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Petrone-García VM, Castellanos-Huerta I, Tellez-Isaias G. Editorial: High-impact respiratory RNA virus diseases. Front Vet Sci 2023; 10:1273650. [PMID: 37675076 PMCID: PMC10478262 DOI: 10.3389/fvets.2023.1273650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
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2
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Sorokin II, Vassilenko KS, Terenin IM, Kalinina NO, Agol VI, Dmitriev SE. Non-Canonical Translation Initiation Mechanisms Employed by Eukaryotic Viral mRNAs. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1060-1094. [PMID: 34565312 PMCID: PMC8436584 DOI: 10.1134/s0006297921090042] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Viruses exploit the translation machinery of an infected cell to synthesize their proteins. Therefore, viral mRNAs have to compete for ribosomes and translation factors with cellular mRNAs. To succeed, eukaryotic viruses adopt multiple strategies. One is to circumvent the need for m7G-cap through alternative instruments for ribosome recruitment. These include internal ribosome entry sites (IRESs), which make translation independent of the free 5' end, or cap-independent translational enhancers (CITEs), which promote initiation at the uncapped 5' end, even if located in 3' untranslated regions (3' UTRs). Even if a virus uses the canonical cap-dependent ribosome recruitment, it can still perturb conventional ribosomal scanning and start codon selection. The pressure for genome compression often gives rise to internal and overlapping open reading frames. Their translation is initiated through specific mechanisms, such as leaky scanning, 43S sliding, shunting, or coupled termination-reinitiation. Deviations from the canonical initiation reduce the dependence of viral mRNAs on translation initiation factors, thereby providing resistance to antiviral mechanisms and cellular stress responses. Moreover, viruses can gain advantage in a competition for the translational machinery by inactivating individual translational factors and/or replacing them with viral counterparts. Certain viruses even create specialized intracellular "translation factories", which spatially isolate the sites of their protein synthesis from cellular antiviral systems, and increase availability of translational components. However, these virus-specific mechanisms may become the Achilles' heel of a viral life cycle. Thus, better understanding of the unconventional mechanisms of viral mRNA translation initiation provides valuable insight for developing new approaches to antiviral therapy.
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Affiliation(s)
- Ivan I Sorokin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Konstantin S Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Natalia O Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Vadim I Agol
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute of Poliomyelitis, Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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Langeberg CJ, Sherlock ME, MacFadden A, Kieft JS. An expanded class of histidine-accepting viral tRNA-like structures. RNA (NEW YORK, N.Y.) 2021; 27:653-664. [PMID: 33811147 PMCID: PMC8127992 DOI: 10.1261/rna.078550.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 05/12/2023]
Abstract
Structured RNA elements are common in the genomes of RNA viruses, often playing critical roles during viral infection. Some viral RNA elements use forms of tRNA mimicry, but the diverse ways this mimicry can be achieved are poorly understood. Histidine-accepting tRNA-like structures (TLSHis) are examples found at the 3' termini of some positive-sense single-stranded RNA (+ssRNA) viruses where they interact with several host proteins, induce histidylation of the RNA genome, and facilitate processes important for infection, to include genome replication. As only five TLSHis examples had been reported, we explored the possible larger phylogenetic distribution and diversity of this TLS class using bioinformatic approaches. We identified many new examples of TLSHis, yielding a rigorous consensus sequence and secondary structure model that we validated by chemical probing of representative TLSHis RNAs. We confirmed new examples as authentic TLSHis by demonstrating their ability to be histidylated in vitro, then used mutational analyses to imply a tertiary interaction that is likely analogous to the D- and T-loop interaction found in canonical tRNAs. These results expand our understanding of how diverse RNA sequences achieve tRNA-like structure and function in the context of viral RNA genomes and lay the groundwork for high-resolution structural studies of tRNA mimicry by histidine-accepting TLSs.
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Affiliation(s)
- Conner J Langeberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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4
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Sherlock ME, Hartwick EW, MacFadden A, Kieft JS. Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. RNA (NEW YORK, N.Y.) 2021; 27:27-39. [PMID: 33008837 PMCID: PMC7749636 DOI: 10.1261/rna.076968.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/26/2020] [Indexed: 05/26/2023]
Abstract
Viruses commonly use specifically folded RNA elements that interact with both host and viral proteins to perform functions important for diverse viral processes. Examples are found at the 3' termini of certain positive-sense ssRNA virus genomes where they partially mimic tRNAs, including being aminoacylated by host cell enzymes. Valine-accepting tRNA-like structures (TLSVal) are an example that share some clear homology with canonical tRNAs but have several important structural differences. Although many examples of TLSVal have been identified, we lacked a full understanding of their structural diversity and phylogenetic distribution. To address this, we undertook an in-depth bioinformatic and biochemical investigation of these RNAs, guided by recent high-resolution structures of a TLSVal We cataloged many new examples in plant-infecting viruses but also in unrelated insect-specific viruses. Using biochemical and structural approaches, we verified the secondary structure of representative TLSVal substrates and tested their ability to be valylated, confirming previous observations of structural heterogeneity within this class. In a few cases, large stem-loop structures are inserted within variable regions located in an area of the TLS distal to known host cell factor binding sites. In addition, we identified one virus whose TLS has switched its anticodon away from valine, causing a loss of valylation activity; the implications of this remain unclear. These results refine our understanding of the structural and functional mechanistic details of tRNA mimicry and how this may be used in viral infection.
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MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Base Sequence
- Binding Sites
- Computational Biology
- Genetic Variation
- Insect Viruses/classification
- Insect Viruses/genetics
- Insect Viruses/metabolism
- Models, Molecular
- Molecular Mimicry
- Phylogeny
- Plant Viruses/classification
- Plant Viruses/genetics
- Plant Viruses/metabolism
- RNA Folding
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Homology, Nucleic Acid
- Valine/metabolism
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Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Erik W Hartwick
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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5
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Guo S, Hsueh YC, Tucker-Kellogg G, Wong SM. Differential expression of novel microRNAs in response to the infection of a TMV mutant with an internal poly(A) tract in N. benthamiana. Virus Res 2017; 239:143-171. [PMID: 28668702 DOI: 10.1016/j.virusres.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/15/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022]
Abstract
We first constructed small RNA libraries of TMV- and TMV-43A-infected N. benthamiana for high throughput sequencing. A total number of 181 novel microRNAs (miRNAs) were identified through an improved miRNAs analysis pipeline. We were able to identify consistent miRNA expression changes induced in TMV and TMV-43A-infected plants, as well as differences associated with the UPD substitution in the TMV-43A viral genome. Virally induced miRNAs are associated with distinct processes and functions of predicted mRNA targets, including relation to host target defense. This study suggests an approach for functional genomics miRNAs in incompletely assembled genomes. These findings provide valuable information for further characterization of miRNAs by two genomic similar viruses, and provide clues to the study of TMV-UPD to find potential defense-related host genes targeted by miRNAs (126 words).
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | | | - Greg Tucker-Kellogg
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore; Temasek Life Sciences Laboratory, Singapore, Republic of Singapore; National University of Singapore Research Institute in Suzhou, Jiangsu, PR China.
