Rapid, DNA-induced interface swapping by DNA gyrase

DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase
formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to
form the active complex. GyrA is usually found as a dimer in solution,
whereas GyrB can exist as a monomer. DNA gyrase is able to loop DNA around
the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a
transient double-strand break (DSB) established in another duplex. This
results in the conversion of a positive loop into a negative one, thereby
introducing negative supercoiling into the bacterial genome, an activity
essential for DNA replication and transcription. The strong protein
interface in the GyrA dimer must be broken to allow passage of the
transported DNA segment and it is generally assumed that the interface is
usually stable and only opens when DNA is transported, to prevent the
introduction of deleterious DSBs in the genome. In this paper we show that
DNA gyrase can exchange its DNA-cleaving interfaces between two active
heterotetramers. This so-called interface “swapping” or “exchange” (IS)
can occur within a few minutes in solution. We also show that bending of
DNA by gyrase is essential for cleavage but not for DNA bindingper seand
favors IS. interface swapping is also favored by DNA wrapping and an
excess of GyrB. We suggest that proximity, promoted by GyrB
oligomerization and binding and wrapping along a length of DNA, between
two heterotetramers favors rapid interface exchange. This exchange does
not require ATP, can occur in the presence of fluoroquinolones, and raises
the possibility of non-homologous recombination solely through gyrase
activity. The ability of gyrase to undergo interface swapping also
explains how gyrase heterodimers, containing a single active-site
tyrosine, can carry out double-strand passage reactions and therefore
suggests an alternative explanation to the recently proposed “swivelling”
mechanism for DNA gyrase (Gubaev, Weidlich, and Klostermeier 2016).