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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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2
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Shao N, Singh NS, Slade SE, Jones AME, Balasubramanian MK. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe. Sci Rep 2015; 5:17196. [PMID: 26597962 PMCID: PMC4657001 DOI: 10.1038/srep17196] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/02/2022] Open
Abstract
The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins.
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Affiliation(s)
- Nan Shao
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK CV4 7AL.,Department of Biological Sciences, National University of Singapore, Singapore 117543.,Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - N Sadananda Singh
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Susan E Slade
- School of Life Sciences, University of Warwick, Coventry, UK CV4 7AL
| | | | - Mohan K Balasubramanian
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK CV4 7AL.,Department of Biological Sciences, National University of Singapore, Singapore 117543.,Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Mechanobiology Institute, 5A Engineering Drive 1, National University of Singapore, Singapore 117411
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Thibodeaux GN, Liang X, Moncivais K, Umeda A, Singer O, Alfonta L, Zhang ZJ. Transforming a pair of orthogonal tRNA-aminoacyl-tRNA synthetase from Archaea to function in mammalian cells. PLoS One 2010; 5:e11263. [PMID: 20582317 PMCID: PMC2889833 DOI: 10.1371/journal.pone.0011263] [Citation(s) in RCA: 9] [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: 04/11/2010] [Accepted: 06/01/2010] [Indexed: 11/19/2022] Open
Abstract
A previously engineered Methanocaldococcus jannaschii tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair orthogonal to Escherichia coli was modified to become orthogonal in mammalian cells. The resulting tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair was able to suppress an amber codon in the green fluorescent protein, GFP, and in a foldon protein in mammalian cells. The methodology reported here will allow rapid transformation of the much larger collection of existing tyrosyl-tRNA synthetases that were already evolved for the incorporation of an array of over 50 unnatural amino acids into proteins in Escherichia coli into proteins in mammalian cells. Thus we will be able to introduce a large array of possibilities for protein modifications in mammalian cells.
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Affiliation(s)
- Gabrielle Nina Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Xiang Liang
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Kathryn Moncivais
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Aiko Umeda
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Oded Singer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Lital Alfonta
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (LA); (ZJZ)
| | - Zhiwen Jonathan Zhang
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (LA); (ZJZ)
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Hino N, Hayashi A, Sakamoto K, Yokoyama S. Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code. Nat Protoc 2007; 1:2957-62. [PMID: 17406555 DOI: 10.1038/nprot.2006.424] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a detailed protocol for incorporating non-natural amino acids, 3-iodo-L-tyrosine (IY) and p-benzoyl-L-phenylalanine (pBpa), into proteins in response to the amber codon (the UAG stop codon) in mammalian cells. These amino acids, IY and pBpa, are applicable for structure determination and the analysis of a network of protein-protein interactions, respectively. This method involves (i) the mutagenesis of the gene encoding the protein of interest to create an amber codon at the desired site, (ii) the expression in mammalian cells of the bacterial pair of an amber suppressor tRNA and an aminoacyl-tRNA synthetase specific to IY or pBpa and (iii) the supplementation of the growth medium with these amino acids. The amber mutant gene, together with these bacterial tRNA and synthetase genes, is introduced into mammalian cells. Culturing these cells for 16-40 h allows the expression of the full-length product from the mutant gene, which contains the non-natural amino acid at the introduced amber position. This method is implemented using the conventional tools for molecular biology and treating cultured mammalian cells. This protocol takes 5-6 d for plasmid construction and 3-4 d for incorporating the non-natural amino acids into proteins.
