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Physical-Chemical Properties

Molecular Structure (Primary and Secondary)

  • Chapter
Book cover The Viroids

Part of the book series: The Viruses ((VIRS))

Abstract

Essential to understanding how viroids function is the determination of their nucleotide sequences. Within each viroid sequence is all the information to allow it to function in vivo. Our major problem is to relate this sequence to the secondary and tertiary structure of the viroid and the way in which this information is encoded, interpreted, and expressed in the plant cell.

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References

  • Barker, J. M., Mclnnes, J. L., Murphy, P. J., and Symons, R. H., 1985, Dot-blot procedure with [32P]DNA probes for the sensitive detection of avocado sunblotch and other viroids in plants, /. Virol Methods 10:87.

    Article  CAS  Google Scholar 

  • Boguski, M. S., Hieter, P. A., and Levy, C. C, 1980, Identification of a cytidine-specific ribonuclease from chicken liver, J. Biol. Chem. 255:2160.

    CAS  Google Scholar 

  • Branch, A. D., Robertson, H. D., and Dickson, E., 1981, Longer-than-unit-length viroid minus strands are present in RNA from infected plants, Proc. Natl. Acad. Sci. USA 78:6381.

    Article  CAS  Google Scholar 

  • Bruening, G., Gould, A. R., Murphy, P. J., and Symons, R. H., 1982, Oligomers of avocado sunblotch viroid are found in infected avocado leaves, FEBS Lett. 148:71.

    Article  CAS  Google Scholar 

  • Colpan, M., Schumacher, J., Bruggemann, W., Sanger, H. L., and Riesner, D., 1983, Largescale purification of viroid RNA using Cs2SO4 gradient centrifugation and high-performance liquid chromatography, Anal. Biochem. 131:257.

    Article  PubMed  CAS  Google Scholar 

  • Comay, E., Nussinov, R., and Comay, O., 1984, An accelerated algorithm for calculating the secondary structure of single stranded RNAs, Nucleic Acids Res. 12:53.

    Article  PubMed  CAS  Google Scholar 

  • Cress, D. E., Kiefer, M. C, and Owens, R. A., 1983, Construction of infectious potato spindle tuber viroid cDNA clones, Nucleic Acids Res. 11:6821.

    Article  PubMed  CAS  Google Scholar 

  • da Graca, J. V., and Mason, T. E., 1983, Detection of avocado sunblotch viroid in flower buds by polyacrylamide gel electrophoresis, Phytopathol. Z. 108:262.

    Article  Google Scholar 

  • da Graca, J. V., and van Vuuren, S.P., 1980, Transmission of avocado sunblotch disease to cinnamon, Plant Dis. 64:475.

    Article  Google Scholar 

  • de Wachter, R., and Fiers, W., 1972, Preparative two-dimensional polyacrylamide gel electrophoresis of 32P-labelled RNA, Anal. Biochem. 49:184.

    Article  PubMed  Google Scholar 

  • Dickson, E., Prensky, W., and Robertson, H. D., 1975, Comparative studies of two viroids: Analysis of potato spindle tuber and citrus exocortis viroids by RNA fingerprinting and polyacrylamide-gel electrophoresis, Virology 68:309.

    Article  PubMed  CAS  Google Scholar 

  • Dickson, E., Diener, T. O., and Robertson, H. D., 1978, Potato spindle tuber and citrus exocortis viroids undergo no major sequence changes during replication in two different hosts, Proc. Natl. Acad. Sci. USA 75:951.

    Article  CAS  Google Scholar 

  • Dickson, E., Robertson, H. D., Niblett, C. L., Horst, R. K., and Zaitlin, M., 1979, Minor differences between nucleotide sequences of mild and severe strains of potato spindle tuber viroid, Nature 277:60.

    Article  CAS  Google Scholar 

  • Diener, T. O., Hadidi, A., and Owens, R. A., 1977, Methods for studying viroids, Methods Virol. 6:185.

    CAS  Google Scholar 

  • Donis-Keller, H., 1980, Phy M: An RNase activity specific for U and A residues useful in RNA sequence analysis, Nucleic Acids Res. 8:3133.

    Article  PubMed  CAS  Google Scholar 

  • Donis-Keller, H., Maxam, A. M., and Gilbert, W., 1977, Mapping adenines, guanines and pyrimidines in RNA, Nucleic Acids Res. 4:2527.

