Auxiliary ATP binding sites support DNA unwinding by RecBCD

Rani Zananiri, Sivasubramanyan Mangapuram Venkata, Vera Gaydar, Dan Yahalom, Omri Malik, Sergei Rudnizky, Oded Kleifeld, Ariel Kaplan () and Arnon Henn ()
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Rani Zananiri: Faculty of Biology, Technion - Israel Institute of Technology
Sivasubramanyan Mangapuram Venkata: Faculty of Biology, Technion - Israel Institute of Technology
Vera Gaydar: Faculty of Biology, Technion - Israel Institute of Technology
Dan Yahalom: Faculty of Biology, Technion - Israel Institute of Technology
Omri Malik: Faculty of Biology, Technion - Israel Institute of Technology
Sergei Rudnizky: Faculty of Biology, Technion - Israel Institute of Technology
Oded Kleifeld: Faculty of Biology, Technion - Israel Institute of Technology
Ariel Kaplan: Faculty of Biology, Technion - Israel Institute of Technology
Arnon Henn: Faculty of Biology, Technion - Israel Institute of Technology

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract The RecBCD helicase initiates double-stranded break repair in bacteria by processively unwinding DNA with a rate approaching ∼1,600 bp·s−1, but the mechanism enabling such a fast rate is unknown. Employing a wide range of methodologies — including equilibrium and time-resolved binding experiments, ensemble and single-molecule unwinding assays, and crosslinking followed by mass spectrometry — we reveal the existence of auxiliary binding sites in the RecC subunit, where ATP binds with lower affinity and distinct chemical interactions as compared to the known catalytic sites. The essentiality and functionality of these sites are demonstrated by their impact on the survival of E.coli after exposure to damage-inducing radiation. We propose a model by which RecBCD achieves its optimized unwinding rate, even when ATP is scarce, by using the auxiliary binding sites to increase the flux of ATP to its catalytic sites.

Date: 2022
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DOI: 10.1038/s41467-022-29387-1

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