viruses of plants: into the battle between viruses and their host...spread of plant viruses through...
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Viruses of Plants:
Into the battle between
viruses and their host
Richard Kormelink
Laboratory of Virology
Wageningen University
Virology Course Rotterdam 2018
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Laboratory of Virology research themes
Virology Course Rotterdam 2018
Plant virus research
● Tomato spotted wilt virus-bunyavirus & Geminiviruspathology
● RNAi, virus resistance and viral counter-defence
● Intercellular movement
● Virus imaging (WEMC)
Insect virus research
● Invertebrate DNA virus genetics and evolution
● Baculovirus and insect behavior
● Protein expression and gene therapy systems
● Mechanism of oral infection
Arbovirus research
● Molecular arbovirus-mosquito interactions (WN, CHIKV)
● Viral vaccines
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Why study plant viruses?
Virology Course Rotterdam 2016
Food
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Why study plant viruses?
Virology Course Rotterdam 2018
• Cause serious losses in food and fiber production
• Excellent models for molecular biology
• Good probes for studying cellular processes
• Vectors for gene expression and synthesis of proteins of commercial
and medical interest in plants.
• Virus-induced gene silencing (VIGS): functional genomics
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Impact of Plant virus diseases
~20 plant viruses cause annual
crop-losses of > $ 20 billion
(Rybicki , 2015)
Cassava
Rice
Tomato
Pepper
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Viruses of plants
Virology Course Rotterdam 2018
Introduction:
− Plant viruses and diseases
Genetic make up of plant viruses:
− Genetic maps and translation
strategies
− Examples
The plant viral replication cycle
− Differences with viruses in animal
hosts
Plant defense against viruses
− RNA interference
− Resistance genes
− Engineered resistance
− VIGS Abutilon mosaic virus
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Examples of plant virus diseases: Tulip
breaking virus
Virology Course Rotterdam 2018
Potyvirus; 750 nm - Ø12 nm
Vector: Aphid
Tulipmania
By 1635, a sale of 40 bulbs for 100,000 florins (70.000
US dollars) was recorded.
A record was the sale of the most famous bulb, the
Semper Augustus, for 6,000 florins (± 4200 US dollars)
in Haarlem
By way of comparison, a ton of butter cost around 100
florins and "eight fat swine" 240 florins.
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Examples of plant virus diseases :
Potato leafroll virus (PLRV)
Virology Course Rotterdam 2018
Isometric (+RNA) 30 nm
Aphid
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Beet necrotic yellow vein virus
Virology Course Rotterdam 2018
Fungus: Polymyxa betaeRoot cells with sporesRhizomania
Rod-shaped (+RNA; segmented): 390, 265, 100, 70nm 20nm
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Tobacco rattle virus
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Rod-shaped (+RNA; segmented):
185-196nm, 50-115nm, 70nm
23nm
Nematode: Paratrichodorus,
Trichodorus
Potato
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Tomato spotted wilt virus (TSWV)
Tomato
PepperAlstroemeria
Iris
Membrane bound (ambisense RNA)
Ø80 - 100 nm
BunyaviridaeTospovirusØ80 - 100 nm
Thrips
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Morphology of plant virus particles
Virology Course Rotterdam 2018
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Means of spread of some representative
plant viruses
Virology Course Rotterdam 2018
Ng and Falk (2006). Annual Review of Phytopathology Vol. 44: 183-212
Different living organisms can act as vectors to spread viruses
Means of Spread Rel. frequency Examples of genera
Humans Rare Tobamovirus, Potexvirus
Fungi Rare Carmovirus, Tombusvirus, Ophiovirus, Furovirus, Bymovirus
Nematodes Few Nepovirus, Tobravirus
Mites Few Rymovirus, Pigeaon pea sterility mosaic virus
Thrips Few Tospovirus
Beetles Few Comovirus, Tymovirus
Whiteflies Many Begomovirus, Crinivirus
Leafhoppers Many Phytoreovirus, Mastrevirus, Tenuivirus
Aphids Most (65%) Potyvirus, Luteovirus, Cucumovirus, Clostreovirus
