Proteomics of Viruses

ANNE PUMFERY REEM BERRO% and FATAH KASHANCHP  

The term proteome was first coined in late 1994 by Marc Wilkins at the Siena two-dimensional gel electrophoresis (2DE) meeting and defines the entire protein complement in a given cell, tissue, or organism [1], In its wider sense, proteomics research also assesses protein activities, modifications and localization, and interactions of proteins in complexes. It relies heavily on technology since it needs to identify proteins and protein complexes in biological samples comprehensively and quantitatively with both high sensitivity and fidelity. 

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Therefore, in this chapter we will discuss some recent findings on the proteomics of DNA and RNA viral infections that are associated with clinically important diseases in humans, including human cytomegalovirus (HCMV), herpes simplex virus (HSV), Epstein-Barr virus (EBV), human immunodeficiency virus (HIV), hepatitis B and C (HBV and HCV, respectively), and adenovirus, as well as the coronavirus that causes severe acute respiratory syndrome (SARS). 

One aspect of viral proteomics has been the characterization of virus particles and virally infected cells. Characterization of purified virions has led to the identification of viral proteins that were not originally identified with the virion as well as the identification of cellular proteins associated with the purified virus. For example, analysis of HCMV viral particles identified 12 additional ORFs not previously known to reside in virions as well as the identification of 71 cellular proteins [6]. The importance of these cellular and viral proteins in viral replication or pathogenesis awaits further analysis. Additionally, 12 unique polypeptides were identified that did not correspond to previously identified ORFs [6], illustrating the fact that despite intensive sequence analysis, sequence characteristics of viral promoters and ORFs are still not entirely understood. Analysis of virally infected cells has also led to the characterization of events leading to EBV-induced transformation [9,10,47], identification of cellular proteins induced in HIV-infected... 

Fontaine-Rodriguez, E.C., Taylor, T.J., Olesky, M. and Knipe, D.M., Proteomics of herpes simplex virus infected cell protein 27 association with translation initiation factors. Virology, 330, 487 92 (2004). 

Feng ZP, Zhang X, Han P, Arora N, Anders RF, Norton RS. Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes. Mol Biochem Parasitol. 2006 150(2) 256-267. Matrosovich M, Herrler G, Klenk HD. Sialic acid receptors of viruses. Top Curr Chem. 2013. 

Toda T et al. Proteomic analysis of Ep-stein-Barr virus-transformed human B-lymphoblastoid cell lines before and after immortalization. Electrophoresis 2000 21 1814-1822. 

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