Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase
Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
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2020
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| Online Access: | https://hdl.handle.net/10356/142876 |
| _version_ | 1811683494403768320 |
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| author | Law, Yee-Song Utt, Age Tan, Yaw Bia Zheng, Jie Wang, Sainan Chen, Ming Wei Griffin, Patrick R. Merits, Andres Luo, Dahai |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Law, Yee-Song Utt, Age Tan, Yaw Bia Zheng, Jie Wang, Sainan Chen, Ming Wei Griffin, Patrick R. Merits, Andres Luo, Dahai |
| author_sort | Law, Yee-Song |
| collection | NTU |
| description | Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3'-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF4 Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general. |
| first_indexed | 2024-10-01T04:13:38Z |
| format | Journal Article |
| id | ntu-10356/142876 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:13:38Z |
| publishDate | 2020 |
| record_format | dspace |
| spelling | ntu-10356/1428762020-11-01T05:16:49Z Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase Law, Yee-Song Utt, Age Tan, Yaw Bia Zheng, Jie Wang, Sainan Chen, Ming Wei Griffin, Patrick R. Merits, Andres Luo, Dahai School of Biological Sciences Lee Kong Chian School of Medicine (LKCMedicine) NTU Institute of Structural Biology Science::Medicine Chikungunya Virus Nonstructural Protein 2 Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3'-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF4 Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general. MOE (Min. of Education, S’pore) MOH (Min. of Health, S’pore) Accepted version 2020-07-06T08:25:07Z 2020-07-06T08:25:07Z 2019 Journal Article Law, Y.-S., Utt, A., Tan, Y. B., Zheng, J., Wang, S., Chen, M. W., . . . Luo, D. (2019). Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase. Proceedings of the National Academy of Sciences, 116(19), 9558-9567. doi:10.1073/pnas.1900656116 0027-8424 https://hdl.handle.net/10356/142876 10.1073/pnas.1900656116 31000599 2-s2.0-85065612168 19 116 9558 9567 en Proceedings of the National Academy of Sciences of the United States of America © 2019 The Author(s). All rights reserved. This paper was published by National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America and is made available with permission of The Author(s). application/pdf |
| spellingShingle | Science::Medicine Chikungunya Virus Nonstructural Protein 2 Law, Yee-Song Utt, Age Tan, Yaw Bia Zheng, Jie Wang, Sainan Chen, Ming Wei Griffin, Patrick R. Merits, Andres Luo, Dahai Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title | Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title_full | Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title_fullStr | Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title_full_unstemmed | Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title_short | Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase |
| title_sort | structural insights into rna recognition by the chikungunya virus nsp2 helicase |
| topic | Science::Medicine Chikungunya Virus Nonstructural Protein 2 |
| url | https://hdl.handle.net/10356/142876 |
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