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Viruses of plants
Virology Course Rotterdam 2018
Introduction:
− History
− Plant viruses and diseases
Genetic make up of plant viruses:
− Genetic maps and translation
strategies
− Examples
The plant viral replication cycle
− Differences with viruses in animal
hosts
Plant defense against viruses
− RNA interference
− Resistance genes
− Engineered resistance
− VIGS
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More than 1000 different plant viruses
have been described ……………
Virology Course Rotterdam 2018
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…… of which 90% has an RNA genome
Virology Course Rotterdam 2018 Baltimore (1971)
e.g. Geminiviruses (4%)
e.g. Caulimoviruses (2%)
e.g. Reoviruses (4%)
Most plant viruses (76%)
Pseudoviridae (2%)
e.g. Plant-infecting
bunyaviruses (TSWV) (14%)
- RNA is directly infectious- RNA can be directly translated
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Genetic maps of plant viruses
Virology Course Rotterdam 2018
..or embedded in
the other genes
Viral genome (RNA or DNA)
Virion
Replication
Vector transport
Movement
RNAisuppressor
Polymerase
Coatprotein
To become a successful plant pathogen; a POL gene, one or more CP genes, and 3 additional genes
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Functions encoded by (RNA) viruses
Virology Course Rotterdam 2018
1. The coat protein(s) cp protect the viral genome
2. RNA-dependent RNA polymerase RdRP replicate the (RNA) genome
subunits: core polymerase pol to synthesize RNA
helicase hel to unfold secondary structure
methyltransferase mt to add cap structure
3. Proteases (some viruses) pro polyprotein processing
4. Terminal protein (some viruses) VPg priming RNA synthesis
5. Movement protein (plant viruses only!) mp for cell-to-cell transport
6. RNAi suppressor protein (plant only?) various counteracting RNAi defence
7. Vector transmission protein various insect transmission
8. Miscellaneous proteins (not conserved among viruses)
In case of enveloped viruses:
9. Envelope glycoproteins G cell attachment
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(Plant) RNA viruses: strategies to
express downstream cistrons
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Strategies to circumvent this problem:
1. Segmentation of the genome (i.e. minimization of downstream cistrons)
2. Translation of subgenomic mRNAs (subgenomic promoter)
3. Read-through translation (leaky stop codon)
4. Polyprotein processing (viral protease)
5. Frame-shifting
General problem of eukaryotic RNA viruses:
the eukaryotic ribosome translates only monocistronic mRNAs, while a viral
RNA genome contains at least 3 genes.
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Genetic map of Brome Mosaic Virus (BMV)
Virology Course Rotterdam 2018
m7GRNAs
ProteinsCP
1 (3234 nt) 2 (2885 nt) 3 (2117 nt)
4 (876 nt)
109 kDa 94 kDa 33 kDa 20 kDa
m7G m7G
m7G
Tyr Tyr Tyr
Tyr
MPpolhelmt
L M H
RNA 1 RNA 3 + 4 RNA 2
Translation strategies:• genome segmentation• subgenomic mRNA
Multi-partite virus
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Advantages of a divided genome
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1. Rapid recombination by RNA reassortment (in mixed infections)
2. Increase of genome size (separate encapsidation: multipartite virus)
3. Reduction of lethality (reduction target size)
4. Regulation of gene expression
5. Facilitation of spreading through plants and/or vectors (smaller entities)
Disadvantage: low efficiency of transmission
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Genetic map of Tobacco Mosaic Virus (TMV)
Virology Course Rotterdam 2018
69
Amber UAG
3417 4917 6396
4903 5707
5712 6189
m7G
126 kDa
183 kDa
30 kDa
17.6 kDa
CP
Proteins
RNA His
30K - mRNA
CP - mRNAHis
Hism7G
m7G
MP
polhel
helmt
mt
Translation strategies:• Read-through translation (through “leaky”stop codon)• Sub-genomic mRNA
(Two 3' co-terminal subgenomic mRNAs to express MP and CP)-
MP: the cell-to-cell movement protein
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Genetic map of Potato Virus Y (PVY)
Virology Course Rotterdam 2018
AAAA 3’
35kDa 52kDa 50kDa 71kDa 6kDa21kDa 27kDa 58kDa 30kDa
AI CI NIa NIb
N-Pro HC-PRO ?? HelicaseATPase
? VPg Protease Polymerase CP
?
