Evolution: Revealing the influence of viruses – Medical News Today

In classifying all living organisms, scientists use taxonomy a naming system to group similar organisms. The largest groupings are called kingdoms. For example, humans, all animals, plants, fungi, and multicellular organisms are members of a kingdom called eukaryotes.

Eukaryotic cells all have one important commonality: they house their DNA in a nucleus. The nucleus of the cell is centrally located and membrane-bound.

Prokaryotes include bacteria and archaea, single-celled organisms whose DNA is loosely packed and surrounded by a cell membrane.

Viruses are even simpler. They comprise only DNA or RNA and solely have one protective protein coat, called a capsid, surrounding them.

What do these distinct organisms have to do with each other and evolution? Quite a bit, according to Oxford University evolutionary biologist and the new studys first author, Dr. Nicholas A. T. Irwin.

Viruses and eukaryotes depend on one another. The former use their host-derived genes for replication and cellular control, often encoding cellular-derived informational and operational genes, allowing viruses to adapt and survive.

Eukaryotes can incorporate viral DNA into their genomes. This new DNA, previously thought to be inactive, has now been found to provide new functionality to their eukaryote hosts.

Colleagues at the Department of Botany at the University of British Columbia in Vancouver, Canada, and the Department of Zoology at the University of Oxford, United Kingdom, collaborated with Dr. Irwin to reveal groundbreaking findings in gene movement between viruses and eukaryotes called horizontal gene transfer.

In the journal Nature Microbiology, Dr. Irwin and his colleagues explained how they used complex computational analyses to search for evidence of identical genes present in viruses and eukaryotes. After studying 201 eukaryotes and 108,842 viruses, the team identified distinct trends in viral-eukaryote gene transfer.

Using well-established computer analyses of the evolutionary development and diversification of species, called phylogenetics, the researchers could delineate how virus and eukaryote bidirectional gene transfers have driven species diversification.

Dr. Irwin explained to Medical News Today that the researchers used computational analyses to search for evidence of transferred genes in the genomes of around 200 eukaryotes and thousands of viruses, which covered the diversity of eukaryotic and viral species whose genomes had been sampled.

We were not only interested in identifying viral genes within eukaryotic genomes, but also detecting the presence of eukaryotic genes in viral genomes.

Medical News Today asked Dr. Irwin how they were able to arrive at such sweeping conclusions about genetic relatedness between eukaryotes and viruses. Dr. Irwin recounted:

One of the important factors that allowed us to conduct this analysis was the enormous amount of genomic data that has now become available from eukaryotes, viruses, and prokaryotes (including bacteria and archaea). These new resources have resulted from major DNA sequencing efforts trying to understand the diversity of genomes across the tree of life.

In addition to this, recent technological advances in high-throughput DNA sequencing and metagenomics, which is the sequencing and assembly of genomes from mixed communities of organisms, such as seawater samples, has accelerated the rate at which these data have become available.

Having a large diversity of high-quality genomic datasets was crucial, as it allowed us to infer which species were participating in these gene transfers, Dr. Irwin added.

The scientists found that both viruses and eukaryotes hijack each others DNA.

But, they found that eukaryotic genes transferred to viruses approximately twice as frequently as viral genes transferred to eukaryotes.

Dr. Irwin explained there might be a few reasons why viruses were the big winners in the gene competition. He noted that genes may frequently transfer from the virus to the eukaryote, but they might not stick around because of natural selection.

But, viruses may retain those genes they acquire from their hosts because they are beneficial to the virus. And, for a gene to persist, the organism must survive and propagate, a trait at which viruses are very skilled.

The researchers then applied all their knowledge of the genetics of these many eukaryotes and viruses and compared them to well-established evolutionary trees. In this way, they could approximate the timing of gene transfer events relative to when species diverged or speciated, which refers to becoming a new type of species. For Medical News Today, Dr. Irwin illustrated:

If we observed a viral gene in a human genome, we would predict that the gene was acquired after humans speciated from other primates. In contrast, if a viral gene was present in all animals, say from sponges to chimps, we would infer that gene to have been derived in the last common ancestor of animals.

Of course, there are different ways to interpret these patterns, but we base our interpretations on the assumption that gaining a gene through gene transfer is more difficult and unlikely than losing a transferred gene.

[D]r. Irwin described three separate incidents in evolution where viral genes are present and exemplify viral-influenced evolution:

Medical News Today asked Dr. Irwin what intrigued him most about his results. He mused,

The most interesting result of the study was being able to identify and visualize the patterns of gene transfer across the eukaryotic tree of life.

One of my main interests is understanding how cellular diversity and complexity have evolved, and I believe that this work has provided strong evidence that host-virus interactions have played an important part in generating the diversity of life that we see today.

I also think this study has interesting implications for how we view viruses. Similar to how the discovery and characterization of the microbiome changed our view of bacteria, I think that revealing the influence that viruses have had on the evolution of life could encourage more nuanced thoughts about the importance of viruses in nature.

Dr. Irwin

Regarding where this research might lead future scientific endeavors, principal author, Professor Patrick Keeling, added: A lot of progress in understanding [h]orizontal gene transfer (HGT) in eukaryotes has focused on the pattern of gene transfers on the tree of eukaryotes now we also have some insights into the process that led to that pattern and the likelihood that viruses are a major route for transfers.

It would be useful to take a few of the lineages where we see a lot of viral HGT and dig deeper, looking at more closely related hosts and viruses to see the process unfolding at different time scales.

And finally, Dr. Keeling noted, identifying which genes are selected for in viruses can tell you a lot about what process makes the virus more successful, and by extension how it uses its host cell.

This study, explaining HGT between eukaryotes and viruses, is the first of its kind to reveal how viruses may have allowed multiple eukaryotic species to diverge and evolve.