Page 6 - Volume 2,Issue 2, July 2009

© Benaki Phytopathological Institute
Van der Vlugt 50
low virus concentrations. At virus concen-
trations more in line with “real-world” situ-
ations, no differences in reactivity between
the strains could be observed.
Genome organization and expression
The genome organization of PepMV (Aguilar
et al ., 2002, Cotillon et al., 2002) is typical for
potexviruses (Verchot-Lubicz et al., 2007).
Its positive single-stranded RNA is capped
at the 5’-end, polyadenylated at the 3’-end
and contains 5’- and 3’-non-translated re-
gions. Its 6410 nucleotides encode five puta-
tive partly overlapping open reading frames
(ORFs 1 to 5, Figure 2). The 5’-nontranlated
region (5’-NTR) of the virus is 85 nts long and
starts with the pentanucleotide GAAAA,
which is typical for potexviruses.
ORF1 (nt 86-4406) encodes a 164 kDa of
1439 amino acids (aa). A putative methyl-
transferase domain (aa 59-224) specific for
the supergroup of ‘Sindbis-like’ viruses (Ro-
zanov et al., 1992), a NTPase/helicase domain
(aa 708-934) with the NTP-binding motifs
GCGGSGKS and VVIFDD (Kadaré and Haen-
ni, 1997) and a RNA-dependent RNA poly-
merase (RdRp) domain (aa1217-1374) char-
acterised by the SGEGPTFDANT-X22-GDD
motif (Kamer and Argos, 1984), can be dis-
tinguished. The stop codon of the first ORF
is followed by a short intergenic region (IR1)
of 25 nts and a set of three partially overlap-
ping ORFs typically known as the triple gene
block (TGB).
ORF2 (nt 4432-5136) encodes the first
TGB protein (TGBp1), a 234 aa protein of
26 kDa. TIt contains a typical NTPase/heli-
case motif (AA26-233) characterised by sev-
en conserved motifs. Two of these motifs
may be involved in NTP binding (Kadaré and
Haenni, 1997). TGBp1 belongs to the super-
family I of RNA helicases.
ORF3 (nt 5117-5488) overlaps 19 nu-
cleotides with the 3’-end of ORF2 and ex-
tends 148 nucleotides past the start codon
of ORF4. It encodes a small 14 kDa protein
of (TGBp2), which contains a potexvirus spe-
cific consensus motif: PxxGDxxHxL/FPxG-
GxYxDGTKxxxY (Wong et al., 1997).
ORF4 (nt 5340-5594) encodes the third
TGB protein (TGBp3), a 85 aa protein of 9
kDa. This protein is the most variable among
potexviruses. It contains a CxV/IxxxG con-
sensus motif among potexvirus TGBp3 pro-
teins.
Following ORF4 is the second intergenic
region (IR2) of 38 nts (nt 5595-5632). This IR2
is highly variable in sequence between the
different strains. It precedes ORF5 (nt 5633-
6346), which encodes the 238 aa coat pro-
tein (CP) of 25 kDa. This CP contains the am-
phipathic core sequence KFAAFDFFDGVT. A
similar sequence is also found in the CP of
other potexviruses (Wong et al., 1997) and
it might be responsible for binding of virus
RNA to the CP through hydrophobic inter-
actions.
The 64 nts long 3’-non-translated region
(3’-NTR: nt 6347-6410) precedes the poly(A)
tail and contains the hexameter 5’-ACUUAA
sequence, which is also present in the 3’-
NTR of all potexviruses sequenced so far.
This motif is proposed to be a cis-acting el-
ement involved in the positive and nega-
tive viral RNA synthesis (Bancroft et al., 1991;
White et al., 1992). The 5’-AAUAAA polyade-
nylation signal terminates the RNA genome,
whereby the AAA portion forms the first A
residues of the poly(A) tail.
Virus isolates and strains
The first described PepMV isolate (BBA1137;
Jones et al., 1980) was found on pepino (S.
muricatum) in Peru. This isolate is now con-
sidered the type isolate of the Peruvian (PE)
strain of PepMV. Its full sequence has been
determined and was published as SM74 (acc
Figure 2. Schematic organization of the RNA genome of Pep-
ino mosaic virus with its five open reading frames (ORFs). M7G
= 5’ cap, AAAAAn = poly(A) tail.