NE, United States of America
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3
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Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proc Natl Acad Sci U S A 2024; 121:e2318008121. [PMID: 38306478 PMCID: PMC10861870 DOI: 10.1073/pnas.2318008121] [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: 10/16/2023] [Accepted: 12/02/2023] [Indexed: 02/04/2024] Open
Abstract
Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "raiA motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.
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Affiliation(s)
- Lucas W. Soares
- Department of Microbial Pathogenesis, Yale University, New Haven, CT06536
| | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Chrishan M. Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
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4
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Zhang X, Liang X, He S, Tian H, Liu W, Jia Y, Zhang L, Zhang W, Kuang H, Chen J. Seed color in lettuce is determined by the LsTT2, LsCHS, and Ls2OGD genes from the flavonoid biosynthesis pathway. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:241. [PMID: 37930450 DOI: 10.1007/s00122-023-04491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE The mutated LsTT2 and Ls2OGD genes are responsible for white seeds and yellow seeds in lettuce, respectively. Three LsCHS genes are involved in the biosynthesis of flavonoid in seed coats. Lettuce seeds have several different colors, including black, yellow, and white. The genetic mechanisms underlying color variations of lettuce seeds remain unknown. We used genome-wide association studies (GWAS) and map-based cloning approaches to clone genes controlling the color of lettuce seeds. LsTT2, which encodes an R2R3-MYB transcription factor and is homologous to the TT2 gene in Arabidopsis, was shown to be the causal gene for the variation of black and white seeds in lettuce. A point mutation leads to the lack of stop codon in the LsTT2 transcript, resulting in white seeds. Knockout of the LsTT2 gene converted black seeds to white seeds. The locus controlling yellow seeds was mapped to Chromosome 2. Knockout of two 2-oxoglutarate-dependent dioxygenases (2OGD) genes from the candidate region converted black seeds to yellow seeds, suggesting that these two 2OGD proteins catalyze the conversion of yellow metabolites to black metabolites. We also showed that three LsCHS genes from the candidate region are associated with flavonoid biosynthesis in seeds. Knockout mutants of the three LsCHS genes decreased color intensity. This study provides new insights into the regulation of flavonoid biosynthesis in plants.
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Affiliation(s)
- Xiaoyan Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiaoli Liang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shuping He
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hao Tian
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wenye Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yue Jia
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Weiyi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jiongjiong Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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5
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Lyu Z, Villanueva P, O’Malley L, Murphy P, Augenstreich J, Briken V, Singh A, Ling J. Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP. Nucleic Acids Res 2023; 51:9905-9919. [PMID: 37670559 PMCID: PMC10570021 DOI: 10.1093/nar/gkad725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/12/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Patricia Villanueva
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Liam O’Malley
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering and Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
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6
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Ochkasova A, Arbuzov G, Malygin A, Graifer D. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Int J Mol Sci 2023; 24:11458. [PMID: 37511213 PMCID: PMC10380927 DOI: 10.3390/ijms241411458] [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: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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7
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Prabhakar A, Pavlov MY, Zhang J, Indrisiunaite G, Wang J, Lawson M, Ehrenberg M, Puglisi JD. Dynamics of release factor recycling during translation termination in bacteria. Nucleic Acids Res 2023; 51:5774-5790. [PMID: 37102635 PMCID: PMC10287982 DOI: 10.1093/nar/gkad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
In bacteria, release of newly synthesized proteins from ribosomes during translation termination is catalyzed by class-I release factors (RFs) RF1 or RF2, reading UAA and UAG or UAA and UGA codons, respectively. Class-I RFs are recycled from the post-termination ribosome by a class-II RF, the GTPase RF3, which accelerates ribosome intersubunit rotation and class-I RF dissociation. How conformational states of the ribosome are coupled to the binding and dissociation of the RFs remains unclear and the importance of ribosome-catalyzed guanine nucleotide exchange on RF3 for RF3 recycling in vivo has been disputed. Here, we profile these molecular events using a single-molecule fluorescence assay to clarify the timings of RF3 binding and ribosome intersubunit rotation that trigger class-I RF dissociation, GTP hydrolysis, and RF3 dissociation. These findings in conjunction with quantitative modeling of intracellular termination flows reveal rapid ribosome-dependent guanine nucleotide exchange to be crucial for RF3 action in vivo.
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Affiliation(s)
- Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
- Program in Biophysics, Stanford University, Stanford, CA 94305-5126, USA
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Jingji Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Gabriele Indrisiunaite
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Michael R Lawson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, Uppsala, Sweden
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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8
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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: 0] [Impact Index Per Article: 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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9
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Korostelev AA. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. BIOCHEMISTRY (MOSCOW) 2021; 86:1107-1121. [PMID: 34565314 DOI: 10.1134/s0006297921090066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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10
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Ataluren-Promising Therapeutic Premature Termination Codon Readthrough Frontrunner. Pharmaceuticals (Basel) 2021; 14:ph14080785. [PMID: 34451881 PMCID: PMC8398184 DOI: 10.3390/ph14080785] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/08/2023] Open
Abstract
Around 12% of hereditary disease-causing mutations are in-frame nonsense mutations. The expression of genes containing nonsense mutations potentially leads to the production of truncated proteins with residual or virtually no function. However, the translation of transcripts containing premature stop codons resulting in full-length protein expression can be achieved using readthrough agents. Among them, only ataluren was approved in several countries to treat nonsense mutation Duchenne muscular dystrophy (DMD) patients. This review summarizes ataluren’s journey from its identification, via first in vitro activity experiments, to clinical trials in DMD, cystic fibrosis, and aniridia. Additionally, data on its pharmacokinetics and mechanism of action are presented. The range of diseases with underlying nonsense mutations is described for which ataluren therapy seems to be promising. What is more, experiments in which ataluren did not show its readthrough activity are also included, and reasons for their failures are discussed.
