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About viruses and viral disease
On episode #261 of the science show This Week in Virology, Vincent meets up with Chantal and Jean-Michel at the first International Symposium on Giant Virus Biology in Tegernsee, Germany, to discuss their work on Mimivirus, Megavirus, and Pandoravirus.
You can find TWiV #261 at www.microbe.tv/twiv.
The discovery of the giant Mimivirus and Megavirus amazed virologists (and also many others). Their virions (750 nanometers) and DNA genomes (1,259,000 base pairs) were the biggest ever discovered, shattering the notions that viruses could not be seen with a light microscope, and that viral genomes were smaller than bacterial genomes. Now two even bigger viruses have been discovered, which are physically and genetically unlike any previously known viruses. They have been called Pandoraviruses.
Both new viruses were isolated by culturing environmental samples in the amoeba Acanthamoeba castellani. Pandoravirus salinus was isolated from shallow marine sediment in a river at the coast of central Chile, and Pandoravirus dulcis was obtained from mud at the bottom of a freshwater pond near Melbourne, Australia. The P. salinus genome is at least 2.77 megabases in length (there is some uncertainty in the actual length due to the presence of repeated sequences at the ends of the DNA), while the P. dulcis genome is 2.47 megabases in length. The smaller P. dulcis genome is a subset of the P. salinus genome.
These new genomes are twice as large as those of previously described viruses, and bigger than the genomes of intracellular bacteria such as Tremblaya (138,927 base pairs) and Rickettsia (1,111,523 bp), some free living bacteria, and many free living Archaea.
While the huge sizes of the Pandoravirus virion and genomes are amazing, I find three other features of these viruses even more remarkable. The first is their atypical replication cycle. The virions are taken into amoebae by phagocytic vacuoles, and upon fusing with the vacuole membrane, the virion contents are released into the cytoplasm via a pore on the virion apex. Within 2-4 hours the cell nucleus is reorganized, and by 8-10 hours new particles appear where the nucleus once was. Pandoravirus DNA and virions are synthesized and assembled simultaneously, in contrast to eukaryotic DNA viruses and phages which fill pre-formed capsids with DNA. Virions are released by 10-15 hours as the cells lyse.
A second amazing feature is that most of the P. salinus open reading frames encode brand-new proteins. Of the 2,556 putative protein coding sequences in the P. salinus genome, 93% have no recognizable counterparts among known proteins. Some of the genes found in large DNA viruses are present, such as those encoding DNA polymerase and DNA-dependent RNA polymerase, and several amino acyl-tRNA synthetases, like members of the Megaviridae. Curiously, many of the Pandoravirus coding regions contain intervening sequences, which must be removed by RNA splicing. This process is known to occur only in the cell nucleus, suggesting that some Pandoravirus transcription occurs in that organelle. The lack of gene homology leads to authors to conclude that ‘no microorganism closely related to P. salinus has ever been sequenced’.
I am also impressed by what the authors describe as the ‘alien morphological features’ of the virions. The oval-shaped particles are 1 micron in length and 0.5 microns in diameter, easily visible by light microscopy. They are wrapped in a three-layered envelope with a pore at one end of the particle, and resemble nothing that has ever been seen before (see photograph).
How much bigger can viruses get? I don’t know the answer but I would guess even bigger than Pandoraviruses. The membranous Pandoravirus particle could easily accommodate even larger genomes. How big can a virus get and still be a virus? The answer to that question is easy: it is a virus as long as it requires a cell for replication.
These remarkable findings further emphasize the need for scientists to pursue their curiosity, and not only work on problems of obvious medical relevance. As the authors write,
This work is a reminder that our census of the microbial diversity is far from comprehensive and that some important clues about the fundamental nature of the relationship between the viral and the cellular world might still lie within unexplored environments.
Continuing their playful naming of giant viruses, the authors note that the name Pandoravirus reflects their ‘lack of similarity with previously described microorganisms and the surprises expected from their future study’.
The mantle of world’s biggest virus has passed from Mimivirus to Megavirus. But in this case, size doesn’t matter. It’s the genes that these viruses share and do not share that make this story important.
