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mRNA-Mediated Duplexes Play Dual Roles in the Regulation of Bidirectional Ribosomal Frameshifting. Int J Mol Sci 2018; 19:ijms19123867. [PMID: 30518074 PMCID: PMC6321510 DOI: 10.3390/ijms19123867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 11/17/2022] Open
Abstract
In contrast to -1 programmed ribosomal frameshifting (PRF) stimulation by an RNA pseudoknot downstream of frameshifting sites, a refolding upstream RNA hairpin juxtaposing the frameshifting sites attenuates -1 PRF in human cells and stimulates +1 frameshifting in yeast. This eukaryotic functional mimicry of the internal Shine-Dalgarno (SD) sequence-mediated duplex was confirmed directly in the 70S translation system, indicating that both frameshifting regulation activities of upstream hairpin are conserved between 70S and 80S ribosomes. Unexpectedly, a downstream pseudoknot also possessed two opposing hungry codon-mediated frameshifting regulation activities: attenuation of +1 frameshifting and stimulation of a non-canonical -1 frameshifting within the +1 frameshift-prone CUUUGA frameshifting site in the absence of release factor 2 (RF2) in vitro. However, the -1 frameshifting activity of the downstream pseudoknot is not coupled with its +1 frameshifting attenuation ability. Similarly, the +1 frameshifting activity of the upstream hairpin is not required for its -1 frameshifting attenuation function Thus, each of the mRNA duplexes flanking the two ends of a ribosomal mRNA-binding channel possesses two functions in bi-directional ribosomal frameshifting regulation: frameshifting stimulation and counteracting the frameshifting activity of each other.
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52
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Peng S, Sun R, Wang W, Chen C. Single-molecule FRET studies on interactions between elongation factor 4 (LepA) and ribosomes. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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53
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Shi XX, Chen H, Xie P. Dynamics of tRNA dissociation in early and later cycles of translation elongation by the ribosome. Biosystems 2018; 172:43-51. [PMID: 30184468 DOI: 10.1016/j.biosystems.2018.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 11/24/2022]
Abstract
Deacylated tRNA dissociation from E site and aminoacyl-tRNA binding to the A site of the ribosome play a critical role in repetitive cycles of protein synthesis. Available experimental data showed that in the small range of aminoacyl-tRNA concentrations, during the first few cycles of translation elongation (initiation phase of translation) the E-site tRNA can be dissociated either before or after the A-site tRNA binding, while during the later cycles of elongation (elongation phase) the E-site tRNA is mostly dissociated before the A-site tRNA binding. Here, based on our proposed model of translation elongation we study analytically the dynamics of the E-site tRNA dissociation and A-site tRNA binding, providing quantitative explanations of the available experimental data in both the initiation and elongation phases. In our model there exist two routes of state transitions within an elongation cycle in the initiation phase, with each route having stochastic E-site tRNA dissociation but with different dissociation rates. Thus, the E-site tRNA dissociation is governed by a stochastic competition between the tRNA dissociation and A-site tRNA association reactions, although in the small range of aminoacyl-tRNA concentrations used in the experiments it seems that such stochastic competition does not exist. Moreover, the detailed comparisons between the dynamics of tRNA dissociation in the initiation phase and that in the elongation phase are made.
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Affiliation(s)
- Xiao-Xuan Shi
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China; Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China
| | - Ping Xie
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China; Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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54
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Bernal-Bernal D, Abellón-Ruiz J, Iniesta AA, Pajares-Martínez E, Bastida-Martínez E, Fontes M, Padmanabhan S, Elías-Arnanz M. Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex. Nucleic Acids Res 2018. [PMID: 29893914 DOI: 10.1093/nar/gky475.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of CRISPR-Cas systems is a prerequisite for their defensive role against invading genetic elements. Yet, much remains unknown about how this crucial step is regulated. We describe a new mechanism controlling CRISPR-cas expression, which requires an extracytoplasmic function (ECF) σ factor (DdvS), its membrane-bound anti-σ (DdvA) and a global regulatory complex (CarD-CarG). Transcriptomic analyses revealed that the DdvS/CarD/CarG-dependent regulon comprises a type III-B CRISPR-Cas system in Myxococcus xanthus. We mapped four DdvS-driven CarD/CarG-dependent promoters, with one lying immediately upstream of the cas cluster. Consistent with direct action, DdvS and CarD-CarG localize at these promoters in vivo. The cas genes are transcribed as a polycistronic mRNA that reads through the leader into the CRISPR array, a putative σA-dependent promoter in the leader having negligible activity in vivo. Consequently, expression of the entire CRISPR-Cas system and mature CRISPR-RNA (crRNA) production is DdvS/CarD/CarG-dependent. DdvA likely uses its large C-terminal domain to sense and transduce the extracytoplasmic signal triggering CRISPR-cas expression, which we show is not starvation-induced multicellular development. An ECF-σ/anti-σ pair and a global regulatory complex provide an effective mechanism to coordinate signal-sensing with production of precursor crRNA, its processing Cas6 endoribonuclease and other Cas proteins for mature crRNA biogenesis and interference.
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Affiliation(s)
- Diego Bernal-Bernal
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Javier Abellón-Ruiz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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55
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Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, Puglisi JD. How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation. Annu Rev Biochem 2018; 87:421-449. [PMID: 29925264 PMCID: PMC6594189 DOI: 10.1146/annurev-biochem-060815-014818] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences. In this review, we highlight how mRNA and nascent-peptide elements manipulate the translation machinery to alter the dynamics and pathway of elongation.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
- Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
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56
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Zhang Y, Hong S, Ruangprasert A, Skiniotis G, Dunham CM. Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel. Structure 2018; 26:437-445.e3. [PMID: 29456023 PMCID: PMC5842130 DOI: 10.1016/j.str.2018.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/14/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.
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Affiliation(s)
- Yan Zhang
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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57
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Fang H, Huang YF, Radhakrishnan A, Siepel A, Lyon GJ, Schatz MC. Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Syst 2018; 6:180-191.e4. [PMID: 29361467 PMCID: PMC5832574 DOI: 10.1016/j.cels.2017.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/24/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein translation; however, sampling errors and biological biases are prevalent and poorly understood. Addressing these issues, we present Scikit-ribo (https://github.com/schatzlab/scikit-ribo), an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols (r = 0.99). Next, we show that the commonly used reads per kilobase of transcript per million mapped reads-derived TE estimation is prone to biases, especially for low-abundance genes. Scikit-ribo introduces a codon-level generalized linear model with ridge penalty that correctly estimates TE, while accommodating variable codon elongation rates and mRNA secondary structure. This corrects the TE errors for over 2,000 genes in S. cerevisiae, which we validate using mass spectrometry of protein abundances (r = 0.81), and allows us to determine the Kozak-like sequence directly from Ribo-seq. We conclude with an analysis of coverage requirements needed for robust codon-level analysis and quantify the artifacts that can occur from cycloheximide treatment.
