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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 comparison of homopolynucleotide (HPN) content in H. pylori 26695 with other bacteria, from Archaea to Eubacteria species.The abbreviations are: AbT469, Aciduliprofundum boonei T469; Ab, Acinetobacter baumannii AB0057; Bq, Bartonella quintana; Cc, Chlamydophila caviae GPIC; Ct, Clostridium thermocellum ATCC 27405; CPCC 7424, Cyanothece sp. PCC 7424; Ch, Cytophaga hutchinsonii ATCC 33406; Lr, Lactobacillus reuteri DSM 20016; Lb, Leptospira biflexa serovar Patoc; Lc, Leuconostoc citreum KM20; Mb, Methanosarcina barkeri; Pm, Proteus mirabilis strain HI4320; Spn, Streptococcus pneumoniae ATCC; Spy, Streptococcus pyogenes M1 GAS; St, Streptococcus thermophilus CNRZ1066; Sd, Sulfurospirillum deleyianum DSM 6946; Tl, Thermotoga lettingae TMO; Vp, Veillonella parvula DSM 2008; As, Aliivibrio salmonicida LFI1238; Cj, Campylobacter jejuni RM1221; EcK12, Escherichia coli K12; Hp, Helicobacter pylori 26695.
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pone-0017300-g010: The comparison of homopolynucleotide (HPN) content in H. pylori 26695 with other bacteria, from Archaea to Eubacteria species.The abbreviations are: AbT469, Aciduliprofundum boonei T469; Ab, Acinetobacter baumannii AB0057; Bq, Bartonella quintana; Cc, Chlamydophila caviae GPIC; Ct, Clostridium thermocellum ATCC 27405; CPCC 7424, Cyanothece sp. PCC 7424; Ch, Cytophaga hutchinsonii ATCC 33406; Lr, Lactobacillus reuteri DSM 20016; Lb, Leptospira biflexa serovar Patoc; Lc, Leuconostoc citreum KM20; Mb, Methanosarcina barkeri; Pm, Proteus mirabilis strain HI4320; Spn, Streptococcus pneumoniae ATCC; Spy, Streptococcus pyogenes M1 GAS; St, Streptococcus thermophilus CNRZ1066; Sd, Sulfurospirillum deleyianum DSM 6946; Tl, Thermotoga lettingae TMO; Vp, Veillonella parvula DSM 2008; As, Aliivibrio salmonicida LFI1238; Cj, Campylobacter jejuni RM1221; EcK12, Escherichia coli K12; Hp, Helicobacter pylori 26695.

Mentions: High number of HPNs in genes should elevate the high HPN proportion in a genome. If this genomic feature is true in H. pylori, it can be extrapolated that all the H. pylori strains should share this feature and the genomes of H. pylori have at least much higher proportion of HPN than other bacterial genomes that contain the similar G+C content. Following this hypothesis, we performed the analysis in two steps: firstly, to compare all Helicobacter pylori genomes with the genomes of closely related species and E. coli; and then to compare a Helicobacter pylori genome with other bacterial genomes from Archaea to Eubacteria species that possess the 38.5–39.5% of G+C content. The G+C contents of 51 genomes were located within this range in the NCBI database. One representative of each species (20 species) was chosen for comparison so that 20 species genomes as well as E. coli were tested. The result demonstrated that all H. pylori strains had a similar proportion of HPN number (Figure 9). When compared to closely related species, the genomes of H. pylori as well as H. acinonychis had higher HPN proportion in all four bases, starting from tri-homopolynucleotides, indicating that it could be the common trait of Helicobacter genus. Campylobacter jejuni genome, with 30.5% of G+C, had much higher poly-A and poly-T than H. pylori genomes but had much less poly-G and poly-C so that its HPN composition was strongly influenced by the lower G+C content of genome. In comparison with E. coli, it clearly showed this feature, higher HPN in all four types of bases in H. pylori, including poly-G and poly-C even though E. coli has much higher G+C content (50.8%). When comparing with other species that contain similar genomic G+C content, it also showed the similar result, much higher HPN from tri-homopolynucleotides in H. pylori (Figure 10).