    Article  PubMed  CAS  Google Scholar 

  • England, T. E., and Uhlenbeck, O. C., 1978, 3’-Terminal labelling of RNA with T4 RNA ligase, Nature 275:560.

    Article  PubMed  CAS  Google Scholar 

  • Frisby, D., 1977, Oligonucleotide mapping of non-radioactive virus and messenger RNAs, Nucleic Acids Res. 4:2975.

    Article  PubMed  CAS  Google Scholar 

  • Goodman, T. C., Nagel, L., Rappold, W., Klotz, G., and Riesner, D., 1984, Viroid replication: Equilibrium association constant and comparative activity measurements for the viroid-polymerase interaction, Nucleic Acids Res. 12:6231.

    Article  PubMed  CAS  Google Scholar 

  • Gross, H. J., Domdey, H., and Sanger, H. L., 1977, Comparative oligonucleotide fingerprints of three plant viroids, Nucleic Acids Res. 4:2021.

    Article  PubMed  CAS  Google Scholar 

  • Gross, H. J., Domdey, H., Lossow, C., Jank, P., Raba, M., Alberty, H., and Sanger, H. L., 1978, Nucleotide sequence and secondary structure of potato spindle tuber viroid, Nature 273:203.

    Article  PubMed  CAS  Google Scholar 

  • Gross, H. J., Liebl, U., Alberty, H., Krupp, G., Domdey, H., Ramm, K., and Sanger, H. L., 1981, A severe and a mild potato spindle tuber viroid isolate differ in three nucleotide exchanges only, Biosci. Rep. 1:235.

    Article  PubMed  CAS  Google Scholar 

  • Gross, H. J., Krupp, G., Domdey, H., Raba, M., fank, P., Lossow, C., Alberty, H., Ramm, K., and Sanger, H. L., 1982, Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid, Eur. J. Biochem 121:249.

    CAS  Google Scholar 

  • Haseloff, J., 1983, Structure of viroids, virusoids and satellites, Ph.D. thesis, University of Adelaide.

    Google Scholar 

  • Haseloff, J., and Symons, R. H., 1981, Chrysanthemum stunt viroid: Primary sequence and secondary structure, Nucleic Acids Res. 9:2741.

    Article  PubMed  CAS  Google Scholar 

  • Haseloff, J., Mohamed, N. A., and Symons, R. H., 1982, Viroid RNAs of cadang-cadang disease of coconuts, Nature 299:316.

    Article  CAS  Google Scholar 

  • Henco, K., Sänger, H. L., and Riesner, D., 1979, Fine structure melting of viroids as studied by kinetic methods, Nucleic Acids Res. 6:3041.

    Article  PubMed  CAS  Google Scholar 

  • Hutchins, C. J., Keese, P., Visvader, J. E., Rathjen, P. D., Mclnnes, J. L., and Symons, R. H., 1985, Comparison of multimeric plus and minus forms of viroids and virusoids, Plant Mol. Biol. 4:293.

    Article  CAS  Google Scholar 

  • Hutchins, C. J., Rathjen, P. D., Forster, A. C., and Symons, R. H., 1986, Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid, Nucleic Acids Res. 14:3627.

    Article  PubMed  CAS  Google Scholar 

  • Imperial, J. S., Rodriguez, M. J. B., and Randies, J. W., 1981, Variation in the viroid-like RNA associated with cadang-cadang disease: Evidence for an increase in molecular weight with disease progress, /. Gen. Virol. 56:77.

    Article  CAS  Google Scholar 

  • Imperial, J. S., Bautista, R. M., and Randies, J. W., 1985, Transmission of the coconut cadang-cadang viroid to six species of palm by inoculation with nucleic acid extracts, Plant Pathol. 34:391.

    Article  CAS  Google Scholar 

  • Ishikawa, M., Meshi, T., Ohno, T., Okada, Y., Sano, T., Ueda, I., and Shikata, E., 1984, A revised replication cycle for viroids: The role of longer than unit length RNA in viroid replication, Mol. Gen. Genet. 196:421.

    Article  CAS  Google Scholar 

  • Kay, E. R. M., Simmons, N. S., and Dounce, A. L., 1952, An improved preparation of sodium desoxyribonuclease, J. Am. Chem. Soc. 74:1724.