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Affiliation(s)
- Han Fang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Aditya Radhakrishnan
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21211, USA.
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58
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Yang JR. Does mRNA structure contain genetic information for regulating co-translational protein folding? Zool Res 2018; 38:36-43. [PMID: 28271668 PMCID: PMC5368379 DOI: 10.13918/j.issn.2095-8137.2017.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of mRNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by mRNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.
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Affiliation(s)
- Jian-Rong Yang
- Department of Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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59
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Qi F, Motz M, Jung K, Lassak J, Frishman D. Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PLoS Comput Biol 2018; 14:e1005987. [PMID: 29389943 PMCID: PMC5811046 DOI: 10.1371/journal.pcbi.1005987] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/13/2018] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion. Polyproline motifs induce ribosome stalling during translation, but the functional significance of this effect remains unclear. Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E. coli proteomes as a consequence of the reduced translation efficiency, supporting the conjecture that translation efficiency-based evolutionary pressure shapes protein sequences. Enrichment of polyproline motifs in the protein regions bracketing structural domains and transmembrane helices indicates their regulatory role in co-translational protein folding and transmembrane helix insertion. Polyproline motifs could thus serve as protein-level cis-acting elements, which directly regulate the rate of translation elongation.
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Affiliation(s)
- Fei Qi
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Magdalena Motz
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,St Petersburg State Polytechnic University, St Petersburg, Russia
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60
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Sharma AK, Ahmed N, O'Brien EP. Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times. Phys Rev E 2018; 97:022409. [PMID: 29548178 DOI: 10.1103/physreve.97.022409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 06/08/2023]
Abstract
Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5.6 AA/s. How these seemingly contradictory results can be reconciled is the focus of this study. Here, we combine knowledge of the molecular factors shown to influence translation speed with genomic information from Escherichia coli, Saccharomyces cerevisiae and Homo sapiens to simulate the synthesis of cytosolic proteins in these organisms. The model recapitulates a near constant average translation rate, which we demonstrate arises because the molecular determinants of translation speed are distributed nearly randomly amongst most of the transcripts. Consequently, codon translation rates are also randomly distributed and fast-translating segments of a transcript are likely to be offset by equally probable slow-translating segments, resulting in similar average elongation rates for most transcripts. We also show that the codon usage bias does not significantly affect the near random distribution of codon translation rates because only about 10% of the total transcripts in an organism have high codon usage bias while the rest have little to no bias. Analysis of Ribo-Seq data and an in vivo fluorescent assay supports these conclusions.
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Affiliation(s)
- Ajeet K Sharma
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nabeel Ahmed
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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61
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Quandt EM, Traverse CC, Ochman H. Local genic base composition impacts protein production and cellular fitness. PeerJ 2018; 6:e4286. [PMID: 29362699 PMCID: PMC5774297 DOI: 10.7717/peerj.4286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/01/2018] [Indexed: 01/25/2023] Open
Abstract
The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.
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Affiliation(s)
- Erik M Quandt
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Charles C Traverse
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
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62
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Barik S. Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias. Heliyon 2017; 3:e00492. [PMID: 29387823 PMCID: PMC5772840 DOI: 10.1016/j.heliyon.2017.e00492] [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: 11/22/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 11/18/2022] Open
Abstract
A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.
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63
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Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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64
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Peng S, Wang W, Chen C. Breaking the Concentration Barrier for Single-Molecule Fluorescence Measurements. Chemistry 2017; 24:1002-1009. [DOI: 10.1002/chem.201704065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
| | - Wenjuan Wang
- School of Life Sciences and Technology Center for Protein Sciences; Tsinghua University; Beijing, 100084 P.R. China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing, 100084 P.R. China
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65
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Puah RY, Jia H, Maraswami M, Toh DFK, Ero R, Yang L, Patil KM, Ong AAL, Krishna MS, Sun R, Tong C, Huang M, Chen X, Loh TP, Gao YG, Liu DX, Chen G. Selective Binding to mRNA Duplex Regions by Chemically Modified Peptide Nucleic Acids Stimulates Ribosomal Frameshifting. Biochemistry 2017; 57:149-159. [PMID: 29116759 DOI: 10.1021/acs.biochem.7b00744] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minus-one programmed ribosomal frameshifting (-1 PRF) allows the precise maintenance of the ratio between viral proteins and is involved in the regulation of the half-lives of cellular mRNAs. Minus-one ribosomal frameshifting is activated by several stimulatory elements such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary structure (hairpin or pseudoknot) that is positioned 2-8 nucleotides downstream from the slippery site. Upon -1 RF, the ribosomal reading frame is shifted from the normal zero frame to the -1 frame with the heptameric slippery sequence decoded as XXX YYY Z instead of X XXY YYZ. Our research group has developed chemically modified peptide nucleic acid (PNA) L and Q monomers to recognize G-C and C-G Watson-Crick base pairs, respectively, through major-groove parallel PNA·RNA-RNA triplex formation. L- and Q-incorporated PNAs show selective binding to double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). The sequence specificity and structural selectivity of L- and Q-modified PNAs may allow the precise targeting of desired viral and cellular RNA structures, and thus may serve as valuable biological tools for mechanistic studies and potential therapeutics for fighting diseases. Here, for the first time, we demonstrate by cell-free in vitro translation assays using rabbit reticulocyte lysate that the dsRNA-specific chemically modified PNAs targeting model mRNA hairpins stimulate -1 RF (from 2% to 32%). An unmodified control PNA, however, shows nonspecific inhibition of translation. Our results suggest that the modified dsRNA-binding PNAs may be advantageous for targeting structured RNAs.
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Affiliation(s)
| | | | | | | | - Rya Ero
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | | | | | | | | | | | | | - Mei Huang
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | | | | | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551.,Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, South China Agricultural University , Guangzhou 510642, Guangdong, People's Republic of China
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66
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Bugaud O, Barbier N, Chommy H, Fiszman N, Le Gall A, Dulin D, Saguy M, Westbrook N, Perronet K, Namy O. Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single-molecule fluorescence microscopy. RNA (NEW YORK, N.Y.) 2017; 23:1626-1635. [PMID: 28768714 PMCID: PMC5648031 DOI: 10.1261/rna.061523.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/27/2017] [Indexed: 05/05/2023]
Abstract
Protein synthesis is a complex multistep process involving many factors that need to interact in a coordinated manner to properly translate the messenger RNA. As translating ribosomes cannot be synchronized over many elongation cycles, single-molecule studies have been introduced to bring a deeper understanding of prokaryotic translation dynamics. Extending this approach to eukaryotic translation is very appealing, but initiation and specific labeling of the ribosomes are much more complicated. Here, we use a noncanonical translation initiation based on internal ribosome entry sites (IRES), and we monitor the passage of individual, unmodified mammalian ribosomes at specific fluorescent milestones along mRNA. We explore initiation by two types of IRES, the intergenic IRES of cricket paralysis virus (CrPV) and the hepatitis C (HCV) IRES, and show that they both strongly limit the rate of the first elongation steps compared to the following ones, suggesting that those first elongation cycles do not correspond to a canonical elongation. This new system opens the possibility of studying both IRES-mediated initiation and elongation kinetics of eukaryotic translation and will undoubtedly be a valuable tool to investigate the role of translation machinery modifications in human diseases.
