Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages
Autor: | Rohan Kapoor, Jueliet Menolascino, Adele Crane, Cyril J. Versoza, Rithik Mehta, Saige Munig, Daniel Sackett, Tiana Hua, Makena Sy, Lillian Lloyd, Zeel Patel, Abraham Morais, Brandon Schmit, Susanne P. Pfeifer |
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Rok vydání: | 2021 |
Předmět: |
AcademicSubjects/SCI01140
genome annotation AcademicSubjects/SCI00010 Mycobacteriophage Mycobacterium smegmatis mycobacteriophages codon usage bias Genome Viral QH426-470 de novo assembly Biology Mycobacterium abscessus AcademicSubjects/SCI01180 phylogeny cluster K Genome Mycobacterium tuberculosis Genetics Humans Codon Usage Molecular Biology Genetics (clinical) Mycobacteriophages biology.organism_classification Genome Report Codon usage bias AcademicSubjects/SCI00960 Mycobacterium |
Zdroj: | G3: Genes|Genomes|Genetics G3: Genes, Genomes, Genetics, Vol 11, Iss 11 (2021) |
ISSN: | 2160-1836 |
Popis: | Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance. |
Databáze: | OpenAIRE |
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