The 5' ends of Hantaan virus (Bunyaviridae) RNAs suggest a prime-and-realign mechanism for the initiation of RNA synthesis

Abstract

We examined the 5 ends of Hantaan virus (HTN) genomes and mRNAs to gain insight into the manner in which these chains were initiated. Like those of all members of the family Bunyaviridae described so far, the HTN mRNAs contained 5 terminal extensions that were heterogeneous in both length and sequence, presumably because HTN also ''cap snatches'' host mRNAs to initiate the viral mRNAs. Unexpectedly, however, almost all of the mRNAs contained a G residue at position ؊1, and a large fraction also lacked precisely one of the three UAG repeats at the termini. The genomes, on the other hand, commenced with a U residue at position ؉1, but only 5 monophosphates were found here, indicating that these chains may not have initiated with UTP at this position. Taken together, these unusual findings suggest a prime-and-realign mechanism of chain initiation in which mRNAs are initiated with a G-terminated host cell primer and genomes with GTP, not at the 3 end of the genome template but internally (opposite the template C at position ؉3), and after extension by one or a few nucleotides, the nascent chain realigns backwards by virtue of the terminal sequence repeats, before processive elongation takes place. For genome initiation, an endonuclease, perhaps that involved in cap snatching, is postulated to remove the 5 terminal extension of the genome, leaving the 5 pU at position ؉1.

Transcription and replication mechanisms of Bunyaviridae and Arenaviridae L proteins

“…Transcription initiation has been proposed to occur by prime and realign for hanta-and orthobunyavirus based on the non-templated sequences consistently detected in viral mRNAs consisting in extra repeated triplets conserved at the genome ends (AUC AUC AUC for hantavirus, UCA UCA UCA for orthobunyavirus, see Fig. 1) (Garcin et al, 1995;Jin and Elliott, 1993). The prime and realign model proposed for the initiation of RNA replication by the arenavirus polymerase differs from the one proposed for Fig.…”

Master sensors of pathogenic RNA – RIG-I like receptors

“…They consist of an N-terminal tandem caspase activation and recruitment domain (CARD) fused to a DExD/H-box helicase domain (composed of Hel1, Hel2 and Hel2i) and the C-terminal domain (CTD; previously called RD = repressor domain) (Luo et al 2013;Saito et al 2007; Yoneyama et al but no recognition by RIG-I or MDA5 in BM-DC or fibroblasts (Zhou and Perlman 2007), recognition by MDA5, not RIG-I in macrophages and microglia (Roth-Cross et al 2008). **Evasion of RIG-I recognition by nuclease 5 end cleavage leaving monophosphate at the 5 end of the viral genome (Garcin et al 1995;Habjan et al 2008). ***Evasion of RIG-I recognition via substitution of 5 triphosphate by Vpg protein at the 5 end of the viral genome (Hruby and Roberts 1978;Lee et al 1977;Rohayem et al 2006).…”

Strategies of highly pathogenic RNA viruses to block dsRNA detection by RIG-I-like receptors: Hide, mask, hit

“…Digestion with a specific 5 0 -3 0 ssRNA exoribonuclease demonstrated that HTNV and CCHFV genomic RNAs bear a monophosphate group at the 5 0 terminus, which may explain why such nucleic acids are not sensed by RIG-I (Habjan et al, 2008). HTNV 5 0 -ppp moieties are trimmed off during the synthesis of viral genome through a ''prime and realign'' process that cleaves the first-incorporated nucleotide leaving a 5 0 monophosphorylated terminus (Garcin et al, 1995). Furthermore, in addition to being devoid of RIG-I-stimulating 5 0 -ppp, the HTNV genome has complementary 5 0 -and 3 0 -strands that form perfectly paired panhandle structures that are promptly encapsidated by viral nucleocapsid proteins (Garcin et al, 1995).…”

“…HTNV 5 0 -ppp moieties are trimmed off during the synthesis of viral genome through a ''prime and realign'' process that cleaves the first-incorporated nucleotide leaving a 5 0 monophosphorylated terminus (Garcin et al, 1995). Furthermore, in addition to being devoid of RIG-I-stimulating 5 0 -ppp, the HTNV genome has complementary 5 0 -and 3 0 -strands that form perfectly paired panhandle structures that are promptly encapsidated by viral nucleocapsid proteins (Garcin et al, 1995). For CCHFV, whose genomic RNA bears a terminal pyrimidine residue at the 5 0 -end, in place of the purine normally used by viral polymerases to initiate RNA synthesis, a similar ''prime and realign'' process likely occurs during replication (Garcin et al, 1995).…”

“…Furthermore, in addition to being devoid of RIG-I-stimulating 5 0 -ppp, the HTNV genome has complementary 5 0 -and 3 0 -strands that form perfectly paired panhandle structures that are promptly encapsidated by viral nucleocapsid proteins (Garcin et al, 1995). For CCHFV, whose genomic RNA bears a terminal pyrimidine residue at the 5 0 -end, in place of the purine normally used by viral polymerases to initiate RNA synthesis, a similar ''prime and realign'' process likely occurs during replication (Garcin et al, 1995). However, the exact mechanism and viral proteins through which CCHFV removes protruding 5 0 -ppp from its genome ends is currently unknown (Habjan et al, 2008).…”