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Affiliation(s)
- Olivier Bugaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Nathalie Barbier
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Hélène Chommy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Nicolas Fiszman
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Antoine Le Gall
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - David Dulin
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Matthieu Saguy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Nathalie Westbrook
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Karen Perronet
- Laboratoire Charles Fabry, Institut d'Optique, CNRS, Université Paris-Saclay, 91127 Palaiseau, France
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
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67
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Svitkin YV, Cheng YM, Chakraborty T, Presnyak V, John M, Sonenberg N. N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. Nucleic Acids Res 2017; 45:6023-6036. [PMID: 28334758 PMCID: PMC5449617 DOI: 10.1093/nar/gkx135] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms. We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | | | | | | | | | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
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68
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Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV. Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA. Mol Cell 2017; 66:558-567.e4. [PMID: 28525745 DOI: 10.1016/j.molcel.2017.04.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022]
Abstract
Ribosome frameshifting during translation of bacterial dnaX can proceed via different routes, generating a variety of distinct polypeptides. Using kinetic experiments, we show that -1 frameshifting predominantly occurs during translocation of two tRNAs bound to the slippery sequence codons. This pathway depends on a stem-loop mRNA structure downstream of the slippery sequence and operates when aminoacyl-tRNAs are abundant. However, when aminoacyl-tRNAs are in short supply, the ribosome switches to an alternative frameshifting pathway that is independent of a stem-loop. Ribosome stalling at a vacant 0-frame A-site codon results in slippage of the P-site peptidyl-tRNA, allowing for -1-frame decoding. When the -1-frame aminoacyl-tRNA is lacking, the ribosomes switch into -2 frame. Quantitative mass spectrometry shows that the -2-frame product is synthesized in vivo. We suggest that switching between frameshifting routes may enrich gene expression at conditions of aminoacyl-tRNA limitation.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- DNA Polymerase III/biosynthesis
- DNA Polymerase III/genetics
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Frameshifting, Ribosomal
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Enzymologic
- Kinetics
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Structure-Activity Relationship
- Tandem Mass Spectrometry
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Affiliation(s)
- Neva Caliskan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Natalia Korniy
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Pearson
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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69
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Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position. Molecules 2017; 22:molecules22091427. [PMID: 28850078 PMCID: PMC5753802 DOI: 10.3390/molecules22091427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/15/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023] Open
Abstract
Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5′- and 3′-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.
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70
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Liu Y, Sharp JS, Do DHT, Kahn RA, Schwalbe H, Buhr F, Prestegard JH. Mistakes in translation: Reflections on mechanism. PLoS One 2017; 12:e0180566. [PMID: 28662217 PMCID: PMC5491249 DOI: 10.1371/journal.pone.0180566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/16/2017] [Indexed: 01/25/2023] Open
Abstract
Mistakes in translation of messenger RNA into protein are clearly a detriment to the recombinant production of pure proteins for biophysical study or the biopharmaceutical market. However, they may also provide insight into mechanistic details of the translation process. Mistakes often involve the substitution of an amino acid having an abundant codon for one having a rare codon, differing by substitution of a G base by an A base, as in the case of substitution of a lysine (AAA) for arginine (AGA). In these cases one expects the substitution frequency to depend on the relative abundances of the respective tRNAs, and thus, one might expect frequencies to be similar for all sites having the same rare codon. Here we demonstrate that, for the ADP-ribosylation factor from yeast expressed in E. coli, lysine for arginine substitutions frequencies are not the same at the 9 sites containing a rare arginine codon; mis-incorporation frequencies instead vary from less than 1 to 16%. We suggest that the context in which the codons occur (clustering of rare sites) may be responsible for the variation. The method employed to determine the frequency of mis-incorporation involves a novel mass spectrometric analysis of the products from the parallel expression of wild type and codon-optimized genes in 15N and 14N enriched media, respectively. The high sensitivity and low material requirements of the method make this a promising technology for the collection of data relevant to other mis-incorporations. The additional data could be of value in refining models for the ribosomal translation elongation process.
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Affiliation(s)
- Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi, United States of America
| | - Duc H-T. Do
- Department of Food Science and Technology, University of Georgia, Athens, Georgia, United States of America
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Florian Buhr
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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71
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Xie P, Chen H. Mechanism of ribosome translation through mRNA secondary structures. Int J Biol Sci 2017; 13:712-722. [PMID: 28655997 PMCID: PMC5485627 DOI: 10.7150/ijbs.19508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/07/2017] [Indexed: 02/03/2023] Open
Abstract
A ribosome is a macromolecular machine that is responsible for translating the genetic codes in messenger RNA (mRNA) into polypeptide chains. It has been determined that besides translating through the single-stranded region, the ribosome can also translate through the duplex region of mRNA by unwinding the duplex. To understand the mechanism of ribosome translation through the duplex, several models have been proposed to study the dynamics of mRNA unwinding. Here, we present a comprehensive review of these models and also discuss other possible models. We evaluate each model and discuss the consistency and/or inconsistency between the theoretical results that are obtained based on each model and the available experimental data, thus determining which model is the most reasonable one to describe the mRNA unwinding mechanism and dynamics of the ribosome. Moreover, a framework for future studies in this subject is provided.
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Affiliation(s)
- Ping Xie
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China.,Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, 528000, China
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72
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Peng S, Sun R, Wang W, Chen C. Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier. Angew Chem Int Ed Engl 2017; 56:6882-6885. [PMID: 28493637 PMCID: PMC5488182 DOI: 10.1002/anie.201702731] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Indexed: 01/01/2023]
Abstract
Single‐molecule fluorescence resonance energy transfer (sm‐FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm‐FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single‐molecule photoactivation FRET (sm‐PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm‐PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm‐FRET measurements. sm‐PAFRET serves as an easy‐to‐implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.
