Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation

A longer‐than‐unit‐length transcript of potato spindle tuber viroid is correctly processed in a potato nuclear extract only if the central conserved region is folded into a multi‐helix junction containing at least one GNRA tetraloop‐hairpin. The cleavage‐ligation site between G95 and G96 was mapped with S1 nuclease and primer extension. The structural motifs involved in the processing mechanism were analysed by UV crosslinking, chemical mapping, phylogenetic comparison and thermodynamic calculations. For processing, the first cleavage occurs within the stem of the GNRA tetraloop; a local conformational change switches the tetraloop motif into a loop E motif, stabilizing a base‐paired 5′ end. The second cleavage yields unit‐length linear intermediates, whose 3′ end is also base‐paired and most probably coaxially stacked in optimum juxtaposition to the 5′ end. They are ligated to mature circles autocatalytically, with low efficiency, or enzymatically, with high efficiency.

[1]  D. Smith,et al.  Mexican papita viroid: putative ancestor of crop viroids. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. Butcher,et al.  Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex. , 1994, Journal of molecular biology.

[3]  J. Kaper,et al.  Small satellite of arabis mosaic virus: autolytic processing of in vitro transcripts of (+) and (-) polarity and infectivity of (+) strand transcripts. , 1995, The Journal of general virology.

[4]  G. Varani,et al.  Structure of an unusually stable RNA hairpin. , 1991, Biochemistry.

[5]  W. Filipowicz,et al.  Circularization of linear viroid RNA via 2'-phosphomonoester, 3', 5'-phosphodiester bonds by a novel type of RNA ligase from wheat germ and Chlamydomonas. , 1982, Nucleic acids research.

[6]  J. Duin,et al.  Secondary Structure Model of the Last Two Domains of Single-stranded RNA Phage Qβ , 1995 .

[7]  R. Simons,et al.  Control of translation by mRNA secondary structure: the importance of the kinetics of structure formation , 1994, Molecular microbiology.

[8]  W. Filipowicz,et al.  Formation of a 2′-phosphomonoester, 3′,5′-phosphodiester linkage by a novel RNA ligase in wheat germ , 1981, Nature.

[9]  J. Semancik.  Viroids and viroid-like pathogens , 1987 .

[10]  D. O. Jordan.  Physico-Chemical Properties of Nucleic Acids , 1950, Nature.

[11]  G. Chanfreau,et al.  An RNA conformational change between the two chemical steps of group II self‐splicing. , 1996, The EMBO journal.

[12]  D Riesner,et al.  Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. , 1991, The EMBO journal.

[13]  I. Tinoco,et al.  Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. , 1992, Nucleic acids research.

[14]  G. Krupp.  RNA synthesis: strategies for the use of bacteriophage RNA polymerases. , 1988, Gene.

[15]  Y. Machida,et al.  THE SEQUENCE IN THE POTATO SPINDLE TUBER VIROID REQUIRED FOR ITS cDNA TO BE INFECTIVE: A PUTATIVE PROCESSING SITE IN VIROID REPLICATION , 1985 .

[16]  G. Steger,et al.  Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. , 1994, Nucleic acids research.

[17]  I. Tinoco,et al.  A thermodynamic study of unusually stable RNA and DNA hairpins. , 1991, Nucleic acids research.

[18]  E Westhof,et al.  Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. , 1994, Journal of molecular biology.

[19]  H. L. Sänger,et al.  Cloned single‐ and double‐stranded DNA copies of potato spindle tuber viroid (PSTV) RNA and co‐inoculated subgenomic DNA fragments are infectious. , 1984, The EMBO journal.

[20]  G. Varani,et al.  The conformation of loop E of eukaryotic 5S ribosomal RNA. , 1993, Biochemistry.

[21]  A. Berk,et al.  Spliced early mRNAs of simian virus 40. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[22]  R. Symons,et al.  Infectivity of linear monomeric transcripts of citrus exocortis viroid: terminal sequence requirements for processing. , 1994, Virology.

[23]  I. Tinoco,et al.  RNA structure at high resolution , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[24]  C. Kundrot,et al.  Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing , 1996, Science.

