A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy

Amaya, I.; Edwards, K.; Wise, B. M.; Bhattacharyya, A.; Pablo, C. H. D.; Mushrush, E.; Coats, A. N.; Dao, S.; Dittmar, G.; Gore, T.; Jarva, T. M.; Kenkebashvili, G.; Rathan-Kumar, S.; Reyes, G. M.; Watts, G. L.; Watts, V. K.; Dubrow, D.; Lewis, G. S.; Stone, B. H.; Xue, B.; Cresawn, S. G.; Mavrodi, D.; Sivanathan, V.; Heller, D.

doi:10.1101/2023.06.21.545952

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bioRxiv · 10.1101/2023.06.21.545952

A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy

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Abstract

During infection, bacteriophages produce diverse gene products to overcome bacterial anti-phage defenses, to outcompete other phages, and take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing 25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known anti-mycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Elucidation by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.

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Amaya, I., Edwards, K., Wise, B. M., Bhattacharyya, A., Pablo, C. H. D., Mushrush, E., Coats, A. N., Dao, S., Dittmar, G., Gore, T., Jarva, T. M., Kenkebashvili, G., Rathan-Kumar, S., Reyes, G. M., Watts, G. L., Watts, V. K., Dubrow, D., Lewis, G. S., Stone, B. H., Xue, B., Cresawn, S. G., Mavrodi, D., Sivanathan, V., Heller, D.. 2023-06-21. A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy. https://doi.org/10.1101/2023.06.21.545952

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