Viruses

The Horton lab uses a variety of biochemical and biophysical methods to investigate DNA binding proteins. Recent projects include the discovery of a novel mechanism of regulation of enzyme activity using filamentation. Filamentation, or self-association into polymers of varied lengths, by enzymes has only recently been appreciated as a widespread phenomenon, although the purpose of filamentation is not known in most cases. We discovered this phenomenon in 2010 in a sequence specific endonuclease, SgrAI, and have now determined its high resolution structure via cryo-electron microscopy. We have also performed a full kinetic analysis showing that filamentation greatly expedites the activation of the enzyme, and also allows for the sequestration of enzyme activity onto only a subset of available substrates. The other major project in the lab concerns the triggering of autoimmune diseases in genetically susceptible individuals. We study proteins from the human parvovirus B19, a virus which often precedes the development of autoimmune diseases like rheumatoid arthritis, autoimmune hepatitis, and lupus. We study how these proteins interact with cellular components to modulate the immune system into loss of self-tolerance.

Michael Worobey, PhD, uses the genomes of viruses to trace the evolution of major communicable diseases, such as HIV/AIDS and influenza. He employs an evolutionary approach to understand the origins, emergence and control of pathogens, in particular RNA viruses and retroviruses such as HIV and influenza virus. The research program integrates fieldwork, theory and methodology, molecular biology, and molecular evolutionary analysis of gene sequences in a phylogenetic framework.Current wet-lab projects in Dr. Worobey’s Biosafety Level 3 facility involve recovery of damaged and/or ancient DNA from a variety of sources including paraffin-embedded human tissue specimens, blood smears, and museum specimens. The two main efforts are: 1) reconstructing the emergence of HIV-1 group M in central Africa and North America using fossil HIV-1 sequences, and 2) investigating the evolution of AIDS-related viruses in wild-living African primates using non-invasively-collected samples.

Papillomaviruses (PVs) are a diverse family of dsDNA viruses infecting most, if not all, amniotes. Papillomaviruses infect cutaneous or mucosal epithelia. While most infections are self-limiting, persistent infection with specific human papillomaviruses has been shown to be the causative agent for cervical cancer. All established oncogenic HPV types belong to a single viral genus (the Alphapapillomaviridae). Of note, phylogenetically, these oncogenic HPV types cluster into a so-called high-risk (HR) clade, indicating an evolutionary relationship between these viruses. Importantly, not all HPV types within this HR clade are associated with cancer. I am intrigued by the observation that only a limited subset of human papillomaviruses is oncogenic. Throughout my studies I have used a combination of biochemical assays and computational analyses to understand why evolutionarily related viruses differ in their ability to cause cancer in humans. It is improbable that the ability to cause cancer provides papillomaviruses with an evolutionary advantage. It is likely that many of the viral functions linked to oncogenesis were evolutionarily beneficial as papillomavirus adapted to novel environmental niches on the host (e.g. external genitalia vs. cervix). Papillomaviruses have evolved to usurp the cellular machinery to complete their life-cycle. The papillomaviral lifecycle perturbs the normal differentiation cycle of the infected cell, forcing cells to divide far beyond their normal lifespan. It is feasible that the continued insult provided by replicating viruses eventually results in malignant transformation of the infected cell. However, while persistent infection is key to viral oncogenesis, many long-term persisting viruses do not cause cancer. By carefully interrogating the differences between these viruses, I believe it will be possible to elucidate which viral phenotypes are associated with oncogenic progression. The pathways targeted by these viruses may represent powerful targets for therapeutic intervention

All viruses hijack host cell machinery to facilitate their replication. Producing infectious viral progeny relies on host cell metabolic pathways to provide energy and building blocks such as nucleotides, amino acids, and lipids. I am interested in investigating the molecular remodeling of cellular metabolic and lipid environments by viruses. The overall goal of my research in dissecting the complex virus-host metabolism interactions is to guide the development of novel antiviral therapies. Keywords: Infectious Disease, Virology, Metabolism, Lipidomics

