Sequence variability in HC-Pro genes of Korean Soybean mosaic virus isolates is associated with differences in gene silencing suppression

Authors: LI, MEIJI - Chungnam National University; KIM, JUNG KYU - Chungnam National University; SEO, EUN-YOUNG - Chungnam National University; HWANG, EUI II - Kt&g R&d; Domier, Leslie; Hammond, John; YOUN, YOUNG-NAM - Chungnam National University; LIM, HYOUN-SUB - Chungnam National University

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2013
Publication Date: 1/1/2014
Publication URL: http://dx.doi.org/10.1007/s00705-013-1964-4
Citation: Li, M., Kim, J., Seo, E., Hwang, E., Domier, L.L., Hammond, J., Youn, Y., Lim, H. 2014. Sequence variability in HC-Pro genes of Korean Soybean mosaic virus isolates is associated with differences in gene silencing suppression. Archives of Virology. 159(6):1373-1383.

Interpretive Summary: Soybean mosaic virus (SMV) causes an important disease of soybean wherever the crop is grown. Different strains of SMV are able to overcome strain-specific resistance genes in particular soybean cultivars, as new strains of the virus evolve or the predominant strains in an area change over time; in response, plant breeders and farmers must deploy new resistance genes to maintain crop yields. The Helper component/Proteinase (HC-Pro) gene varies between strains, and is one factor in overcoming SMV resistance genes; HC-Pro also has a role in transmission of SMV by aphids. A survey of SMV isolates occurring in Korea in 2012 examined variability in the HC-Pro gene, by comparison to previously characterized SMV isolates from the U.S., China, and Korea. A new mild SMV strain was identified among 60 Korean isolates examined, and was found to have weaker RNA silencing suppression activity of the HC-Pro gene. The three single amino acid differences of the HC-Pro gene of the new isolate were separately substituted into a previously characterized severe SMV isolate, and one particular amino acid variation was shown to be largely responsible for the weaker RNA silencing suppression activity. When expressed in the context of the severe SMV isolate, initial symptoms were mild, but eventually the mutant reverted to produce severe symptoms in upper leaves. Thus although the original mild isolate was stable during passage in soybean, the HC-Pro mutant reverted to wild-type severity over time, suggesting that other changes present elsewhere in genome of the original mild strain are required to maintain stability of the mild symptoms. Further examination of this phenomenon, and of the transmissibility of the mild isolate by different aphid species, may explain how the mild isolate is maintained in nature, and may lead to identification of additional resistance genes of value to soybean breeders. The current information will be of most value to other virologists, and to soybean breeders.

Technical Abstract: Soybean mosaic virus (SMV), a member of the family Potyviridae, is an important viral pathogen affecting soybean production in Korea. The variability in helper component proteinase (HC-Pro) sequence and pathogenicity of SMV isolates from seven provinces of Korea was investigated and compared with those of previously characterized virus isolates from the United States and Korea. Phylogenetic analysis of 16 representative newly characterized Korean SMV isolates revealed clustering into two groups. Most of the isolates selected in Korea belonged to Group II and these were very similar to U.S. isolates G7 and C14. To test whether sequence variability in HC-Pro affected gene silencing suppressor activity among Group II, we examined isolate A297-13, which differed at three positions (L54F, N286D, D369N) from HC-Pro of 413 severe SMV strain, and showed very weak silencing suppressor activity. Point mutation of each variant amino acid showed that reduced silencing suppressor function was found in HC-Pro(N286D) but activity was not reduced as much as in HC-Pro of A297-13 in a transient assay; intact smGFP RNA was decreased five-fold with HC-Pro(N286D) and forty-fold with HC-Pro(L54F, N286D, D369N) with respect to 413 HC-Pro(L54, N286, D369). In addition, RNA accumulation of an HC-Pro(L54F, N286D, D369N)-substituted SMV infectious clone was reduced to less than 3% of the level of the wild-type at 10 dpi but increased to c.40% of WT at 40 dpi; RNA accumulated to a similar level as wild type at 50 dpi, but the sequence was found to have reverted to N286 at 50 dpi. The results showed that a naturally occurring novel HC-Pro mutation is unique in maintaining infectivity while significantly reducing silencing suppression function, but that replacement of HC-Pro in wild type HC-Pro may result in reversion to the typical N286 and higher RNA accumulation.