GENERAL PROPERTIES OF

PLANT VIRAL GENOMES

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 The viral genome comprises coding regions that express the

proteins required for
• the viral infection cycle,
• movement through the plant,
• interactions with the host and
• movement between hosts,

 and non-coding regions that

• control the expression and replication of the genome;
• control sequences can also be found in the coding regions.

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 Background
 In theory, the same nucleotide sequence in a viral genome
could code for up to 12 or more polypeptides.
• There could be an open reading frame (ORF) in each of the
three reading frames of both the positive (+) and negative (-)
sense strands, giving six polypeptides.

• Usually an ORF is defined as a sequence commencing with

an AUG initiation codon and capable of expressing a
protein of 10 kDa or more.

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 If each of these ORFs had a leaky termination signal, they

could give rise to a second read-through polypeptide;

 Frameshift to a downstream ORF also gives a second

polypeptide.

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• However, in nature, there must be severe evolutionary

constraints on such multiple use of a nucleotide sequence

• Because even a single base change could have consequences

for several gene products.

• However, two overlapping genes in different reading frames

do occasionally occur, as do genes on both (+) and (-) sense
strands.

• Read-through and frameshift proteins are quite common (will

discuss in later lectures)

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• The number of genes found in plant viruses ranges from 0I for
the satellite virus; tobacco necrosis virus (STNV), to 12 for
some closteroviruses and reoviruses.

• Most of the ss (+) sense RNA genomes code for about four to
seven proteins.

• In addition to coding regions for proteins, genomic nucleic

acids contain nucleotide sequences with recognition and
control functions that are important for virus replication.
• These control and recognition functions are mainly found in
the 5' and 3‘ non-coding sequences of the ssRNA viruses, but
they may also occur internally, even in coding sequences.

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 Economy in the use of genomic
nucleic acids
• Viruses make very efficient use of the limited amount of
genomic nucleic acids they possess.

• Eukaryote genomes may have a content of introns that is 10-

30 times larger than that of the coding sequences.

• Like prokaryote cells, most plant viruses lack introns but there
are some ( will discuss in later lectures)

• Plant viruses share with viruses of other host kingdoms several

other features that indicate very efficient use of the genomic
nucleic acids:
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1. Coding sequences are usually very closely packed, with a rather

small number of noncoding nucleotides between genes.

2. Coding regions for two different genes may overlap in different

reading frames (e.g. in Beet necrotic yellow vein virus (BNYVV)
(Benyvirus)) or one gene may be contained entirely within another
in a different reading frame (e.g. the Luteovirus genome)

3. Read-through of a 'leaky' termination codon may give rise to a

second, longer readthrough polypeptide that is co-terminal at the
amino end with the shorter protein.
This is quite common among the virus groups with ss (+) sense RNA
genomes.
Frameshift proteins in which the ribosome avoids a stop codon by
switching to another reading frame have a result that is similar to a
'leaky' termination signal; these are described in later lectures.
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4. A single gene product may have more than one function.

For example, the coat protein of Alfalfa mosaic virus (AMV) has
1. a protective function in the virus particle,
2. a function in insect transmission and
3. a function in the initiation of infection by the viral RNAs.

The coat protein of Maize streak virus (MSV) has

4. a protective function,
5. involved in insect vector specificity
6. cell-to-cell transport of the virus
7. Nuclear transport of the viral DNA
8. and possibly in symptom expression and in control of
replication.
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5. Functional introns have been found in several geminiviruses, in Rice

tungro bacilliform virus (RTBV) and in Cauliflower mosaic virus
(CaMV).

• Thus, mRNA splicing, a process that can increase the diversity of

mRNA transcripts available and therefore the number of gene
products, may be a feature common in viruses with a DNA genome.

6. A functional viral enzyme may use a host coded protein in combination

with a virus coded polypeptide (e.g. the replicase of Tobacco mosaic virus
(TMV).

7. Regulatory functions in the nucleotide sequence may overlap with

coding sequences (e.g. the signals for subgenomic RNA synthesis in
TMV).
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8. In the 5' and 3' non-coding sequences of the ssRNA viruses, a

given sequence of nucleotides may be involved in more than one
function.

For example, in genomic RNA, the 5'-terminal non-coding

sequences may provide a ribosome recognition site, and at the
same time contain the complementary sequence for a replicase
recognition site in the 3' region of the ( - ) strand.

In members of the Potexvirus genus the origin of assembly is

also at the 5' end of the genome

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Thank you

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