Absence in Helicobacter pylori of an uptake sequence for enhancing uptake of homospecific DNA during transformation

Abstract

Uptake sequences are abundant sequence motifs, often located downstream of ORFs, that are used to facilitate the within-species horizontal transfer of DNA. A frequent word analysis of the complete genome sequence of Helicobacter pylori strain 26685 was performed to search for and determine the identity of an uptake sequence in this species. The results demonstrated that Hel. pylori does not possess an uptake sequence. This is the first naturally transformable Gram-negative species shown to lack such a transformation-targeting system. Keywords : uptake sequence, Helicobacter pylori, transformation INTRODUCTIONHelicobacter pylori is a Gram-negative bacterial species which demonstrates a wide spectrum of genetic diversity (Marshall et al., 1998) : its genome size ranges from 1n0 to 1n8 Mb (Takami et al., 1993), extensive intra-strain variability is revealed by RFLP (Akopyanz et al., 1992) and there is little conservation of gene order in unrelated strains (Jiang et al., 1996). The index of association (I A ) is a measure of linkage equilibrium between alleles and this provides a means to measure the genetic relatedness of bacterial strains. The extent to which bacterial populations can then be considered to be ' clonal ' (high linkage disequilibrium\low frequency of horizontal exchange) or ' panmictic ' (linkage equilibrium\high frequency of horizontal exchange) populations can then be determined (Smith et al., 1993). The I A , determined following analysis by multilocus enzyme electrophoresis, does not differ significantly from zero. This indicates that the clonal population structure of Hel. pylori has been completely disrupted due to frequent recombination between strains (Go et al., 1996) and that the population can therefore be considered ' panmictic '. Furthermore, several genes investigated in Hel. pylori demonstrate a large degree of sequence divergence (Marshall et al., 1998), as well as mosaicism (Atherton et al., 1995). Finally, there is a clearly documented example of strains that have undergone horizontal exchange during co-infection of a human host (Kersulyte et al., 1999) Hel. pylori being a population of bacteria that exchange DNA horizontally within the species at a high frequency. Most strains of Hel. pylori are naturally transformable (Nedenskov-Sorensen et al., 1990 ;Wang et al., 1993 ;Tsuda et al., 1993). Naturally transformable bacteria are able to take up DNA readily from their environment and have the capacity to use it as a means of horizontal exchange of genetic information. Other naturally transformable bacteria have developed strategies to increase the likelihood that the substrate for recombination is derived from related bacteria (Solomon & Grossman 1996 ;Saunders et al., 1999). In Grampositive bacteria this is typically achieved through signals of growth phase and cell density that foster transformation only when the majority of the potential donor bacteria are the same species. In Gram-negative bacteria, as exemplified by Haemophilus and Neisseria spp., it is achieved by using uptake...

Natural Transformation of Gallibacterium anatis

“…This shows that the presence of overabundant kmers is not always a good indicator of whether an organism will show uptake specificity. This was previously observed for Helicobacter pylori, which shows uptake specificity but has no overabundant k-mers (17,34). Because neither pBA1100 nor the linear constructs used for targeted mutagenesis of G. anatis contained detectable Hin-or Apltype uptake sequences, uptake specificity is unlikely to present any practical problems for strain construction.…”

Natural Competence and the Evolution of DNA Uptake Specificity

“…Since the USS and DUS are distinct sequences and uptake sequences have not been identified in other groups, the self-specificities of the two families are likely to be of independent evolutionary origins. The only other bacterial species with demonstrated self-specificity are within the epsilonproteobacteria, Campylobacter and Helicobacter, but these have no strongly overrepresented genomic motif (94)(95)(96). The many similarities between the USS and DUS described below suggest that they are convergent products of the same evolutionary forces.…”

“…The epsilonproteobacteria Helicobacter pylori and Campylobacter jejuni have been shown to have uptake specificity, but the mechanism is unclear since no uptake sequences have been identified in their genomes (95,96). Although this may simply reflect lower enrichment or less-specific biases that are not as readily detected as those of the Pasteurellaceae and Neisseriaceae, these species could also require specific DNA modifications for efficient uptake.…”

Critical Role of RecN in Recombinational DNA Repair and Survival of Helicobacter pylori

“…H. pylori is naturally competent for uptake of exogenous DNA, and a special apparatus homologous to type IV secretion systems (comB locus) has a dedicated role in DNA uptake (17). Unlike several other bacterial species, H. pylori does not seem to require specific DNA sequences for uptake of related DNA (38). Thus, small DNA segments could be taken up from neighboring cells of the same strain (homologous recombination) or from cocolonizing strains (homeologous recombination) and then used to repair damaged genes by recombination.…”