Estudios genómicos y dinámica evolutiva en Helicobacter pylori

Abstract

In this thesis we have carried out a genomic, population and evolutionary analysis of the H. pylori bacteria together with several species of the same genus. H. pylori is recognized as one of the most common human obligate pathogens that colonizes the stomach and duodenum in half the human population, causing inflammation that can lead to ulcers and gastric cancer. This species presents a panmictic population behavior, with frequent mutual homologous recombination and showing great diversity in terms of genome structure and gene composition, as well as high variation in nucleotide sequence due to the high rate of mutation and recombination. As we have been able to verify, the genome of this bacterium has an average length of 1,621,671 + - 43,785 bp with an average G / C content of 40%, which is why it falls within the group of small bacterial genomes of ∼2 Mb. This reduction in size is in concordance with other free-living pathogenic bacteria in extreme environments. Likewise, the gene content is also low, having an average of 1,551 + - 42 genes per genome and a central genome made up of 802 genes. Both values obtained in this Thesis are lower than in other previous studies of this same species. These differences could be due to several causes including: the different number of strains included in each analysis, the calculation program and the respective significance filters of the central genome used, as well as the inclusion in some of these studies of paralogue and orthologous genes. jointly. However, we can point out that the size of 802 genes for the central genome is not extraordinary since, for example, the free-living Actinobacteria have a genome of approximately 800 genes. However, despite the small size of its genome in nucleotides and genes, this bacterium shows enormous variability, which is manifested in the large number of SNPs that the genes of the central genome present in the set of 53 strains analyzed. This great variability makes it possible to classify the different geographic subpopulations in an increasing number than the one initially proposed based on the analysis for only seven genes of the genome. This observation of such high variability is not exceptional for H. pylori since the sequencing of a large number of prokaryotic genomes and the comparison of sequences of closely related species have revealed a high frequency in a large repertoire of genomic variations, which can ranging from single nucleotide variations to large chromosome block insertion-deletion events. The origin of this large amount of variability can have several explanations, none of them mutually exclusive. Among these we can point out: I) lifestyle II) illegitimate recombination by-products (homologous recombination) III) imprecise non-homologous repair mechanism during aberrant DNA replication to repair broken replication forks and IV) presence of repeated elements in its genome. As a result of the erroneous recombination processes, we have been able to verify that inversions are the most frequent chromosomal mutation, existing inversions characteristic of each region, and there are subgroups within them that could have been produced by genetic drift processes. This same association occurs when a structural and phylogenetic analysis is carried out based on the SNPs detected, since we can observe a geographical pattern in which it is possible, in general, to assign each strain according to its origin. We also identified up to six hybrid strains, four of them for the first time in this work and whose genome is the result of the recombination of at least three genomes of different geographical origin. In this sense, we have also verified the great influence that gene flow has on the population structure of this species, producing a large amount of mix between different geographic regions, with donor and other recipient regions. We have also been able to verify that, in addition to the aforementioned mechanisms that contribute to the conformation of the genome, in H. pylori concerted evolution and selection play an important role in its evolutionary dynamics. Thus, for seven duplicated genes, we found evidence of concerted evolution, that is, of homogenization of intergenic sequences for those regions of the gene in which it was possible to verify that recombination occurred. In order to have a broader vision of the evolution of this species and its relationship with other species of the genus Helicobacter, we have carried out a comparative analysis of H. pylori with seven species of the genus. From these analyzes, we can deduce that the African strains of H. pylori are the most related to H. acinonychis species also from the gastric environment. Finally, we have carried out a study on the different immune systems that the genus presents. We have verified that they present a great diversity of systems in the set of species and that almost all species have more than three immune systems, which allows them a better defense against phage attacks.