My thesis work will evaluate the role of CyclophilinA (CypA) in the evolution of retroviral restriction. I will evaluate CypA in the form of the fusion gene TRIMCyp. Additionally, I will study the interaction between CypA and retroviral capsid (CA) to understand the nature of that relationship. CypA, a peptidyl prolyl isomerase protein encoded by host genomes, interacts with specific retroviral proteins, most notably the CA protein of the lentiviruses HIV-1. In human cells, this interaction results in a 2- to 5-fold increase in HIV infectivity. However, in other primate cells, the same interaction results in a decrease in infectivity in the presence of TRIM5a. Thus, while CypA supports lentiviral infection in some species, it inhibits the same infection in others. TRIMCyp is a variant of TRIM5a that has novel retroviral restriction abilities. TRIMCyp provides an evolutionary alternative for a host challenged by a retrovirus, specifically a lentivirus, by taking advantage of the naturally occurring interaction between lentivirus CA and host CypA. In a remarkable case of convergent evolution, TRIMCyp has occurred at least twice in two independent primate lineages: in Actus spp. (owl monkeys) and in the Asian population of macaques. Hypothesis 1: A TRIMCyp gene fusion is an alternative evolutionary solution to retroviral challenges that has evolved multiple times in primates.
Specific Aim 1. 1: TRIMCyp Screen. A screen of primate genomes covering old world monkeys, new world monkeys, and hominoids should reveal additional incidences of TRIMCyp.
Specific Aim 1. 2: TRIMCyp Characterization. For any new TRIMCyp identified it will be important to characterize the TRIMCyp by: (I) locating the CypA insertion in genomic context and (II) assaying TRIMCyp for an effect against lentivirus infectivity. Hypothesis 2: Retroviruses confronted with TRIMCyp in the host will respond by forfeiting CypA binding.
Specific Aim 2. 1: Screen for retroviruses that do not bind CypA. As a result of the genetic conflict between retroviruses and host restriction factors, the retrovirus is under pressure to adapt or face eradication. If a retrovirus is pressured by host TRIMCyp, then it may forfeit binding to CypA in order to evade the host restriction factor, even though the retrovirus may incur a partial loss in infectivity as a result. The gene fusion of TRIM5 and CypA functions as an evolutionary solution by a host in response to a retroviral challenge, specifically lentiviruses such as HIV-1. Understanding the nature of TRIMCyps and how they arose will provide insight into their history and role in primate genomes and in defeating retroviruses.
I will receive training in bioinformatics as well as molecular biology to identify new instances where Trim- CyclophilinA gene fusions contribute to host defense against retroviruses under Dr. Malik's mentorship. Additionally, I will learn state-of-the-art virological techniques using an array of different transgenic viruses under Dr. Michael Emerman, who is a world-leading expert in the design and use of such virology techniques. I will regularly be presenting my research at both Malik and Emerman lab meetings, and to the Genome Sciences department. I will also present current literature to my graduate department as a part of Journal club. Along with coursework in genomics and molecular evolution, I will be attending classes in virology and career development classes (ran by the student-post-doc association at the Fred Hutchinson Cancer Research Center) focused on public speaking, grant writing, paper writing and networking with other scientists. I will also participate in day-long seminars on how to carve an academic career (including choosing post-doc advisors). I will attend one national/international conference each year to gain prestigious avenues to present my research. I will also be assisting Dr. Malik in mentoring and speaking to minority students as part of the Hutch Summer Students program. Earning a NRSA Fellowship will ensure that I am able to commit the next several years to the work that I have outlined, and through my work I will be contributing to the scientific community and general public.
