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A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.

Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K, Ohnishi M, Hayashi T, Thomson NR - DNA Res. (2014)

Bottom Line: Furthermore, phylogenetic analysis of all the E. coli O-serogroup reference strains revealed that the nearly one-quarter of the 184 serogroups were found in the ST10 lineage, which may have a unique genetic background allowing a more successful exchange of O-AGCs.Our data provide a complete view of the genetic diversity of O-AGCs in E. coli showing a stronger association between host phylogenetic lineage and O-serogroup diversification than previously recognized.These data will be a valuable basis for developing a systematic molecular O-typing scheme that will allow traditional typing approaches to be linked to genomic exploration of E. coli diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan iguchi@med.miyazaki-u.ac.jp.

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Sixteen Escherichia coli O-AGC groups identified in this study. Group members have different O serogroups in each group, but these share nearly identical or highly similar genetic organizations. Group names (Gp) are indicated at the left side. DNA sequence identities (%) between group members are indicated in each group.
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DSU043F1: Sixteen Escherichia coli O-AGC groups identified in this study. Group members have different O serogroups in each group, but these share nearly identical or highly similar genetic organizations. Group names (Gp) are indicated at the left side. DNA sequence identities (%) between group members are indicated in each group.

Mentions: On the basis of sequences and genetic structures of the entire O-AGC regions, in addition to 145 unique O-AGCs from different E. coli O serogroups, the O-AGCs from 37 O serogroups could be placed into 16 groups (named Gp1–Gp16) with the members of each group having identical or very similar O-AGC genes (mostly sharing ≥95% DNA sequence identity) (Fig. 1). This included nine groups with members of different serogroups but which carried identical O-AGC gene sets (Gp1–Gp9) and one group, Gp10, where two strains (O13 and O129) of the three-member group carried an identical O-AGC gene set (sharing 98.3–99.9% DNA sequence identity) (Fig. 1). The reason(s) why they belong to different O serogroups even though they have identical O-AGCs are discussed in the Discussion section. Indels or exchange of one or more genes was also shown to explain the differences between O135 and other members of Gp10 and members Gp11–Gp16, which otherwise carried highly conserved orthologous genes (summarized in Fig. 1). Simple insertions of insertion sequence (IS) elements containing one or two transposase genes were found in three groups without any gene disruption: an IS629 insertion in O18ab of Gp12, ISEc11 in O164 of Gp13, and IS1 in O62 of Gp14. IS element-associated replacement of the right-end portion of the O-AGC had occurred in three groups, Gp14, Gp15, and Gp16, resulting in the replacement (or deletion) of glycosyltransferase gene(s). Exchange of the wzx gene had also occurred in Gp16. These data suggest that IS elements are important drivers for generating O-antigen biosynthesis gene replacement and therefore diversity.Figure 1.


A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.

Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K, Ohnishi M, Hayashi T, Thomson NR - DNA Res. (2014)

Sixteen Escherichia coli O-AGC groups identified in this study. Group members have different O serogroups in each group, but these share nearly identical or highly similar genetic organizations. Group names (Gp) are indicated at the left side. DNA sequence identities (%) between group members are indicated in each group.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379981&req=5

DSU043F1: Sixteen Escherichia coli O-AGC groups identified in this study. Group members have different O serogroups in each group, but these share nearly identical or highly similar genetic organizations. Group names (Gp) are indicated at the left side. DNA sequence identities (%) between group members are indicated in each group.
Mentions: On the basis of sequences and genetic structures of the entire O-AGC regions, in addition to 145 unique O-AGCs from different E. coli O serogroups, the O-AGCs from 37 O serogroups could be placed into 16 groups (named Gp1–Gp16) with the members of each group having identical or very similar O-AGC genes (mostly sharing ≥95% DNA sequence identity) (Fig. 1). This included nine groups with members of different serogroups but which carried identical O-AGC gene sets (Gp1–Gp9) and one group, Gp10, where two strains (O13 and O129) of the three-member group carried an identical O-AGC gene set (sharing 98.3–99.9% DNA sequence identity) (Fig. 1). The reason(s) why they belong to different O serogroups even though they have identical O-AGCs are discussed in the Discussion section. Indels or exchange of one or more genes was also shown to explain the differences between O135 and other members of Gp10 and members Gp11–Gp16, which otherwise carried highly conserved orthologous genes (summarized in Fig. 1). Simple insertions of insertion sequence (IS) elements containing one or two transposase genes were found in three groups without any gene disruption: an IS629 insertion in O18ab of Gp12, ISEc11 in O164 of Gp13, and IS1 in O62 of Gp14. IS element-associated replacement of the right-end portion of the O-AGC had occurred in three groups, Gp14, Gp15, and Gp16, resulting in the replacement (or deletion) of glycosyltransferase gene(s). Exchange of the wzx gene had also occurred in Gp16. These data suggest that IS elements are important drivers for generating O-antigen biosynthesis gene replacement and therefore diversity.Figure 1.

Bottom Line: Furthermore, phylogenetic analysis of all the E. coli O-serogroup reference strains revealed that the nearly one-quarter of the 184 serogroups were found in the ST10 lineage, which may have a unique genetic background allowing a more successful exchange of O-AGCs.Our data provide a complete view of the genetic diversity of O-AGCs in E. coli showing a stronger association between host phylogenetic lineage and O-serogroup diversification than previously recognized.These data will be a valuable basis for developing a systematic molecular O-typing scheme that will allow traditional typing approaches to be linked to genomic exploration of E. coli diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan iguchi@med.miyazaki-u.ac.jp.

Show MeSH
Related in: MedlinePlus