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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.

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.

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Target sites : duplications and conservations. Consensus sequences of in silico reconstructed and aligned target sites (5' to 3') typical for each subgroup or family. Only ISs found at least at five different genomic locations and flanked by DRs were considered, as well as elements described previously in literature. Each box represents one base position. Target sites are divided in three parts. The central sequence, which is duplicated upon insertion, is flanked by one upstream (left) and one downstream (right) target arm. Ten bps of each arm are shown. The number of target sites considered for each element is indicated. If more than one element displayed similar insertion specificity, their insertion sites were combined into a single line and their names listed above it. Gray boxes inside a duplication consensus indicate that DRs of variable length can be found for the given element. W, A or T; S, G or C; R, A or G; Y, T or C. * 'IS231' stands for following elements: IS231A, C, F, M, S, T, U, Y, ISBce4, 5, 6, 11, 12 and ISBth5. ** For the 6000 sites, see references [75–77].
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Figure 3: Target sites : duplications and conservations. Consensus sequences of in silico reconstructed and aligned target sites (5' to 3') typical for each subgroup or family. Only ISs found at least at five different genomic locations and flanked by DRs were considered, as well as elements described previously in literature. Each box represents one base position. Target sites are divided in three parts. The central sequence, which is duplicated upon insertion, is flanked by one upstream (left) and one downstream (right) target arm. Ten bps of each arm are shown. The number of target sites considered for each element is indicated. If more than one element displayed similar insertion specificity, their insertion sites were combined into a single line and their names listed above it. Gray boxes inside a duplication consensus indicate that DRs of variable length can be found for the given element. W, A or T; S, G or C; R, A or G; Y, T or C. * 'IS231' stands for following elements: IS231A, C, F, M, S, T, U, Y, ISBce4, 5, 6, 11, 12 and ISBth5. ** For the 6000 sites, see references [75–77].

Mentions: To validate this clustering, established groups were analysed independently for conservation of specific transposase domains as well as length and specificity of target site duplications. Analysis of transposase DDE catalytic regions (N2, N3 and C1) revealed a perfect conservation of the DDE motif (Figure 2), while the size and sequence of the spacers that separate these catalytic residues differed among the ten groups. The YREK motif was partially lacking in three groups, where either its tyrosine, arginine or lysine residue was not conserved. According to the definition of IS families, IS groups sharing the same catalytic site structure were assigned together. Seven clusters displayed the complete YREK motif; and were named subgroups IS231, ISH8, IS4Sa, IS4, ISPepr1, IS10 and IS50. The three remaining groups all displayed a distinct variation of the YREK motif and were therefore assigned to different and new families, namely IS701, ISH3 and IS1634, referred as emerging families. Finally, while IS4 family members generated about 10 bp target duplications, i.e. the approximate length of a complete DNA helix turn, those from emerging families displayed direct repeats (DRs) of around five bps, which corresponds approximately to half a DNA helix turn (Figures 1 &3).


IS4 family goes genomic.

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

Target sites : duplications and conservations. Consensus sequences of in silico reconstructed and aligned target sites (5' to 3') typical for each subgroup or family. Only ISs found at least at five different genomic locations and flanked by DRs were considered, as well as elements described previously in literature. Each box represents one base position. Target sites are divided in three parts. The central sequence, which is duplicated upon insertion, is flanked by one upstream (left) and one downstream (right) target arm. Ten bps of each arm are shown. The number of target sites considered for each element is indicated. If more than one element displayed similar insertion specificity, their insertion sites were combined into a single line and their names listed above it. Gray boxes inside a duplication consensus indicate that DRs of variable length can be found for the given element. W, A or T; S, G or C; R, A or G; Y, T or C. * 'IS231' stands for following elements: IS231A, C, F, M, S, T, U, Y, ISBce4, 5, 6, 11, 12 and ISBth5. ** For the 6000 sites, see references [75–77].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Target sites : duplications and conservations. Consensus sequences of in silico reconstructed and aligned target sites (5' to 3') typical for each subgroup or family. Only ISs found at least at five different genomic locations and flanked by DRs were considered, as well as elements described previously in literature. Each box represents one base position. Target sites are divided in three parts. The central sequence, which is duplicated upon insertion, is flanked by one upstream (left) and one downstream (right) target arm. Ten bps of each arm are shown. The number of target sites considered for each element is indicated. If more than one element displayed similar insertion specificity, their insertion sites were combined into a single line and their names listed above it. Gray boxes inside a duplication consensus indicate that DRs of variable length can be found for the given element. W, A or T; S, G or C; R, A or G; Y, T or C. * 'IS231' stands for following elements: IS231A, C, F, M, S, T, U, Y, ISBce4, 5, 6, 11, 12 and ISBth5. ** For the 6000 sites, see references [75–77].
Mentions: To validate this clustering, established groups were analysed independently for conservation of specific transposase domains as well as length and specificity of target site duplications. Analysis of transposase DDE catalytic regions (N2, N3 and C1) revealed a perfect conservation of the DDE motif (Figure 2), while the size and sequence of the spacers that separate these catalytic residues differed among the ten groups. The YREK motif was partially lacking in three groups, where either its tyrosine, arginine or lysine residue was not conserved. According to the definition of IS families, IS groups sharing the same catalytic site structure were assigned together. Seven clusters displayed the complete YREK motif; and were named subgroups IS231, ISH8, IS4Sa, IS4, ISPepr1, IS10 and IS50. The three remaining groups all displayed a distinct variation of the YREK motif and were therefore assigned to different and new families, namely IS701, ISH3 and IS1634, referred as emerging families. Finally, while IS4 family members generated about 10 bp target duplications, i.e. the approximate length of a complete DNA helix turn, those from emerging families displayed direct repeats (DRs) of around five bps, which corresponds approximately to half a DNA helix turn (Figures 1 &3).

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