Abstract
Virus assembly is a crucial step for the completion of the viral replication cycle. In addition to ensuring efficient incorporation of viral genomes into nascent virions, high specificity is required to prevent incorporation of host nucleic acids. For picornaviruses, including FMDV, the mechanisms required to fulfil these requirements are not well understood. However, recent evidence has suggested that specific RNA sequences dispersed throughout picornavirus genomes are involved in packaging. Here, we have shown that such sequences are essential for FMDV RNA packaging and have demonstrated roles for both the pseudoknot (PK) region and the poly-(C) tract in this process, where the length of the poly-(C) tract was found to influence the efficiency of RNA encapsidation. Sub-genomic replicons containing longer poly-(C) tracts were packaged with greater efficiency in trans, and viruses recovered from transcripts containing short poly-(C) tracts were found to have greatly extended poly-(C) tracts after only a single passage in cells, suggesting that maintaining a long poly-(C) tract provides a selective advantage. We also demonstrated a critical role for a packaging signal (PS) located in the pseudoknot (PK) region, adjacent to the poly-(C) tract, as well as several other non-essential but beneficial PSs elsewhere in the genome. Collectively, these PSs greatly enhanced encapsidation efficiency, with the poly-(C) tract possibly facilitating nearby PSs to adopt the correct conformation. Using these data, we have proposed a model where interactions with capsid precursors control a transition between two RNA conformations, directing the fate of nascent genomes to either be packaged or alternatively to act as templates for replication and/or for protein translation.
Original language | English |
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Article number | e1012283 |
Journal | PLoS Pathogens |
Volume | 20 |
Issue number | 12 |
ISSN | 1553-7366 |
DOIs | |
Publication status | Published - Dec 2024 |
Bibliographical note
Funding Information:This work was funded by BBSRC (BB/V008323/1), TJT, and internal funding from The Pirbright Institute (BBS/E/I/00007034 and BBS/E/PI/230002A), the National Veterinary Institute at the Technical University of Denmark (DTU) and the University of Copenhagen, GJB. Experimental work was carried out in the High Containment Facility at The Pirbright Institute (BBS/E/I/00007037 and BBS/E/PI/23NB0004). The authors would like to acknowledge the Bioinformatics, Sequencing and Proteomics unit and support through the Core capability grant (BBS/E/I/00007039). At DTU and UCPH, work was funded by the Danish Veterinary and Food Administration (FVST) as part of the agreement for commissioned work between the Danish Ministry of Food and Agriculture and Fisheries and DTU and then with the University of Copenhagen. NJS and DJR received funding from BBSRC (BB/K003801/1 and BB/T015748/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors would also like to acknowledge Prof. Stephen Curry for his support as a supervisor to CN during his PhD.
Publisher Copyright:
© 2024 Neil et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.