A Phylogenetic Analysis of Borrelia Burgdorferi Sensu Lato Based on Sequence Information from the hbb Gene, Coding for A Histone-Like Protein

Abstract

We describe a phylogenetic investigation of Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, based on a DNA sequence analysis of the hbb gene, which encodes protein HBb, a member of the family of histone-like proteins. Because of. their intimate contact with the DNA molecule, these proteins are believed to be fairly conserved through evolution. In this study we proved that the hbb gene is suitable for phylogenetic inference in the genus Borrelia. The hbb gene, which is 327 bp long and encodes 108 amino acids, was sequenced for 39 strains, including 37 strains of B. burgdorferi sensu lato, 1 strain of Borrelia turicatae, and 1 strain of Borrelia parkeri. Genetic variability was determined at the sequence level by computational analysis. Briefly, 81 substitutions were scored at the DNA level. Only 25 of these substitutions were responsible for amino acid substitutions at the translational level. The signature region for bacterial histone-like proteins was found in hbb. Although variable at the nucleotide level, it was highly conserved at the deduced amino acid level. A phylogenetic tree for the genus Borrelia that was generated from multiple sequence alignments was consistent with previously published data derived from DNA-DNA hybridization and multilocus enzyme electrophoresis analyses. The subdivision of B. burgdorferi sensu lato into five species (B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afielii, Borrelia japonica, and "Borrelia andersonii") and at least four genomic groups (groups PotiB2, VS116, CA2, and DN127) was confirmed.A large portion of our phylogenetic knowledge in the field of bacterial evolution is based on sequence data for the 16s rRNA subunit (56) common to all bacteria. An amazing amount of phylogenetic information, ranging from conserved spots to highly variable spots, is condensed in this genomic region. However, the usefulness of other genomic regions for evolutionary studies of microorganisms has been emphasized in several studies. Following this theme, phylogenies substantially different from the Woese concept have been proposed based on alignments of several housekeeping genes. These include the genes for the 70-kDa heat shock proteins (20), the 60-kDa heat shock proteins (homologs of Escherichia coli GroEL) (20, 52), elongation factor EF-Tu (40), glutamate dehydrogenase (7), glutamine synthetase (10, 29,48), and RecA (27). These studies and a variety of others have clearly shown that phylogenies based on different genes may differ. Although there are virtually no rational grounds for choosing the right phylogeny, we speculate that a target genomic region for DNA sequence alignment can be more or less suitable for phylogenetic analysis of a particular group of organisms. While some genes might be appropriate for phylogenetic inference at the phylum level, other genes might be more appropriate at lower taxonomic levels, such as the family or genus level. In our phylogenetic approach we have focused on the use of bacterial histone-like proteins (also known...

Delineation of Borrelia burgdorferi sensu lato species by multilocus sequence analysis and confirmation of the delineation of Borrelia spielmanii sp. nov.

“…The strains used in this study (Table 1) belong to five species endemic to Europe, B. burgdorferi s.s., B. garinii, B. afzelii, B. valaisiana and B. lusitaniae. Information regarding DNA-DNA reassociation was available for each of these strains (Postic et al, 1990;Baranton et al, 1992;Canica et al, 1993;Le Fleche et al, 1997;Wang et al, 1997) and sequences at several of the selected loci were accessible from the literature or databases (Postic et al, 1994;Le Fleche et al, 1997;Valsangiacomo et al, 1997;Wang et al, 1997;Casati et al, 2004;Park et al, 2004). For the delineation of 'B.…”

Comparative genetic diversity of Lyme disease bacteria in Northern Californian ticks and their vertebrate hosts

“…Haplotype 28 grouped with CA2, an unclassified Borrelia sp. that previous studies found forms a group distinct from B. burgdorferi s.s. based on DNA-DNA hybridization and sequencing analyses (Valsangiacomo et al, 1997;Postic et al, 1998). Haplotypes 29 and 30 grouped with an uncharacterized Borrelia sp.…”

Comparative sequence analyses of the ribonuclease P (RNase P) RNA genes from LL-2,6-diaminopimelic acid-containing actinomycetes.

“…In the meantime, DNA-DNA hybridization and some useful gene fragments are used for elucidating genetic relationships or in phylogenetic studies. Such gene fragments include genes for rRNAs (Woese, 1987), the β-subunit of ATPsynthase (Amann et al, 1988), tRNA (Hofle, 1990), glutamine synthetase (Brown et al, 1994), elongation factor Tu (Kamla et al, 1996), a 65 kDa heat-shock protein (hsp65) (Swanson et al, 1997) and a histonelike protein (hbb) (Valsangiacomo et al, 1997 The GenBank accession numbers for the sequences of the RNase P RNA genes determined in this study are listed in Table 1. these, 16S rRNA or 16S rDNA have been extensively studied and have become important as target genes in the phylogeny and classification of prokaryotic organisms (Woese & Fox, 1977 ;Woese, 1987 ;Stackebrandt et al, 1997). Nevertheless, there is a general consensus that 16S rRNA gene sequences may be inappropriate for elucidating the relationships between closely related organisms and may be insufficient to guarantee species identity (Fox et al, 1992).…”

“…In the meantime, DNA-DNA hybridization and some useful gene fragments are used for elucidating genetic relationships or in phylogenetic studies. Such gene fragments include genes for rRNAs (Woese, 1987), the β-subunit of ATPsynthase (Amann et al, 1988), tRNA (Hofle, 1990), glutamine synthetase (Brown et al, 1994), elongation factor Tu (Kamla et al, 1996), a 65 kDa heat-shock protein (hsp65) (Swanson et al, 1997) and a histonelike protein (hbb) (Valsangiacomo et al, 1997) Abbreviations : LL-A 2 pm, LL-2,6-diaminopimelic acid ; ITS, internally transcribed spacer.…”