scholarly journals The Mu transpososome structure sheds light on DDE recombinase evolution

Nature ◽  
2012 ◽  
Vol 491 (7424) ◽  
pp. 413-417 ◽  
Author(s):  
Sherwin P. Montaño ◽  
Ying Z. Pigli ◽  
Phoebe A. Rice
Keyword(s):  
Mu Transpososome

scholarly journals Path of DNA within the Mu Transpososome

Cell ◽  
2002 ◽  
Vol 109 (4) ◽  
pp. 425-436 ◽  
Author(s):  
Shailja Pathania ◽  
Makkuni Jayaram ◽  
Rasika M Harshey
Keyword(s):  
Mu Transpososome

Determining the topology of stable protein–DNA complexes

2013 ◽  
Vol 41 (2) ◽  
pp. 601-605 ◽  
Author(s):  
Isabel K. Darcy ◽  
Mariel Vazquez
Keyword(s):  
Present Article ◽  
Experimental Technique ◽  
Topological Structure ◽  
Reaction Pathway ◽  
Dna Supercoiling ◽  
Dna Complexes ◽  
Nucleoprotein Complex ◽  
Mu Transpososome ◽  
Dna Complex

Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in a stable protein–DNA complex. Difference topology has also been used to detect intermediates in a reaction pathway and to investigate the role of DNA supercoiling. In the present article, we review difference topology as applied to the Mu transpososome. The tools discussed can be applied to any stable nucleoprotein complex.

scholarly journals A topological analysis of difference topology experiments of condensin with Topoisomerases II

2019 ◽  
Author(s):  
Soojeong Kim ◽  
Isabel K. Darcy
Keyword(s):  
Simple Model ◽  
Experimental Technique ◽  
Topological Analysis ◽  
Simple Experiment ◽  
Dna Complexes ◽  
3 Dimensional ◽  
Model Protein ◽  
Summary Statement ◽  
Mu Transpososome ◽  
Dimensional Ball

ABSTRACTAn experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time-consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.SUMMARY STATEMENTTangles are used to model protein-DNA complexes: A 3-dimensional ball represents protein while strings embedded in this ball represent protein-bound DNA. We use this simple model to analyze experimental results.

scholarly journals Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
James R Fuller ◽  
Phoebe A Rice
Keyword(s):  
Reaction Rate ◽  
Dna Bending ◽  
Target Site ◽  
Strand Transfer ◽  
Bacteriophage Mu ◽  
Target Dna ◽  
Order Of Magnitude ◽  
Mu Transpososome ◽  
Transposition Reaction ◽  
Selection Of

The transposition of bacteriophage Mu serves as a model system for understanding DDE transposases and integrases. All available structures of these enzymes at the end of the transposition reaction, including Mu, exhibit significant bends in the transposition target site DNA. Here we use Mu to investigate the ramifications of target DNA bending on the transposition reaction. Enhancing the flexibility of the target DNA or prebending it increases its affinity for transpososomes by over an order of magnitude and increases the overall reaction rate. This and FRET confirm that flexibility is interrogated early during the interaction between the transposase and a potential target site, which may be how other DNA binding proteins can steer selection of advantageous target sites. We also find that the conformation of the target DNA after strand transfer is involved in preventing accidental catalysis of the reverse reaction, as conditions that destabilize this conformation also trigger reversal.

scholarly journals The AAA+ ClpX machine unfolds a keystone subunit to remodel the Mu transpososome

2010 ◽  
Vol 107 (6) ◽  
pp. 2437-2442 ◽  
Author(s):  
A. H. Abdelhakim ◽  
R. T. Sauer ◽  
T. A. Baker
Keyword(s):  
Mu Transpososome

scholarly journals Mu transpososome and RecBCD nuclease collaborate in the repair of simple Mu insertions

2014 ◽  
Vol 111 (39) ◽  
pp. 14112-14117 ◽  
Author(s):  
Wonyoung Choi ◽  
Sooin Jang ◽  
Rasika M. Harshey
Keyword(s):  
Mu Transpososome
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