Virology meets Proteomics

Abstract

Ileana M. Cristea David Graham Recent years have witnessed the significant contribution of proteomics to understanding important concepts in virology. Viruses have co-evolved with their hosts, acquiring mechanisms to capture and manipulate host cellular processes for their replication and spread. Similarly, host cells respond by deploying defense mechanisms or by adapting to the infection environment. Proteomics has delivered powerful tools for characterizing this dynamic interaction between viruses and hosts. This success was driven by improvements in proteomic workflows and mass spectrometry instrumentation, as well as by the increased awareness of these valuable proteomic methods within the virology community. Indeed, in recent years, mass spectrometry (MS) has progressed from being a sparsely used technology, hidden in the supplementary material of some virology studies, to being a major contributor to fundamental discoveries in virology. For example, MS-based analyses have been used to characterize the composition of virions, define virus-host protein interactions, map global proteome or secretome changes following infection, determine the function of posttranslational modifications during infection, and define novel mechanisms of host defense against viruses. Our Special Issue aims to celebrate and highlight the integration of these two fields of research, Proteomics and Virology, as well as to raise awareness in both communities of the opportunities present in Viral Proteomics research. The issue contains 15 manuscripts that reflect the impressive diversity of virology studies that benefit from the wide range of available proteomic-based approaches. The elegant merge of these two fields of research is illustrated by the fact that these manuscripts come from both virology and mass spectrometry laboratories. While, of course, not all of the leading laboratories were able to contribute to this issue, we are very pleased to say that, as detailed below, the investigators highlighted in this issue represent some of the major supporters of proteomics for virology studies. We have organized this issue using classical virology taxonomy by dividing the issue into two main sections communicating reports describing either DNA or RNA viruses and a third section on non-MS based proteomics. Section 1, DNA viruses, begins with an informative review discussing the biological discoveries made possible by MS-based proteomics when studying alpha herpesviruses, a major family of human pathogens. This review comes from one of the world-leading virology groups in this area - the Enquist laboratory. Extending the theme of alpha herpesviruses, the two next research papers uncovered protein interactions during infection with herpes simplex virus 1 (HSV-1). First, from the laboratory of David Knipe, one of the first to use MS in protein interaction studies during infection. This study identified an important viral-viral protein interaction for the HSV-1 tegument protein VP16, and proposed an expanded role for VP16 in transactivation of viral gene expression. Second is a paper by Rowles et al. which highlights the value of immunoaffinity purification (IP) and MS for defining virus-host interactions, identifying the association of HSV-1 proteins with an important cellular epigenetic factor. This study adds to the growing interest in the scientific community in understanding the impact of viral infection on the epigenetic landscape of a cell, and comes from a group that was the first to use IP-MS, a now central tool in the field, to study temporal virus-host protein interactions during the progression of an infection. The next three manuscripts focus on the beta herpesvirus, human cytomegalovirus (HCMV). The Moorman lab elegantly demonstrates the importance of studying RNA-protein interactions, identifying a new mechanism through which a viral factor regulates translation during HCMV infection. The next two papers characterize changes in both the proteome and posttranslational modifications. The Terhune lab used metabolic labeling in conjunction with cellular fractionation to build a valuable repository of changes occurring in the nuclei of HCMV infected cells, discovering nuclear import factors that are required for effective HCMV replication. The final beta herpesvirus manuscript comes from the laboratory of Tom Shenk, a world-recognized expert in HCMV biology. Metabolic labeling and phosphopeptide enrichment approaches uncovered the impact of a viral kinase on the cellular phosphoproteome and a novel phosphorylation motif. Further emphasizing the broad contribution of proteomics to herpesvirus studies, the next paper focused on a human cancer virus, the gamma herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV). The Robertson group investigated cellular proteins that bind to the SUMO-interaction motif of the viral latent nuclear antigen (LANA), expanding the current understanding of the role of SUMOylation in KSHV infect