A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi

Abstract

We have determined that Borrelia burgdorferi strain B31 MI carries 21 extrachromosomal DNA elements, the largest number known for any bacterium. Among these are 12 linear and nine circular plasmids, whose sequences total 610 694 bp. We report here the nucleotide sequence of three linear and seven circular plasmids (comprising 290 546 bp) in this infectious isolate. This completes the genome sequencing project for this organism; its genome size is 1 521 419 bp (plus about 2000 bp of undetermined telomeric sequences). Analysis of the sequence implies that there has been extensive and sometimes rather recent DNA rearrangement among a number of the linear plasmids. Many of these events appear to have been mediated by recombinational processes that formed duplications. These many regions of similarity are reflected in the fact that most plasmid genes are members of one of the genome's 161 paralogous gene families; 107 of these gene families, which vary in size from two to 41 members, contain at least one plasmid gene. These rearrangements appear to have contributed to a surprisingly large number of apparently non‐functional pseudogenes, a very unusual feature for a prokaryotic genome. The presence of these damaged genes suggests that some of the plasmids may be in a period of rapid evolution. The sequence predicts 535 plasmid genes ≥300 bp in length that may be intact and 167 apparently mutationally damaged and/or unexpressed genes (pseudogenes). The large majority, over 90%, of genes on these plasmids have no convincing similarity to genes outside Borrelia, suggesting that they perform specialized functions.

Biology of Infection with Borrelia burgdorferi

“…Although the underlying genetic traits contributing to the differences in disease have not been identified, the release of three Borrelia genome sequences (one from each 21 species) should aid in this endeavor [5,[11][12][13]. These genomes have several common features, including a linear chromosome and a large number of smaller DNA molecules (plasmids), some of which are linear and others circular [14][15][16][17].…”

“…The genes encoded on the plasmid component of the genome are less recognizable and the majority of these appear to be unique to the genus Borrelia [4,5]. Additionally, several plasmid-encoded genes have been shown to be required for infectivity or persistence in the tick or the mammalian host (discussed below).…”

“…The genome sequence of the Lyme disease spirochete revealed several interesting features [4,5]. First, no classically-defined virulence factors were identifiable, probably because B. burgdorferi did not evolve to cause disease in mammals.…”

“…However, a sizable number of putative lipoproteins were recognized and some have been shown to trigger components of the mammalian innate immune system (discussed below). Finally, the plasmids appear to be in a state of rapid evolution, as many genes appear to be mutationally inactivated, whereas others have been duplicated and may be functionally diverging from each other [5]. Perhaps reflecting this evolving state, the number of plasmids, their sizes, and the gene order varies substantially among strains and between species; in some cases, plasmids or portions of some plasmids are absent [18,19].…”

“…Consistent with the pathogenesis of Lyme disease, bacterial products that allow B. burgdorferi to replicate and survive, rather than true "virulence factors," appear to be primarily what is required for the bacterium to cause disease in a susceptible host. In support of this idea, the genome sequence of B31, the type strain of B. burgdorferi sensu stricto [4,5], revealed that the bacterium lacks factors common to many bacterial pathogens, such as lipopolysaccharide, toxins, and specialized secretion systems. In this chapter, we will describe the basic biology of B. burgdorferi, and some of the bacterial components required to infect and survive in the mammalian and tick hosts.…”