[25]  R. Symons,et al.  Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites , 1987, Cell.

[26]  O. Uhlenbeck,et al.  Characterization of RNA hairpin loop stability. , 1988, Nucleic acids research.

[27]  H. Robertson,et al.  Cell-Free Circularization of Viroid Progeny RNA by an RNA Ligase from Wheat Germ , 1982, Science.

[28]  M. Schmitz,et al.  Base-pair probability profiles of RNA secondary structures , 1992, Comput. Appl. Biosci..

[29]  G. Steger,et al.  Structural requirements for viroid processing by RNase T1. , 1992, Journal of molecular biology.

[30]  T. Cech,et al.  GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. , 1994, Journal of molecular biology.

[31]  H. Domdey,et al.  Nucleotide sequence and secondary structure of potato spindle tuber viroid , 1978, Nature.

[32]  H. L. Sänger,et al.  A single nucleotide substitution converts potato spindle tuber viroid (PSTVd) from a noninfectious to an infectious RNA for nicotiana tabacum. , 1996, Virology.

[33]  J. Langowski,et al.  Common structural features of different viroids: serial arrangement of double helical sections and internal loops. , 1978, Nucleic acids research.

[34]  H. Robertson,et al.  A replication cycle for viroids and other small infectious RNA's. , 1984, Science.

[35]  K. Flaherty,et al.  Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix , 1994, Nature.

[36]  F. Michel,et al.  Frequent use of the same tertiary motif by self‐folding RNAs. , 1995, The EMBO journal.

[37]  T. O. Diener.  The Viroids , 1987, The Viruses.

[38]  Oligomeric potato spindle tuber viroid (PSTV) RNA does not process autocatalytically under conditions where other RNAs do. , 1987, Virology.

[39]  Murray N. Schnare,et al.  A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993 , 1993, Nucleic Acids Res..

[40]  T. O. Diener.  Circular RNAs: relics of precellular evolution? , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[41]  N. Davidson,et al.  Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide. , 1977, Nucleic acids research.

[42]  I. Petersen,et al.  Direct DNA sequencing following SSCP analysis. , 1994, Analytical biochemistry.

[43]  T. Candresse,et al.  The role of the viroid central conserved region in cDNA infectivity. , 1990, Virology.

[44]  R. Symons,et al.  Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. , 1986, Nucleic acids research.

[45]  E. Westhof,et al.  Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs. , 1994, Journal of molecular biology.

[46]  J. M. Buzayan,et al.  Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA , 1986, Nature.

[47]  T. Baumstark,et al.  Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract. , 1995, Nucleic acids research.

[48]  C. Hernández,et al.  Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[49]  J. Daròs,et al.  Replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[50]  B. J. Benenfeld,et al.  Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[51]  S. Butcher,et al.  A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme. , 1994, Biochemistry.

[52]  J. van Duin,et al.  Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? , 1995, RNA.

[53]  G. Steger,et al.  High resolution SSCP by optimization of the temperature by transverse TGGE. , 1995, Nucleic acids research.

[54]  E. Westhof,et al.  Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. , 1990, Journal of molecular biology.

[55]  T. O. Diener.  Viroid processing: a model involving the central conserved region and hairpin I. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[56]  H. Robertson,et al.  Transcripts of the viroid central conserved region contain the local tertiary structural element found in full‐length viroid , 1992, FEBS letters.

[57]  P. Moore,et al.  The sarcin/ricin loop, a modular RNA. , 1995, Journal of molecular biology.

[58]  D. Riesner,et al.  CHAPTER 15 – Thermodynamics and Kinetics of Conformational Transitions in Oligonucleotides and tRNA , 1973 .

[59]  S. Coutts.  Thermodynamics and kinetics of G-C base pairing in the isolated extra arm of serine-specific transfer RNA from yeast. , 1971, Biochimica et biophysica acta.

[60]  B. Dujon,et al.  Conservation of RNA secondary structures in two intron families including mitochondrial‐, chloroplast‐ and nuclear‐encoded members. , 1983, The EMBO journal.

[61]  G. Steger,et al.  Analysis of RNA structures by temperature-gradient gel electrophoresis: viroid replication and processing. , 1988, Gene.