    Article  CAS  Google Scholar 

  • Keese, P., and Symons, R. H., 1985, Domains in viroids: Evidence of intermolecular RNA rearrangements and their contribution to viroid evolution, Proc. Natl. Acad. Sci. USA 82:4582.

    Article  CAS  Google Scholar 

  • Keese, P., and Symons, R. H., 1986, The structure of viroids and virusoids, in: Viroids and Viroid-like Pathogens (J. S. Semancik, ed.), CRC Press, Boca Raton, Fla.

    Google Scholar 

  • Kiberstis, P. A., Haseloff, J., and Zimmern, D., 1985, 2‘ phosphomonoester, 3’-5 phosphodiester bond at a unique site in a circular viral RNA, EMBO J. 4:817.

    PubMed  CAS  Google Scholar 

  • Kiefer, M. C., Owens, R. A., and Diener, T. O., 1983, Structural similarities between viroids and transposable genetic elements, Proc. Natl. Acad. Sci. USA 80:6234.

    Article  PubMed  CAS  Google Scholar 

  • Kramer, F. R., and Mills, D. R., 1978, RNA sequencing with radioactive chain-terminating ribonucleotides, Proc. Natl. Acad. Sci. USA 75:5334.

    Article  CAS  Google Scholar 

  • Laulhere, J.-P., and Rozier, C., 1976, One-step extraction of plant nucleic acids, Plant Sci. Lett. 6:237.

    Article  CAS  Google Scholar 

  • Lockard, R. E., Alzner-Deweerd, B., Heckman, J. E., MacGee, J., Tabor, M. W., and Raj-Bhandary, U. L., 1978, Sequence analysis of 5’[32P]-labelled mRNA and tRNA using polyacrylamide gel electrophoresis, Nucleic Acids Res. 5:37.

    Article  PubMed  CAS  Google Scholar 

  • McClements, W. L., and Kaesberg, P., 1977, Size and secondary structure of potato spindle tuber viroid, Virology 76:477.

    Article  PubMed  CAS  Google Scholar 

  • Maxam, A. M., and Gilbert, W., 1977, A new method for sequencing DNA, Proc. Natl. Acad. Sci. USA 74:560.

    Article  CAS  Google Scholar 

  • Mohamed, N. A., Haseloff, J. ,Imperial, f. S., and Symons, R. H., 1982, Characterization of the different electrophoretic forms of the cadang-cadang viroid, J. Gen. Virol. 63:181.

    Article  CAS  Google Scholar 

  • Muhlbach, H.-P., Faustmann, O., and Sänger, H. L., 1983, Conditions for optimal growth of a PSTV-infected potato cell suspension and detection of viroid-complementary longer-than-unit-length RNA in these cells, Plant Mol. Biol 2:239.

    Article  Google Scholar 

  • Niblett, C. L., Dickson, E., Horst, R. K., and Romaine, C. P., 1980, Additional hosts and an efficient purification procedure for four viroids, Phytopathology 70:610.

    Article  CAS  Google Scholar 

  • Nussinov, R., and Jacobson, A. B., 1980, Fast algorithm for predicting the secondary structure of single-stranded RNA, Proc. Natl. Acad. Sci. USA 77:6309.

    Article  CAS  Google Scholar 

  • Ohno, T., Akiya, J., Higuchi, M., Okada, Y., Yoshikawa, N., Takahashi, T., and Hashimoto, J., 1982, Purification and characterization of hop stunt viroid, Virology 118:54.

    Article  PubMed  CAS  Google Scholar 

  • Ohno, T., Takamatsu, N., Meshi, T., and Okada, Y., 1983, Hop stunt viroid: Molecular cloning and nucleotide sequence of the complete cDNA copy, Nucleic Acids Res. 11:6185.

    Article  PubMed  CAS  Google Scholar 

  • Okayama, H., and Berg, P., 1982, High-efficiency cloning of full-length cDNA, Mol. Cell. Biol. 2:161.

    CAS  Google Scholar 

  • Owens, R. A., and Cress, D. E., 1980, Molecular cloning and characterization of potato spindle tuber viroid cDNA sequences, Proc. Natl. Acad. Sci. USA 77:5302.

    Article  CAS  Google Scholar 

  • Owens, R. A., and Diener, T. O., 1982, RNA intermediates in potato spindle tuber viroid replication, Proc. Natl. Acad. Sci. USA 79:113.

