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IS4 family goes genomic.

De Palmenaer D, Siguier P, Mahillon J - BMC Evol. Biol. (2008)

Bottom Line: Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution.The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing.Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.

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Affiliation: Laboratoire de microbiologie alimentaire et environnementale, Université catholique de Louvain, Croix du Sud 2/12, B-1348 Louvain-la-Neuve, Belgium. daniel.depalmenaer@uclouvain.be

ABSTRACT

Background: Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of approximately 70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family.

Results: A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus.

Conclusion: The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.

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Transposases vs. IRs and DRs. Comparative overview of IS sequence features. A. Dendrogram representing an alignment of 227 transposases. The first common node of each family was pointed out on the left tree side. Subgroups of family IS4 are mentioned on the right tree side. Individual IS names were removed for clarity. B. Consensus sequences (5' to 3') of left (upper line) and right (lower line) DNA extremities of distinct subgroups/families. '+' symbols are used when the highest conservation level is shared by more than one residue. Percentages of nucleotide conservation at all positions are indicated by black bars. Decimal nucleotide numbering is marked by dotted vertical lines. Full alignments that generated each consensus can be found in Additional files 1 to 10. Note that in the case of family IS701, the exposed consensus does not represent the entire family. For further details, see Additional file 8. IRL, left TIR; IRR, right TIR. C. Target duplication length range in bps.
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Figure 1: Transposases vs. IRs and DRs. Comparative overview of IS sequence features. A. Dendrogram representing an alignment of 227 transposases. The first common node of each family was pointed out on the left tree side. Subgroups of family IS4 are mentioned on the right tree side. Individual IS names were removed for clarity. B. Consensus sequences (5' to 3') of left (upper line) and right (lower line) DNA extremities of distinct subgroups/families. '+' symbols are used when the highest conservation level is shared by more than one residue. Percentages of nucleotide conservation at all positions are indicated by black bars. Decimal nucleotide numbering is marked by dotted vertical lines. Full alignments that generated each consensus can be found in Additional files 1 to 10. Note that in the case of family IS701, the exposed consensus does not represent the entire family. For further details, see Additional file 8. IRL, left TIR; IRR, right TIR. C. Target duplication length range in bps.

Mentions: The present assignment of families and subgroups is primarily based on transposase and DNA end sequence data. Analysis of transposases was performed by multiple sequence alignments and clustering methods followed by dendrogram construction to set up clusters of related proteins (see Methods). Left and right DNA extremities flanking transposase genes were aligned (i) to each other to facilitate observation of terminal inverted repeats (TIRs) and (ii) with TIRs from other ISs to detect DNA extremity conservations. Together, these approaches split the initial IS set into ten groups. In each of them, the percentage of residue identity among transposase pairs often varied between 20 % and 50 %, highlighting the magnitude of divergence occurring among elements of a same IS group. The length of TIRs ranged from 10 to 40 bp and many of them were imperfect. Comparison of TIRs from different elements of a given IS group uncovered unique and conserved signatures in each of them, illustrating the relationship between the transposase sequence and the IS terminal repeats (Figure 1).


IS4 family goes genomic.

De Palmenaer D, Siguier P, Mahillon J - BMC Evol. Biol. (2008)

Transposases vs. IRs and DRs. Comparative overview of IS sequence features. A. Dendrogram representing an alignment of 227 transposases. The first common node of each family was pointed out on the left tree side. Subgroups of family IS4 are mentioned on the right tree side. Individual IS names were removed for clarity. B. Consensus sequences (5' to 3') of left (upper line) and right (lower line) DNA extremities of distinct subgroups/families. '+' symbols are used when the highest conservation level is shared by more than one residue. Percentages of nucleotide conservation at all positions are indicated by black bars. Decimal nucleotide numbering is marked by dotted vertical lines. Full alignments that generated each consensus can be found in Additional files 1 to 10. Note that in the case of family IS701, the exposed consensus does not represent the entire family. For further details, see Additional file 8. IRL, left TIR; IRR, right TIR. C. Target duplication length range in bps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2266710&req=5

Figure 1: Transposases vs. IRs and DRs. Comparative overview of IS sequence features. A. Dendrogram representing an alignment of 227 transposases. The first common node of each family was pointed out on the left tree side. Subgroups of family IS4 are mentioned on the right tree side. Individual IS names were removed for clarity. B. Consensus sequences (5' to 3') of left (upper line) and right (lower line) DNA extremities of distinct subgroups/families. '+' symbols are used when the highest conservation level is shared by more than one residue. Percentages of nucleotide conservation at all positions are indicated by black bars. Decimal nucleotide numbering is marked by dotted vertical lines. Full alignments that generated each consensus can be found in Additional files 1 to 10. Note that in the case of family IS701, the exposed consensus does not represent the entire family. For further details, see Additional file 8. IRL, left TIR; IRR, right TIR. C. Target duplication length range in bps.
Mentions: The present assignment of families and subgroups is primarily based on transposase and DNA end sequence data. Analysis of transposases was performed by multiple sequence alignments and clustering methods followed by dendrogram construction to set up clusters of related proteins (see Methods). Left and right DNA extremities flanking transposase genes were aligned (i) to each other to facilitate observation of terminal inverted repeats (TIRs) and (ii) with TIRs from other ISs to detect DNA extremity conservations. Together, these approaches split the initial IS set into ten groups. In each of them, the percentage of residue identity among transposase pairs often varied between 20 % and 50 %, highlighting the magnitude of divergence occurring among elements of a same IS group. The length of TIRs ranged from 10 to 40 bp and many of them were imperfect. Comparison of TIRs from different elements of a given IS group uncovered unique and conserved signatures in each of them, illustrating the relationship between the transposase sequence and the IS terminal repeats (Figure 1).

Bottom Line: Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution.The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing.Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire de microbiologie alimentaire et environnementale, Université catholique de Louvain, Croix du Sud 2/12, B-1348 Louvain-la-Neuve, Belgium. daniel.depalmenaer@uclouvain.be

ABSTRACT

Background: Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of approximately 70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family.

Results: A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus.

Conclusion: The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.

Show MeSH
Related in: MedlinePlus