The Evolution of Viruses - Zhdanov, V. M. 1990

Special Section
RNA-Containing Isometric Viruses

This chapter examines Introduction/7.html">RNA-containing Viruses with icosahedral virion Structure, which represent a diverse group with undoubtedly varied origins and evolutionary pathways. Despite our long-standing familiarity with most of them, they remain insufficiently studied. All of them possess a positive-sense single-stranded RNA genome with a molecular weight ranging from 1.2 x 106 to 3.2 x 10⁶, and a virion diameter of 23–35 nm [Matthews R., 1982].

The smallest are viruses of the family Leviviridae, which infect various species of Bacteria. Their genome has a Molecular Weight of 1.2 x 10⁶, accounting for 30% of the virion mass, and encodes 4 Proteins: a capsid protein (12,000–14,000), a maturation protein (35,000–44,000), a replicase, and a lysis protein. Each virion contains 180 molecules of the capsid protein and a single molecule of the maturation protein. The replicase is synthesized during infection. Virions are icosahedra with a diameter of 23 nm, composed of 32 capsomers. This group of phages comprises about 40 viruses and exhibits narrow Specificity, infecting male Cells of enteric bacteria, caulobacters, and pseudomonads.

Viruses of the Nudaurelia ß group (6 viruses) infect insects (various lepidopteran species). The molecular weight of the RNA is 1.8 x 10⁶, which constitutes 10–11% of the virion mass. Virions contain a single capsid protein (60,000–70,000) arranged in 240 subunits (T=4), with a diameter of 35 nm. Most viruses in this group are immunologically related.

Six different viruses have been isolated from the insect Nudaurelia cytherea capensis. Among them, the Cu virus has been described in the greatest detail, possessing a protein with a molecular weight of 65,000 [Hendry D. et al., 1985].

Among plant viruses, three groups show similarities. The first group comprises maize chlorotic dwarf virus (MCDV) and the similar rice tungro virus. The Genome has a molecular weight of 3.2 x 106, and its proteins remain unstudied. The virions are polyhedra with a diameter of 30 nm and are transmitted by aphids. The genus Luteovirus is represented by barley yellow dwarf virus (BYDV) and about 40 other plant viruses. Their genome has a molecular weight of 2.0 x 106, and the capsid protein is 24,000. Virions are isometric, with a diameter of 25–30 nm, and replicate in the plant phloem. They are transmitted by aphids, in which the viruses persist. The host specificity spectrum varies among different members of this genus, a significant portion of which have been assigned to it provisionally.

The genus Tombusvirus includes about 11 plant-infecting viruses, including tomato bushy stunt virus (TBSV). They have a small genome with a molecular weight of approximately 1.5 x 10⁶, accounting for 17% of the virion mass, and a single capsid protein (41,000). The virion contains 180 molecules of the capsid protein, forming spherical particles with a diameter of 30 nm. Most viruses in this genus are cross-immunogenic. Their Replication resembles that of Caliciviruses: it produces a subgenomic RNA alongside the full-length double-stranded genome. These viruses infect a wide range of plants and are transmitted mechanically.

The tombusvirus group includes 6 serologically related viruses, with most showing significant nucleic acid Homology, even though genome sizes range from 3,500 (galinsoga mosaic virus) to 4,700 (tomato bushy stunt virus) NUCLEOTIDES. However, the antigenically closest viruses that form the core group have a Genome Size of 4,700 nucleotides [Gallitelli D. et al., 1985]. Using the Ouchterlony double immunodiffusion test, serological differentiation indices for tombusviruses were determined, based on which a dendrogram of serological relationships among 10 tombusviruses was constructed (Fig. 7). These data correlate with Amino acid sequences and may serve as a basis for hypotheses regarding tombusvirus evolution [Koenig R., Gibbs A., 1986].

It is appropriate to discuss a few more groups of positive-sense single-stranded RNA viruses.

