Genome Sequences of Five B1 Subcluster Mycobacteriophages

Breakwell, Donald P.; Barrus, E. Zane; Benedict, Alex B.; Brighton, Alicia K.; Fisher, Joshua N. B.; Gardner, Adam; Kartchner, Brittany; Ladle, Kara C.; Lunt, Bryce L.; Merrill, Bryan D.; Morrell, John D.; Burnett, Sandra H.; Grose, Julianne H.

doi:10.1128/genomea.00968-13

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“…While isolating mycobacteriophages from the soil samples collected from different regions in and around Delhi, India, using M. smegmatis (mc 2 155) as the bacterial host, we found B1 phages to be more in number (a frequency of 1 in 3). Information on B1 phages is available in a few earlier reports (10)(11)(12)(13), however a detailed insight into their genome and experimental data is limited. In this study, 30 new mycobacteriophages were isolated from 160 soil samples and were screened by a PCR-based method (14) for cluster classification, where primers specific to a conserved region in the tape measure protein of B1 sub-cluster phages were used.…”

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confidence: 99%

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

Das,

Arora,

Nadar

et al. 2023

Preprint

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BackgroundA large number (about 1200) of mycobacteriophages (phages) have been isolated onMycobacterium smegmatismc2155. Their genome analysis shows high sequence diversity; therefore, based on nucleotide sequence similarity and genomic architecture, the related phages have been grouped in clusters and sub-clusters. However, a deeper study of mycobacteriophages has been conducted only for a few clusters. This study explores the traits of phages belonging to the B1 sub-cluster. We have attempted to functionally annotate and experimentally characterize B1 phages to get an insight into their biology and explore their therapeutic potential.MethodsAnalysis of B1 sub-cluster phage genomes to understand their key characteristics & lifestyle and to determine the putative function of hypothetical proteins (HPs), we developed a framework with a specific set of computational tools available online. For the experimental characterization, mycobacteriophages were isolated from environmental samples and were examined for their morphology, lysogeny status, effect on biofilm and activity against drug-resistantM. smegmatis. The B1 sub-cluster phages were identified by PCR using the specific primers.ResultsWe have predicted the function of about 55% of the 77 representative proteins in B1 phages, which were previously deemed hypothetical. We studied ten B1 phages (Phages 1-10)which included their morphological characteristics, lysogeny status and antibiofilm activity. TEM analysis, showing an average head & tail size of 65 nm and 202.12 nm, respectively. The turbid morphology of several plaques suggested these phages to be temperate. To verify, we tested their potential to lysogenizeM. smegmatisand later found the spontaneous release from the putative lysogens. Interestingly, a putative RepA-like protein was identified in B1 phage genomes, indicating a possibility of extrachromosomal replication of prophages. Further, the impact ofPhages 1-10onM. smegmatisbiofilm was found to be potent; the highest inhibitory and disruptive effect of phages (at a fixed titre of 108pfu/ml) was 64% and 46%, respectively. Also, all ten phages could kill 4XR1 (the isoniazid-resistantM. smegmatisstrain).ConclusionWe believe this combination of experimental analysis and exploration of genomic features of mycobacteriophages belonging to a sub-cluster can provide deeper insights into mycobacteriophage biology and also help in understanding their therapeutic potential.

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