Scientists have isolated from the metagenomic data genome 501 new large nuclear-cytoplasmic DNA-containing viruses (subgroup of giant viruses) and built their phylogenetic tree. Giant virus found genes that are associated with many metabolic pathways: nutrition, photosynthesis, nitrogen metabolism and even carbon metabolism (including glycolysis and the Krebs cycle). Metabolism genes were derived from cellular organisms in the distant past, evolved and acquired specific groups of viruses features. Thus, giant viruses may have the power to rebuild the livelihoods of the infected cell. Article published in the journal Nature Communications.
Large nuclear-cytoplasmic DNA viruses (NCLDV) — a group of giant viruses of eukaryotes, it consists of several families whose representatives are very large (up to 1.5 micrometers — they can be visible even in optical microscope) and have a large genome (approximately 2.5 million bases). Giant viruses are including a set of metabolic genes, they encode proteins that are involved, for example, in nitrogen metabolism and fermentation. Likely, these genes contribute to changing physiology of the host cell. Most likely, the majority of metabolism genes of viruses are borrowed from cellular organisms as a result of horizontal gene transfer, however, the origin of most of them and how they are characteristic of the NCLDV genomes is unknown.
A group of scientists from the United States under the leadership of Muhammad Moniruzzaman (Mohammad Moniruzzaman) from the Polytechnic University of Virginia was looking for NCLDV genomes in 1545 public metagenomic samples. Were selected those stretches of DNA that contained at least four out of five genes characteristic of the NCLDV, and was not less than 100 thousand base pairs.
121 using the genome of known viruses, the authors constructed a phylogenetic tree, and then confirmed this classification by analyzing the similarity of amino acids and the sizes of genomes. In order to evaluate the evolutionary relationships of the treasure, found the group orthologic proteins (homologous, but diverged during the evolution).
Scientists were able to identify 501 new genome from samples from 400 to 1400 thousand pairs of bases, a large part came from samples of marine and freshwater bodies (444 and 36, respectively). A large part of the genome attributed to the family of mimivirus (Mimiviridae) or phycodnaviruses (Phycodnaviridae), among the latter identified two monophyletic subgroups. The analysis of similarity of the amino acids showed large variation (from 26 to 100 percent), even within the same family, so the researchers divided existing groups 54 a narrower treasures. Interestingly, for 31 hoards not isolated in culture representatives.