Rna Virus Genomes Positive-Strand rna Viruses:
The ultimate size of single-stranded RNA genomes is limited by the fragility of RNA & the tendency of long strands to break. In addition, RNA genomes tend to have higher mutation rates than those composed of DNA because they are copied less accurately, which also tends to drive RNA viruses towards smaller genomes.
Single-stranded RNA genomes vary in size from those of Coronaviruses at approximately 30kb long to those of bacteriophages such as MS2 & Qβ at about 3.5kb. Such genomes from different virus families share a number of common features:
Purified (+)sense vRNA is directly infectious when applied to susceptible host cells in the absence of any virus proteins (although it is about one million times less infectious than virus particles).
There is an untranslated region (UTR) at the 5' end of the genome which does not encode any proteins & a shorter UTR at the 3' end. These regions are functionally important in virus replication & are thus conserved in spite of the pressure to reduce genome size.
Both ends of (+)stranded eukaryotic virus genomes are often modified, the 5' end by a small, covalently attached protein or a methylated nucleotide 'cap' structure & the 3' end by polyadenylation. These signals allow vRNA to be recognised by host cells & to function as mRNA.
Negative-Strand rna Viruses:
Viruses with negative-sense RNA genomes are a little more diverse than positive-stranded viruses. Possibly because of the difficulties of expression, they tend to have larger genomes encoding more genetic information. Because of this, segmentation is a common though not universal feature of such viruses.
Negative-sense RNA genomes are not infectious as purified RNA. This is because such virus particles all contain a virus-specific polymerase. The first event when the virus genome enters the cell is that the (-)sense genome is copied by the polymerase, forming either (+)sense transcripts which are used directly as mRNA, or a double-stranded molecule known either as the replicative intermediate (RI) or replicative form (RF), which serves as a template for further rounds of mRNA synthesis. Therefore, since purified negative-sense genomes cannot be directly translated & are not replicated in the absence of the virus polymerase, these genomes are inherently non-infectious.
Ambisense Genome Organization:
Some RNA viruses are not strictly 'negative-sense' but ambisense, since they are part (-)sense & part (+)sense:
Dna Virus Genomes 'Small' dna Genomes:
Bacteriophages have been extensively studied as examples of DNA virus genomes. Although they vary considerably in size, in general terms they tend to be relatively small.
The structure of the bacteriophage M13 genome has been studied in great detail & modified extensively for use as a vector for DNA sequencing. The genome of this virus is:
circular
single-stranded DNA
approximately 7,200 nucleotides long
Unlike other virion structures, the filamentous M13 capsid can be lengthened by the addition of further protein subunits. The genome size of this virus can also be increased by the addition of extra sequences in the non-essential intergenic region without the penalty of becoming incapable of being packaged into the capsid. This is very unusual. In other viruses, the packaging constraints are much more rigid, e.g. in phage λ, only DNA of between approximately 95% - 110% (approximately 46kbp - 54kbp) of the normal genome size (49kbp) can be packaged into the virus particle.
Not all bacteriophages have such simple genomes as M13, e.g. the genome of lambda is approximately 49kbp & that of phage T4 about 160kbp double-stranded DNA. These latter two bacteriophages also illustrate another common feature of linear virus genomes - the importance of the sequences present at the ends of the genome:
In the case of lambda, the substrate which is packaged into the phage heads during assembly consists of long concatemers of phage DNA which are produced during the later stages of vegetative replication. The DNA is 'reeled in' by the phage head & when a complete genome has been incorporated, cleaved at a specific sequence by a phage-encoded endonuclease. This enzymes leaves a 12bp 5' overhang on the end of each of the cleaved strands, known as the cos site. Hydrogen bond formation between these 'sticky ends' can result in the formation of a circular molecule. In a newly infected cell, the gaps on either side of the cos site are closed by DNA ligase & it is this circular DNA which is undergoes vegetative replication or integration into the bacterial chromosome.
Bacteriophage T4 illustrates another molecular feature of certain linear virus genomes, terminal redundancy. Replication of the T4 genome also produces long concatemers of DNA. These are cleaved by a specific endonuclease, but unlike the lamda genome, the lengths of DNA incorporated into the particle are somewhat longer than a complete genome length. Therefore, some genes are repeated at each end of the genome, & the DNA packaged into the phage particles contains reiterated information.
As further examples of small DNA genomes, consider those of two families of animal viruses, the parvoviruses & polyomaviruses:
|
Parvovirus genomes are:
|
These are very small genomes, & even the replication-competent parvoviruses contain only two genes, rep, which encodes proteins involved in transcription & cap, which encodes the coat proteins. The ends of the genome have palindromic sequences of about 115nt, which form 'hairpins'. These structures are essential for the initiation of genome replication, once again emphasising the importance of the sequences at the ends of the genome.
The genomes of polyomaviruses consist of double-stranded, circular DNA molecules, approximately 5kbp in size:
The entire nucleotide sequence of all the viruses in the family is known & the architecture of the polyomavirus genome (i.e. number & arrangement of genes & function of the regulatory signals & systems) has been studied in great detail at a molecular level. Within the particles, the virus DNA is associated with four cellular histones. The genomic organization of these viruses has evolved to pack maximal information (6 genes) into minimal space (5kbp). This has been achieved by the use of both strands of the genome DNA & overlapping genes.