Bacterial Insertion Sequences

Ohtsubo, Eiichi; Sekine, Yoshiaki

doi:10.1007/978-3-642-79795-8_1

Cited by 51 publications

(49 citation statements)

References 150 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although a member of the IS3 family, IS2 differs significantly from its better-characterized relatives, IS3 and IS911. For example, IS2 transposition is associated with a 5 bp target site duplication (Rosenberg et al, 1978;Sengstag et al, 1983;Lewis et al, 1994a), whereas both IS3 and IS911 are associated with 3 bp duplications (Sommer et al, 1979, see also Ohtsubo and Sekine, 1996;Prere et al, 1990) In this paper, we have examined the effect of pre-engineering the orfA-orfB frameshift on transposition of IS2. We can readily detect both IS minicircles and figure-eight molecules, extending the IS911 findings to a second member of the IS3 family.…”

Section: Fig 1 Derivatives Of Is2mentioning

confidence: 99%

“…Its 1.3-kb DNA sequence indicates that it is a member of the large IS3 family, which includes IS elements from a wide variety of bacteria from E. coli to mycobacteria and mycoplasma (for reviews see Polard and Chandler, 1995a;Ohtsubo and Sekine, 1996). The transposase proteins of IS3 family members have a catalytic domain that is homologous to those of certain other bacterial transposons, such as phage Mu, Tn7 and Tn552, and to the catalytic domains of the integrases of retroviruses, such as HIV and ASV, and retrotransposons, such as the yeast Ty elements Rowland and Dyke, 1990;Kahn et al, 1991;Kulkosky et al, 1992;Baker and Luo, 1994;see Craig, 1996).…”

Section: Introductionmentioning

confidence: 99%

“…1) to produce an OrfAB fusion protein. A second common feature of these IS elements is the conservation of the dinucleotide, 5Ј-CA-3Ј, at the 3Ј ends of the element (Polard and Chandler, 1995a;Ohtsubo and Sekine, 1996). Transposase-mediated cleavage occurs to the 3Ј side of this dinucleotide and the resulting -CA OH is the active species in the subsequent insertion into target DNA (see Mizuuchi, 1992).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway

Lewis

Grindley

1997

Molecular Microbiology

View full text Add to dashboard Cite

SummaryThe Escherichia coli insertion sequence, IS2, is a member of the IS3 family of bacterial transposable elements. Its transposase is a fusion protein, OrfAB, made by a programmed ¹1 translational frameshift near to the end of orfA and just after the start of orfB. We have characterized two major products of IS2 intramolecular transposition, which accumulate in cells that express the IS2 OrfAB fusion protein at elevated levels. The more abundant product is a minicircle composed of the complete IS2 with just a single basepair (occasionally 2 bp) separating the two IS ends. In all cases, this basepair is derived from the vector sequence immediately adjacent to the left IS2 end (IRL). The second product is a figure-eight molecule that contains all the IS2 and vector sequences present in the parental plasmid. One DNA strand contains the parental sequences unrearranged. The other contains a single-stranded version of the minicircle junction -the precise 3Ј end of IRR has been cleaved and joined to a target just outside the 5Ј end of IRL; the remaining vector sequences have a free 5Ј end, derived from cleavage at the 3Ј end of IRR, and a free 3Ј end, released upon cleavage of the target site adjacent to IRL. We propose that figure-eight molecules are the precursor to IS2 minicircles and that the formation of these two products is the initial step in IS2 intermolecular transposition. This proposed transposition pathway provides a means for a transposase that can cleave only one strand at each IS end to produce simple insertions and avoid forming co-integrates.

show abstract

Section: Fig 1 Derivatives Of Is2mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway

Lewis

Grindley

1997

Molecular Microbiology

View full text Add to dashboard Cite

show abstract

“…The first group of transposons consists of the cut-and-paste elements, which move strictly through DNA intermediates. Examples of this type of transposon include the bacterial insertion sequences, the eukaryotic Tc1/Mariner elements, maize Ac/Ds elements, and Drosophila P elements (8,20,24,29,32). The second group, the retrotransposons, transpose through an RNA intermediate.…”

mentioning

confidence: 99%

Target Specificity of the Endonuclease from theXenopus laevisNon-Long Terminal Repeat Retrotransposon, Tx1L

