Genomic organization of plant viruses

1. GENOME ORGANIZATION OF DNA VIRUSES
Presented by,
Swathi Mohan P M
2nd MSc Biology

2. CONTENTS
• BUNCHY TOP VIRUS OF BANANA
• POTATO VIRUS Y
• CITRUS TRISTEZA VIRUS

3. BUNCHY TOP VIRUS OF BANANA
• Banana bunchy top disease (BBTD), caused by Banana Bunchy Top
Virus (BBTV), is the most devastating viral disease of bananas.
• BBTD develops from Banana Bunchy top Virus (BBTV), which is a
member of the genus Babuvirus in Nanoviridae family
• Banana Bunchy Top Virus (BBTV) is a multipartite circular single-
stranded (CSS) DNA virus with six DNA components that are each
about 1 Kb in size.

4. • comprises six circular single-stranded (ss) DNA components, namely
DNA-R, C, S, M, U3, and N.
• The complete BBTV genome consists of six ssDNA components,
including DNA-R, S, C, N, and M, which encodes the master
replication initiation protein (M-Rep), capsid protein, (CP) cell–cycle
link protein (Clink), nuclear–shuttle protein (NSP), and movement
protein (MP), respectively, while DNA-U3 encodes a protein for which
no function has been found.
• Each component may encode one large gene and contain an
intergenic region with two homology regions, stem–loop common
region (CR-SL) and the major common region (CR-M).

5. • BBTV and other related multipartite viruses enclose their genomic
components into distinct virions to preserve the integrity of the viral
genome.
• Gene expression in multipartite DNA viruses is highly flexible due to
variations in the copy number ad transcript levels of individual
genomic components.
• This enables them to adapt to changing conditions and maintain
optimal fitness.
• In the current study, the copy number of each genetic component of
BBTV and its transcript level were determined in the leaf, midrib, and
root tissue of the infected banana plant.

6. • In contrast, the transcript level was highest in the root (312.45 ±
106.69) and lowest in the midrib (0.72 ± 0.16).
• This suggests that BBTV independently regulates the transcriptional
level of each DNA component. The distribution of BBTV in different
tissues assists the identification of significantly higher viral load
tissues for early and sensitive disease diagnosis, which will be
beneficial for better disease management.

7. POTATO VIRUS Y
• Potato Virus Y (PVY) is a monopartite, single stranded RNA virus that
infects mainly Solanaceous plants including, potato, tomato, pepper,
tobacco and eggplant.
• There are multiple strains of the virus including the common strain,
PVYO, which causes mosaic symptoms in most hosts.
• The necrotic strains PVYN and PVYNTN both cause a veinal necrosis
on tobacco; PVYNTN also causes a tuber necrosis in certain potato
varieties.

8. • The PVY presents a single-stranded positive sense RNA genome of
10000 bases in length.
• The 5’-end of the viral genome is covalently linked to the viral
encoded VPg protein.
• The 3’-end is constituted by a polyadenylated sequence.A single Open
Reading Frame is present on the PVY genome.
• This ORF encodes a polyprotein (3063 residues) cleaved by
three viral protease (P1, HC-Pro and Nib) to produce nine
functional proteins (P1, HC-Pro, P3, 6k1, CI, 6k2, NIa, NIb et
CP).

9. • These viral proteins are involved in different steps of the viral cycle.
• They consist of a 10-kb positive-sense RNA, with a 5′-covalently linked
protein (VPg) and a 3′ poly (A) tail

10. • This RNA is enclosed in a protein capsid (CP) composed of up to 2000
subunits of 30–37 kDa.
• The gene products of the potyviral genome from the 5′ to the 3′ are:
the P1 protein that contains a protease domain at its C-terminal
region, cleaving itself from the adjacent helper component protease
(HC-Pro) protein, with another presently unknown function.
• The HC-Pro protein is multifunctional—it is involved in aphid
transmission of the virus, movement of the virus in the plant and is a
suppressor of the RNA-dependent gene silencing antivirus defense.

11. • The C-terminal part of the HC-protein also acts as a protease, cleaving
itself from the precursor polyprotein, the P3 protein of unknown
function, which is a “replication complex block” composed of the CI
protein, VPg protease, and polymerase.
• The CI protein forms pinwheels, it has an associated helicase activity,
and is perhaps involved in viral cell-to-cell movement.
• CI is bordered by two small proteins 6K1 and 6K2 of unknown
function.

12. CITRUS TRISTEZA VIRUS
• Citrus tristeza virus (CTV) is a viral species of the
genus Closterovirus that causes the most economically damaging
disease to its namesake plant genus, Citrus.
• The 2000 x 11 nm long bipolar flexuous filamentous particles of Citrus
tristeza virus (CTV) (genus Closterovirus,
family Closteroviridae) contain a single-stranded positive-sense RNA
genome of 19.3 kb, which is encapsidated in two different capsid
proteins that coat the opposite ends of the virions.
• CTV is the largest identified RNA virus infecting plants and the second
largest worldwide after the animal Coronaviruses.

13. • The CTV RNA genome structure resembles that of Coronaviruses, and
it is organized in twelve open reading frames (ORFs) and two non-
translated regions (NTR) at the 5´ and 3´ terminus.
• The 5´ termini of the CTV genome is protected with a cap structure.
• The CTV genome maintains the two characteristic clusters of genes of
the family Closteroviridae .