The Detection of Inherent Homologous Recombination Between Repeat Sequences in H. pylori 26695 by the PCR-Based Method

Abstract

Helicobacter pylori infects more than half of the world's population, making it the most widespread infection of bacteria. It has high genetic diversity and has been considered as one of the most variable bacterial species. In the present study, a PCR-based method was used to detect the presence and the relative frequency of homologous recombination between repeat sequences (>500 bp) in H. pylori 26695. All the recombinant structures have been confirmed by sequencing. The inversion generated between inverted repeats showed distinct features from the recombination for duplication or deletion between direct repeats. Meanwhile, we gave the mathematic reasoning of a general formula for the calculation of relative recombination frequency and indicated the conditions for its application. This formula could be extensively applied to detect the frequency of homologous recombination, site-specific recombination, and other types of predictable recombination. Our results should be helpful for better understanding the genome evolution and adaptation of bacteria.

Analysis of a single Helicobacter pylori strain over a 10-year period in a primate model

“…These include a high frequency of spontaneous mutation, gene conversion, transposition, and natural competence (Fu et al, 2014). H. pylori is missing several of the genes that are important for mismatch repair, which may result in the higher rate of spontaneous mutation (Garcia-Ortiz et al, 2011; Tomb et al, 1997).…”

“…In addition to inter-strain rearrangements, H. pylori has several direct and indirect repeat sequences that can result in intragenomic rearrangements (Fu et al, 2014; Kennemann et al, 2011). These gene conversion events have been documented in at least two outer membrane protein (OMP) groups, the bab genes (Solnick et al, 2004) and the sab genes (Talarico et al, 2012).…”

Functional Identification and Evolutionary Analysis of Two Novel Plasmids Mediating Quinolone Resistance in Proteus vulgaris

“…DNA recombination is one of the most important factors that lead to changes of bacterial genetic information, during which DR play an important role [ 24 , 25 , 45 ]. In this study, we found that the existence of DR is a common feature of these plasmids containing qnrD , providing the potential to form a new plasmid when needed and showing that the conserved genes could be transferred and also substituted.…”

Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli

“…In the E. coli genomes, a few TRIP1 repeats were found at the junction of flanking genes from two separate loci. This is a typical result of intra-chromosomal rearrangement caused by repeat sequences [6,43,44]. To determine the frequency and influence of chromosomal arrangement caused by TRIP1 repeats, we scanned all genomes for the relative position of the 10 flanking genes from the five loci.…”