Characterization and genomic analysis of the Lyme disease spirochete bacteriophage phiBB-1

Faith, D. R.; Kinnersley, M.; Brooks, D. M.; Drecktrah, D.; Hall, L. S.; Luo, E.; Santiago-Frangos, A.; Wachter, J.; Samuels, S.; Secor, P. R.

doi:10.1101/2024.01.08.574763

bioRxiv · 10.1101/2024.01.08.574763

Characterization and genomic analysis of the Lyme disease spirochete bacteriophage phiBB-1

Faith, D. R.·Kinnersley, M.·Brooks, D. M.·Drecktrah, D.·Hall, L. S.·Luo, E.·Santiago-Frangos, A.·Wachter, J.·Samuels, S.·Secor, P. R.

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Abstract

Lyme disease is a tick-borne infection caused by the spirochete Borrelia (Borreliella) burgdorferi. Borrelia species have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids some of which are required throughout the enzootic cycle. Included in this plasmid repertoire by almost all Lyme disease spirochetes are the 32-kb circular plasmid cp32 prophages that are capable of lytic replication to produce infectious virions called {phi}BB-1. While the B. burgdorferi genome contains evidence of horizontal transfer, the mechanisms of gene transfer between strains remain unclear. While we know that {phi}BB-1 transduces cp32 and shuttle vector DNA during in vitro cultivation, the extent of {phi}BB-1 DNA transfer is not clear. Herein, we use proteomics and long-read sequencing to further characterize {phi}BB-1 virions. Our studies identified the cp32 pac region and revealed that {phi}BB-1 packages linear cp32s via a headful mechanism with preferentially packaging of plasmids containing the cp32 pac region. Additionally, we find {phi}BB-1 packages fragments of the linear chromosome and full-length plasmids including lp54, cp26, and others. Furthermore, sequencing of {phi}BB-1 packaged DNA allowed us to resolve the covalently closed hairpin telomeres for the linear B. burgdorferi chromosome and most linear plasmids in strain CA-11.2A. Collectively, our results shed light on the biology of the ubiquitous {phi}BB-1 phage and further implicates {phi}BB-1 in the generalized transduction of diverse genes and the maintenance of genetic diversity in Lyme disease spirochetes.

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Faith, D. R., Kinnersley, M., Brooks, D. M., Drecktrah, D., Hall, L. S., Luo, E., Santiago-Frangos, A., Wachter, J., Samuels, S., Secor, P. R.. 2024-01-09. Characterization and genomic analysis of the Lyme disease spirochete bacteriophage phiBB-1. https://doi.org/10.1101/2024.01.08.574763

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