A small group (6 species) of insect-infecting viruses are also bisegmented and form the family Nodaviridae. Their genome consists of two RNA segments with molecular weights of 1.15 x 10⁶ and 0.5 x 10⁶, both packaged within a single particle of 29 nm diameter. The RNA lacks poly(A) tails. The first segment encodes a protein with a molecular weight of 105,000 (likely a replicase), and the second encodes a precursor protein (43,000) of the capsid protein. The major protein has a molecular weight of 40,000, and the minor protein is 43,000 (or two at 39,000 each). In addition, low-molecular-weight Peptides with molecular weights of 10,000 and 5,000 are produced in infected cells; the former is involved in replication, while the latter is a component of virions. These viruses infect Diptera, Lepidoptera, and Hymenoptera, and typically have a wide host range.

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Fig. 7. Dendrogram illustrating the relationships among 10 tombusviruses based on reciprocal tests.

1 — TBSV; 2— TBS K-BS3; 3 — AMC V; 4 — PAMV; 5 — PLCV; 6 — MPV; 7 — EMCV; 8 — CIRV; 9 — TNV; 10 — Cyb RSV.

The genus Dianthovirus is represented by carnation ringspot virus and two other viruses. Their genome is bipartite, with RNA segments of 1.5 x 106 and 0.5 x 106, with the first segment harboring the Gene for the capsid protein (40,000). The particles are polyhedral with a diameter of 31–34 nm. The host range is broad, and the viruses are transmitted mechanically.

The pea enation mosaic virus group currently includes a single representative, which is a bipartite virus. Its RNA1 has a molecular weight of 1.77 x 10⁶ and encodes two major proteins, P2 (88,000) and P4 (369,000), and one minor protein, P1 (147,000). The genes for these proteins are arranged in the following order: P4 — P2 — P1. RNA2 has a molecular weight of 1.2 x 10⁶ and encodes the P3 protein (45,000). The capsid protein is VP2 [Gabriel C., De Zolten C., 1984].

The velvet tobacco mottle virus group comprises 4 representatives and possesses two RNA fragments (1.5 x 106 and 0.12 x 10⁶), the second of which is circular. Both fragments are packaged in separate particles with a diameter of 30 nm. The reproduction cycle is complex, involving both nuclear and cytoplasmic synthesis. These viruses are transmitted by beetles and mirids, as well as mechanically.

Pea enation mosaic virus has been classified into a separate group. Its genome is also bipartite, with RNA segments of 1.7 x 106 and 1.3 x 10⁶. There are two capsid proteins: a major one (22,000) and a minor one (28,000). The RNA is encapsidated in polyhedral particles 28 nm in diameter. The virus is transmitted by aphids, in which it persists.

Viruses of the genus Ilarvirus are bipartite. They contain 4 RNA molecules with molecular weights of 1.1 x 10⁶, 0.9 x 10⁶, and 0.7 x 10⁶, while the 4th RNA is an mRNA (0.3 x 10⁶) for the Synthesis of the capsid protein (25,000). Particles containing different RNAs have a diameter of 26–35 nm. The reproduction cycle is quite complex. Fifteen viruses in this group infect a wide range of plants and are transmitted either mechanically or through seeds.

The tripartite alfalfa mosaic virus contains three RNAs that encode proteins with molecular weights of 126,000 (RNA1), 90,000 (RNA2), and 32,000 (RNA3); the 4th component is an mRNA (RNA4) homologous to the 3'-terminal sequence of RNA3. The first two proteins drive viral RNA Synthesis, whereas the third protein regulates the balance between plus- and minus-strands of viral RNA. RNA4 encodes the synthesis of the capsid protein [Sarachu A. et al., 1985].

