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Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell 2015; 59:744-54. [PMID: 26321254 DOI: 10.1016/j.molcel.2015.07.018] [Citation(s) in RCA: 353] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/08/2015] [Accepted: 07/20/2015] [Indexed: 12/20/2022]
Abstract
Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy, and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance the rate of translation elongation, whereas non-optimal codons slow elongation. Codon usage also controls ribosome traffic on mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase the signal-to-noise ratio. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding.
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152
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Abstract
Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis.
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153
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Hattab G, Warschawski DE, Moncoq K, Miroux B. Escherichia coli as host for membrane protein structure determination: a global analysis. Sci Rep 2015; 5:12097. [PMID: 26160693 PMCID: PMC4498379 DOI: 10.1038/srep12097] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/11/2015] [Indexed: 11/13/2022] Open
Abstract
The structural biology of membrane proteins (MP) is hampered by the difficulty in producing and purifying them. A comprehensive analysis of protein databases revealed that 213 unique membrane protein structures have been obtained after production of the target protein in E. coli. The primary expression system used was the one based on the T7 RNA polymerase, followed by the arabinose and T5 promoter based expression systems. The C41λ(DE3) and C43λ(DE3) bacterial mutant hosts have contributed to 28% of non E. coli membrane protein structures. A large scale analysis of expression protocols demonstrated a preference for a combination of bacterial host-vector together with a bimodal distribution of induction temperature and of inducer concentration. Altogether our analysis provides a set of rules for the optimal use of bacterial expression systems in membrane protein production.
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Affiliation(s)
- Georges Hattab
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Dror E Warschawski
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL research university, Paris, France
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154
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Voorhees RM, Hegde RS. Structures of the scanning and engaged states of the mammalian SRP-ribosome complex. eLife 2015; 4. [PMID: 26158507 PMCID: PMC4497383 DOI: 10.7554/elife.07975] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/07/2015] [Indexed: 12/11/2022] Open
Abstract
The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting. DOI:http://dx.doi.org/10.7554/eLife.07975.001 Proteins are long chain-like molecules built from smaller building blocks, called amino acids, by a large molecular machine known as a ribosome. Although all proteins are assembled inside cells, some of them must be delivered to the outside or inserted into cell membranes. It is important to understand how this selective delivery system works because secreted proteins (i.e., those delivered outside) and membrane-embedded proteins are essential for cells to communicate with their surroundings. Proteins destined for secretion or membrane insertion contain characteristic stretches of amino acids that act as a targeting signal for delivery to the membrane. These targeting signals are recognized by the ‘signal recognition particle’ (or SRP for short), a large complex found in all living organisms. The SRP has the task of finding ribosomes that are assembling proteins with a targeting signal, and then taking them to the membrane. The protein being assembled can then either cross the membrane for secretion by the cell, or get embedded within the membrane. So, how can the SRP scan the broad range of proteins that are made by the ribosome and engage with only those containing targeting signals? Voorhees and Hegde investigated this question by analyzing SRPs bound to ribosomes that were at different stages of building a membrane protein. The experiment was devised so that SRP would be in two different states: in the first state, the SRP was scanning for its targeting signal and, in the second, it was engaged with the targeting signal. Voorhees and Hegde took many thousands of pictures of these samples using a technique called cryo-electron microscopy, and reconstructed the three-dimensional structures of both states. This revealed fine details of how SRP positions itself immediately next to the part of the ribosome where newly formed protein chains emerge. From here, the SRP scans the protein until the targeting signal emerges and then it engages with the protein. Engaging the targeting signal just as it emerges from the ribosome is probably important because targeting signals tend to aggregate if they are exposed to the contents of a cell. The new structures show how SRP cradles the targeting signal inside a binding groove and covers it with a protective lid to minimize its risk of aggregation. The next challenges are to figure out how SRP chooses which ribosomes to scan, and how it releases the targeting signal when it has delivered it to the membrane. DOI:http://dx.doi.org/10.7554/eLife.07975.002
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155
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López D, Pazos F. Protein functional features are reflected in the patterns of mRNA translation speed. BMC Genomics 2015; 16:513. [PMID: 26155933 PMCID: PMC4497413 DOI: 10.1186/s12864-015-1734-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 06/29/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. RESULTS We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. CONCLUSIONS This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.
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Affiliation(s)
- Daniel López
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), c/ Darwin, 3, Madrid, 28049, Spain.
- Current address: BacMine, S.L. c/ Santiago Grisolía, lab 151, Parque Científico de Madrid, Tres Cantos, Madrid, 28760, Spain.
| | - Florencio Pazos
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), c/ Darwin, 3, Madrid, 28049, Spain.