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11
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Impact of Hydrogen Peroxide on Protein Synthesis in Yeast. Antioxidants (Basel) 2021; 10:antiox10060952. [PMID: 34204720 PMCID: PMC8231629 DOI: 10.3390/antiox10060952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Cells must be able to respond and adapt to different stress conditions to maintain normal function. A common response to stress is the global inhibition of protein synthesis. Protein synthesis is an expensive process consuming much of the cell's energy. Consequently, it must be tightly regulated to conserve resources. One of these stress conditions is oxidative stress, resulting from the accumulation of reactive oxygen species (ROS) mainly produced by the mitochondria but also by other intracellular sources. Cells utilize a variety of antioxidant systems to protect against ROS, directing signaling and adaptation responses at lower levels and/or detoxification as levels increase to preclude the accumulation of damage. In this review, we focus on the role of hydrogen peroxide, H2O2, as a signaling molecule regulating protein synthesis at different levels, including transcription and various parts of the translation process, e.g., initiation, elongation, termination and ribosome recycling.
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12
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Tamilmaran N, Sankaranarayanan R, Selvakumar A S P, Munavar MH. Horizontal transfer of domains in ssrA gene among Enterobacteriaceae. Genes Cells 2021; 26:541-550. [PMID: 33971069 DOI: 10.1111/gtc.12869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/29/2022]
Abstract
The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3' end than 5' end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.
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Affiliation(s)
- Nagarajan Tamilmaran
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | | | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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13
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Carbone CE, Demo G, Madireddy R, Svidritskiy E, Korostelev AA. ArfB can displace mRNA to rescue stalled ribosomes. Nat Commun 2020; 11:5552. [PMID: 33144582 PMCID: PMC7641280 DOI: 10.1038/s41467-020-19370-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
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Affiliation(s)
- Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Rohini Madireddy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Medicago Inc., 7 Triangle drive, Durham, NC, 27713, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
- Sanofi, 49 New York Ave, Suite 3660, Framingham, MA, 01701, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
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14
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Saito K, Green R, Buskirk AR. Ribosome recycling is not critical for translational coupling in Escherichia coli. eLife 2020; 9:59974. [PMID: 32965213 PMCID: PMC7538156 DOI: 10.7554/elife.59974] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter assays or in ribosome density genome-wide. These findings argue that re-initiation is not a major mechanism of translational coupling in E. coli. Finally, RRF depletion has dramatic effects on the activity of ribosome rescue factors tmRNA and ArfA. Our results provide a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.
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Affiliation(s)
- Kazuki Saito
- Department of Molecular Biology and Genetics, Baltimore, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Baltimore, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Baltimore, United States
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15
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Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc Natl Acad Sci U S A 2020; 117:22167-22172. [PMID: 32839318 DOI: 10.1073/pnas.2013543117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial cells. However, little is known about how environmental factors affect the level and heterogeneity of stop-codon readthrough. In this study, we have combined dual-fluorescence reporters, mass spectrometry, mathematical modeling, and single-cell approaches to demonstrate that a metabolic stress caused by excess carbon substantially increases both the level and heterogeneity of stop-codon readthrough. Excess carbon leads to accumulation of acid metabolites, which lower the pH and the activity of release factors to promote readthrough. Furthermore, our time-lapse microscopy experiments show that single cells with high readthrough levels are more adapted to severe acid stress conditions and are more sensitive to an aminoglycoside antibiotic. Our work thus reveals a metabolic stress that promotes translational heterogeneity and phenotypic diversity.
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16
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Kurita D, Abo T, Himeno H. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue. J Biol Chem 2020; 295:13326-13337. [PMID: 32727848 DOI: 10.1074/jbc.ra120.014664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/27/2020] [Indexed: 02/01/2023] Open
Abstract
Translation termination in bacteria requires that the stop codon be recognized by release factor RF1 or RF2, leading to hydrolysis of the ester bond between the peptide and tRNA on the ribosome. As a consequence, normal termination cannot proceed if the translated mRNA lacks a stop codon. In Escherichia coli, the ribosome rescue factor ArfA releases the nascent polypeptide from the stalled ribosome with the help of RF2 in a stop codon-independent manner. Interestingly, the reaction does not proceed if RF1 is instead provided, even though the structures of RF1 and RF2 are very similar. Here, we identified the regions of RF2 required for the ArfA-dependent ribosome rescue system. Introduction of hydrophobic residues from RF2 found at the interface between RF2 and ArfA into RF1 allowed RF1 to associate with the ArfA-ribosome complex to a certain extent but failed to promote peptidyl-tRNA hydrolysis, whereas WT RF1 did not associate with the complex. We also identified the key residues required for the process after ribosome binding. Our findings provide a basis for understanding how the ArfA-ribosome complex is specifically recognized by RF2 and how RF2 undergoes a conformational change upon binding to the ArfA-ribosome complex.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan.
| | - Tatsuhiko Abo
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan.
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17
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Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Nat Commun 2019; 10:5397. [PMID: 31776341 PMCID: PMC6881298 DOI: 10.1038/s41467-019-13408-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled ribosomes, recruits RF2 but not RF1, and induces transition of the ribosome into an open active conformation.
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18
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Ge X, Oliveira A, Hjort K, Bergfors T, Gutiérrez-de-Terán H, Andersson DI, Sanyal S, Åqvist J. Inhibition of translation termination by small molecules targeting ribosomal release factors. Sci Rep 2019; 9:15424. [PMID: 31659219 PMCID: PMC6817905 DOI: 10.1038/s41598-019-51977-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/10/2019] [Indexed: 11/18/2022] Open
Abstract
The bacterial ribosome is an important drug target for antibiotics that can inhibit different stages of protein synthesis. Among the various classes of compounds that impair translation there are, however, no known small-molecule inhibitors that specifically target ribosomal release factors (RFs). The class I RFs are essential for correct termination of translation and they differ considerably between bacteria and eukaryotes, making them potential targets for inhibiting bacterial protein synthesis. We carried out virtual screening of a large compound library against 3D structures of free and ribosome-bound RFs in order to search for small molecules that could potentially inhibit termination by binding to the RFs. Here, we report identification of two such compounds which are found both to bind free RFs in solution and to inhibit peptide release on the ribosome, without affecting peptide bond formation.
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Affiliation(s)
- Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Ana Oliveira
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
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19
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Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. Extensive ribosome and RF2 rearrangements during translation termination. eLife 2019; 8:46850. [PMID: 31513010 PMCID: PMC6742477 DOI: 10.7554/elife.46850] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.
