Analysis of gene content in sweet potato chlorotic stunt virus RNA1 reveals the presence of the p22 RNA silencing suppressor in only a few isolates: implications for viral evolution and synergism
Sweet potato chlorotic stunt virus (genus Crinivirus) belongs to the family Closteroviridae, members of which have a conserved overall genomic organization but are variable in gene content. In the bipartite criniviruses, heterogeneity is pronounced in the 3′-proximal region of RNA1, which in sweet potato chlorotic stuat virus (SPCSV) encodes two novel proteins, RNase3 (RNase III endonuclease) and p22 (RNA silencing suppressor). This study showed that two Ugandan SPCSV isolates contained the p22 gene, in contrast to three isolates of the East African strain from Tanzania and Peru and an isolate of the West African strain from Israel, which were missing a 767 nt fragment of RNA1 that included the p22 gene. Regardless of the presence of p22, all tested SPCSV isolates acted synergistically with potyvirus sweet potato feathery mottle virus (SPFMV; genus Potyvirus, family Potyviridae) in co-infected sweetpotato plants (Ipomoea batatas), which greatly enhanced SPFMV titres and caused severe sweetpotato virus disease (SPVD). Therefore, the results indicate that any efforts to engineer pathogen-derived RNA silencing-based resistance to SPCSV and SPVD in sweetpotato should not rely on p22 as the transgene. The data from this study demonstrate that isolates of this virus species can vary in the genes encoding RNA silencing suppressor proteins. This study also provides the first example of intraspecific variability in gene content of the family Closteroviridae and may be a new example of the recombination-mediated gene gain that is characteristic of virus evolution in this virus family.
AguilarJ. M.,
FrancoM.,
MarcoC. F.,
BerdialesB.,
Rodriguez-CerezoE.,
TrunigerV.,
ArandaM. A.2003; Further variability within the genus Crinivirus , as revealed by determination of the complete RNA genome sequence of Cucurbit yellow stunting disorder virus . J Gen Virol 84:2555–2564[CrossRef]
AlicaiT.,
FenbyN. S.,
GibsonR. W.,
AdipalaE.,
VettenH. J.,
FosterG. D.,
SealS. E.1999; Occurrence of two serotypes of sweet potato chlorotic stunt virus in East Africa and their associated differences in coat protein and HSP70 homologue gene sequences. Plant Pathol 48:718–726[CrossRef]
Bar-JosephM.,
YangG.,
GafnyR.,
MawassiM.1997; Subgenomic RNAs: the possible building blocks for modular recombination of Closteroviridae genomes. Semin Virol 8:113–119[CrossRef]
CohenJ.,
FranckA.,
VettenH. J.,
LesemannD. E.,
LoebensteinG.1992; Purification and properties of closterovirus-like particles associated with a whitefly-transmitted disease of sweet potato. Ann Appl Biol 121:257–268[CrossRef]
FauquetC. M.,
MayoM. A.,
ManiloffJ.,
DesselbergerU.,
BallL. A.eds.2005Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses San Diego: Elsevier Academic Press;
FenbyN. S.,
FosterG. D.,
GibsonR. W.,
SealS. E.2002; Partial sequence of HSP70 homologue gene shows diversity between West African and East African isolates of sweet potato chlorotic stunt virus. Tropical Agric 79:26–30
GibsonR. W.,
MpembeI.,
AlicaiT.,
CareyE. E.,
MwangaR. O. M.,
SealS. E.,
VettenH. J.1998; Symptoms, aetiology and serological analysis of sweet potato virus disease in Uganda. Plant Pathol 47:95–102[CrossRef]
HernandezC.,
CaretteJ. E.,
BrownD. J.,
BolJ. F.1996; Serial passage of tobacco rattle virus under different selection conditions results in deletion of structural and nonstructural genes in RNA 2. J Virol 70:4933–4940
HoyerU.,
JelkmannW.,
MaissE.,
VettenH. J.1996a; Sweet potato sunken vein virus (SPSVV): another bipartite closterovirus transmitted by Bemisia tabaci . In Abstracts of Presentations on Plant Protection Issues, Xth International Congress of Virology Jerusalem: Israel. Phytoparasitica 26, issue 1: http://www.phytoparasitica.org/phyto/
HoyerU.,
MaissE.,
JelkmannW.,
LesemannD.-E.,
VettenH. J.1996b; Identification of the coat protein gene of a sweet potato sunken vein closterovirus isolate from Kenya and evidence for serological relationship among geographically diverse closterovirus isolates from sweet potato. Phytopathology 86:744–750[CrossRef]
IsHakJ. A.,
KreuzeJ. F.,
JohanssonA.,
MukasaS. B.,
TairoF.,
Abo El-AbbasF. M.,
ValkonenJ. P. T.2003; Some molecular characteristics of three viruses from SPVD-affected sweet potato plants in Egypt. Arch Virol 148:2449–2460[CrossRef]
