TY - JOUR
T1 - To Knot or Not to Knot
T2 - Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element
AU - Schlick, Tamar
AU - Zhu, Qiyao
AU - Dey, Abhishek
AU - Jain, Swati
AU - Yan, Shuting
AU - Laederach, Alain
N1 - Funding Information:
We gratefully acknowledge funding from the National Science Foundation RAPID Award 2030377 from the Divisions of Mathematical Science and of Chemistry, National Institutes of Health R35GM122562 Award from the National Institute of General Medical Sciences, and Philip-Morris International to T. Schlick, and National Institutes of Health grants R35 GM140844, R01 GM101237, and R01 HL111527 to A. Laederach.
Publisher Copyright:
©
PY - 2021/8/4
Y1 - 2021/8/4
N2 - The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG"(RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
AB - The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG"(RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
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U2 - 10.1021/jacs.1c03003
DO - 10.1021/jacs.1c03003
M3 - Article
C2 - 34283611
AN - SCOPUS:85111330959
VL - 143
SP - 11404
EP - 11422
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
SN - 0002-7863
IS - 30
ER -