    Article  CAS  Google Scholar 

  • Owens, R. A., Erbe, E., Hadidi, A., Steere, R. L., and Diener, T. O., 1977, Separation and infectivity of circular and linear forms of potato spindle tuber viroid, Proc. Natl. Acad. Sci. USA 74:3859.

    Article  CAS  Google Scholar 

  • Palukaitis, P., and Symons, R. H., 1980, Purification and characterization of the circular and linear forms of chrysanthemum stunt viroid, J. Gen. Virol. 46:477.

    Article  CAS  Google Scholar 

  • Palukaitis, P., Hatta, T., Alexander, D. McE., and Symons, R. H., 1979, Characterization of a viroid associated with avocado sunblotch disease, Virology 99:145.

    Article  PubMed  CAS  Google Scholar 

  • Peattie, D. A., 1979, Direct chemical method for sequencing RNA, Proc. Natl. Acad. Sci. USA 76:1760.

    Article  CAS  Google Scholar 

  • Pilly, D., Niemeyer, A., Schmidt, M., and Bargetzi, J. P., 1978, Enzymes for RNA sequence analysis, preparation and specificity of exoplasmodial ribonucleases I and II from Physarum polycephalum, J. Biol. Chem. 253:437.

    CAS  Google Scholar 

  • Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R., and Bruening, G., 1986, Autolytic processing of dimeric plant virus satellite RNA, Science 231:1577.

    Article  PubMed  CAS  Google Scholar 

  • Randies, J. W., and Hatta, T., 1979, Circularity of the ribonucleic acids associated with cadang-cadang disease, Virology 96:47.

    Article  Google Scholar 

  • Riesner, D., and Gross, H. J., 1985, Viroids, Annu. Rev. Biochem. 54:531.

    Article  CAS  Google Scholar 

  • Riesner, D., Henco, K., Rokohl, U., Klotz, G., Kleinschmidt, A. K., Domdey, H., Jank, P., Gross, H. J., and Sanger, H. L., 1979, Structure and structure formation of viroids, J. Mol. Biol. 133:85.

    Article  CAS  Google Scholar 

  • Riesner, D., Colpan, M., Goodman, T. C., Nagel, L., Schumacher, J., Steger, G., and Hofmann, H., 1983, Dynamics and interactions of viroids, J. Biomol. Struct. Dyn. 1:669.

    PubMed  CAS  Google Scholar 

  • Runia, W. Th., and Peters, D., 1980, The response of plant species used in agriculture and horticulture to viroid infections, Neth. J. Plant Pathol. 86:135.

    Google Scholar 

  • Sanger, F., Coulson, A. R., Barrell, B. G., Smith, A. J. H., and Roe, B. A., 1980, Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing, J. Mol. Biol. 143:161.

    Article  CAS  Google Scholar 

  • Sanger, H. L., 1982, Biology, structure, functions and possible origin of viroids, in: Encyclopedia of Plant Physiology New Series ,Vol. 14B (B. Parthier and D. Boulter, eds.), pp. 368–454, Springer-Verlag, Berlin.

    Google Scholar 

  • Sanger, H. L., 1984, Minimal infectious agents: The viroids, in: The Microbe, 1984: Part I Viruses (B. W. J. Mahy and J. R. Pattison, eds.), Society for General Microbiology Symposium 36, pp. 281–334, Cambridge University Press, London.

    Google Scholar 

  • Sanger, H. L., Klotz, G., Riesner, D., Gross, H. J., and Kleinschmidt, A. K., 1976, Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures, Proc. Natl. Acad. Sci. USA 73:3852.

    Article  CAS  Google Scholar 

  • Sano, T., Uyeda, I., Shikata, E., Ohno, T., and Okada, Y., 1984, Nucleotide sequence of cucumber pale fruit viroid: Homology to hop stunt viroid, Nucleic Acids Res. 12:3427.

    Article  PubMed  CAS  Google Scholar 

  • Semancik, J. S., Morris, T. J., Weathers, L. G., Rodorf, B. F., and Kearns, D. R., 1975, Physical properties of a minimal infectious RNA (viroid) associated with the exocortis disease, Virology 63:160.

    Article  PubMed  CAS  Google Scholar 

  • Simoncsits, A., Brownlee, G. G., Brown, R. S., Rubin, J. R., and Guilley, H., 1977, New rapid gel sequencing method for RNA, Nature 269:833.

