Comparative Study of Synonymous Codon Usage Variations Between the Nucleocapsid and Spike Genes of Coronavirus, and C-type Lectin Domain Genes of Human and Mouse

Overview

Journal Exp Mol Med

Specialties Biochemistry
Molecular Biology

Date 2009 Jun 30

PMID 19561398

Citations 3

Authors

Insung Ahn

Byeong-Jin Jeong

Hyeon Seok Son

Affiliations

Soon will be listed here.

Abstract

Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.

Citing Articles

Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.

Gao W, Chen X, He J, Sha A, Luo Y, Xiao W BMC Genomics. 2024; 25(1):456.

PMID: 38730418 PMC: 11084086. DOI: 10.1186/s12864-024-10374-3.

Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.

Sheikh A, Al-Taher A, Al-Nazawi M, Al-Mubarak A, Kandeel M J Virol Methods. 2020; 277:113806.

PMID: 31911390 PMC: 7119019. DOI: 10.1016/j.jviromet.2019.113806.

Gaining insights into the codon usage patterns of TP53 gene across eight mammalian species.

Mazumder T, Chakraborty S PLoS One. 2015; 10(3):e0121709.

PMID: 25807269 PMC: 4373688. DOI: 10.1371/journal.pone.0121709.

References

Shields D, Sharp P . Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res. 1987; 15(19):8023-40. PMC: 306324. DOI: 10.1093/nar/15.19.8023. View

Zelensky A, Gready J . The C-type lectin-like domain superfamily. FEBS J. 2005; 272(24):6179-217. DOI: 10.1111/j.1742-4658.2005.05031.x. View

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

Stenico M, LLOYD A, Sharp P . Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res. 1994; 22(13):2437-46. PMC: 308193. DOI: 10.1093/nar/22.13.2437. View

Lynn D, Singer G, Hickey D . Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 2002; 30(19):4272-7. PMC: 140546. DOI: 10.1093/nar/gkf546. View

Catanzaro A, Roederer M, Koup R, Bailer R, Enama M, Nason M . Phase I clinical evaluation of a six-plasmid multiclade HIV-1 DNA candidate vaccine. Vaccine. 2007; 25(20):4085-92. DOI: 10.1016/j.vaccine.2007.02.050. View

Shackelton L, Parrish C, Holmes E . Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol. 2006; 62(5):551-63. DOI: 10.1007/s00239-005-0221-1. View

Gao W, Tamin A, Soloff A, DAiuto L, Nwanegbo E, Robbins P . Effects of a SARS-associated coronavirus vaccine in monkeys. Lancet. 2003; 362(9399):1895-6. PMC: 7112457. DOI: 10.1016/S0140-6736(03)14962-8. View

Yang Z, Kong W, Huang Y, Roberts A, Murphy B, Subbarao K . A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice. Nature. 2004; 428(6982):561-4. PMC: 7095382. DOI: 10.1038/nature02463. View

10.

Woo P, Lau S, Huang Y, Tsoi H, Chan K, Yuen K . Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia. Arch Virol. 2005; 150(11):2299-311. PMC: 7086700. DOI: 10.1007/s00705-005-0573-2. View

11.

Donnelly J, Berry K, Ulmer J . Technical and regulatory hurdles for DNA vaccines. Int J Parasitol. 2003; 33(5-6):457-67. DOI: 10.1016/s0020-7519(03)00056-0. View

12.

McInerney J . Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci U S A. 1998; 95(18):10698-703. PMC: 27958. DOI: 10.1073/pnas.95.18.10698. View

13.

DODD R, Drickamer K . Lectin-like proteins in model organisms: implications for evolution of carbohydrate-binding activity. Glycobiology. 2001; 11(5):71R-9R. DOI: 10.1093/glycob/11.5.71r. View

14.

Riley S, Fraser C, Donnelly C, Ghani A, Abu-Raddad L, Hedley A . Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions. Science. 2003; 300(5627):1961-6. DOI: 10.1126/science.1086478. View

15.

Ye Y, Hauns K, Langland J, Jacobs B, Hogue B . Mouse hepatitis coronavirus A59 nucleocapsid protein is a type I interferon antagonist. J Virol. 2006; 81(6):2554-63. PMC: 1865977. DOI: 10.1128/JVI.01634-06. View

16.

Schulze K, Staib C, Schatzl H, Ebensen T, Erfle V, Guzman C . A prime-boost vaccination protocol optimizes immune responses against the nucleocapsid protein of the SARS coronavirus. Vaccine. 2008; 26(51):6678-84. PMC: 7115531. DOI: 10.1016/j.vaccine.2008.09.006. View

17.

Gallagher T, Buchmeier M . Coronavirus spike proteins in viral entry and pathogenesis. Virology. 2001; 279(2):371-4. PMC: 7133764. DOI: 10.1006/viro.2000.0757. View

18.

Spiegel M, Schneider K, Weber F, Weidmann M, Hufert F . Interaction of severe acute respiratory syndrome-associated coronavirus with dendritic cells. J Gen Virol. 2006; 87(Pt 7):1953-1960. DOI: 10.1099/vir.0.81624-0. View

19.

Cella M, Sallusto F, Lanzavecchia A . Origin, maturation and antigen presenting function of dendritic cells. Curr Opin Immunol. 1997; 9(1):10-6. DOI: 10.1016/s0952-7915(97)80153-7. View

20.

Ahn I, Son H . Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques. Can J Microbiol. 2007; 53(7):830-9. DOI: 10.1139/W07-044. View