Genome Analysis of Epsilon CrAss-like Phages

CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found....

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Bibliographic Details
Published in:Viruses Vol. 16; no. 4; p. 513
Main Authors: Babkin, Igor V., Tikunov, Artem Y., Baykov, Ivan K., Morozova, Vera V., Tikunova, Nina V.
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 27.03.2024
MDPI
Subjects:
Amino acids
Analysis
Bacteriophages
Bacteriophages - classification
Bacteriophages - genetics
Comparative analysis
crAss-like phages
diversity-generating retroelements
DNA
DNA polymerase
DNA polymerases
DNA primase
DNA Primase - genetics
DNA Primase - metabolism
DNA, Viral - genetics
domain
ecological balance
Ecology
family
Genes
Genetic aspects
Genetic diversity
Genetic Variation
genome
Genome, Viral
Genomes
Genomics
Genomics - methods
humans
intestinal microorganisms
lifestyle
Microbiomes
monophyly
Nucleotide sequence
Phages
Phylogeny
Primase
Prophages - genetics
Protein binding
Proteins
Repressors
repressors/anti-repressors
Retroelements
reverse transcriptase
RNA polymerase
RNA-directed DNA polymerase
RNA-Directed DNA Polymerase - genetics
RNA-Directed DNA Polymerase - metabolism
sequence analysis
Software
Transfer RNA
Viral Proteins - genetics
Viral Proteins - metabolism
virus taxonomy
Russia
United States > US
genome
repressors/anti-repressors
virus taxonomy
reverse transcriptase
diversity-generating retroelements
crAss-like phages
ISSN:1999-4915, 1999-4915
Online Access:Get full text
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Summary:CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
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ISSN:1999-4915
1999-4915
DOI:10.3390/v16040513