Monsters from the sewers

Giant viruses were called the product of "gene robbery"

Anna Kaznadzei, N+1

American scientists have described a new group of giant viruses that encode a variety of unusual genes, including a number of components of the translation apparatus, which were not previously described in viruses. Phylogenetic analysis has shown that such diversity does not support the theory of the cellular or independent origin of the virus domain, but is a consequence of an increase in the genome of smaller ancestors. The study was published in Science (Schulz et al., Giant viruses with an expanded complement of translation system components).

The origin of viruses is still a mystery. There are at least three hypotheses describing this process. According to the first, viruses were once small cells that parasitize inside larger ones, and have lost most of their own genes and, as a result, other organelles. According to the second hypothesis, viruses in the past were fragments of DNA or RNA of normal cells that separated from their hosts in the form of plasmids (small circular DNA that can be transmitted from cell to cell) or transposons (independent DNA elements that can move from place to place within the genome and replicate separately from the rest). According to the third hypothesis, viruses arose independently during the origin of life on the planet and from the very beginning lead a parasitic lifestyle.

Most of the known viruses have a diameter of up to 300 nm, but there are also so-called giant viruses reaching 300 nm or more (the record holder is the Pithovirus found in 2014 in the permafrost of Siberia, reaching 1.5 microns in length and 0.5 microns in diameter). Giant viruses are often carriers of genes atypical for their fellows, including genes of the translation apparatus necessary for protein synthesis. According to various hypotheses, they again could have arisen due to the simplification of the ancient cellular form, or due to the collection of genes from other organisms initially by small viruses.

Picture: Carla Schaffer / AAAS – VM

By examining the metagenomes of samples from the Austrian sewage treatment plants of the city of Klosterneuburg, scientists have discovered a new giant virus called Klosneuvirus. The collected genome of this species turned out to be large (1.57 MB). Meta-transcriptomic data have shown that at least 15% of the genes of this virus are working. The images obtained using electron microscopy suggested the presence of a typical icosahedral structure with a size of about 300 nm.

Based on the results of the search for relatives Klosneuvirus, among 7000 metagenomes, three were found, with sizes of 0.86 Mb (Indivirus) to 1.33 Mb (Hokovirus) and 1.53 Mb (Catovirus). In their genomes, scientists have identified about 2,500 new gene families that have never been described for viruses before. 355 of them were families known among eukaryotes, but only 14 such eukaryotic families were found in all four new viruses at the same time. This highlights the diversity of the Klosneuviruses group, and indicates that their hosts are most likely different. The taxonomic classification of the metagenome, made using the analysis of 18s RNA, showed that their hosts apparently belong to the Cercozoa type. This distinguishes Klosneuviruses from other giant viruses that parasitize amoebas from the genus Acanthamoeba, and once again emphasizes the importance of the methodology for studying viruses separately, without initial binding to the host.

Evolution of genomes and phylogenetic position of Klosneuviruses based on comparison of orthologous genes of giant viruses. The right panel reflects the number of mapped orthologs (from an article in Science).

Most of all, the new viruses were similar to viruses of the Mimiviridae family. The constructed phylogenetic trees allowed them to be placed between the Cafeteria roenbergensis virus (CroV) and the genus Mimiviruses. After that, scientists began to track the course of evolution, as a result of which these viruses presumably arose, starting with the last common ancestor of SroV, Mimiviruses and Klosneuviruses. Apparently, it was a virus with a small genome. The results of the analysis showed that over time, all three lines independently acquired more and more genes, and Klosneuviruses were particularly successful in their growth. At some points, genes were lost (perhaps such stages are associated with a change of host, scientists note), but, on average, the increase was stronger than the losses.

Interestingly, the presence of giant viruses related to Mimiviruses has already been predicted before. Scientists believed that the newly described species containing a large number of genes uncharacteristic for viruses would confirm the theory of the origin of viruses by simplifying cellular forms, but the phylogenetic data obtained during this study do not support it.

Many components of the translation system are encoded in the Klosneuvirus genome, including twenty-five transport RNAs with anticodons to at least fourteen different amino acids, as well as aminoacyl-tRNA synthetases with specificity to all major amino acids, translation initiation factors and many others. If they represented a jointly evolving group, separate from all other branches of the phylogenetic tree, this would indicate in favor of another hypothesis, according to which the virus domain arose independently and independently. However, it turned out that most of these components, according to comparative genomics, are collected from a variety of organisms, including amoebas and unicellular algae. Thus, Klosneuviruses evolved from small viruses that, with the course of evolution, gained more and more genes from various hosts, following the path of complication rather than simplification.

Why giant viruses need so many "looted" parts of the translational apparatus, despite the fact that ribosomal genes and RNA have never been found in viruses, remains unclear. Perhaps they come in handy when the hosts are trying to turn off their own translation system to cope with a viral infection.

Portal "Eternal youth" http://vechnayamolodost.ru  07.04.2017