Biology Reference
In-Depth Information
that greatly affects packaging accuracy is the coupling of encapsida-
tion and synthesis of the genome as found in many (
) strand RNA
viruses, for example the influenza A virus. In a similar manner, seques-
tration of the viral RNA and capsid/coat protein in vesicles as found
in cells infected with polio virus greatly improve packaging efficiency
by increasing the local concentration of the correct components while
keeping competing cellular material at low concentrations.
The following sections will provide an overview of the molecular-
level interactions that control packaging in four well-studied model
systems: The MS2 bacteriophage, the alfalfa mosaic virus (AMV), and
the retroviruses HIV and moloney murine leukemia virus (MMV).
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The MS2 Phage
The MS2 phage is a group I bacteriophage with a positive single-
stranded RNA genome comprising 3569 nucleotides. The major gene
products that are expressed upon viral infection of
E. coli
cells are the
393-amino acid maturation protein, a 60.7 kDa replicase subunit, the
13.75 kDa phage coat protein and the 75-amino acid lysis protein.
During the packaging of the genomic RNA a signal sequence
within the genomic RNA forms a specific complex with a coat protein
dimer as the intra-cellular concentration of coat protein increases. The
RNA-protein complex acts as a repressor of the translation of the viral
replicase gene by binding to an element in the initiation codon. This
is a key interaction in the regulation of virus assembly. The MS2 system
has been widely used to study sequence-specific interactions between
RNA and protein using biochemical and biophysical methods.
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The RNA Packaging Signal
The coat protein of the MS2 phage interacts specifically with a
19-nucleotide RNA hairpin that is located at the 5´ end of the viral
replicase gene. The hairpin consists of a seven-base pair stem closed
by a four-nucleotide loop. The stem is interrupted by an unpaired
nucleotide between base pairs five and six (Fig. 1). The stem sequence
includes the Shine-Dalgarno sequence and initiation codon of the