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Affiliation(s)
- Nobumasa Hino
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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Zhang Z, Alfonta L, Tian F, Bursulaya B, Uryu S, King DS, Schultz PG. Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells. Proc Natl Acad Sci U S A 2004; 101:8882-7. [PMID: 15187228 PMCID: PMC428441 DOI: 10.1073/pnas.0307029101] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Indexed: 11/18/2022] Open
Abstract
An orthogonal tryptophanyl-transfer RNA (tRNA) synthetase (TrpRS)-mutant opal suppressor tRNA(Trp) (mutRNA(UCA)(Trp)) pair was generated for use in mammalian cells. The anticodon loop of the Bacillus subtilis tRNA(Trp) was mutated to UCA, three positions in the D arm were mutated to generate an internal promoter sequence, and the mutRNA(UCA)(Trp) gene was inserted between the 5' and 3' flanking sequences of the tRNA(Trp-1) gene from Arabidopsis to enhance its expression in mammalian cells. In vitro aminoacylation assays and in vivo opal suppression assays showed that B. subtilis TrpRS (BsTrpRS) charges only the cognate mutRNA(UCA)(Trp) and no endogenous mammalian tRNAs. Similarly, the mutRNA(UCA)(Trp) is specifically charged by B. subtilis TrpRS and not by endogenous synthetases in mammalian cells. Site-directed mutagenesis was then used to alter the specificity of BsTrpRS to uniquely charge 5-hydoxy-l-tryptophan. The resulting mutant BsTrpRS-mutRNA(UCA)(Trp) pair allows the efficient and selective incorporation of 5-hydroxy-l-tryptophan into mammalian proteins in response to the codon, TGA. This amino acid can be used as a fluorescence probe and also undergoes electrochemical oxidation in situ to generate an efficient protein crosslinking.
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Affiliation(s)
- Zhiwen Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, Soma A, Kobayashi T, Kitabatake M, Takio K, Saito K, Shirouzu M, Hirao I, Yokoyama S. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 2002; 30:4692-9. [PMID: 12409460 PMCID: PMC135798 DOI: 10.1093/nar/gkf589] [Citation(s) in RCA: 189] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Revised: 08/23/2002] [Accepted: 08/23/2002] [Indexed: 11/13/2022] Open
Abstract
A suppressor tRNA(Tyr) and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA(Tyr) gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRNA, together with the cognate TyrRS, failed to exhibit suppressor activity in mammalian cells. Then, we found that amber suppression can occur with the heterologous pair of E.coli TyrRS and Bacillus stearothermophilus suppressor tRNA(Tyr), which naturally contains the promoter sequence. Furthermore, the efficiency of this suppression was significantly improved when the suppressor tRNA was expressed from a gene cluster, in which the tRNA gene was tandemly repeated nine times in the same direction. For incorporation of 3-iodo-L-tyrosine, its specific E.coli TyrRS variant, TyrRS(V37C195), which we recently created, was expressed in mammalian cells, together with the B.stearothermophilus suppressor tRNA(Tyr), while 3-iodo-L-tyrosine was supplied in the growth medium. 3-Iodo-L-tyrosine was thus incorporated into the proteins at amber positions, with an occupancy of >95%. Finally, we demonstrated conditional 3-iodo-L-tyrosine incorporation, regulated by inducible expression of the TyrRS(V37C195) gene from a tetracycline-regulated promoter.
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Affiliation(s)
- Kensaku Sakamoto
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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7
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Li K, Zhang J, Buvoli M, Yan XD, Leinwand L, He H. Ochre suppressor transfer RNA restored dystrophin expression in mdx mice. Life Sci 2000; 61:PL 205-9. [PMID: 9328234 DOI: 10.1016/s0024-3205(97)00714-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The mdx mouse is an animal model for human Duchenne muscular dystrophy. The lack of dystrophin in mdx mice is caused by an ochre mutation in exon 23 of the dystrophin gene. This study tested the feasibility of inhibiting translational termination as an approach for genetic therapy for diseases caused by nonsense mutations. We evaluated both the in vitro and in vivo efficiencies of readthrough of ochre codons in 2 genes with the tRNA suppressor gene. The first target was a CAT reporter gene bearing an ochre mutation at the 5' end (CATochre). The second target was the dystrophin gene in mdx mice. The readthrough efficiencies were about 20% in COS cells and 5.5% in rat hearts. At four weeks after a direct injection of plasmid DNA encoding the tRNA suppressor into mdx mice, dystrophin positive fibers were detected by sarcolemmal immunostaining. This is the first convincing data that a tRNA suppressor gene might be a useful in vivo treatment for the genetic disorders caused by nonsense mutations.