RNA
PROTEINS
145 9306
POLYPROTEIN
Proteolytic cleavage
VPg
Translation strategy:polyprotein processing
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Recombinative nature of potyviruses
Virology Course Rotterdam 2018
Evolved by recombinationCore modules
A very successful group of plant pathogenic viruses
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Genetic Map of TSWV
Virology Course Rotterdam 2018
vcRNA
vRNA
Gn/Gc (glycoproteins)
3’
5’
M RNA
5’
3’
NSm (movement protein)
(-) (+)
3’
5’3’
5’
N (nucleoprotein)
S RNA
vcRNA
vRNA
NSs (suppressor of silencing)
(-) (+)
L RNA
L (RNA-dependent RNA polymerase)
vcRNA 5’
vRNA 3’ 5’
3’
(-)
Membrane bound Ø80 - 100 nm
Family BunyaviridaeGenus TospovirusNegative & Ambisense RNA
Translation strategies:• Segmented RNA genome• Subgenomic mRNAs• Processing precursor proteins (GP)
Ambisense
RNA segments
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Comparison of an animal- and plant-
infecting Bunyavirus: NSm is the major
genetic difference
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BUNYAVIRUS HOSTS VECTORSOrthobunya-/Nairo-/Phlebovirus Mammals, Birds Moquitoes, sandflies, ticksHantavirus Rodents Rodent-borneTomato Spotted Wilt Virus Plants Thrips
NSm is the plant viral movement protein Bunyaviruses replicate in their insect vector !!
NSs 32 kDa)
N (28 kDa)
Phlebovirus
RdRp (241 kDa)
Gn-Gc (139 kDa)
Orthobunyavirus/Hantavirus/Nairovirus
RdRp (247-459 kDa)
L RNAv
vc
M RNAGc-Gn (108-160 kDa)
vvc
S RNA
NSs (11-13 kDa)
N (26-50 kDa)
vvc
RdRp (331.5 kDa)
NSm (33.6 kDa)
Gn-Gc (127.4 kDa)
NSs (52.4 kDa)
N (28.8 kDa)
Tospovirus
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Viruses of plants
Virology Course Rotterdam 2018
Introduction:
− History
− Plant viruses and diseases
Genetic make up of plant viruses:
− Genetic maps and translation
strategies
− Examples
The plant viral replication cycle
− Differences with viruses in animal
hosts
Plant defense against viruses
− RNA interference
− Resistance genes
− Engineered resistance
− VIGS
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Infection cycle of plant viruses
Virology Course Rotterdam 2018
Penetration into plant cell
Uncoating/translation
Intracellular multiplication
Transport: cell-to-cell
long-distance
Vector
-arthropods
-nematodes
-fungi
Acquisition
Inoculation
Plant host
Nonpersistent transmission
Persistent transmission
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Plant virus infection: Initial interactions
Virology Course Rotterdam 2018
• No receptor-mediated uptake
plasma membrane covered by rigid cell wall
• Penetration not by endocytosis
but by transient wounding of cell wall/membrane
• Uncoating occurs by ribosomes
“co-translational disassembly”
TMV
Ribosomes
Ontmanteling en vroege translatie
cell wall
co-translationaldisassembly
early translation
Uncoating andtranslation
Entry
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Replication cycle of TMV as function of time
Virology Course Rotterdam 2018
5’ 3’
126 kDa 183 kDa read through CP
MP3419
4919 5709
6191
OAS
0 min parental virus
5’ - 3’ disassembly(cotranslational)
2-3 min
3-5 min
20-30 min
25-35 min all coat protein subunits removed
10 min 3’ - 5’ disassembly (coreplicational?)
