Figure 2: RNA-dependent mRNA amplification can result in a 5’-truncated molecule encoding C-terminal fragment of a conventionally encoded polypeptide.

Boxed line-sense strand RNA. Single line-antisense strand RNA. “AUG”- functional translation initiation codon (could be other than AUG). “TCE”–3’-terminal complementary element; “ICE”– internal complementary element, both on the antisense RNA strand. Yellow circle – helicase/ modifying activity complex. Blue lines (both single and boxed) – RNA strand modified and separated from its complement by a helicase complex. Red arrow – position of cleavage of the chimeric intermediate. Step 1: Synthesis of antisense strand; step 2: Strand separation; step 3: Folding of antisense strand into self-priming configuration; step 4: Extension of self-primed antisense RNA; step 5: Strand separation; step 6: Cleavage of the chimeric intermediate; step 7: End-products of RNA amplification. Steps 3’–7’ correspond to steps 3–7. Top panel: Conventional, genome-transcribed mRNA molecule. Middle panel: Projected stages of RNA-dependent mRNA amplification. “ICE” is located within a segment of antisense RNA corresponding to the 5’UTR of conventional mRNA; the chimeric RNA end product contains the entire coding content of conventional mRNA. Bottom panel: “ICE” is located within a segment of antisense RNA corresponding to the coding region of conventional mRNA. The amplified chimeric end product contains a 5’-truncated coding region of conventional mRNA. The translational outcome is decided by position of the first functional translation initiation codon; if in-frame, a CTF of conventional polypeptide is produced.