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New implications on genomic adaptation derived from the Helicobacter pylori genome comparison.

Lara-Ramírez EE, Segura-Cabrera A, Guo X, Yu G, García-Pérez CA, Rodríguez-Pérez MA - PLoS ONE (2011)

Bottom Line: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence.Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome.Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, México.

ABSTRACT

Background: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.

Principal findings: We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, homological recombination contributed to events of inversion. Based on the information of genomic rearrangement, the first genome scaffold structure of H. pylori last common ancestor was produced. The core genome consists of 1186 genes, of which 22 genes could particularly adapt to human stomach niche. H. pylori contains high proportion of pseudogenes whose genesis was principally caused by homopolynucleotide (HPN) mutations. Such mutations are reversible and facilitate the control of gene expression through the change of DNA structure. The reversible mutations and a quasi-panmictic feature could allow such genes or gene fragments frequently transferred within or between populations. Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome.

Conclusion: Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style.

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Related in: MedlinePlus

The portions of types of premature mutations in pseudogenes.a. premature mutations in pseudogenes in strain B38. b. premature mutations in pseudogenes in other strains.
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pone-0017300-g007: The portions of types of premature mutations in pseudogenes.a. premature mutations in pseudogenes in strain B38. b. premature mutations in pseudogenes in other strains.

Mentions: Therefore, that H. pylori genomes possess the high proportion of pseudogenes in the intraspecies strains is an ideal model for detecting the recent genomic evolution of species. We firstly analyzed the pseudogenes in B38. The 59 fragmented genes (28 hypothetic proteins, 11 membrane proteins, 11 restriction-modification system proteins and 9 others) were chosen for comparison because the orthologous sequences exist in other strains. The multi-alignment analysis of the 59 pseudogenes demonstrated that the mutations were generally resulted from frameshift: except 4 genes interrupted by ISHp609 and 4 gene with the occurrence of new stop codon by point mutations, 60 premature mutations were formed by frameshifts (Figure 7a, Table S3). These frameshifts were caused by indels of homonucleotides, heteronucleotides, short tandem repeats, short direct repeats and recombination with other fragments. However, the indel of homonucleotides were the principal contribution, 60% of total frameshifts (36/60). As the consequence of such indels, one or more nucleotide differences existed at the mutation sites of homopolynucleotide (HPN) when compared to normal sequences. We further analyzed the 50 pseudogenes that were randomly selected from other strains and showed that up to 90% of prematures were responsible for homonucleotide indel (Figure 7b. Table S4).


New implications on genomic adaptation derived from the Helicobacter pylori genome comparison.

Lara-Ramírez EE, Segura-Cabrera A, Guo X, Yu G, García-Pérez CA, Rodríguez-Pérez MA - PLoS ONE (2011)

The portions of types of premature mutations in pseudogenes.a. premature mutations in pseudogenes in strain B38. b. premature mutations in pseudogenes in other strains.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3046158&req=5

pone-0017300-g007: The portions of types of premature mutations in pseudogenes.a. premature mutations in pseudogenes in strain B38. b. premature mutations in pseudogenes in other strains.
Mentions: Therefore, that H. pylori genomes possess the high proportion of pseudogenes in the intraspecies strains is an ideal model for detecting the recent genomic evolution of species. We firstly analyzed the pseudogenes in B38. The 59 fragmented genes (28 hypothetic proteins, 11 membrane proteins, 11 restriction-modification system proteins and 9 others) were chosen for comparison because the orthologous sequences exist in other strains. The multi-alignment analysis of the 59 pseudogenes demonstrated that the mutations were generally resulted from frameshift: except 4 genes interrupted by ISHp609 and 4 gene with the occurrence of new stop codon by point mutations, 60 premature mutations were formed by frameshifts (Figure 7a, Table S3). These frameshifts were caused by indels of homonucleotides, heteronucleotides, short tandem repeats, short direct repeats and recombination with other fragments. However, the indel of homonucleotides were the principal contribution, 60% of total frameshifts (36/60). As the consequence of such indels, one or more nucleotide differences existed at the mutation sites of homopolynucleotide (HPN) when compared to normal sequences. We further analyzed the 50 pseudogenes that were randomly selected from other strains and showed that up to 90% of prematures were responsible for homonucleotide indel (Figure 7b. Table S4).

Bottom Line: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence.Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome.Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, México.

ABSTRACT

Background: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.

Principal findings: We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, homological recombination contributed to events of inversion. Based on the information of genomic rearrangement, the first genome scaffold structure of H. pylori last common ancestor was produced. The core genome consists of 1186 genes, of which 22 genes could particularly adapt to human stomach niche. H. pylori contains high proportion of pseudogenes whose genesis was principally caused by homopolynucleotide (HPN) mutations. Such mutations are reversible and facilitate the control of gene expression through the change of DNA structure. The reversible mutations and a quasi-panmictic feature could allow such genes or gene fragments frequently transferred within or between populations. Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome.

Conclusion: Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style.

Show MeSH
Related in: MedlinePlus