45 min
30-40 min initiation of assembly
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Replication of a single stranded
(+) RNA virus
Virology Course Rotterdam 2018
5’ 3’(+)
5’3’(-)
(-)
RIReplicative Intermediate
5’ 3’(+)
3’
5’
RI
5’3’(-)
(+)5’
3’
RF(+)
(-)viral polymerase(RdRp)
helicase
Disassembly and early translation(synthesis of viral polymerase)
?
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Difference between a (+)-sense and (-)-sense RNA virus
Virology Course Rotterdam 2018
Plus-strand RNA virus
[ RNA is directly infectious[ RNA is directly translatable
Minus-strand RNA virus
[ RNA is not infectious[ RNA is not directly translatable
5’3’(-)
lipid membranepolymerase
5’3’
(+)
5’
3’
(-)
ORFtranslation
(more polymerase etc.)
glycoproteins
nucleocapsid
polymerase
Virus particles must carry some molecules of the viral polymerase
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RNA viruses replicate in the cytoplasm ……
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Nucleusgeminivirusrhabdovirus
Chloroplasttymovirus
Vacuolecucumovirusalfamovirus
GolgiTospovirus
Endoplasmic reticulumcomovirusbromovirus
Cytoplasm/viroplasmpotyvirus (pinwheels?)potexvirustobamovirus (X-bodies)tospovirus
Mitochondriontombusvirus
DNA/RNAvirus
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.…… at cellular membranes
Virology Course Rotterdam 2018
Chloroplast
Cytoplasm
Cytoplasm
Vacuole
Cowpea mosaic virus replication at the ER membranes
Cucumber mosaic virus replication at the vacuole membraneTurnip yellow
mosaic virus
replication at the
chloroplast
membrane
uninfected infected
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After multiplication in the primary cell,
the virus spreads
Virology Course Rotterdam 2018
Primary infection
vector
Early processesdisassemblymultiplication in the first cell
Active transport(viral function)
Defence response(tobacco: N gene)
Passive transportPhloem (xylem)
Systemic infection
AND NEXT OVER LONG DISTANCEUSING THE VASCULAR SYSTEM (Fast)
… MOVE FROM CELL-TO-CELL (Slow)
Local lesion
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Long- distance transport: viruses follow
the route of assimilates
Virology Course Rotterdam 2018
sink
source
sink
Most plant viruses move over long distances through the phloem (sieve elements).
Vascular transport in a plant:
Xylem: water and minerals
Phloem: metabolites
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During systemic infection plant viruses
have to pass the thick cell wall
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Plant cell
Chloroplast
Plasmodesma
Cell wall
PMCW
ER
ER
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Spread of plant viruses through
plasmodesma: a complex pore
Virology Course Rotterdam 2018
Rod shaped viruses Ø10-20 nm
Icosahedral virusesØ20-80 nm
Cell 1
Cell 2
ER
Viral RNAØ10 nm
2 nm
plasmodesmain cell wall
The problem!
