The Evolution of Viruses - Zhdanov V. M. 1990

Special Section
Viroids

Diseases caused by viroids do not differ significantly from other viral plant diseases. The first of these to draw the attention of virologists was potato spindle tuber viroid (PSTV), followed later by the discovery of citrus diseases (such as citrus exocortis) and others [Diener T., 1982]. These pathogens attracted scientific interest because they turned out to be not conventional Viruses, but relatively small, covalently closed single-stranded RNA molecules with a Molecular Weight of 100,000–120,000. In PSTV, the viroid consists of 359 ribonucleotides. The circularization of the RNA and The complexity of its Secondary Structure provide viroids with unusual stability. Such a small RNA molecule cannot encode even a "minor" protein molecule, perhaps only a short polypeptide. In reality, viroid RNA lacks any Genetic Code and does not even contain AUG codons.

Naturally, viroids lack their own RNA Replication Enzymes, meaning replication must be carried out by cellular enzyme systems. Exactly how this occurs remains unclear, although it is logical to assume the existence of a replicative intermediate in the form of an RNA template complementary to either the virion RNA or double-stranded RNA. Such double-stranded RNA was isolated from PSTV-infected tomatoes using Polyacrylamide gel Electrophoresis and DNA–RNA Hybridization. Multiple loops of newly synthesized daughter RNA have been detected on the circular or linear strand of the replicative intermediate. Thus, the rolling-circle model can serve as a model for viroid RNA replication [Owens R., Diener T., 1982]. However, another possibility cannot be ruled out—replication via a DNA intermediate, which is indirectly supported by its sensitivity to actinomycin D.

In this regard, studying the cadang-cadang viroid, which infects coconut palms in the Philippines, is of particular interest. Investigations of this disease revealed four types of low-molecular-weight RNAs consisting of 250 and 500 NUCLEOTIDES (Cytology/cytology/16.html">Early stages of the disease), and 300 and 600 nucleotides (late stages). Apparently, the first members of these pairs are monomers, and the second are dimers of the former. A high degree of Homology has been found between these Viroids and other known viroids (PSTV, CSV, CEV, ASDV). Closely related to them are virusoids—encapsidated virus-like RNAs (VTMOV, SNMY, Subterranean clover mottle virus). None of these contain a genetic code. It is hypothesized that their replication is mediated by The Cell via a replicative intermediate, namely oligomeric RNA [Haseloff J. et al., 1982].

As already noted, the Introduction/11.html">Secondary structure of viroids is quite complex and includes numerous complementary regions, which also makes The formation of dimers possible [Diener T., 1986]. Based on sequencing data, viroids are predicted to contain five domains: a conserved central region, a pathogenicity region, a variable domain, and two terminal domains that undergo mutual exchange among viroids. Domain rearrangement is illustrated by the cadang-cadang viroid of coconut palm, which appears de novo upon each infection. This mechanism explains THE ORIGIN OF viroids and viruses through genetic exchange between the pathogen and host RNA [Keese P. et al., 1985]. Figures 4 and 5 show the domain structures of the viroids listed in Table 4.

Thus, viroids are autonomous fragments (hardly even classifiable as genes) of cellular genetic material transcribed into single-stranded RNA. The complexity of their secondary structure protects viroids from Nucleases and provides an opportunity for molecular evolution. It remains unclear what underlies the Pathogenesis of the diseases they cause. Most likely, this is not a primary property of the genetic elements from which viroids originated, but rather an acquired property that may have provided these autonomous structures with ecological and evolutionary advantages. There are compelling reasons to believe that viroids originate from introns or Transposons—Mobile Genetic Elements. This hypothesis is supported by the structural similarities between viroids and transposons. A comparison of four viroids—tomato stunt/apical stunt viroid (TASV), citrus exocortis (CEV), potato spindle tuber (PSTV), tomato "plantain macho" (TPMV), and chrysanthemum stunt viroid (CSV)—revealed five similar sequences ranging from 11 to 15 nucleotides in length, with an overall homology of 73–83%.

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Fig. 4. SCHEMATIC STRUCTURE OF a viroid.

Five homology regions among viroids are indicated; arrows denote inverted repeats; 1 — left terminal region; 2 — pathogenicity region; 3 — conserved central nucleoid (domain); 4 — variable region; 5 — right terminal region.

Fig. 5. Secondary STRUCTURE OF THE central conserved region of various viroids.

