Pulling apart catalytically active Tn5 synaptic complexes using magnetic tweezers

Transposon Tn5

Tn5 was one of the first transposons to be identified ( 10 ). As a result of Tn5's early discovery and its simple macromolecular requirements for transposition, the Tn5 system has been a very productive tool for studying the molecular mechanism of DNA transposition. These studies are of broad value because they offer insights into DNA transposition in general, because DNA transposition is a useful model with which to understand other types of protein-DNA interactions such as retroviral DNA integration and the DNA cleavage events involved in immunoglobulin gene formation, and because Tn5-derived tools are useful adjuncts in genetic experimentation.

The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system

The histone-like nucleoid structuring protein (H-NS) is an important regulator of stress response and virulence genes in gram-negative bacteria. In addition to binding regulatory regions of genes in a structure-specific manner, H-NS also binds in a structure-specific manner to sites in the Tn10 transpososome, allowing it to act as a positive regulator of Tn10 transposition. This is the only example to date of H-NS regulating a transposition system by interacting directly with the transposition machinery. In general, transposition complexes tend to include segments of deformed DNA and given the capacity of H-NS to bind such structures, and the results from the Tn10 system, we asked if H-NS might regulate another transposition system (Tn5) by directly binding the transposition machinery. We show in the current work that H-NS does bind Tn5 transposition complexes and use hydroxyl radical footprinting to characterize the H-NS interaction with the Tn5 transpososome. We also show that H-NS can promote Tn5 transpososome formation in vitro, which correlates with the Tn5 system showing a dependence on H-NS for transposition in vivo. Taken together the results suggest that H-NS might play an important role in the regulation of many different bacterial transposition systems and thereby contribute directly to lateral gene transfer.

Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements

Single-DNA stretching and twisting experiments provide a sensitive means to detect binding of proteins, via detection of their modification of DNA mechanical properties. However, it is often difficult or impossible to determine the numbers of proteins bound in such experiments, especially when the proteins interact nonspecifically (bind stably at any sequence position) with DNA. Here we discuss how analogs of the Maxwell relations of classical thermodynamics may be defined and used to determine changes in numbers of bound proteins, from measurements of extension as a function of bulk protein concentration. We include DNA twisting in our analysis, which allows us to show how changes in torque along single DNA molecules may be determined from measurements of extension as a function of DNA linking number. We focus on relations relevant to common experimental situations (e.g., magnetic and optical tweezers with or without controlled torque or linking number). The relation of our results to Gibbs adsorption is discussed.