Nucleotide Sequence and Secondary Structure of Citrus Exocortis and Chrysanthemum Stunt Viroid

Abstract

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 vilro 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 U l a RNA found for a region highly conserved in the three viroids.

Common structural features of the genes for two stable RNAs fromHalobacterium halobium

“…The length of the gene (304 bp) correlates well with the length of the RNA suggesting that the gene for the 7S RNA does not contain intron(s) although extremely small introns (less than 10 bp) can not be excluded by these data. This was further confirmed by sequencing fragments of 7S RNA obtained by partial digestion of this RNA with RNases U2, Ti and A (21,22,23). These partial RNA sequences covered 92 % of the total DNA sequence identified as the gene for the 7S RNA without any interruption.…”

“…Isolation of DNA was carried out as previously described (9 (20) and Gross et al (21). Partial enzymatic digestion of RNA.…”

“…Partial enzymatic digestion of RNA. Partial enzymatic digestion of RNA with RNase A, Ti and U2 was performed essentially as described (21,22,23).…”

A citrus exocortis viroid variant from broad bean (Vicia faba L.): infectivity and pathogenesis

“…Sequence analysis demonstrated that the nucleic acid detected in broad bean was a variant of CEVd containing 373 nucleotides with ten differences as compared with CEVd-C (Fig. 2a, b) (Gross et al, 1982). Six of these variations (see asterisks in Fig.…”

“…Moreover, the characterization of most viroids, including CEVd, has been accomplished after their purification from alternative herbaceous hosts which provided high viroid titres (Semancik & Weathers, 1972;Gross et al, 1982;Visvader et al, 1982). Since the viroid population of a given isolate can be modified as a result of host and tissue selection its biological properties may also vary depending on the host chosen for its characterization (Semancik et al, 1993).…”