Let us briefly review three additional groups of isometric RNA-containing plant viruses. One of these, the genus Necrovirus, includes tobacco necrosis virus and cucumber necrosis virus. The RNA (1.3 x 106, 1.6 x 106) has a ppApGpUp structure at its 5'-end. There is a single capsid protein (22,000). Virions are 28 nm polyhedral particles that infect angiosperms and are transmitted by the fungus Olpidium. The second group, the genus Tymovirus, is represented by turnip yellow mosaic virus and 17 other viruses. The RNA (2 x 10⁶) accounts for 35% of the virion mass and features a m7G5'ppp5'Gp cap structure at the 5'-end and a tRNA-like structure at the 3'-end. Some particles contain mRNA (0.2x10⁶–0.3x10⁶) for the synthesis of the capsid protein—180 molecules per virion. Of the two particle types, ß-particles contain the complete genome, whereas T-particles are products of unbalanced synthesis. Morphologically, they are 29 nm icosahedra composed of 20 hexamers and 12 pentamers. Members of this genus show immunological relationships. These viruses infect dicotyledonous plants and are transmitted mechanically or by beetles. The viruses of the third group—cucumber mosaic viruses (genus Cucumovirus)—comprise 4 species and are tripartite: 1.25 x 10⁶ (RNA1); 1.13 x 10⁶ (RNA2); 0.82 x 10⁶ (RNA3). A fourth particle type contains mRNA (0.35 x 10⁶) for capsid Protein Synthesis. Unlike the RNA of the previous virus group, all 5'-ends of the RNAs possess a m7G5'ppp5'Np cap structure, and the 3'-end features a tRNA-like structure that accepts Tyrosine. The RNA fragments are enclosed in 29 nm icosahedral particles. Each RNA translates into a separate protein, with the first three encoding proteins of 105,000, 120,000, and 34,000 molecular weight [Afanasyev B. N. et al., 1986]. These viruses are transmitted mechanically, through seeds, and by aphids.

The viruses compared in this chapter share certain features while differing in others that define subgroups. Common characteristics include positive-sense RNA polarity, the absence of 5'-terminal proteins, and an isometric virion structure (or particle Morphology). Next come the differences.

In the first 5 groups, no mechanism for the compartmentalized synthesis of individual gene products has been discovered yet, although studies on small isometric phages have shown that The activity of each of the 4 genes is regulated during Translation. For instance, the synthesis of the polymerase halts the activity of its own gene by blocking the initiation site. A similar regulatory mechanism likely governs the few genes present in the remaining three virus groups. Their ecological niches are diverse: bacteria, insects, and plants (transmitted by aphids with persistent retention, as well as by Fungi).

Tombusviruses and tymoviruses already possess a distinct mechanism for separating the activities of different genes—namely, the synthesis of subgenomic RNA, even though the same sequence of identical positive polarity is present on the genomic RNA. The synthesis of subgenomic RNAs is mirrored in caliciviruses, whose genome also has a positive polarity but is distinguished by the presence of a protein covalently linked to its 5'-end.

Multipartite viruses can be viewed as a further evolutionary step in the functional Separation of individual genes; therefore, viruses with divided genomes are placed in a third category. This group includes, first, insect-infecting nodaviruses, whose genome is split into two fragments, although both fragments are packaged within the same capsid; the large fragment encodes the polymerase, while the small one encodes the capsid protein. Three groups of plant viruses with bipartite genomes package their complete genome across separate particles; the pea enation mosaic virus may also contain a 3rd RNA component. Groups of tripartite plant viruses can form a 4th component—an mRNA for capsid protein synthesis. All or nearly all genes are physically (spatially) separated.

Thus, the examined groups of small RNA-containing viruses illustrate one of the possible evolutionary pathways of their genome, ensuring the separate synthesis of proteins encoded by different genes, the quantitative ratios of which are, naturally, non-equimolar. From this perspective, the functioning of small genomes containing no more than 4–5 genes is more easily regulated if they are compartmentalized, which is almost ideally achieved in multipartite viruses. However, multipartity has a flip side: efficient infection requires the simultaneous entry of all multipartite virus components into a new host Organism. The specified virus groups do not appear to be closely related to one another; some, such as leviviruses, are highly specialized groups infecting only male individuals of certain bacterial species. Two groups of viruses infect insects. Of the remaining 7 plant-infecting groups, 4 are transmitted by insects, predominantly aphids. This may point to a potential mechanism by which these viruses colonize new ecological niches.