Felicia Goodrum earned her Ph.D. from Wake Forest University School of Medicine studying cell cycle restrictions to adenovirus replication. She trained as a postdoctoral fellow at Princeton University in the laboratory of Dr. Thomas Shenk studying human cytomegalovirus latency. Dr. Goodrum joined the faculty at the University of Arizona in 2006. Dr. Goodrum is the recipient of the Howard Temin Award from the National Cancer Institute, the Pew Scholar in Biomedical Sciences Award, and the Presidential Award for Early Career Scientists and Engineers.Dr. Goodrum's research focuses on the complex host-virus interactions that result in viral persistence. Progress in understanding latent programs of persistence have been impeded by the inherent complexity of the herpesviruses and that paucity of adequate model systems. Herpesviruses are extraordinary for their ability to coexist with their host by establishing life-long latent infections. Latency is defined as a reversibly quiescent state during which viral gene expression and replication is highly restricted. Her laboratory studies cytomegalovirus or CMV, one of eight human herpesviruses. CMV is remarkable in that it persists latently in 60-99% of the population, generally in the absence of disease in the immunocompetent host. Reactivation of CMV from latency poses life-threatening disease risks in immunocompromised individuals, particularly transplant patients. CMV infection is also the leading cause of infectious disease-related birth defects, affecting ~1% of live births in the US. Further, the health cost of the latent coexistence of CMV is just beginning to emerge in an association to age-related pathologies including vascular disease, immune dysfunction and frailty. The key to eradicating CMV lies in understanding latency in order to ultimately develop novel antiviral strategies targeting latently infected cells or to prevent reactivation. Our studies aim to define the molecular basis of persistence by defining viral and cellular determinants important to viral persistence and the mechanisms by which these determinants function in relevant cell models. In turn, our work will provide critical insights into how CMV assimilates into and impacts human biology.

Bentley A. Fane, PhD, is a Professor in the School of Plant Sciences, College of Agriculture and Life Sciences and holds a joint appointment in the Department of Immunobiology, Arizona College of Medicine. Dr. Fane has an international reputation for his research into virus structure, assembly and evolution. His research focuses on the viruses of the Microviridae, of which he is considered one of the leading experts. He has been instrumental in defining the biochemical and structural parameters that allow these viruses to replicate and produce progeny in as little as five minutes. The rapid lifecycle has facilitated in depth studies into how viruses evolved resistance mechanism to anti-viral proteins targeting particle assembly.He has published over 60 original research paper in leading scientific journals, including Nature, Molecular Cell, and Journal of Virology, in which his publications on the evolution of resistance mechanisms and kinetic traps have been selected by the journal editors as articles of “significant interest.” He is a frequent presenter at national and international meetings, and has been invited to State of the Art and plenary talks at give the American Society for Virology. He presently serves on the Editorial Boards of two leading virology journals: Virology and the Journal of Virology. At the University of Arizona, Dr. Fane has been actively involved in promoting undergraduate research has been honored with teaching awards on the department, college, and university levels. Keywords: Virus structure and assembly, Viral DNA translocation, Viral evolution

Samuel Campos, PhD, studies early events of Human Papillomavirus (HPV) infection. HPVs are small, non-enveloped DNA viruses that cause a variety of lesions ranging from benign waters to cervical cancers. Although over 100 types of HPVs have been identified, HPV16 is the most prevalent, and is alone responsible for more than 50% of cervical cancers in women worldwide. Dr. Campos and his lab study the mechanisms of HPV virus transmission at a cellular level, in hopes to discover new approaches for the prevention and treatment of HPV.HPV16 virions consist of an ~8kb circular dsDNA genome packaged into a ~60 nm protein capsid. The genome is condensed with cellular histones and exists in a chromatin-like state. The capsid is comprised of 72 pentamers of the major capsid protein L1 and up to 72 molecules of the minor capsid protein L2, localized along the inner capsid surface, within the central cavities beneath the L1 pentamers. Mature HPV16 virions exist in an oxidized state, with adjacent L1 pentamers crosslinked together by disulfide bonds to stabilize the capsid. In order to establish an infection, HPV16 virions must bind and penetrate host cells, ultimately delivering their genomes to the host cell nucleus to initiate early gene expression, cell cycle progression, and genome replication. Non-enveloped viruses are faced with the challenge of getting their genetic material across a cellular membrane and often overcome this by disrupting the endosomal or lysosomal membranes and translocating to the cellular cytoplasm during the course of intracellular virion trafficking. Keywords: virology, microbiology, virus-host interaction, HPV