Anatomy of a preferred target site for the bacterial insertion sequence IS90311Edited by M. Gottesman

Hu, Wen-Yuan; Thompson, W. A.; Lawrence, Charles E.; Derbyshire, Keith M.

doi:10.1006/jmbi.2000.4421

Cited by 20 publications

(21 citation statements)

References 45 publications

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“…Mating-out assays were performed as described previously (52). The target conjugative plasmid was pUBF101, which contains a region preferred by IS903 for insertion (25), and the recipient was DH1 (Nal r ). pKD498 was used as the transposon delivery plasmid.…”

Section: Reagents and Chemicalsmentioning

confidence: 99%

Genetic Evidence that GTP Is Required for Transposition of IS 903 and Tn 552 in Escherichia coli

et al. 2005

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Surprisingly little is known about the role of host factors in regulating transposition, despite the potentially deleterious rearrangements caused by the movement of transposons. An extensive mutant screen was therefore conducted to identify Escherichia coli host factors that regulate transposition. An E. coli mutant library was screened using a papillation assay that allows detection of IS903 transposition events by the formation of blue papillae on a colony. Several host mutants were identified that exhibited a unique papillation pattern: a predominant ring of papillae just inside the edge of the colony, implying that transposition was triggered within these cells based on their spatial location within the colony. These mutants were found to be in pur genes, whose products are involved in the purine biosynthetic pathway. The transposition ring phenotype was also observed with Tn552, but not Tn10, establishing that this was not unique to IS903 and that it was not an artifact of the assay. Further genetic analyses of purine biosynthetic mutants indicated that the ring of transposition was consistent with a GTP requirement for IS903 and Tn552 transposition. Together, our observations suggest that transposition occurs during late stages of colony growth and that transposition occurs inside the colony edge in response to both a gradient of exogenous purines across the colony and the developmental stage of the cells.Transposons are defined as distinct regions of DNA that have the ability to move from one genomic location to another, a process mediated by element-encoded transposases (8, 9). While the main focus of transposition research has been in determining the detailed mechanisms of transposition, relatively little attention has been paid to how transposition is regulated in vivo or the in vivo requirements for the process (35). Transposon movement can result in gene inactivation (by insertional inactivation or deletion) or activation (by creation or introduction of promoters upstream of genes). In addition, intramolecular transposition can result in extensive DNA rearrangements, including deletions, inversions, and duplications of chromosome segments; these events are thought to play an important role in facilitating genome evolution (7-9). As the consequences of transposition can be either dire or favorable for the host organism, it is intuitive that the host has the capability to regulate this process. There are multiple examples of how transposons regulate their own movement, but very little work has focused on the role played by the host in regulating transposition. To address this, we have generated an insertion mutant library of Escherichia coli, which we have used to screen for host genes involved in regulation of IS903 transposition (E. Twiss, A. Coros, N. Tavakoli, and K. M. Derbyshire, unpublished data).The first comprehensive genetic screen for host mutants affecting transposition was carried out in 1985; it revealed a role for dam methylation in decreasing the rate of IS10, IS903, and IS50 transposi...

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Section: Reagents and Chemicalsmentioning

confidence: 99%

Genetic Evidence that GTP Is Required for Transposition of IS 903 and Tn 552 in Escherichia coli

et al. 2005

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“…Conversely, several recent studies have shown that the transfer from nonspecific to specific sites involves multiple dissociation͞ reassociations (25)(26)(27). For instance, the processivity of the EcoRV nuclease, its ability to cleave two recognition sites during one DNA-binding event, decreased as the separation of the sites was increased from 50 to 750 bp in a manner that excluded sliding from being the only route (25).…”

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confidence: 99%

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Gowers

Wilson

Halford

2005

Proc. Natl. Acad. Sci. U.S.A.

