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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
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Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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Zhao Y, Lindberg BG, Esfahani SS, Tang X, Piazza S, Engström Y. Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development. BMC Biol 2021; 19:185. [PMID: 34479564 PMCID: PMC8417969 DOI: 10.1186/s12915-021-01106-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Background A number of cellular processes have evolved in metazoans that increase the proteome repertoire in relation to the genome, such as alternative splicing and translation recoding. Another such process, translational stop codon readthrough (SCR), generates C-terminally extended protein isoforms in many eukaryotes, including yeast, plants, insects, and humans. While comparative genome analyses have predicted the existence of programmed SCR in many species including humans, experimental proof of its functional consequences are scarce. Results We show that SCR of the Drosophila POU/Oct transcription factor Ventral veins lacking/Drifter (Vvl/Dfr) mRNA is prevalent in certain tissues in vivo, reaching a rate of 50% in the larval prothoracic gland. Phylogenetically, the C-terminal extension is conserved and harbors intrinsically disordered regions and amino acid stretches implied in transcriptional activation. Elimination of Vvl/Dfr translational readthrough by CRISPR/Cas9 mutagenesis changed the expression of a large number of downstream genes involved in processes such as chromatin regulation, neurogenesis, development, and immune response. As a proof-of-principle, we demonstrate that the C-terminal extension of Vvl/Dfr is necessary for correct timing of pupariation, by increasing the capacity to regulate its target genes. The extended Vvl/Dfr isoform acts in synergy with the transcription factor Molting defective (Mld) to increase the expression and biosynthesis of the steroid hormone ecdysone, thereby advancing pupariation. Consequently, late-stage larval development was prolonged and metamorphosis delayed in vvl/dfr readthrough mutants. Conclusions We demonstrate that translational recoding of a POU/Oct transcription factor takes place in a highly tissue-specific and temporally controlled manner. This dynamic and regulated recoding is necessary for normal expression of a large number of genes involved in many cellular and developmental processes. Loss of Vvl/Dfr translational readthrough negatively affects steroid hormone biosynthesis and delays larval development and progression into metamorphosis. Thus, this study demonstrates how SCR of a transcription factor can act as a developmental switch in a spatiotemporal manner, feeding into the timing of developmental transitions between different life-cycle stages. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01106-0.
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Affiliation(s)
- Yunpo Zhao
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Department of Molecular Biology, Umeå University, SE-901 87, Umeå, SE, Sweden
| | - Bo Gustav Lindberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Shiva Seyedoleslami Esfahani
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Xiongzhuo Tang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Stefano Piazza
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.,Present address: Research and Innovation Centre, Fondazione Edmund Mach, via E Mach 1, 38010, San Michele a/Adige, Italy
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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Rodnina MV, Korniy N, Klimova M, Karki P, Peng BZ, Senyushkina T, Belardinelli R, Maracci C, Wohlgemuth I, Samatova E, Peske F. Translational recoding: canonical translation mechanisms reinterpreted. Nucleic Acids Res 2020; 48:1056-1067. [PMID: 31511883 PMCID: PMC7026636 DOI: 10.1093/nar/gkz783] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
During canonical translation, the ribosome moves along an mRNA from the start to the stop codon in exact steps of one codon at a time. The collinearity of the mRNA and the protein sequence is essential for the quality of the cellular proteome. Spontaneous errors in decoding or translocation are rare and result in a deficient protein. However, dedicated recoding signals in the mRNA can reprogram the ribosome to read the message in alternative ways. This review summarizes the recent advances in understanding the mechanisms of three types of recoding events: stop-codon readthrough, –1 ribosome frameshifting and translational bypassing. Recoding events provide insights into alternative modes of ribosome dynamics that are potentially applicable to other non-canonical modes of prokaryotic and eukaryotic translation.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Bee-Zen Peng
