London School of Hygiene & Tropical Medicine

The structure of the proteins that trigger genome replication in rotavirus is described for the first time by scientists at the London School of Hygiene & Tropical Medicine and University of California, Los Angeles. The research examined the virus in action and deciphers how its genome replicates using proteins it recruits to form a specialised production line in its core.

Genomes hold an organism’s blueprint for replication and transcription. Viral genome could be either DNA or RNA. Understanding its replication could enable interventions to stop the beginning of the process, preventing further viral infection. Though there are vaccines, there are currently no treatments for rotavirus, which has an RNA genome.

Their work, published in the open access journal Nature Communications, could inform drug development efforts to counter the virus that is responsible for up to half a million children’s deaths globally each year.

In a second paper, published in the Proceedings of the National Academy of Sciences, the team report the structure and replication process of the same key enzymes in bluetongue virus, a member of the same viral family. This insight into its genome replication could be exploited to design new antiviral treatments which again could stop replication and infection and protect against the disease.

Bluetongue virus is a major threat to livestock around the world, infecting cows, goats, sheep, along with wild animals like deer, buffalo and camels. It is spread by biting insects, particularly midges, and causes fever, sores, lameness, deformities in young and ultimately death.

There is no treatment for bluetongue, but animals often require antibiotics to treat secondary bacterial infections. Developing antivirals to treat the disease would have the additional benefit of reducing antibiotic use, which is a critical factor in antibiotic resistance.

Polly Roy, Professor of Virology at the London School of Hygiene & Tropical Medicine, who is part of the research team, said: “The ability to see viral structures in context and in action has come with recent technological advances. Our research details how these two RNA viruses replicate their genome for the first time, providing information that could be used to design drugs to treat and prevent rotavirus in humans and bluetongue in livestock.”

Rotavirus and bluetongue are in the Reoviridae family which can infect insects, plants and animals - including humans, and have unique structures. Rather than DNA, they are formed of RNA and an essential protein called ‘RNA dependent RNA polymerase’ plays a crucial role in their replication.

In order to study these proteins within the viruses, the team used cryo-electron microscopy, which enables researchers to look at proteins in cells in their active states, how they interact and perform their functions. Cryo-electron microscopy is a 30-year technology with revolutionary recent development and won the 2017 Nobel Prize in Chemistry.

As well as viewing the rotavirus’ “hand-shaped” core structure, the team show the function of two previously undescribed domains - one opens the two strands of RNA and the other triggers the start of viral replication.

With bluetongue, the team again identify two unique structures, not found in similar viruses: a ‘fingernail’ attached to part of the “hand-shaped” core structure, and a bundle of three novel structures, stemming from different parts of the centre. They show structural changes that take place during viral entry and the ripples they induce. This understanding could provide insights into similar viruses.

Z. Hong Zhou, Professor of Microbiology, Immunology and Molecular Genetics and Director of the Electron Imaging Center for Nanomachines at University of California, Los Angeles, said: “The complementary expertise between our two teams, one in the USA and the other in the UK, is key to the success. It involved a timely application of cutting-edge nano-scale technologies to pressing public health problems.”

Publications

Ke Ding, Cristina C. Celma, Xing Zhang, Thomas Chang, Wesley Shen, Ivo Atanasov, Polly Roy & Z. Hong Zhou. In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. Nature Communications.

Yao He, Sakar Shivakoti, Ke Ding, Yanxiang Cui, Polly Roy, and Z. Hong Zhou. In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating. Proceedings of the National Academy of Sciences. DOI:10.1073/pnas.1905849116