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Affiliation(s)
- Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Chen Xu
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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20
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Ribosomal protein eL42 contributes to the catalytic activity of the yeast ribosome at the elongation step of translation. Biochimie 2018; 158:20-33. [PMID: 30550856 DOI: 10.1016/j.biochi.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022]
Abstract
The GGQ minidomain of the ribosomal protein eL42 was previously shown to contact the CCA-arm of P-site bound tRNA in human ribosome, indicating a possible involvement of the protein in the catalytic activity. Here, using Schizosaccharomyces pombe (S. pombe) cells, we demonstrate that the GGQ minidomain and neighboring region of eL42 is critical for the ribosomal function. Mutant eL42 proteins containing amino acid substitutions within or adjacent to the GGQ minidomain failed to complement the function of wild-type eL42, and expression of the mutant eL42 proteins led to severe growth defects. These results suggest that the mutations in eL42 interfere with the ribosomal function in vivo. Furthermore, we show that some of the mutations associated with the conserved GGQ region lead to reduced activities in the poly(Phe) synthesis and/or in the peptidyl transferase reaction with respect to puromycin, as compared with those of the wild-type ribosomes. A pK value of 6.95 was measured for the side chain of Lys-55/Arg-55, which is considerably less than that of a Lys or Arg residue. Altogether, our findings suggest that eL42 contributes to the 80S ribosome's peptidyl transferase activity by promoting the course of the elongation cycle.
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21
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Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Cell Rep 2018; 20:161-172. [PMID: 28683310 DOI: 10.1016/j.celrep.2017.06.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/06/2017] [Accepted: 06/09/2017] [Indexed: 01/24/2023] Open
Abstract
During termination of translation, the nascent peptide is first released from the ribosome, which must be subsequently disassembled into subunits in a process known as ribosome recycling. In bacteria, termination and recycling are mediated by the translation factors RF, RRF, EF-G, and IF3, but their precise roles have remained unclear. Here, we use single-molecule fluorescence to track the conformation and composition of the ribosome in real time during termination and recycling. Our results show that peptide release by RF induces a rotated ribosomal conformation. RRF binds to this rotated intermediate to form the substrate for EF-G that, in turn, catalyzes GTP-dependent subunit disassembly. After the 50S subunit departs, IF3 releases the deacylated tRNA from the 30S subunit, thus preventing reassembly of the 70S ribosome. Our findings reveal the post-termination rotated state as the crucial intermediate in the transition from termination to recycling.
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22
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Zeng F, Jin H. Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination. Sci Rep 2018; 8:2349. [PMID: 29403017 PMCID: PMC5799190 DOI: 10.1038/s41598-018-20107-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/12/2018] [Indexed: 11/24/2022] Open
Abstract
The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N5 position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.
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Affiliation(s)
- Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA.
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23
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Hoernes TP, Clementi N, Juen MA, Shi X, Faserl K, Willi J, Gasser C, Kreutz C, Joseph S, Lindner H, Hüttenhofer A, Erlacher MD. Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release. Proc Natl Acad Sci U S A 2018; 115:E382-E389. [PMID: 29298914 PMCID: PMC5776981 DOI: 10.1073/pnas.1714554115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons.
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Affiliation(s)
- Thomas Philipp Hoernes
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Xinying Shi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Jessica Willi
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias David Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria;
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24
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Buskirk AR, Green R. Ribosome pausing, arrest and rescue in bacteria and eukaryotes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0183. [PMID: 28138069 DOI: 10.1098/rstb.2016.0183] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Ribosomes translate genetic information into polypeptides in several basic steps: initiation, elongation, termination and recycling. When ribosomes are arrested during elongation or termination, the cell's capacity for protein synthesis is reduced. There are numerous quality control systems in place to distinguish between paused ribosomes that need some extra input to proceed and terminally stalled ribosomes that need to be rescued. Here, we discuss similarities and differences in the systems for resolution of pauses and rescue of arrested ribosomes in bacteria and eukaryotes, and how ribosome profiling has transformed our ability to decipher these molecular events.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, MD, USA
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25
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Evans CR, Ling J. Visualizing translational errors: one cell at a time. Curr Genet 2017; 64:551-554. [PMID: 29159424 DOI: 10.1007/s00294-017-0784-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/04/2023]
Abstract
Physiological heterogeneity among single cells with identical genetic information has been observed in a large number of bacterial phenotypes, including growth, stress responses, cell size, and antibiotic tolerance. Despite the widespread observation of this phenomenon in bacterial populations, not much is known about the molecular mechanisms behind phenotypic heterogeneity. Currently, our understanding is primarily limited to transcriptional profile of single cells using fluorescence reporters. Although the development of these tools has been extremely informative, it cannot fully explain the heterogeneity seen in populations. In a recent publication, Fan et al. have developed a dual-fluorescent reporter system that is capable of quantitatively measuring translational fidelity in single cells. It is shown that translational fidelity is heterogeneous and affects the growth characteristics of single cells. The development of tools for analysis of molecular heterogeneity downstream of transcription may play an important role in advancing our understanding of the physiology of bacterial populations.
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Affiliation(s)
- Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX, 77030, USA.,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX, 77030, USA. .,Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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26
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Enabling stop codon read-through translation in bacteria as a probe for amyloid aggregation. Sci Rep 2017; 7:11908. [PMID: 28928456 PMCID: PMC5605706 DOI: 10.1038/s41598-017-12174-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/05/2017] [Indexed: 11/23/2022] Open
Abstract
Amyloid aggregation of the eukaryotic translation terminator eRF3/Sup35p, the [PSI+] prion, empowers yeast ribosomes to read-through UGA stop codons. No similar functional prion, skipping a stop codon, has been found in Escherichia coli, a fact possibly due to the efficient back-up systems found in bacteria to rescue non-stop complexes. Here we report that engineering hydrophobic amyloidogenic repeats from a synthetic bacterial prion-like protein (RepA-WH1) into the E. coli releasing factor RF1 promotes its aggregation and enables ribosomes to continue with translation through a premature UAG stop codon located in a β-galactosidase reporter. To our knowledge, intended aggregation of a termination factor is a way to overcome the bacterial translation quality checkpoint that had not been reported so far. We also show the feasibility of using the amyloidogenic RF1 chimeras as a reliable, rapid and cost-effective system to screen for molecules inhibiting intracellular protein amyloidogenesis in vivo, by testing the effect on the chimeras of natural polyphenols with known anti-amyloidogenic properties. Resveratrol exhibits a clear amyloid-solubilizing effect in this assay, showing no toxicity to bacteria or interference with the enzymatic activity of β-galactosidase.
