Homologs of RNA ligase 2 of the bacteriophage T4 in metagenomes of ocean microbiota

A. A. Zimin ; N. A. Nikulin ; N. N. Nazipova

Matematičeskaâ biologiâ i bioinformatika, Tome 14 (2019) no. 2, pp. 683-704.

Résumé

RNA ligase 2 from a T4 phage RNA ligase 2 is a unique enzyme that is, unlike other RNA ligases, functionally similar to the DNA ligases, as well as it is related to editing RNA ligases of parasitic Trypanosoma and Leishmania. RNA ligases 2 are present in a limited (small) number of genomes, which, moreover, are strongly scattered throughout the tree of life. A search was made for homologs of T4 phage RNA ligase 2 in the databases of pelagic oceanic genetic data (GOS) and deep-sea sedimentary microbiota (LCGC14). In the metagenomes of the pelagic and sedimentary deep-water microbiota, 6 and 15 homologs, respectively, of RNA ligase 2 of bacteriophage T4 were found , suitable for analysis. Phylogenetic analysis of the detected amino acid sequences showed that most of them are similar to the homologs of RNA ligase 2 from bacteria and fungi. Five homologues of oceanic origin were found on a branch of a phylogenetic tree common to homologs from Tevenvirinae subfamily and Euglenozoa phylum. This result indicates the presence both in the water column of the open ocean and at its bottom of new, still unknown, organisms whose genomes encode this rare enzyme.

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