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

Abstract

Lyme disease is a tick-borne infection caused by the spirocheteBorrelia(Borreliella)burgdorferi.Borreliaspecies have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids that encode diverse outer membrane lipoproteins, which facilitate movement of the spirochete between its tick vector and a vertebrate host in an enzootic cycle. TheB. burgdorferigenome shows evidence of horizontal transfer between strains, but the mechanisms remain poorly defined. Almost all Lyme disease spirochetes are infected by 32-kp circular plasmid (cp32) prophages that undergo lytic replication and produce infectious virions called ϕBB-1. In the laboratory, ϕBB-1 transduces cp32s and shuttle vectors between spirochetes. However, the extent that ϕBB-1 participates in horizontal gene transfer between Lyme disease spirochetes is not known. Here, we use proteomics and long-read sequencing to characterize ϕBB-1 virions and the genetic material they package. Our studies reveal that ϕBB-1 packages linear cp32s via a headful mechanism. We identify the cp32pacregion and show that plasmids containing the cp32pacregion are preferentially packaged into ϕBB-1 virions. Additionally, we find ϕBB-1 packages fragments of the linear chromosome and other plasmids including lp54, cp26, and others. Furthermore, sequencing of ϕBB-1 packaged DNA allowed us to resolve the covalently closed hairpin telomeres for the linearB. burgdorferichromosome and most linear plasmids in strain CA-11.2A. Collectively, our results shed light on the biology of the ubiquitous ϕBB-1 phage and further implicates ϕBB-1 in the generalized transduction of diverse genes between spirochetes and the maintenance of genetic diversity in Lyme disease spirochetes.