Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351

Dong, Qinghan; Sadouk, A.; Lelie, Daniël van der; Taghavi, Safiyh; Ferhat, A; Nuyten, J M; Borremans, B.; Mergeay, Max; Toussaint, Ariane

doi:10.1128/jb.174.24.8133-8138.1992

Cited by 50 publications

(27 citation statements)

References 31 publications

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“…That SpVl-R8A2 B viral DNA has an exactly analogous structure, but with a 1 bp spacer (Dong et al, 1992), suggests that it too is a packaged version of an IS element. The borders of many (Table 2, junctions Cl, C3, C6, E2, and X), though not all (Table 2, junctions El, Dl, and D8), chromosomal SpVl-R8A2 B sequences with other chromosomal sequences occur precisely at the IRR and IRL sequences (Bébéar et al, 1996;Laigret et al, 1996).…”

Section: Resultsmentioning

confidence: 99%

“…The substitutions detected relative to SpVl-R8A2 B made it unlikely that the elements function as proviruses. The ends of LI and LIO (Table 2, junctions Cl, C3, C6, and X) sequences were the IS30-like IRR or IRL sequences (Dong et al, 1992;Bébéar et al, 1996) expected from the transposase-mediated insertion of the SpVl-R8A2 B DNA in the chromosome.…”

Section: Resultsmentioning

confidence: 99%

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Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

Melcher¹,

Sha²,

Ye³

et al. 1999

Microbial & Comparative Genomics

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Genomes of Spiroplasma citri strains have rearranged frequently during their evolution, partly due to multiple integrated sequences of spiroplasma viruses. To understand better the role of viral sequences in genome evolution, we examined available nucleotide sequences of viruslike elements in the S. citri chromosome. Comparison of integrated and nonintegrated sequences of spiroplasma virus SpV1-C74 DNA suggested that it is an encapsidated form of the circular transposition intermediate belonging to an insertion sequence (IS3) family member. One SpV1-C74 viral DNA fragment was identified as interrupting the remains of a DNA adenine modification methylase gene. A viral DNA insertion of SpV1-R8A2 B DNA had hallmarks of having suffered an internal deletion by a site-specific recombination system. Homologous recombination likely was responsible for several deletions within viral DNA. A homologous recombination event was inferred between part of a viral DNA insertion and a similar chromosomal sequence. Dispersed sequences from SpV1-like C4 open reading frames (ORFs) were identified as involved in a complex deletion-inversion event. Thus, SpV1-like sequences likely have altered spiroplasma genomes by inserting within active genes, destroying their function, by providing targets for site-specific recombination, by mediating deletions of sequences adjacent to their integration sites, and by providing targets for homologous recombination, leading to inversions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

Melcher¹,

Sha²,

Ye³

et al. 1999

Microbial & Comparative Genomics

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show abstract

“…It contains copies of IS1086 (Dong et al 1992;Taghavi et al 1997) and Tn6049 ). Besides the hypothetical genes, some typical plasmid-related genes are present, such as repA, traY, mobA (likely knocked out by Tn6049), and mobB.…”

Section: Cmgi-5: a Plasmid Remnant?mentioning

confidence: 99%

New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria

Houdt

Monchy

Leys

et al. 2009

Antonie van Leeuwenhoek

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Cupriavidus metallidurans strain CH34 is a beta-Proteobacterium that thrives in low concentrations of heavy metals. The genetic determinants of resistance to heavy metals are located on its two chromosomes, and are particularly abundant in the two megaplasmids, pMOL28 and pMOL30. We explored the involvement of mobile genetic elements in acquiring these and others traits that might be advantageous in this strain using genome comparison of Cupriavidus/Ralstonia strains and related beta-Proteobacteria. At least eleven genomic islands were identified on the main replicon, three on pMOL28 and two on pMOL30. Multiple islands contained genes for heavy metal resistance or other genetic determinants putatively responding to harsh environmental conditions. However, cryptic elements also were noted. New mobile genetic elements (or variations of known ones) were identified through synteny analysis, allowing the detection of mobile genetic elements outside the bias of a selectable marker. Tn4371-like conjugative transposons involved in chemolithotrophy and degradation of aromatic compounds were identified in strain CH34, while similar elements involved in heavy metal resistance were found in Delftia acidovorans SPH-1 and Bordetella petrii DSM12804. We defined new transposons, viz., Tn6048 putatively involved in the response to heavy metals and Tn6050 carrying accessory genes not classically associated with transposons. Syntenic analysis also revealed new transposons carrying metal response genes in Burkholderia xenovorans LB400, and other bacteria. Finally, other putative mobile elements, which were previously unnoticed but apparently common in several bacteria, were also revealed. This was the case for triads of tyrosine-based site-specific recombinases and for an int gene paired with a putative repressor and associated with chromate resistance.

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“…Di¡erent from the results in which the transposition frequency of the insertion sequence IS1086 was 1000 times greater at 37 ‡C compared to that at 30 ‡C, the Tn3 translocation varied between 26 and 30 ‡C [23]. Above 30 ‡C the frequency dropped drastically up to null when the temperature was 37 ‡C [24].…”

Section: Strains With Primer Tnp 1 -Ampli¢ed Sequencesmentioning

confidence: 78%

Transposon Tn1721 distribution among strains of Xylella fastidiosa

Ferreira

2002

FEMS Microbiology Letters

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Transposons are mobile genetic elements found within the genomes of various organisms including bacteria, fungi, plants and animals. Fragments of the transposon Tn1721 were found included in the genome of Xylella fastidiosa strain 9a5c. Regions from such fragments were PCR-amplified using specially designed primers (TNP 1 and TNP 2 ). In order to detect insertions of the Tn1721 element, both primers were used and one of them included a region of the transposon (TNP 1 ) and the other one had the right repeat and part of the bacterial chromosome (TNP 2 ). The PCR products obtained from strain 9a5c were used as a pattern for fragment size comparisons when DNA samples from other X. fastidiosa strains were used as template for the PCR assays. Differences were observed concerning the PCR products of such amplifications when some X. fastidiosa strains isolated from grapevine and plum were used. For the citrus-derived strains only the strains U187d and GP920b produced fragments with different sizes or weak band intensity. Such variations in the X. fastidiosa genome related to disrupted Tn1721 copies are probably due to the possibility of such a transposon element being still able to duplicate even after deletion events might have taken place and also because the bacterial strains in which the main differences were detected are derived from different host plants cultivated under different climate conditions from the one used as reference. ß

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Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351

Cited by 50 publications

References 31 publications

Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria

Transposon Tn1721 distribution among strains of Xylella fastidiosa

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