Genetic variability and evolutionary implications of RNA silencing suppressor genes in RNA1 of sweet potato chlorotic stunt virus isolates infecting sweetpotato and related wild species

Arthur K Tugume; Robert Amayo; Isabel Weinheimer; Settumba B Mukasa; Patrick R Rubaihayo; Jari P T Valkonen

doi:10.1371/journal.pone.0081479

Genetic variability and evolutionary implications of RNA silencing suppressor genes in RNA1 of sweet potato chlorotic stunt virus isolates infecting sweetpotato and related wild species

PLoS One. 2013 Nov 22;8(11):e81479. doi: 10.1371/journal.pone.0081479. eCollection 2013.

Authors

Arthur K Tugume¹, Robert Amayo, Isabel Weinheimer, Settumba B Mukasa, Patrick R Rubaihayo, Jari P T Valkonen

Affiliation

¹ Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland ; Department of Biological Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala, Uganda.

Abstract

Background: The bipartite single-stranded RNA genome of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus; Closteroviridae) encodes a Class 1 RNase III (RNase3), a putative hydrophobic protein (p7) and a 22-kDa protein (p22) from genes located in RNA1. RNase3 and p22 suppress RNA silencing, the basal antiviral defence mechanism in plants. RNase3 is sufficient to render sweetpotato (Ipomoea batatas) virus-susceptible and predisposes it to development of severe diseases following infection with unrelated virus. The incidence, strains and gene content of SPCSV infecting wild plant species have not been studied.

Methodology/principal findings: Thirty SPCSV isolates were characterized from 10 wild Ipomoea species, Hewittia sublobata or Lepistemon owariensis (family Convolvulaceae) in Uganda and compared with 34 local SPCSV isolates infecting sweetpotatoes. All isolates belonged to the East African (EA) strain of SPCSV and contained RNase3 and p7, but p22 was not detected in six isolates. The three genes showed only limited genetic variability and the proteins were under purifying selection. SPCSV isolates lacking p22 synergized with Sweet potato feathery mottle virus (SPFMV, genus potyvirus; Potyviridae) and caused severe symptoms in co-infected sweetpotato plants. One SPCSV isolate enhanced accumulation of SPFMV, but no severe symptoms developed. A new whitefly-transmitted virus (KML33b) encoding an RNase3 homolog (<56% identity to SPCSV RNase3) able to suppresses sense-mediated RNA silencing was detected in I. sinensis.

Conclusions/significance: SPCSV isolates infecting wild species and sweetpotato in Uganda were genetically undifferentiated, suggesting inter-species transmission of SPCSV. Most isolates in Uganda contained p22, unlike SPCSV isolates characterized from other countries and continents. Enhanced accumulation of SPFMV and increased disease severity were found to be uncoupled phenotypic outcomes of RNase3-mediated viral synergism in sweetpotato. A second virus encoding an RNase3-like RNA silencing suppressor was detected. Overall, results provided many novel and important insights into evolutionary biology of SPCSV.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Crinivirus / genetics*
Evolution, Molecular*
Genes, Suppressor*
Genetic Variation*
Ipomoea batatas / classification
Ipomoea batatas / virology*
Molecular Sequence Data
Phenotype
Phylogeny
Plant Diseases / virology*
RNA, Viral / genetics*
Selection, Genetic
Sequence Alignment
Serotyping
Viral Proteins / genetics

Substances

RNA, Viral
Viral Proteins

Grants and funding

Financial support from the Academy of Finland (grants #1110797 and 1134335 to JPTV) and Viikki Graduate Programme in Molecular Biosciences (to IW) is gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.