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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 phylogenic tree of repeats HP0227 and HP1342 with their homologs in different genomes.The arrows indicate the homologs in strain HPAG1.
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pone-0017300-g003: The phylogenic tree of repeats HP0227 and HP1342 with their homologs in different genomes.The arrows indicate the homologs in strain HPAG1.

Mentions: The majority of inverted repeats did not lead to inversion, as shown in Figure 2. Thus, the inverted repeat sequences on genomes were further studied. The strains 26695, HPAG1, P12, J99 and B38 have two paralogs, respectively called HP0227 and HP1342, HPAG1_0230 and HPAG1_1289, HPP12_0227 and HPP12_1305, jhp0212 and jhp1261, HELPY_0231 and HELPY_1317 but the strains G27, Shi470, 51 and 52 have only one homolog. The genomic structure analysis showed that HP0227, HPAG1_0230, HPP12_0227, jhp0212, and HELPY_0231 with their neighbor genes have the similar structure to the homologs HPG27_0207 in G27, HPSH_01180 in Shi470, KHP_0226 in strain 51 and HPKB_0236 in strain 52, indicating that HP0227, HPAG1_0230, HPP12_0227, jhp0212, and HELPY_0231 are the original, and the duplications are the paralogs HP1342, HPAG1_1289, HPP12_1305, jhp1261 and HELPY_1317. The original and its paralog are the inverted repeats. Actually, the repeat sequences are a little larger than the coding region. In strain 26695, the repeat region is 2114 bp long, including the whole sequence of coding region 2076 bp. Multi-alignment showed that the original segments have two types of sequences in strains, one as representative in 26695 and the other as in P12, J99 and Shi470. The inverted sequences in each strain are almost identical, indicating that the new copy is of intragenomic origin (duplication). But the strain HPAG1contains these two types of sequences (Figure 3), implying that one of the paralogs could be of exotic origin realized by horizontal transfer. Therefore, it is very possible the first introduction of new copy to the new site that resulted in inverted repeats with identical sequences and then the occurrence of recombination to integrate exotic homologs through horizontal transfer.


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 phylogenic tree of repeats HP0227 and HP1342 with their homologs in different genomes.The arrows indicate the homologs in strain HPAG1.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017300-g003: The phylogenic tree of repeats HP0227 and HP1342 with their homologs in different genomes.The arrows indicate the homologs in strain HPAG1.
Mentions: The majority of inverted repeats did not lead to inversion, as shown in Figure 2. Thus, the inverted repeat sequences on genomes were further studied. The strains 26695, HPAG1, P12, J99 and B38 have two paralogs, respectively called HP0227 and HP1342, HPAG1_0230 and HPAG1_1289, HPP12_0227 and HPP12_1305, jhp0212 and jhp1261, HELPY_0231 and HELPY_1317 but the strains G27, Shi470, 51 and 52 have only one homolog. The genomic structure analysis showed that HP0227, HPAG1_0230, HPP12_0227, jhp0212, and HELPY_0231 with their neighbor genes have the similar structure to the homologs HPG27_0207 in G27, HPSH_01180 in Shi470, KHP_0226 in strain 51 and HPKB_0236 in strain 52, indicating that HP0227, HPAG1_0230, HPP12_0227, jhp0212, and HELPY_0231 are the original, and the duplications are the paralogs HP1342, HPAG1_1289, HPP12_1305, jhp1261 and HELPY_1317. The original and its paralog are the inverted repeats. Actually, the repeat sequences are a little larger than the coding region. In strain 26695, the repeat region is 2114 bp long, including the whole sequence of coding region 2076 bp. Multi-alignment showed that the original segments have two types of sequences in strains, one as representative in 26695 and the other as in P12, J99 and Shi470. The inverted sequences in each strain are almost identical, indicating that the new copy is of intragenomic origin (duplication). But the strain HPAG1contains these two types of sequences (Figure 3), implying that one of the paralogs could be of exotic origin realized by horizontal transfer. Therefore, it is very possible the first introduction of new copy to the new site that resulted in inverted repeats with identical sequences and then the occurrence of recombination to integrate exotic homologs through horizontal transfer.

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