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Mechanisms for Defining Supercoiling Set Point of DNA Gyrase Orthologs

E. Tretter,J. Berger

Published 2012 in Journal of Biological Chemistry

ABSTRACT

Background: The mechanisms controlling DNA supercoiling efficiency by gyrase are not understood. Results: A nonconserved C-terminal tail in GyrA controls DNA binding, wrapping, and supercoiling set point. Conclusion: The tail is a novel regulatory element that modulates gyrase activity. Significance: Intrinsic properties of gyrase can be fine-tuned to boost enzyme output. DNA topoisomerases manage chromosome supercoiling and organization in all cells. Gyrase, a prokaryotic type IIA topoisomerase, consumes ATP to introduce negative supercoils through a strand passage mechanism. All type IIA topoisomerases employ a similar set of catalytic domains for function; however, the activity and specificity of gyrase are augmented by a specialized DNA binding and wrapping element, termed the C-terminal domain (CTD), which is appended to its GyrA subunit. We have discovered that a nonconserved, acidic tail at the extreme C terminus of the Escherichia coli GyrA CTD has a dramatic and unexpected impact on gyrase function. Removal of the CTD tail enables GyrA to introduce writhe into DNA in the absence of GyrB, an activity exhibited by other GyrA orthologs, but not by wild-type E. coli GyrA. Strikingly, a “tail-less” gyrase holoenzyme is markedly impaired for DNA supercoiling capacity, but displays normal ATPase function. Our findings reveal that the E. coli GyrA tail regulates DNA wrapping by the CTD to increase the coupling efficiency between ATP turnover and supercoiling, demonstrating that CTD functions can be fine-tuned to control gyrase activity in a highly sophisticated manner.

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