Later On

A blog written for those whose interests more or less match mine.

Giant Viruses and the Tree of Life

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Patrick Forterre writes in Inference:

SCIENTISTS HAVE ALWAYS thought viruses much smaller than bacteria. And with good reason. Most bacteriophages are 100 times smaller than the bacteria that they infect. Bacteria can be viewed under an optical microscope; but an electron microscope is required in order to see a viral particle. When giant viruses were discovered in 2003, they came as a surprise. The giant mimivirus, for example, had actually been discovered in 1992, but misidentified as a bacterium—Bradfordcoccus.1 The confusion was understandable. Mimivirus particles are 750 nanometers long—easily visible with an optical microscope; and, what is more, the dye used to reveal bacterial cell walls also stained mimivirus particles.

A number of other monster viruses have been discovered in the last decade.2 Most of them have been isolated and described by Didier Raoult and Jean-Michel Claverie in Marseille. If Marseille is now the Mecca of giant virus research, Vancouver is something of a mini Mecca. It is there that Curtis Suttle and his team isolated and described both Cafeteria roenbergensis and Bodo saltans.3 Most giant viruses observed in the laboratory have been studied in amoebae,4 but giant viruses are found in extraordinarily diverse terrestrial and aquatic environments.5 Some infect algae, and there is some suspicion that the mimivirus infects human cells as well.6 All giant viruses infect eukaryotes.

Viruses closely related to the mimivirus have been grouped into the family Mimiviridae. The other giant viruses have been classified into three families: MolliviridaePandoraviridae, and Pithoviridae.

Mimiviridae and Molliviridae produce virions, or viral particles, with a characteristically icosahedral shape. Pandoraviridae and Pithoviridae produce strange ovoid particles that have often been confused for intracellular protists.7 One of the most unusual of the giant viruses is a member of Mimiviridae. Discovered in Brazil, the Tupanvirus contains a virion featuring a gigantic head and an equally gigantic membranous tail. Such a shape is without precedent in the viral world.

Giant viruses contain linear or double-stranded DNA that encode for 500 to 2,500 proteins. The Pandoravirus encodes 2,000 genes, which is only 10 times fewer than a human cell, and, at roughly 2.5 million base pairs, its genome is the largest of any known virus. The mimivirus genome encodes about half that number. Produced by a Pithovirus, the largest known virion is an ovoid particle with a length of 1.5 micrometers and a width of 0.5 micrometers. The size of a virion and the size of its genome are not necessarily correlated. They are no good guide to the threshold beyond which a virus is counted giant.8

Five years after giant viruses were discovered, researchers learned that giant viruses can themselves become infected by smaller viruses.9 The virophages that infect them have genomes that code for only about twenty genes. These virophages, unable to infect amoebae by themselves, are transported inside amoebae by their giant virus hosts.10 Once inside, the virophages transcribe and replicate their genes using the machinery of the giant virus, the giant virus then using the amoeba’s machinery to transcribe and replicate its own genes.11 The three known virophages—Mavirus, Sputnik, and Zamilon—happen to infect members of the Mimiviridae family, but virophages targeting other giant viruses are likely to be identified.


THE DISCOVERY OF giant viruses and their virophages immediately reopened an old question: are viruses alive? Viruses had been excluded from the tree of life because they lacked the machinery needed either to reproduce or to synthesize proteins. A virus must hijack a cell before it can do either. But when scientists realized that viruses are more complex than originally presumed—encoding several thousand genes and becoming infected by other viruses—they began to suspect that viruses might be alive after all. When a virophage infects a Mimiviridae, it seems to become ill, its virions manifesting an abnormal morphology.

How can something be ill if it is not alive?12

Viruses had been excluded from living systems for another reason. They did not seem to share proteins that are universal across the three cellular domains: Archaea, Bacteria, and Eukarya. Yet many giant viruses do encode universal proteins, including RNA polymerase, some aminoacyl tRNA synthetases, and a few proteins involved in protein synthesis or DNA replication. Some phylogenetic analysts now place giant viruses in a fourth monophyletic group somewhere between Archaea and Eukarya.13 For all that, the fact remains that giant viruses lack the capacity to synthesize their own proteins without parasitizing a cell. Purificación López-García and David Moreira have thus disputed the phylogenetic analysis behind the phylogenetic analysts, arguing that the giant viruses are nothing more than genetic pickpockets, their genes acquired from a cellular origin in yet another triumph of theft over honest toil.14

Chantal Abergel and Claverie have also argued for the cellular origin of viral genes. But they have noticed, in addition, that most of the genes that giant viruses encode lack homologues in both modern cellular organisms and giant viruses from other families. Giant viruses, they suggest, might have arisen by regressive evolution—features lost instead of gained—from cellular lineages that diverged from modern cellular organisms before the advent of the last universal common ancestor of Archaea, Bacteria, and Eukarya. Claverie predicts that, as new giants are discovered, the distinction between viruses and cells will blur even further.15

Virus, Virion, and Virocell

WHEN IN DOUBT, define. The existence of giant viruses prompted virologists to search for a definition that could encompass the whole range of viruses, from the smallest, with genomes encoding two genes, to the largest, encoding thousands. All viruses produce virions—a viral particle consisting of a core of nucleic acid surrounded by a capsid protein shell.16 It is the capsid that distinguishes viruses from other mobile genetic elements, such as plasmids. The smallest virus and the smallest plasmid both have one gene coding for a replication protein. The virus has an additional gene that codes for a capsid.17

All virions have at least one capsid. For this reason, Raoult and I initially suggested defining viruses as capsid-encoding organisms.18 Some small virions are formed by one or more DNA- or RNA-binding proteins; others, by several capsid proteins, with a lipid membrane inside or outside the shell. The virions of giant viruses are elaborate structures involving hundreds of proteins and a lipid membrane that is often decorated with polysaccharide extensions. Virions and viruses are not the same thing. Confusion between the two is pervasive. The confusion is easy to understand. Virions can be easily isolated, they are infectious, and they can be photographed.

But they are not viruses.

Claverie was the first to emphasize the distinction.19 Within the cytoplasm of an infected cell, the mimivirus produces a large compartment called a viral factory, where the viral DNA, while being transcribed and replicated, is shielded from the cell’s defense mechanisms. Many RNA and DNA viruses produce viral factories.20 But in the mimivirus, the factory is huge—the size of the infected amoeba’s nucleus. Claverie suggested that the viral factory is the actual virus, and that virions are the equivalent of the spores or gametes of cellular organisms.21

After Claverie published this argument, I observed that bacterial and archaeal viruses do not produce an isolated viral factory inside the cytoplasm of the infected cell: they transform the entire cell into a factory.22 I suggested calling the infected cell a virocell.23 Adopting Claverie’s idea, I argued that . . .

Continue reading. There’s more.

Written by Leisureguy

14 September 2021 at 1:07 pm

Posted in Evolution, Science

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