The diversity in shape and structure of viruses is immense rev. in Ref. [1]. Viruses can be envel-
oped or non-enveloped. Their genome can be com- posed of single or double stranded DNA or RNA;
it can be monopartite plant and animal viruses or multipartite plant viruses, rarely animal
viruses. In viruses with a single stranded RNA, the genome can be of positive or of negative
polarity, or it can be ambisense.
To date, the vast majority of plant viruses — the topic of the present review — that have been
investigated contain an RNA genome. Conse- quently, it is among such viruses that many strate-
gies of expression were first described and have been the most thoroughly examined. Plant viral
genomes are small, generally ranging from 4 to 15 kb or kbp. They code for four to 12 proteins.
These include proteins involved in RNA replica- tiontranscription, as for example the RNA-depen-
dent RNA polymerase RdRp among RNA viruses or the reverse transcriptase activity in
Caulimoviruses, transport of the infectious agent from cell to cell by the movement protein MP,
encapsidation of the viral genome by the coat protein CP, vector transmission of the virus by a
protein frequently referred to as the helper compo- nent, proteolytic maturation of viral precursor
polyproteins by viral proteinases, and transactiva- tors that facilitate translation of downstream open
reading frames ORFs. As mentioned above, syn- thesis of the viral proteins is ensured by the host
translation machinery.
Recently, other reviews have dealt with the syn- thesis and function of plant virus proteins [3 – 6].
The aim of the present review is to offer an overview of the strategies of expression as found
in plant viruses. For the sake of convenience, four levels are distinguished at which regulation of gene
expression can occur. These are at the level of the genome segments, transcription and translation,
and at the post-translational level.
2. Regulation of gene expression at the level of the genome segments
In the case of multipartite genomes, each genome segment can contain one or more ORF.
Although still hypothetical because sparsely inves- tigated, one can postulate that regulation of syn-
thesis of the proteins deriving from distinct genome segments could be cell-type specific, and
could depend on such features as the nature of the leader sequence the 5 untranslated region, UTR
or the nature of the initiation codon and its nucle- otide environment.
3. Regulation of gene expression at the transcription level
Regulation at the level of transcription can oc- cur by splicing of viral mRNAs thereby generating
new ORFs, the production of subgenomic sg RNAs i.e. mRNAs produced from the genomic
g RNA template and consisting of viral genomes truncated to varying degrees in their 5 region, the
ambisense strategy in which both viral and viral complementary gRNAs code for viral proteins,
and cap-snatching, a mechanism by which the virus ‘snatches’ the 5 end of host mRNAs to
prime synthesis of the viral mRNAs. Editing of viral RNAs is observed only in the animal
Paramyxo6iridae rev. in Ref. [7]. It results in the introduction of generally one or two nucleotides
most frequently G residues in a population of newly synthesized viral RNAs probably as a result
of ‘stuttering’ of the RdRp at the level of a run of G’s. However, since no plant viruses belonging to
this genus have been described to date, editing will not be discussed here.
3
.
1
. Splicing Splicing of mRNAs is encountered in DNA-
containing plant viruses. It has been described among certain single strand DNA-containing
Gemini6iridae, and among the double strand DNA-containing
Caulimoviruses and
Bad- naviruses. Splicing is required for replication of
Wheat dwarf geminivirus WDV; [8] and for in- fectivity
of Cauliflower
mosaic caulimovirus
CaMV; [9]. In Rice tungro bacilliform bad- navirus RTBV it is required for the expression of
the otherwise silent ORF IV [10]. Splicing in the monocot Gemini6iridae is illus-
trated in Fig. 1A for WDV. The Gemini6iridae that infect monocot plants contain a monopartite, sin-
gle stranded, circular DNA genome. Two of the ORFs, ORF III and ORF IV, overlap. An intron
is located within ORF III in a region that partly overlaps ORF IV. Excision of this intron results in
a fusion product of ORF III and IV that presents maximum homology to the corresponding contin-
uous ORF of dicot Gemini6iridae. The sequences surrounding the intron fit the consensus sequences
of splice donor and acceptor sites, and are con- served among monocot Gemini6iridae, as is also a
lariat sequence positioned upstream of the accep- tor site. Both unspliced and spliced forms of the
corresponding mRNA are detected in infected plants, even though the fused protein is sufficient
for DNA replication of the virus in vivo [8]. It thus seems quite likely that expression of ORF III
from unspliced RNA as well as the fusion protein resulting from processed RNA are important for
the monocot infecting Gemini6iridae, i.e. in host specificity [8].
