The Cap-Snatching Mechanism of Bunyaviruses

Abstract

In common with all segmented negative-sense RNA viruses, bunyavirus transcripts contain heterologous sequences at their 5′ termini originating from capped host cell RNAs. These heterologous sequences are acquired by a socalled cap-snatching mechanism. Whereas for nuclear replicating influenza virus the source of capped primers as well as the cap-binding and endonuclease activities of the viral polymerase needed for cap snatching have been functionally and structurally well characterized, our knowledge on the expected counterparts of cytoplasmic replicating bunyaviruses is still limited and controversial. This review focuses on the cap-snatching mechanism of bunyaviruses in the light of recent structural and functional data. Bunyavirus Transcription and Genome Replication The order of Bunyavirales, which was established in 2018, accommodates a diverse group of viruses formerly separated into the Arenaviridae and Bunyaviridae families [1]. The Bunyavirales order contains important human pathogens such as Lassa virus (LASV; family Arenaviridae), Crimean-Congo hemorrhagic fever virus (family Nairoviridae), Rift Valley fever virus (RVFV, family Phenuiviridae), Hantaan virus (family Hantaviridae), and La Crosse virus (family Peribunyaviridae). Highlights Endonuclease domains have been located in many different bunyavirus L proteins and can be classified as His+ or His-metal-dependent endonucleases. An active cap-binding domain (CBD) has been identified in the C-terminal region of bunyavirus L protein. Despite very low sequence identity, this domain is very similar to influenza virus PB2 CBD on the structural level. Atomic structures of bunyavirus N protein do not provide evidence for the hypothesized N protein cap-binding site. It remains unclear whether a functionally relevant cap-specific binding site exists in any bunyavirus N protein. The comparably low affinity of bunyavirus CBD for cap-structures indicates the necessity for further regions of the L protein or other viral or cellular proteins to be involved in cap binding.

Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes

“…It is currently unclear which cytoplasmic capped RNAs are accessed by bunyavirus polymerases, and in what context, and if the polymerase contains specific domains that interact with host capped-RNA-bound proteins. Second, the length of the host-derived capped RNA primer generated after cleavage by the endonuclease differs between families 5 , 0–7 in Arenaviridae , 10–18 in Peribunyaviridae , 10–14 in Orthomyxoviridae , suggesting differences in the relative position of the endonuclease, CBD and polymerase active site. Third, CBD localization within L proteins remains unclear for several viral families primarily due to the absence of a definitive motif for the cap-binding site and because of the high divergence in sequence between polymerases, particularly in their C-terminal region.…”

“…Replication generates full-length genome or antigenome copies (vRNA and cRNA, respectively), whereas transcription produces capped viral mRNA that are recognized by the cellular translation machinery to produce viral proteins. Transcription is initiated by a "cap-snatching" mechanism, whereby host 5′ capped RNAs are bound by the L cap-binding domain (CBD), cleaved by the L endonuclease domain several nucleotides downstream, and then used to prime synthesis of mRNA 2,5,6 .…”

Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes

“…This leads us to hypothesize that it might act as a platform to recruit cytoplasmic proteins recognising capped RNA or be involved in replication-related activities. It might as well interact with host translation factors, thus mediating the transcription-translation coupling observed in Bunyavirales 5, 18 .…”

“…Replication generates full-length genome or antigenome copies (vRNA and cRNA respectively), whereas transcription produces capped viral mRNA that are recognized by the cellular translation machinery to produce viral proteins. Transcription is initiated by a “cap-snatching” mechanism, whereby host 5′ capped RNAs are bound by the L cap-binding domain (CBD), cleaved by the L endonuclease domain several nucleotides downstream, and then used to prime synthesis of mRNA 2, 5, 6 . Although the overall mechanism of transcription initiation is likely conserved between sNSVs, several elements suggest some divergences between viral families.…”

“…Whereas influenza polymerase interacts directly with the host polymerase II to snatch the caps of nascent transcripts in the nucleus 7 , it is currently unclear which and in what context cytoplasmic capped RNAs are accessed by bunyavirus polymerases and if the polymerase contains specific domains that would serve as platforms to interact with host capped-RNA-bound proteins. Second, the length of the host-derived capped RNA primer generated after cleavage by the endonuclease differs between families 5 , 0 to 7 in Arenaviridae, 10 to 18 in Peribunyaviridae , 10 to 14 in Orthomyxoviridae, suggesting differences in the relative position of the endonuclease, CBD and polymerase active site. Third, CBD localization within L proteins remains unclear for several viral families primarily due to the absence of a definitive motif for the cap-binding site and because of the high divergence in sequence between polymerases, particularly in their C-terminal region.…”