Visualizing Mu transposition: assembling the puzzle pieces

Rice, Phoebe A.

doi:10.1101/gad.1309305

Cited by 6 publications

(4 citation statements)

References 21 publications

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“…that of retroviral integrase; Nowotny, 2009; Hickman et al , 2010). The wide range of sequences that can be recognized and distinguished is readily understood by the fact that these enzymes are multidomain proteins containing dedicated sequence‐specific DNA‐binding domains (Davies et al , 2000; Watkins et al , 2004; Rice, 2005; Richardson et al , 2009). Therefore, successfully identifying their own transposon ends does not appear to be a conceptually sophisticated matter.…”

Section: Discussionmentioning

confidence: 99%

DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans

Hickman

James

Barábas

et al. 2010

EMBO J

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Bacterial insertion sequences (ISs) from the IS200/IS605 family encode the smallest known DNA transposases and mobilize through single-stranded DNA transposition. Transposition by one particular family member, ISDra2 from Deinococcus radiodurans, is dramatically stimulated upon massive c irradiation. We have determined the crystal structures of four ISDra2 transposase/IS end complexes; combined with in vivo activity assays and fluorescence anisotropy binding measurements, these have revealed the molecular basis of strand discrimination and transposase action. The structures also show that previously established structural rules of target site recognition that allow different specific sequences to be targeted are only partially conserved among family members. Furthermore, we have captured a fully assembled active site including the scissile phosphate bound by a divalent metal ion cofactor (Cd 2 þ ) that supports DNA cleavage. Finally, the observed active site rearrangements when the transposase binds a metal ion in which it is inactive provide a clear rationale for metal ion specificity.

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Section: Discussionmentioning

confidence: 99%

DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans

Hickman

James

Barábas

et al. 2010

EMBO J

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“…( B ) Domain and subdomain organization of MuA as assigned by partial proteolysis (140). NMR and crystal structures for the individual (except IIIβ) are available (9, 62, 141). The subdomain IIβ was observed in crystal structures (142), while IIIα and IIIβ were delineated by mutagenesis and functional studies (9).…”

Section: Figmentioning

confidence: 99%

Transposable Phage Mu

Harshey

2014

Microbiol Spectr

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Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.

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“…The sequence-specific DNA binding function that allows the transposase to locate the ends of its mobile element can reside in a single domain or be distributed among several domains. For example, MuA transposase recognizes its transposon ends using a winged helix DNA binding domain followed by an HTH domain (reviewed in Chaconas and Harshey, 2002; Rice, 2005); members of the mariner family use two HTH domains (reviewed in Plasterk et al , 1999; van Pouderoyen et al , 1997; Watkins et al , 2004; Richardson et al , 2009); and OrfAB, the transposase of IS 911 , uses a single HTH domain (Rousseau et al , 2002). …”

Section: Rnase H-like Dna Transposases Are Modular Proteinsmentioning

confidence: 99%

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

Hickman

Chandler

Dyda

2010

Critical Reviews in Biochemistry and Molecular Biology

132

165

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DNA rearrangements are important in genome function and evolution. Genetic material can be rearranged inadvertently during processes such as DNA repair, or can be moved in a controlled manner by enzymes specifically dedicated to the task. DNA transposases comprise one class of such enzymes. These move DNA segments known as transposons to new locations, without the need for sequence homology between transposon and target site. Several biochemically distinct pathways have evolved for DNA transposition, and genetic and biochemical studies have provided valuable insights into many of these. However, structural information on transposases – particularly with DNA substrates – has proven elusive in most cases. On the other hand, large-scale genome sequencing projects have led to an explosion in the number of annotated prokaryotic and eukaryotic mobile elements. Here, we briefly review biochemical and mechanistic aspects of DNA transposition, and propose that integrating sequence information with structural information using bioinformatics tools such as secondary structure prediction and protein threading can lead not only to an additional level of understanding but possibly also to testable hypotheses regarding transposition mechanisms. Detailed understanding of transposition pathways is a prerequisite for the long-term goal of exploiting DNA transposons as genetic tools and as a basis for genetic medical applications.

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Visualizing Mu transposition: assembling the puzzle pieces

Cited by 6 publications

References 21 publications

DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans

DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans

Transposable Phage Mu

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

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