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27
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Korkmaz G, Sanyal S. R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteria Escherichia coli. J Biol Chem 2017; 292:15134-15142. [PMID: 28743745 DOI: 10.1074/jbc.m117.785238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/23/2017] [Indexed: 11/06/2022] Open
Abstract
The current understanding of the specificity of the bacterial class I release factors (RFs) in decoding stop codons has evolved beyond a simple tripeptide anticodon model. A recent molecular dynamics study for deciphering the principles for specific stop codon recognition by RFs identified Arg-213 as a crucial residue on Escherichia coli RF2 for discriminating guanine in the third position (G3). Interestingly, Arg-213 is highly conserved in RF2 and substituted by Ile-196 in the corresponding position in RF1. Another similar pair is Leu-126 in RF1 and Asp-143 in RF2, which are also conserved within their respective groups. With the hypothesis that replacement of Arg-213 and Asp-143 with the corresponding RF1 residues will reduce G3 discrimination by RF2, we swapped these residues between E. coli RF1 and RF2 by site-directed mutagenesis and characterized their preference for different codons using a competitive peptide release assay. Among these, the R213I mutant of RF2 showed 5-fold improved reading of the RF1-specific UAG codon relative to UAA, the universal stop codon, compared with the wild type (WT). In-depth fast kinetic studies revealed that the gain in UAG reading by RF2 R213I is associated with a reduced efficiency of termination on the cognate UAA codon. Our work highlights the notion that stop codon recognition involves complex interactions with multiple residues beyond the PXT/SPF motifs. We propose that the R213I mutation in RF2 brings us one step forward toward engineering an omnipotent RF in bacteria, capable of reading all three stop codons.
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Affiliation(s)
- Gürkan Korkmaz
- From the Department of Cell and Molecular Biology, Uppsala University, Box-596, 75124 Uppsala, Sweden
| | - Suparna Sanyal
- From the Department of Cell and Molecular Biology, Uppsala University, Box-596, 75124 Uppsala, Sweden
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28
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Huter P, Müller C, Arenz S, Beckert B, Wilson DN. Structural Basis for Ribosome Rescue in Bacteria. Trends Biochem Sci 2017. [PMID: 28629612 DOI: 10.1016/j.tibs.2017.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems.
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Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Feodor-Lynenstr. 25, 81377 München, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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29
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Eustache S, Créchet JB, Bouceba T, Nakayama JI, Tanaka M, Suzuki M, Woisard A, Tuffery P, Baouz S, Hountondji C. A Functional Role for the Monomethylated Gln-51 and Lys-53 Residues of the 49GGQTK53 Motif of eL42 from Human 80S Ribosomes. Open Biochem J 2017; 11:8-26. [PMID: 28567122 PMCID: PMC5418926 DOI: 10.2174/1874091x01711010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/06/2017] [Accepted: 01/10/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND We have previously demonstrated that the eukaryote-specific ribosomal protein eL42 of the human 80S ribosome contains seven monomethylated residues, among which are the Gln-51 and Lys-53 residues contained in the 47GFGGQTK53 sequence conserved in all eukaryotic 80S ribosomes. This sequence contains the methylated and universally conserved GGQ motif common for all class-1 translation termination factors responsible for stop codon recognition and for triggering the hydrolysis of the P site-bound peptidyl-tRNA. We have also recently reported a model of ribosomal ternary eL42-tRNA-eRF1 complex where specific regions of all three macromolecules (the comparably flexible GGQ domains of eRF1 and eL42 and the CCA-arm of tRNA) are involved in interactions. METHOD Here, we have studied the interactions between recombinant eL42 and eRF1 proteins and the tRNA substrate by means of the Biacore assay, using the wild-type eL42 protein, the eL42-Δ(GGQTK) mutant (the eL42 protein whose GGQTK motif has been deleted), the single Q51E and K53Q mutants (eL42-Q51E and eL42-K53Q, respectively), as well as the double Q51A/K53A mutant (eL42-Q51A/K53A). RESULTS Our results show that the monomethylated Gln-51 and Lys-53 residues contained in the 47GFGGQTK53 sequence of eL42 and the monomethylated GGQ motif of eRF1 represents the sites of interaction between these two proteins through hydrophobic contacts between methyl groups. We also demonstrate that the interactions between eL42 and tRNA or 28S rRNA are characterized by strong binding affinities (KD values in the nanomolar or picomolar range, respectively) which argue for specific interactions. Strong interactions between eL42 and tRNA are likely to be responsible for the decrease in the poly(U)-dependent poly(Phe) synthesis activity of human 80S or E. coli 70S ribosomes in the presence of added human recombinant eL42. It is proposed that the decrease of the activity of the ribosome is caused by the sequestration of the substrate Phe-tRNAPhe by the added eL42 protein. CONCLUSION Interactions between the monomethylated Gln-51 and Lys-53 residues of the 49GGQTK53 motif of the human eL42 protein and the methylated GGQ motif of eRF1 are likely to play a functional role on translating human 80S ribosomes.
