RT Journal Article
SR Electronic
T1 Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.08.13.249771
DO 10.1101/2020.08.13.249771
A1 Stracy, Mathew
A1 Schweizer, Jakob
A1 Sherratt, David J
A1 Kapanidis, Achillefs N
A1 Uphoff, Stephan
A1 Lesterlin, Christian
YR 2020
UL http://biorxiv.org/content/early/2020/08/13/2020.08.13.249771.abstract
AB Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Towards identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions, rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid does not pose a physical barrier for protein diffusion, but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58-99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome-crowding likely has important implications for the function of all DNA-binding proteins.Competing Interest StatementThe authors have declared no competing interest.