Nearly precise excision: a new type of DNA alteration associated with the translocatable element Tn10

Ross, Donald G.; Swan, Judith; Kleckner, Nancy

doi:10.1016/0092-8674(79)90089-8

Cited by 61 publications

(22 citation statements)

References 13 publications

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“…This synthesis must open the template duplex and is likely to be prone to template switching, which has been observed in many situations, especially for the PolA repair polymerase (Ross et al 1979;Ahmed and Podemski 1998;Pinder et al 1998;Lovett 2004;Lee et al 2007). Strand extension after this template switch generates a branched structure that can be resolved either by chromosome replication or by repair of the three-way junction to yield a symmetrical inversion duplication (see nick indicated in Figure 2).…”

Section: Resultsmentioning

confidence: 99%

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

et al. 2010

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During growth under selection, mutant types appear that are rare in unselected populations. Stressinduced mechanisms may cause these structures or selection may favor a series of standard events that modify common preexisting structures. One such mutation is the short junction (SJ) duplication with long repeats separated by short sequence elements: AB*(CD)*(CD)*E (* ¼ a few bases). Another mutation type, described here, is the tandem inversion duplication (TID), where two copies of a parent sequence flank an inverse-order segment: AB(CD)(E9D9C9B9)(CD)E. Both duplication types can amplify by unequal exchanges between direct repeats (CD), and both are rare in unselected cultures but common after prolonged selection for amplification. The observed TID junctions are asymmetric (aTIDs) and may arise from a symmetrical precursor (sTID)-ABCDE(E9D9C9B9A9)ABCDE-when sequential deletions remove each palindromic junction. Alternatively, one deletion can remove both sTID junctions to generate an SJ duplication. It is proposed that sTID structures form frequently under all growth conditions, but are usually lost due to their instability and fitness cost. Selection for increased copy number helps retain the sTID and favors deletions that remodel junctions, improve fitness, and allow higher amplification. Growth improves with each step in formation of an SJ or aTID amplification, allowing selection to favor completion of the mutation process.

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Section: Resultsmentioning

confidence: 99%

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

et al. 2010

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“…Note that similar effects are also known to occur by homologous recombination between two inverted or directly repeated IS copies in a replicon. Other known mechanisms such as cut-and-paste, or Copy out-Paste in (donor primed transposon replication) (34) would not generate this type of genomic rearrangement but could contribute to genomic modifications in other ways such as "nearly precise excision" (123,124) or by using alternative sequences that resemble their IR (125,126). …”

Section: Influence Of Transposition Mechanismsmentioning

confidence: 99%

Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

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“…Excision of transposable elements can also dramatically affect gene activity. Excision is imprecise for most transposons, and this results in sequence alterations remaining at the sites of excision (2,5,9,12,53,58,61,67,69). Imprecise excision of transposable elements can lead to proteins that have altered molecular weights (63), enzymatic activities (14,69), and developmental patterns of gene expression (10,40).…”

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confidence: 99%

Insertion and excision of Caenorhabditis elegans transposable element Tc1.

Eide

Anderson

1988

Mol. Cell. Biol.

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The transposable element Tcl is responsible for most spontaneous mutations that occur in Caenorhabditis ekgans variety Bergerac. We investigated the genetic and molecular properties of Tcl transposition and excision. We show that Tcl insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tcl insertion sites were similar to each other, and we present a consensus sequence for Tcl insertion that describes these similarities. We show that Tcl excision was usually imprecise. Tcl excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tcl somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tcl excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tcl transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specffic manner as germ-line excision was. In a genetic background where Tcl transposition and excision in the germ line was not detectable, Tcl excision in the soma still occurred at high frequency.

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Nearly precise excision: a new type of DNA alteration associated with the translocatable element Tn10

Cited by 61 publications

References 13 publications

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

The Tandem Inversion Duplication inSalmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types

Everyman's Guide to Bacterial Insertion Sequences

Insertion and excision of Caenorhabditis elegans transposable element Tc1.

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