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Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons.

Tourasse NJ, Stabell FB, Kolstø AB - Nucleic Acids Res. (2014)

Bottom Line: IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS).Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified.In addition, introns and IS elements related to those that were at the origin of IStrons were also identified.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway Institut de Biologie Physico-Chimique, UMR CNRS 7141, Université Pierre et Marie Curie, Paris, France nicolas.tourasse@ibpc.fr.

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Predicted secondary structure of the BcISt1 IStron and comparison of key structural features of group A and B IStrons. In the BcISt1 structure, labels P1 to P9 indicate the group I intron domains and subdomains. The IR and DR motifs in the IR stem-loop region of BcISt1 are colored in red and blue. The boxed inset shows the predicted structure of IRs in the ORF-less copies of BcISt1 that were obtained experimentally in this study (see Figure 7) and that were also identified in the genome sequences of emetic strains of B. cereus. The IGS stem is colored in orange. Exon sequences are in lowercase. Splice sites are indicated by arrows. A comparison of the P1 subdomains of various IStrons is shown to illustrate that the U–G pair that is critical for 5′ splice site recognition is surrounded by flanking base-pairs within the IGS stem in group A IStrons, whereas it is predicted to be immediately followed by an internal loop in group B elements, where it is shifted by one bp relative to the splice site. For group A IStrons, bases corresponding to the subterminal palindromes that are required for IS200/IS605 elements (see Figure 3) are highlighted in purple. A comparison of the IR regions is also shown to illustrate that the IR stem is short and compositionally balanced in group A IStrons, in contrast to the long and extremely AU-rich stem in group B elements. The IS (transposase) component is represented by a circle. The structural models shown are from selected representatives that illustrate the variability in sequence and structure. Sequences of the 5′ and 3′ ends of the other IStrons, which are highly similar to those shown here, can be seen in Figure 3. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses.
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Figure 4: Predicted secondary structure of the BcISt1 IStron and comparison of key structural features of group A and B IStrons. In the BcISt1 structure, labels P1 to P9 indicate the group I intron domains and subdomains. The IR and DR motifs in the IR stem-loop region of BcISt1 are colored in red and blue. The boxed inset shows the predicted structure of IRs in the ORF-less copies of BcISt1 that were obtained experimentally in this study (see Figure 7) and that were also identified in the genome sequences of emetic strains of B. cereus. The IGS stem is colored in orange. Exon sequences are in lowercase. Splice sites are indicated by arrows. A comparison of the P1 subdomains of various IStrons is shown to illustrate that the U–G pair that is critical for 5′ splice site recognition is surrounded by flanking base-pairs within the IGS stem in group A IStrons, whereas it is predicted to be immediately followed by an internal loop in group B elements, where it is shifted by one bp relative to the splice site. For group A IStrons, bases corresponding to the subterminal palindromes that are required for IS200/IS605 elements (see Figure 3) are highlighted in purple. A comparison of the IR regions is also shown to illustrate that the IR stem is short and compositionally balanced in group A IStrons, in contrast to the long and extremely AU-rich stem in group B elements. The IS (transposase) component is represented by a circle. The structural models shown are from selected representatives that illustrate the variability in sequence and structure. Sequences of the 5′ and 3′ ends of the other IStrons, which are highly similar to those shown here, can be seen in Figure 3. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses.

Mentions: Multiple sequence alignment showing the IStron target sites, boundaries and sequence ends. Omitted regions are indicated by the sign ‘[…]’. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses next to IStron names. IStron-less sequences homologous to IStron flanking exons are included to confirm IStron boundaries (sequences named by their GenBank accession numbers only). Also included are IS elements (ISDra2 and ISBth15 from D. radiodurans and B. thuringiensis, respectively, taken from the ISfinder database) and group I introns (GenBank accessions ACJY01000107 and ADMN01000043 from F. periodonticum and T. sanguinis, respectively) with ends and target sites similar to those of IStrons. Group A and B IStrons are inserted next to T-rich pentanucleotide and GG-containing sites, respectively, which are boxed in cyan. Note that the target site of group B IStrons does not end with a U, unlike for virtually all known group I introns. In group A IStrons, the regions corresponding to the subterminal palindromes that are recognized by the ORF A transposase during transposition of IS200/IS605 elements are highlighted in yellow. For group B IStrons, imperfect AT-rich IR motifs that are presumed to be recognized by the ORF A transposase during transposition of IS607 elements are highlighted in light blue. IR motifs forming the IR stem in the group I intron structure of IStrons (see Figure 4) are boxed in black. The direct repeat sequence (3′ DR) that is similar to part of the 5′ IR motif (5′ IR/5′ DR) and that is located immediately upstream of, and is globally complementary to, the 3′ IR motif in group B IStrons is boxed in yellow.


Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons.

