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Ariza-Mateos A, Briones C, Perales C, Domingo E, Gómez J. The archaeology of coding RNA. Ann N Y Acad Sci 2019; 1447:119-134. [PMID: 31237363 DOI: 10.1111/nyas.14173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/18/2019] [Accepted: 05/29/2019] [Indexed: 12/16/2022]
Abstract
Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto-tRNA-like structures. Different biochemical and biophysical tools have been used to search for ancient-like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as "archaeological," and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA-like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon-alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA-like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA-like motif next to the tRNA-like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny-based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent "the losers" in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain.,Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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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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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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Brulé H, Grosjean H, Giegé R, Florentz C. A pseudoknotted tRNA variant is a substrate for tRNA (cytosine-5)-methyltransferase from Xenopus laevis. Biochimie 1998; 80:977-85. [PMID: 9924976 DOI: 10.1016/s0300-9084(99)80003-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
tRNA post-transcriptional modification enzymes of Xenopus laevis were proposed previously to belong to two major groups according to their sensitivity to structural perturbations in their substrates. To further investigate the structural variations tolerated by these enzymes, the tRNA-like domain of turnip yellow mosaic virus RNA (88 nucleotides in length) has been microinjected into the oocytes of Xenopus laevis. This RNA possesses 12 potential target nucleotides for modification within a structure including a pseudoknotted folding, an extended anticodon stem, and unusual D-loop/T-loop interactions. Results indicate that only cytosine-42, a position equivalent to C-49 in canonical tRNAs, was quantitatively modified into m5C in the microinjected RNA. Modification was detected to high levels, indicating that at least one enzyme tolerates non-canonical structural features.
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Affiliation(s)
- H Brulé
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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Canady MA, Day J, McPherson A. Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV). Proteins 1995; 21:78-81. [PMID: 7716173 DOI: 10.1002/prot.340210111] [Citation(s) in RCA: 13] [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
Turnip yellow mosaic virus (TYMV) was purified from Chinese cabbage and crystallized in a form that permits high resolution structural analysis using X-ray diffraction. The crystals have a hexagonal bipyramidal morphology and often achieve dimensions of 1.0 x 1.0 x 0.5 mm. The crystals appear to be of hexagonal space group P6(2)22 with a=b=525 A, c=315 A, but we cannot strictly rule out the possibility that the space group is P622. They appear different than any crystals of TYMV previously reported. There are three T = 3 virus particles in the unit cell, which implies that one quarter of the particle, or 45 protein subunits, comprises the asymmetric unit of the crystal. Native data have been collected using synchrotron radiation to a resolution of 3.2 A.
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Affiliation(s)
- M A Canady
- Department of Biochemistry, University of California, Riverside 92521, USA
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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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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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Mans RM, Pleij CW, Bosch L. tRNA-like structures. Structure, function and evolutionary significance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 201:303-24. [PMID: 1935928 DOI: 10.1111/j.1432-1033.1991.tb16288.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R M Mans
- Department of Biochemistry, State University of Leiden, The Netherlands
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Gargouri R, Joshi RL, Bol JF, Astier-Manifacier S, Haenni AL. Mechanism of synthesis of turnip yellow mosaic virus coat protein subgenomic RNA in vivo. Virology 1989; 171:386-93. [PMID: 2763458 DOI: 10.1016/0042-6822(89)90606-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Turnip yellow mosaic virus (TYMV) possesses a monopartite single-stranded (+) sense RNA genome in which the coat protein (cp) gene is 3' proximal and is expressed in vivo via a subgenomic RNA. Evidence is presented here that this subgenomic RNA is synthesized in vivo by internal initiation of replication on (-) RNA strands of genomic length. The double-stranded RNAs (dsRNAs) from TYMV-infected plants have been isolated, purified, and characterized. Under native conditions, no dsRNAs (replicative intermediates and/or replicative forms) of subgenomic length corresponding to subgenomic cp RNA can be detected by ethidium bromide staining of RNA-sizing gels or by Northern blot hybridization using RNA probes. The presence of nascent subgenomic cp (+) RNA strands on the dsRNA of genomic length has been demonstrated using two different approaches: (1) Northern blot hybridization using (-) RNA probes under denaturing conditions and (2) characterization of the 5' ends of nascent (+) RNA strands upon labeling by vaccinia virus nucleoside-2'-methyltransferase.
