The 5BSL3.2 Functional RNA Domain Connects Distant Regions in the Hepatitis C Virus Genome

Abstract

Viral genomes are complexly folded entities that carry all the information required for the infective cycle. The nucleotide sequence of the RNA virus genome encodes proteins and functional information contained in discrete, highly conserved structural units. These so-called functional RNA domains play essential roles in the progression of infection, which requires their preservation from one generation to the next. Numerous functional RNA domains exist in the genome of the hepatitis C virus (HCV). Among them, the 5BSL3.2 domain in the cis-acting replication element (CRE) at the 3′ end of the viral open reading frame has become of particular interest given its role in HCV RNA replication and as a regulator of viral protein synthesis. These functionalities are achieved via the establishment of a complex network of long-distance RNA–RNA contacts involving (at least as known to date) the highly conserved 3′X tail, the apical loop of domain IIId in the internal ribosome entry site, and/or the so-called Alt region upstream of the CRE. Changing contacts promotes the execution of different stages of the viral cycle. The 5BSL3.2 domain thus operates at the core of a system that governs the progression of HCV infection. This review summarizes our knowledge of the long-range RNA–RNA interaction network in the HCV genome, with special attention paid to the structural and functional consequences derived from the establishment of different contacts. The potential implications of such interactions in switching between the different stages of the viral cycle are discussed.

Hepatitis C Virus Translation Regulation

“…Long-range RNA-RNA interactions are very important in HCV replication. Several such putative interactions have been described [24,45,63,82,[98][99][100][101][102][103][104][105][106][107][108]. By far the most important interactions (see Figure 1) that have been demonstrated to be functionally relevant by several studies are the following.…”

“…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].…”

The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle

“…These networks of contacts include both intra-and intermolecular connections, adding a new level of complexity to the architecture of the RNA genome. The interactions that occur generate different RNA structures that perform tasks added to the storage of information [2,3]. Understanding RNA folding has, therefore, become an area of major interest, in which further knowledge is sought on the role of RNA in transcription elongation, splicing, translation and the synthesis of different protein isoforms, etc.…”

“…RNA viruses have evolved to acquire a supra-coding information system defined by discrete, complexly folded and highly conserved RNA structural/functional domains that overlap with the protein-coding sequence. These domains interact with proteins and other macromolecules, and establish long-distance interactions with other genomic RNA elements to control the synthesis of viral proteins, the replication of the viral genome, and its encapsidation [2,3].…”