Transposition of Cyanobacterium Insertion Element ISY<i>100</i>in<i>Escherichia coli</i>

Urasaki, Akihiro; Sekine, Yoshiaki; Ohtsubo, Eiichi

doi:10.1128/jb.184.18.5104-5112.2002

Cited by 13 publications

(19 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, based on previous reports that many IS110/IS492 family elements do not generate duplication of the target site sequence upon insertion (14,23,30), we cannot exclude the possibility that 1,279-bp-long IS621 is inserted into the target site without duplication. We have been trying to develop a system for transposing IS621 into the target plasmid with or without a REP sequence by using methods that have been used previously to transpose IS elements, such as IS1, IS3, and ISY100 (41,42,48), but we have failed to do so. IS492, an IS110/IS492 family element, is known to generate circular IS492 molecules with an extra 5-bp sequence immediately adjacent to the element (35).…”

Section: Discussionmentioning

confidence: 99%

A Novel IS Element, IS 621 , of the IS 110 /IS 492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli

2003

Self Cite

View full text Add to dashboard Cite

An Escherichia coli strain, ECOR28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. This insertion sequence (named IS621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. A computer-aided homology search using the DNA sequence as the query revealed that IS621 was homologous to the piv genes, encoding pilin gene invertase (PIV). A homology search using the amino acid sequence of the putative protein encoded by IS621 as the query revealed that the protein also has partial homology to transposases encoded by the IS110/IS492 family elements, which were known to have partial homology to PIV. This indicates that IS621 belongs to the IS110/IS492 family but is most closely related to the piv genes. In fact, a phylogenetic tree constructed on the basis of amino acid sequences of PIV proteins and transposases revealed that IS621 belongs to the piv gene group, which is distinct from the IS110/IS492 family elements, which form several groups. PIV proteins and transposases encoded by the IS110/IS492 family elements, including IS621, have four acidic amino acid residues, which are conserved at positions in their N-terminal regions. These residues may constitute a tetrad D-E(or D)-D-D motif as the catalytic center. Interestingly, IS621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS621 may not recognize the entire REP sequence in transposition, but it recognizes a 15-bp sequence conserved in the REP sequences around the target site. There are several elements belonging to the IS110/IS492 family that also transpose to specific sites in the repeated sequences, as does IS621. IS621 does not have terminal inverted repeats like most of the IS110/IS492 family elements. The terminal sequences of IS621 have homology with the 26-bp inverted repeat sequences of pilin gene inversion sites that are recognized and used for inversion of pilin genes by PIV. This suggests that IS621 initiates transposition through recognition of their terminal regions and cleavage at the ends by a mechanism similar to that used for PIV to promote inversion at the pilin gene inversion sites.

show abstract

Section: Discussionmentioning

confidence: 99%

A Novel IS Element, IS 621 , of the IS 110 /IS 492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli

2003

Self Cite

View full text Add to dashboard Cite

show abstract

“…Southern hybridization was carried out against PCR products on 0.8% agarose gels according to Urasaki et al (2002), using a p-SINE1 probe that had been labeled with digoxigenin using a DIG-oligonucleotide 3' end labeling kit (Roche).…”

Section: Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism

Kurata

Akimoto

et al. 2005

Genes Genet. Syst.

Self Cite

View full text Add to dashboard Cite

Of the rice species with an AA genome, Oryza meridionalis has been identified in northern Australia as a species of the annual type, among those previously classified as Oryza perennis , Oryza rufipogon or Oryza nivara . This notion has, however, led to some confusion to determine which strains belong to O. meridionalis and how different these strains are from the O. rufipogon strains of the annual type. In this paper, we examined Australian wild rice strains for the presence or absence of p-SINE1 members, which have been used for identification of the strains of species with the AA genome, by PCR using primers that hybridize to the sequences flanking each p-SINE1 member. The rice strains examined include perennial and annual strains, which have previously been described as O. rufipogon . We found that all the annual strains and other strains, whose types have not been determined, have p-SINE1 members that are specifically present at the corresponding loci in the standard strains of O. meridionalis , but do not have those which are specifically present at the corresponding loci in the strains of the other species with the AA genome. The perennial strains, however, have p-SINE1 members that are specifically present at the corresponding loci in the standard O. rufipogon strains of either the annual or the perennial type, but do not have those which are specifically present at the corresponding loci in the strains of the other species with the AA genome, including O. meridionalis . These findings support the previous notion that O. meridionalis consists of the annual strains and is a distinct species from O. rufipogon . The p-SINE1 members used in this study appear to be very useful for classification of any wild rice strains of the AA-genome species, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains.

show abstract

“…IS14999 is thought not to need any host factors in its transposition because it has been reported that IS630/Tc1 superfamily elements do not require any host factors (Craig, 1997;Urasaki et al, 2002). This would be an advantage for using IS14999 as a tool for genetic manipulation in various bacteria.…”

Section: Discussionmentioning

confidence: 97%

“…Moreover, Tc1/mariner family elements, like IS630 family elements, also have conserved DDE or DDD triad amino acids as an essential part of their catalytic site, and mutations in the triad abolished transposase activity (Lohe et al, 1997). Consequently, these two families form a mega-family, the IS630/Tc1 superfamily, whose elements share a similar signature sequence or motif in the catalytic domain of their respective transposases (Shao & Tu, 2001;Urasaki et al, 2002). The only difference is that Tc1/mariner family elements appear to be excised from their donor molecules, leaving an empty site with an extra sequence, called a footprint (Plasterk, 1996), like those of other element families.…”

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

Transposition of Cyanobacterium Insertion Element ISY100inEscherichia coli

Cited by 13 publications

References 44 publications

A Novel IS Element, IS 621 , of the IS 110 /IS 492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli

A Novel IS Element, IS 621 , of the IS 110 /IS 492 Family Transposes to a Specific Site in Repetitive Extragenic Palindromic Sequences in Escherichia coli

Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism

A new insertion sequence, IS14999, from Corynebacterium glutamicum

Contact Info

Product

Resources

About