The evolutionary implications of viral life

By Maryam Chaib de Mares

As biologists, we think about living things all the time, and yet is still tricky business trying to define life. In fact, there is no single defining property of life as we know it—all we can do currently is describe life as we know it on Earth. The issue becomes even trickier when you consider forms at the boundaries of life, such as viruses. Traditionally, viruses have been seen as parasitic genetic material. Because they can only reproduce within other living beings, viruses have been excluded from many definitions of life. Recently, many researchers have begun distinguishing between life and cellular life, and they argue that viruses are microorganisms whose lifestyle is restricted to intracellular parasitism. Regardless of their definition, it is agreed that viruses can infect organisms from all three domains of life (Bacteria, Archea, and Eukarya) and even other viruses. Therefore, viruses may influence the evolution of cellular organisms.

Chaib_EvolutionaryViralLife_bacteriophages_intext
Bacteriophages, viruses that infect bacteria, use an E. coli cell to reproduce and then burst out to infect other cells.

Nasir et al. explored the distribution of viral diversity among cellular organisms. They tested whether viruses with different replication strategies prefer certain hosts and contrasted virion morphologies (the shapes of the infective particles) of virus families infecting different domain groups. In a nutshell, their result show that specific groups of hosts have unique distributions of replicon types (A, below). For instance, Archaea completely lack RNA viruses, while Bacteria have only a few, and Eukaryotes such as vertebrates play host to numerous viruses of this type. Different types of viruses can also make big jumps between ‘divisions’ within a domain. The same virus can sometimes infect both plant and animal cells when these are linked by their mode of life, such as when. But some limits to ‘jumpiness’ seem to exist: viruses jump hosts over shorter evolutionary time spans. No modern virus is known to cross the barrier between domains.

Pie-charts show the abundance of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, ssRNA(+) and ssRNA(−), where + and – refer to the orientation of the strand relative to coding DNA, and retrotranscribing viruses in Archaea, Bacteria, and Eukarya, and within the major eukaryal divisions. Corresponds to Figure 1(A) in Nasir et al. (2014).
Pie-charts show the abundance of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, ssRNA(+) and ssRNA(−), where + and – refer to the orientation of the strand relative to coding DNA, and retrotranscribing viruses in Archaea, Bacteria, and Eukarya, and within the major eukaryal divisions. Corresponds to Figure 1(A) in Nasir et al. (2014).

More intriguing patterns emerge when you look at the distribution of viruses among hosts. They identified only 63 archaeoviruses – viruses exclusive to the archaeal domain –, in comparison to 1251 bacterioviruses and 2321 eukaryoviruses. These figures are biased: there are simply fewer archaeal species that have been screened for viral infections. Despite this bias, however, archaeoviruses clearly have more diverse shapes than bacterioviruses, with 4 unique virion shapes in Archaea versus only one in Bacteria. The results by Nasir et al. suggest that Archaea are likely infected by a greater number of viral lineages than Bacteria. They pose the invention of the peptidoglycan-containing cell wall in Bacteria as a potential explanation for this pattern: Fewer viruses have been able to cope with this barrier, resulting in the low diversity of bacterioviruses.

The different virion morphologies (virus shapes) found in the three domains of life, Bacteria, Archaea, and Eukarya. Corresponds to Fig. 1(B) in Nasir et al. (2014).
The different virion morphologies (virus shapes) found in the three domains of life, Bacteria, Archaea, and Eukarya. Corresponds to Fig. 1(B) in Nasir et al. (2014).

Nasir et al.’s study is largely descriptive and mostly presents trends that will have to be validated experimentally. Nevertheless, it is a thought-provoking piece of work that makes use of the best of our current knowledge. This study opens new avenues of research in a long overlooked field, the evolutionary implications of viral ‘life’. Several studies have demonstrated the role of viruses in introducing genetic diversity into their host genomes. But their work suggests other major potential roles of viruses in the evolution of other domains. For instance, they conjecture that RNA viruses could be one major trigger for the evolution of modern Archaea. Because RNA viruses infect both Bacteria and Eukarya, their ancestors likely originated from a putative ancient world of cells with RNA genomes and RNA viruses. Archaea, however, are only infected by viruses with DNA genomes. The pattern we observe points to the ancient existence of RNA viruses and suggests their loss from Archaea, since it is more likely they were lost in one domain than that they were gained independently in two. The authors propose that the complete absence of RNA viruses in Archaea may be due to the instability of RNA at high temperatures, since it is likely that the last common ancestor of Archaea was a heat-lover, or hyperthermophile.

The steaming waters of Silex Spring in Yellowstone National Park are just right for heat-loving Archaea, which cause the red color on the bank. Their preference for high temperatures may explain why no one has ever found an RNA virus that infects Archaea. (Image by Brocken Inaglory via Wikimedia Commons)

DNA viruses are more widely distributed Archaea and Bacteria, whereas in Eukarya, RNA viruses are predominant and exhibit unique virion types not observed in prokaryotic viruses. Eukaryoviruses are also unequally distributed in the major eukaryal groups. For example, fungi and plants (including algae) have few or none of the double-stranded DNA viruses that other eukaryotic lineages have. There, again, it seems that the evolution of cell walls forms a barrier against particular types of viruses.

Finally, the authors report a puzzling tendency for both viral genomes and virion shapes to get more diverse as their eukaryotic hosts get more complex. The authors go as far as to suggest a possible scenario of co-evolution between viruses and their hosts that may have led to organism complexity in the eukaryotic domain. However, it is not clear from the correlation alone whether the viruses have driven the increasing complexity of eukaryotes, the eukaryotes have driven the diversification of viruses, or some other factor has caused them both to become more complex. Surely, this ever increasing data will continue to spawn interesting hypotheses, but, above all, these findings should urge us to develop better model systems that will allow us to test hypotheses emerging from these data.

Maryam Chaib de Mares is a graduate student at the University of Groningen in the Netherlands.

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