Physical pore size 2 nm
Size exclusion limit ~1 kDa
Plant-infecting viruses must modify the PD
For this they have movement proteins
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Modification of plasmodesmata
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Plasmodesma modified
by Tobamovirus
Plasmodesma modified
by Comovirus/Tospovirus
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Cowpea mosaic virus: movement of
mature virions
Virology Course Rotterdam 2018
Cell wallCell 1
Cell 2
Transport tubule (MP) with virions
MP structurally modifies the plasmodesma and formsa virion-containing tubule
Electron tomogram of an isolated tubule
PM
Tubule
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The TMV MP enlarges the diffusion limits
of plasmodesmata
Virology Course Rotterdam 2018
LYCH-10 kDa dextran
Wildtypeplant
MP transgenicplant
T=30’T= 0
Micro-injected probe LYCH (450 Da)
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To remember
Virology Course Rotterdam 2018
• Most plant viruses are transmitted by insects (but do not replicate)
• No receptor-mediated entry, but entry through wounding (insect’s
stylet)
• Plant viruses move through plasmodesmata that are modified by a
viral movement protein. Move as genome or virion.
• Long-distance transport follows the route of metabolites (through the
phloem)
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Viruses of plants
Virology Course Rotterdam 2018
Introduction:
− History
− Plant viruses and diseases
Genetic make up of plant viruses:
− Genetic maps and translation
strategies
− Examples
The plant viral replication cycle
− Differences with viruses in animal
hosts
Plant defense against viruses
− RNA interference
− Resistance genes
− Engineered resistance
− VIGS
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Defense in plants
Virology Course Rotterdam 2018
Against Viruses
First line of defence:
RNA interference (RNAi)
(RNA silencing)
Second line of defence:
Resistance (R)-genes
multigenic (hard to breed, but durable)
monogenic (easy to breed, but less durable)
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Principle of RNAi
Virology Course Rotterdam 2018
dsRNA
Dicer/DCL
I.
II. 21-24 nt siRNAs
III. Activation of RISC AGO
IV. Translational inhibition Cleavage
AGO AGO
AAA40S
60SAAA
40S
60S
mRNAstarget
mRNAstarget
21 nt siRNAs
Translational arrest or
cleavage or target RNAs
22 nt miRNAs (host encoded)
Translational arrest or
cleavage or target RNAs
24 nt siRNAs
DNA and histone methylation
(epigenetics)
• Gene regulation
• Development and regulation
of chromosome dynamics
Defense against molecular parasites (viruses and transposable elements)
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Antiviral RNAi
Virology Course Rotterdam 2018
Replication
dsRNA intermediates
AAA
Viral mRNAs
Dicer/DCL
I.
II. 21 nt siRNAs
III. Antiviral RISC AGO
IV. Translational inhibition Cleavage
AGO AGO
AAA40S
60SAAA
40S
60S
mRNAsViral
mRNAsViral
RNA virus
(-)RI
5’ 3’(+)
3’
5’
Trigger is dsRNA
RF (+)
(-)
21-25 nt siRNA
Hamilton et al., 1999
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Antiviral RNAi
Virology Course Rotterdam 2018
Replication
dsRNA intermediates
AAA
Viral mRNAs
Dicer/DCL
I.
II. 21 nt siRNAs
III. Antiviral RISC AGO
IV. Translational inhibition Cleavage
AGO AGO
AAA40S
60SAAA
40S
60S
mRNAsViral
mRNAsViral
RNA virus
Post transcriptional gene silencing
(PTGS)
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Virus-induced antiviral RNAi
Virology Course Rotterdam 2018
PVX
TMV – “PVX”
STOP
STOP
21-24 nt (siRNA)
Hamilton et al., 1999
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Antiviral RNAi in plants, insects….
Virology Course Rotterdam 2018
AND mammals
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Plant host defence against viral invasion
AAA
Dicing by DCL4 (2)
21 nt siRNAs
AGO1
AGO1
AAA40S
60S
AGO1
AAA40S
60S
Cell-to-cell spread
AGO1
AGO1
Cell-to-cell spread
Immunization
Immunization
Amplification
RDRs
DCL4
Secondary siRNAs
RDR (1,2,6): host-encoded RNA-dependent RNA polymerase
Aberrant/cleaved Viral RNA
Cytoplasm
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Amplification is essential for a strong
antiviral response
AAA
Dicing by DCL4 (2)
21 nt siRNAs
AGO1
AGO1
AAA40S
60S
AGO1
AAA40S
60S
Cell-to-cell spread
AGO1
AGO1
Cell-to-cell spread
Immunization
Immunization
Amplification
RDRs
DCL4
Secondary siRNAs
Plants become highly susceptible
to RNA viruses
RDR (1,2,6): host-encoded RNA-dependent RNA polymerase
Cytoplasm
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How come viruses still achieve a
successful infection?
