A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA.

A three-dimensional model of the histidylable 3'-terminal tRNA-like domain of tobacco mosaic virus RNA is proposed on the basis of a comparative structural analysis, chemical and enzymatic probing, combined with graphical modeling of three RNA constructs of increasing size (38, 108, and 182 nt) derived from the 3'-terminal viral RNA sequence. The comparison between the probing patterns of the three RNAs allowed the determination of the relative orientation of these structural domains in the full-length viral tRNA-like structure. Modeling data indicate that only one of the two possible isomers of the three-way junction located at a central position of the tRNA-like domain is in agreement with structural data. Interestingly, this isomer gives rise to a molecule bearing a structural mimicry with the L-shape of canonical tRNAs. A pseudoknotted acceptor branch containing a T-like loop is located perpendicularly to an anticodon-like branch. Moreover, a single-stranded RNA stretch belonging to the pseudoknotted central core mimics a D-like loop and it is proposed that it interacts via two conserved guanosines with nucleotides of the T-like loop as found in canonical tRNAs. This model is valid for the 3' noncoding regions of tobamoviral RNAs as well as for the tRNA-like domain of the satellite tobacco mosaic virus RNA. All three molecules are substrates for yeast HisRS; however, whereas the complete viral genome is required for optimal histidylation capacities, both charging levels and affinity constants are decreased for the three RNA transcripts, suggesting that additional contacts located outside the tRNA-like domain are needed for an optimal aminoacylation process.

[1]  L. Philipson,et al.  Binding of histidine to tobacco mosaic virus RNA. , 1972, Biochemical and biophysical research communications.

[2]  A. Rich,et al.  Transfer RNA: molecular structure, sequence, and properties. , 1976, Annual review of biochemistry.

[3]  O. Uhlenbeck,et al.  Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. , 1978, Biochemistry.

[4]  K. Richards,et al.  Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA. , 1979, Nucleic acids research.

[5]  C. Pleij,et al.  Three‐dimensional models of the tRNA‐like 3′ termini of some plant viral RNAs. , 1983, The EMBO journal.

[6]  K. Watanabe,et al.  Role of the extra G-C pair at the end of the acceptor stem of tRNA(His) in aminoacylation. , 1989, Nucleic acids research.

[7]  J. Diaz‐ruiz,et al.  Nucleotide sequences of 5' and 3' non-coding regions of pepper mild mottle virus strain S RNA. , 1989, The Journal of general virology.

[8]  D. Lilley,et al.  The three‐way DNA junction is a Y‐shaped molecule in which there is no helix‐helix stacking. , 1990, The EMBO journal.

[9]  F. García-Arenal,et al.  The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus. , 1990, Virology.

[10]  C. Francklyn,et al.  Enzymatic aminoacylation of an eight-base-pair microhelix with histidine. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Ebel,et al.  Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides. , 1990, Biochimie.

[12]  A. T. Perrotta,et al.  A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA , 1991, Nature.

[13]  J. Puglisi,et al.  Synthesis and purification of large amounts of RNA oligonucleotides. , 1991, BioTechniques.

[14]  C. Pleij,et al.  tRNA‐like structures , 1991 .

[15]  E. Dam,et al.  Structural and functional aspects of RNA pseudoknots. , 1992, Biochemistry.

[16]  A model for the solution structure of a branched, three-strand DNA complex. , 1993, Journal of biomolecular structure & dynamics.

[17]  C Massire,et al.  DRAWNA: a program for drawing schematic views of nucleic acids. , 1994, Journal of molecular graphics.

[18]  C. Florentz,et al.  Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context. , 1994, Nucleic acids research.