Mass Spectrometry Analysis Coupled with De Novo Sequencing Reveals Amino Acid Substitutions in Nucleocapsid Protein from Influenza A Virus

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2014 Feb 14

PMID 24521884

Citations 3

Authors

Zijian Li

Wanchun Sun

Donglin Wu

Xiang Gao

Ningning Sun

Ning Liu

Affiliations

Soon will be listed here.

Abstract

Amino acid substitutions in influenza A virus are the main reasons for both antigenic shift and virulence change, which result from non-synonymous mutations in the viral genome. Nucleocapsid protein (NP), one of the major structural proteins of influenza virus, is responsible for regulation of viral RNA synthesis and replication. In this report we used LC-MS/MS to analyze tryptic digestion of nucleocapsid protein of influenza virus (A/Puerto Rico/8/1934 H1N1), which was isolated and purified by SDS poly-acrylamide gel electrophoresis. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. The obtained results provided experimental evidence that amino acid substitutions resulted from non-synonymous gene mutations could be directly characterized by mass spectrometry in proteins of RNA viruses such as influenza A virus.

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References

Takayama I, Nakauchi M, Fujisaki S, Odagiri T, Tashiro M, Kageyama T . Rapid detection of the S247N neuraminidase mutation in influenza A(H1N1)pdm09 virus by one-step duplex RT-PCR assay. J Virol Methods. 2012; 188(1-2):73-5. DOI: 10.1016/j.jviromet.2012.12.005. View

Tang J, Shetty N, Lam T, Hon K . Emerging, novel, and known influenza virus infections in humans. Infect Dis Clin North Am. 2010; 24(3):603-17. PMC: 7127320. DOI: 10.1016/j.idc.2010.04.001. View

Liu N, Song W, Lee K, Wang P, Chen H, Cai Z . Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS. J Am Soc Mass Spectrom. 2008; 20(2):312-20. DOI: 10.1016/j.jasms.2008.10.010. View

Mitchell R, Taylor G, McGeer A, Frenette C, Suh K, Wong A . Understanding the burden of influenza infection among adults in Canadian hospitals: a comparison of the 2009-2010 pandemic season with the prepandemic and postpandemic seasons. Am J Infect Control. 2013; 41(11):1032-7. DOI: 10.1016/j.ajic.2013.06.008. View

Mahony J . Nucleic acid amplification-based diagnosis of respiratory virus infections. Expert Rev Anti Infect Ther. 2010; 8(11):1273-92. DOI: 10.1586/eri.10.121. View

Haynes C, Guerra S, Fontana J, DeJesus V . HPLC-ESI-MS/MS analysis of hemoglobin peptides in tryptic digests of dried-blood spot extracts detects HbS, HbC, HbD, HbE, HbO-Arab, and HbG-Philadelphia mutations. Clin Chim Acta. 2013; 424:191-200. DOI: 10.1016/j.cca.2013.06.007. View

Lalle E, Bordi L, Castilletti C, Meschi S, Selleri M, Carletti F . Design and clinical application of a molecular method for detection and typing of the influenza A/H1N1pdm virus. J Virol Methods. 2009; 163(2):486-8. DOI: 10.1016/j.jviromet.2009.10.004. View

Dortmans J, Dekkers J, Ambepitiya Wickramasinghe I, Verheije M, Rottier P, van Kuppeveld F . Adaptation of novel H7N9 influenza A virus to human receptors. Sci Rep. 2013; 3:3058. PMC: 3808826. DOI: 10.1038/srep03058. View

Rodriguez-Sanchez B, Alonso M, Catalan P, Sanchez Conde M, Gonzalez-Candelas F, Giannella M . Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009. J Clin Virol. 2011; 52(2):129-32. DOI: 10.1016/j.jcv.2011.07.001. View

10.

Crusat M, Liu J, Palma A, Childs R, Liu Y, Wharton S . Changes in the hemagglutinin of H5N1 viruses during human infection--influence on receptor binding. Virology. 2013; 447(1-2):326-37. PMC: 3820038. DOI: 10.1016/j.virol.2013.08.010. View

11.

Punpanich W, Chotpitayasunondh T . A review on the clinical spectrum and natural history of human influenza. Int J Infect Dis. 2012; 16(10):e714-23. DOI: 10.1016/j.ijid.2012.05.1025. View

12.

Sheu T, Fry A, Garten R, Deyde V, Shwe T, Bullion L . Dual resistance to adamantanes and oseltamivir among seasonal influenza A(H1N1) viruses: 2008-2010. J Infect Dis. 2010; 203(1):13-7. PMC: 3086447. DOI: 10.1093/infdis/jiq005. View

13.

Roth M, Parks B, Ferguson J, Boyne 2nd M, Kelleher N . "Proteotyping": population proteomics of human leukocytes using top down mass spectrometry. Anal Chem. 2008; 80(8):2857-66. PMC: 2615201. DOI: 10.1021/ac800141g. View

14.

Liu N, Wang G, Lee K, Guan Y, Chen H, Cai Z . Mutations in influenza virus replication and transcription: detection of amino acid substitutions in hemagglutinin of an avian influenza virus (H1N1). FASEB J. 2009; 23(10):3377-82. DOI: 10.1096/fj.09-134072. View

15.

Theberge R, Infusini G, Tong W, McComb M, Costello C . Top-Down Analysis of Small Plasma Proteins Using an LTQ-Orbitrap. Potential for Mass Spectrometry-Based Clinical Assays for Transthyretin and Hemoglobin. Int J Mass Spectrom. 2011; 300(2-3):130-142. PMC: 3098445. DOI: 10.1016/j.ijms.2010.08.012. View

16.

Sheynkman G, Shortreed M, Frey B, Scalf M, Smith L . Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J Proteome Res. 2013; 13(1):228-40. PMC: 3947302. DOI: 10.1021/pr4009207. View