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Affiliation(s)
- Stéphanie Eustache
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
- Université Paris-Diderot, Sorbonne-Paris-Cité, INSERM-UMR-S973 and RPBS, Paris, France
| | | | - Tahar Bouceba
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine (IBPS) Plateforme d’interactions moléculaires, CNRS-FR3631; 7, Quai Saint Bernard, F-75252, Paris Cedex 05, France
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Mayo Tanaka
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Mieko Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501 Japan
| | - Anne Woisard
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
| | - Pierre Tuffery
- Université Paris-Diderot, Sorbonne-Paris-Cité, INSERM-UMR-S973 and RPBS, Paris, France
| | - Soria Baouz
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
| | - Codjo Hountondji
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire “Enzymologie de l’ARN”, UPMC-UR6, (Tour 32), Case courrier 60 - 4, Place Jussieu, F-75252, Paris Cedex 05, France
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30
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Baggett NE, Zhang Y, Gross CA. Global analysis of translation termination in E. coli. PLoS Genet 2017; 13:e1006676. [PMID: 28301469 PMCID: PMC5373646 DOI: 10.1371/journal.pgen.1006676] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/30/2017] [Accepted: 03/08/2017] [Indexed: 01/01/2023] Open
Abstract
Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. We performed ribosome profiling on a set of isogenic strains with well-characterized release factor mutations to determine how they alter translation globally. Consistent with their known defects, strains with increasingly severe release factor defects exhibit increasingly severe accumulation of ribosomes over stop codons, indicative of an increased duration of the termination/release phase of translation. Release factor mutant strains also exhibit increased occupancy in the region following the stop codon at a significant number of genes. Our global analysis revealed that, as expected, translation termination is generally efficient and accurate, but that at a significant number of genes (≥ 50) the ribosome signature after the stop codon is suggestive of translation past the stop codon. Even native E. coli K-12 exhibits the ribosome signature suggestive of protein extension, especially at UGA codons, which rely exclusively on the reduced function RF2 variant of the K-12 strain for termination. Deletion of RF3 increases the severity of the defect. We unambiguously demonstrate readthrough and frameshifting protein extensions and their further accumulation in mutant strains for a few select cases. In addition to enhancing recoding, ribosome accumulation over stop codons disrupts attenuation control of biosynthetic operons, and may alter expression of some overlapping genes. Together, these functional alterations may either augment the protein repertoire or produce deleterious proteins. Proteins are the cellular workhorses, performing essentially all of the functions required for cell and organismal survival. But, it takes a great deal of energy to make proteins, making it critical that proteins are made accurately and in the proper time frame. After a ribosome synthesizes a protein, release factors catalyze the accurate and timely release of the finished protein from the ribosome, a process called termination. Ribosomes are then recycled and start the next protein. We utilized ribosome profiling, a method that allows us to follow the position of every ribosome that is making a protein, to globally investigate and strengthen insights on termination fidelity for cells with and without mutant release factors. We find that as we decrease release factor function, the time to terminate/release a protein increases across the genome. We observe that the accuracy of terminating a protein at the correct place decreases on a global scale. Using this metric we identify genes with inherently low termination efficiency and confirm two novel events resulting in extended protein products. In addition we find that beyond disrupting accurate protein synthesis, release factor mutations can alter expression of genes involved in the production of key amino acids.
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Affiliation(s)
- Natalie E. Baggett
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Yan Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
- California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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31
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Huter P, Müller C, Beckert B, Arenz S, Berninghausen O, Beckmann R, Wilson DN. Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons. Nature 2016; 541:546-549. [PMID: 27906161 DOI: 10.1038/nature20821] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
In bacteria, ribosomes stalled on truncated mRNAs that lack a stop codon are rescued by the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB systems. Although tmRNA-ribosome and ArfB-ribosome structures have been determined, how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is unclear. Here we present a cryo-electron microscopy reconstruction of the Escherichia coli 70S ribosome stalled on a truncated mRNA in the presence of ArfA and RF2. The structure shows that the C terminus of ArfA binds within the mRNA entry channel on the small ribosomal subunit, and explains how ArfA distinguishes between ribosomes that bear truncated or full-length mRNAs. The N terminus of ArfA establishes several interactions with the decoding domain of RF2, and this finding illustrates how ArfA recruits RF2 to the stalled ribosome. Furthermore, ArfA is shown to stabilize a unique conformation of the switch loop of RF2, which mimics the canonical translation termination state by directing the catalytically important GGQ motif within domain 3 of RF2 towards the peptidyl-transferase centre of the ribosome. Thus, our structure reveals not only how ArfA recruits RF2 to the ribosome but also how it promotes an active conformation of RF2 to enable translation termination in the absence of a stop codon.
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Affiliation(s)
- Paul Huter
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Claudia Müller
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bertrand Beckert
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Stefan Arenz
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Daniel N Wilson
- Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
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32
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Shi X, Joseph S. Mechanism of Translation Termination: RF1 Dissociation Follows Dissociation of RF3 from the Ribosome. Biochemistry 2016; 55:6344-6354. [PMID: 27779391 DOI: 10.1021/acs.biochem.6b00921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Release factors 1 and 2 (RF1 and RF2, respectively) bind to ribosomes that have a stop codon in the A site and catalyze the release of the newly synthesized protein. Following peptide release, the dissociation of RF1 and RF2 from the ribosome is accelerated by release factor 3 (RF3). The mechanism for RF3-promoted dissociation of RF1 and RF2 is unclear. It was previously proposed that RF3 hydrolyzes GTP and dissociates from the ribosome after RF1 dissociation. Here we monitored directly the dissociation kinetics of RF1 and RF3 using Förster resonance energy transfer-based assays. In contrast to the previous model, our data show that RF3 hydrolyzes GTP and dissociates from the ribosome before RF1 dissociation. We propose that RF3 stabilizes the ratcheted state of the ribosome, which consequently accelerates the dissociation of RF1 and RF2.