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 comparison of homopolynucleotide (HPN) content in H. pylori 26695 with other bacteria, from Archaea to Eubacteria species.The abbreviations are: AbT469, Aciduliprofundum boonei T469; Ab, Acinetobacter baumannii AB0057; Bq, Bartonella quintana; Cc, Chlamydophila caviae GPIC; Ct, Clostridium thermocellum ATCC 27405; CPCC 7424, Cyanothece sp. PCC 7424; Ch, Cytophaga hutchinsonii ATCC 33406; Lr, Lactobacillus reuteri DSM 20016; Lb, Leptospira biflexa serovar Patoc; Lc, Leuconostoc citreum KM20; Mb, Methanosarcina barkeri; Pm, Proteus mirabilis strain HI4320; Spn, Streptococcus pneumoniae ATCC; Spy, Streptococcus pyogenes M1 GAS; St, Streptococcus thermophilus CNRZ1066; Sd, Sulfurospirillum deleyianum DSM 6946; Tl, Thermotoga lettingae TMO; Vp, Veillonella parvula DSM 2008; As, Aliivibrio salmonicida LFI1238; Cj, Campylobacter jejuni RM1221; EcK12, Escherichia coli K12; Hp, Helicobacter pylori 26695.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017300-g010: The comparison of homopolynucleotide (HPN) content in H. pylori 26695 with other bacteria, from Archaea to Eubacteria species.The abbreviations are: AbT469, Aciduliprofundum boonei T469; Ab, Acinetobacter baumannii AB0057; Bq, Bartonella quintana; Cc, Chlamydophila caviae GPIC; Ct, Clostridium thermocellum ATCC 27405; CPCC 7424, Cyanothece sp. PCC 7424; Ch, Cytophaga hutchinsonii ATCC 33406; Lr, Lactobacillus reuteri DSM 20016; Lb, Leptospira biflexa serovar Patoc; Lc, Leuconostoc citreum KM20; Mb, Methanosarcina barkeri; Pm, Proteus mirabilis strain HI4320; Spn, Streptococcus pneumoniae ATCC; Spy, Streptococcus pyogenes M1 GAS; St, Streptococcus thermophilus CNRZ1066; Sd, Sulfurospirillum deleyianum DSM 6946; Tl, Thermotoga lettingae TMO; Vp, Veillonella parvula DSM 2008; As, Aliivibrio salmonicida LFI1238; Cj, Campylobacter jejuni RM1221; EcK12, Escherichia coli K12; Hp, Helicobacter pylori 26695.
Mentions: High number of HPNs in genes should elevate the high HPN proportion in a genome. If this genomic feature is true in H. pylori, it can be extrapolated that all the H. pylori strains should share this feature and the genomes of H. pylori have at least much higher proportion of HPN than other bacterial genomes that contain the similar G+C content. Following this hypothesis, we performed the analysis in two steps: firstly, to compare all Helicobacter pylori genomes with the genomes of closely related species and E. coli; and then to compare a Helicobacter pylori genome with other bacterial genomes from Archaea to Eubacteria species that possess the 38.5–39.5% of G+C content. The G+C contents of 51 genomes were located within this range in the NCBI database. One representative of each species (20 species) was chosen for comparison so that 20 species genomes as well as E. coli were tested. The result demonstrated that all H. pylori strains had a similar proportion of HPN number (Figure 9). When compared to closely related species, the genomes of H. pylori as well as H. acinonychis had higher HPN proportion in all four bases, starting from tri-homopolynucleotides, indicating that it could be the common trait of Helicobacter genus. Campylobacter jejuni genome, with 30.5% of G+C, had much higher poly-A and poly-T than H. pylori genomes but had much less poly-G and poly-C so that its HPN composition was strongly influenced by the lower G+C content of genome. In comparison with E. coli, it clearly showed this feature, higher HPN in all four types of bases in H. pylori, including poly-G and poly-C even though E. coli has much higher G+C content (50.8%). When comparing with other species that contain similar genomic G+C content, it also showed the similar result, much higher HPN from tri-homopolynucleotides in H. pylori (Figure 10).

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