Virology Course Rotterdam 2018
Wild type PVY reverses GFP silencing ........and so does CMV
Viral counter-defence!!
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Genetic maps of plant viruses
Virology Course Rotterdam 2018
..or embedded in
the other genes
Viral genome (RNA or DNA)
Virion
Replication
Vector transport
Movement
RNAisuppressor
Polymerase
Coatprotein
To become a successful plant pathogen; a POL gene, one or more CP genes, and 3 additional genes
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P0
Viral counter-defence by RNA viruses
AAA
Dicing by DCL4 (2)
21 nt siRNAs
AGO1
AGO1
AAA40S
60S
AGO1
AAA40S
60S
Cell-to-cell spread
AGO1
AGO1
Cell-to-cell spread
Immunization
Immunization
Amplification
RDRs
DCL4
Secondary siRNAs
P19
NSs
2b
NSs
P38
P19
2b
NSs
2b
HC-Pro
P38
SPCSV RNaseIIIHC-Pro
P1
RDR (1,2,6): host-encoded RNA-dependent RNA polymerase
Cytoplasm
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Side effects?
Virology Course Rotterdam 2018
RNAi suppressors that sequester siRNAs often bind the structurally resembling miRNAs as well
Interference on the miRNA pathway
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Plant Virus RNA silencing suppressors
(RSS)
Virology Course Rotterdam 2018
RNAi suppressor activityembedded in viral geneswith diverse functions
(polymerase, movement protein, capsid protein…
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Also animal/human virus RSS!
Virology Course Rotterdam 2018
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Mutant plant viruses
lacking a RSS....
Virology Course Rotterdam 2018
Wang et al. (2010)
.....are less virulent, and viral titersin the host are lower
......unless the host’s RNAi system is compromised as well
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Mutant animal-infecting
viruses lacking a RSS....
Virology Course Rotterdam 2018
HIV Tat is a suppressor of RNAi, anda mutant lacking Tat replicates tolower titers.......
........but replicates to wild type levelsagain when trans-complemented withEbola VP35 (RSS) or Rice hoja blanca virus NS3 (RSS).
RNAi suppressor proteins act cross-kingdom!!
Schnettler et al. (2009)
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Complication: Animal-virus RSS often
are IFN-anatagonists as well.
Virology Course Rotterdam 2018
Cullen et al. (2014)
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Antiviral RNAi against DNA viruses
AAA
Dicing by DCL4 (2)
21 nt siRNAs
AGO1
AGO1
AAA40S
60S
AGO1
AAA40S
60S
Cell-to-cell spread
siRNAs
AGO1
Cell-to-cell spread
Immunization
RDRs
DCL4
RDR (1,2,6): host-encoded RNA-dependent RNA polymerase
Nucleus
Caulimovirus
Geminivirus
Transcription
Dicing by DCL3/4/2
21 nt siRNAs
24 nt siRNAs
Antiviral RITS
AGO4
Cytoplasm
DN
A/h
isto
ne
meth
yla
tion
An epigenetic antiviral defence mechanism
(Transcriptional Gene Silencing)
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Antiviral RNAi against DNA viruses
AAA
Dicing by DCL4 (2)
21 nt siRNAs
AGO1
AGO1
AAA40S
60S
AGO1
AAA40S
60S
Cell-to-cell spread
siRNAs
AGO1
Cell-to-cell spread
Immunization
RDRs
DCL4
RDR (1,2,6): host-encoded RNA-dependent RNA polymerase
Nucleus
Caulimovirus
Geminivirus
Transcription
Dicing by DCL3/4/2
21 nt siRNAs
24 nt siRNAs
Antiviral RITS
AGO4
Cytoplasm
DN
A/h
isto
ne
meth
yla
tion
V2
P6
C2
βC1
V2
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Transcriptional gene silencing (TGS) of
geminiviruses
Rodriguez-Negrete et al. (2009)
Involving siRNA-dependent DNA methylation (RdDM) of corresponding viral DNA sequences.
