Molecular cloning and characterization of potato spindle tuber viroid cDNA sequences

Cloning and Sequencing of Viroids

Determining the sequence identity of viroid RNAs present in symptomatic or asymptomatic plant tissues is critical to obtain knowledge of their distribution. It enables the development of tools for diagnostics and for studying the basic biology of viroids. With the advent of cDNA-based methods for cloning RNAs and cloning strategies that do not require prior knowledge of the viroid sequence, characterization of several newly discovered viroids has rapidly expanded our knowledge of these unusual pathogenic RNAs. This chapter describes two methods, using random primers or viroid-specific primers, to generate complementary DNA (cDNA) copies of viroid RNAs for subsequent cloning and sequence analysis.

Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation

Viroids are non-encapsidated, single-stranded, circular RNAs consisting of 246-434 nucleotides. Despite their non-protein-encoding RNA nature, viroids replicate autonomously in host cells. To date, more than 25 diseases in more than 15 crops, including vegetables, fruit trees, and flowers, have been reported. Some are pathogenic but others replicate without eliciting disease. Viroids were shown to have one of the fundamental attributes of life to adapt to environments according to Darwinian selection, and they are likely to be living fossils that have survived from the pre-cellular RNA world. In 50 years of research since their discovery, it was revealed that viroids invade host cells, replicate in nuclei or chloroplasts, and undergo nucleotide mutation in the process of adapting to new host environments. It was also demonstrated that structural motifs in viroid RNAs exert different levels of pathogenicity by interacting with various host factors. Despite their small size, the molecular mechanism of viroid pathogenicity turned out to be more complex than first thought.

Are viroids escaped introns?

A complex of considerable stability is possible between the 5' end of U1 RNA and a specific nucleotide sequence of the potato spindle tuber viroid complement. Because base-pairing between the 5' end of U1 RNA and the ends of introns is believed by some to be responsible for the precise alignment and correct excision of introns, the U1-related sequence may represent the two ends of a presumed intron ancestor of the viroid complement after circularization.

Longer-than-unit-length viroid minus strands are present in RNA from infected plants

Nucleic acids isolated from uninfected and potato spindle tuber viroid-infected Rutgers tomato plants were fractionated on agarose gels under two different sets of denaturing conditions and hybridized to (125)I-labeled viroid in a series of blot hybridization experiments. Complementary strand nucleic acids detected in extracts of infected plants were heterogeneous in size, with four discrete bands containing molecules approximately 700, 1050, 1500, and 1800 nucleotides long. Enzymatic studies indicated that these viroid minus strands are composed exclusively of RNA and, as extracted, are present in complexes containing extensive double-stranded regions. After treatment with several RNases under conditions favoring digestion of single-stranded regions, the high molecular weight minus strands can no longer be detected and roughly unit-length minus strands appear. A model for the structure of the viroid replication intermediate is proposed.

Evidence for a single rolling circle in the replication of potato spindle tuber viroid

We analyzed in vivo-labeled RNA to determine which of the two proposed rolling-circle models is more likely to depict the replication cycle of potato spindle tuber viroid. A key feature distinguishing the two models is the presence of a circular monomeric minus strand in one and not the other. Chromatography on cellulose CF11 was used to purify a fraction containing the replication intermediates free from single-stranded progeny. Heat denaturation followed by gel electrophoresis was used to seek possible circular templates-species required for rolling-circle replication to take place. Upon heating, a (32)P-labeled RNA was released. Limited nuclease digestion ("nicking") revealed that this was a unitlength circular RNA. Fingerprinting identified it as a plus strand. No circular minus strands were detected in this population or in nuclease-treated samples containing RNase T1-resistant cores of the replication complex. Thus, potato spindle tuber viroid appears to use an asymmetric pathway in which minus strands are synthesized by rolling-circle copying, but plus strands are not. More details of the replication pathways used by various viroid-like RNAs are needed and will help to establish the evolutionary relationships among these infectious agents.