KarasevA. V.,
NikolaevaO. V.,
MushegianA. R.,
LeeR. F.,
DawsonW. O.1996; Organization of the 3′-terminal half of beet yellow stunt virus genome and implications for the evolution of closteroviruses. Virology 221:199–207[CrossRef]
KaryeijaR. F.,
KreuzeJ. F.,
GibsonR. W.,
ValkonenJ. P. T.2000; Synergistic interactions of a potyvirus and a phloem-limited crinivirus in sweet potato plants. Virology 269:26–36[CrossRef]
KokkinosC. D.,
ClarkC. A.2006; Interactions among Sweet potato chlorotic stunt virus and different potyviruses and potyvirus strains infecting sweetpotato in the United States. Plant Dis 90:1347–1352[CrossRef]
KreuzeJ. F.,
KaryeijaR. F.,
GibsonR. W.,
ValkonenJ. P. T.2000; Comparisons of coat protein gene sequences show that East African isolates of Sweet potato feathery mottle virus form a genetically distinct group. Arch Virol 145:567–574[CrossRef]
KreuzeJ. F.,
SavenkovE. I.,
ValkonenJ. P. T.2002; Complete genome sequence and analyses of the subgenomic RNAs of Sweet potato chlorotic stunt virus reveal several new features for the genus Crinivirus . J Virol 76:9260–9270[CrossRef]
KreuzeJ. F.,
SavenkovE. I.,
CuellarW.,
LiX.,
ValkonenJ. P. T.2005; Viral class 1 RNase III involved in suppression of RNA silencing. J Virol 79:7227–7238[CrossRef]
LakatosL.,
CsorbaT.,
PantaleoV.,
ChapmanE. J.,
CarringtonJ. C.,
LiuY. P.,
DoljaV. V.,
CalvinoL. F.,
Lopez-MoyaJ. J.,
BurgyanJ.2006; Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25:2768–2780[CrossRef]
LivakK. J.,
SchmittgenT. D.2001; Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method. Methods 25:402–408[CrossRef]
LuR.,
FolimonovA.,
ShintakuM.,
LiW. X.,
FalkB. W.,
DawsonW. O.,
DingS. W.2004; Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci U S A 101:15742–15747[CrossRef]
MéraiZ.,
KerényiZ.,
KertészS.,
MagnaM.,
LakatosL.,
SilhavyD.2006; Double-stranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing. J Virol 80:5747–5756[CrossRef]
MilgramM.,
CohenJ.,
LoebensteinG.1996; Effects of sweet potato feathery mottle virus and sweet potato sunken vein virus on sweet potato yields and rates of reinfection of virus-free planting material in Israel. Phytoparasitica 24:189–193[CrossRef]
MukasaS. B.,
RubaihayoP. R.,
ValkonenJ. P. T.2006; Interactions between a crinivirus, an ipomovirus and a potyvirus in coinfected sweet potato plants. Plant Pathol 55:458–467[CrossRef]
PeremyslovV. V.,
HagiwaraY.,
DoljaV. V.1998; Genes required for replication of the 15.5-kilobase RNA genome of a plant closterovirus. J Virol 72:5870–5876
Pio-RibeiroG.,
WinterS.,
JarretR. L.,
DemskiJ. W.,
HamiltonR. I.1996; Detection of sweet potato virus disease-associated closterovirus in a sweet potato accession in the United States. Plant Dis 80:551–554[CrossRef]
QuF.,
MorrisT. J.2002; Efficient infection of Nicotiana benthamiana by Tomato bushy stunt virus is facilitated by the coat protein and maintained by p19 through suppression of gene silencing. Mol Plant Microbe Interact 15:193–202[CrossRef]
SandgrenM.,
SavenkovE. I.,
ValkonenJ. P. T.2001; The readthrough region of Potato mop-top virus (PMTV) coat protein encoding RNA, the second largest RNA of PMTV genome, undergoes structural changes in naturally infected and experimentally inoculated plants. Arch Virol 146:467–477[CrossRef]
SimonA. E.,
RoossinckM. J.,
HaveldaZ.2004; Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu Rev Phytopathol 42:415–437[CrossRef]
TairoF.,
MukasaS. B.,
JonesR. A.,
KullayaA.,
RubaihayoP. R.,
ValkonenJ. P. T.2005; Unravelling the genetic diversity of the three main viruses involved in sweet potato virus disease (SPVD), and its practical implications. Mol Plant Pathol 6:199–211[CrossRef]
VettenH. J.,
HoyerU.,
MaissE.,
LesemannD. E.,
JelkmannW.1996; Serological detection and discrimination of geographically diverse isolates of sweet potato sunken vein closterovirus. Phytopathology 86:891A[CrossRef]
WinterS.,
PuracA.,
LeggettF.,
FrisonE. A.,
RosselH. W.,
HamiltonR. I.1992; Partial characterization and molecular cloning of a closterovirus from sweet potato infected with the sweet potato virus disease complex from Nigeria. Phytopathology 82:869–875[CrossRef]
Analysis of gene content in sweet potato chlorotic stunt virus RNA1 reveals the presence of the p22 RNA silencing suppressor in only a few isolates: implications for viral evolution and synergism