Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand
Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA that serves as a template for synthesis of more positive strand progeny. Structural RNA elements are important for genome replication, but while they are readily observed in the positive strand, evidence of their existence in the negative strand is more limited. We hypothesized that this was due to viruses differing in their capacity to allow this latter RNA to adopt structural folds. To investigate this, ribozymes were introduced into the negative strand of different viral constructs; the expectation being that if RNA folding occurred, negative strand cleavage and suppression of replication would be seen. Indeed, this was what happened with hepatitis C virus (HCV) and feline calicivirus (FCV) constructs. However, little or no impact was observed for chikungunya virus (CHIKV), human rhinovirus (HRV), hepatitis E virus (HEV), and yellow fever virus (YFV) constructs. Reduced cleavage in the negative strand proved to be due to duplex formation with the positive strand. Interestingly, ribozyme-containing RNAs also remained intact when produced in vitro by the HCV polymerase, again due to duplex formation. Overall, our results show that there are important differences in the conformational constraints imposed on the folding of the negative strand between different positive strand RNA viruses.
double-stranded RNA, positive strand RNA virus, replication, replication intermediate, ribozyme
1359-1376
Herod, Morgan R.
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Ward, Joseph C.
18411518-2ae4-47bb-9944-f853658e8196
Tupin, Andrew
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Harris, Mark
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Stonehouse, Nicola J.
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Mccormick, Christopher J.
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October 2022
Herod, Morgan R.
ee407974-577f-4529-ab16-271f6d04c5c1
Ward, Joseph C.
18411518-2ae4-47bb-9944-f853658e8196
Tupin, Andrew
94f18f2e-18d8-4fbe-b9a1-6b2dae8c6871
Harris, Mark
3e8c70ec-34ae-4197-8a10-1c545207c665
Stonehouse, Nicola J.
d384d16a-fea8-460e-8896-1c153369722b
Mccormick, Christopher J.
0fce14bf-2f67-4d08-991f-114dd1e7f0bd
Herod, Morgan R., Ward, Joseph C., Tupin, Andrew, Harris, Mark, Stonehouse, Nicola J. and Mccormick, Christopher J.
(2022)
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand.
RNA, 28 (10), .
(doi:10.1261/rna.079125.122).
Abstract
Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA that serves as a template for synthesis of more positive strand progeny. Structural RNA elements are important for genome replication, but while they are readily observed in the positive strand, evidence of their existence in the negative strand is more limited. We hypothesized that this was due to viruses differing in their capacity to allow this latter RNA to adopt structural folds. To investigate this, ribozymes were introduced into the negative strand of different viral constructs; the expectation being that if RNA folding occurred, negative strand cleavage and suppression of replication would be seen. Indeed, this was what happened with hepatitis C virus (HCV) and feline calicivirus (FCV) constructs. However, little or no impact was observed for chikungunya virus (CHIKV), human rhinovirus (HRV), hepatitis E virus (HEV), and yellow fever virus (YFV) constructs. Reduced cleavage in the negative strand proved to be due to duplex formation with the positive strand. Interestingly, ribozyme-containing RNAs also remained intact when produced in vitro by the HCV polymerase, again due to duplex formation. Overall, our results show that there are important differences in the conformational constraints imposed on the folding of the negative strand between different positive strand RNA viruses.
Text
RNA-2022-Herod-1359-76
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Accepted/In Press date: 22 July 2022
Published date: October 2022
Additional Information:
Funding Information:
We would like to thank Professors A. Firth and D. Rowlands for helpful discussions. We are grateful to Professors T. Wakita, R. Bartenschlager, K. Green, and Andres Merits, Drs. T. Tuthill, P. Bredenbeek, and P. Farci for the gift of HCV gt2a, HCV gt1b, FCV, CHIKV, HRV, YFV, and HEV constructs. We thank Dr. V. Lohmann for the JFH-1 NS5B expression construct. This work was supported by the Medical Research Council (G0701215 to C.J.M.; MR/S007229/1 to M.R.H.; MR/S001026/1 to M.H.) and the Royal Society (RGS\R2\202376 to M.R.H.).
Publisher Copyright:
© 2022 Herod et al.
Keywords:
double-stranded RNA, positive strand RNA virus, replication, replication intermediate, ribozyme
Identifiers
Local EPrints ID: 469912
URI: http://eprints.soton.ac.uk/id/eprint/469912
ISSN: 1355-8382
PURE UUID: 16abe03f-0e8a-4032-ba2e-a73a58e8731c
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Date deposited: 28 Sep 2022 16:56
Last modified: 17 Mar 2024 03:03
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Contributors
Author:
Morgan R. Herod
Author:
Joseph C. Ward
Author:
Andrew Tupin
Author:
Mark Harris
Author:
Nicola J. Stonehouse
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