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Affiliation(s)
- Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Ruirui Sun
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
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73
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Peng S, Sun R, Wang W, Chen C. Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Sijia Peng
- School of Life Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing China
| | - Ruirui Sun
- School of Life Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing China
| | - Wenjuan Wang
- School of Life Sciences; Technology Center for Protein Sciences; Tsinghua University; Beijing China
| | - Chunlai Chen
- School of Life Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Advanced Innovation Center for Structural Biology; Tsinghua University; Beijing China
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74
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Po P, Delaney E, Gamper H, Szantai-Kis DM, Speight L, Tu L, Kosolapov A, Petersson EJ, Hou YM, Deutsch C. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. J Mol Biol 2017; 429:1873-1888. [PMID: 28483649 DOI: 10.1016/j.jmb.2017.04.019] [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: 01/23/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 12/17/2022]
Abstract
All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the life-sustaining tasks of faithfully decoding mRNA and catalyzing peptide bond formation at the peptidyl transferase center (PTC). The ribosome has evolved an exit tunnel to host the elongating new peptide, protect it from proteolytic digestion, and guide its emergence. It is here that the nascent chain begins to fold. This folding process depends on the rate of translation at the PTC. We report here that besides PTC events, translation kinetics depend on steric constraints on nascent peptide side chains and that confined movements of cramped side chains within and through the tunnel fine-tune elongation rates.
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Affiliation(s)
- Pengse Po
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Delaney
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lee Speight
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - LiWei Tu
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrey Kosolapov
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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75
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RPLP1 and RPLP2 Are Essential Flavivirus Host Factors That Promote Early Viral Protein Accumulation. J Virol 2017; 91:JVI.01706-16. [PMID: 27974556 DOI: 10.1128/jvi.01706-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue viruses (DENV), yellow fever virus (YFV), and Zika virus (ZIKV). In order to understand how these viruses replicate in human cells, we previously conducted genome-scale RNA interference screens to identify candidate host factors. In these screens, we identified ribosomal proteins RPLP1 and RPLP2 (RPLP1/2) to be among the most crucial putative host factors required for DENV and YFV infection. RPLP1/2 are phosphoproteins that bind the ribosome through interaction with another ribosomal protein, RPLP0, to form a structure termed the ribosomal stalk. RPLP1/2 were validated as essential host factors for DENV, YFV, and ZIKV infection in two human cell lines: A549 lung adenocarcinoma and HuH-7 hepatoma cells, and for productive DENV infection of Aedes aegypti mosquitoes. Depletion of RPLP1/2 caused moderate cell-line-specific effects on global protein synthesis, as determined by metabolic labeling. In A549 cells, global translation was increased, while in HuH-7 cells it was reduced, albeit both of these effects were modest. In contrast, RPLP1/2 knockdown strongly reduced early DENV protein accumulation, suggesting a requirement for RPLP1/2 in viral translation. Furthermore, knockdown of RPLP1/2 reduced levels of DENV structural proteins expressed from an exogenous transgene. We postulate that these ribosomal proteins are required for efficient translation elongation through the viral open reading frame. In summary, this work identifies RPLP1/2 as critical flaviviral host factors required for translation. IMPORTANCE Flaviviruses cause important diseases in humans. Examples of mosquito-transmitted flaviviruses include dengue, yellow fever and Zika viruses. Viruses require a plethora of cellular factors to infect cells, and the ribosome plays an essential role in all viral infections. The ribosome is a complex macromolecular machine composed of RNA and proteins and it is responsible for protein synthesis. We identified two specific ribosomal proteins that are strictly required for flavivirus infection of human cells and mosquitoes: RPLP1 and RPLP2 (RPLP1/2). These proteins are part of a structure known as the ribosomal stalk and help orchestrate the elongation phase of translation. We show that flaviviruses are particularly dependent on the function of RPLP1/2. Our findings suggest that ribosome composition is an important factor for virus translation and may represent a regulatory layer for translation of specific cellular mRNAs.
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76
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Seo YS, Shon MY, Kong R, Kang OH, Zhou T, Kim DY, Kwon DY. Black ginseng extract exerts anti-hyperglycemic effect via modulation of glucose metabolism in liver and muscle. JOURNAL OF ETHNOPHARMACOLOGY 2016; 190:231-240. [PMID: 27260409 DOI: 10.1016/j.jep.2016.05.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 04/29/2016] [Accepted: 05/29/2016] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ginseng (Panax ginseng C. A. Meyer, Araliaceae) has been used as a traditional medicine for thousands of years for the treatment of a wide variety of diseases, including diabetes. Processed ginseng named Black ginseng exhibits more potent biological activities than white and red ginseng. The aim of this study was to investigate the effects of black ginseng extract (GBG05-FF) on hyperglycemia and glucose tolerance in streptozotocin (STZ)-induced diabetic mice. MATERIALS AND METHODS Black ginseng was produced by a repeated steaming and drying process, subsequent extraction with 70% ethanol, filtration, and lyophilization. The effect of GBG05-FF on glucose uptake and related protein expression and phosphorylation were determined in C2C12 cells. Furthermore, we evaluated the anti-diabetic effects of GBG05-FF in STZ-induced diabetic mice. RESULTS GBG05-FF significantly (p<0.05) increased glucose uptake in C2C12 myotubes via AMPK, Sirt1 and PI3-K pathway. In addition, GBG05-FF improved the fasting blood glucose levels and glucose tolerance in STZ-induced diabetic mice. GBG05-FF decreased blood parameters such as glycated hemoglobin, triglyceride and total cholesterol. Quantitative RT-PCR assay revealed that in the STZ-induced diabetic mice treated with GBG05-FF, the expression of hepatic genes involved in gluconeogenesis (phosphoenolpyruvate carboxykinase (PEPCK), glucose 6-phosphatase (G6Pase)), glycogenolysis (liver glycogen phosphorylase (LGP)) and glycogenesis (glycogen synthase (GS)) was suppressed, while the expression of the genes involved in glucose uptake (glucose transporter (GLUT) 1, GLUT4) and β-oxidation (acyl-CoA oxidase (ACO), carnitine palmitoyl transferase 1a (CPT1a), mitochondrial medium chain acyl-CoA dehydrogenase (MCAD)) in muscle were increased. GBG05-FF delayed diabetes-associated muscle atrophy by activating mTOR. The major bioactive compounds including ginsenoside Rg1, Rg3(S), Rg3(R), Rg5, Rk1 and Rh4 were evaluated for glucose uptake effect in C2C12 myotubes; the data indicated that Rh4 significantly (p<0.05) increased glucose uptake. CONCLUSION Collectively, the results suggested that GBG05-FF is a potentially useful agent for treatment of diabetes by increasing glucose uptake.