The consensus sequences are conserved across all viroids; 1 — PSTV, TPMV; 2 — CEV, TASV; 3 — CCCV; 4 — HSV.

At the same time, sequences typical of transposon termini have been identified, as well as inverted sequences ending in the dinucleotides UG and CA. Based on these data, it has been suggested [Kiefer M. et al., 1983] that viroids originate from transposons or retroviral proviruses that have lost their internal coding regions. Another hypothesis proposes that viroids—which are covalently closed circular RNA molecules with a molecular weight of 1.1 × 10⁵–1.3 × 10⁵—arose through the circularization of excised introns. This model was put forward based on studies of the potato spindle tuber viroid [Diener T., 1986; Dinter-Gottlieb F., 1986].

Table 4. Viroids and their isolates with established nucleotide sequences

On the other hand, viroids share A number of properties with certain satellite viruses, and both groups of structures show similarities with nuclear and Mitochondrial DNA introns [Gollmer C. et al., 1985]. The cited authors studied a satellite of cucumovirus—Peanut stunt virus-associated RNA (PARNAb). Its linear RNA has a 5'-cap structure and a 3'–OH group; its 5'- and 3'-termini are homologous to the RNA of another pea mosaic virus satellite. Furthermore, up to 90% of the PARNA5 nucleotides are homologous to certain plant viroids as well as to certain introns (Fig. 6). These data lead to the Conclusion that PARNA5 and viroids originate from nuclear and mitochondrial DNA introns and have evolutionarily diverged.

Plant virus satellites possess a small RNA of 400 nucleotides or more and replicate in the presence of helper viruses belonging to the cucumovirus, nepovirus, sobemovirus, and tombusvirus groups. The satellite RNA of tobacco ringspot virus has a molecular weight of 115,000 and consists of 352 nucleotides. Only the plus strand is encapsidated in monomeric or multimeric form [Gerlach W. et al., 1986]. The helper virus belongs to the nepoviruses and provides not only the replication of the satellite RNA but also its encapsidation, with the satellite virus reducing the pathogenicity of its supporting virus. Dimeric RNA forms yield two active satellite RNA molecules upon autolysis [Buzayan J. et al., 1986].

Fig. 6. Schematic representation of potential base-pairing between conserved sequences of PARNA5 introns compared with mitochondrial introns. Conserved sequences are boxed.

Along with satellite viruses, RNA-containing Viruses are frequently "accompanied" by satellite RNAs. For instance, the tobacco ringspot virus provirus is associated with a circular satellite RNA that is replicated by the master virus via a rolling-circle mechanism. Such satellite RNAs have been designated as virusoids and are frequently detected in virus-infected plants [Lin- thorst H., Kapar J., 1984]. The satellite RNA (RNA2) detected in plants infected with sobemoviruses differs from their genomic RNA (RNA1), which has a linear structure and a molecular weight of 1.4 × 10⁶. In contrast, the satellite RNA is small, possesses a circular structure, and is similar to viroids [Jones A., Mayo M., 1984].

Tobacco necrosis satellite virus multiplies in the presence of its helper virus, yet it encodes its own capsid protein. While tobacco necrosis virus has a sedimentation coefficient of 130S, the satellite virus sediments at 58S. The serological Proteins of both viruses show no relationship; the virion size is about 30 nm, whereas that of the satellite is 17 nm. The satellite RNA has a molecular weight of 0.4 × 10⁶, which corresponds to 1200 nucleotides [Kassanis B., 1981]. Studies of cucumber mosaic virus satellite RNA have demonstrated a high degree of homology with the 3'-terminal part of tRNA and corresponding plant genes [Gordon K., Symons R., 1983].

Unique relationships have been revealed between the quadripartite bee virus of chronic paralysis (chronic bee paralysis virus) and its satellite. Their capsid proteins are distinct and serologically unrelated. Chronic bee paralysis virus acts as a helper for its associated satellite virus, which is incapable of independent reproduction. Co-infection leads to competition for polymerase utilization, resulting in a decreased titer of the helper virus [Ball B. et al., 1985].

Thus, viroids and virusoids can be regarded as the earliest stages in the formation of autonomous genetic structures from which classical viruses may subsequently have evolved. Their origin from cellular genetic elements is unquestionable; at the same time, even at this initial stage, they are characterized by evolutionary autonomy.