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6
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Dewan V, Reader J, Forsyth KM. Role of aminoacyl-tRNA synthetases in infectious diseases and targets for therapeutic development. Top Curr Chem (Cham) 2013; 344:293-329. [PMID: 23666077 DOI: 10.1007/128_2013_425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play a pivotal role in protein synthesis and cell viability. These 22 "housekeeping" enzymes (1 for each standard amino acid plus pyrrolysine and o-phosphoserine) are specifically involved in recognizing and aminoacylating their cognate tRNAs in the cellular pool with the correct amino acid prior to delivery of the charged tRNA to the protein synthesis machinery. Besides serving this canonical function, higher eukaryotic AARSs, some of which are organized in the cytoplasm as a multisynthetase complex of nine enzymes plus additional cellular factors, have also been implicated in a variety of non-canonical roles. AARSs are involved in the regulation of transcription, translation, and various signaling pathways, thereby ensuring cell survival. Based in part on their versatility, AARSs have been recruited by viruses to perform essential functions. For example, host synthetases are packaged into some retroviruses and are required for their replication. Other viruses mimic tRNA-like structures in their genomes, and these motifs are aminoacylated by the host synthetase as part of the viral replication cycle. More recently, it has been shown that certain large DNA viruses infecting animals and other diverse unicellular eukaryotes encode tRNAs, AARSs, and additional components of the protein-synthesis machinery. This chapter will review our current understanding of the role of host AARSs and tRNA-like structures in viruses and discuss their potential as anti-viral drug targets. The identification and development of compounds that target bacterial AARSs, thereby serving as novel antibiotics, will also be discussed. Particular attention will be given to recent work on a number of tRNA-dependent AARS inhibitors and to advances in a new class of natural "pro-drug" antibiotics called Trojan Horse inhibitors. Finally, we will explore how bacteria that naturally produce AARS-targeting antibiotics must protect themselves against cell suicide using naturally antibiotic resistant AARSs, and how horizontal gene transfer of these AARS genes to pathogens may threaten the future use of this class of antibiotics.
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Affiliation(s)
- Varun Dewan
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Center for RNA Biology, and Center for Retroviral Research, The Ohio State University, Columbus, OH, 43210, USA
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7
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Characterization of a novel tymovirus on tomato plants in Brazil. Virus Genes 2012; 46:190-4. [DOI: 10.1007/s11262-012-0830-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/20/2012] [Indexed: 11/25/2022]
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8
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Molecular basis for RNA polymerization by Qβ replicase. Nat Struct Mol Biol 2012; 19:229-37. [PMID: 22245970 DOI: 10.1038/nsmb.2204] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 11/15/2011] [Indexed: 12/17/2022]
Abstract
Core Qβ replicase comprises the Qβ virus-encoded RNA-dependent RNA polymerase (β-subunit) and the host Escherichia coli translational elongation factors EF-Tu and EF-Ts. The functions of the host proteins in the viral replicase are not clear. Structural analyses of RNA polymerization by core Qβ replicase reveal that at the initiation stage, the 3'-adenine of the template RNA provides a stable platform for de novo initiation. EF-Tu in Qβ replicase forms a template exit channel with the β-subunit. At the elongation stages, the C-terminal region of the β-subunit, assisted by EF-Tu, splits the temporarily double-stranded RNA between the template and nascent RNAs before translocation of the single-stranded template RNA into the exit channel. Therefore, EF-Tu in Qβ replicase modulates RNA elongation processes in a distinct manner from its established function in protein synthesis.
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9
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Dreher TW. Viral tRNAs and tRNA-like structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:402-14. [PMID: 21956939 DOI: 10.1002/wrna.42] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viruses commonly exploit or modify some aspect of tRNA biology. Large DNA viruses, especially bacteriophages, phycodnaviruses, and mimiviruses, produce their own tRNAs, apparently to adjust translational capacity during infection. Retroviruses recruit specific host tRNAs for use in priming the reverse transcription of their genome. Certain positive-strand RNA plant viral genomes possess 3'-tRNA-like structures (TLSs) that are built quite differently from authentic tRNAs, and yet efficiently recapitulate several properties of tRNAs. The structures and roles of these TLSs are discussed, emphasizing the variety in both structure and function.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology and Center for Genome Research and Bioinformatics, Oregon State University, Corvallis, OR 97331, USA.
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10
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Ahlquist P, French R, Janda M, Loesch-Fries LS. Multicomponent RNA plant virus infection derived from cloned viral cDNA. Proc Natl Acad Sci U S A 2010; 81:7066-70. [PMID: 16593527 PMCID: PMC392077 DOI: 10.1073/pnas.81.22.7066] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro transcripts from mixtures of appropriate brome mosaic virus (BMV) cDNA clones are infectious when inoculated onto barley plants. Infectivity depends on in vitro transcription and on the presence of transcripts from clones of all three BMV genetic components. Infectivity is destroyed by RNase after transcription, but it is insensitive to RNase before or to DNase after transcription. Virion RNAs from plants infected with cDNA transcripts hybridize to BMV-specific probes and coelectrophorese with virion RNAs propagated from conventional inoculum. Direct RNA sequencing shows that a deletion in the noncoding region of one infectious BMV clone is preserved in viral RNA from plants systemically infected with transcript mixtures representing that clone.
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Affiliation(s)
- P Ahlquist
- Biophysics Laboratory and Plant Pathology Department, University of Wisconsin-Madison, Madison, WI 53706
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11
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Joshi RL, Faulhammer H, Chapeville F, Sprinzl M, Haenni AL. Aminoacyl RNA domain of turnip yellow mosaic virus Val-RNA interacting with elongation factor Tu. Nucleic Acids Res 2010; 12:7467-78. [PMID: 16617475 PMCID: PMC320175 DOI: 10.1093/nar/12.19.7467] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Turnip yellow mosaic virus (TYMV) Val-RNA forms a complex with the peptide elongation factor Tu (EF-Tu) in the presence of GTP: the Val-RNA is protected by EF-Tu.GTP from non-enzymatic deacylation and nuclease digestion. The determination of the length of the shortest TYMV Val-RNA fragment that binds EF-Tu.GTP leads us to conclude that the valylated aminoacyl RNA domain equivalent in tRNAs to the continuous helix formed by the acceptor stem and the T arm is sufficient for complex formation. Since the aminoacyl RNA domain is also sufficient for adenylation by the ATP(CTP):tRNA nucleotidyltransferase, an analogy can be drawn between these two tRNA-specific proteins.
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Affiliation(s)
- R L Joshi
- Institut Jacques Monod, CNRS and Université Paris VII, 2 Place Jussieu, 75251 Paris Cedex 05, France
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12
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Collmer CW, Kaper JM. Double-stranded RNAs of cucumber mosaic virus and its satellite contain an unpaired terminal guanosine: implications for replication. Virology 2008; 145:249-59. [PMID: 18640549 DOI: 10.1016/0042-6822(85)90158-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/1985] [Accepted: 05/23/1985] [Indexed: 11/25/2022]
Abstract
Terminal sequences of the double-stranded (ds) forms of RNAs 3 and 4 and the satellite RNA (CARNA 5) of cucumber mosaic virus (CMV) have been determined. The ds forms of both CARNA 5 and RNA 3 contain an unpaired guanosine (G) at the 3' end of the minus (-) strand, a feature also present in the replicative forms (RFs) of several animal alphaviruses. The unpaired G present in the CMV-related ds RNAs suggests that these molecules represent RFs and that viral and satellite RNAs share common replicative machinery. The 3' terminus of the (-) strand of ds RNA 4 is heterogeneous, with and without the added G. The existence of these two ds RNA 4 molecules suggests that replication of the subgenomic RNA 4 proceeds through a mechanism different from that of the genomic RNAs. The plus (+) strands of the ds forms of RNAs 3 and 4 and CARNA 5 are uncapped at the 5' termini and all end with a 3'-terminal cytosine (C. The 3'-terminal adenosine (A) present on most single-stranded (ss), encapsidated, CMV RNAs 3 and 4 is therefore added post-transcriptionally, and a possible control function for such a 3' terminus is discussed. The lack of an added 3'-terminal A on ss, encapsidated, CARNA 5 could result in its high replicative efficiency through escape from such a control.
