Newly discovered Medusavirus turns evolutionary theory to stone

Eukaryotic genes in newly discovered Medusavirus hints at devolution and not evolution

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Published: 23 May 2019 (GMT+10)
Yoshikawa, G., et al., Medusavirus, a novel large DNA virus discovered from hot spring water, J. Virol., 2019 | doi:10.1128/JVI.02130-18.Icosahedral
Figure 1: Icosahedral structure of Medusavirus

A novel ‘giant virus’ (diameter 260 nanometers, 1 nanometer is 10-9 meters) has recently been discovered in a Japanese hot spring. Masaharu Takemaru, a virologist at the Tokyo University of Science, named it Medusavirus after the Greek legend of the Medusa, who was so ugly that people looking at her would turn to stone. Researchers have cultured Medusavirus inside the amoeba Acanthamoeba castellanii. The virus induces the amoeba to dehydrate and harden in self-defense (a process known as encystment).1 If they fail to do this, these amoebae will be invaded by the virus, which hijacks the reproductive machinery to produce more viruses. Then the amoeba bursts to release the new viruses.2

This virus belongs to the family of nucleocytoplasmic large DNA viruses (NCLDVs) but was the first NCLDV to be isolated from a thermal environment, i.e. hot springs. Medusavirus looks like a 20-sided die (otherwise known as an icosahedron, see figure 1), and has a genome 381,000 letters long, with 461 putative (hypothetical) protein-coding genes.

Medusavirus has several very interesting genetic features. For example, its genome size (and physical size) is much, much larger than that of regular viruses. For example, the un-spliced genome of the HIV has only 9,200 nucleotides, and influenza viruses have about 13,000. But it has a much larger number of genes as well: 461 compared to the 9 genes of the HIV or 11 of influenza. Furthermore, 279 of the 461 genes (61%) of Medusavirus are ORFan genes, which are genes unique to a specific taxon and therefore are without any detectable homologs in any other taxa. ORFan genes can also be restricted to a specific taxonomic level. They pose a problem for evolutionary theory in that it is hard to explain how hundreds of genes could possibly appear all of a sudden via rapid, unobserved mutations. ORFan genes are very common for NCLDVs,3,4 meaning they are extremely difficult to classify taxonomically and are nearly impossible to fit into the evolutionary story.

Medusavirus has some 279 ORFan genes, making up a staggering 61% of its genes. The large number of ORFans in its genome sets it far apart from all small-sized viruses. How can so many genes exist in the Medusavirus genome which do not resemble any other gene in any other organism? This implies that there are no lineages leading from any other NCLDV to Medusavirus. It appears that the origin of Medusavirus is separate from all other NCLDVs, which implies special creation, not gradual evolution. Indeed, the discoverers placed it in its own family, Medusaviridae.

There is also evidence that the virus has exchanged genes with its host. The researchers at Tokyo University speculate that out of 57 supposed examples of gene transfer between Medusavirus and its amoeba host, 13 transfers happened from the host to the virus, 12 genes were transferred from the virus to the host, with the directionality of the transfer of the remaining 32 genes undecided.1 Since the amoeba is arguably not the original host (Medusavirus was cultured in it only in the lab), it is possible that the transfer of these genes between the virus and the host happened very quickly, and are not remnants of its co-existence over millions of years. It will be interesting to see what they learn as this exotic and enigmatic virus is studied in more detail.