Nevertheless, there are reasons to suggest evolutionary links among different plant virus groups. In particular, this was demonstrated through comparative studies of the Amino Acid Composition of bromoviruses (tripartite, capped with tRNA-like structures), cucumoviruses (tripartite, capped with tRNA-like structures), and alfalfa mosaic virus (multipartite, capped structures). The dendrogram in Fig. 8 illustrates the possible divergence of these entities from a common ancestor [Dale J. et al., 1985].

These considerations are likely sufficient when analyzing the potential origins of the virus groups under consideration. Evolutionary relationships among various viruses displaying immunological affinity may well be uncovered not only through genome sequencing, but also by comparing the putative evolutionary pathways of both the Viruses and Their hosts. For instance, analyzing the Nudaurelia ß group of viruses clearly requires studying the geographical distribution and phylogeny of their hosts, namely Lepidoptera. Furthermore, phylogenetic correlations among enterobacteria, the genera Саulobacter and Pseudomonas, alongside the ecological interactions between Escherichia and Podellvibrio, can prove highly useful when examining isometric RNA-containing phages. It is also insightful to compare the serological relatedness among barley yellow dwarf virus strains with the cultivation history of cereals, carrots, turnips, peas, soybeans, clover, and other crops, as well as the parasitism spectrum of aphids infesting these plants.

Fig. 8. A dendrogram illustrating the Classification of brome mosaic virus, cucumovirus, and avian myeloblastosis virus proteins, whose amino acid compositions were determined computationally.

1 — BBM 1; 2 — BBM 2; 3 — BBM 3; 4 — CCM 1; 5 — CCM 2; 6 — CCM 3; 7 — BM; 8 — CYB; 9 — AMVS- 10 — AMV-425; 11, 12 — cucumber mosaic virus 1 and 2; 13 — PS; 14 — tomato aspermy virus.

When discussing small isometric RNA-containing viruses, we proceeded on the assumption that they lack both cap structures and 5'-terminal proteins. Further research will determine whether this holds true for all viral groups under review. However, explicitly highlighting two KEY FEATURES OF viral RNA replication may help in better understanding the material presented. Specifically, these features include: 1. RNA-dependent RNA synthesis lacks a proofreading mechanism to correct replication errors (the "typo" frequency can reach 10^-3 compared to 10^-7–10^-10 for DNA). 2. The absence of an enzymatic machinery to degrade extensive double-stranded RNA structures. Consequently, the genome replication strategy shifts, giving rise to specialized mechanisms and structures that prevent The formation of extended RNA duplexes during replication (such as tRNA-like terminal structures, simultaneous interaction with multiple replicase molecules, and the translation of growing plus-sense RNA strands, etc.).

Homology between viral and cellular proteins has also been observed in prokaryotic viruses [Koji O., 1985]. For instance, the ß-subunit of the MS2 phage replicase shares homology with the a-subunit of the Escherichia coli RNA polymerase; homology exists between the C-terminus of the aforementioned viral polymerase, the DNA primase (the product of the dnaG gene), and the a-subunit of the E. coli polymerase; and homology is likewise found between the ß-re-plicase of phage MS2, the DNA polymerase of phage T7, and the N-terminus of the bacterial polymerase a-subunit. These Examples suggest that evolution proceeds via blocks (modules) that can be utilized by viruses originating from cellular elements—sometimes quite distinct ones (such as the RNA-containing phage MS2 and the DNA-containing phage T7)—or, alternatively, we may be dealing once again with molecular convergence. Further elaboration on these replication features in chapters dedicated to The structure of RNA-containing viruses may provide deeper insight into The Emergence of fragmented genomes, the necessity of Genetic information compaction, and other related phenomena.

Finally, certain features of economical genome utilization should be highlighted (the mechanisms found in DNA viruses are listed below): 1) structural gene frame shifting (MS2, J2 RNA, ФX174 DNA); 2) different stop signals with identical METABOLISM/31.html">Transcription initiation sites (Qß, TYMV, RNA, ФX174 DNA); 3) transcription signals (JD, RNA, ФX174 DNA); 4) alternative reading directions (phage lambda). More detailed commentary [Reanney D., 1984] pertains to RNA-containing viruses.