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Affiliation(s)
- Xinying Shi
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0314, United States
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0314, United States
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33
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Simms CL, Thomas EN, Zaher HS. Ribosome-based quality control of mRNA and nascent peptides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27193249 DOI: 10.1002/wrna.1366] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 11/06/2022]
Abstract
Quality control processes are widespread and play essential roles in detecting defective molecules and removing them in order to maintain organismal fitness. Aberrant messenger RNA (mRNA) molecules, unless properly managed, pose a significant hurdle to cellular proteostasis. Often mRNAs harbor premature stop codons, possess structures that present a block to the translational machinery, or lack stop codons entirely. In eukaryotes, the three cytoplasmic mRNA-surveillance processes, nonsense-mediated decay (NMD), no-go decay (NGD), and nonstop decay (NSD), evolved to cope with these aberrant mRNAs, respectively. Nonstop mRNAs and mRNAs that inhibit translation elongation are especially problematic as they sequester valuable ribosomes from the translating ribosome pool. As a result, in addition to RNA degradation, NSD and NGD are intimately coupled to ribosome rescue in all domains of life. Furthermore, protein products produced from all three classes of defective mRNAs are more likely to malfunction. It is not surprising then that these truncated nascent protein products are subject to degradation. Over the past few years, many studies have begun to document a central role for the ribosome in initiating the RNA and protein quality control processes. The ribosome appears to be responsible for recognizing the target mRNAs as well as for recruiting the factors required to carry out the processes of ribosome rescue and nascent protein decay. WIREs RNA 2017, 8:e1366. doi: 10.1002/wrna.1366 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Erica N Thomas
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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34
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Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3. Proc Natl Acad Sci U S A 2015; 112:3038-43. [PMID: 25733896 DOI: 10.1073/pnas.1424127112] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Premature termination codons (PTCs) in an mRNA ORF inactivate gene function by causing production of a truncated protein and destabilization of the mRNA. Readthrough of a PTC allows ribosomal A-site insertion of a near-cognate tRNA, leading to synthesis of a full-length protein from otherwise defective mRNA. To understand the mechanism of such nonsense suppression, we developed a yeast system that allows purification and sequence analysis of full-length readthrough products arising as a consequence of endogenous readthrough or the compromised termination fidelity attributable to the loss of Upf (up-frameshift) factors, defective release factors, or the presence of the aminoglycoside gentamicin. Unlike classical "wobble" models, our analyses showed that three of four possible near-cognate tRNAs could mispair at position 1 or 3 of nonsense codons and that, irrespective of whether readthrough is endogenous or induced, the same sets of amino acids are inserted. We identified the insertion of Gln, Tyr, and Lys at UAA and UAG, whereas Trp, Arg, and Cys were inserted at UGA, and the frequency of insertion of individual amino acids was distinct for specific nonsense codons and readthrough-inducing agents. Our analysis suggests that the use of genetic or chemical means to increase readthrough does not promote novel or alternative mispairing events; rather, readthrough effectors cause quantitative enhancement of endogenous mistranslation events. Knowledge of the amino acids incorporated during readthrough not only elucidates the decoding process but also may allow predictions of the functionality of readthrough protein products.
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35
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Indrisiunaite G, Pavlov MY, Heurgué-Hamard V, Ehrenberg M. On the pH dependence of class-1 RF-dependent termination of mRNA translation. J Mol Biol 2015; 427:1848-60. [PMID: 25619162 DOI: 10.1016/j.jmb.2015.01.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/05/2015] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
We have studied the pH dependence of the rate of termination of bacterial protein synthesis catalyzed by a class-1 release factor (RF1 or RF2). We used a classical quench-flow technique and a newly developed stopped-flow technique that relies on the use of fluorescently labeled peptides. We found the termination rate to increase with increasing pH and, eventually, to saturate at about 70 s(-1) with an apparent pKa value of about 7.6. From our data, we suggest that class-1 RF termination is rate limited by the chemistry of ester bond hydrolysis at low pH and by a stop-codon-dependent and pH-independent conformational change of RFs at high pH. We propose that RF-dependent termination depends on the participation of a hydroxide ion rather than a water molecule in the hydrolysis of the ester bond between the P-site tRNA and its peptide chain. We provide a simple explanation for why the rate of termination saturated at high pH in our experiments but not in those of others.
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Affiliation(s)
- Gabriele Indrisiunaite
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden
| | - Valérie Heurgué-Hamard
- Centre National de la Recherche Scientifique, FRE3630, University Paris Diderot Sorbonne Paris Cité Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Biomedicinskt Centrum, Box 596, 75124 Uppsala, Sweden.
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36
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Transposon mutagenesis of the extremely thermophilic bacterium Thermus thermophilus HB27. Extremophiles 2014; 19:221-8. [PMID: 24948436 DOI: 10.1007/s00792-014-0663-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °C and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. Multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in T. thermophilus and Escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not been developed. Here we report a detailed method of transposon mutagenesis of T. thermophilus HB27 based on the EZ-Tn5 system from Epicentre Biotechnologies. We were able to generate insertion mutations throughout the chromosome by in vitro transposition and transformation with mutagenized genomic DNA. We also report that an additional step, one that fills in single stranded gaps in donor DNA generated by the transposition reaction, was essential for successful mutagenesis. We anticipate that our method of transposon mutagenesis will enable further genetic development of T. thermophilus and may also be valuable for similar endeavors with other under-developed organisms.
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37
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Theoretical Study on Two-Step Mechanisms of Peptide Release in the Ribosome. J Phys Chem B 2014; 118:5717-29. [DOI: 10.1021/jp501246a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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38
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Petropoulos AD, McDonald ME, Green R, Zaher HS. Distinct roles for release factor 1 and release factor 2 in translational quality control. J Biol Chem 2014; 289:17589-96. [PMID: 24798339 DOI: 10.1074/jbc.m114.564989] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bacteria, stop codons are recognized by two similar class 1 release factors, release factor 1 (RF1) and release factor 2 (RF2). Normally, during termination, the class 2 release factor 3 (RF3), a GTPase, functions downstream of peptide release where it accelerates the dissociation of RF1/RF2 prior to ribosome recycling. In addition to their canonical function in termination, both classes of release factor are also involved in a post peptidyl transfer quality control (post PT QC) mechanism where the termination factors recognize mismatched (i.e. error-containing) ribosome complexes and promote premature termination. Here, using a well defined in vitro system, we explored the role of release factors in canonical termination and post PT QC. As reported previously, during canonical termination, RF1 and RF2 recognize stop codons in a similar manner, and RF3 accelerates their rate of dissociation. During post PT QC, only RF2 (and not RF1) effectively binds to mismatched ribosome complexes; and whereas the addition of RF3 to RF2 increased its rate of release on mismatched complexes, the addition of RF3 to RF1 inhibited its rate of release but increased the rate of peptidyl-tRNA dissociation. Our data strongly suggest that RF2, in addition to its primary role in peptide release, functions as the principle factor for post PT QC.
