title: Structural and functional analyses of stem-loop 1 of the Sindbis virus genome.
abstract: Alphavirus genome function is controlled by elements at both the 5' and 3' ends. The 5' 220 nt of the Sindbis virus genome is predicted to consist of four stem-loop structures the first of which has been demonstrated to be required for efficient minus-strand RNA synthesis. To understand the role of the structure of the first stem-loop (SL1) in regulating genome function, we performed enzymatic and chemical probing analyses. There were significant differences between the computer-predicted structures and our experimental data. In the 5' terminus, two loop regions appear to be interacting in a complex and interdependent fashion with non-Watson-Crick interactions involving multiple adenosine residues playing a critical role in determining the overall structure. Some of the mutations that disrupted these interactions had significant affects, both positive and negative, on minus-strand synthesis, and translational efficiency was generally increased. In the context of full-length virus, these structural changes resulted in reduced virus growth kinetics particularly in mosquito cells suggesting host-specific effects of mutations in this region of the viral genome. Possible SL1 structures based on our experimental data are discussed.
authors: Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA.
authors: David G
authors: DG
authors: Nickens
authors: Richard W
authors: RW
authors: Hardy
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D006224:Cricetinae; D009033:Culicidae / Q000821:virology; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012845:Sindbis Virus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral