The DNA of a Plant Retroviroid-Like Element Is Fused to Different Sites in the Genome of a Plant Pararetrovirus and Shows Multiple Forms with Sequence Deletions

Abstract

Carnation small viroid-like RNA (CarSV RNA) and its homologous DNA are the two forms of a unique plant retroviroid-like system. CarSV RNA is a 275-nucleotide noninfectious viroid-like RNA, present in certain carnation plants, which can adopt hammerhead structures in both polarity strands and self-cleave accordingly. CarSV DNA is organized as a series of head-to-tail multimers forming part of extrachromosomal elements in which CarSV DNA sequences are fused to sequences of carnation etched ring virus (CERV), a plant pararetrovirus. Analysis of more than 30 CarSV-CERV DNA junctions showed that distinct regions of the viral genome seem able to interact with CarSV DNA. All these junctions were short nucleotide stretches common to both CarSV and CERV DNAs. This suggests a polymerase-driven mechanism for their origin involving an enzyme with low processivity, most likely the viral reverse transcriptase. This view was further supported by the observation that most of CarSV sequences forming part of the junctions correspond either to strong secondary structure motifs in the conformation proposed for CarSV RNA or to its self-cleavage sites, which may have facilitated polymerase jumping. Accompanying the most-abundant CarSV RNA, a series of CarSV RNAs with sequence deletions were previously characterized. Here we have identified some of their corresponding DNA forms, together with other CarSV DNA forms with deletions not found in any CarSV RNA species identified so far. Some of these CarSV DNA forms have also been detected fused to CERV sequences. The existence of these shortened CarSV DNA versions may provide a continuous input of their corresponding transcripts and explain the persistence of CarSV RNAs with defective hammerhead structures for which an RNA-RNA model of amplification seems unlikely.Carnation small viroid-like RNA (CarSV RNA) and its homologous DNA, have been proposed as the two forms of a unique plant retroviroid-like system (5). CarSV RNA is a 275-nucleotide (nt) circular RNA present in certain carnation plants which can form hammerhead structures in both polarity strands and self-cleave in vitro as predicted by these ribozymes (16). Despite the structural similarities that CarSV RNA shares with viroid and viroid-like satellite RNAs (for reviews on these pathogens, see references 2, 9, 14, 15, and 31), two main differences separate them: CarSV RNA lacks an extracellular infectious phase, i.e., it cannot be transmitted horizontally from plant to plant, and also it exists as a homologous DNA counterpart (5; L. Palkovics, K. Salánki, A. Wittner, E. Tóth, and E. Balázs, 5th Int. Cong. Plant Mol. Biol., abstr. 1019, 1997). CarSV DNA accumulates at low levels in carnation since it is only detectable by PCR amplification, and examination of the patterns of PCR-amplified products indicates that CarSV DNA is organized as a series of head-to-tail multimers (5). The CarSV RNA-DNA element bears a close resemblance to two small linear RNAs from the newt (330 nt) and schistosomes (335 nt), which are also able to adopt ...

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