Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis

Abstract

The main Borrelia species causing Lyme borreliosis in Europe and Asia are Borrelia afzelii, B. garinii, B. burgdorferi and B. bavariensis. This is in contrast to the United States, where infections are exclusively caused by B. burgdorferi. Until to date the genome sequences of four B. afzelii strains, of which only two include the numerous plasmids, are available. In order to further assess the genetic diversity of B. afzelii, the most common species in Europe, responsible for the large variety of clinical manifestations of Lyme borreliosis, we have determined the full genome sequence of the B. afzelii strain K78, a clinical isolate from Austria. The K78 genome contains a linear chromosome (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309 open reading frames of which 496 are located on plasmids. With the exception of lp28-8, all linear replicons in their full length including their telomeres have been sequenced. The comparison with the genomes of the four other B. afzelii strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of B. burgdorferi strain B31, confirmed a high degree of conservation within the linear chromosome of B. afzelii, whereas plasmid encoded genes showed a much larger diversity. Since some plasmids present in B. burgdorferi are missing in the B. afzelii genomes, the corresponding virulence factors of B. burgdorferi are found in B. afzelii on other unrelated plasmids. In addition, we have identified a species specific region in the circular plasmid, cp26, which could be used for species determination. Different non-coding RNAs have been located on the B. afzelii K78 genome, which have not previously been annotated in any of the published Borrelia genomes.

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

“…Other plasmids are found in fewer than 10% of the analyzed Bbsl strains, while some plasmids are nearly always present but vary by size, gene content and copy number [21]. Cross species genomic comparisons suggest gene duplication/loss and differential expression patterns in addition to sequence variation in conserved lipoproteins are the primary drivers of differing tissue tropisms rather than gain of virulence genes [21–23]. …”

A Borrelia burgdorferi mini‐vls system that undergoes antigenic switching in mice: investigation of the role of plasmid topology and the long inverted repeat

“…The IRs would appear to be an important component of the vls system as they are present adjacent to all vlsE genes sequenced thus far (see Introduction). The question of why the IR is required for switching on a circular but not linear plasmid is vexing, especially since all vls loci found to date have been found on linear replicons ,b, Casjens et al, 2012Schüler et al, 2015;Kingry et al, 2016). Some possible explanations for our results regarding the IR in the mini-vls system are:…”

“…The first is whether the topology of the vls locus is important or not. In B. burgdorferi, all vls loci sequenced to date are found on linear DNA molecules and near the hairpin telomeres (Casjens et al, ,b; Casjens et al, ; Schüler et al, ; Kingry et al, ). A direct comparison between a linear and circular mini‐ vls (both carrying the 100 bp inverted repeat) revealed no significant difference in switching between them (Fig.…”

“…The IRs would appear to be an important component of the vls system as they are present adjacent to all vlsE genes sequenced thus far (see Introduction). The question of why the IR is required for switching on a circular but not linear plasmid is vexing, especially since all vls loci found to date have been found on linear replicons (Casjens et al, ,b, Casjens et al, ; Schüler et al, ; Kingry et al, ). Some possible explanations for our results regarding the IR in the mini‐ vls system are: The vls locus is normally present on a linear replicon and the IR may not be needed for recombinational switching, but may instead be required for regulated transcription of the vlsE gene. Replication of linear replicons in Borrelia species involves circular replication intermediates, if telomere resolution does not precede completion of replication at both ends (Chaconas and Kobryn, ).…”

“…The segmented B. burgdorferi genome has a number of linear replicons terminated by covalently closed hairpin ends (Chaconas and Kobryn, ) with similar but non‐identical sequences (Tourand et al, ). Another important feature is that the vls locus has always been found at the end of linear plasmids or the linear chromosome (Casjens et al, ,b; Casjens et al, ; Schüler et al, ; Kingry et al, ), and hence DNA topology may be important for switching at vlsE . In contrast other bacterial antigenic variation systems are present on circular molecules (Vink et al, ).…”