Land plants are (almost) never virus-free

Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes

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This project started as a bioinformatic study of the enigmatic 30K superfamily of plant virus movement proteins (MP). This protein superfamily is widespread in viruses with different kinds of genomes, but, despite their important role in enabling productive virus infections in plants, not much is known about these proteins’ structure, mechanism of action, and evolutionary origins. The last review of sequence similarities within the 30K superfamily has been published in 2000, and we wanted to update the picture of sequence conservation and evolution in the 30K MPs. At the very least, we expected to sort through all the homologs, build multiple alignments and perhaps predict the spatial fold of the family.

We also knew that plant pararetroviruses (Caulimoviridae) encode 30K MPs and that in some plant genomes one finds the complete copies of integrated Caulimoviridae members. Upon a closer look, we found that in fact such endogeneous pararetroviruses are found in all ferns, gymnosperms and angiosperms for which enough of genome or transcriptome sequence is available. One exception thus far are two carnivorous plants with small genomes, which do not have integrated pararetroviruses (though they have retroelements of other kinds). Going back to the MPs of these integrated viruses, we found many mRNAs matching their genes. Moreover, analysis of periodic positive selection in MP genes indicates that in some lineages such selection takes place, making it likely that these proteins are expressed too.

These findings are interesting, because, possibly for the first time, they indicate that virtually no euphyllophyte plant is ever “virus-free”: integrated pararetroviruses are in nearly every genome, sometimes in several copies, at least one of which seems to be expressed. MPs are known to modify cytoskeleton, intracellular membrane and plasmodesmata, and it is possible that the endopararetrovirus proteins are doing that in all plants, if perhaps only in some cells. These findings suggests many new experiments to plant virologists.

There were no major technical bottlenecks – mostly a matter of applying the most appropriate methods for each kind of sequence analysis – but, as always with comparative genomics, there is still not enough sequence in the databases. In particular, we are not sure what is going on with viruses and proviruses in primitive land plants, such as mosses and horsetails.

Introducing the Authors

santiagoSantiago has been studying virus evolution for years. Arcady has published on virus evolution too, but his current job is to manage programs and research awards at the U.S. National Science Foundation (NSF). The agency wants its program officers to be practicing scientists, and generously provides some protected time for that.


Arcady decided to use it to revisit the question of evolution of proteins that mediate cell-to-cell movement in plant viruses, and thought that Santiago’s lab would be a perfect place to do it. So he introduced himself to Santiago, received a warm invitation to visit, and came to Valencia in the summer of 2014.

About the Research

Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes
Virology, Volume 476, February 2015, Pages 304 – 315
Arcady R. Mushegian, Santiago F. Elena 

Read the full article on ScienceDirect


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