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MESH Headings
- Animals
- Biomarkers/blood
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- Cell Line
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/enzymology
- Dose-Response Relationship, Drug
- Gene Expression Regulation, Enzymologic/drug effects
- Glycated Hemoglobin/metabolism
- Hypoglycemic Agents/isolation & purification
- Hypoglycemic Agents/pharmacology
- Insulin/blood
- Liver/drug effects
- Liver/enzymology
- Male
- Mice, Inbred ICR
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/enzymology
- Panax/chemistry
- Panax/classification
- Phosphorylation
- Phytotherapy
- Plant Extracts/isolation & purification
- Plant Extracts/pharmacology
- Plants, Medicinal
- Signal Transduction/drug effects
- Streptozocin
- Time Factors
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Affiliation(s)
- Yun-Soo Seo
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang-Oriental Medicines Research Institute, Wonkwang University, Iksan, Jeonbuk 570-749, Republic of Korea
| | - Mi-Yae Shon
- International Ginseng and Herb Research Institute, Geumsan, 312-804, Republic of Korea
| | - Ryong Kong
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang-Oriental Medicines Research Institute, Wonkwang University, Iksan, Jeonbuk 570-749, Republic of Korea
| | - Ok-Hwa Kang
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang-Oriental Medicines Research Institute, Wonkwang University, Iksan, Jeonbuk 570-749, Republic of Korea
| | - Tian Zhou
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang-Oriental Medicines Research Institute, Wonkwang University, Iksan, Jeonbuk 570-749, Republic of Korea
| | - Do-Yeon Kim
- International Ginseng and Herb Research Institute, Geumsan, 312-804, Republic of Korea
| | - Dong-Yeul Kwon
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang-Oriental Medicines Research Institute, Wonkwang University, Iksan, Jeonbuk 570-749, Republic of Korea.
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77
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Xie P. On the pathway of ribosomal translocation. Int J Biol Macromol 2016; 92:401-415. [PMID: 27431796 DOI: 10.1016/j.ijbiomac.2016.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/29/2022]
Abstract
The translocation of tRNAs coupled with mRNA in the ribosome is a critical process in the elongation cycle of protein synthesis. The translocation entails large-scale conformational changes of the ribosome and involves several intermediate states with tRNAs in different positions with respect to 30S and 50S ribosomal subunits. However, the detailed role of the intermediate states is unknown and the detailed mechanism and pathway of translocation is unclear. Here based on previous structural, biochemical and single-molecule data we present a translocation pathway by incorporating several intermediate states. With the pathway, we study theoretically (i) the kinetics of 30S head rotation associated with translocation catalyzed by wild-type EF-G, (ii) the dynamics of fluctuations between different tRNA states during translocation interfered with EF-G mutants and translocation-specific antibiotics, (iii) the kinetics of tRNA movement in 50S subunit and mRNA movement in 30S subunit in the presence of wild-type EF-G, EF-G mutants and translocation-specific antibiotics, (iv) the dynamics of EF-G sampling to the ribosome during translocation, etc., providing consistent and quantitative explanations of various available biochemical and single-molecule experimental data published in the literature. Moreover, we study the kinetics of 30S head rotation in the presence of EF-G mutants, providing predicted results. These have significant implications for the molecular mechanism and pathway of ribosomal translocation.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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78
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Kutchko KM, Laederach A. Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27396578 PMCID: PMC5179297 DOI: 10.1002/wrna.1374] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
Selective 2′‐hydroxyl acylation analyzed by primer extension (SHAPE) provides information on RNA structure at single‐nucleotide resolution. It is most often used in conjunction with RNA secondary structure prediction algorithms as a probabilistic or thermodynamic restraint. With the recent advent of ultra‐high‐throughput approaches for collecting SHAPE data, the applications of this technology are extending beyond structure prediction. In this review, we discuss recent applications of SHAPE data in the transcriptomic context and how this new experimental paradigm is changing our understanding of these experiments and RNA folding in general. SHAPE experiments probe both the secondary and tertiary structure of an RNA, suggesting that model‐free approaches for within and comparative RNA structure analysis can provide significant structural insight without the need for a full structural model. New methods incorporating SHAPE at different nucleotide resolutions are required to parse these transcriptomic data sets to transcend secondary structure modeling with global structural metrics. These ‘multiscale’ approaches provide deeper insights into RNA global structure, evolution, and function in the cell. WIREs RNA 2017, 8:e1374. doi: 10.1002/wrna.1374 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Katrina M Kutchko
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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79
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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80
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Elongation factor G initiates translocation through a power stroke. Proc Natl Acad Sci U S A 2016; 113:7515-20. [PMID: 27313204 DOI: 10.1073/pnas.1602668113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
During the translocation step of prokaryotic protein synthesis, elongation factor G (EF-G), a guanosine triphosphatase (GTPase), binds to the ribosomal PRE-translocation (PRE) complex and facilitates movement of transfer RNAs (tRNAs) and messenger RNA (mRNA) by one codon. Energy liberated by EF-G's GTPase activity is necessary for EF-G to catalyze rapid and precise translocation. Whether this energy is used mainly to drive movements of the tRNAs and mRNA or to foster EF-G dissociation from the ribosome after translocation has been a long-lasting debate. Free EF-G, not bound to the ribosome, adopts quite different structures in its GTP and GDP forms. Structures of EF-G on the ribosome have been visualized at various intermediate steps along the translocation pathway, using antibiotics and nonhydolyzable GTP analogs to block translocation and to prolong the dwell time of EF-G on the ribosome. However, the structural dynamics of EF-G bound to the ribosome have not yet been described during normal, uninhibited translocation. Here, we report the rotational motions of EF-G domains during normal translocation detected by single-molecule polarized total internal reflection fluorescence (polTIRF) microscopy. Our study shows that EF-G has a small (∼10°) global rotational motion relative to the ribosome after GTP hydrolysis that exerts a force to unlock the ribosome. This is followed by a larger rotation within domain III of EF-G before its dissociation from the ribosome.
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81
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Jacobson GN, Clark PL. Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons. Curr Opin Struct Biol 2016; 38:102-10. [PMID: 27318814 PMCID: PMC5010456 DOI: 10.1016/j.sbi.2016.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022]
Abstract
Protein folding occurs on a time scale similar to peptide bond formation by the ribosome, which has long sparked speculation that altering translation rate could alter the folding mechanism or even the final folded structure of a protein in vivo. Recent results have provided strong support for this model: synonymous substitutions to codons with different usage frequency, which are often translated at different rates, have been shown to significantly alter the co-translational folding mechanism of some proteins, leading to altered cell function. Here we review recent progress towards understanding the connections between synonymous codon usage, translation rate and co-translational protein folding mechanisms.
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Affiliation(s)
- Giselle N Jacobson
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patricia L Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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82
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Shebl B, Menke DE, Pennella M, Poudyal RR, Burke DH, Cornish PV. Preparation of ribosomes for smFRET studies: A simplified approach. Arch Biochem Biophys 2016; 603:118-30. [PMID: 27208427 DOI: 10.1016/j.abb.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/18/2022]
Abstract
During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET). The recent advances in fluorescently labeled ribosomes and translation components have resulted in success of smFRET experiments. Various methods have been employed to target fluorescent dyes to specific locations within the ribosome. Primarily, these methods have involved additional steps including subunit dissociation and/or full reconstitution, which could result in ribosomes of reduced activity and translation efficiency. In addition, substantial time and effort are required to produce limited quantities of material. To enable rapid and large-scale production of highly active, fluorescently labeled ribosomes, we have developed a procedure that combines partial reconstitution with His-tag purification. This allows for a homogeneous single-step purification of mutant ribosomes and subsequent integration of labeled proteins. Ribosomes produced with this method are shown to be as active as ribosomes purified using classical methods. While we have focused on two labeling sites in this report, the method is generalizable and can in principle be extended to any non-essential ribosomal protein.
