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: linear non-segmented (+)sense single-stranded DNA about 5kb long

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.

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