    Article  PubMed  CAS  Google Scholar 

  • Steger, G., Hofmann, H., Fortsch, J., Gross, H. J., Randies, J. W., Sänger, H. L., and Riesner, D., 1984, Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data, J. Biomol. Struct. Dyn. 2:543.

    CAS  Google Scholar 

  • Symons, R. H., 1979, Extensive sequence homology at the 3’-termini of the four RNAs of cucumber mosaic virus, Nucleic Acids Res. 7:825.

    Article  PubMed  CAS  Google Scholar 

  • Symons, R. H., 1981, Avocado sunblotch viroid: Primary sequence and proposed secondary structure, Nucleic Acids Res. 9:6527.

    Article  PubMed  CAS  Google Scholar 

  • Symons, R. H., Haseloff, J., Visvader, J. E., Keese, P., Murphy, P. J., Gill, D. S., Gordon, K. H. J., and Bruening, G., 1985, On the mechanism of replication of viroids, virusoids, and satellite RNAs, in: Subviral Pathogens of Plants and Animals: Viroids and Prions (K. Maramorosch and J. J. McKelvey, Jr., eds.), pp. 235–263, Academic Press, New York.

    Google Scholar 

  • Tabler, M., and Sanger, H. L., 1984, Cloned single- and double-stranded DNA copies of potato spindle tuber viroid (PSTV) RNA and co-inoculated subgenomic DNA fragments are infectious, EMBO J. 3:3055.

    PubMed  CAS  Google Scholar 

  • Tinoco, I., Jr., Uhlenbeck, O. C., and Levine, M. D., 1971, Estimation of secondary structure in ribonucleic acids, Nature 230:362.

    Article  PubMed  CAS  Google Scholar 

  • van Wezenbeek, P., Vos, P., van Boom, J., and van Kammen, A., 1982, Molecular cloning and characterization of a complete DNA copy of potato spindle tuber viroid RNA, Nucleic Acids Res. 10:7947.

    Article  PubMed  Google Scholar 

  • Visvader, J. E., and Symons, R. H., 1983, Comparative sequence and structure of different isolates of citrus exocortis viroid, Virology 130:232.

    Article  PubMed  CAS  Google Scholar 

  • Visvader, J. E., and Symons, R. H., 1985, Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity, Nucleic Acids Res. 13:2907.

    Article  PubMed  CAS  Google Scholar 

  • Visvader, J. E., and Symons, R. H., 1986, Replication of in vitro constructed viroid mutants: Location of the pathogenicity-modulating domain of citrus exocortis viroid, EMBO J. 5:2051.

    PubMed  CAS  Google Scholar 

  • Visvader, J. E., Gould, A. R., Bruening, G. E., and Symons, R. H., 1982, Citrus exocortis viroid: Nucleotide sequence and secondary structure of an Australian isolate, FEBS Lett. 137:288.

    Article  PubMed  CAS  Google Scholar 

  • Visvader, J. E., Forster, A. C., and Symons, R. H., 1985, Infectivity and in vitro mutagenesis of monomeric cDNA clones of citrus exocortis viroid indicates the site of processing of viroid precursors, Nucleic Acids Res. 13:5843.

    Article  PubMed  CAS  Google Scholar 

  • Zimmern, D., and Kaesberg, P., 1978, 3’-Terminal nucleotide sequence of encephalomy-ocarditis virus RNA determined by reverse transcriptase and chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 75:4257.

    Article  CAS  Google Scholar 

  • Zuker, M., and Stiegler, P., 1981, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Res. 9:133.

    Article  PubMed  CAS  Google Scholar 

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Author notes

  1. Paul Keese

    Present address: Research School of Biological Sciences, Australian National University, Canberra, A.C.T., 2600, Australia

Authors and Affiliations

  1. Department of Biochemistry, University of Adelaide, Adelaide, 5000, South Australia, Australia

    Paul Keese & Robert H. Symons

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  1. Paul Keese
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  2. Robert H. Symons
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Editors and Affiliations

  1. Microbiology and Plant Pathology Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, 20705, USA

    T. O. Diener

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© 1987 Plenum Press, New York

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Keese, P., Symons, R.H. (1987). Physical-Chemical Properties. In: Diener, T.O. (eds) The Viroids. The Viruses. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-1855-2_3

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  • DOI: https://doi.org/10.1007/978-1-4613-1855-2_3

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