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Affiliation(s)
- Bassem Shebl
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Drew E Menke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Min Pennella
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Raghav R Poudyal
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Peter V Cornish
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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83
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Trotta E. Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. BMC Genomics 2016; 17:366. [PMID: 27188984 PMCID: PMC4869280 DOI: 10.1186/s12864-016-2692-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. RESULTS In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. CONCLUSIONS In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.
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Affiliation(s)
- Edoardo Trotta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche (CNR), Rome, 00133, Italy.
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84
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Protein Elongation, Co-translational Folding and Targeting. J Mol Biol 2016; 428:2165-85. [DOI: 10.1016/j.jmb.2016.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 11/18/2022]
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85
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Tinoco I, Kim HK, Yan S. Frameshifting dynamics. Biopolymers 2016; 99:1147-66. [PMID: 23722586 DOI: 10.1002/bip.22293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/14/2013] [Accepted: 05/20/2013] [Indexed: 01/26/2023]
Abstract
Translation of messenger RNA by a ribosome occurs three nucleotides at a time from start signal to stop. However, a frameshift means that some nucleotides are read twice or some are skipped, and the following sequence of amino acids is completely different from the sequence in the original frame. In some messenger RNAs, including viral RNAs, frameshifting is programmed with RNA signals to produce specific ratios of proteins vital to the replication of the organism. The mechanisms that cause frameshifting have been studied for many years, but there are no definitive conclusions. We review ribosome structure and dynamics in relation to frameshifting dynamics provided by classical ensemble studies, and by new single-molecule methods using optical tweezers and FRET.
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Affiliation(s)
- Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460
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86
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Ishimura R, Nagy G, Dotu I, Chuang JH, Ackerman SL. Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation. eLife 2016; 5. [PMID: 27085088 PMCID: PMC4917338 DOI: 10.7554/elife.14295] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/14/2016] [Indexed: 12/17/2022] Open
Abstract
Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of C57BL/6J-Gtpbp2nmf205-/- mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNAArgUCU tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in C57BL/6J-Gtpbp2nmf205-/- mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress. DOI:http://dx.doi.org/10.7554/eLife.14295.001 Information stored in DNA is used to make proteins in a two-step process. First, the DNA is copied to make molecules of messenger ribonucleic acid (or messenger RNA for short). Next, machines called ribosomes use the messenger RNAs as templates to assemble chains of amino acids – the building blocks of proteins – in a process called translation. Another type of RNA molecule called transfer RNA carries each amino acid to the ribosomes. If a specific transfer RNA is not available for translation at the right time, the ribosome might stall as it moves along the messenger RNA. At this point, the ribosome needs to be restarted or it will fall off the mRNA without finishing the protein. In 2014, a group of researchers reported that certain types of brain cells are very sensitive to ribosome stalling, and tend to die if translation does not continue. A protein called GTPBP2 was shown to play an important role in restarting stalled ribosomes in these cells. Here, Ishimura, Nagy et al. – including some of the researchers from the earlier work – investigated the molecular pathways that ribosome stalling triggers in brain cells using mutant mice that lacked the GTPBP2 protein. The experiments show that ribosome stalling activates an enzyme known as GCN2, which was already known to sense other types of malfunctions in cellular processes. Ishimura, Nagy et al. also show that GCN2 triggers stress responses in the cells by activating a communication system called the ATF4 pathway. This pathway protects the cells from damage, and its absence results in more rapid cell deterioration and death. The next challenges are to understand the exact mechanism by which GCN2 senses stalled ribosomes, and to find out how ribosome stalling causes the death of brain cells. DOI:http://dx.doi.org/10.7554/eLife.14295.002
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Affiliation(s)
- Ryuta Ishimura
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Gabor Nagy
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Ivan Dotu
- Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, United States.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, United States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States.,Department of Cell and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, United States.,Section of Neurobiology, University of California, La Jolla, United States
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87
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Xie P. Model of the pathway of -1 frameshifting: Long pausing. Biochem Biophys Rep 2016; 5:408-424. [PMID: 28955849 PMCID: PMC5600365 DOI: 10.1016/j.bbrep.2016.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/25/2022] Open
Abstract
It has been characterized that the programmed ribosomal -1 frameshifting often occurs at the slippery sequence on the presence of a downstream mRNA pseudoknot. In some prokaryotic cases such as the dnaX gene of Escherichia coli, an additional stimulatory signal-an upstream, internal Shine-Dalgarno (SD) sequence-is also necessary to stimulate the efficient -1 frameshifting. However, the molecular and physical mechanism of the -1 frameshifting is poorly understood. Here, we propose a model of the pathway of the -1 translational frameshifting during ribosome translation of the dnaX -1 frameshift mRNA. With the model, the single-molecule fluorescence data (Chen et al. (2014) [29]) on the dynamics of the shunt either to long pausing or to normal translation, the tRNA transit and sampling dynamics in the long-paused rotated state, the EF-G sampling dynamics, the mean rotated-state lifetimes, etc., are explained quantitatively. Moreover, the model is also consistent with the experimental data (Yan et al. (2015) [30]) on translocation excursions and broad branching of frameshifting pathways. In addition, we present some predicted results, which can be easily tested by future optical trapping experiments.
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88
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Bartholomäus A, Del Campo C, Ignatova Z. Mapping the non-standardized biases of ribosome profiling. Biol Chem 2016; 397:23-35. [DOI: 10.1515/hsz-2015-0197] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 08/25/2015] [Indexed: 01/30/2023]
Abstract
Abstract
Ribosome profiling is a new emerging technology that uses massively parallel amplification of ribosome-protected fragments and next-generation sequencing to monitor translation in vivo with codon resolution. Studies using this approach provide insightful views on the regulation of translation on a global cell-wide level. In this review, we compare different experimental set-ups and current protocols for sequencing data analysis. Specifically, we review the pitfalls at some experimental steps and highlight the importance of standardized protocol for sample preparation and data processing pipeline, at least for mapping and normalization.
