Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

Abstract

Hepatitis C virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5′ untranslated region (5′ UTR), while also downstream elements like the cis-replication element (CRE) in the coding region and the 3′ UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5′- and 3′-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA–RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5′ end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3′ UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in question acts on HCV replication when physically present in the plus strand genome or in the minus strand antigenome. Therefore, it may be required to use reduced systems that selectively focus on the analysis of HCV minus strand initiation and/or plus strand initiation.

Global importance of RNA secondary structures in protein-coding sequences

“…Some viral RNA genomes contain known functional RNA secondary structures. For a proof of principle, we therefore analyzed the 3'region of the Hepatitis C Virus RNA genome which contains RNA secondary structure elements known to be involved in genome replication (Niepmann et al, 2018). The results show that in two regions containing functional signals (J7880 and J8880) class c 1 is strongly under-represented, whereas in the coding sequence (CDS) region containing the so-called CRE and encoding the hydrophobic transmembrane region of the protein, class c 2 is strongly under-represented, with high values in class c 1 ( Supplementary Fig.…”

Hepatitis C Virus Translation Regulation

“…First, the interaction between the apical loop of the CRE 5BSL3.2 and the apical loop of the SL 2 in the 3 UTR (also named "kissing loop" interaction) [98,99] is important for HCV replication. Second, the interaction between the bulge of the CRE 5BSL3.2 (GCCCG) with a sequence about 200 nts upstream (CGGGC) ("9170" in Figure 1 and in [23]) was also shown to be important for replication [100,103] and third, the internal CRE 5BSL3.2 bulge can alternatively interact with the apical loop of the SL IIId (UGGGU) in the IRES [101].…”

“…The HCV plus strand RNA genome. The internal ribosome entry site (IRES) in the HCV 5 -untranslated region (5 UTR), the entire 3 UTR and the cis-acting replication element (CRE) in the NS5B coding region are involved in translation regulation [22][23][24]. Those regions of the 5 UTR, 3 UTR, and CRE that bind to the ribosomal 40S subunit are underlayed in light yellow.…”

“…Each incoming plus strand which survived cellular immune responses [5,38,39] and degradation is replicated by the NS5B replicase and gives rise to one antigenome minus strand copy, which in turn generates about 10 progeny plus strands [30]. HCV RNA synthesis is regulated by a variety of RNA signals that reside close to the very 3 -and 5 -ends of the genome, but also sequence and RNA secondary structure elements in the coding region (largely in the 3 -terminal NS5B coding sequence) contribute to the regulation of RNA synthesis [23,30,[40][41][42][43][44][45]. Bulk translation from the progeny plus strand genomes, then, yields a vast excess of viral proteins over the number of genomes [30,46].…”

“…The first advantage is that in particular the very ends of the RNA genome do not need to serve functions in translation control such as in capped and polyadenylated cellular mRNAs. Instead, RNA signals that are involved in genome replication can be directly placed at the very genome ends [23,30,45]. The second benefit of cap-independent translation is that the virus escapes antiviral countermeasures of the cell in terms of the downregulation of cap-dependent translation, which is largely conferred by phosphorylation of eIF2 and the resulting inhibition of cap-dependent translation initiation [56].…”