The discovery of Mimivirus in a French cooling tower amazed virologists. At 750 nanometers in diameter, it dwarfed all other known viruses and shattered the notion of viruses as ‘filterable agents’. That definition came from using filters that exclude any particle larger than 200 nanometers. The 1.2 million base pair Mimivirus DNA genome was found to encode 979 proteins – more than any other virus. This treasure chest included some proteins never found in any viral genome, such as amino-acyl tRNA synthetases, the enzymes that attach amino acids to transfer RNAs in preparation for protein synthesis. Many other cellular genes were also encoded in the Mimivirus genome, as well as proteins that had never been seen before. This discovery led to the idea that Mimivirus evolved from an ancestral cellular organism by losing genes. The alternative idea is that viruses are ‘pickpockets’ – they began as small pieces of DNA that escaped from cells, acquired a capsid, and then slowly stole genes from other organisms.
The problem with the idea that Mimivirus is a gene loser is that it was the only really big virus of its kind – until Megavirus was discovered in the ocean off the coast of Chile. At 680 nm in diameter, Megavirus is slightly smaller than Mimivirus, but the DNA genome is larger – 1,259,197 base pairs versus 1,182,000. The Megavirus genome encodes 1,120 putative proteins compared with 979 for Mimivirus. What is significant about Megavirus is that its genome resembles that of Mimivirus, including the presence of cellular genes such as those encoding amino-acyl tRNA synthetases. Also important is the fact that 258 of the Megavirus proteins have no counterparts in Mimivirus, including three amino-acyl tRNA synthetases.
When Mimivirus was first discovered, it was not clear if it was an anomaly, or if it would provide information on the emergence of viruses. Other giant viruses were subsequently discovered, but they were either nearly identical to Mimivirus (Mamavirus) or little genome sequence was available (Terra, Courdo, Moumou). The evolutionary distance of Megavirus and Mimivirus is sufficient to allow identification of similar features and the selection forces that lead to their emergence. A comparison of their DNA sequences reveals a set of genes in common between the two viruses, such as those that function during protein synthesis. These observations suggest that Megavirus and Mimivirus arose from a common cellular ancestor – one that could carry out protein synthesis – and lost the genes that were no longer needed. The alternative scenario, that these giant viruses started out small and acquired additional genes, seems unlikely. Seven different gene acquisition events would have been needed to acquire just the genes encoding amino-acyl tRNA synthetases.
More details about how Megavirus and Mimivirus emerged from a cellular ancestor will require the isolation of other giant DNA viruses. Which leads to the inevitable question – what is the biggest virus on earth? Have we reached the limit of viral genome size? Probably not, but I doubt that we will find viruses with much larger genomes that encode almost all the genes needed for independent replication. Such viruses likely evolved from primitive cells a very long time ago, and only the evolutionary descendants remain on Earth today.
If you are wondering how these giant viruses are named, the authors provide revealing background:
We believe it is useful and desirable that the name of a newly isolated microorganism convey some of its most distinctive properties. After the initial naming of Mimivirus (for “microbe mimickingâ€), already not a very good name because the prefix “mimi†does not convey a helpful scientific notion, newly isolated related viruses are receiving increasingly random/funny names such as “Mamavirus,†“Moumouvirus,†“Courdovirus,†and “Terraâ€. …we believe the current trend is counterproductive and should give way to more informative names….a distinctive feature of the above giant viruses (or of their close ancestors) is to possess genome in excess of a “megabaseâ€. Hence, the term “Megavirus,†and the proposed family/genus “Megaviridae†that will be proposed… “Chilensis†then refers to the location where this virus was first isolated.
The authors did not incorporate the species of the viral host in the name of the virus. They justify this break with tradition because the natural host of  Megavirus chilensis is not known – it was isolated from the ocean by co-culture with acanthamoeba, a procedure the authors will continue to use to identify giant DNA viruses.
Arslan D, Legendre M, Seltzer V, Abergel C, & Claverie JM (2011). Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proceedings of the National Academy of Sciences of the United States of America, 108 (42), 17486-91 PMID: 21987820