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Affiliation(s)
- K Li
- Department of Drug Development and Therapeutics, Sun Yet-Sen University of Medical Science, Guangzhou, P.R. China
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Buzina A, Shulman MJ. Infrequent translation of a nonsense codon is sufficient to decrease mRNA level. Mol Biol Cell 1999; 10:515-24. [PMID: 10069800 PMCID: PMC25184 DOI: 10.1091/mbc.10.3.515] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In many organisms nonsense mutations decrease the level of mRNA. In the case of mammalian cells, it is still controversial whether translation is required for this nonsense-mediated RNA decrease (NMD). Although previous analyzes have shown that conditions that impede translation termination at nonsense codons also prevent NMD, the residual level of termination was unknown in these experiments. Moreover, the conditions used to impede termination might also have interfered with NMD in other ways. Because of these uncertainties, we have tested the effects of limiting translation of a nonsense codon in a different way, using two mutations in the immunoglobulin mu heavy chain gene. For this purpose we exploited an exceptional nonsense mutation at codon 3, which efficiently terminates translation but nonetheless maintains a high level of mu mRNA. We have shown 1) that translation of Ter462 in the double mutant occurs at only approximately 4% the normal frequency, and 2) that Ter462 in cis with Ter3 can induce NMD. That is, translation of Ter462 at this low (4%) frequency is sufficient to induce NMD.
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Affiliation(s)
- A Buzina
- Departments of Immunology and Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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9
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Saks ME, Sampson JR, Nowak MW, Kearney PC, Du F, Abelson JN, Lester HA, Dougherty DA. An engineered Tetrahymena tRNAGln for in vivo incorporation of unnatural amino acids into proteins by nonsense suppression. J Biol Chem 1996; 271:23169-75. [PMID: 8798511 DOI: 10.1074/jbc.271.38.23169] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A new tRNA, THG73, has been designed and evaluated as a vehicle for incorporating unnatural amino acids site-specifically into proteins expressed in vivo using the stop codon suppression technique. The construct is a modification of tRNAGln(CUA) from Tetrahymena thermophila, which naturally recognizes the stop codon UAG. Using electrophysiological studies of mutations at several sites of the nicotinic acetylcholine receptor, it is established that THG73 represents a major improvement over previous nonsense suppressors both in terms of efficiency and fidelity of unnatural amino acid incorporation. Compared with a previous tRNA used for in vivo suppression, THG73 is as much as 100-fold less likely to be acylated by endogenous synthetases of the Xenopus oocyte. This effectively eliminates a major concern of the in vivo suppression methodology, the undesirable incorporation of natural amino acids at the suppression site. In addition, THG73 is 4-10-fold more efficient at incorporating unnatural amino acids in the oocyte system. Taken together, these two advances should greatly expand the range of applicability of the in vivo nonsense suppression methodology.
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Affiliation(s)
- M E Saks
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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10
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Hatfield DL, Smith DW, Lee BJ, Worland PJ, Oroszlan S. Structure and function of suppressor tRNAs in higher eukaryotes. Crit Rev Biochem Mol Biol 1990; 25:71-96. [PMID: 2183969 DOI: 10.3109/10409239009090606] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- D L Hatfield
- Laboratory of Experimental Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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11
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Laski FA, Ganguly S, Sharp PA, RajBhandary UL, Rubin GM. Construction, stable transformation, and function of an amber suppressor tRNA gene in Drosophila melanogaster. Proc Natl Acad Sci U S A 1989; 86:6696-8. [PMID: 2505255 PMCID: PMC297912 DOI: 10.1073/pnas.86.17.6696] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Drosophila melanogaster strains with a stably incorporated amber suppressor tRNA gene have been generated. A tRNATyr gene was site specifically mutated to produce an anticodon sequence that recognizes the amber codon and then introduced into Drosophila by using P-element-mediated transformation. Transformants from four integration events were recovered. Two integrations resulted in both male and female sterility, whereas the other two resulted in male sterility but female fertility. Strains derived from the two female-fertile integration events were shown to have a low level of amber-suppressing activity by their ability to suppress an amber mutation in a chloramphenicol acetyltransferase gene.