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89
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Hu HT, Cho CP, Lin YH, Chang KY. A general strategy to inhibiting viral -1 frameshifting based on upstream attenuation duplex formation. Nucleic Acids Res 2015; 44:256-66. [PMID: 26612863 PMCID: PMC4705660 DOI: 10.1093/nar/gkv1307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022] Open
Abstract
Viral −1 programmed ribosomal frameshifting (PRF) as a potential antiviral target has attracted interest because many human viral pathogens, including human immunodeficiency virus (HIV) and coronaviruses, rely on −1 PRF for optimal propagation. Efficient eukaryotic −1 PRF requires an optimally placed stimulator structure downstream of the frameshifting site and different strategies targeting viral −1 PRF stimulators have been developed. However, accessing particular −1 PRF stimulator information represents a bottle-neck in combating the emerging epidemic viral pathogens such as Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, an RNA hairpin upstream of frameshifting site was shown to act as a cis-element to attenuate −1 PRF with mechanism unknown. Here, we show that an upstream duplex formed in-trans, by annealing an antisense to its complementary mRNA sequence upstream of frameshifting site, can replace an upstream hairpin to attenuate −1 PRF efficiently. This finding indicates that the formation of a proximal upstream duplex is the main determining factor responsible for −1 PRF attenuation and provides mechanistic insight. Additionally, the antisense-mediated upstream duplex approach downregulates −1 PRF stimulated by distinct −1 PRF stimulators, including those of MERS-CoV, suggesting its general application potential as a robust means to evaluating viral −1 PRF inhibition as soon as the sequence information of an emerging human coronavirus is available.
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Affiliation(s)
- Hao-Teng Hu
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Che-Pei Cho
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Ya-Hui Lin
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
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90
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Li R, Zhang Q, Li J, Shi H. Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator. Nucleic Acids Res 2015; 44:2554-63. [PMID: 26602687 PMCID: PMC4824070 DOI: 10.1093/nar/gkv1285] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 11/05/2015] [Indexed: 01/25/2023] Open
Abstract
An experimental system was designed to measure in vivo termination efficiency (TE) of the Rho-independent terminator and position–function relations were quantified for the terminator tR2 in Escherichia coli. The terminator function was almost completely repressed when tR2 was located several base pairs downstream from the gene, and TE gradually increased to maximum values with the increasing distance between the gene and terminator. This TE–distance relation reflected a stochastic coupling of the ribosome and RNA polymerase (RNAP). Terminators located in the first 100 bp of the coding region can function efficiently. However, functional repression was observed when the terminator was located in the latter part of the coding region, and the degree of repression was determined by transcriptional and translational dynamics. These results may help to elucidate mechanisms of Rho-independent termination and reveal genomic locations of terminators and functions of the sequence that precedes terminators. These observations may have important applications in synthetic biology.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qing Zhang
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Junbai Li
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hualin Shi
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
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91
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Koch M, Clementi N, Rusca N, Vögele P, Erlacher M, Polacek N. The integrity of the G2421-C2395 base pair in the ribosomal E-site is crucial for protein synthesis. RNA Biol 2015; 12:70-81. [PMID: 25826414 PMCID: PMC4615901 DOI: 10.1080/15476286.2015.1017218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
During the elongation cycle of protein biosynthesis, tRNAs traverse through the ribosome by consecutive binding to the 3 ribosomal binding sites (A-, P-, and E- sites). While the ribosomal A- and P-sites have been functionally well characterized in the past, the contribution of the E-site to protein biosynthesis is still poorly understood in molecular terms. Previous studies suggested an important functional interaction of the terminal residue A76 of E-tRNA with the nucleobase of the universally conserved 23S rRNA residue C2394. Using an atomic mutagenesis approach to introduce non-natural nucleoside analogs into the 23S rRNA, we could show that removal of the nucleobase or the ribose 2'-OH at C2394 had no effect on protein synthesis. On the other hand, our data disclose the importance of the highly conserved E-site base pair G2421-C2395 for effective translation. Ribosomes with a disrupted G2421-C2395 base pair are defective in tRNA binding to the E-site. This results in an impaired translation of genuine mRNAs, while homo-polymeric templates are not affected. Cumulatively our data emphasize the importance of E-site tRNA occupancy and in particular the intactness of the 23S rRNA base pair G2421-C2395 for productive protein biosynthesis.
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Affiliation(s)
- Miriam Koch
- a Department of Chemistry and Biochemistry; University of Bern ; Bern , Switzerland
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92
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Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z. Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function. PLoS Genet 2015; 11:e1005613. [PMID: 26495981 PMCID: PMC4619774 DOI: 10.1371/journal.pgen.1005613] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/28/2015] [Indexed: 01/30/2023] Open
Abstract
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.
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Affiliation(s)
- Cristian Del Campo
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
| | - Alexander Bartholomäus
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
| | - Ivan Fedyunin
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zoya Ignatova
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry and Molecular Biology, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
- * E-mail:
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93
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Functional Importance of Mobile Ribosomal Proteins. BIOMED RESEARCH INTERNATIONAL 2015; 2015:539238. [PMID: 26457300 PMCID: PMC4592705 DOI: 10.1155/2015/539238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/12/2015] [Indexed: 01/07/2023]
Abstract
Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins), whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.
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94
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Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex. Int J Mol Sci 2015; 16:23723-44. [PMID: 26473825 PMCID: PMC4632723 DOI: 10.3390/ijms161023723] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by "hungry" codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.
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95
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Rudorf S, Lipowsky R. Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage. PLoS One 2015; 10:e0134994. [PMID: 26270805 PMCID: PMC4535986 DOI: 10.1371/journal.pone.0134994] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/15/2015] [Indexed: 11/18/2022] Open
Abstract
To synthesize a protein, a ribosome moves along a messenger RNA (mRNA), reads it codon by codon, and takes up the corresponding ternary complexes which consist of aminoacylated transfer RNAs (aa-tRNAs), elongation factor Tu (EF-Tu), and GTP. During this process of translation elongation, the ribosome proceeds with a codon-specific rate. Here, we present a general theoretical framework to calculate codon-specific elongation rates and error frequencies based on tRNA concentrations and codon usages. Our theory takes three important aspects of in-vivo translation elongation into account. First, non-cognate, near-cognate and cognate ternary complexes compete for the binding sites on the ribosomes. Second, the corresponding binding rates are determined by the concentrations of free ternary complexes, which must be distinguished from the total tRNA concentrations as measured in vivo. Third, for each tRNA species, the difference between total tRNA and ternary complex concentration depends on the codon usages of the corresponding cognate and near-cognate codons. Furthermore, we apply our theory to two alternative pathways for tRNA release from the ribosomal E site and show how the mechanism of tRNA release influences the concentrations of free ternary complexes and thus the codon-specific elongation rates. Using a recently introduced method to determine kinetic rates of in-vivo translation from in-vitro data, we compute elongation rates for all codons in Escherichia coli. We show that for some tRNA species only a few tRNA molecules are part of ternary complexes and, thus, available for the translating ribosomes. In addition, we find that codon-specific elongation rates strongly depend on the overall codon usage in the cell, which could be altered experimentally by overexpression of individual genes.
