Research output: Contribution to journal › Article › peer-review
Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes. / Babkin, Igor; Tikunov, Artem; Morozova, Vera et al.
In: International Journal of Molecular Sciences, Vol. 24, No. 20, 15302, 18.10.2023.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 57531115