Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

• Published in: Molecular cell Vol. 81; no. 7; pp. 1499 - 1514.e6
• Main Authors: Stracy, Mathew, Schweizer, Jakob, Sherratt, David J., Kapanidis, Achillefs N., Uphoff, Stephan, Lesterlin, Christian
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.04.2021; Cell Press
• Subjects: Chromosome-crowding; chromosome-free cells; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; single-molecule tracking; target search of bacterial DNA-binding proteins; target search of bacterial DNA-binding proteins; single-molecule tracking; Chromosome-crowding; chromosome-free cells
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2021.01.039

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. Toward 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 is not 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. [Display omitted] •Protein motion was compared between unperturbed cells and DNA-free cells•Protein mobility was dictated by DNA interactions rather than molecular weight•The nucleoid is not a physical barrier for protein diffusion•The proteins studied spend most (58%–99%) of their search time bound to DNA To understand how DNA-binding proteins find their target sites, Stracy et al. tracked the motion of 11 diverse proteins in living Escherichia coli. By comparing protein behavior in normal cells and cells without chromosomes, they showed that the DNA-binding proteins spend most of their search time bound to DNA.