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Affiliation(s)
- C W Collmer
- Plant Virology Laboratory, Plant Protection Institute, Agricultural Research Service, U. S Department of Agriculture, Beltsville, Maryland 20705, USA
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13
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Dreher TW. Role of tRNA-like structures in controlling plant virus replication. Virus Res 2008; 139:217-29. [PMID: 18638511 DOI: 10.1016/j.virusres.2008.06.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 06/14/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
Transfer RNA-like structures (TLSs) that are sophisticated functional mimics of tRNAs are found at the 3'-termini of the genomes of a number of plant positive strand RNA viruses. Three natural aminoacylation identities are represented: valine, histidine, and tyrosine. Paralleling this variety in structure, the roles of TLSs vary widely between different viruses. For Turnip yellow mosaic virus, the TLS must be capable of valylation in order to support infectivity, major roles being the provision of translational enhancement and down-regulation of minus strand initiation. In contrast, valylation of the Peanut clump virus TLS is not essential. An intermediate situation seems to exist for Brome mosaic virus, whose RNAs 1 and 2, but not RNA 3, need to be capable of tyrosylation to support infectivity. Other known roles for certain TLSs include: (i) the recruitment of host CCA nucleotidyltransferase as a telomerase to maintain intact 3' CCA termini, (ii) involvement in the encapsidation of viral RNAs, and (iii) presentation of minus strand promoter elements for replicase recognition. In the latter role, the promoter elements reside within the TLS but are not functionally dependent on tRNA mimicry. The phylogenetic distribution of TLSs indicates that their evolutionary history includes frequent horizontal exchange, as has been observed for protein-coding regions of plant positive strand RNA viruses.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology and Center for Genome Research & Bioinformatics, 220 Nash Hall, Oregon State University, Corvallis, OR 97331, USA.
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14
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Kopeina GS, Afonina ZA, Gromova KV, Shirokov VA, Vasiliev VD, Spirin AS. Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA. Nucleic Acids Res 2008; 36:2476-88. [PMID: 18310103 PMCID: PMC2377419 DOI: 10.1093/nar/gkm1177] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The time course of polysome formation was studied in a long-term wheat germ cell-free translation system using sedimentation and electron microscopy techniques. The polysomes were formed on uncapped luciferase mRNA with translation-enhancing 5' and 3' UTRs. The formation of fully loaded polysomes was found to be a long process that required many rounds of translation and proceeded via several phases. First, short linear polysomes containing no more than six ribosomes were formed. Next, folding of these polysomes into short double-row clusters occurred. Subsequent gradual elongation of the clusters gave rise to heavy-loaded double-row strings containing up to 30-40 ribosomes. The formation of the double-row polysomes was considered to be equivalent to circularization of polysomes, with antiparallel halves of the circle being laterally stuck together by ribosome interactions. A slow exchange with free ribosomes and free mRNA observed in the double-row type polysomes, as well as the resistance of translation in them to AMP-PNP, provided evidence that most polysomal ribosomes reinitiate translation within the circularized polysomes without scanning of 5' UTR, while de novo initiation including 5' UTR scanning proceeds at a much slower rate. Removal or replacements of 5' and 3' UTRs affected the initial phase of translation, but did not prevent the formation of the double-row polysomes during translation.
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Affiliation(s)
- Gelina S Kopeina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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15
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Tsonis PA, Dwivedi B. Molecular mimicry: structural camouflage of proteins and nucleic acids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1783:177-87. [PMID: 18068679 DOI: 10.1016/j.bbamcr.2007.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 11/05/2007] [Accepted: 11/06/2007] [Indexed: 11/28/2022]
Abstract
When it comes to protein specificity and function their three-dimensional structure is the ultimate determinant. Thus, sequences that participate in key parts, such as catalytic sites or DNA binding have been favored and maintained highly conserved during evolution. However, in a reversal of fortune, selection has favored conservation of shapes over sequence, especially when proteins look like nucleic acids. Proteins from pathogens evade the host's defenses because they are shaped as DNA; others use such a disguise for transcriptional regulation. Several factors are tRNA look-alikes so that they can efficiently control the process of protein synthesis. Molecular mimicry among RNAs could result in a new unexplored level in gene regulation. This comprehensive review outlines this important area and aims to emphasize that molecular mimicry could in fact be more widespread than initially thought and eventually adds a new layer of genetic regulation.
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16
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Matsuda D, Dreher TW. Cap- and initiator tRNA-dependent initiation of TYMV polyprotein synthesis by ribosomes: evaluation of the Trojan horse model for TYMV RNA translation. RNA (NEW YORK, N.Y.) 2007; 13:129-37. [PMID: 17095542 PMCID: PMC1705754 DOI: 10.1261/rna.244407] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Turnip yellow mosaic virus (TYMV) RNA directs the translation of two overlapping open reading frames. Competing models have been previously published to explain ribosome access to the downstream polyprotein cistron. The Trojan horse model, based on cell-free experiments, proposes noncanonical cap-independent initiation in which the 3'-terminal tRNA-like structure (TLS) functionally replaces initiator tRNA, and the valine bound to the TLS becomes cis-incorporated into viral protein. The initiation coupling model, based on in vivo expression and ribosome toe-printing studies, proposes a variation of canonical leaky scanning. Here, we have re-examined the wheat germ extract experiments that led to the Trojan horse model, incorporating a variety of controls. We report that (1) translation in vitro from the polyprotein AUG of TYMV RNA is unchanged after removal of the 3' TLS but is stimulated by the presence of a 5'-cap; (2) the presence of free cap analog or edeine (which interferes with initiation at the ribosomal P site and its tRNA(i) (Met) involvement) inhibits translation from the polyprotein AUG; (3) the toe-prints of immediately post-initiation ribosomes on TYMV RNA are similar with and without an intact TLS; and (4) significant deacylation of valyl-TYMV RNA in wheat germ extract can complicate the detection of cis-incorporation. These results favor the initiation coupling model.
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Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331-3804, USA
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17
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Shaloiko LA, Granovsky IE, Ivashina TV, Ksenzenko VN, Shirokov VA, Spirin AS. Effective non-viral leader for cap-independent translation in a eukaryotic cell-free system. Biotechnol Bioeng 2005; 88:730-9. [PMID: 15532099 DOI: 10.1002/bit.20267] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 61 nt 5'-untranslated region (5'-UTR) of mRNA encoding for a light-emitting protein of hydroid polyp Obelia longissima, obelin, is shown to provide a high level of cap-independent translation of heterologous mRNAs in cell-free translation systems based on wheat germ extracts. The inhibition of translation typically observed when excess mRNA is present or produced in a eukaryotic system (the so-called self-inhibition phenomenon) is found abated with mRNA constructs carrying the obelin mRNA leader. The role of the sequestration of a limiting initiation factor, probably eIF4F, in the self-inhibition phenomenon and the possible independence of the obelin mRNA leader from eIF4F are discussed. We propose the obelin mRNA leader be used for effective cap-independent translation in eukaryotic cell-free systems, including combined transcription-translation systems with uncontrolled phage polymerase-catalyzed accumulation of mRNA.
