Viral proteomics: The emerging cutting-edge of virus research

Zhou, ShengTao; Liu, Rui; Zhao, Xia; Huang, CanHua; Wei, YuQuan

Bacteriophages (phages) are the most abundant and diverse form of life and have indispensable roles in the microbial world. A series of studies have examined the structural proteomes of bacteriophages. Savalia et al. [31] utilized liquid chromatography and electrospray ionization mass spectrometry to analyze the virion proteins of phiEco32, a novel Escherichia coli bacteriophage. Two phiEco32-encoded proteins that interact with the host RNA polymerase were defined. One is an ECF family σ factor that might be responsible for the transcription of certain viral genes, and the other is a novel RNA polymerase-binding protein and transcription. Roberts et al. [32] explored the proteome of coliphage T1 using isoelectric focusing to separate the components of the virion, followed by MALDI-TOF. T1 was expected to consist of 13−15 structural proteins in the mature virion. Correspondingly, the 2DE analysis of the T1 virion performed in the same study resolved 15 proteins. Subsequent mass spectrometry revealed four abundantly expressed proteins: the major tail protein (gp41), a major capsid component (gp49), the major head subunit (gp47), and a protein associated with the major head subunit (gp48) [10] . In 2006, Naryshkina et al. [33] determined the sequence of the 152372 bp genome of pYS40, a lytic tailed bacteriophage of Thermus thermophilus. pYS40 contains 170 putative ORFs and three tRNA genes. Functions for a quarter of the pYS40 gene products were putatively attributed, based on similarity to proteins of known function from diverse phages and bacteria. A cluster of proteins was identified as being involved in nucleotide salvage, such as flavin-dependent thymidylate synthase, thymidylate kinase, ribonucleotide reductase, and deoxycytidylate deaminase. Others were involved in DNA replication, such as DNA primase, helicase, type A DNA polymerase. The increasing number of such studies will provide invaluable knowledge complementing the annotation of phage genomes and allowing for comparative genomics studies.