Christensen

Pont-Kingdon

Carroll

2000

Molecular and Cellular Biology

View full text Add to dashboard Cite

Elements of the Tx1L family are non-long terminal repeat retrotransposons (NLRs) that are dispersed in the genome of Xenopus laevis. Essentially all genomic copies of Tx1L are found inserted at a specific site within another family of transposable elements (Tx1D). This suggests that Tx1L is a site-specific retrotransposon. Like many (but not all) other NLRs, the Xenopus element encodes an apparent endonuclease that is related in sequence to the apurinic-apyrimidinic endonucleases that participate in DNA repair. This enzyme is thought to introduce the single-strand break in target DNA that initiates transposition by the target-primed reverse transcription (TPRT) mechanism. To explore the issue of target specificity more fully, we expressed the polypeptide encoded by the endonuclease domain of open reading frame 2 from Tx1L (Tx1L EN) and characterized its cleavage capabilities. This endonuclease makes a specific nick in the bottom strand precisely at one end of the presumed Tx1L target duplication. Because this activity leaves a 5-phosphate and 3-hydroxyl at the nick, it has the location and chemistry required to initiate new insertion events by TPRT. Tx1L EN does not make a specific cut at a preferred target site for Tx1D elements, ruling out the alternative possibility that the composite Tx1L-Tx1D element moves as a unit under the control of functions encoded by Tx1L. Further characterization revealed that the endonuclease remains active for many hours at room temperature and that it is capable of enzymatic turnover. Scanning substitution mutagenesis located the recognition site for Tx1L EN within 10 bp surrounding the primary nick site. Implications of these features for natural transposition events are discussed.Transposons are ubiquitous mobile genetic elements found in the genomes of most, if not all, organisms. They can be grouped into two main categories based on sequence organization and mode (or presumed mode) of transposition (3). The first group of transposons consists of the cut-and-paste elements, which move strictly through DNA intermediates. Examples of this type of transposon include the bacterial insertion sequences, the eukaryotic Tc1/Mariner elements, maize Ac/Ds elements, and Drosophila P elements (8,20,24,29,32). The second group, the retrotransposons, transpose through an RNA intermediate.The retrotransposons can be further subdivided into two subgroups that differ in sequence organization and mechanisms of retrotransposition. The retrovirus-like long terminal repeat (LTR) retrotransposons reverse transcribe their RNA genome in the cytoplasm, producing a double-stranded DNA copy with terminal direct repeats. This species is transported to the cell nucleus, where it is integrated into chromosomal DNA courtesy of an element-encoded integrase. Examples of this type of retrotransposon are Ty1 and Ty3 of Saccharomyces cerevisiae, Copia and 412 from Drosophila, and Tf1 from Schizosaccharomyces pombe (3).Although they also rely on reverse transcription, the non-LTR retrotransposons (NLRs) transpose...

show abstract

“…IS630 family elements are known to preferentially transpose to and consequently duplicate upon insertion a 59-TA-39 dinucleotide sequence (Ohtsubo & Sekine, 1996;Mahillon & Chandler, 1998). This feature is recognized also in eukaryotic Tc1/mariner family elements (Plasterk et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

A new insertion sequence, IS14999, from Corynebacterium glutamicum

et al. 2005

View full text Add to dashboard Cite

A new insertion sequence from Corynebacterium glutamicum ATCC 14999 was isolated and characterized. This IS element, designated IS14999, comprised a 1149 bp nucleotide sequence with 22 bp imperfect terminal inverted repeats. IS14999 carries a single open reading frame of 345 amino acids encoding a putative transposase that appears to have partial homology to IS642, an IS630/Tc1 superfamily element, at the C-terminal region in the amino acid sequence. This indicated that IS14999 belonged to the IS630/Tc1 superfamily, which was first identified in C. glutamicum. IS14999 has a unique distance of 38 amino acid residues between the second and third amino acids in the DDE motif, which is well known as the catalytic centre of transposase. This suggested that IS14999 constituted a new subfamily of the IS630/Tc1 superfamily. A phylogenetic tree constructed on the basis of amino acid sequences of transposases revealed that this new transposable element was more similar to eukaryotic Tc1/mariner family elements than to prokaryotic IS630 family elements. Added to the fact that IS14999 was present in only a few C. glutamicum strains, this implies that IS14999 was probably acquired by a recent lateral transfer event from eukaryotic cells. Analysis of the insertion site in C. glutamicum R revealed that IS14999 appeared to transpose at random and always caused a target duplication of a 59-TA-39 dinucleotide upon insertion, like the other IS630/Tc1 family elements. These findings indicated that IS14999 could be a powerful tool for genetic manipulation of corynebacteria and related species.

show abstract

Bacterial Insertion Sequences

Cited by 51 publications

References 150 publications

Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway

Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway

Target Specificity of the Endonuclease from theXenopus laevisNon-Long Terminal Repeat Retrotransposon, Tx1L

A new insertion sequence, IS14999, from Corynebacterium glutamicum

Contact Info

Product

Resources

About