Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn 5 transposase 1 1Edited by G. Smith

Zhou, Maggie; Bhasin, Archna; Reznikoff, William S.

doi:10.1006/jmbi.1997.1579

Cited by 72 publications

(52 citation statements)

References 35 publications

(58 reference statements)

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“…The recognition of these borders in different combinations could result in the transposition of larger plasmid segments; however, such events would be dependent on the specificity of the IS801 transposase, which is currently unknown. Some transposases, such as that of Tn5, have been shown to have low specificities (53,86), while others, such as that of transposon Tn10, are capable of excision irrespective of the position or orientation of their terminal repeats (12). Thus, transposase transactivation and border specificity may play an important role in plasmid evolution.…”

Section: Resultsmentioning

confidence: 99%

Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

Stavrinides

Guttman

2004

J Bacteriol

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Plasmids are transmissible, extrachromosomal genetic elements that are often responsible for environmental or host-specific adaptations. In order to identify the forces driving the evolution of these important molecules, we determined the complete nucleotide sequence of the five-plasmid complement of the radish and Arabidopsis pathogen Pseudomonas syringae pv. maculicola ES4326 and conducted an intraspecific comparative genomic analysis. To date, this is the most complex fully sequenced plasmid complement of any gram-negative bacterium. The plasmid complement comprises two pPT23A-like replicons, pPMA4326A (46,697 bp) and pPMA4326B (40,110 bp); a pPS10-like replicon, pPMA4326C (8,244 bp); and two atypical, replicase-deficient replicons, pPMA4326D (4,833 bp) and pPMA4326E (4,217 bp). A complete type IV secretion system is found on pPMA4326A, while the type III secreted effector hopPmaA is present on pPMA4326B. The region around hopPmaA includes a shorter hopPmaA homolog, insertion sequence (IS) elements, and a three-element cassette composed of a resolvase, an integrase, and an exeA gene that is also present in several human pathogens. We have also identified a novel genetic element (E622) that is present on all but the smallest plasmid (pPMA4326E) that has features of an IS element but lacks an identifiable transposase. This element is associated with virulence-related genes found in a wide range of P. syringae strains. Comparative genomic analyses of these and other P. syringae plasmids suggest a role for recombination and integrative elements in driving plasmid evolution.

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Section: Resultsmentioning

confidence: 99%

Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

Stavrinides

Guttman

2004

J Bacteriol

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“…However, even if there is no direct evidence, some interesting mutant TEs have already been studied. Artificial changes in the sequence of some DNA transposons do seem to improve the cis-interaction between the element and the transposase protein, e.g., for the mariner element (Augé-Gouillou et al 2001), the Tn5 bacterial insertion sequence (Zhou et al 1998), or the reconstituted Sleeping Beauty element (Cui et al 2002). Furthermore, in Drosophila, some mutant elements could be able to replace the wild copies at the population scale, such as the hobo element (Souames et al 2003).…”

Section: Discussionmentioning

confidence: 99%

Population Genetics Models of Competition Between Transposable Element Subfamilies

Rouzic

Capy

2006

Genetics

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Transposable elements are one of the major components of genomes. Some copies are fully efficient; i.e., they are able to produce the proteins needed for their own transposition, and they can move and duplicate into the genome. Other copies are mutated. They may have lost their moving ability, their coding capacity, or both, thus becoming pseudogenes slowly eliminated from the genome through deletions and natural selection. Little is known about the dynamics of such mutant elements, particularly concerning their interactions with autonomous copies. To get a better understanding of the transposable elements' evolution after their initial invasion, we have designed a population genetics model of transposable elements dynamics including mutants or nonfunctional sequences. We have particularly focused on the case where these sequences are nonautonomous elements, known to be able to use the transposition machinery produced by the autonomous ones. The results show that such copies generally prevent the system from achieving a stable transposition-selection equilibrium and that nonautonomous elements can invade the system at the expense of autonomous ones. The resulting dynamics are mainly cyclic, which highlights the similarities existing between genomic selfish DNA sequences and host-parasite systems.

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“…This mutant is termed EK/LP and is the standard for this and other studies of Tn5 Tnp. The rate of transposition is further increased by replacing the naturally occurring end sequences with a 19-bp site termed the mosaic end (ME) (7). The combination of Tnp EK/LP and ME sequences has allowed the development of an efficient series of in vitro assays used to study the individual steps of the transposition process via gel shift (3) and catalytic assays (2,6,8,9).…”

Section: Tn5 Transposase (Tnp)mentioning

confidence: 99%

Tn5 Transposase Active Site Mutations Suggest Position of Donor Backbone DNA in Synaptic Complex

Peterson

Reznikoff

2003

Journal of Biological Chemistry

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Tn5 transposase (Tnp), a 53.3-kDa protein, enables the movement of transposon Tn5 by a conservative mechanism. Within the context of a protein and DNA synaptic complex, a single Tnp molecule catalyzes four sequential DNA breaking and joining reactions at the end of a single transposon. The three amino acids of the DDE motif (Asp-97, Asp-188, and Glu-326), which are conserved among transposases and retroviral integrases, have been shown previously to be absolutely required for all catalytic steps. To probe the effect of active site geometry on the ability to form synaptic complexes and perform catalysis, single mutations at each position of the DDE motif were constructed. The aspartates were changed to glutamates, and the glutamate was changed to an aspartate. These mutants were studied by performing in vitro binding assays using short oligonucleotide substrates simulating the natural substrates for the synaptic complex formation and subsequent transposition steps. The results indicate that the aspartate to glutamate mutations restrict synaptic complex formation with substrates resembling the natural transposon prior to transferred strand nicking. This suggests a structural model in which the donor backbone DNA, prior to nicking, occupies the same space that is invaded by the longer side chains present in the aspartate to glutamate mutants. Additionally, catalytic assays support the previous proposal that the active site coordinates two divalent metal ions.

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Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn 5 transposase 1 1Edited by G. Smith

Cited by 72 publications

References 35 publications

Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

Population Genetics Models of Competition Between Transposable Element Subfamilies

Tn5 Transposase Active Site Mutations Suggest Position of Donor Backbone DNA in Synaptic Complex

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