Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

Abstract

Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5 ′ untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3 ′ UTR. We propose an alternative structure in the 5 ′ UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3 ′ end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5 ′ and 3 ′ UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5 ′ -3 ′ UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.

Functional RNA structures throughout the Hepatitis C Virus genome

“…Despite these differences between HCV and flaviruses, structural elements identified in one type of virus can provide valuable mechanistic insights into potential mechanisms for the function of other viruses. For example, cyclization elements between the 5′ and 3′ UTR have been proposed for HCV [41]. A distinctive feature of Flavivirus structure is the sfRNA element in the 3′-UTR that blocks cellular exonucleases.…”

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

“…The search for unique RNA elements within the HCV genome has spanned the better part of two decades. By using bioinformatic tools and ribonuclease mapping, several groups have contributed to the identification of RNA structures in untranslated regions (UTRs) as well as the core and NS5B-encoding regions (Fricke et al, 2015; Tuplin et al, 2004). Many of these structures have since been validated by mutational analysis in cell culture models of HCV replication and infectivity, and they have helped assign functional roles for specific RNA structural elements (Diviney et al, 2008; Friebe and Bartenschlager, 2002; Friebe et al, 2005; Friebe et al, 2001; Kolykhalov et al, 2000; Lee et al, 2004; McMullan et al, 2007; Oakland et al, 2013; Vassilaki et al, 2008; You and Rice, 2008; You et al, 2004).…”

What can pestiviral endonucleases teach us about innate immunotolerance?

“…This is confirmed by the fact that in vitro transcribed ssRNA of the BVD viral genome possess highly structured regions resistant to serum RNases and to RNase A (preferentially ssRNases) that are able to induce activation of TLR-3 [20,48]. The 5 0 -und 3 0 -UTRs and long-range interactions between these two regions might be especially immunostimulatory [49,50], but most regions within the BVD viral genome seem to possess high-ordered structures able to induce TLR activation [48].…”