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Tamara Senyushkina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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Kleppe AS, Bornberg-Bauer E. Robustness by intrinsically disordered C-termini and translational readthrough. Nucleic Acids Res 2019; 46:10184-10194. [PMID: 30247639 PMCID: PMC6365619 DOI: 10.1093/nar/gky778] [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: 04/18/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
During protein synthesis genetic instructions are passed from DNA via mRNA to the ribosome to assemble a protein chain. Occasionally, stop codons in the mRNA are bypassed and translation continues into the untranslated region (3′-UTR). This process, called translational readthrough (TR), yields a protein chain that becomes longer than would be predicted from the DNA sequence alone. Protein sequences vary in propensity for translational errors, which may yield evolutionary constraints by limiting evolutionary paths. Here we investigated TR in Saccharomyces cerevisiae by analysing ribosome profiling data. We clustered proteins as either prone or non-prone to TR, and conducted comparative analyses. We find that a relatively high frequency (5%) of genes undergo TR, including ribosomal subunit proteins. Our main finding is that proteins undergoing TR are highly expressed and have a higher proportion of intrinsically disordered C-termini. We suggest that highly expressed proteins may compensate for the deleterious effects of TR by having intrinsically disordered C-termini, which may provide conformational flexibility but without distorting native function. Moreover, we discuss whether minimizing deleterious effects of TR is also enabling exploration of the phenotypic landscape of protein isoforms.
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Affiliation(s)
- April Snofrid Kleppe
- Institute of Biodiversity and Evolution, University of Münster, Hüfferstr. 1, 48151 Münster, Germany
| | - Erich Bornberg-Bauer
- Institute of Biodiversity and Evolution, University of Münster, Hüfferstr. 1, 48151 Münster, Germany
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Li C, Zhang J. Stop-codon read-through arises largely from molecular errors and is generally nonadaptive. PLoS Genet 2019; 15:e1008141. [PMID: 31120886 PMCID: PMC6550407 DOI: 10.1371/journal.pgen.1008141] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/05/2019] [Accepted: 04/16/2019] [Indexed: 12/02/2022] Open
Abstract
Stop-codon read-through refers to the phenomenon that a ribosome goes past the stop codon and continues translating into the otherwise untranslated region (UTR) of a transcript. Recent ribosome-profiling experiments in eukaryotes uncovered widespread stop-codon read-through that also varies among tissues, prompting the adaptive hypothesis that stop-codon read-through is an important, regulated mechanism for generating proteome diversity. Here we propose and test a competing hypothesis that stop-codon read-through arises mostly from molecular errors and is largely nonadaptive. The error hypothesis makes distinct predictions about the probability of read-through, frequency of sequence motifs for read-through, and conservation of the read-through region, each of which is supported by genome-scale data from yeasts and fruit flies. Thus, except for the few cases with demonstrated functions, stop-codon read-through is generally nonadaptive. This finding, along with other molecular errors recently quantified, reveals a much less precise or orderly cellular life than is commonly thought. The stop codon gives the translating ribosome the signal for the termination of peptide synthesis, but occasionally the ribosome goes past the stop codon and continues translating into the otherwise untranslated region of a transcript. Stop-codon read-through generates an elongated peptide, which could be beneficial under certain circumstances. Although stop-codon read-through was thought to be rare, recent ribosome-profiling experiments in eukaryotes discovered hundreds of genes that undergo stop-codon read-through at a detectable rate. It is unclear whether most of these observed read-through events have biological functions or reflect cellular errors. The error hypothesis makes a set of distinct predictions about the probability of read-through, frequency of sequence motifs for read-through, and conservation of the read-through region. Our analysis of genome-scale data from yeasts and fruit flies verifies each of these predictions, suggesting that most stop-codon read-through events are nonadaptive cellular errors. These and related findings of various molecular errors in transcription and posttranscriptional modification paint a much less precise or orderly cellular life than is commonly portrayed.
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Affiliation(s)
- Chuan Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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