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Affiliation(s)
- L A Shaloiko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 142290
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18
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Dreher TW. Turnip yellow mosaic virus: transfer RNA mimicry, chloroplasts and a C-rich genome. MOLECULAR PLANT PATHOLOGY 2004; 5:367-75. [PMID: 20565613 DOI: 10.1111/j.1364-3703.2004.00236.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
SUMMARY Taxonomy: Turnip yellow mosaic virus (TYMV) is the type species of the genus Tymovirus, family Tymoviridae. TYMV is a positive strand RNA virus of the alphavirus-like supergroup. Physical properties: Virions are non-enveloped 28-nm T = 3 icosahedrons composed of a single 20-kDa coat protein that is clustered in 20 hexameric and 12 pentameric subunits. Infectious particles and empty capsids coexist in infected tissue. The genomic RNA is 6.3 kb long, with a 5'(m7)GpppG cap and a 3' untranslated region ending in a tRNA-like structure to which valine can be covalently added. The genome has a distinctive skewed C-rich, G-poor composition (39% C, 17% G). Viral proteins: Two proteins, whose open reading frames extensively overlap, are translated from the genomic RNA. p206, which contains sequences indicative of RNA capping, NTPase/helicase and polymerase activities, is the only viral protein that is necessary for genome replication in single cells. It is produced as a polyprotein and self-cleaved to yield 141- and 66-kDa proteins. p69 is required for virus movement within the plant and is also a suppressor of gene silencing. The coat protein is expressed from the single subgenomic RNA. Hosts and symptoms: TYMV has a narrow host range almost completely restricted to the Cruciferae. Experimental host species are Brassica pekinensis (Chinese cabbage) or B. rapa (turnip), in which diffuse chlorotic local lesions and systemic yellow mosaic symptoms appear. Arabidopsis thaliana can also be used. Clumping of chloroplasts and the accumulation of vesicular invaginations of the chloroplast outer membranes are distinctive cytopathological symptoms. High yields of virus are produced in all leaf tissues, and the virus is readily transmissible by mechanical inoculation. Localized transmission by flea beetles may occur in the field.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
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19
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Matsuda D, Dreher TW. The tRNA-like structure of Turnip yellow mosaic virus RNA is a 3'-translational enhancer. Virology 2004; 321:36-46. [PMID: 15033563 DOI: 10.1016/j.virol.2003.10.023] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2003] [Revised: 10/22/2003] [Accepted: 10/23/2003] [Indexed: 02/07/2023]
Abstract
Many positive stand RNA viral genomes lack the poly(A) tail that is characteristic of cellular mRNAs and that promotes translation in cis. The 3' untranslated regions (UTRs) of such genomes are expected to provide similar translation-enhancing properties as a poly(A) tail, yet the great variety of 3' sequences suggests that this is accomplished in a range of ways. We have identified a translational enhancer present in the 3' UTR of Turnip yellow mosaic virus (TYMV) RNA using luciferase reporter RNAs with generic 5' sequences transfected into plant cells. The 3' terminal 109 nucleotides comprising the tRNA-like structure (TLS) and an upstream pseudoknot (UPSK) act in synergy with a 5'-cap to enhance translation, with a minor contribution in stabilizing the RNA. Maximum enhancement requires that the RNA be capable of aminoacylation, but either the native valine or engineered methionine is acceptable. Mutations that decrease the affinity for translation elongation factor eEF1A (but also diminish aminoacylation efficiency) strongly decrease translational enhancement, suggesting that eEF1A is mechanistically involved. The UPSK seems to act as an important, though nonspecific, spacer element ensuring proper presentation of a functional TLS. Our studies have uncovered a novel type of translational enhancer and a new role for a plant viral TLS.
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Affiliation(s)
- Daiki Matsuda
- Department of Microbiology, Oregon State University, Corvallis, OR 97331-3804, USA
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20
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Abstract
Turnip yellow mosaic virus (TYMV) has a genomic plus-strand RNA with a 5' cap followed by overlapping and different reading frames for the movement protein and polyprotein, while the distal coat protein cistron is translated from a subgenomic RNA. The 3'-untranslated region harbors a tRNA-like structure (TLS) to which a valine moiety can be added and it is indispensable for virus viability. Here, we report about a surprising interaction between TYMV-RNA-programmed ribosomes and 3'-valylated TLS that yields polyprotein with the valine N terminally incorporated by a translation mechanism resistant to regular initiation inhibitors. Disruption of the TLS exclusively abolishes polyprotein synthesis, which can be restored by adding excess TLS in trans. Our observations imply a novel eukaryotic mechanism for internal initiation of mRNA translation.
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Affiliation(s)
- Sharief Barends
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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21
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22
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23
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24
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Fechter P, Giegé R, Rudinger-Thirion J. Specific tyrosylation of the bulky tRNA-like structure of brome mosaic virus RNA relies solely on identity nucleotides present in its amino acid-accepting domain. J Mol Biol 2001; 309:387-99. [PMID: 11371160 DOI: 10.1006/jmbi.2001.4654] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Residues specifying aminoacylation by yeast tyrosyl-tRNA synthetase (TyrRS) of the tRNA-like structure present at the 3'-end of brome mosaic virus (BMV) RNA were determined by the in vitro approach using phage T7 transcripts. They correspond to nucleotides equivalent to base-pair C1-G72 and discriminator base A73 in the amino acid-acceptor branch of the molecule. No functional equivalents of the tyrosine anticodon residues, shown to be weakly involved in tyrosine identity of canonical tRNA(Tyr), were found in the BMV tRNA-like structure. This indicates a behaviour of this large and intricate molecule reminiscent of that of a minihelix derived from an amino acid-acceptor branch. Furthermore, iodine footprinting experiments performed on a tyrosylable BMV RNA transcript of 196 nt complexed to yeast TyrRS indicate that the amino acid-acceptor branch of the viral RNA is protected against cleavages as well as a hairpin domain, which is possibly located perpendicularly to its accepting branch. This domain without the canonical anticodon loop or the tyrosine anticodon acts as an anchor for TyrRS interaction leading to a better efficiency of tyrosylation.
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Affiliation(s)
- P Fechter
- Département "Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse", UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Strasbourg Cedex F-67084, France
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25
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Abstract
In this article, I review how our research on RNA began, how it led us to demonstrate the single-stranded nature of RNA, and the ways in which it differs from double-stranded DNA. It was based on the development of a method for the isolation of undegraded rRNA and the observation that in rRNA preparations due to their viscosity behavior resemble a flexible, contractile coil. In support of this assumption, birefringence of flow measurements showed that rRNA solutions gave moderate positive values, which disappeared upon addition of salt. This is in contrast with DNA solutions where considerable negative birefringence persists even in the presence of salt. Further studies on RNA showed a close correlation of the ionic strength dependencies of optical rotation, optical density and hydrodynamic properties. These early results indicated that rRNA and tRNA possess a significant secondary structure. I then review the basis of the hairpin model for the secondary structure of RNA and finally, summarize current understanding of the tertiary structure of RNA.
