1887

Abstract

is a chromosomal ∼155 bp repeated element found uniquely and ubiquitously in the group of Gram-positive bacteria; it exhibits several features characteristic of mobile elements, including a variable distribution pattern between strains. Here, highly similar elements in non-conserved genomic loci are identified in a set of closely related and strains near the phylogenetic cluster. It is also shown that may be present on small RNA transcripts in the 100–400 bp size range. folding of at the RNA level indicated that transcripts may form a double-hairpin-like structure predicted to have high structural stability. A functional role of at the RNA level is supported by multiple cases of G–U base-pairing, and compensatory mutations maintaining structural stability of the RNA fold. folding at the DNA level produced similar predicted structures, with the potential to form a cruciform structure at open DNA complexes. The predicted structural stability was greater for elements showing high sequence identities to elements in non-conserved chromosomal loci in other strains, relative to other copies. mobility could thus be dependent on the formation of a stable DNA or RNA intermediate. Furthermore, elements potentially encoding structurally stable and less stable transcripts were phylogenetically intermixed, indicating that loss of mobility may have occurred multiple times during evolution. Repeated elements with similar features in other bacteria have been shown to provide functions such as mRNA stabilization, transcription termination and/or promoter function. Similarly, may constitute a mobile element which occasionally gains a function when it enters an appropriate chromosomal locus.

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2007-11-01
2019-11-19
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Chromosomal coordinates of 159 full-length repeats in the genomes of ATCC 10987 (Cereus_10987; 84 full-length repeats; AE017194), Ames (Ba_Ames; 15 full-length repeats; AE016879), 97-27 (Bt_Konkukian; 29 full-length repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 31 full-length repeats; CP000001). [ PDF] (13 kb) Chromosomal coordinates of 493 partial repeats in the genomes of ATCC 10987 (Cereus_10987; 212 partial repeats; AE017194), Ames (Banthracis_Ames; 91 partial repeats; AE016879), 97-27 (Bt_konkukian; 93 partial repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 97 partial repeats; CP000001). [ PDF] (30 kb) Multiple sequence alignment of 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L and ATCC 10987, abbreviated as Ba, Btk, E33L and Bce, respectively. Sequences were aligned using CLUSTAL W (Thompson , 1994) followed by manual editing using SEAVIEW (Galtier , 1996). A plot of the conservation of each site was generated by CLUSTAL_X (Thompson , 1997) and is shown below the alignment. Nucleotides are coloured by the following scheme: dA (red), dC (cyan), dG (orange), dT (green). Sequence lengths are given to the left of the alignment. Indels are represented by dashes. The asterisk at the top of the alignment indicates the only site conserved in all sequences. [ PDF] (2.2 Mb) Predicted RNA folding, using MFOLD (Zuker, 2003), of the 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L (Cereus ZK) and ATCC 10987, with predicted Δ (dg) values (kcal mol ; 1 kcal=4.184 kJ). [ PDF] (2.9 Mb) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. , 543-548. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 4673-4680. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 4876-4882. Mfold web server for nucleic acid folding and hybridization prediction. , 3406-3415.

PDF

Chromosomal coordinates of 159 full-length repeats in the genomes of ATCC 10987 (Cereus_10987; 84 full-length repeats; AE017194), Ames (Ba_Ames; 15 full-length repeats; AE016879), 97-27 (Bt_Konkukian; 29 full-length repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 31 full-length repeats; CP000001). [ PDF] (13 kb) Chromosomal coordinates of 493 partial repeats in the genomes of ATCC 10987 (Cereus_10987; 212 partial repeats; AE017194), Ames (Banthracis_Ames; 91 partial repeats; AE016879), 97-27 (Bt_konkukian; 93 partial repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 97 partial repeats; CP000001). [ PDF] (30 kb) Multiple sequence alignment of 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L and ATCC 10987, abbreviated as Ba, Btk, E33L and Bce, respectively. Sequences were aligned using CLUSTAL W (Thompson , 1994) followed by manual editing using SEAVIEW (Galtier , 1996). A plot of the conservation of each site was generated by CLUSTAL_X (Thompson , 1997) and is shown below the alignment. Nucleotides are coloured by the following scheme: dA (red), dC (cyan), dG (orange), dT (green). Sequence lengths are given to the left of the alignment. Indels are represented by dashes. The asterisk at the top of the alignment indicates the only site conserved in all sequences. [ PDF] (2.2 Mb) Predicted RNA folding, using MFOLD (Zuker, 2003), of the 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L (Cereus ZK) and ATCC 10987, with predicted Δ (dg) values (kcal mol ; 1 kcal=4.184 kJ). [ PDF] (2.9 Mb) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. , 543-548. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 4673-4680. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 4876-4882. Mfold web server for nucleic acid folding and hybridization prediction. , 3406-3415.

