Exploring the biology of multipartite viruses – Nano

Three main categories of virus genome structure and organization, independently of whether the nucleic acid is single- or double-stranded RNA or DNA, can be distinguished. The “monopartite” viruses have a single chromosome bearing all genetic information and packaged in a single virus particle. The “segmented” viruses have two or more chromosomes, which are all encapsidated together in a single virion. Finally, the “multipartite” viruses also have more than one chromosome, from 2 to 10 depending on the viral species, but each is encapsidated individually in distinct virus particles. Multipartite viruses are extremely frequent in plants, where they induce numerous diseases in major crops around the world. They also infect fungi and have recently been reported in insects.

Because of this puzzling compartmentalization of the genetic information of multipartite viruses into several virus particles, the functioning of their genome is intricately linked to that of their populations. Theoretical studies have proposed putative advantages of such viral systems, like enhanced stability, replication and/or recombination/shuffling of smaller nucleic acid segments; the counterpart costs being the reduced chances to infect new cells and new hosts with at least one copy of each, thus with no information loss. The current view of the way multipartite viral systems can be functional largely suffers from the lack of experimental data which would support any of the proposed benefits or even the actual existence of the above mentioned cost at new cell and host infection.

We have recently demonstrated that the multipartite Faba bean necrotic stunt virus (FBNSV, Family Nanoviridae) reproducibly accumulates its eight genes (or genome segments) within host plants with different and specific relative frequencies, some genes being frequent and others rare. We here refer to the specific pattern of the frequencies of the eight segments as the “genome formula”. This discovery suggests an unforeseen putative benefit in multipartite viral systems, that is the capability to differentially control the copy number of each gene/segment, which in turn drives the virus population in the situation of maximum costs, due to the increased risk of losing rare segments.

We here propose a research program that experimentally addresses in parallel the relationship between the various genome segments and the population dynamics/genetics of multipartite viruses, using FBNSV as a model system. We will investigate:

i) the link between the gene/segment copy number (genome formula), the regulation of gene expression, and the expression of viral phenotypes (accumulation, aggressiveness, transmission by aphid vectors)

ii) the actual distribution of distinct genomic segments in cells of the host and of the vectors, in order to reveal whether they are all always together in individual cells at all steps of the life cycle, or whether the genetic information can be temporarily separated in distinct locations of the host or vector

iii) the way ssDNA segments, mRNA and proteins actually traffic within hosts and vectors to investigate whether the various segments can complement each other only within cells or also across cells

iv) the plastictity of the genome formula in response to environmental changes and its evolution during adaptation to new host species.

The project will provide key information on the basic “way of life” of multipartite viruses. In particular, the proposed experiments will inform on both the putative benefits and costs in these enigmatic biological systems, for which decades of theoretical studies led to the recent conclusion that the current conceptual framework of virology cannot explain their existence.