Current projects

2) Genome Structure, Transcription, and Packaging of dsRNA viruses               Project number: 5R01AI094386-11 

Double-stranded RNA (dsRNA)
viruses comprise a large group of non-enveloped viruses characterized by their ability to transcribe their RNA within an intact capsid (i.e., endogenous RNA transcription), thus evading cellular antiviral responses to dsRNA. Among them, members of the Reoviridae family of dsRNA viruses are of significance in both public health and basic science, exemplified respectively by the gastroenteritis-causing rotavirus which is responsible for approximately half a million child deaths annually worldwide and the insect-killing cytoplasmic polyhedrosis virus (CPV), which was used historically as a model in the discovery of RNA capping. 

We have studied non-enveloped dsRNA viruses with single-layered (CPV), double-layered [mammalian reovirus (MRV) and aquareovirus (ARV)], and triple-layered [rhesus rotavirus (RRV), bluetongue virus (BTV)] capsid. These viruses could also be classified based on the presence (such as CPV and reoviruses) or absence (such as BTV and RRV) of an mRNA-capping turret on the icosahedral vertices of their innermost shell. Results from the prior funding cycles have uncovered that BTV and CPV both use surface trimers bearing similarities to fusion proteins of enveloped viruses (e.g., flu, AIDS and COVID-19 viruses) for cell entry. 

We have also captured the asymmetrically attached transcriptional enzyme complex (TEC) at the quiescent, initiation and transcribing stages of CPV, BTV and RRV; and identified both conserved and diverse features among their structures and organizations of TEC and RNA capping. Our studies showed that, upon cell entry, these viruses sense different environmental cues for internal transcription activation; and in the case of CPV, sensing of SAM and ATP by the RNA-capping turret triggers a cascade of events: opening of the turret iris, detachment of the trimeric spike, and initiation of endogenous transcription. 

The need to conserve endogenous RNA transcription and the structural diversities uncovered in our prior studies have led to our overall hypothesis: genomes of dsRNA viruses have diverged substantially to allow incorporation of RNA segments encoding the distinct proteins required to interact with different host cells, giving rise to different genome and TEC organizations and variations to both RNA unwinding during transcription and RNA capping during release. 

We aim to test this hypothesis with state-of-the-art cryoEM and cryoET by determining representative dsRNA viruses’ genome organizations during quiescence, unwinding and capping during transcription, and genome packing during assembly. We will model the genomes inside CPV, BTV, as well as dsRNA viruses with one and two dsRNA segments for comparison (Aim 1). Capping and cap-snatching during RNA transcription will then be investigated (Aim 2). Finally, we will visualize how different genomic RNA and capsid proteins assemble to form infectious virion particles (Aim 3).

Select publications:

Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.
Stevens, A., Cui, Y., Shivakoti, S. & Zhou, Z. H. (2023). Protein & Cell
Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins.
Pan, M., Alvarez-Cabrera, A. L., Kang, J. S., Wang, L., Fan, C. & Zhou, Z. H. (2021). Nature Communications
Atomic Structure of the Trichomonas vaginalis Double-Stranded RNA Virus 2.
Stevens, A., Muratore, K., Cui, Y., Johnson, P. J. & Zhou, Z. H. (2021).  mBio
In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.
Zhang, X., Ding, K., Yu, X., Chang, W., Sun, J. & Zhou, Z. H. (2015). Nature

Research & Facilities 

Zhou Lab
California Nanosystems Institute (CNSI)
University of California Los Angeles (UCLA)
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