PDF

Chromosomal coordinates of 159 full-length repeats in the genomes of ATCC 10987 (Cereus_10987; 84 full-length repeats; AE017194), Ames (Ba_Ames; 15 full-length repeats; AE016879), 97-27 (Bt_Konkukian; 29 full-length repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 31 full-length repeats; CP000001). [ PDF] (13 kb) Chromosomal coordinates of 493 partial repeats in the genomes of ATCC 10987 (Cereus_10987; 212 partial repeats; AE017194), Ames (Banthracis_Ames; 91 partial repeats; AE016879), 97-27 (Bt_konkukian; 93 partial repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 97 partial repeats; CP000001). [ PDF] (30 kb) Multiple sequence alignment of 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L and ATCC 10987, abbreviated as Ba, Btk, E33L and Bce, respectively. Sequences were aligned using CLUSTAL W (Thompson , 1994) followed by manual editing using SEAVIEW (Galtier , 1996). A plot of the conservation of each site was generated by CLUSTAL_X (Thompson , 1997) and is shown below the alignment. Nucleotides are coloured by the following scheme: dA (red), dC (cyan), dG (orange), dT (green). Sequence lengths are given to the left of the alignment. Indels are represented by dashes. The asterisk at the top of the alignment indicates the only site conserved in all sequences. [ PDF] (2.2 Mb) Predicted RNA folding, using MFOLD (Zuker, 2003), of the 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L (Cereus ZK) and ATCC 10987, with predicted Δ (dg) values (kcal mol ; 1 kcal=4.184 kJ). [ PDF] (2.9 Mb) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. , 543-548. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 4673-4680. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 4876-4882. Mfold web server for nucleic acid folding and hybridization prediction. , 3406-3415.

PDF

Chromosomal coordinates of 159 full-length repeats in the genomes of ATCC 10987 (Cereus_10987; 84 full-length repeats; AE017194), Ames (Ba_Ames; 15 full-length repeats; AE016879), 97-27 (Bt_Konkukian; 29 full-length repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 31 full-length repeats; CP000001). [ PDF] (13 kb) Chromosomal coordinates of 493 partial repeats in the genomes of ATCC 10987 (Cereus_10987; 212 partial repeats; AE017194), Ames (Banthracis_Ames; 91 partial repeats; AE016879), 97-27 (Bt_konkukian; 93 partial repeats; AE017355), E33L (formerly known as Zebra Killer, Cereus_ZK; 97 partial repeats; CP000001). [ PDF] (30 kb) Multiple sequence alignment of 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L and ATCC 10987, abbreviated as Ba, Btk, E33L and Bce, respectively. Sequences were aligned using CLUSTAL W (Thompson , 1994) followed by manual editing using SEAVIEW (Galtier , 1996). A plot of the conservation of each site was generated by CLUSTAL_X (Thompson , 1997) and is shown below the alignment. Nucleotides are coloured by the following scheme: dA (red), dC (cyan), dG (orange), dT (green). Sequence lengths are given to the left of the alignment. Indels are represented by dashes. The asterisk at the top of the alignment indicates the only site conserved in all sequences. [ PDF] (2.2 Mb) Predicted RNA folding, using MFOLD (Zuker, 2003), of the 159 full-length repeats identified in the genomes of Ames, subsp. (97-27), E33L (Cereus ZK) and ATCC 10987, with predicted Δ (dg) values (kcal mol ; 1 kcal=4.184 kJ). [ PDF] (2.9 Mb) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. , 543-548. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 4673-4680. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 4876-4882. Mfold web server for nucleic acid folding and hybridization prediction. , 3406-3415.

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