Viral Nucleic Acids: DNA, RNA, secondary and tertiary structures

Viral nucleic acids

DNA or RNA. In viruses genetic information is carried by either DNA or RNA. Double stranded DNA carries information in the cell. Highly stable in its double stranded form, it is complemented, for the transfer of information to the protein, by messangers, transfer and ribosomal RNAs. Viral genomes are present in more varied forms; they are made up of DNA or RNA and either of these supports can be single-stranded or double-stranded.In plants only viruses in the families Caulimovirideae, Geminivirideae and Nanovirideae have DNA genomes. The other viruses have RNA genomes, most of which are single stranded. Single stranded RNAs can be positive sense or negative sense. Viral RNAs can also be double-stranded (Reovirideae). In 1956, it was established that the viral RNAs carry their own genetic information unlike the cellular RNAs where the primary support is the DNA. In evolutionary terms, the success of the RNA genomes indicates that it is advantageous for a virus to use this support. Its chemical fragility in the single-stranded form, especially its sensitivity to the ribonucleases, is probably counterbalanced by the formation of secondary double stranded structures and the close association with the proteins. All the viruses need mRNA to express their genes. Those viruses in which the genome is not directly messanger use different mechanisms to transcribe their genome into RNAs.

Cellular mRNA ends. Because of the process of synthesis, the chain of nucleotides that constitute RNA is oriented. The first triphosphate nucleoside positioned carries the phosphate residues on the 5′ carbon of ribose, and this end is called 5′. The chain grows by the formation of phosphodiester linkages between the 3′ carbon and the 5′ carbon of the subsequent triphosphate nucleoside. The last nucleoside has ribose carrying an –OH on the 3′ carbon and this is the 3′ end. These ends carry the structures that protect the RNAs from the action of the exonucleases and directly intervene in the initiation of protein synthesis. The 5′ end of the mRNA carries a cap made up of methylated guanosine in position 7 and inverted, forming a triphosphate bond with the first nucleotide of the chain. The first two bases are also methylated. The 3′ carries a poly A of variable length (20 to 40 amino acids). Certain viral transcripts have the same terminal structures as the cellular ends. The cellular mRNA begins and ends with non-coding regions of variable lengths that flank the coding region in which an open reading frame (ORF) opens, beginning generally with the start codon AUG in a favourable context, and ending in a termination codon (UAG, UAA, UGA).

Extremities of genomic viral RNA. The ends of the single-stranded genomic viral RNAs of the positive polarity carry diverse structures. At the 5′ end there is a cap but here the X and Y are not methylated, or a viral protein linked to the RNA by a covalent bond is present (VP_g), or even any particular structure. The VP_g is coded by the viral genome. It is not necessary for the translation of viral RNA. It is cleaved from the polypeptide in which it is part of the replication module (Fellers et al., 1998). Because of its role as a primer in the replication, it is linked to the 5′ end of the RNA by a covalent bond with a tyrosine (Potyviruses and poliovirus) or a serine (Comovirus). Its size ranges from 3.5 to 24 kDa depending on the virus. At the 3′ end is a poly (A) of the variable length, or a t-RNA like structure, or a particular structure (-Y). The t-RNA like structure was discovered on the RNA of the TYMV. The sequence of 159 nucleotides of the 3′ end leads to the folding of the chain by several series of base pairing that give it a part of the structure and functionality of the valine tRNA. The 3′ region of the viral RNA is the place where the replication enzymes recognize specifically to make a copy.

Six combinations have been found between the various structures of the 5′ and the 3′ ends:

§  5′ cap----3′ poly(A): Potexvirus, Trichovirus, Benyvirus

§  5′ cap----3′ tRNA like structure: Bromovirus, Cucumovirus, Hordeivirus

§  5′ cap----3′ Y: Alfamovirus, Carmovirus

§  5′ VP_g ----3′ poly(A): Comovirus, Potyviridae

§  5′ VP_g ----3′Y: Sobemovirus. Enamovirus

§  5′ X ----3′Y: Luteovirus, Necrivirus

where, X and Y represent structure that are still not precisely described.

The genomes of the plant viruses code 4 to 12 proteins, and many mechanisms are used by the viruses to express the large amount of the information in a minimum of sequences. Their genes are always very nearly spaced and it is not rare to found the overlapping ORFs. The genetic information is carried by a single molecule (undivided or monopartite) or by several molecules (multipartite). In the last case, the terminal structures of different RNAs are most often identical or very similar.

Secondary and tertiary structures. Some elements of the RNA structures can be predicted by the observation of sequences, by mutation experiments and by phylogenetic analyses. Statistical programs can be used to visualize folds and suggest optimal and sub-optimal structures. The secondary structures in the hairpin or stem-loop form are constituted when a single chain presents complementary inverse sequences, which in pairing will form a stem in a double helix, separated by a few nucleotides forming a loop. These are sites of interaction with the cellular and the viral proteins, and with other nucleotide sequences. A pseudo-knot is formed when the loop of a hairpin pairs with a nearby or more distant nucleotide sequence forming a tertiary structure. The tRNA like structures carried by certain viral RNAs at the 3′ end are formed of hairpins and pseudo-knots, the latter being absent in the cellular tRNA. Hairpins and pseudo-knots are present in different locations on the RNA, in relation with the translation, replication, encapsidation and other processes. The ultimate three dimensional structure is thus determined by its sequences, then the secondary structures and finally by the relationship between the secondary structures themselves and between them and the immediate or general environment.