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Affiliation(s)
- Alexandros D Petropoulos
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Megan E McDonald
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Rachel Green
- From the Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Hani S Zaher
- the Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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39
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Koutmou KS, McDonald ME, Brunelle JL, Green R. RF3:GTP promotes rapid dissociation of the class 1 termination factor. RNA (NEW YORK, N.Y.) 2014; 20:609-620. [PMID: 24667215 PMCID: PMC3988563 DOI: 10.1261/rna.042523.113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/24/2014] [Indexed: 05/29/2023]
Abstract
Translation termination is promoted by class 1 and class 2 release factors in all domains of life. While the role of the bacterial class 1 factors, RF1 and RF2, in translation termination is well understood, the precise contribution of the bacterial class 2 release factor, RF3, to this process remains less clear. Here, we use a combination of binding assays and pre-steady state kinetics to provide a kinetic and thermodynamic framework for understanding the role of the translational GTPase RF3 in bacterial translation termination. First, we find that GDP and GTP have similar affinities for RF3 and that, on average, the t1/2 for nucleotide dissociation from the protein is 1-2 min. We further show that RF3:GDPNP, but not RF3:GDP, tightly associates with the ribosome pre- and post-termination complexes. Finally, we use stopped-flow fluorescence to demonstrate that RF3:GTP enhances RF1 dissociation rates by over 500-fold, providing the first direct observation of this step. Importantly, catalytically inactive variants of RF1 are not rapidly dissociated from the ribosome by RF3:GTP, arguing that a rotated state of the ribosome must be sampled for this step to efficiently occur. Together, these data define a more precise role for RF3 in translation termination and provide insights into the function of this family of translational GTPases.
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Affiliation(s)
- Kristin S. Koutmou
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Megan E. McDonald
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Julie L. Brunelle
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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40
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Abo T, Chadani Y. The fail-safe system to rescue the stalled ribosomes in Escherichia coli. Front Microbiol 2014; 5:156. [PMID: 24782844 PMCID: PMC3989581 DOI: 10.3389/fmicb.2014.00156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022] Open
Abstract
Translation terminates at stop codon. Without stop codon, ribosome cannot terminate translation properly and reaches and stalls at the 3′-end of the mRNA lacking stop codon. Bacterial tmRNA-mediated trans-translation releases such stalled ribosome and targets the protein product to degradation by adding specific “degradation tag.” Recently two alternative ribosome rescue factors, ArfA (YhdL) and ArfB (YaeJ), have been found in Escherichia coli. These three ribosome rescue systems are different each other in terms of molecular mechanism of ribosome rescue and their activity, but they are mutually related and co-operate to maintain the translation system in shape. This suggests the biological significance of ribosome rescue.
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Affiliation(s)
- Tatsuhiko Abo
- Graduate School of Natural Science and Technology, Okayama University Okayama, Japan ; Department of Biology, Faculty of Science, Okayama University Okayama, Japan
| | - Yuhei Chadani
- Graduate School of Natural Science and Technology, Okayama University Okayama, Japan
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41
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Lentini L, Melfi R, Di Leonardo A, Spinello A, Barone G, Pace A, Palumbo Piccionello A, Pibiri I. Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay. Mol Pharm 2014; 11:653-64. [PMID: 24483936 PMCID: PMC4167060 DOI: 10.1021/mp400230s] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 12/17/2013] [Accepted: 01/31/2014] [Indexed: 01/28/2023]
Abstract
The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.
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Affiliation(s)
- Laura Lentini
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Centro di OncoBiologia
Sperimentale (COBS), via San Lorenzo
Colli, 90145 Palermo, Italy
| | - Angelo Spinello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Andrea Pace
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
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Kumal SR, Kobayashi R, Ueno S, Ichiki T. Photo-assisted Fabrication of Ribosome Display Microarray. J PHOTOPOLYM SCI TEC 2014. [DOI: 10.2494/photopolymer.27.459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Peske F, Kuhlenkoetter S, Rodnina MV, Wintermeyer W. Timing of GTP binding and hydrolysis by translation termination factor RF3. Nucleic Acids Res 2013; 42:1812-20. [PMID: 24214994 PMCID: PMC3919579 DOI: 10.1093/nar/gkt1095] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein synthesis in bacteria is terminated by release factors 1 or 2 (RF1/2), which, on recognition of a stop codon in the decoding site on the ribosome, promote the hydrolytic release of the polypeptide from the transfer RNA (tRNA). Subsequently, the dissociation of RF1/2 is accelerated by RF3, a guanosine triphosphatase (GTPase) that hydrolyzes GTP during the process. Here we show that—in contrast to a previous report—RF3 binds GTP and guanosine diphosphate (GDP) with comparable affinities. Furthermore, we find that RF3–GTP binds to the ribosome and hydrolyzes GTP independent of whether the P site contains peptidyl-tRNA (pre-termination state) or deacylated tRNA (post-termination state). RF3–GDP in either pre- or post-termination complexes readily exchanges GDP for GTP, and the exchange is accelerated when RF2 is present on the ribosome. Peptide release results in the stabilization of the RF3–GTP–ribosome complex, presumably due to the formation of the hybrid/rotated state of the ribosome, thereby promoting the dissociation of RF1/2. GTP hydrolysis by RF3 is virtually independent of the functional state of the ribosome and the presence of RF2, suggesting that RF3 acts as an unregulated ribosome-activated switch governed by its internal GTPase clock.
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Affiliation(s)
- Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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44
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Dujeancourt L, Richter R, Chrzanowska-Lightowlers ZM, Bonnefoy N, Herbert CJ. Interactions between peptidyl tRNA hydrolase homologs and the ribosomal release factor Mrf1 in S. pombe mitochondria. Mitochondrion 2013; 13:871-80. [PMID: 23892058 PMCID: PMC3919214 DOI: 10.1016/j.mito.2013.07.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 06/19/2013] [Accepted: 07/18/2013] [Indexed: 11/22/2022]
Abstract
Mitochondrial translation synthesizes key subunits of the respiratory complexes. In Schizosaccharomyces pombe, strains lacking Mrf1, the mitochondrial stop codon recognition factor, are viable, suggesting that other factors can play a role in translation termination. S. pombe contains four predicted peptidyl tRNA hydrolases, two of which (Pth3 and Pth4), have a GGQ motif that is conserved in class I release factors. We show that high dosage of Pth4 can compensate for the absence of Mrf1 and loss of Pth4 exacerbates the lack of Mrf1. Also Pth4 is a component of the mitochondrial ribosome, suggesting that it could help recycling stalled ribosomes. In S. pombe the peptidyl tRNA hydrolases Pth3 and Pth4 are mitochondrial proteins. Pth3 and Pth4 are associated with the mitochondrial ribosome and the large subunit. Deletion of pth4 and mrf1, encoding the mitochondrial release factor, is co-lethal. Over-expression of pth4 compensates for the deletion of mrf1. Pth4 can act as a release factor in S. pombe mitochondria.
