Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid.

The complete nucleotide sequence of citrus exocortis viroid (CEV, propagated in Gymura) and chrysanthemum stunt viroid (CSV, propagated in Cineraria) has been established, using labelling in vitro and direct RNA sequencing methods and a new screening procedure for the rapid selection of suitable RNA fragments from limited digests. The covalently closed circular single-stranded viroid RNAs consist of 371 (CEV) and 354 (CSV) nucleotides, respectively. As previously shown for potato spindle tuber viroid (PSTV, 359 nucleotides), CEV and CSV also contain a long polypurine sequence. Maximal base-pairing of the established CEV and CSV sequences results in an extended rod-like secondary structure similar to that previously established for PSTV and as predicted from detailed physicochemical studies of all these viroids. Although the three viroid species sequenced to date differ in size and nucleotide sequence, there is 60--73% homology between them. As PSTV, CEV and CSV also contain conserved complementary sequences which are separated from each other in the native secondary structure. We postulate that the resulting 'secondary' hairpins, being formed and observed in vitro during the complex process of thermal denaturation of viroid RNA, must have a vital, although yet unknown, function in vivo. The possible origin and function of viroids are discussed on the basis of the characteristic structural features and of a considerable homology with U1a RNA found for a region highly conserved in the three viroids.

Nucleotide sequence and secondary structure of potato spindle tuber viroid.

The viroid of the potato spindle tuber disease (PSTV) is a covalently closed ring of 359 ribonucleotides. As a result of intramolecular base pairing, a serial arrangement of double-helical sections and internal loops form a unique rod-like secondary structure. PSTV is the first pathogen of a eukaryotic organism for which the complete molecular structure has been established.

Amino-acid incorporation into tRNA fragments and into heterologous combinations of fragments.

When the CCA-halves of tRNAAla1(yeast) and tRNAVal1(Escherichia coli) were incubated with the pG-halves of tRNAVal1 (E.coli) and trnaala1 (yeast), respectively, heterologous complexes were detected. When a 10-fold excess of one half was applied, up to 50% of the other half could be complexed. 5--12% alanine and valine incorporation was observed into the heterolgous combinations in which the pG-halves were derived from tRNAAla1 (yeast) and tRNAVal1 (E.coli), respectively. Although the values are small they appear to be significant considering the results of a number of control experiments. The CCA-half of tRNASer1,2(yeast) and another fragment of this tRNA which extends from the dihydrouridine region to the CCA-terminus were inactive in the aminoacylation assay but they could be converted into a form which accepted serine under standard conditions even in the absence of a complementary fragment. One activation procedure involved the addition of MgCl2 to Mg2+-free fragment solutions, the other consisted in a brief heating-cooling cycle of the fragment solutions at low Mg2+ concentrations. With the two procedures up to 20% or up to 40%, respectively, of the maximal serine incorporation were achieved. At 37 degrees C the active conformation of the fragments persisted only for a few minutes. Analogously, the CCA-halves of tRNAPhe (yeast), tRNAAla1 (yeast), and tRNAVal1 (E.coli)could be activated although here the extent of aminoacylation varied greatly from one experiment to the other. Mischarging of the activated CCA-halves of tRNASer1,2 (yeast) and tRNAPhe (yeast) with phenylalanine and serine, respectively, was not observed. The results obtained with the hererologous fragment combinations and with the CCA-halves alone, which at first sight seem to contradict each other, are discussed with respect to the conformational requirements of synthetase-tRNA recognition.