223

257

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Proteins that act at specific DNA sequences bind DNA randomly and then translocate to the target site. The translocation is often ascribed to the protein sliding along the DNA while maintaining continuous contact with it. Proteins also can move on DNA by multiple cycles of dissociation͞reassociation within the same chain. To distinguish these pathways, a strategy was developed to analyze protein motion between DNA sites. The strategy reveals whether the protein maintains contact with the DNA as it transfers from one site to another by sliding or whether it loses contact by a dissociation͞reassociation step. In reactions at low salt, the test protein stayed on the DNA as it traveled between sites, but only when the sites were <50 bp apart. Transfers of >30 bp at in vivo salt, and over distances of >50 bp at any salt, always included at least one dissociation step. Hence, for this enzyme, 1D sliding operates only over short distances at low salt, and 3D dissociation͞ reassociation is its main mode of translocation.DNA-protein interaction ͉ recognition sequence ͉ restriction enzyme

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“…Most YPAL targets overlap or coincide with palindromic sequences. This finding is not novel, since IS30 (25), IS1397 (29), IS903 (18), and IS621 (10) similarly tend to insert into regions of dyad symmetry. The notion that many YPAL targets may coincide with rho-independent transcriptional terminators also is not unprecedented, since Y. pestis IS1541 (23) and Mycoplasma fermentans IS1630 (6) have also been found inserted at rho-independent transcriptional terminators.…”

Section: Resultsmentioning

confidence: 87%

Structural Organization and Functional Properties of Miniature DNA Insertion Sequences in Yersiniae

et al. 2006

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YPALs (Yersinia palindromic sequences) are miniature DNA insertions scattered along the chromosomes of yersiniae. The spread of these intergenic repeats likely occurred via transposition, as suggested by the presence of target site duplications at their termini and the identification of syntenic chromosomal regions which differ in the presence/absence of YPAL DNA among Yersinia strains. YPALs tend to be inserted closely downstream from the stop codon of flanking genes, and many YPAL targets overlap rho-independent transcriptional terminator-like sequences. This peculiar pattern of insertion supports the hypothesis that most of these repeats are cotranscribed with upstream sequences into mRNAs. YPAL RNAs fold into stable hairpins which may modulate mRNA decay. Accordingly, we found that YPAL-positive transcripts accumulate in Yersinia enterocolitica cells at significantly higher levels than homologous transcripts lacking YPAL sequences in their 3 untranslated region.Bacterial insertion sequences (ISs) are mobile genetic elements ranging in size from 800 to 2,500 bp which are widely distributed among bacteria (21, 5). Typically, ISs encode a transposase which mediates their movement and feature terminal inverted repeats (TIRs) 10 to 50 bp long, which serve as recognition sites for the transposase. Most ISs generate short direct repeats (target site duplications [TSDs]) at the point of insertion. For each element, the length of the TSD is fixed and ranges from 2 to 13 bp. Differences in the structural organization, coding capacity, and transposition properties make it possible to sort ISs into approximately 20 major subfamilies (21).In recent years, it has emerged that small IS-like sequences called MITEs (for miniature transposable elements) may be a relevant genome component in several eukaryotic species (16,20). These elements characteristically measure 150 to 400 bp, carry long TIRs, and are flanked by TSDs of variable lengths. MITEs likely represent deletion derivatives of longer, autonomous ISs, which have been mobilized by tranposases encoded by partly related mobile donor elements (20). Several MITE families have also been identified in archaeabacteria (5). Three families of MITEs have been described for eubacteria. RUP (repeat unit of pneumococcus) elements are spread in ϳ100 copies in the genome of the Streptococcus pneumoniae 4 strain, and it has been proposed that their mobilization is mediated by the IS630-Spn1 element (24). NEMIS (Neisseria miniature insertion sequences) are 108-to 158-bp-long repeats which make up ϳ2% of the Neisseria meningitidis genome. In contrast to RUP elements, which are mostly interspersed with other repeated DNA sequences, NEMIS sequences are frequently located next to Neisseria genes and are transcribed into mRNAs. Hairpins formed by the pairing of NEMIS TIRs are targeted by RNase III, and this interaction regulates sets of N. meningitidis genes at the posttranscriptional level (12, 13).A different type of eubacterial MITE is represented by ERIC (enterobacterial repetitive i...

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Anatomy of a preferred target site for the bacterial insertion sequence IS90311Edited by M. Gottesman

Cited by 20 publications

References 45 publications

Genetic Evidence that GTP Is Required for Transposition of IS 903 and Tn 552 in Escherichia coli

Genetic Evidence that GTP Is Required for Transposition of IS 903 and Tn 552 in Escherichia coli

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Structural Organization and Functional Properties of Miniature DNA Insertion Sequences in Yersiniae

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