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Finding traces of large DNA viruses in plants

Little by little, the recently discovered large DNA viruses are revealing their secrets. For the first time, researchers from INRA Versailles-Grignon and CNRS have shown that gene transfer from these viruses occurred in the genome of the moss Physcomitrella patens. This phenomenon can be explained by genes being transferred during an infection.

Photo of the moss Physcomitrella patens. Protonemata (filaments) and gametophores (stems with leaves).. © INRA, Fabien Nogué
By INRA News Office
Updated on 01/05/2015
Published on 10/24/2014

Nucleocytoplasmic large DNA viruses (NCLDVs), sometimes called “giant viruses”, are known for infecting animals and various single-celled organisms. They have never been detected in plants. Researchers at INRA Versailles-Grignon and CNRS explored this peculiarity as it pertains to genomics and bioinformatics. They performed genome sequences analysis on 13 plants that were representative of various phylogenetic taxonomic groups, including mosses and flowering plants. They then looked at possible genetic relationships between certain plant genes and those found in various organisms such as viruses and eukaryotes.

Traces of large DNA viruses in plants

The scientists were able to demonstrate the presence of 20 gene families related to large DNA virus genes within the Physcomitrella patens moss genome. These gene families were involved in fundamental viral life cycle biological processes, from DNA replication to protein synthesis and RNA transcription. Genes from viruses – between 8 and 19 copies depending on the families – were clustered in separate areas from the chromosomes, which suggests that they are derived from repeated insertion by a single viral genome.

By comparing these insertions within different areas, the researchers were able to recreate a viral genome with a genetic composition related to that of large DNA viruses. The scientists have hypothesised that these viral areas were acquired by the moss more than four million years ago due to physical contact which would have supported gene transfer from the virus to the plant. These data suggest that the moss was infected by these NCLDV-related viruses.

In plants, during the stage when reproductive cells are produced, any modification to the genetic makeup of the plant due to a viral infection will have direct consequences on the reproductive cells, thereby transferring these changes to future generations. The duration of this stage, critical in moss and fleeting in flowering plants, could explain the presence of genes related to viral genes in moss and their absence in the other plants studied. The shift towards a shorter stage in such plants could have helped counteract any possible impact of the virus on their genomes and populations.

Epigenetic regulation of viral gene expression in plants

In moss, the expression of these large DNA virus-related genes is strongly regulated because they are suppressed. The researchers showed that the DNA structure of these genes is altered (methylation of certain cytosines) without being able to find the molecules (small RNAs) responsible for this modification. These observations suggest that the regulation of viral gene expression in plants is epigenetic in nature, meaning the DNA structure is modified without affecting the sequence. However, further study is required to determine the metabolic pathway at the origin of this structural modification.

These results are a major step forward in the study and understanding of interactions between plants and their pathogens. They show for the first time that certain plants – in this case, Physcomitrella patens moss – are susceptible to infection by NCLDVs.

Scientific contact(s):

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INRA News Office
Associated Division(s):
Plant Biology and Breeding
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Florian Maumus, Aline Epert, Fabien Nogué & Guillaume Blanc. Plant genomes enclose footprints of past infections by giant virus relatives. Nature Communications 5, Article number: 4268 doi:10.1038/ncomms5268.

About large DNA viruses

Nucleocytoplasmic large DNA viruses (NCLDVs) were first described in the early 2000s. Scientists were able to establish a new viral family that includes Mimivirus, Megavirus and Pandoravirus. Structurally speaking, these viruses are both larger than their virus peers (over 0.2 µm) and have a complex genome, the size of which (0.1 to 2.5 million base pairs) is similar to the smallest bacterial genomes. Functionally, NCLDVs use a multiplication process that takes place in the cell’s cytoplasm and does not rely (or very little) on the transcription and replication mechanisms of the infected cell. Although not well known amongst the general public, they have received considerable coverage in scientific journals and their specific characteristics bring up new questions regarding their origins and evolution.