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Affiliation(s)
- F A Laski
- Department of Biochemistry, University of California, Berkeley 94720
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12
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Chejanovsky N, Carter BJ. Replication of a human parvovirus nonsense mutant in mammalian cells containing an inducible amber suppressor. Virology 1989; 171:239-47. [PMID: 2545030 DOI: 10.1016/0042-6822(89)90531-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
When recombinant plasmids containing the entire adeno-associated virus (AAV) genome are transfected into permissive cells infected with a helper adenovirus, infectious AAV particles are efficiently generated. These plasmids can be used to generate mutant AAV genomes or recombinant AAV vectors. Packaging of mutant AAV genomes has required complementation with a second AAV plasmid in the transfection assay which may lead to generation of significant amounts of wild-type AAV recombinants. One approach to alleviate this problem was to generate conditional lethal mutants. We constructed an AAV plasmid recombinant having a nonsense mutation in the AAV rep gene by using oligonucleotide-directed mutagenesis to convert a serine codon to an amber codon. We show that this mutant AAV can be grown on monkey cell lines containing an inducible human serine tRNA amber suppressor. The amber suppression is quite efficient and yields a burst of mutant AAV particles at about 10% of the titer of wild-type AAV. The reversion frequency of the amber mutation appears to be less than 10(-5).
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Affiliation(s)
- N Chejanovsky
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, Maryland 20892
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Abstract
This chapter discusses some observations concerning the natural occurrence and structural organization of polycistronic animal virus mRNAs, and the mechanisms by which they may be translated to yield two or more unique polypeptide products. In most polycistronic viral mRNAs, initiation of translation of both the 5’-proximal, upstream cistron and the internal, downstream cistron(s) likewise occurs at an AUG codon. Animal viruses encoding polycistronic mRNAs in which translation-initiation occurs alternatively at one or more AUG initiation sites, include members of several virus families that utilize a variety of different replication strategies as parts of their life cycles. They include: 1. viruses with DNA genomes and viruses with RNA genomes; 2. viruses with circular genomes and viruses with linear genomes; 3. viruses whose genomes are constituted by a single piece of nucleic acid, as well as viruses with segmented genomes; and 4. viruses that utilize the cell nucleus as the site for mRNA biogenesis, as well as viruses whose mRNA is synthesized in the cytoplasm. Furthermore, many different biochemical mechanisms may exist in animal cells to permit the expression of functionally polycistronic viral mRNAs.
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Sedivy JM, Capone JP, RajBhandary UL, Sharp PA. An inducible mammalian amber suppressor: propagation of a poliovirus mutant. Cell 1987; 50:379-89. [PMID: 3038332 DOI: 10.1016/0092-8674(87)90492-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We describe a general protocol for controlled gene amplification, which allows conditional expression of high levels of amber suppressor activity in monkey kidney cells, and we demonstrate its use in the genetic analysis of animal viruses by the generation and propagation of the first nonsense mutant of poliovirus. A human amber suppressor tRNASer gene linked to the SV40 origin of replication and a second DNA carrying a temperature-sensitive SV40 large T antigen gene were cotransfected into monkey cells. Cell lines having stably integrated the DNAs were isolated. Shifting the cells from the nonpermissive temperature to a lower permissive temperature caused the amplification of the suppressor tRNA gene, which resulted in suppression efficiencies at amber codons of 50%-70%, as measured by suppression of an amber codon in the E. coli chloramphenicol acetyltransferase gene. A mutant of poliovirus, in which a serine codon in the replicase gene was converted to an amber codon, was efficiently propagated on the suppressor-positive cell lines. The mutant virus reverted to wild-type by a single base change to a serine codon at a frequency of approximately 2.5 x 10(-6), surprisingly low for a RNA genome.
