Nucleotide sequence and secondary structure of potato spindle tuber viroid

Groß, H.; Domdey, Horst; Lossow, Christine; Jank, Peter; Raba, Manfred; Alberty, Heidemarie; Sänger, Heinz L.

doi:10.1038/273203a0

Cited by 481 publications

(266 citation statements)

References 46 publications

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“…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.…”

Section: Methodsmentioning

confidence: 72%

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

Moritz¹,

Lankat–Buttgereit²,

Groß³

et al. 1985

Nucl Acids Res

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The genes coding for the 5S rRNA and another stable RNA, termed 7S RNA, in Halobacterium halobium were isolated from a genomic library of this archaebacterium and their nucleotide sequences determined. Both genes are colinear with their transcripts (5S rRNA and 7S RNA), but 5S rRNA and possibly also 7S RNA isolated from other halobacteria carry additional nucleotides within the RNA transcript. Both genes are located in the G+C rich chromosomal fraction I of H. halobium. Comparison of the 3' non-coding regions of both genes shows a 20 bp sequence of high homology immediately at the 3' ends which is almost symmetrically flanked by two stem-loop structures, one being situated close to the 3' end but within the coding region and the other downstream of the common 20 bp sequence. INTRODUCTIONAs first shown by Woese (1), 16S ribosomal RNAs from archaebacteria differ considerably in their nucleotide sequence from those of normal eubacteria. More recent reports on the sequences of 5S rRNA from various archaebacteria, such as Thermoplasma acidophilum, Halobacterium cutirubrum and Halococcus morrhuae showed also substantial differences in their primary sequences as well as in their putative secondary structures compared to those of eubacteria and eukaryotes. Moreover it was demonstrated that the 5S

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Section: Methodsmentioning

confidence: 72%

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

Section: Methodsmentioning

confidence: 99%

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

Moritz¹,

Lankat–Buttgereit²,

Groß³

et al. 1985

Nucl Acids Res

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“…1) that show sequence homologies with stretches of U3B snRNA are drawn in bold-face. The figures with the arrows indicate the first and last nucleotide residues in the circular molecule according to the conventional numbering system [2]. Size of matrix 359 x 216, order of matches 2, size of boxes 30 x 30.…”

Section: Resultsmentioning

confidence: 99%

“…Viroids [l], a distinct class of plant pathogenic agents, are covalently closed circular singlestranded RNA molecules [2] with a particular, DNA-like secondary structure [3]. The complete nucleotide sequence and secondary structure of some of them are known [2,4-81. Eukaryotic small nuclear RNAs (snRNAs), of a largely unknown function, are linear singlestranded RNA molecules with a hairpin-like secondary structure (cf.…”

Section: Introductionmentioning

confidence: 99%

Sequence homology between potato spindle tuber viroid and U3B snRNA

1983

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Sequence homology was found by computer analysis between potato spindle tuber viroid (PSTV) RNA and U3B snRNA of Novikoff hepatoma cells. This homology is colinear in arrangement, extends in length to 81% of the entire U3B snRNA molecule and is involved in the PSTV molecule unique sites which, if depicted in terms of the secondary structure of the circular PSTV molecule, reveal a conspicuous regularity in their location. A strong relation in primary structure between PSTV and U3B snRNA is demonstrated by statistical analysis. PSTV 1138 snRNA

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“…In addition, four of the last six P47A clones had specific changes, prominent among which were: A9o -> G (clone 9) and G2~ a ~ U (clone 10) in the upper and lower strands, respectively, of the central conserved region (CCR) characteristic of the members of the apple scar skin viroid (ASSVd) group (Hashimoto & Koganezawa, 1987;Koltunow & Rezaian, 1988), and GI~-+U (clone 7) affecting the terminal conserved region (TCR) present Short communication in two viroid groups whose type members are ASSVd and potato spindle tuber viroid (PSTVd) (Gross et al, 1978). Substitutions in the lower strand of the CCR have been found in some PSTVd isolates (Owens et al, 1992), but not in viroids of the ASSVd group.…”

mentioning

confidence: 99%

Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

Ambrós

Desvignes

Llácer

et al. 1995

Journal of General Virology

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The sequences of several cDNA clones of pear blister canker viroid (PBCVd) P1914T and P47A isolates have been determined. Seven out of eight P1914T clones analysed have a constant sequence which differs at six positions from that of the P2098T isolate reported previously. The remaining P1914T clone (8) has a single nucleotide substitution. The same six changes have been also observed in most of the ten P47A clones sequenced.However, some P47A clones show additional variability in positions on both strands of the central conserved region (CCR) and in another conserved sequence at the left-terminal region. This is the first report of a change affecting the upper strand of a viroid CCR. Reasons why such a change is tolerated are discussed. Infectivity bioassays have demonstrated that PBCVd is the causal agent of PBC disease.

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Nucleotide sequence and secondary structure of potato spindle tuber viroid

Cited by 481 publications

References 46 publications

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

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

Sequence homology between potato spindle tuber viroid and U3B snRNA

Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

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