B.Sc. Molecular Biology - University College London - 2002
Ph.D. Neuroscience - University of California, San Francisco - 2008
How do viruses reprogram host gene expression ?
I am interested in how viruses, and particularly the oncogenic gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV), alter cellular gene expression in a broad manner at the transcriptional and posttranscriptional level. This is a new way to look at host-pathogen interactions, as most studies focus on specific effects of viral proteins on immune signaling. However, a growing body of literature points at the existence of more general effects of viral proteins on gene expression. In particular, during KSHV infection, cells infected in a productive (lytic) manner are believed to provided paracrine factors that support the proliferation and tumor phenotype of cells infected in a latent manner. This process contributes to the development of KSHV-induced tumors (Kaposi's sarcoma and some type of B-cell lymphomas). Therefore, studying how KSHV controls host gene expression may also help identify target genes that are important for the tumor maintenance process.
1) How does the KSHV RNA endonuclease SOX target host transcripts for degradation?
KSHV and other gammaherpesviruses cause widespread degradation of host messenger RNAs through the action of a viral protein termed SOX. This process has an important role in the life cycle of the virus and its ability to disseminate within the body of the infected host. Despite its importance, the mechanism of action of SOX has remained elusive, because the weak RNase activity this protein displays in vitro cannot account for the extensive RNA degradation in cells. Together with Sergio Covarrubias, a former student in the Glaunsinger lab, I have investigated how SOX degrades mRNA in cells. Through a combination of reporter and siRNA knockdown approaches, we found that SOX preferentially targets RNAs that are transcribed by RNA polymerase II and are competent for translation. We also showed that SOX-mediated degradation is a two-step process. First, SOX acts as a RNA endonuclease cleaving RNAs internally, then cellular RNases like the 5'-3' exonuclease Xrn1 degrade the body of the message. Normally Xrn1 cannot degrade mRNAs because their 5' end is protected by a 7-methyl guanosine cap, and regulated sequential removal of the 3' poly(A) tail and of the cap controls RNA degradation kinetics. By cleaving RNAs internally SOX bypasses these regulatory steps and forces the host machinery to degrade host transcripts.
To our surprise, SOX does not indiscriminately cut along the mRNA but targets specific sequences on the transcripts. My current research focuses on characterizing the element that is targeted by SOX. Preliminary data with reporters suggest that a complex element, perhaps a structure, of >25 nucleotides is required for the cleavage. We suspect this element is highly degenerate because it must be present on the ~60% of mRNAs that are targeted by SOX. I am using a deep-sequencing based approach to map the SOX cleavage sites across the transcriptome and then search for motifs surrounding the cut sites.
Our interest in SOX specificity is two-fold. On the one hand, we would like to better understand the function of this protein and how this previously unappreciated target selectivity plays out in the context of viral infection. On the other hand, not much is known about the regulation and targeting of eukaryotic RNA endonucleases in general, despite a renewed interest in these enzymes as regulators of eukaryotic RNA decay. This could be a great opportunity to identify mechanisms of targeting for RNA endonucleases.
2) Is the mechanism of action of KSHV SOX similar to that of RNA endonucleases from other viruses?
"Host shutoff", the reduction of host gene expression by viruses, can be achieved by interfering with any of the steps of gene expression. Besides KSHV, other viruses accomplish host shutoff by inducing degradation of host transcripts, including other gammaherpesviruses like Epstein Barr virus (EBV), the more distantly related alphaherpesviruses like herpes simplex virus (HSV) and completely unrelated viruses like SARS coronavirus. Strikingly, all of the viral factors that trigger host shutoff through mRNA degradation are reported to act as or recruit RNases, although some of the proteins are completely unrelated. I was intrigued by this observation and decided to investigate whether the overall mechanism of mRNA degradation was similar by testing the factors in parallel. Indeed, all of the host shutoff RNases specifically target RNAs that are competent for translation (although translation itself or even ribosome binding is not always required) and they all rely on host machinery, specifically Xrn1, to degrade the body of the messages. The cut site, however, is divergent even between the closely related homologs SOX (from KSHV) and BGLF5 (from EBV). Our conclusion is that several viruses from divergent families have evolved slightly different ways to tap into the same basic cellular mechanism of RNA degradation and thus broadly target host transcripts.
Interestingly, since our work was published, a new viral RNase encoded by influenza A virus was described. Thus, this mechanism of host shutoff may be even more widespread than previously appreciated.
3) Are there other broad regulators of host gene expression in KSHV and how do they function?
Besides SOX, could KSHV encode other host shutoff factors or other proteins with broad effects on host gene regulation? Some of the discrepancies between the effects of SOX in transfected cells and in KSHV-infected cells strongly suggest this is likely. Also, 40% of gammaherpesviral proteins are predicted to have a role in interactions with the infected host, but many KSHV proteins are largely uncharacterized. Through a multi-tiered screen, I identified several KSHV genes that may suppress or enhance host gene expression in a promoter-independent, UTR-independent and coding region-independent manner. I am now working on characterizing the molecular mechanism of action of these proteins and their role in viral infection. Several of the proteins I identified have no known function or have functions that are inferred solely on homology to genes from alpha- or betaherpesviruses, suggesting this approach could ascribe functions to previously uncharacterized viral proteins.
KSHV host shutoff:
Marta M. Gaglia, Sergio Covarrubias, Wesley Wong, Britt A. Glaunsinger, A common strategy for host RNA degradation by divergent viruses (2012) Journal of Virology, 86:9527-30. Highlighted in Spotlight section.
Sergio Covarrubias*, Marta M. Gaglia*, G. Renuka Kumar, Wesley Wong, Andrew O. Jackson, Britt A. Glaunsinger, Coordinated Destruction of Cellular Messages in Translation Complexes by the Gammaherpesvirus Host Shutoff Factor and the Mammalian Exonuclease Xrn1 (2011) PLOS Pathogens, 7: e1002339. (*co-first authors) (Link)
Marta M. Gaglia and Britt A. Glaunsinger, Viruses and the cellular RNA decay machinery (2010) WIREs RNA 1: 47-59 [invited review]
Genetics of aging and behavior:
Marta M. Gaglia*, Dae-Eun Jeong*, Eun-A Ryu*, Dongyeop Lee, Cynthia Kenyon, Seung-Jae Lee, Genes that act downstream of sensory neurons to influence longevity, dauer formation and pathogen responses in Caenorhabditis elegans (2012) PLOS Genetics (in press) (*co-first authors)
Tracy M Yamawaki, Jennifer R. Berman, Monika Suchanek-Kavipurapu, Mark McCormick, Marta M. Gaglia, Seung-Jae Lee, Cynthia Kenyon, The Somatic Reproductive Tissues of C. elegans Promote Longevity through Steroid Hormone Signaling (2010) PLoS Biol 8: e1000468 (Link)
Marta M. Gaglia and Cynthia Kenyon, Stimulation of movement in a quiescent, hibernation-like form of C. elegans by dopamine signaling (2009) Journal of Neuroscience 29: 7302-14 (Link)