Han Xiao PhD thesis - Research@StAndrews:FullText - University of ...

1.2.4 Genome organization
The genome of paramyxoviruses is single-stranded, non-segmented, negative-sense RNA
ranging in length from 15 kb to 19 kb (see Fig. 1.5). Flanking the genome is a 3’
extracistronic region of ∼ 50 nucleotides known as the leader, and 5’ extracistronic region
of 50 to 161 nucleotides known as the trailer. These regions are essential for virus
transcription and replication. The genome contains 6 to 10 tandem linked genes,
depending on species. At the beginning and end of each gene are conserved
transcriptional control sequences that are transcribed into mRNA. These genes are
separated by intergenic regions that vary in length depending on virus species.
Paramyxovirus helical nucleocapsids, rather than the free RNA genome, are the template
for all RNA synthesis. The genomic RNA complexed with the NP (or N), P and L
proteins (Holonucleocapsids) are thought to have the capacity to transcribe mRNAs in
vitro. A major characteristic used to help classify paramyxoviruses into different
subfamilies and genera is the structure of P genes. In certain paramyxoviruses, P gene
encodes more than one protein by overlapping open reading frames (ORFs) through
“RNA editing” or pseudotemplated addition of nucleotides (Kolakofsky and Lamb,
2001). In the genus Rubulavirus, PIV5, mumps virus P gene encodes both the P and V
genes. The P and V proteins have a common N-terminal domain (1-164 aa), but after the
editing site, viral polymerase could insert two additional non-templated G nucleotides
into the mRNA that shift the translational reading frames (ORF) (Vidal, Curran, and
Kolakofsky, 1990a; Vidal, Curran, and Kolakofsky, 1990b). As a result, the C-terminus
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