3
.
2
. Subgenomic RNAs In addition to gRNAs, a large number of
viruses, whether of positive or negative polarity, also produce one or more sgRNA species that
derive from the genome by internal initiation of RNA synthesis on the complementary gRNA
strand; sgRNAs are not required for replication. They allow expression of cistrons which occupy
internal positions in the genome. When several genes are present in the 3 region of the gRNA, as
in the case of Tobacco mosaic tobamovirus TMV illustrated in Fig. 1B, a family of 3 colin-
ear sgRNAs is frequently produced, such that each gene to be expressed is located at the 5 end
of one sgRNA, a position required for optimal expression in eukaryotes. The sgRNAs are or are
not encapsidated, depending on whether they har- bor the encapsidation site.
In general, sgRNAs are the mRNAs for the 3 proximal genes on polycistronic viral RNAs, and
are identical in sequence to the 3 end of the gRNAs. Barley stripe mosaic hordeivirus BSMV
is an exception. All three segments terminate by a tRNA-like structure and contain a polyA stretch
about 200 nucleotides upstream from the 3 end. It has been reported that the sgRNAs deriving from
RNAb have the expected tRNA-like structure at their 3 end, whereas surprisingly, the sgRNA
derived from RNAg terminates at its 3 end by the polyA stretch [11].
3
.
3
. Ambisense and cap-snatching A particular case of sgRNA synthesis is that
encountered in viruses which resort to the am- bisense strategy. Since among the plant viruses
this strategy is accompanied by cap-snatching, these two aspects are discussed together. The seg-
ments of the RNA genome of Tospoviruses rev. in Ref. [12] and Tenuiviruses rev. in Ref. [13]
are either of negative polarity or are ambisense. The viral RNA contains an ORF in its 5 region,
whereas another ORF is located in the 5 region of
Fig. 1. Regulation of gene expression at the level of transcrip- tion. A Splicing in WDV ORF III and ORF IV. Expression
from the unspliced and spliced mRNAs relevant regions is shown. The spliced region in ORF III overlapping ORF IV is
indicated. B Subgenomic RNAs of TMV. C Ambisense strategy and cap-snatching in Tenuivirus RNA4. Horizontal
line, mRNA; asterisk, cap structure; vertical bar at 3 end of RNA, tRNA-like structure; expressed ORFs, white rectan-
gles; non-expressed ORFs, grey rectangles; horizontal arrows, translation products. In C: v, viral; vc, viral complementary;
IR, intergenic region; NS4 and NSvc4, non-structural protein synthesized from v- and vc-RNA, respectively; dashed arrow,
synthesis of protein is postulated;
, cap and snatched RNA sequence. Not to scale.
the viral complementary RNA. The two ORFs are separated by an intergenic region. This is illus-
trated for RNA4 of Tenuiviruses in Fig. 1C. Viruses using this strategy have evolved a unique
mechanism to produce the sgRNAs which direct the synthesis of their proteins. Contrary to initia-
tion by classical RdRps, initiation of synthesis of the mRNAs by a mechanism known as cap-
snatching is primer-dependent, the primers deriv- ing from the 5 end of host mRNAs. Thus, the
viral mRNAs are capped as opposed to the viral and viral complementary RNAs that are not
capped. Nevertheless, as shown in vitro for Tenuiviruses, the uncapped viral RNAs can serve
directly as templates in translation, and translation follows the scanning mode of initiation [14]. The
mechanism whereby cap-snatching occurs among plant viruses is unknown.
4. Regulation of gene expression at the translation level
