Until fairly recently, only suppressible UAG and UGA codons had been described. However
suppression at the level of a UAA codon has been proposed for Beet soil-borne furovirus [45] and for
Beet virus Q, a furo-like virus [46]. In addition to the termination codon, other elements on the
mRNA
are required
in cis
for efficient
readthrough. In the case of TMV RNA, the na- ture of the two codons following the suppressible
UAG codon are crucial for efficient readthrough [47,48]. The requirements in BYDV are totally
different. Here, two elements, both located down- stream of the suppressible UAG codon terminat-
ing the CP gene are mandatory for readthrough in vitro and in vivo [49]. The proximal element is
located six to 15 nucleotides downstream of the UAG, and is composed of 16 repeats of the se-
quence CCN NNN N: any nucleotide; deletion of the 5 proximal third of these repeats dramati-
cally reduces readthrough. The distal element is about 60 nucleotides long and is located nearly
700 nucleotides downstream of the UAG codon, in the readthrough ORF. Deletions within this
element also strongly impair readthrough. The distal element is well conserved among Lute-
oviruses and in Pea enation mosaic enamovirus, lending weight to the possibility that a similar role
may also be ascribed to the corresponding region in these viruses. It will be interesting to establish
whether the proximal and distal regions interact by long-distance base-pairing. As opposed to the
situation observed in animal viruses in which a hairpin and even a pseudoknot structure down-
stream of the suppressible termination codon are frequently required for readthrough, among plant
viruses there has to date been no report that regions downstream of the suppressible termina-
tion codon could adopt secondary structures im- portant for efficient readthrough.
tRNAs have been isolated from various plant tissues that act as suppressor tRNAs and misread
termination codons in trans [5]. These are two Tyr accepting tRNAs for the UAG codon in TMV
RNA, as well as a Trp and a Cys accepting tRNA for the UGA codon in the Tobacco rattle to-
bravirus RNA. To date, no suppressor tRNA has been isolated that specifically recognizes suppress-
ible UAA codons. Nevertheless, the fact that mu- tating the suppressible UAG codon in TMV RNA
to a UAA codon leads to virion formation in plants, suggests that a tRNA is present in the host
that can recognize UAA or UAG containing TMV RNA [50].
5. Regulation of gene expression at the post-translational level
Proteolytic processing of precursor polyproteins is a crucial process among many viruses [51]. It
results in the production of mature as well as intermediate-sized viral proteins. The activity of a
processed protein may be different from its activ- ity when in a precursor form. Cleavage which is
triggered by viral-encoded proteinases, can occur in cis andor in trans; it can be a co- andor
post-translational event. The viral proteinases can be grouped on the basis of their relatedness to
cellular proteinases. Hence, DNA containing viruses possess pepsin-like proteinases, whereas
the RNA containing viruses possess either chy- motrypsin-like Como6iridae, Poty6iridae or pa-
pain-like Poty6iridae, Tymoviruses proteinases.
Fig. 3 provides a schematic representation of the genome organization of Potyviruses. Processing of
the polyprotein of these viruses requires three dis- tinct
proteinases, P1
a chymotrypsin-like
Fig. 3. Regulation at the post-translation level: proteolytic processing. Example of the maturation sites on the polyprotein of a Potyvirus. The abbreviations of the names of the viral proteins are indicated within the ORF, except for VPg whose position is
indicated below by a thin vertical arrow, and 6K1 and 6K2 which are indicated below their respective ORFs. The positions at which cleavage occurs are indicated by vertical lines within the large ORF. The viral proteinases in italics and the point at which
they cleave the polyprotein vertical arrow are presented above the ORF; NIa cleaves at all sites dashed line except those cleaved by P1 and HC-Pro.
Fig. 4. ORFs of Grapevine fleck virus. The ORFs 1, 2 and 3 are in different reading frames. The function of ORFs 3 and
5 is unknown. Other indications are as in Fig. 1.
from two distinct ORFs Bromo6iridae, or result from
frameshift or
from readthrough
Furoviruses, Necroviruses, Tobamoviruses, To- braviruses, Tombusviruses. This illustrates the
fascinating flexibility of protein expression among different viruses.
Probably the highest level of sophistication with respect to the use of multiple strategies by a single
virus, is to be found among the Luteoviruses Fig. 6. The ingenuity of the Luteovirus genome of
B 6000 nucleotides is extreme: it resorts to over-
lapping ORFs, frameshift, readthrough, the pro- duction of a sgRNA, and proteolytic processing to
release its VPg for attachment to the 5 end of the genome. In addition, as outlined above, for at
least one Luteovirus, BYDV-PAV whose genome proteinase and HC-Pro a papain-like proteinase
which cleave themselves at their C-terminus, and NIa a chymotrypsin-like proteinase which is re-
sponsible for all the other cleavages in the polyprotein, and hence operates in cis and in trans.
6. Conclusions
