Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment

International Journal of Molecular Sciences

David H. Mathews¹  Barbara Szutkowska²  Pawel Zmora²  Klaudia Wieczorek²  Ryszard Kierzek²  Elzbieta Kierzek²  Walter N. Moss³  Jake M. Peterson³ 

[1] Department of Biochemistry & Biophysics and Center for RNA Biology, 601 Elmwood Avenue, Box 712, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA;Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA;

关键词: influenza A virus;    IAV;    RNA virus;    RNA secondary structure;    RNA chemical mapping;   

DOI  :  10.3390/ijms23052452

来源: DOAJ

【 摘 要 】

Influenza A virus (IAV) is a member of the single-stranded RNA (ssRNA) family of viruses. The most recent global pandemic caused by the SARS-CoV-2 virus has shown the major threat that RNA viruses can pose to humanity. In comparison, influenza has an even higher pandemic potential as a result of its high rate of mutations within its relatively short (<13 kbp) genome, as well as its capability to undergo genetic reassortment. In light of this threat, and the fact that RNA structure is connected to a broad range of known biological functions, deeper investigation of viral RNA (vRNA) structures is of high interest. Here, for the first time, we propose a secondary structure for segment 8 vRNA (vRNA8) of A/California/04/2009 (H1N1) formed in the presence of cellular and viral components. This structure shows similarities with prior in vitro experiments. Additionally, we determined the location of several well-defined, conserved structural motifs of vRNA8 within IAV strains with possible functionality. These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted. This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA level.

【 授权许可】

Unknown