Virology Course Rotterdam 2018
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Second line of defence:
Dominant Resistance (R) genes-
sensors of innate immunity
Virology Course Rotterdam 2018
HRN CCC NB-ARC LRR
Breeding companies (Rijk Zwaan, Enza Seeds, Bejo Seeds etc.):
single dominant R genes
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Innate immune sensors in plants and
mammals
Virology Course Rotterdam 2018
(Plants: intracellular NLRs = dominant R genes)
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The Bunyaviridae: Genome organization
Virology Course Rotterdam 2018
NSs 32 kDa)
N (28 kDa)
Phlebovirus
RdRp (241 kDa)
Gn-Gc (139 kDa)
Orthobunyavirus/Hantavirus/Nairovirus
RdRp (247-459 kDa)
L RNAv
vc
M RNAGc-Gn (108-160 kDa)
vvc
S RNA
NSs (11-13 kDa)
N (26-50 kDa)
vvc
RdRp (331.5 kDa)
NSm (33.6 kDa)
Gn-Gc (127.4 kDa)
NSs (52.4 kDa)
N (28.8 kDa)
Tospovirus
NSs: viral defence against host innate immune responses
NSm: facilitates movement of viral entity between plant cells
Kormelink et al. (2011), Vir. Research
Kormelink (2011) in “ The Bunyaviridae” (Elliott & Plyusnin, eds.)
• The TSWV NSs is an RNAi suppressor
• The vertebrate-infecting bunyavirus NSs proteins acts
as IFN antagonists
• The TSWV tospovirus non-structural proteins NSs and
NSm trigger the resistance genes Tsw- and Sw-5
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Exploiting RNAi:
Engineering multiple virus resistance
Virology Course Rotterdam 2018
Transgene cassette with
target gene sequences from serveral viruses
Transcription
dsRNADICER
Viral specific siRNAs
TYRV-t WSMoV TCSV TSWV GRSV
Transgenic line
Wild type
High efficiency of resistance (66-73%) due to dsRNA
constructs
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Virus-induced gene silencing (VIGS)
Virology Course Rotterdam 2018
Defining gene functions using VIGS
pTRV2LB RB
MCS2x35S CP Rz NOSt
pTRV1RBLB
2x35S NOStRzRdRp
MP
16K
pTRV2LB RB
PDS2x35S CP Rz NOSt
+ PDS
pTRV1
+
pTRV2
At different time points:
Observe virus symptoms and
silencing effect
T=0
Inject A. tumefaciens suspensions
with TRV1 and TRV2 expression
cassette to N. benthamiana plants.
•pTRV1+ pTRV2-PDS• Plant viruses
Control
PDS silenced
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Discovery and Identification of (new)
viruses by deep-sequencing of siRNAs
Virology Course Rotterdam 2017
Li et al. (2012)Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation
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To remember
Virology Course Rotterdam 2018
• Plants have different mechanisms of defense against virus
infections (RNA interference, resistance genes)
• Plant viruses express factors that trigger these defense
mechanisms
• But also express factors that counteract (suppress) these
defense mechanisms
• Plant viruses can effectively be stopped by inducing RNAi
(transgenic resistance; hairpin constructs)
• VIGS is a powerful tool to identify gene functions
• sRNA sequencing is a powerful tool for virus discovery