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Affiliation(s)
- Sophia Rudorf
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SR); (RL)
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SR); (RL)
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96
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Hemmati M, Zohoori E, Mehrpour O, Karamian M, Asghari S, Zarban A, Nasouti R. Anti-atherogenic potential of jujube, saffron and barberry: anti-diabetic and antioxidant actions. EXCLI JOURNAL 2015; 14:908-15. [PMID: 26600752 PMCID: PMC4650949 DOI: 10.17179/excli2015-232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/26/2015] [Indexed: 11/10/2022]
Abstract
Atherogenic dyslipidemia, characterized by an increased level of lipoprotein (a) and a decreased level of adiponectin, is a major risk factor for cardiovascular diseases in diabetic patients. To reduce cardiovascular risk in diabetic patients, use of agents with antidiabetic and anti-atherogenic potential is required. Using an animal model of diabetes, we investigated the antiatherogenic potential of extracts of three medicinal plants: jujube, barberry, and saffron. For this, serum level of fasting blood glucose, lipid profile, malondialdehyde, total antioxidant capacity, adiponectin and lipoprotein (a) in diabetic control and extract treated groups were measured. Statistical analysis of measurements showed that serum levels of fasting blood glucose, triglyceride, and VLDL decreased significantly (P < 0.05) in all treated groups. Treatment with all extracts reduced lipid peroxidation and increased antioxidant capacity of the experimental diabetic groups. Serum adiponectin levels increased in all treated groups, whereas lipoprotein (a) levels decreased, most markedly when treated with jujube extract. Jujube, saffron, and barberry extracts are beneficial in ameliorating oxidative stress and atherogenic risk of diabetic rats. This highlights the benefits of further investigating the cardio-protective potential of medicinal plant extracts and evaluating their usefulness as cardio protective agents in clinical practice.
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Affiliation(s)
- Mina Hemmati
- Atherosclerosis and Coronary Artery Research Center, Birjand University of Medical Sciences, Birjand, Iran ; Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Elham Zohoori
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Omid Mehrpour
- Atherosclerosis and Coronary Artery Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Mehdi Karamian
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Somaye Asghari
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Asghar Zarban
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Roya Nasouti
- Department of Biochemistry, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
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97
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Dunkle JA, Dunham CM. Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code. Biochimie 2015; 114:90-6. [PMID: 25708857 PMCID: PMC4458409 DOI: 10.1016/j.biochi.2015.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/11/2015] [Indexed: 01/26/2023]
Abstract
Important viral and cellular gene products are regulated by stop codon readthrough and mRNA frameshifting, processes whereby the ribosome detours from the reading frame defined by three nucleotide codons after initiation of translation. In the last few years, rapid progress has been made in mechanistically characterizing both processes and also revealing that trans-acting factors play important regulatory roles in frameshifting. Here, we review recent biophysical studies that bring new molecular insights to stop codon readthrough and frameshifting. Lastly, we consider whether there may be common mechanistic themes in -1 and +1 frameshifting based on recent X-ray crystal structures of +1 frameshift-prone tRNAs bound to the ribosome.
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Affiliation(s)
- Jack A Dunkle
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA
| | - Christine M Dunham
- Emory University School of Medicine, Department of Biochemistry, 1510 Clifton Road NE, Suite G223, Atlanta, GA 30322, USA.
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98
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Xie P. A unified model of nucleic acid unwinding by the ribosome and the hexameric and monomeric DNA helicases. J Theor Biol 2015; 380:359-66. [PMID: 26092375 DOI: 10.1016/j.jtbi.2015.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/05/2015] [Indexed: 11/18/2022]
Abstract
DNA helicases are enzymes that use the chemical energy to separate DNA duplex into their single-stranded forms. The ribosome, which catalyzes the translation of messenger RNAs (mRNAs) into proteins, can also unwind mRNA duplex. According to their structures, the DNA helicases can fall broadly into hexameric and monomeric forms. A puzzling issue for the monomeric helicases is that although they have similar structures, in vitro biochemical data showed convincingly that in the monomeric forms some have very weak DNA unwinding activities, some have relatively high unwinding activities while others have high unwinding activities. However, in the dimeric or oligomeric forms all of them have high unwinding activities. In addition, in the monomeric forms all of them can translocate efficiently along the single-stranded DNA (ssDNA). Here, we propose a model of the translocation along the ssDNA and DNA unwinding by the monomeric helicases, providing a consistent explanation of these in vitro experimental data. Moreover, by comparing the present model for the monomeric helicases with the model for the hexameric helicases and that for the ribosome which were proposed before, a unified model of nucleic acid unwinding by the three enzymes is proposed.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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99
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Caliskan N, Peske F, Rodnina MV. Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting. Trends Biochem Sci 2015; 40:265-74. [PMID: 25850333 PMCID: PMC7126180 DOI: 10.1016/j.tibs.2015.03.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022]
Abstract
–1PRF occurs when ribosomes move over a slippery sequence. A frameshifting pseudoknot/stem-loop element stalls ribosomes in a metastable state. –1PRF may contribute to the quality-control machinery in eukaryotes. Trans-acting factors (proteins, miRNAs, or antibiotics) can modulate –1PRF.
Programmed −1 ribosomal frameshifting (−1PRF) is an mRNA recoding event commonly utilized by viruses and bacteria to increase the information content of their genomes. Recent results have implicated −1PRF in quality control of mRNA and DNA stability in eukaryotes. Biophysical experiments demonstrated that the ribosome changes the reading frame while attempting to move over a slippery sequence of the mRNA – when a roadblock formed by a folded downstream segment in the mRNA stalls the ribosome in a metastable conformational state. The efficiency of −1PRF is modulated not only by cis-regulatory elements in the mRNA but also by trans-acting factors such as proteins, miRNAs, and antibiotics. These recent results suggest a molecular mechanism and new important cellular roles for −1PRF.
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Affiliation(s)
- Neva Caliskan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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100
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Mizuuchi R, Ichihashi N, Usui K, Kazuta Y, Yomo T. Adaptive evolution of an artificial RNA genome to a reduced ribosome environment. ACS Synth Biol 2015; 4:292-8. [PMID: 24933578 DOI: 10.1021/sb5000884] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reconstitution of an artificial system that has the same evolutionary ability as a living thing is a major challenge in the in vitro synthetic biology. In this study, we tested the adaptive evolutionary ability of an artificial RNA genome replication system, termed the translation-coupled RNA replication (TcRR) system. In a previous work, we performed a study of the long-term evolution of the genome with an excess amount of ribosome. In this study, we continued the evolution experiment in a reduced-ribosome environment and observed that the mutant genome compensated for the reduced ribosome concentration. This result demonstrated the ability of the TcRR system to adapt and may be a step toward generating living things with evolutionary ability.
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Affiliation(s)
- Ryo Mizuuchi
- Department
of Bioinformatics Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Department
of Bioinformatics Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kimihito Usui
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuaki Kazuta
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Department
of Bioinformatics Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate
School of Frontier Biosciences, Osaka University University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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