Coronavirus Nucleocapsid Protein Facilitates Template Switching and is Required for Efficient Transcription

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2009 Dec 4

PMID 19955314

Citations 137

Authors

Sonia Zuniga

Jazmina L G Cruz

Isabel Sola

Pedro A Mateos-Gomez

Lorena Palacio

Luis Enjuanes

Affiliations

Soon will be listed here.

Abstract

Purified nucleocapsid protein (N protein) from transmissible gastroenteritis virus (TGEV) enhanced hammerhead ribozyme self-cleavage and favored nucleic acid annealing, properties that define RNA chaperones, as previously reported. Several TGEV N-protein deletion mutants were expressed in Escherichia coli and purified, and their RNA binding ability and RNA chaperone activity were evaluated. The smallest N-protein domain analyzed with RNA chaperone activity, facilitating DNA and RNA annealing, contained the central unstructured region (amino acids 117 to 268). Interestingly, N protein and its deletion mutants with RNA chaperone activity enhanced template switching in a retrovirus-derived heterologous system, reinforcing the concept that TGEV N protein is an RNA chaperone that could be involved in template switching. This result is in agreement with the observation that in vivo, N protein is not necessary for TGEV replication, but it is required for efficient transcription.

Citing Articles

A Comparison of Conserved Features in the Human Coronavirus Family Shows That Studies of Viruses Less Pathogenic than SARS-CoV-2, Such as HCoV-OC43, Are Good Model Systems for Elucidating Basic Mechanisms of Infection and Replication in Standard....

Heffner A, Rouault T Viruses. 2025; 17(2).

PMID: 40007010 PMC: 11860170. DOI: 10.3390/v17020256.

Structural proteins of human coronaviruses: what makes them different?.

Minigulov N, Boranbayev K, Bekbossynova A, Gadilgereyeva B, Filchakova O Front Cell Infect Microbiol. 2024; 14:1458383.

PMID: 39711780 PMC: 11659265. DOI: 10.3389/fcimb.2024.1458383.

Regulation viral RNA transcription and replication by higher-order RNA structures within the nsp1 coding region of MERS coronavirus.

Terada Y, Amarbayasgalan S, Matsuura Y, Kamitani W Sci Rep. 2024; 14(1):19594.

PMID: 39179600 PMC: 11343750. DOI: 10.1038/s41598-024-70601-5.

Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2.

Patarca R, Haseltine W Int J Mol Sci. 2024; 25(15).

PMID: 39125583 PMC: 11311688. DOI: 10.3390/ijms25158012.

Unraveling the assembly mechanism of SADS-CoV virus nucleocapsid protein: insights from RNA binding, dimerization, and epitope diversity profiling.

Zhang Y, Wu F, Han Y, Wu Y, Huang L, Huang Y J Virol. 2024; 98(8):e0092624.

PMID: 39082816 PMC: 11334509. DOI: 10.1128/jvi.00926-24.

References

Tang T, Wu M, Chen S, Hou M, Hong M, Pan F . Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory syndrome and 229E human coronaviruses. Proteomics. 2005; 5(4):925-37. PMC: 7167620. DOI: 10.1002/pmic.200401204. View

Zuniga S, Sola I, Alonso S, Enjuanes L . Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. J Virol. 2003; 78(2):980-94. PMC: 368802. DOI: 10.1128/jvi.78.2.980-994.2004. View

Terribilini M, Sander J, Lee J, Zaback P, Jernigan R, Honavar V . RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 2007; 35(Web Server issue):W578-84. PMC: 1933119. DOI: 10.1093/nar/gkm294. View

Schelle B, Karl N, Ludewig B, Siddell S, Thiel V . Selective replication of coronavirus genomes that express nucleocapsid protein. J Virol. 2005; 79(11):6620-30. PMC: 1112145. DOI: 10.1128/JVI.79.11.6620-6630.2005. View

Almazan F, Galan C, Enjuanes L . The nucleoprotein is required for efficient coronavirus genome replication. J Virol. 2004; 78(22):12683-8. PMC: 525053. DOI: 10.1128/JVI.78.22.12683-12688.2004. View

Fan H, Ooi A, Tan Y, Wang S, Fang S, Liu D . The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties. Structure. 2005; 13(12):1859-68. PMC: 7126683. DOI: 10.1016/j.str.2005.08.021. View

Takeda M, Chang C, Ikeya T, Guntert P, Chang Y, Hsu Y . Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method. J Mol Biol. 2008; 380(4):608-22. PMC: 7094413. DOI: 10.1016/j.jmb.2007.11.093. View

Huang Q, Yu L, Petros A, Gunasekera A, Liu Z, Xu N . Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein. Biochemistry. 2004; 43(20):6059-63. DOI: 10.1021/bi036155b. View

Thiel V, Herold J, Schelle B, Siddell S . Viral replicase gene products suffice for coronavirus discontinuous transcription. J Virol. 2001; 75(14):6676-81. PMC: 114390. DOI: 10.1128/JVI.75.14.6676-6681.2001. View

10.

Ivanyi-Nagy R, Lavergne J, Gabus C, Ficheux D, Darlix J . RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae. Nucleic Acids Res. 2007; 36(3):712-25. PMC: 2241907. DOI: 10.1093/nar/gkm1051. View

11.

Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O . RNA chaperones, RNA annealers and RNA helicases. RNA Biol. 2008; 4(3):118-30. DOI: 10.4161/rna.4.3.5445. View

12.

van Hemert M, van den Worm S, Knoops K, Mommaas A, Gorbalenya A, Snijder E . SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro. PLoS Pathog. 2008; 4(5):e1000054. PMC: 2322833. DOI: 10.1371/journal.ppat.1000054. View

13.

Mark J, Li X, Cyr T, Fournier S, Jaentschke B, Hefford M . SARS coronavirus: unusual lability of the nucleocapsid protein. Biochem Biophys Res Commun. 2008; 377(2):429-433. PMC: 7092863. DOI: 10.1016/j.bbrc.2008.09.153. View

14.

Dyson H, Wright P . Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol. 2005; 6(3):197-208. DOI: 10.1038/nrm1589. View

15.

Thiel V, Karl N, Schelle B, Disterer P, Klagge I, Siddell S . Multigene RNA vector based on coronavirus transcription. J Virol. 2003; 77(18):9790-8. PMC: 224574. DOI: 10.1128/jvi.77.18.9790-9798.2003. View

16.

Tan Y, Fang S, Fan H, Lescar J, Liu D . Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells. Nucleic Acids Res. 2006; 34(17):4816-25. PMC: 1635287. DOI: 10.1093/nar/gkl650. View

17.

Sola I, Moreno J, Zuniga S, Alonso S, Enjuanes L . Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis. J Virol. 2005; 79(4):2506-16. PMC: 546574. DOI: 10.1128/JVI.79.4.2506-2516.2005. View

18.

Guo J, Henderson L, Bess J, Kane B, LEVIN J . Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J Virol. 1997; 71(7):5178-88. PMC: 191753. DOI: 10.1128/JVI.71.7.5178-5188.1997. View

19.

Wang Y, Wu X, Wang Y, Li B, Zhou H, Yuan G . Low stability of nucleocapsid protein in SARS virus. Biochemistry. 2004; 43(34):11103-8. DOI: 10.1021/bi049194b. View

20.

Herschlag D . RNA chaperones and the RNA folding problem. J Biol Chem. 1995; 270(36):20871-4. DOI: 10.1074/jbc.270.36.20871. View