Structural and functional analyses of stem–loop 1 of the Sindbis virus genome

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.