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Affiliation(s)
- Laurent Dujeancourt
- Centre de Génétique Moléculaire, UPR3404, FRC3115, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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45
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome. J Phys Chem B 2013; 117:3503-15. [DOI: 10.1021/jp3110248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
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46
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Jeudy S, Abergel C, Claverie JM, Legendre M. Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. PLoS Genet 2012; 8:e1003122. [PMID: 23271980 PMCID: PMC3521657 DOI: 10.1371/journal.pgen.1003122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/12/2012] [Indexed: 12/04/2022] Open
Abstract
Mimivirus and Megavirus are the best characterized representatives of an expanding new family of giant viruses infecting Acanthamoeba. Their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. These giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. The presence of those genes, thought to be hallmarks of cellular organisms, revived fundamental interrogations on the evolutionary origin of these viruses and the link they might have with the emergence of eukaryotes. In this work, we focused on the Mimivirus-encoded translation termination factor gene, the detailed primary structure of which was elucidated using computational and experimental approaches. We demonstrated that the translation of this protein proceeds through two internal stop codons via two distinct recoding events: a frameshift and a readthrough, the combined occurrence of which is unique to these viruses. Unexpectedly, the viral gene carries an autoregulatory mechanism exclusively encountered in bacterial termination factors, though the viral sequence is related to the eukaryotic/archaeal class-I release factors. This finding is a hint that the virally-encoded translation functions may not be strictly redundant with the one provided by the host. Lastly, the perplexing occurrence of a bacterial-like regulatory mechanism in a eukaryotic/archaeal homologous gene is yet another oddity brought about by the study of giant viruses. Giant viruses, such as Mimivirus and Megavirus, have huge near-micron-sized particles and possess more genes than several cellular organisms. Furthermore their genomes encode functions not supposed to be in a virus, such as components of the protein translation apparatus. Since Lwoff in 1957, viruses are defined as ultimate obligate intracellular parasites from their need to hijack the peptide synthesis machinery of their host to replicate. We looked at the Mimivirus and Megavirus proteins that recognize the stop codons, the translation termination factors. We found that these genes contain two internal stop codons, meaning that their translation bypasses two distinct stop codons to produce a functional translation termination factor. These types of autoregulatory mechanisms are found in bacterial termination factors, although it involves only a single internal stop codon and not two, and are absent from their eukaryotic and archaeal homologs. Despite these bacterial-like features, giant viruses' termination factors have sequences that do not resemble bacterial genes but are clearly related to the eukaryotic and archaeal termination factors. Thus, giant viruses' termination factors surprisingly combine elements from eukaryotes/archaea and bacteria.
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Affiliation(s)
- Sandra Jeudy
- CNRS, Aix-Marseille Université, IGS UMR7256, Marseille, France
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47
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Abstract
The interplay of translation and mRNA turnover has helped unveil how the regulation of gene expression is a continuum in which events that occur during the birth of a transcript in the nucleus can have profound effects on subsequent steps in the cytoplasm. Exemplifying this continuum is nonsense-mediated mRNA decay (NMD), the process wherein a premature stop codon affects both translation and mRNA decay. Studies of NMD helped lead us to the therapeutic concept of treating a subset of patients suffering from multiple genetic disorders due to nonsense mutations with a single small-molecule drug that modulates the translation termination process at a premature nonsense codon. Here we review both translation termination and NMD, and our subsequent efforts over the past 15 years that led to the identification, characterization, and clinical testing of ataluren, a new therapeutic with the potential to treat a broad range of genetic disorders due to nonsense mutations.
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Affiliation(s)
- Stuart W Peltz
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA.
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48
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Keeling KM, Wang D, Conard SE, Bedwell DM. Suppression of premature termination codons as a therapeutic approach. Crit Rev Biochem Mol Biol 2012; 47:444-63. [PMID: 22672057 PMCID: PMC3432268 DOI: 10.3109/10409238.2012.694846] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. A number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (PTCs; also known as nonsense mutations) in mammalian cells. We discuss efforts to utilize these drugs to suppress disease-causing PTCs that result in the loss of protein expression and function. In-frame PTCs represent a genotypic subset of mutations that make up ~11% of all known mutations that cause genetic diseases, and millions of patients have diseases attributable to PTCs. Current approaches aimed at reducing the efficiency of translation termination at PTCs (referred to as PTC suppression therapy) have the goal of alleviating the phenotypic consequences of a wide range of genetic diseases. Suppression therapy is currently in clinical trials for treatment of several genetic diseases caused by PTCs, and preliminary results suggest that some patients have shown clinical improvements. While current progress is promising, we discuss various approaches that may further enhance the efficiency of this novel therapeutic approach.
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Affiliation(s)
- Kim M. Keeling
- Dept. of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dan Wang
- Dept. of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sara E. Conard
- Dept. of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David M. Bedwell
- Dept. of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
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49
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Chadani Y, Ito K, Kutsukake K, Abo T. ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis inEscherichia coli. Mol Microbiol 2012; 86:37-50. [DOI: 10.1111/j.1365-2958.2012.08190.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Johnson DBF, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. Release factor one is nonessential in Escherichia coli. ACS Chem Biol 2012; 7:1337-44. [PMID: 22662873 PMCID: PMC3423824 DOI: 10.1021/cb300229q] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recoding a stop codon to an amino acid may afford orthogonal genetic systems for biosynthesizing new protein and organism properties. Although reassignment of stop codons has been found in extant organisms, a model organism is lacking to investigate the reassignment process and to direct code evolution. Complete reassignment of a stop codon is precluded by release factors (RFs), which recognize stop codons to terminate translation. Here we discovered that RF1 could be unconditionally knocked out from various Escherichia coli stains, demonstrating that the reportedly essential RF1 is generally dispensable for the E. coli species. The apparent essentiality of RF1 was found to be caused by the inefficiency of a mutant RF2 in terminating all UAA stop codons; a wild type RF2 was sufficient for RF1 knockout. The RF1-knockout strains were autonomous and unambiguously reassigned UAG to encode natural or unnatural amino acids (Uaas) at multiple sites, affording a previously unavailable model for studying code evolution and a unique host for exploiting Uaas to evolve new biological functions.
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Affiliation(s)
| | | | | | - Matthew D. Schultz
- Bioinformatics
Program, University of California at San Diego, La Jolla, California
92093, United States
| | | | - Joseph R. Ecker
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland
20815, United States
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