When Felix d’Herelle, a seminal figure in the history of molecular biology, discovered the first bacteriophage in French soldiers in 1917, writes Carl Zimmer in A Planet of Viruses, “many scientists refused to believe that such a thing actually existed. A century later, it’s clear that Herelle had found the most abundant life form on Earth. What’s more, marine viruses have a massive influence on the planet. Marine phages influence the ecology of the world’s oceans. They leave their mark on Earth’s global climate. And they have been playing a crucial part in the evolution of life for billions of years. They are, in other words, biology’s living matrix.”
Scientists have started to ask if some genes in living organisms actually came from ancient viruses. In 2013, the discovery of two giant viruses unlike anything seen before blurred the line between the viral and cellular world. These pandoraviruses are as big as bacteria, and contain genomes that are more complex than those found in some eukaryotic organisms (whose cells contain nuclei, unlike the two other kingdoms of living organisms, bacteria and archaea). Their strange amphora shape and enormous, atypical genome led scientists to wonder where they came from.
“Viruses are not traditionally considered alive,” writes Sarah Zang in The Atlantic, “because they lack the cellular machinery to replicate on their own. But scientists have found giant viruses with genes for building proteins, which are necessary for replication.
In the 11 June 2018 edition of Nature Communications, researchers proposed that these freaks of nature, pandoviruses appear to be factories for new genes – as evolutionary innovators, giant viruses continue to shake branches on the tree of life.these new members contain a large number of orphan genes, i.e. genes which encode proteins that have no equivalent in other living organisms (this was already the case for the two previously discovered pandoraviruses). This unexplained characteristic is at the heart of many a debate over the origin of viruses. What most surprised researchers was that the orphan genes differed from one pandoravirus to another, making it less and less likely that they were inherited from a common ancestor!
“If living organisms got genes from viruses, that would be a radical inversion of previous hypotheses about their origin,” continues Zang. “Scientists have suggested that viruses might be degenerate versions of living cells that lost most of their cellular machinery, retaining only their protein capsule and genetic material. Or that viruses might be mere fragments of cells that broke off and are unable to replicate on their own.
“But if histones and enzymes for synthesizing DNA originated in viruses, then they might have been present when life first began in primordial soup. They might be one reason life on this planet exists at all.”
The discovery of the Medusavirus, writes Zang, holds clues to the evolution of more complex life as more and more giant viruses have been discovered, scientists have started to wonder whether some genes in living organisms actually came from ancient viruses.. The paper published in the Journal of Virology in 2019 went viral so to speak because of the ability of the Medusavirus to turn amoeba into “stone.” However, the bigger discovery is the possible relationship between the Medusavirus and the evolution of complex life.
A team of scientists led by virologist Masaharu Takemura at Tokyo University of Science and Hiroyuki Ogata at Kyoto University in Japan have discovered a giant virus that, much like the mythical monster Medusa, can turn almost amoeba to a stone-like cyst. Isolated from a hot spring in Japan and eponymously dubbed Medusavirus, this virus infects a species of amoeba known as Acanthamoeba castellanii and causes it to develop a hard, stony shell.
With the Medusavirus, scientists discovered that DNA replication occurred in the nucleus of the host amoeba and observed evidence of exchange of genetic information between the host and the virus as they coevolved. They also found that the giant virus harbors in its ancient genome some of the complex proteins that make up the building blocks of eukaryotic organisms such as animals, plants, and humans. Understanding the presence of these proteins in the virus’ genome may help scientists tackle some of the hardest questions about our origins. In fact, “genomics research of the giant virus indicates that there is likely a relationship between the Medusavirus and the origin of eukaryotic life,” says Takemura.
A 3D reconstruction of the Medusavirus particle showcases its thousands of external spikes, which protrude roughly 14 nanometres from the particle’s surface. Credit: G. Yoshikawa et al./J. Virol. (CC BY 4.0)
A virus does not have the necessary “machinery” to replicate. It does this inside its host cell, by releasing its genome and “hijacking” the cell’s machinery. When a virus invades an organism, it uses some of the host genes in order to replicate itself. This can leave a mark, like a fingerprint, on the host’s DNA, which is then passed on for generations. The host also interacts with the virus, and the virus adopts new sequences that are preserved through time. The host and virus coevolve, and it is this “coevolution” that is at the forefront of this insightful study.
Viruses are classified based on their genetic characteristics, that is, by how they generate mRNA to produce proteins and genetic material. The Medusavirus is a nucleocytoplasmic large DNA virus, which belongs to a group of recently discovered eukaryotic viruses with large and complex double-stranded DNA (dsDNA) genomes. It is interesting because, unlike most viruses, it contains genes that encode for proteins involved in DNA packaging.
The Medusavirus has a full set of histones, which are proteins that have evolved to keep the DNA folded inside the nucleus and regulate gene expression. This is particularly strange when you consider that viruses have no nucleus; this could mean that during the coevolution, the virus might have acquired the genes that encode these histones. With these findings, this study also makes a claim that the Medusavirus is a completely different family of viruses.
When the Medusavirus petrifies the amoeba, it does so by hijacking the cell directly from its nucleus. The virus transfers its DNA to initiate replication and uses its own DNA polymerase (enzyme that synthesizes DNA) and histones, but overall, it relies on the host to complete the process.
The results of an evolutionary analysis done by the authors suggest that in the evolution tree, the Medusavirus DNA polymerase lies at the origin of the DNA polymerase found in eukaryotes. As one of the authors, Dr Genki Yoshikwa from Kyoto University, observes, this could mean that our DNA polymerase “probably originated from Medusavirus or one of its relatives.”
Image credit top of page with thanks to Pixabay