04/03/2016

• Begomoviruses, have emerged as serious pathogens of

agronomic and horticultural crops in subtropical and
tropical regions of the Americas, Africa and Asia

• Begomoviruses have circular, single-stranded DNA

(ssDNA) genomes that replicate through double-
stranded DNA (dsDNA) intermediates by a rolling
circle mechanism.

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• The genomes of begomoviruses are approximately 2.6

to 3.0 kb in size.

• Bipartite genomes share a common region (CR) of

approximately 200 nucleotides (nt) that is highly
conserved among cognate components of a viral
species, while the analogous region in monopartite
viruses is referred to as the large intergenic region
(LIR).

Conti....

• The CR and LIR contain modular cis-acting elements

of the origin of replication (ori) and promoter
elements

• Four to six open reading frames (ORFs) capable of

encoding proteins >10 kDa in size are present on the
DNA A component or monopartite genome.

• The viral capsid protein (CP) is encoded by the ORF

CP, which is the most highly conserved begomovirus
gene

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• The CP of begomoviruses is required for

encapsidation of ssDNA and for whitefly-mediated
transmission.

• The CP is also necessary for systemic spread of all

monopartite and some bipartite viruses, depending
upon the degree of virus-host adaptation

• The Rep ORF encodes Rep, a replication initiation

protein, and specificity is mediated through sequence-
specific interactions with cis-acting elements of the
ori.

• The TrAP ORF encodes a transcription activator

(TrAP) required for gene expression, and the REn
ORF encodes a replication enhancer (REn)

• Movement and systemic infection in bipartite viruses

is accomplished by DNA B component; ORFs NSP
and MP, which are responsible for nuclear transport of
ssDNA and cell-to-cell movement functions

• For monopartite viruses, several ORFs are involved in

movement functions, including the CP, V2, and
translation products of the C4 ORF, which exert host-
specific effects on symptom severity, virus
accumulation, and movement

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Gene Protein Functions

(A)V2 V2 Symptoms determination, movement and involve in CP expression.
(A)V1/ CP Whitefly-mediated transmission, encapsidation and movement, nuclear
CP localisation.
(A)C1/ Rep Essential for replication, initiation of virion-strand DNA replication, control
Rep of cell cycle, hydrolyzes ATP, has a site-specific topoisomerase activity

(A)C2/ TrAP Transcriptional activator for the virion-sense (and host) genes, suppresses
TrAP RNA silencing and other host defense responses, overcomes programmed
cell death, can be a pathogenicity factor
(A)C3/ REn Enhances viral DNA replication.
REn
(A)C4 C4 Involved in symptom determinant, movement and suppression of PTGS
synergistically with TrAP in ACMV.
(B)V1/ NSP Transport of viral DNA between the nucleus and cytoplasm and host range
NSP properties of the virus, pathogenicity determinant.
(B)C1/ MP Mediates the cell-to-cell movement and pathogenicity determinant.
MP

• With the recognition of diversity within

begomoviruses has come the development of standard
approaches to identify new and resurgent viruses.

• For most plant viruses, serology has traditionally been

the method of choice for identification of new and
resurgent viruses.

• However, virus-specific antiserum for begomoviruses

is not available because the CP is extremely conserved
across all species.

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Conti....

• DNA-based diagnostics, including

1. polymerase chain reaction (PCR) and
2. nucleotide sequencing of viral amplicons, have
supplanted serology for detection, identification, and
classification of this group.

• Sequence alignments are conveniently presented as

phylogenetic trees to illustrate predicted relationships,
and distances can be calculated to estimate divergence

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Conti....

• Sequences associated with functional domains of

viral polypeptides,

• nucleotide sequence motifs or

• regulatory elements that are conserved within the

genus or groups of species or strains,

• and sequences that are highly variable have been

explored

Conti....

• A second potentially informative sequence is

located within the Rep ORF, which encodes the
Rep-associated protein.

• The N-terminal 189 to 200 aa region of this

polypeptide contains “virus-specific” motifs, while
more conserved sequences are present in the
midregion and C-terminal amino acids.

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Conti....

• A third prospective informative region is a

nontranslated CR/LIR sequence of begomoviruses.

• All geminiviruses contain a conserved consensus

sequence of approximately 30 nt in length in this
region.

• This sequence contains the TAATATT/AC

cleavage site at which rolling-circle replication is
initiated,
• and this conserved feature led to early speculation
that recombination might occur frequently at this
site.

• In addition, virus-specific, directly repeated sequences

(iterons) that bind Rep during replication initiation are
also present in this region

• Iterons are considered highly useful for determining

virus identity,
• identifying virus relationships,
• providing clues as to the likelihood that bipartite
genomes may interact with others in trans to form a
reassortant.

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• Natural Host Range

• Natural hosts of begomoviruses are plant species in which the
virus can replicate, cause systemic infection, and encapsidate,
and from which virions are ingested and transmitted to a
susceptible host by the whitefly vector.

• Because the genomes of plant viruses are exceedingly small

and limited in the number and function of coding and
regulatory sequences, their replication depends nearly entirely
on plant regulatory and metabolic processes

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Conti....

• Much attention has been given to determining experimental host

ranges of begomoviruses, but little is known about the natural
reservoirs or the role they may play in the epidemiology of
begomovirus-incited diseases.

• For the majority of begomoviruses, weed reservoirs remain

unexplored or unidentified, making it difficult to draw important
epidemiological and ecological conclusions in relation to disease
spread.

• For most other begomoviruses known in crops today, it seems

likely that they have been associated with that crop species for
some time, and that cultivated, not wild, hosts are the primary
sources of inocula for subsequent infections of crop and weed
hosts.

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