RNA intermediates in potato spindle tuber viroid replication

Two double-stranded RNA intermediates of viroid replication have been isolated from potato spindle tuber viroid (PSTV)-infected tomato tissue and characterized by polyacrylamide gel electrophoresis and DNA-RNA hybridization techniques. These replicative intermediates contain monomeric circular or linear PSTV strands complexed with a multimeric complementary RNA strand. Synchronous synthesis of single-stranded PSTV is accompained by a simultaneous marked increase in double-stranded PSTV RNA; thus, in vivo precursors of the characterized double-stranded PSTV RNAs seem to be involved in PSTV replication. A "rolling circle" model for viroid replication on a circular PSTV template can accommodate the double-stranded PSTV RNA species characterized.

Viroids and the nature of viroid diseases

In its methodology, the unexpected discovery of the viroid in 1971 resembles that of the virus by Beijerinck some 70 years earlier. In either case, a novel type of plant pathogen was recognized by its ability to penetrate through a medium with pores small enough to exclude even the smallest previously known pathogen: bacteria as compared with the tobacco mosaic agent; viruses as compared with the potato spindle tuber agent. Interestingly, one of the two methods used by Beijerinck, diffusion of the tobacco mosaic agent into agar gels, is conceptually similar to one method used to establish the size of the potato spindle tuber agent, namely polyacrylamide gel electrophoresis. Further work demonstrated that neither agent is an unusually small conventional pathogen (a microbe in the case of the tobacco mosaic agent; a virus in the case of the potato spindle tuber agent), but that either agent represents the prototype of a fundamentally distinct class of pathogen, the viruses and the viroids, respectively. With the viroids, this distinction became evident once their unique molecular structure, lack of mRNA activity, and autonomous replication had become elucidated. Functionally, viroids rely to a far greater extent than viruses on their host's biosynthetic systems: Whereas translation of viral genetic information is essential for virus replication, viroids are totally dependent on their hosts' transcriptional system and, in contrast to viruses, no viroid-coded proteins are involved. Because of the viroids' simplicity and extremely small size they approach more closely even than viruses Beijerinck's concept of a contagium vivum fluidum.

The antigen of hepatitis delta virus: examination of in vitro RNA-binding specificity

The only known protein of hepatitis delta virus (HDV), the delta antigen, is found both within virus particles and within the nucleus of the infected cell, where it has one or more roles essential for RNA genome replication. Others have demonstrated that the antigen has the ability, in vitro, to specifically bind HDV RNA species. We report a further examination of this phenomenon, using partially purified recombinant protein, expressed as a fusion with the staphylococcal protein A. From Northwestern (RNA-immunoblot) analyses with both complete and various subdomains of HDV genomic and antigenomic RNAs, we found that a necessary feature for specific binding was that the RNA be able to fold to some extent into the so-called rodlike structure; this structure is a predicted intramolecular partial base-pairing of the circular RNA, with about 70% of all bases involved, so as to produce an unbranched rodlike structure. Six different subregions of the HDV rodlike structure, three on the genomic RNA and three on its complement, the antigenomic RNA, were tested and found to be sufficient for antigen binding. However, features in addition to the rodlike structure may also be necessary for specific binding, because we found that a similar structure present in the RNA of the potato spindle tuber viroid did not allow binding.

Subviral pathogens of plants: the viroids

Research during the last 15 years has conclusively shown that viroids are not only fundamentally different from viruses at the molecular level, but that they are most likely not directly related to viruses in an evolutionary sense. Today, viroids are among the most thoroughly studied biological macromolecules. Their molecular structures have been elucidated to a large extent, but much needs to be learned regarding the correlation between molecular structure and biological function. The availability of the tools of recombinant DNA technology in viroid research promises rapid progress in these areas of inquiry.

The electrophoretic analysis of low molecular weight nucleic acids from Crohn's disease tissues in the search for an unconventional small infectious agent. Brief report

A small unconventional, viroid-like aetiological agent might initiate Crohn's disease (CD). Electrophoresis of radiolabelled low molecular weight nucleic acids from mesenteric lymph nodes and leucocytes did not distinguish CD-specific sequences compatible with a viroid-like agent.

