Research & Publications
Without capsid proteins and glycoproteins, oncogenic herpesvirus genomes (EBV and KSHV) will remain trapped in cells that are destined to die. The Guindy laboratory uses various genomic (RNA-seq and ChIP-seq) and proteomic (mass spec) approaches to investigate the involvement of several viral protein suspects and their cellular comrades in The Great Escape of viruses from cells. Our current viral suspects include, a viral protein kinase and six other companions with no molecular finger prints - based on blast searches. Current intel suggests that suspect proteins are important in transcribing messages of viral capsid proteins and glycoproteins once they receive The Signal. Identifying the signal and understanding the role of these viral and cellular proteins will enable us to keep viral genomes cell-trapped.
Specialized Terms: DNA replication; Tumor virus; Herpesvirus; Oncogenic; Transcription factor; Replication protein; Phosphorylation; Protein modifications; Kinase
Extensive Research Description
Epstein-Barr virus (EBV) is etiologically linked to the development of several forms of lymphoma and carcinoma. EBV causes lymphoproliferative diseases in organ transplant and AIDS patients. Available anti-herpesvirus drugs, namely acyclovir and foscarnet, which inhibit the viral DNA polymerase, have poor efficacy and adverse side effects. Thus, it is imperative to study other virally encoded proteins, particularly enzymes, as potential targets for developing new anti-viral therapies.
EBV infection has latent and lytic forms (Fig 1). Both forms of infection contribute to the oncogenic capacity of the virus. Latent infection is characterized by expression of a small subset of viral genes that cause cell proliferation. Lytic infection is the stage at which virus particles are assembled and released to infect new cells. During lytic infection, expression of viral genes is divided into two phases, early and late, relative to onset of viral DNA replication. Early genes encode proteins mainly involved in viral DNA replication. Late genes encode structural proteins (capsid proteins and glycoproteins) that form virus particles and immunomodulators that subvert the immune system. Late genes represent more than one third of all herpesvirus genes. Despite the importance of late genes, little is known about the mechanisms that regulate their expression.
The research in the Guindy laboratory focuses on studying the mechanisms that regulate expression of viral late genes. Late genes are transcribed only after the virus replicates its genome; inhibition of viral DNA replication abolishes synthesis of late products - as if the virus knows how to tell time. This problem of understanding the timing of late gene expression is common to all DNA viruses. Abrogating late gene expression has detrimental effects on production of new virus particles. Also, disrupting the dependency of late gene expression on viral DNA replication is likely to be deleterious to infected cells as these cells will become subject to recognition by the immune system. In our research, we discovered two viral proteins that are essential regulators for transcription of late genes, BGLF4, a viral protein kinase, and BGLF3, a protein with no cellular homologs or identifiable domains. Five additional factors have also been identified, by other colleagues in the field, as regulators of late gene expression. All late gene regulators have orthologs in both beta and gamma herpesviruses. The current model suggests that late gene regulators assemble on late promoters to form a viral pre-initiation complex (vPIC) dedicated for transcription of late genes. vPIC recruits the basic transcription machinery, including RNAPII, to late promoters for transcription to ensue. While expression of each late gene regulator is essential for transcription of late genes, the exact role of each proteins is still ambiguous.
In our current research we are using mass spectrometry to study the dynamics of vPIC assembly and the role of each protein in recruiting members of the basic transcription machinery to form a functional pre-initiation complex on late gene promoters. Understanding the dynamics of vPIC assembly requires knowing the post-translational modifications that regulate interactions among various subunits of the complex. One of the questions we are interested in addressing is, why does vPIC become functional only after viral DNA replication? Recently, we identified a single phosphorylation site in the BGLF3 protein and demonstrated that phospho-Thr42 is essential for transcription of late genes and production of new virus particles (Fig 2). We are interested in mapping additional post-translational modifications in other late gene regulators and determining their potential role as checkpoints for synthesis of viral late structural proteins. Furthermore, we are studying the role of BGLF4, a serine/threonine protein kinase encoded by EBV in regulation of late gene expression. Our approach involves studying the phosphoproteomics of EBV infected cells in the absence and presence of the kinase activity of BGLF4. This approach has the potential to inform the development of a new class of drugs against EBV and its associated malignancies.
A separate project in the Guindy laboratory involves the importance of a viral long non-coding RNA referred to as BHLF1 that is expressed at high levels during lytic infection. We have generated modified oligos that specifically target BHLF1 for degradation. We are currently using these mOligos to assess the role of BHLF1 in viral reactivation and de novo infection. The fact that BHLF1 is expressed at high levels suggests that we can use this molecule as a bio-marker to determine whether a patient is undergoing active lytic reactivation. BHLF1 is the precursor of circular RNA, a form of RNA that is currently receiving much attention in terms of cancer bio-markers.
Oncogenic Viruses; Pediatrics; Protein Processing, Post-Translational; Mass Spectrometry; Tumor Virus Infections; Epstein-Barr Virus Infections; Infectious Disease Medicine