The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

Abstract

RNA is a versatile macromolecule that accommodates functional information in primary sequence and secondary and tertiary structure. We use a combination of chemical probing, RNA structure modeling, comparative sequence analysis, and functional assays to examine the role of RNA structure in the hepatitis C virus (HCV) genome. We describe a set of conserved but functionally diverse structural RNA motifs that occur in multiple coding regions of the HCV genome, and we demonstrate that conformational changes in these motifs influence specific stages in the virus' life cycle. Our study shows that these types of structures can pervade a genome, where they play specific mechanistic and regulatory roles, constituting a "code within the code" for controlling biological processes.

Figure 1. Genome-wide analysis of HCV RNA structure

(A) Experimental overview. HCV RNA was in vitro transcribed and folded, then modified with NAI. Reverse transcription (RT) of modified and unmodified RNA generated fluorescent cDNA fragments that were analyzed by capillary electrophoresis (CE) to provide a SHAPE reactivity map. Reactivities were used to calculate candidate secondary structures. We performed covariation analyses to identify conserved structures, then examined functional relevance of structures by reverse genetics. (B) Summary of SHAPE reactivity and covariation analysis. Regions of low reactivity (≤ 0.7) are colored blue, high reactivity (> 0.7) in red, and regions missing SHAPE data in gray. Each bar represents two nucleotides. Yellow boxes denote regions of the genome containing RNA motifs with covarying mutations present across all HCV genotypes. (C) Positions of peptidase/protease cleavage sites in translated polyprotein (triangles). (D) SHAPE reactivity profiles of regions containing highly conserved RNA motifs (average of two data sets). For reference a dotted line is drawn through a reactivity of 0.7.

Figure 2. Conserved RNA motifs in the core-encoding region

(A) Covariation analysis of core-encoding region RNA structures. Kissing interaction highlighted in red. Nucleotides are colored by degree of conservation. Basepairs are colored based on the presence of covarying mutations. ΔG’s (kcal/mol) are reported for the tested structures calculated by thermodynamic modeling of each full stem loop. Dashes mark every tenth nucleotide. (B) SL588A and SL783A mutant designs with the resulting ΔG’s of each full stem loop. The SL588A lock construct contains mutations that extend into the B region, which replaces a series of mismatches with base pairing nucleotides in order to stabilize the helix. (C) Mutant designs probing kissing interaction between SL427 and SL588. (D) Replication and infectivity time courses for SL588A and SL783A mutants. GNN is a mutation that disrupts the active site of the NS5B RNA-dependent RNA polymerase. Replication measurements were made at 12, 24, 48, 72, 96, and 120 h post-transfection. Samples collected at each timepoint were used to infect naive cells and assayed 72 h post-infection. (E) Replication and infectivity time courses for SL427/SL588 kissing mutants. Data are represented as the mean of three experiments +/− SEM. See also Figure S1B and S4A.

Figure 3. Conformational sampling of RNA structure in NS4B-encoding region

(A) Covariation analysis of SL6038 in NS4B-encoding region. Structures are annotated as in Figure 2. (B) SL6038 mutant designs. The SL6038 unzip construct contains mutations that extend beyond the predicted structure in order to prevent alternate basepairs to form within the region. (C), (D), (E), Replication and infectivity time courses for SL6038 mutants, mismatch mutants and mismatch mutants in stem versus cloverleaf context. Data are represented as the mean of three experiments +/− SEM.

Figure 4. RNA motifs within the NS5B and E1-encoding regions

(A) Covariation analysis of SL8001 in NS5B-encoding region. Structures are annotated as in Figure 2. (B) SL8001 mutant designs. (C) Early replication time course for SL8001 mutants. Measurements were made in 8 h intervals over 48 h. (D) Full replication and infectivity time course for SL8001 mutants over 120 h. (E) Covariation analysis of SL1412 in E1-encoding region. (F) SL1412 mutant designs. (G) Replication and infectivity time course for SL1412 mutants. Data are represented as the mean of three experiments +/− SEM.