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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

Distribution of inverted sequences on H. pylori genomes.The REPuter output files were combined with the Mauve alignment “coordinates output file” to make a plot with java script codes. The grey background figure shows the conserved blocks between genomes produced by Mauve. All the color lines indicate a pair of inverted repeats (>25 bp) at the position of genomes. Red arrows show the positions of some repeats mentioned in the text.
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pone-0017300-g002: Distribution of inverted sequences on H. pylori genomes.The REPuter output files were combined with the Mauve alignment “coordinates output file” to make a plot with java script codes. The grey background figure shows the conserved blocks between genomes produced by Mauve. All the color lines indicate a pair of inverted repeats (>25 bp) at the position of genomes. Red arrows show the positions of some repeats mentioned in the text.

Mentions: The distribution of inverted repeats (>25 bp) of nine genomes was shown in Figure 2. We first noticed the inverted rDNA repeated sequences. Each H. pylori strain normally has two sets of rRNA genes locating on complementary strand, of which 5S rDNAs are generally sited together with 23S rDNA to form a gene cluster. However, strains B38, G27 and 26695 have an additional 5S rDNA on sequence strand with 17 bp less in size. Further analysis showed that an inversion occurred between two 5S rDNA copies (HELPY_5S_2 and HELPY_5S_3 in B38; HPG27_rRNA1 and HPG27_rRNA2 in G27). The inverted repeat sequences are, respectively, 189 bp in B38 and 518 bp in G27, both of which exactly start from the first base of the 5S rDNAs, the junction point of the inversion. The situation in strain 26695 is more complicated. One 5S rDNA (HP_r02) has been translocated to the new site with coordinate number 448451 and 448585, comparing with genomes of G27 and B38. Some features of this new site need to be mentioned. Firstly, the rDNA cluster here is on the sequence strand, different from the region of the cluster in other genomes; Secondly, the rDNA cluster is included in a pair of inverted repeat fragments with the size of 10.5 kb (coordinate number: c1483962-1473496; 438181- 448645); Thirdly, several genes (HP0428-HP0435) at the downstream of 5S rDNA in strain 26695, has their homologs positioned (coordinate number about 1000000) within the inversion between 5S rDNA repeats in G27 and B38. The above information suggests that the novel architecture of the additional rDNA in strain 26695 should be involved in another inversion, resulting in the movement of fragments. In other words, this recurrent inversion occurred after the formation of 5S rDNA duplication in strain 26695.


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)

Distribution of inverted sequences on H. pylori genomes.The REPuter output files were combined with the Mauve alignment “coordinates output file” to make a plot with java script codes. The grey background figure shows the conserved blocks between genomes produced by Mauve. All the color lines indicate a pair of inverted repeats (>25 bp) at the position of genomes. Red arrows show the positions of some repeats mentioned in the text.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017300-g002: Distribution of inverted sequences on H. pylori genomes.The REPuter output files were combined with the Mauve alignment “coordinates output file” to make a plot with java script codes. The grey background figure shows the conserved blocks between genomes produced by Mauve. All the color lines indicate a pair of inverted repeats (>25 bp) at the position of genomes. Red arrows show the positions of some repeats mentioned in the text.
Mentions: The distribution of inverted repeats (>25 bp) of nine genomes was shown in Figure 2. We first noticed the inverted rDNA repeated sequences. Each H. pylori strain normally has two sets of rRNA genes locating on complementary strand, of which 5S rDNAs are generally sited together with 23S rDNA to form a gene cluster. However, strains B38, G27 and 26695 have an additional 5S rDNA on sequence strand with 17 bp less in size. Further analysis showed that an inversion occurred between two 5S rDNA copies (HELPY_5S_2 and HELPY_5S_3 in B38; HPG27_rRNA1 and HPG27_rRNA2 in G27). The inverted repeat sequences are, respectively, 189 bp in B38 and 518 bp in G27, both of which exactly start from the first base of the 5S rDNAs, the junction point of the inversion. The situation in strain 26695 is more complicated. One 5S rDNA (HP_r02) has been translocated to the new site with coordinate number 448451 and 448585, comparing with genomes of G27 and B38. Some features of this new site need to be mentioned. Firstly, the rDNA cluster here is on the sequence strand, different from the region of the cluster in other genomes; Secondly, the rDNA cluster is included in a pair of inverted repeat fragments with the size of 10.5 kb (coordinate number: c1483962-1473496; 438181- 448645); Thirdly, several genes (HP0428-HP0435) at the downstream of 5S rDNA in strain 26695, has their homologs positioned (coordinate number about 1000000) within the inversion between 5S rDNA repeats in G27 and B38. The above information suggests that the novel architecture of the additional rDNA in strain 26695 should be involved in another inversion, resulting in the movement of fragments. In other words, this recurrent inversion occurred after the formation of 5S rDNA duplication in strain 26695.

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