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November 19, 2012

Virus in the Room

I am the Lorax, I speak for the trees. I speak for the trees, for the trees have no tongues, and I'm asking you, sir, at the top of my lungs.
from The Lorax by Dr. Seuss

by Welkin Johnson

Figure1
Figure 1: A non-virus. Source.

As biologists, we divvy the biological realm up into domains using a formula that frankly, smacks of nepotism, bestowing three glorious domains upon our closest relatives—the Eucaryota, the Archaea, and the Bacteria—while committing an injustice to the so-called viruses, lumping them together in a miscellaneous catch-all category (“viruses” from Latin for poison and other noxious substances) with contemptible disregard for phylogeny or any true measure of diversity.

Imagine that viruses, like Dr. Seuss’s Truffula Trees, had a vocal advocate like The Lorax. Undoubtedly, through the agency of their outspoken mouthpiece, they would protest these gerrymandered borders and laugh at our skewed notions of biological diversity. After all (the viruses would argue), just consider the platypus, the coelacanth, the earthworm, and the bacillus. All these organisms have double-stranded DNA genomes, whose lengths all fall within roughly the same order of magnitude, which they replicate using evolutionarily customized versions of what amounts to the same basic enzymatic apparatus. How boring! How unimaginative! Now consider this (the viruses go on to say): the giant Mimivirus, 1256 nm of girth enfolding >1,000,000 base pairs of DNA, and the tiny Circovirus, with a mere 1,800 bases of single-stranded DNA tucked inside a 20nm-wide shell, are neither more nor less related to one another than either one is to an elephant! (For those who are not familiar with the elephant, it is a relative of the platypus, the coelacanth, the earthworm, and the bacillus)

Figure2
Figure 2: The virus scale. Some representative viruses are shown, arranged according to genome size. Collectively, viral genome lengths span three orders of magnitude.

Let us thumb through the catalogue of viral genomes: here we find the familiar double-stranded DNA, including both linear and circular genomes, but also some with not-so-familiar twists—poxviruses, for example, covalently closing both ends of their linear double-stranded DNA genomes. We also find an abundance of themes not found anywhere among the domains of cellular ife: thus, there are viruses with single-stranded DNA genomes, and viruses with single-stranded RNA genomes, the latter including some that are negative-sense, some positive-sense, and some part positive and part negative (ambisense). Additionally, there also viruses with double-stranded RNA genomes, and if that isn’t bizarre enough, there are viruses with segmented RNA genomes (to which the influenza virus, whose virions incorporate a precise complement of eight different RNA segments [figure 3], will bear witness).

Figure3
Figure 3: Images of influenza virions Note the eight individually packaged genome segments within each virion. Each of these encodes a different protein or proteins, all of which are essential to the virus. Source.

Equally impressive are the Reoviruses with genomes composed of a dozen different segments of double-stranded RNA. Replicate that! And there are retroviruses, whose genomes are sometimes RNA (in the virion), and at other times double-stranded DNA (upon entering a host cell). Hepadnaviruses, possible cousins to the retroviruses, have gapped double-stranded DNA genomes with a bit of RNA thrown in, which they, too, convert to DNA by means of reverse transcriptase.

This diversity of genome styles each comes with its own uniquely-tailored replication system dictated in part by the need (shared by all viruses) to generate mRNA (because all viruses rely on host cells for translation). Importantly, there is very little if any phylogenetic evidence for a common ancestry connecting all the different viral types, or for grouping viruses together. Attempts to prove the existence of a last universal common ancestor of all viruses may be folly, as it is entirely possible that no such ancestor ever existed (that is, what we lump together as “viruses” actually represent uniquely evolved biological entities that happen, just by chance, to have taken on obligate intracellular parasitism as a mode of existence). At best, and by stretching the limits of phylogenetic comparisons, some of the RNA viruses can be combined into hypothetical “supergroups”.

Figure4 Figure 4: The Baltimore Classification system. The Baltimore scheme is a nifty tool for memorizing the steps each kind of virus must take in order to use the translation machinery of its host’s cell. Thus far, all known viruses (including bacteriophage) fit into one of the seven categories. Modified from: Source.

The tables thus turned, the viruses demand a fair redistricting, with the viral realm to include no fewer than seven domains to our three. They also ask that we wear name-tags, since they are having trouble remembering how to tell an elephant from a bacillus.

 

Welkin

Welkin Johnson is on the faculty of Boston College and an associate blogger of Small Things Considered.

Comments

I love this article and am so glad it ran in Microbe because I missed it online.

Giant DNA viruses are in line for a domain all their own --and once that glass ceiling is breached who knows what else will happen? Maybe other viruses will be lined up for domains as well.

Here's a link to the giant virus website: http://www.giantvirus.org/ Talented little fellows.

Wow, just wow. I had no idea of how much variation is in viruses. Would it be fair to say then that maybe the one common characteristic of all viruses, namely their dependence of a cellular host is a result of multiple examples of convergent evolution? Thanks for the post!

The variety of replication strategies exhibited by viruses brings to mind the variety of body plans found among the organisms of the Cambrian explosion, as described by Stephen J. Gould in his book, Wonderful Life. In the same way that the majority of those body plans became evolutionary dead ends and are no longer represented in nature, could the unusual viral replication strategies be leftovers from a time when a whole slew of strategies were tolerated, most of which became dead ends except for those that escaped extinction through obligate intracellular parasitism? Fun to think about . . .

Agreed. But what impresses me is that all viruses have to achieve the same result (an absolutely unbroken chain of transmission from one host to the next, indefinitely). How does a Circovirus do the same thing as a Mimivirus (and do it just as well) with 1/1000th the genome? That thing is barely the equivalent of a single gene!

To be fair, as far as physical size and genome size go, cellular life has an even wider range than viruses. 160 kbp to 150 Gbp currently. Although one might argue that plants cheat when it comes to genome size, what with all the polyploidy going on...

But, as you say, our core biochemistry is all sadly unimaginative, compared to viruses.

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