RNA Structure in the 5′ Untranslated Region of Enterovirus D68 Strains with Differing Neurovirulence Phenotypes

Figures

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  Figure 1. Multiple sequence alignment (MSA) of EV-D68 5′ UTRs. The sequence alignment shows base substitutions, insertions and deletions in the 2014 strain as compared to the original Fermon isolate. The MSA was generated using Clustal Omega. Using the Fermon strain as a reference, nucleotide alterations are colored based on the 5′ UTR domain: domain I = red, domain II = light blue, domain III = light green, domain IV = purple, domain V = sage green, domain VI = pink, and long-range interaction (LR) = khaki.

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  Figure 2. Secondary structure models of EV-D68 5′ UTRs. (a) and (b) represent the secondary structure of EV-D68 Fermon and 2014 strains, respectively. The shape reactivity of each nucleotide is indicated by colored shading. Grey shading indicates little reactivity, with reactivity values below 0.40. Orange shading indicates moderate reactivity, with reactivity values between 0.40 and 0.85. Red shading indicates high reactivity, with values greater than 0.85. Domains I through VI are labeled along with the long-range interaction (LR) and intrinsically disordered RNA region (IDRR). Line-art depictions with 5′ UTR of both the Fermon and 2014 strains are depicted in panel (c) and structural features are colored and labeled accordingly: domain I = red, domain II = light blue, domain III = light green, domain IV = purple, domain V = sage green, domain VI = pink, long-range interaction (LR) = khaki, and intrinsically disordered RNA region (IDRR) = orange.

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  Figure 3. Tertiary structure models of the 5′ UTRs of EV-D68 Fermon and 2014 strains. Panels (a) and (b) represent the tertiary structure predictions generated using 3DRNAv2.0 for the 5′ UTRs of the Fermon and 2014 strains, respectively. Structural predictions were visualized and pseudocolored using PyMOL. Pseudocoloring follows the same coloring pattern as shown in panel (c) of Figure 2, and structures of interest are labeled as shown in panels of Figure 2.

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  Figure 4. Secondary structure of domains I and II of EV-D68 5′ UTRs. (a) and (b) represent domains I and II of the 5′ UTR of the Fermon and 2014 strains of EV-D68, respectively. The shape reactivity of each nucleotide is indicated by colored shading. Grey shading indicates little reactivity, with reactivity values below 0.40. Orange shading indicates moderate reactivity, with reactivity values between 0.40 and 0.85. Red shading indicates high reactivity, with values greater than 0.85.

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  Figure 5. Tertiary structures of domains I, II and III of the Fermon and 2014 EV-D68 strains. Panels (a,b) represent the tertiary structure predictions generated using 3DRNAv2.0 for domains I, II and III of the 5′ UTRs of the Fermon and 2014 strains. Structural predictions were visualized and pseudocolored using PyMOL. The red regions represent domain I, the light blue regions represent domain II, and the light green region represent domain III. Domains and regions outside of I, II and III in this figure are colored grey.

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  Figure 6. Secondary structures of domains IV and V of EV-D68 Fermon and 2014 Strains. (a) and (b) represent domains IV and V of the 5′ UTR of the Fermon and 2014 strains of EV-D68, respectively. The shape reactivity of each nucleotide is indicated by colored shading. Grey shading indicates little reactivity, with reactivity values below 0.40. Orange shading indicates moderate reactivity, with reactivity values between 0.40 and 0.85. Red shading indicates high reactivity, with values greater than 0.85.

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  Figure 7. Tertiary structures domains IV and V of EV-D68 Fermon and 2014 Strains. Panels (a–d) represent the tertiary structure predictions generated using 3DRNAv2.0 for domains IV and V of the 5′ UTRs of the Fermon and 2014 strains. Structural predictions were visualized and pseudocolored using PyMOL. The coloring of the domains follows the pattern set in Figure 1. Structures of interest are labeled within each panel. Panels (b) and (d) represent the Fermon and 2014 5′ UTR structures, respectively, viewed from a different angle.