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156
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Aeschimann F, Xiong J, Arnold A, Dieterich C, Großhans H. Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling. Methods 2015; 85:75-89. [PMID: 26102273 DOI: 10.1016/j.ymeth.2015.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/10/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023] Open
Abstract
Gene expression profiling provides a tool to analyze the internal states of cells or organisms, and their responses to perturbations. While global measurements of mRNA levels have thus been widely used for many years, it is only through the recent development of the ribosome profiling technique that an analogous examination of global mRNA translation programs has become possible. Ribosome profiling reveals which RNAs are being translated to what extent and where the translated open reading frames are located. In addition, different modes of translation regulation can be distinguished and characterized. Here, we present an optimized, step-by-step protocol for ribosome profiling. Although established in Caenorhabditis elegans, our protocol and optimization approaches should be equally usable for other model organisms or cell culture with little adaptation. Next to providing a protocol, we compare two different methods for isolation of single ribosomes and two different library preparations, and describe strategies to optimize the RNase digest and to reduce ribosomal RNA contamination in the libraries. Moreover, we discuss bioinformatic strategies to evaluate the quality of the data and explain how the data can be analyzed for different applications. In sum, this article seeks to facilitate the understanding, execution, and optimization of ribosome profiling experiments.
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Affiliation(s)
- Florian Aeschimann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Jieyi Xiong
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931 Cologne, Germany
| | - Andreas Arnold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Christoph Dieterich
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9b, 50931 Cologne, Germany.
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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157
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Wilusz JE. Controlling translation via modulation of tRNA levels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:453-70. [PMID: 25919480 DOI: 10.1002/wrna.1287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are critical adaptor molecules that carry amino acids to a messenger RNA (mRNA) template during protein synthesis. Although tRNAs have commonly been viewed as abundant 'house-keeping' RNAs, it is becoming increasingly clear that tRNA expression is tightly regulated. Depending on a cell's proliferative status, the pool of active tRNAs is rapidly changed, enabling distinct translational programs to be expressed in differentiated versus proliferating cells. Here, I highlight several post-transcriptional regulatory mechanisms that allow the expression or functions of tRNAs to be altered. Modulating the modification status or structural stability of individual tRNAs can cause those specific tRNA transcripts to selectively accumulate or be degraded. Decay generally occurs via the rapid tRNA decay pathway or by the nuclear RNA surveillance machinery. In addition, the CCA-adding enzyme plays a critical role in determining the fate of a tRNA. The post-transcriptional addition of CCA to the 3' ends of stable tRNAs generates the amino acid attachment site, whereas addition of CCACCA to unstable tRNAs prevents aminoacylation and marks the tRNA for degradation. In response to various stresses, tRNAs can accumulate in the nucleus or be further cleaved into small RNAs, some of which inhibit translation. By implementing these various post-transcriptional control mechanisms, cells are able to fine-tune tRNA levels to regulate subsets of mRNAs as well as overall translation rates.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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158
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Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol 2015; 64:58-74. [PMID: 25817479 DOI: 10.1016/j.biocel.2015.03.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/02/2015] [Accepted: 03/14/2015] [Indexed: 02/07/2023]
Abstract
SCOPE Synonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health. PURPOSE This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics. PHYSIOLOGICAL AND MEDICAL RELEVANCE Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.
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159
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Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane. Proc Natl Acad Sci U S A 2015; 112:E1678-87. [PMID: 25775549 DOI: 10.1073/pnas.1424655112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chloroplast genomes encode ∼ 37 proteins that integrate into the thylakoid membrane. The mechanisms that target these proteins to the membrane are largely unexplored. We used ribosome profiling to provide a comprehensive, high-resolution map of ribosome positions on chloroplast mRNAs in separated membrane and soluble fractions in maize seedlings. The results show that translation invariably initiates off the thylakoid membrane and that ribosomes synthesizing a subset of membrane proteins subsequently become attached to the membrane in a nuclease-resistant fashion. The transition from soluble to membrane-attached ribosomes occurs shortly after the first transmembrane segment in the nascent peptide has emerged from the ribosome. Membrane proteins whose translation terminates before emergence of a transmembrane segment are translated in the stroma and targeted to the membrane posttranslationally. These results indicate that the first transmembrane segment generally comprises the signal that links ribosomes to thylakoid membranes for cotranslational integration. The sole exception is cytochrome f, whose cleavable N-terminal cpSecA-dependent signal sequence engages the thylakoid membrane cotranslationally. The distinct behavior of ribosomes synthesizing the inner envelope protein CemA indicates that sorting signals for the thylakoid and envelope membranes are distinguished cotranslationally. In addition, the fractionation behavior of ribosomes in polycistronic transcription units encoding both membrane and soluble proteins adds to the evidence that the removal of upstream ORFs by RNA processing is not typically required for the translation of internal genes in polycistronic chloroplast mRNAs.
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160
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Gorochowski TE, Ignatova Z, Bovenberg RAL, Roubos JA. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 2015; 43:3022-32. [PMID: 25765653 PMCID: PMC4381083 DOI: 10.1093/nar/gkv199] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/26/2015] [Indexed: 01/28/2023] Open
Abstract
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
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Affiliation(s)
| | - Zoya Ignatova
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Johannes A Roubos
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
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161
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Morgunov AS, Babu MM. Optimizing membrane-protein biogenesis through nonoptimal-codon usage. Nat Struct Mol Biol 2015; 21:1023-5. [PMID: 25469841 DOI: 10.1038/nsmb.2926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Alexey S Morgunov
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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162
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Protein translocation: Slowly (translate) but surely (translocate). Nat Rev Mol Cell Biol 2014; 16:2-3. [PMID: 25491102 DOI: 10.1038/nrm3921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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