Tourasse NJ, Stabell FB, Kolstø AB - Nucleic Acids Res. (2014)

Predicted secondary structure of the BcISt1 IStron and comparison of key structural features of group A and B IStrons. In the BcISt1 structure, labels P1 to P9 indicate the group I intron domains and subdomains. The IR and DR motifs in the IR stem-loop region of BcISt1 are colored in red and blue. The boxed inset shows the predicted structure of IRs in the ORF-less copies of BcISt1 that were obtained experimentally in this study (see Figure 7) and that were also identified in the genome sequences of emetic strains of B. cereus. The IGS stem is colored in orange. Exon sequences are in lowercase. Splice sites are indicated by arrows. A comparison of the P1 subdomains of various IStrons is shown to illustrate that the U–G pair that is critical for 5′ splice site recognition is surrounded by flanking base-pairs within the IGS stem in group A IStrons, whereas it is predicted to be immediately followed by an internal loop in group B elements, where it is shifted by one bp relative to the splice site. For group A IStrons, bases corresponding to the subterminal palindromes that are required for IS200/IS605 elements (see Figure 3) are highlighted in purple. A comparison of the IR regions is also shown to illustrate that the IR stem is short and compositionally balanced in group A IStrons, in contrast to the long and extremely AU-rich stem in group B elements. The IS (transposase) component is represented by a circle. The structural models shown are from selected representatives that illustrate the variability in sequence and structure. Sequences of the 5′ and 3′ ends of the other IStrons, which are highly similar to those shown here, can be seen in Figure 3. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses.
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Figure 4: Predicted secondary structure of the BcISt1 IStron and comparison of key structural features of group A and B IStrons. In the BcISt1 structure, labels P1 to P9 indicate the group I intron domains and subdomains. The IR and DR motifs in the IR stem-loop region of BcISt1 are colored in red and blue. The boxed inset shows the predicted structure of IRs in the ORF-less copies of BcISt1 that were obtained experimentally in this study (see Figure 7) and that were also identified in the genome sequences of emetic strains of B. cereus. The IGS stem is colored in orange. Exon sequences are in lowercase. Splice sites are indicated by arrows. A comparison of the P1 subdomains of various IStrons is shown to illustrate that the U–G pair that is critical for 5′ splice site recognition is surrounded by flanking base-pairs within the IGS stem in group A IStrons, whereas it is predicted to be immediately followed by an internal loop in group B elements, where it is shifted by one bp relative to the splice site. For group A IStrons, bases corresponding to the subterminal palindromes that are required for IS200/IS605 elements (see Figure 3) are highlighted in purple. A comparison of the IR regions is also shown to illustrate that the IR stem is short and compositionally balanced in group A IStrons, in contrast to the long and extremely AU-rich stem in group B elements. The IS (transposase) component is represented by a circle. The structural models shown are from selected representatives that illustrate the variability in sequence and structure. Sequences of the 5′ and 3′ ends of the other IStrons, which are highly similar to those shown here, can be seen in Figure 3. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses.
Mentions: Multiple sequence alignment showing the IStron target sites, boundaries and sequence ends. Omitted regions are indicated by the sign ‘[…]’. GenBank accession numbers of genomic sequences encoding the IStrons shown are given in parentheses next to IStron names. IStron-less sequences homologous to IStron flanking exons are included to confirm IStron boundaries (sequences named by their GenBank accession numbers only). Also included are IS elements (ISDra2 and ISBth15 from D. radiodurans and B. thuringiensis, respectively, taken from the ISfinder database) and group I introns (GenBank accessions ACJY01000107 and ADMN01000043 from F. periodonticum and T. sanguinis, respectively) with ends and target sites similar to those of IStrons. Group A and B IStrons are inserted next to T-rich pentanucleotide and GG-containing sites, respectively, which are boxed in cyan. Note that the target site of group B IStrons does not end with a U, unlike for virtually all known group I introns. In group A IStrons, the regions corresponding to the subterminal palindromes that are recognized by the ORF A transposase during transposition of IS200/IS605 elements are highlighted in yellow. For group B IStrons, imperfect AT-rich IR motifs that are presumed to be recognized by the ORF A transposase during transposition of IS607 elements are highlighted in light blue. IR motifs forming the IR stem in the group I intron structure of IStrons (see Figure 4) are boxed in black. The direct repeat sequence (3′ DR) that is similar to part of the 5′ IR motif (5′ IR/5′ DR) and that is located immediately upstream of, and is globally complementary to, the 3′ IR motif in group B IStrons is boxed in yellow.

Bottom Line: IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS).Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified.In addition, introns and IS elements related to those that were at the origin of IStrons were also identified.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Oslo, Norway Institut de Biologie Physico-Chimique, UMR CNRS 7141, Université Pierre et Marie Curie, Paris, France nicolas.tourasse@ibpc.fr.

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Related in: MedlinePlus