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16
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Ho YS, Kan YW. In vivo aminoacylation of human and Xenopus suppressor tRNAs constructed by site-specific mutagenesis. Proc Natl Acad Sci U S A 1987; 84:2185-8. [PMID: 3031670 PMCID: PMC304613 DOI: 10.1073/pnas.84.8.2185] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Amber suppressor tRNA genes were constructed by site-specific mutagenesis of the anticodons of human lysine-inserting tRNA (tRNA(Lys)) and glutamine-inserting tRNA (tRNA(Gln)) genes, and a Xenopus laevis tyrosine-inserting tRNA (tRNA(Tyr)) gene. As previous in vitro studies in prokaryotes have shown that substitution of nucleotides in the anticodon region can profoundly affect tRNA aminoacylation, it is important to determine whether the mutation affects aminoacylation of these eukaryotic tRNAs. We present a method for quantitating the tRNA aminoacylation in vivo in mammalian cells, and we have determined that the suppressor tRNA(Tyr) is fully aminoacylated and suppressor tRNA(Lys) and tRNA(Gln) are aminoacylated 40-50% and 80%, respectively. This in vivo method of estimating aminoacylation may be applied to other mutations in the tRNA genes.
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17
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Introduction of UAG, UAA, and UGA nonsense mutations at a specific site in the Escherichia coli chloramphenicol acetyltransferase gene: use in measurement of amber, ochre, and opal suppression in mammalian cells. Mol Cell Biol 1986. [PMID: 3023959 DOI: 10.1128/mcb.6.9.3059] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have used oligonucleotide-directed site-specific mutagenesis to convert serine codon 27 of the Escherichia coli chloramphenicol acetyltransferase (cat) gene to UAG, UAA, and UGA nonsense codons. The mutant cat genes, under transcriptional control of the Rous sarcoma virus long terminal repeat, were then introduced into mammalian cells by DNA transfection along with UAG, UAA, and UGA suppressor tRNA genes derived from a human serine tRNA. Assay for CAT enzymatic activity in extracts from such cells allowed us to detect and quantitate nonsense suppression in monkey CV-1 cells and mouse NIH3T3 cells. Using such an assay, we provide the first direct evidence that an opal suppressor tRNA gene is functional in mammalian cells. The pattern of suppression of the three cat nonsense mutations in bacteria suggests that the serine at position 27 of CAT can be replaced by a wide variety of amino acids without loss of enzymatic activity. Thus, these mutant cat genes should be generally useful for the quantitation of suppressor activity of suppressor tRNA genes introduced into cells and possibly for the detection of naturally occurring nonsense suppressors.
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18
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Capone JP, Sedivy JM, Sharp PA, RajBhandary UL. Introduction of UAG, UAA, and UGA nonsense mutations at a specific site in the Escherichia coli chloramphenicol acetyltransferase gene: use in measurement of amber, ochre, and opal suppression in mammalian cells. Mol Cell Biol 1986; 6:3059-67. [PMID: 3023959 PMCID: PMC367040 DOI: 10.1128/mcb.6.9.3059-3067.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have used oligonucleotide-directed site-specific mutagenesis to convert serine codon 27 of the Escherichia coli chloramphenicol acetyltransferase (cat) gene to UAG, UAA, and UGA nonsense codons. The mutant cat genes, under transcriptional control of the Rous sarcoma virus long terminal repeat, were then introduced into mammalian cells by DNA transfection along with UAG, UAA, and UGA suppressor tRNA genes derived from a human serine tRNA. Assay for CAT enzymatic activity in extracts from such cells allowed us to detect and quantitate nonsense suppression in monkey CV-1 cells and mouse NIH3T3 cells. Using such an assay, we provide the first direct evidence that an opal suppressor tRNA gene is functional in mammalian cells. The pattern of suppression of the three cat nonsense mutations in bacteria suggests that the serine at position 27 of CAT can be replaced by a wide variety of amino acids without loss of enzymatic activity. Thus, these mutant cat genes should be generally useful for the quantitation of suppressor activity of suppressor tRNA genes introduced into cells and possibly for the detection of naturally occurring nonsense suppressors.