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MESH Headings
- History, 20th Century
- Israel
- Nucleic Acid Conformation
- Osmolar Concentration
- RNA/chemistry
- RNA/history
- RNA/isolation & purification
- RNA, Bacterial/chemistry
- RNA, Bacterial/history
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/history
- RNA, Ribosomal/isolation & purification
- RNA, Transfer/chemistry
- RNA, Transfer/history
- RNA, Viral/chemistry
- RNA, Viral/history
- Viscosity
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Affiliation(s)
- U Z Littauer
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
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26
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Gonzalez RL, Tinoco I. Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot. J Mol Biol 1999; 289:1267-82. [PMID: 10373367 DOI: 10.1006/jmbi.1999.2841] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Identification and characterization of a metal ion binding site in an RNA pseudoknot was accomplished using cobalt (III) hexammine, Co(NH3)63+, as a probe for magnesium (II) hexahydrate, Mg(H2O)62+, in nuclear magnetic resonance (NMR) structural studies. The pseudoknot causes efficient -1 ribosomal frameshifting in mouse mammary tumor virus. Divalent metal ions, such as Mg2+, are critical for RNA structure and function; Mg2+preferentially stabilizes the pseudoknot relative to its constituent hairpins. The use of Co(NH3)63+as a substitute for Mg2+was investigated by ultraviolet absorbance melting curves, NMR titrations of the imino protons, and analysis of NMR spectra in the presence of Mg2+or Co (NH3)63+. The structure of the pseudoknot-Co(NH3)63+complex reveals an ion-binding pocket formed by a short, two-nucleotide loop and the major groove of a stem. Co(NH3)63+stabilizes the sharp loop-to-stem turn and reduces the electrostatic repulsion of the phosphates in three proximal strands. Hydrogen bonds are identified between the Co(NH3)63+protons and non-bridging phosphate oxygen atoms, 2' hydroxyl groups, and nitrogen and oxygen acceptors on the bases. The binding site is significantly different from that previously characterized in the major groove surface of tandem G.U base-pairs, but is similar to those observed in crystal structures of a fragment of the 5 S rRNA and the P5c helix of the Tetrahymena thermophila group I intron. Changes in chemical shifts occurred at the same pseudoknot protons on addition of Mg2+as on addition of Co(NH3)63+, indicating that both ions bind at the same site. Ion binding dissociation constants of approximately 0.6 mM and 5 mM (in 200 mM Na+and a temperature of 15 degrees C) were obtained for Co(NH3)63+and Mg2+, respectively, from the change in chemical shift as a function of metal ion concentration. An extensive array of non-sequence-specific hydrogen bond acceptors coupled with conserved structural elements within the binding pocket suggest a general mode of divalent metal ion stabilization of this type of frameshifter pseudoknot. These results provide new thermodynamic and structural insights into the role divalent metal ions play in stabilizing RNA tertiary structural motifs such as pseudoknots.
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Affiliation(s)
- R L Gonzalez
- Berkeley and Structural Biology Department, Physical Biosciences Division, University of California, Berkeley, CA, 94720-1460, USA
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27
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Chapman MR, Kao CC. A minimal RNA promoter for minus-strand RNA synthesis by the brome mosaic virus polymerase complex. J Mol Biol 1999; 286:709-20. [PMID: 10024445 DOI: 10.1006/jmbi.1998.2503] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The approximately 150 nt tRNA-like structure present at the 3' end of each of the brome mosaic virus (BMV) genomic RNAs is sufficient to direct minus-strand RNA synthesis. RNAs containing mutations in the tRNA-like structure that decrease minus-strand synthesis were tested for their ability to interact with RdRp (RNA-dependent RNA polymerase) using a template competition assay. Mutations that are predicted to disrupt the pseudoknot and stem B1 do not affect the ability of the tRNA-like structure to interact with RdRp. Similarly, the +1 and +2 nucleotides are not required for stable template-RdRp interaction. Mutations in the bulge and hairpin loops of stem C decreased the ability of the tRNA-like structure to interact with RdRp. Furthermore, in the absence of the rest of the BMV tRNA, stem C is able to interact with RdRp. The addition of an accessible initiation sequence containing ACCA3' to stem C created an RNA capable of directing RNA synthesis. Synthesis from this minimal minus-strand template is dependent on sequences in the hairpin and bulged loops.
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Affiliation(s)
- M R Chapman
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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28
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Becker HF, Motorin Y, Florentz C, Giegé R, Grosjean H. Pseudouridine and ribothymidine formation in the tRNA-like domain of turnip yellow mosaic virus RNA. Nucleic Acids Res 1998; 26:3991-7. [PMID: 9705510 PMCID: PMC147804 DOI: 10.1093/nar/26.17.3991] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The last 82 nucleotides of the 6.3 kb genomic RNA of plant turnip yellow mosaic virus (TYMV), the so-called 'tRNA-like' domain, presents functional, structural and primary sequence homologies with canonical tRNAs. In particular, one of the stem-loops resembles the TPsi(pseudouridine)-branch of tRNA, except for the presence of a guanosine at position 37 (numbering is from the 3'-end) instead of the classical uridine-55 in tRNA (numbering is from the 5'-end). Both the wild-type TYMV-RNA fragment and a variant, TYMV-mut G37U in which G-37 has been replaced by U-37, have been tested as potential substrates for the yeast tRNA modification enzymes. Results indicate that two modified nucleotides were formed upon incubation of the wild-type TYMV-fragment in a yeast extract: one Psi which formed quantitatively at position 65, and one ribothymidine (T) which formed at low level at position U-38. In the TYMV-mutant G37U, besides the quantitative formation of both Psi-65 and T-38, an additional Psi was detected at position 37. Modified nucleotides Psi-65, T-38 and Psi-37 in TYMV RNA are equivalent to Psi-27, T-54 and Psi-55 in tRNA, respectively. Purified yeast recombinant tRNA:Psisynthases (Pus1 and Pus4), which catalyze respectively the formation of Psi-27 and Psi-55 in yeast tRNAs, are shown to catalyze the quantitative formation of Psi-65 and Psi-37, respectively, in the tRNA-like 3'-domain of mutant TYMV RNA in vitro . These results are discussed in relation to structural elements that are needed by the corresponding enzymes in order to catalyze these post-transcriptional modification reactions.
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Affiliation(s)
- H F Becker
- Laboratoire d'Enzymologie et Biochimie Structurales du CNRS, 1, avenue de la Terrasse, Bâtiment 34,F-91198 Gif-sur-Yvette, France
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29
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Lai MM. Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription. Virology 1998; 244:1-12. [PMID: 9581772 DOI: 10.1006/viro.1998.9098] [Citation(s) in RCA: 219] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Viral RNA replication and transcription involves not only viral RNA-dependent RNA polymerases, but also cellular proteins, the majority of which are subverted from the RNA-processing or translation machineries of host cells. These factors interact with viral RNA or polymerases to form transcription or replication ribonucleoprotein complexes and may provide template specificity for RNA-dependent RNA synthesis, suggesting a close parallel to the mechanism of DNA-dependent RNA synthesis. The types of cellular proteins involved and their modes of action are reviewed.
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Affiliation(s)
- M M Lai
- Howard Hughes Medical Institute and Department of Molecular Microbiology and Immunology, University of Southern California School of Medicine, Los Angeles 90033-1054, USA.