Medusavirus contains a lot of genes which are specific to eukaryotes (the closest homolog of 115 of its 182 non-ORFan genes (63.2%) are eukaryotic), such as ones involved in DNA structuring, replication and protein translation. For example, the Medusavirus genome contains all five eukaryotic histone proteins (H1, H2A, H2B, H3 and H4), which is the most for any known NCLDV species. It also contains a gene which codes for a DNA polymerase. Table 1 lists several eukaryotic genes which are present in both Medusavirus and its host. Although the Medusavirus DNA polymerase resembles ones found in eukaryotes, it didn’t particularly resemble animal (e.g. its host amoeba) or plant versions. Therefore, some evolutionists think that this polymerase gene arose early on, before eukaryotes evolved many millions of years ago.2 However, Medusavirus is also missing certain proteins, which are present only in the host genome, and which are necessary for DNA replication, for example DNA topoisomerase II and also a DNA-dependent RNA polymerase. The lack of these enzyme genes in Medusavirus implies that it is dependent on the host nucleus for DNA replication. Furthermore, since the Medusavirus DNA polymerase also has orthologs (genes with the same function) in plants and animals, this would argue for the conservation of genes, which is an oxymoron: evolution is the opposite of stasis or conservation.5

It is still a question as to what Medusavirus is exactly. The researchers who isolated this species claim that they isolated only Medusavirus from the hot springs, and not the amoeba2. This is because the hot springs would be too much of an extreme environment for the amoeba to survive in6. Thus, a giant question remains as to what the exact relationship is between Medusavirus and A. castellanii, apart from the amoeba being a host in which Medusavirus can be cultured. Medusavirus is likely not a true virus, but a degraded single-celled eukaryotic organism. The strongest evidence for this is its high eukaryotic gene content. This idea had been suggested by creation scientists about other large-sized “viruses”.7 This kind of organismal degeneration is like what we see in bacteria where wild bacteria undergo gene loss and become parasitic.8 Or, perhaps Medusavirus was designed to be a symbiotic regulator of the amoeba.

All we know is that we have a new species of NCLDV, distinct from all other NCLDV species, implying its special creation. Genetics again vindicates the Bible.

Table 1. Eukaryotic genes present in either the host (Acanthamoeba castellanii) and Medusavirus or just the host

GenePresent in
BCS1 host and Medusavirus
Cyclin B host and Medusavirus
deoxycytidylate deaminase host and Medusavirus
DNA primase host and Medusavirus
dUTPase host and Medusavirus
Family B DNA polymerase host and Medusavirus
GTP-binding Ras-related nuclear protein host and Medusavirus
Histones H1, 2A/B, 3, 4 host and Medusavirus
Holliday junction resolvase host and Medusavirus
Metacaspase host and Medusavirus
nucleoside diphosphate kinase host and Medusavirus
poly(A) polymerase regulatory subunit host and Medusavirus
Polymerase delta host and Medusavirus
Rho transcription termination factor host and Medusavirus
ribonuclease HII host and Medusavirus
ribonucleotide reductase (large and small subunits) host and Medusavirus
sliding clump proteins host and Medusavirus
thymidylate synthase host and Medusavirus
transcription elongation factor S-II host and Medusavirus
viral late transcription factors 2, 3 host and Medusavirus
DNA topoisomerase II host only
DNA-dependent RNA polymerase host only
mRNA capping enzyme host only

References and notes

  1. Zhang, S., Beware the Medusavirus, Atlantic, 20 March 2019. Return to text.
  2. Yoshikawa, G. et al., Medusavirus, a novel large DNA virus discovered from hot spring water, J. Virol., 2019 | doi:10.1128/JVI.02130-18. Return to text.
  3. O’Micks, J., Creation perspective of nucleocytoplasmic large DNA viruses, J. Creation 30(3):110–117, 2016. Return to text.
  4. Koonin, E.V., Senkevich, T.G., and Dolja, V.V., The ancient Virus World and evolution of cells. Biol Direct. 1:29, 2006. Return to text.
  5. Cserháti, M., Creation aspects of conserved non-coding sequences, J. Creation 21(2):101–108, 2007. Return to text.
  6. Dr. Masaharu Takemura, personal communication. Return to text.
  7. Wieland, C., and Batten, D. Creation in the research lab. Creation 21(2):16-17, March 1999. Return to text.
  8. O’Micks, J., Bacterial genome decay from a baraminological viewpoint, J. Creation 29(2):122–130, 2015. Return to text.

Readers’ comments

Peter H.
Fascinating. Thank you.

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