Molecular cloning of potato spindle tuber viroid (PSTV) cDNA synthesized by enzymatic elongation of PSTV-specific DNA primers: a general strategy for viroid cloning

Different cDNAs were synthesized by primer extension from the RNA of the severe strain KF 440 of potato spindle tuber viroid (PSTV) with the aid of reverse transcriptase using three PSTV-specific DNA molecules as primers. The cDNAs were made double-stranded and cloned into plasmid pBR 322. Various overlapping subgenomic DNA fragments were prepared from these clones and recombined in two different ways. In both cases a PSTV DNA copy was obtained which represented the entire PSTV RNA genome. The sequence of the DNA of one of the resulting full-length clones was identical with the original PSTV isolate, whereas the other clone showed one nucleotide change. On the basis of these results the advantages and problems of different strategies for the molecular cloning of the circular viroid RNA genome are discussed.

Construction of infectious potato spindle tuber viroid cDNA clones

Contiguous restriction fragments from two cloned partial-length potato spindle tuber viroid (PSTV) cDNAs were used to construct recombinant DNAs containing full-length monomeric and dimeric PSTV cDNA. When five different PSTV cDNA plasmids and RNA isolated from E. coli cells harboring these plasmids were tested for infectivity on tomato, plasmid DNAs containing PSTV cDNA dimers were infectious. RNA transcripts containing the sequence of PSTV from these plasmids were also infectious. The sequences of the viroid progeny and the cloned DNA were identical. In vitro mutagenesis of infectious PSTV cDNAs will allow systematic investigation of the role of specific sequences in viroid replication and pathogenesis.

Structural similarities between viroids and transposable genetic elements

The primary structures of the tomato planta macho and tomato apical stunt viroids have been determined, and probable secondary structures are proposed. Both viroids can assume the rodlike conformation with extensive base-pairing characteristic of all known viroids. Sequence homologies between the two viroids (75%) and with members of the potato spindle tuber viroid group (73-83%) indicate that they both belong to this group. Comparative sequence analysis of all members of the group reveals striking similarities with the ends of transposable genetic elements. These similarities, the presence of inverted repeats often ending with the dinucleotides U-G and C-A, and flanking imperfect direct repeats suggest that viroids may have originated from transposable elements or retroviral proviruses by deletion of interior portions of the viral (or element) DNA.

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region.

Nuclear DNA from uninfected or potato spindle tuber viroid-infected tomato plants contains no detectable sequences complementary to cloned double-stranded viroid cDNA

High molecular weight tomato nuclear DNA was isolated from uninfected and potato spindle tuber viroid (PSTV)-infected tomato leaves. Restriction digests were fractionated on agarose gels, denatured and transferred to diazobenzyloxymethylpaper, and hybridized to 32P-labeled cloned double-stranded PSTV cDNA. No hybridization to DNA from either uninfected or infected tissue could be detected under conditions that permitted detection of cloned double-stranded PSTV cDNA at a concentration equivalent to one-fifth copy of PSTV-related DNA per haploid tomato genome. Hybridization of tomato DNA to 32P-labeled cloned soybean 18S and 28S ribosomal DNA sequences showed that the restricted nuclear DNA was suitable for hybridization to probes containing homologous sequences. Our results indicate that neither PSTV nor its complementary strand is transcribed from nuclear DNA but do not rule out the possibility of sequence homology between host DNA and a small portion of PSTV or its complement.

Specifically primed synthesis in vitro of full-length DNA complementary to potato-spindle-tuber viroid

Potato spindle tuber viroid (PSTV) RNA is transcribed in vitro by reverse transcriptase into complementary DNA in the presence of synthetic oligodeoxyribonucleotides as primers. In the case of priming with the pentadecadeoxyribonucleotide d(T-T-C-T-T-T-T-T-T-C-T-T-T-T-C) complementary to PSTV RNA from nucleotides 49 to 63, specificity of transcription initiation allows rapid sequencing of part of the viroid genome using chain-terminating dideoxyribonucleoside triphosphates. The DNA transcripts obtained represent distinct molecular species with the largest product being a full-length copy of the viroid RNA template. Molecular hybridization with 32P-labeled complementary DNA detects sequence homologies among different viroid species.