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30
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Hsue B, Masters PS. A bulged stem-loop structure in the 3' untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J Virol 1997; 71:7567-78. [PMID: 9311837 PMCID: PMC192104 DOI: 10.1128/jvi.71.10.7567-7578.1997] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The 3' untranslated region (UTR) of the positive-sense RNA genome of the coronavirus mouse hepatitis virus (MHV) contains sequences that are necessary for the synthesis of negative-strand viral RNA as well as sequences that may be crucial for both genomic and subgenomic positive-strand RNA synthesis. We have found that the entire 3' UTR of MHV could be replaced by the 3' UTR of bovine coronavirus (BCV), which diverges overall by 31% in nucleotide sequence. This exchange between two viruses that are separated by a species barrier was carried out by targeted RNA recombination. Our results define regions of the two 3' UTRs that are functionally equivalent despite having substantial sequence substitutions, deletions, or insertions with respect to each other. More significantly, our attempts to generate an unallowed substitution of a particular portion of the BCV 3' UTR for the corresponding region of the MHV 3' UTR led to the discovery of a bulged stem-loop RNA secondary structure, adjacent to the stop codon of the nucleocapsid gene, that is essential for MHV viral RNA replication.
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Affiliation(s)
- B Hsue
- Department of Biomedical Sciences, University at Albany, State University of New York, 12201, USA
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31
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Houser-Scott F, Ansel-McKinney P, Cai JM, Gehrke L. In vitro genetic selection analysis of alfalfa mosaic virus coat protein binding to 3'-terminal AUGC repeats in the viral RNAs. J Virol 1997; 71:2310-9. [PMID: 9032367 PMCID: PMC191340 DOI: 10.1128/jvi.71.3.2310-2319.1997] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The coat proteins of alfalfa mosaic virus (AMV) and the related ilarviruses bind specifically to the 3' untranslated regions of the viral RNAs, which contain conserved repeats of the tetranucleotide sequence AUGC. The purpose of this study was to develop a more detailed understanding of RNA sequence and/or structural determinants required for coat protein binding by characterizing the role of the AUGC repeats. Starting with a complex pool of 39-nucleotide RNA molecules containing random substitutions in the AUGC repeats, in vitro genetic selection was used to identify RNAs that bound coat protein. After six iterative rounds of selection, amplification, and reselection, 25% of the RNAs selected from the randomized pool were wild type; that is, they contained all four AUGC sequences. Among the 31 clones analyzed, AUGC was clearly the preferred selected sequence at the four repeats, but some nucleotide sequence variability was observed at AUGC(865-868) if the other three AUGC repeats were present. Variant RNAs that bound coat protein with affinities equal to or greater than that of the wild-type molecule were not selected. To extend the in vitro selection results, RNAs containing specific nucleotide substitutions were transcribed in vitro and tested in coat protein and peptide binding assays. The data strongly suggest that the AUGC repeats provide sequence-specific determinants and contribute to a structural platform for specific coat protein binding. Coat protein may function in maintaining the 3' ends of the genomic RNAs during replication by stabilizing an RNA structure that defines the 3' terminus as the initiation site for minus-strand synthesis.
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Affiliation(s)
- F Houser-Scott
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
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32
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cis-Acting Signals in Bromovirus RNA Replication and Gene Expression: Networking with Viral Proteins and Host Factors. ACTA ACUST UNITED AC 1997. [DOI: 10.1006/smvy.1997.0125] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Giegé R. Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries. Proc Natl Acad Sci U S A 1996; 93:12078-81. [PMID: 8901535 PMCID: PMC37945 DOI: 10.1073/pnas.93.22.12078] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- R Giegé
- Unité Propre de Recherche 9002 Structures des Macromolécules Biologiques et Mécanismes de Reconnaissance, Centre National de la Recherche Scientifique, Strasbourg, France
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34
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Klaff P, Riesner D, Steger G. RNA structure and the regulation of gene expression. PLANT MOLECULAR BIOLOGY 1996; 32:89-106. [PMID: 8980476 DOI: 10.1007/bf00039379] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RNA secondary and tertiary structure is involved in post-transcriptional regulation of gene expression either by exposing specific sequences or through the formation of specific structural motifs. An overview of RNA secondary and tertiary structures known from biophysical studies is followed by a review of examples of the elements of RNA processing, mRNA stability and translation of the messenger. These structural elements comprise sense-antisense double-stranded RNA, hairpin and stem-loop structures, and more complex structures such as bifurcations, pseudoknots and triple-helical elements. Metastable structures formed during RNA folding pathway are also discussed. The examples presented are mostly chosen from plant systems, plant viruses, and viroids. Examples from bacteria or fungi are discussed only when unique regulatory properties of RNA structures have been elucidated in these systems.
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Affiliation(s)
- P Klaff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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35
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Tanguay RL, Gallie DR. Isolation and characterization of the 102-kilodalton RNA-binding protein that binds to the 5' and 3' translational enhancers of tobacco mosaic virus RNA. J Biol Chem 1996; 271:14316-22. [PMID: 8663059 DOI: 10.1074/jbc.271.24.14316] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Tobacco mosaic virus (TMV) is a positive-sense, single-stranded RNA virus the genome of which acts as a mRNA in the cytoplasm. On infection, TMV mRNA is efficiently and selectively translated by the host translation machinery despite the lack of a poly(A) tail, which is normally required for efficient translation. Both the 68-base 5' leader (Omega) and the 205-base 3' untranslated region of TMV promote efficient translation. A 25-base poly(CAA) region within Omega and the upstream pseudoknot domain, a 72-base region composed of three RNA pseudoknots, are responsible for the translational regulation. We have identified, purified, and characterized a 102-kDa RNA-binding protein (p102) from wheat that binds specifically to the poly(CAA) region within Omega and the upstream pseudoknot domain within the TMV 3' untranslated region. Polyclonal antibodies raised against wheat p102 were used to demonstrate that p102 is widely conserved in plant species. Moreover, specific RNA binding activity was detected in all plant species tested. Addition of anti-p102 antibodies to an in vitro translation lysate derived from wheat germ repressed translation, which was subsequently reversed by supplementing the lysate with p102. These findings suggest that this protein may play an important role in determining translational efficiency in plants.
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Affiliation(s)
- R L Tanguay
- Department of Biochemistry, University of California, Riverside, California 92521-0129, USA
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36
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Affiliation(s)
- D C Yang
- Department of Chemistry, Georgetown University, Washington DC 20057, USA
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37
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Brigotti M, Carnicelli D, Alvergna P, Pallanca A, Sperti S, Montanaro L. Differential up-regulation by tRNAs of ribosome-inactivating proteins. FEBS Lett 1995; 373:115-8. [PMID: 7589447 DOI: 10.1016/0014-5793(95)01023-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Some plant ribosome-inactivating proteins (RIPs) with RNA-N-glycosidase activity on 28S RNA require, for the inactivation of ribosomes, the presence of macromolecular cofactors present in post-ribosomal supernatants. In the case of gelonin one of the cofactors is tRNATrp lacking one or two nucleotides at the 3'-CCA end [Brigotti, M., Carnicelli, D., Alvergna, P., Pallanca, A., Lorenzetti, R., Denaro, M., Sperti, S. and Montanaro, L. (1995) Biochem. J. 310, 249-253]. In the present study it is shown that tRNAs are involved in the up-regulation of all the cofactor-requiring RIPs up to now identified (agrostin, barley RIP, PAP and tritin, besides gelonin). Polyacrylamide gel electrophoresis shows that tRNA fractions with different mobilities stimulate different RIPs. With the identification of agrostin, the cofactor-requiring RIPs (italics) add to five out of a total of thirteen investigated: barley RIP, bryodin-R, gelonin, lychnin, momordin, momorcochin-S, PAP, saporin-6, tritin [Carnicelli, D., Brigotti, M., Montanaro, L. and Sperti, S. (1992) Biochem. Biophys. Res. Commun. 182, 579-582], agrostin, luffin, trichokirin and trichosanthin (present study).
