Structural and Functional Motifs in Influenza Virus RNAs

Abstract

Influenza A viruses (IAV) are responsible for recurrent influenza epidemics and occasional devastating pandemics in humans and animals. They belong to the Orthomyxoviridae family and their genome consists of eight (-) sense viral RNA (vRNA) segments of different lengths coding for at least 11 viral proteins. A heterotrimeric polymerase complex is bound to the promoter consisting of the 13 5′-terminal and 12 3′-terminal nucleotides of each vRNA, while internal parts of the vRNAs are associated with multiple copies of the viral nucleoprotein (NP), thus forming ribonucleoproteins (vRNP). Transcription and replication of vRNAs result in viral mRNAs (vmRNAs) and complementary RNAs (cRNAs), respectively. Complementary RNAs are the exact positive copies of vRNAs; they also form ribonucleoproteins (cRNPs) and are intermediate templates in the vRNA amplification process. On the contrary, vmRNAs have a 5′ cap snatched from cellular mRNAs and a 3′ polyA tail, both gained by the viral polymerase complex. Hence, unlike vRNAs and cRNAs, vmRNAs do not have a terminal promoter able to recruit the viral polymerase. Furthermore, synthesis of at least two viral proteins requires vmRNA splicing. Except for extensive analysis of the viral promoter structure and function and a few, mostly bioinformatics, studies addressing the vRNA and vmRNA structure, structural studies of the influenza A vRNAs, cRNAs, and vmRNAs are still in their infancy. The recent crystal structures of the influenza polymerase heterotrimeric complex drastically improved our understanding of the replication and transcription processes. The vRNA structure has been mainly studied in vitro using RNA probing, but its structure has been very recently studied within native vRNPs using crosslinking and RNA probing coupled to next generation RNA sequencing. Concerning vmRNAs, most studies focused on the segment M and NS splice sites and several structures initially predicted by bioinformatics analysis have now been validated experimentally and their role in the viral life cycle demonstrated. This review aims to compile the structural motifs found in the different RNA classes (vRNA, cRNA, and vmRNA) of influenza viruses and their function in the viral replication cycle.

Influenza A Virus Ribonucleoproteins Form Liquid Organelles at Endoplasmic Reticulum Exit Sites

“…The remaining sequence attaches several copies of unevenly-bound nucleoprotein (NP) 2 . The advantages of having a segmented genome are evident for viral evolution 3 and for better gene expression control 4 , but increase the complexity of the assembly of fully infectious virions 5-8 .…”

“…Viral assembly occurs at the plasma membrane and, in 80% of the cases, 8 distinct vRNPs are packaged selectively into a budding membrane 9 . Seminal work established the requirement of cis-acting and intersegment RNA-RNA interactions for the formation of this supra-molecular complex (reviewed in 5-8 ). However, it is under debate if vRNPs reach the plasma membrane already as complete genome bundles.…”

A single dose of a vesicular stomatitis virus-based influenza vaccine confers rapid protection against H5 viruses from different clades

“…Influenza A viruses, which belong to the family Orthomyxoviridae, have a single-stranded negative-sense RNA genome consisting of eight segments. 1 They are important zoonotic pathogens, with high morbidity in pigs, horses, poultry, and humans. 2 Influenza A viruses have two envelope glycoproteins (GPs), hemagglutinin (HA) and neuraminidase (NA), and are divided into subtypes based on antigenicity.…”

Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses

“…Actually, mutations at the nucleotide level may also influence the pathogenicity of IAV. They can affect the packaging, transcription and translation of the virus, and interfere with the hosts' immune response (Ferhadian, et al, 2018;Ingle, et al, 2015;Wang, et al, 2017;Williams, et al, 2018;Zhao, et al, 2014 protein, which could enhance the pathogenicity of H9N2 virus in mice (Sediri, et al, 2016), had little impact on the pathogenesis of the 2009 pandemic H1N1 virus in both mice and ferrets (Jagger, et al, 2010). Computational identification of the molecular marker by integrating data from multiple sources or diverse genetic background may be benefit for recognizing those with more general impact.…”

“…Mutations at the nucleotide sites were reported to affect the transcription, translation and packaging process of IAV (Ferhadian, et al, 2018;Kobayashi, et al, 2016).…”