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Asfaw B. A new hominid parietal from Bodo, Middle Awash Valley, Ethiopia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1983; 61:367-71. [PMID: 6412559 DOI: 10.1002/ajpa.1330610311] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A piece of left parietal of a Middle Pleistocene hominid, recovered from the Upper Bodo Sand Unit, in the Middle Awash, Ethiopia, is described anatomically and compared to Middle Pleistocene hominids and modern Homo sapiens. It bears several primitive features and has important implications for the original Bodo skull, found at the same stratigraphic level in the same area. The new fossil skull represents a different individual from the original Bodo skull.
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Joshi S, Chapeville F, Haenni AL. Length requirements for tRNA-specific enzymes and cleavage specificity at the 3' end of turnip yellow mosaic virus RNA. Nucleic Acids Res 1982; 10:1947-62. [PMID: 6176943 PMCID: PMC320582 DOI: 10.1093/nar/10.6.1947] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This paper describes the minimum length of the turnip yellow mosaic virus (TYMV) RNA necessary to fulfill the tRNA-like properties of the viral RNA: 50 to 75 nucleotides and 86 nucleotides from the 3' end of TYMV RNA are sufficient for adenylation and valylation respectively by the Escherichia coli system. The size of the tRNA-like fragments obtained in vitro in the presence of an E. coli, a reticulocyte or a chinese cabbage leaf extract has also been determined. Among the major fragments liberated from the 3' end of TYMV RNA by the three systems are fragments of 117 and 112 nucleotides. In addition, the E. coli extract liberates fragments of 139 and 61 nucleotides, and the reticulocyte lysate fragments of 109, 94, 84, 73 and 46 nucleotides. The cleavage of the viral RNA by several systems in vitro to yield RNA fragments encompassing the tRNA-like sequence suggests that such fragments might also be liberated in vivo.
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Haenni AL, Joshi S, Chapeville F. tRNA-like structures in the genomes of RNA viruses. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1982; 27:85-104. [PMID: 6285419 DOI: 10.1016/s0079-6603(08)60598-x] [Citation(s) in RCA: 131] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Littauer UZ, Soreq H. The regulatory function of poly(A) and adjacent 3' sequences in translated RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1982; 27:53-83. [PMID: 7048421 DOI: 10.1016/s0079-6603(08)60597-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Goldberg EZ, Naroditsky BS, Felgenhauer PE, Garaev MM, Tikchonenko TI. Replication of heterologous DNA in Xenopus laevis oocytes. FEBS Lett 1981; 124:215-8. [PMID: 6262120 DOI: 10.1016/0014-5793(81)80140-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Joshi S, Haenni AL. Fluorographic detection of nucleic acids labelled with weak beta-emitters in gels containing high acrylamide concentrations. FEBS Lett 1980; 118:43-6. [PMID: 7409190 DOI: 10.1016/0014-5793(80)81214-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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De Robertis EM, Olson MV. Transcription and processing of cloned yeast tyrosine tRNA genes microinjected into frog oocytes. Nature 1979; 278:137-43. [PMID: 368655 DOI: 10.1038/278137a0] [Citation(s) in RCA: 124] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Xenopus oocytes transcribe cloned yeast tyrosine tRNA genes and process the RNA. The processing includes base modifications, addition of the CCA end, and splicing of the intervening sequence. The primary transcript has a 5' leader extension which varies considerably in seuqence and in length between different tRNATyr loci, but is nevertheless present in all of them.
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