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Affiliation(s)
- M Brigotti
- Dipartimento di Patologia sperimentale dell'Università di Bologna, Italy
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38
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Quadt R, Ishikawa M, Janda M, Ahlquist P. Formation of brome mosaic virus RNA-dependent RNA polymerase in yeast requires coexpression of viral proteins and viral RNA. Proc Natl Acad Sci U S A 1995; 92:4892-6. [PMID: 7761419 PMCID: PMC41813 DOI: 10.1073/pnas.92.11.4892] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In this report we show that yeast expressing brome mosaic virus (BMV) replication proteins 1a and 2a and replicating a BMV RNA3 derivative can be extracted to yield a template-dependent BMV RNA-dependent RNA polymerase (RdRp) able to synthesize (-)-strand RNA from BMV (+)-strand RNA templates added in vitro. This virus-specific yeast-derived RdRp mirrored the template selectivity and other characteristics of RdRp from BMV-infected plants. Equivalent extracts from yeast expressing 1a and 2a but lacking RNA3 contained normal amounts of 1a and 2a but had no RdRp activity on BMV RNAs added in vitro. To determine which RNA3 sequences were required in vivo to yield RdRp activity, we tested deletions throughout RNA3, including the 5',3', and intercistronic noncoding regions, which contain the cis-acting elements required for RNA3 replication in vivo. RdRp activity was obtained only from cells expressing 1a, 2a, and RNA3 derivatives retaining both 3' and intercistronic noncoding sequences. Strong correlation between extracted RdRp activity and BMV (-)-strand RNA accumulation in vivo was found for all RNA3 derivatives tested. Thus, extractable in vitro RdRp activity paralleled formation of a complex capable of viral RNA synthesis in vivo. The results suggest that assembly of active RdRp requires not only viral proteins but also viral RNA, either to directly contribute some nontemplate function or to recruit essential host factors into the RdRp complex and that sequences at both the 3'-terminal initiation site and distant internal sites of RNA3 templates may participate in RdRp assembly and initiation of (-)-strand synthesis.
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Affiliation(s)
- R Quadt
- Institute for Molecular Virology, University of Wisconsin-Madison 53706-1596, USA
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39
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Felden B, Florentz C, McPherson A, Giegé R. A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA. Nucleic Acids Res 1994; 22:2882-6. [PMID: 8065897 PMCID: PMC310250 DOI: 10.1093/nar/22.15.2882] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.
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Affiliation(s)
- B Felden
- Unité Propre de Recherche Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Centre National de la Recherche Scientifique, Strasbourg, France
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40
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Maizels N, Weiner AM. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci U S A 1994; 91:6729-34. [PMID: 8041690 PMCID: PMC44276 DOI: 10.1073/pnas.91.15.6729] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We propose a phylogeny for the evolution of tRNA that is based on the ubiquity and conservation of tRNA-like structures in the replication of contemporary genomes. This phylogeny is unique in suggesting that the function of tRNA in replication dates back to the very beginnings of life on earth, before the advent of templated protein synthesis. The origin we propose for tRNA has distinct implications for the order in which other components of the modern translational apparatus evolved. We further suggest that the "top half" of modern tRNA-a coaxial stack of the acceptor stem on the T psi C arm--is the ancient structural and functional domain and that the "bottom half" of tRNA--a coaxial stack of the dihydrouracil arm on the anticodon arm--arose later to provide additional specificity.
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Affiliation(s)
- N Maizels
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06510-8024
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41
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Gallie DR, Kobayashi M. The role of the 3'-untranslated region of non-polyadenylated plant viral mRNAs in regulating translational efficiency. Gene 1994; 142:159-65. [PMID: 8194747 DOI: 10.1016/0378-1119(94)90256-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tobacco mosaic virus (TMV) is a positive-sense RNA virus in which the single genomic RNA functions as a messenger RNA. It is a member of a class of plant viral RNAs that are the only known non-polyadenylated mRNAs in plants. The 3'-untranslated region (UTR) of TMV genomic RNA is the functional equivalent of a poly(A) tail in that it increases mRNA stability and regulates translational efficiency. To determine whether the 3'-UTR of other non-polyadenylated plant viral mRNAs regulate translation, those from turnip yellow mosaic (TYMV), brome mosaic (BMV), and alfalfa mosaic (AlMV) viruses were investigated. Chimeric gene constructs were made in which the viral 3'-UTRs were introduced immediately downstream from the reporter genes encoding beta-glucuronidase (GUS) and luciferase (LUC), and were translated in plant protoplasts following delivery of the mRNA using electroporation. The 3'-UTR from BMV RNA3 regulated reporter gene expression in vivo to an extent comparable to that observed for the TMV 3'-UTR. The BMV 3'-UTR increased both message stability and translational efficiency. As regulators of translation, the BMV and TMV 3'-UTR were dependent on the presence of a cap at the 5' terminus for function. The 3' UTR of TYMV or AlMV RNA4 had little impact on translation or transcript stability. These data suggest that although the TMV 3'-UTR is not unique in regulating translation, the 3'-UTR of plant viral mRNAs do vary in their regulatory ability.
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Affiliation(s)
- D R Gallie
- Department of Biochemistry, University of California, Riverside 92521-0129
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42
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Abstract
It is well known that DNA-based organisms rearrange and repair their genomic DNA through recombination processes, and that these rearrangements serve as a powerful source of variability and adaptation for these organisms. In RNA viruses' genetic recombination is defined as any process leading to the exchange of information between viral RNAs. There are two types of recombination events: legitimate and illegitimate. While legitimate (homologous) recombination occurs between closely related sequences at corresponding positions, illegitimate (nonhomologous) recombination could happen at any position among the unrelated RNA molecules. In order to differentiate between the symmetrical and asymmetrical homologous crosses, Lai defined the former as homologous recombination and the latter as aberrant homologous recombination. This chapter uses brome mosaic virus (BMV), a multicomponent plant RNA virus, as an example to discuss the progress in studying the mechanism of genetic recombination in positive-stranded RNA viruses. Studies described in this chapter summarize the molecular approaches used to increase the frequency of recombination among BMV RNA segments and, more importantly, to target the sites of crossovers to specific BMV RNA regions. It demonstrates that the latter can be accomplished by introducing local complementarities to the recombining substrates.
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Affiliation(s)
- J J Bujarski
- Plant Molecular Biology Center, Northern Illinois University, De Kalb 60115
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43
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A phylogenetically conserved sequence within viral 3' untranslated RNA pseudoknots regulates translation. Mol Cell Biol 1993. [PMID: 8355685 DOI: 10.1128/mcb.13.9.5331] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Both the 68-base 5' leader (omega) and the 205-base 3' untranslated region (UTR) of tobacco mosaic virus (TMV) promote efficient translation. A 35-base region within omega is necessary and sufficient for the regulation. Within the 3' UTR, a 52-base region, composed of two RNA pseudoknots, is required for regulation. These pseudoknots are phylogenetically conserved among seven viruses from two different viral groups and one satellite virus. The pseudoknots contained significant conservation at the secondary and tertiary levels and at several positions at the primary sequence level. Mutational analysis of the sequences determined that the primary sequence in several conserved positions, particularly within the third pseudoknot, was essential for function. The higher-order structure of the pseudoknots was also required. Both the leader and the pseudoknot region were specifically recognized by, and competed for, the same proteins in extracts made from carrot cell suspension cells and wheat germ. Binding of the proteins is much stronger to omega than the pseudoknot region. Synergism was observed between the TMV 3' UTR and the cap and to a lesser extent between omega and the 3' UTR. The functional synergism and the protein binding data suggest that the cap, TMV 5' leader, and 3' UTR interact to establish an efficient level of translation.
