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Journal of Virology, April 2006, p. 3395-3405, Vol. 80, No. 7
0022-538X/06/$08.00+0     doi:10.1128/JVI.80.7.3395-3405.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Analyses of Subgenomic Promoters of Hibiscus Chlorotic Ringspot Virus and Demonstration of 5' Untranslated Region and 3'-Terminal Sequences Functioning as Subgenomic Promoters

Weimin Li1 and Sek-Man Wong1,2*

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543,1 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 1176042

Received 9 November 2005/ Accepted 12 January 2006

Hibiscus chlorotic ringspot virus (HCRSV), which belongs to the genus Carmovirus, generates two 3'-coterminal subgenomic RNAs (sgRNAs) of 1.4 kb and 1.7 kb. Transcription start sites of the two sgRNAs were identified at nucleotides (nt) 2178 and 2438, respectively. The full promoter of sgRNA1, a 118-base sequence, is localized between positions +6 and –112 relative to its transcription start site (+1). Similarly, a 132-base sequence, from +6 to –126, defines the sgRNA2 promoter. Computer analysis revealed that both sgRNA promoters share a similar two-stem-loop (SL1 + SL2) structure, immediately upstream of the transcription start site. Mutational analysis of the primary sequence and secondary structures showed further similarities between the two subgenomic promoters. The basal portion of SL2, encompassing the transcription start site, was essential for transcription activity in each promoter, while SL1 and the upper portion of SL2 played a role in transcription enhancement. Both the 5' untranslated region (UTR) and the last 87 nt at the 3' UTR of HCRSV genomic RNA are likely to be the putative genomic plus-strand and minus-strand promoters, respectively. They function well as individual sgRNA promoters to produce ectopic subgenomic RNAs in vivo but not to the same levels of the actual sgRNA promoters. This suggests that HCRSV sgRNA promoters share common features with the promoters for genomic plus-strand and minus-strand RNA synthesis. To our knowledge, this is the first demonstration that both the 5' UTR and part of the 3' UTR can be duplicated and function as sgRNA promoters within a single viral genome.

* Corresponding author. Mailing address: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore. Phone: 65-65162976. Fax: 65-67792486. E-mail: dbswsm{at}nus.edu.sg.

Journal of Virology, April 2006, p. 3395-3405, Vol. 80, No. 7
0022-538X/06/$08.00+0     doi:10.1128/JVI.80.7.3395-3405.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Zhang, X., Wong, S.-M. (2009). Hibiscus chlorotic ringspot virus upregulates plant sulfite oxidase transcripts and increases sulfate levels in kenaf (Hibiscus cannabinus L.). J. Gen. Virol. 90: 3042-3050 [Abstract] [Full Text]  
  • Li, W., Wong, S.-M. (2007). Host-dependent effects of the 3' untranslated region of turnip crinkle virus RNA on accumulation in Hibiscus and Arabidopsis. J. Gen. Virol. 88: 680-687 [Abstract] [Full Text]  


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