TY - JOUR

T1 - Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes

AU - Babkin, Igor

AU - Tikunov, Artem

AU - Morozova, Vera

AU - Matveev, Andrey

AU - Morozov, Vitaliy V

AU - Tikunova, Nina

N1 - Virome sequencing, genome assembly, annotation, and analysis were funded by the Russian Science Foundation; Project No. 21-14-00360. Phylogenetic analysis and 3D modeling were supported by the Ministry of Education and Science, Project No. 121031300043-8.

PY - 2023/10/18

Y1 - 2023/10/18

N2 - Metagenomics provides detection of phage genome sequences in various microbial communities. However, the use of alternative genetic codes by some phages precludes the correct analysis of their genomes. In this study, the unusual phage genome (phAss-1, 135,976 bp) was found after the de novo assembly of the human gut virome. Genome analysis revealed the presence of the TAG stop codons in 41 ORFs, including characteristic phage ORFs, and three genes of suppressor tRNA. Comparative analysis indicated that no phages with similar genomes were described. However, two phage genomes (BK046881_ctckW2 and BK025033_ct6IQ4) with substantial similarity to phAss-1 were extracted from the human gut metagenome data. These two complete genomes demonstrated 82.7% and 86.4% of nucleotide identity, respectively, similar genome synteny to phAss-1, the presence of suppressor tRNA genes and suppressor TAG stop codons in many characteristic phage ORFs. These data indicated that phAss-1, BK046881_ctckW2, and BK025033_ct6IQ4 are distinct species within the proposed Phassvirus genus. Moreover, a monophyletic group of divergent phage genomes containing the proposed Phassvirus genus was found among metagenome data. Several phage genomes from the group also contain ORFs with suppressor TAG stop codons, indicating the need to use various translation tables when depositing phage genomes in GenBank.

AB - Metagenomics provides detection of phage genome sequences in various microbial communities. However, the use of alternative genetic codes by some phages precludes the correct analysis of their genomes. In this study, the unusual phage genome (phAss-1, 135,976 bp) was found after the de novo assembly of the human gut virome. Genome analysis revealed the presence of the TAG stop codons in 41 ORFs, including characteristic phage ORFs, and three genes of suppressor tRNA. Comparative analysis indicated that no phages with similar genomes were described. However, two phage genomes (BK046881_ctckW2 and BK025033_ct6IQ4) with substantial similarity to phAss-1 were extracted from the human gut metagenome data. These two complete genomes demonstrated 82.7% and 86.4% of nucleotide identity, respectively, similar genome synteny to phAss-1, the presence of suppressor tRNA genes and suppressor TAG stop codons in many characteristic phage ORFs. These data indicated that phAss-1, BK046881_ctckW2, and BK025033_ct6IQ4 are distinct species within the proposed Phassvirus genus. Moreover, a monophyletic group of divergent phage genomes containing the proposed Phassvirus genus was found among metagenome data. Several phage genomes from the group also contain ORFs with suppressor TAG stop codons, indicating the need to use various translation tables when depositing phage genomes in GenBank.

KW - Humans

KW - Bacteriophages/genetics

KW - Virome

KW - Codon, Terminator/genetics

KW - Genome, Viral

KW - Genetic Code

KW - RNA, Transfer/genetics

KW - Phylogeny

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85175272372&origin=inward&txGid=19f1769a246512b6ab1e235fb75d8a87

U2 - 10.3390/ijms242015302

DO - 10.3390/ijms242015302

M3 - Article

C2 - 37894982

VL - 24

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 20

M1 - 15302

ER -