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Leathers V, Tanguay R, Kobayashi M, Gallie DR. A phylogenetically conserved sequence within viral 3' untranslated RNA pseudoknots regulates translation. Mol Cell Biol 1993; 13:5331-47. [PMID: 8355685 PMCID: PMC360232 DOI: 10.1128/mcb.13.9.5331-5347.1993] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Both the 68-base 5' leader (omega) and the 205-base 3' untranslated region (UTR) of tobacco mosaic virus (TMV) promote efficient translation. A 35-base region within omega is necessary and sufficient for the regulation. Within the 3' UTR, a 52-base region, composed of two RNA pseudoknots, is required for regulation. These pseudoknots are phylogenetically conserved among seven viruses from two different viral groups and one satellite virus. The pseudoknots contained significant conservation at the secondary and tertiary levels and at several positions at the primary sequence level. Mutational analysis of the sequences determined that the primary sequence in several conserved positions, particularly within the third pseudoknot, was essential for function. The higher-order structure of the pseudoknots was also required. Both the leader and the pseudoknot region were specifically recognized by, and competed for, the same proteins in extracts made from carrot cell suspension cells and wheat germ. Binding of the proteins is much stronger to omega than the pseudoknot region. Synergism was observed between the TMV 3' UTR and the cap and to a lesser extent between omega and the 3' UTR. The functional synergism and the protein binding data suggest that the cap, TMV 5' leader, and 3' UTR interact to establish an efficient level of translation.
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Affiliation(s)
- V Leathers
- Department of Biochemistry, University of California, Riverside 92521-0129
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45
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Felden B, Florentz C, Westhof E, Giegé R. Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA. Biochimie 1993; 75:1143-57. [PMID: 8199250 DOI: 10.1016/0300-9084(93)90014-j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicularly and mimicking a tRNA structure, and a fifth domain which makes the connection with the rest of the viral RNA. After recalling the different steps that led to the present structural knowledge of the BMV tRNA-like domain, we review its novel structural features revealed by the modelling and that did not appear in older versions of 3-D models of this structure. These features comprise additional base-pairs, hairpin loops, new tertiary long-range interactions, and a second pseudoknot. The main goal of this paper is to strengthen the validity of the model by establishing correlations between the putative 3-D conformation and the functional properties of the domain. For that, we show how the present structural model rationalises mutagenic and footprinting data that have established the importance of specific regions of the RNA for its recognition and aminoacylation by yeast tyrosyl-tRNA synthetase. We discuss further how the model corroborates mutational analyses performed to understand recognition of this RNA domain by the (ATP,CTP):tRNA nucleotidyl-transferase and by the viral replicase. The published mutants of the BMV tRNA-like domain fall into two classes. In one class, the mutants leave unchanged the overall architecture of the molecule, thereby affecting functions directly. In the second class, the overall architecture of the mutants is perturbed, and thus functions are affected indirectly.
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Affiliation(s)
- B Felden
- Unité Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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46
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Abstract
The genomic RNA from turnip yellow mosaic virus presents a 3'-end functionally and structurally related to tRNAs. This report summarizes our knowledge about the peculiar structure of the tRNA-like domain and its interaction with tRNA specific proteins, like RNAse P, tRNA nucleotidyl-transferase, aminoacyl-tRNA synthetases, and elongation factors. It discusses also the biological role of this structure in the viral life cycle. A brief survey of our knowledge of other tRNA mimicries in biological systems, as well as their relevance for understanding canonical tRNA, will also be presented.
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Key Words
- turnip yellow mosaic virus rna
- trna-like structure
- aminoacylation
- replication
- tymv, turnip yellow mosaic virus
- bmv, brome mosaic virus
- tmv, tobacco mosaic virus
- tymc, corvallis strain of tymv rna
- ty-alu, clones of cdna fragments of different length starting at restriction sites alu containing the trna-like domain of tymv rna
- ty-dde, clones of cdna fragments of different length starting at restriction sites dde containing the trna-like domain of tymv rna
- ty-dra, clones of cdna fragments of different length starting at restriction sites dra containing the trna-like domain of tymv rna
- ty-sma, clones of cdna fragments of different length starting at restriction sites sma containing the trna-like domain of tymv rna
- ty-aa, clone of cdna containing the amino acid accepting branch of tymv rna
- aars, aminoacyl-trna synthetase (amino acids are abbreviated by the three-letter code)
- cp, coat protein
- orf, open reading frame
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Affiliation(s)
- R Giegé
- Unité Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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47
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Dreher TW, Tsai CH, Florentz C, Giegé R. Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides. Biochemistry 1992; 31:9183-9. [PMID: 1390705 DOI: 10.1021/bi00153a010] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].
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Affiliation(s)
- T W Dreher
- Department of Agricultural Chemistry, Oregon State University, Corvallis 97331
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48
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Jacob AN, Murthy MR, Savithri HS. Nucleotide sequence of the 3' terminal region of belladonna mottle virus-Iowa (renamed Physalis mottle virus) RNA and an analysis of the relationships of tymoviral coat proteins. Arch Virol 1992; 123:367-77. [PMID: 1562236 DOI: 10.1007/bf01317270] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.
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Affiliation(s)
- A N Jacob
- Department of Biochemistry, Indian Institute of Science, Bangalore
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49
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Rudinger J, Florentz C, Dreher T, Giegé R. Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA. Nucleic Acids Res 1992; 20:1865-70. [PMID: 1579487 PMCID: PMC312299 DOI: 10.1093/nar/20.8.1865] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.
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Affiliation(s)
- J Rudinger
- UPR Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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50
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Pilipenko EV, Maslova SV, Sinyakov AN, Agol VI. Towards identification of cis-acting elements involved in the replication of enterovirus and rhinovirus RNAs: a proposal for the existence of tRNA-like terminal structures. Nucleic Acids Res 1992; 20:1739-45. [PMID: 1315956 PMCID: PMC312265 DOI: 10.1093/nar/20.7.1739] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
On the basis of a comparative analysis of published sequences, models for the secondary structure of the 3'-terminal [poly(A)-preceding] untranslated region of the entero- and rhinovirus RNAs were worked out. The models for all these viruses share a common core element, but there are an extra enterovirus-specific element and still an additional element characteristic of a subset of enterovirus RNAs. The two latter models were verified for poliovirus and coxsackievirus B genomes by testing with single-strand and double-strand specific enzymatic and chemical probes. A tRNA-like tertiary structure model for the 3'-terminal folding of enterovirus RNAs was proposed. A similar folding was proposed for the 3' termini of the negative RNA strands as well as for the 5' termini of the positive strand of all entero- and rhinovirus RNAs. Implications of these data for template recognition during negative and positive RNA strands synthesis and for the evolution of the picornavirus genomes are discussed.
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Affiliation(s)
- E V Pilipenko
- Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow
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