Classical swine fever virus (CSFV) is a member of the pestivirus
family, which shares many features in common with hepatitis
C virus (HCV). It is shown here that CSFV has an exceptionally
efficient cis-acting internal ribosome entry segment
(IRES), which, like that of HCV, is strongly influenced by the
sequences immediately downstream of the initiation codon, and
is optimal with viral coding sequences in this position. Constructs
that retained 17 or more codons of viral coding sequence exhibited
full IRES activity, but with only 12 codons, activity was ∼66%
of maximum in vitro (though close to maximum in transfected
BHK cells), whereas with just 3 codons or fewer, the activity
was only ∼15% of maximum. The minimal coding region elements
required for high activity were exchanged between HCV and CSFV.
Although maximum activity was observed in each case with the
homologous combination of coding region and 5′ UTR, the
heterologous combinations were sufficiently active to rule out
a highly specific functional interplay between the 5′
UTR and coding sequences. On the other hand, inversion of the
coding sequences resulted in low IRES activity, particularly
with the HCV coding sequences. RNA structure probing showed
that the efficiency of internal initiation of these chimeric
constructs correlated most closely with the degree of
single-strandedness of the region around and immediately downstream
of the initiation codon. The low activity IRESs could not be
rescued by addition of supplementary eIF4A (the initiation factor
with ATP-dependent RNA helicase activity). The extreme sensitivity
to secondary structure around the initiation codon is likely
to be due to the fact that the eIF4F complex (which has eIF4A
as one of its subunits) is not required for and does not
participate in initiation on these IRESs.