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19
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Homa FL, Purifoy DJ, Glorioso JC, Levine M. Molecular basis of the glycoprotein C-negative phenotypes of herpes simplex virus type 1 mutants selected with a virus-neutralizing monoclonal antibody. J Virol 1986; 58:281-9. [PMID: 3009845 PMCID: PMC252911 DOI: 10.1128/jvi.58.2.281-289.1986] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previously (Holland et al., J. Virol. 52:566-574, 1984; Kikuchi et al., J. Virol. 52:806-815, 1984) we described the isolation and partial characterization of over 100 herpes simplex virus type 1 mutants which were resistant to neutralization by a pool of glycoprotein C- (gC) specific monoclonal antibodies. The genetic basis for the inability of several of these gC- mutants to express an immunoreactive envelope form of gC is reported here. Comparative nucleotide sequence analysis of the gC gene of the six mutants gC-3, gC-8, gC-49, gC-53, gC-85, and synLD70, which secrete truncated gC polypeptides, with that of the wild-type KOS 321 gC gene revealed that these mutant phenotypes were caused by frameshift or nonsense mutations, resulting in premature termination of gC translation. Secretion of the gC polypeptide from cells infected with these mutants was due to the lack of a functional transmembrane anchor sequence. The six secretor mutants were tested for suppression of amber mutations in mixed infection with a simian virus 40 amber suppressor vector. Mutant gC-85 was suppressed and produced a wild-type-sized membrane-bound gC. Nucleotide sequence analysis of the six gC deletion mutants gC-5, gC-13, gC-21, gC-39, gC-46, and gC-98 revealed that they carried identical deletions which removed 1,702 base pairs of the gC gene. The deletion, which was internal to the gC gene, removed the entire gC coding sequence and accounted for the novel 1.1-kilobase mRNA previously seen in infections with these mutants. The mutant gC-44 was previously shown to produce a membrane-bound gC protein indistinguishable in molecular weight from wild-type gC. This mutant differed from wild-type virus in that it had reduced reactivity with virus-neutralizing monoclonal antibodies. Nucleotide sequence analysis of the gC gene of mutant gC-44 demonstrated a point mutation which changed amino acid 329 of gC from a serine to a phenylalanine.
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Abstract
Oligonucleotide-directed mutagenesis was used to construct a nonsense mutation in open reading frame (ORF) E2 of bovine papillomavirus DNA. A single base substitution mutation was constructed which converted a TAC codon into a TAG amber stop codon at a position in the ORF that did not overlap with any other viral ORFs. Full-length viral DNA containing the mutation induced only approximately 2% of the transformed foci of mouse C127 cells that were induced by wild-type DNA. In a different transformation assay, approximately one-half of the C127 cells which had acquired the mutant DNA gave rise to colonies containing at least some cells with transformed morphology. The constructed mutation was maintained in cell lines derived from cells which had acquired the mutant viral DNA, but the viral DNA appeared to be integrated into the host cell genome. Genetic mapping experiments proved that the constructed amber mutation caused the decrease in focus-forming activity and the integration of the mutant viral DNA. These results suggest that ORF E2 encodes a protein which is involved either directly or indirectly in some aspects of oncogenic transformation by bovine papillomavirus and in maintaining the viral DNA as a plasmid in transformed cells.
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Pratt K, Eden FC, You KH, O'Neill VA, Hatfield D. Conserved sequences in both coding and 5' flanking regions of mammalian opal suppressor tRNA genes. Nucleic Acids Res 1985; 13:4765-75. [PMID: 4022772 PMCID: PMC321825 DOI: 10.1093/nar/13.13.4765] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The rabbit genome encodes an opal suppressor tRNA gene. The coding region is strictly conserved between the rabbit gene and the corresponding gene in the human genome. The rabbit opal suppressor gene contains the consensus sequence in the 3' internal control region but like the human and chicken genes, the rabbit 5' internal control region contains two additional nucleotides. The 5' flanking sequences of the rabbit and the human opal suppressor genes contain extensive regions of homology. A subset of these homologies is also present 5' to the chicken opal suppressor gene. Both the rabbit and the human genomes also encode a pseudogene. That of the rabbit lacks the 3' half of the coding region. Neither pseudogene has homologous regions to the 5' flanking regions of the genes. The presence of 5' homologies flanking only the transcribed genes and not the pseudogenes suggests that these regions may be regulatory control elements specifically involved in the expression of the eukaryotic opal suppressor gene. Moreover the strict conservation of coding sequences indicates functional importance for the opal suppressor tRNA genes.
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O'Neill VA, Eden FC, Pratt K, Hatfield DL. A human opal suppressor tRNA gene and pseudogene. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89581-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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