Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching

Year: 2018

Authors: Tempestini A., Monico C., Gardini L., Vanzi F., Pavone FS., Capitanio M.

Autors Affiliation: LENS European Lab Nonlinear Spect, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy; Univ Florence, Dept Phys & Astron, Via Sansone 1, I-50019 Sesto Fiorentino, Italy; CNR, Natl Inst Opt, Largo Fermi 6, I-50125 Florence, Italy; Dept Biol, Via Madonna Piano 6, I-50019 Sesto Fiorentino, Italy; Int Ctr Computat Neurophoton, Via Nello Carrara 1, I-50019 Sesto Fiorentino, FI, Italy.

Abstract: In any living cell, genome maintenance is carried out by DNA-binding proteins that recognize specific sequences among a vast amount of DNA. This includes fundamental processes such as DNA replication, DNArepair, and gene expression and regulation. Here, we study the mechanism of DNA target search by a single lac repressor protein (LacI) with ultrafast force-clamp spectroscopy, a sub-millisecond and few base-pair resolution technique based on laser tweezers. We measure 1D-diffusion of proteins on DNA at physiological salt concentrations with 20 bp resolution and find that sliding of LacI along DNA is sequence dependent. We show that only allosterically activated LacI slides along non-specific DNA sequences during target search, whereas the inhibited conformation does not support sliding and weakly interacts with DNA. Moreover, we find that LacI undergoes a load-dependent conformational change when it switches between sliding and strong binding to the target sequence. Our data reveal how DNA sequence and molecular switching regulate LacI target search process and provide a comprehensive model of facilitated diffusion for LacI.

Journal/Review: NUCLEIC ACIDS RESEARCH

Volume: 46 (10)      Pages from: 5001  to: 5011

More Information: European Union´s Horizon 2020 Research and Innovation Programme [654148 Laserlab-Europe]; Italian Ministry of University and Research (FIRB ´Futuro in Ricerca´ 2013 [RBFR13V4M2], and Flagship Project NANOMAX); Ente Cassa di Risparmio di Firenze. Funding for open access charge: Italian Ministry of University and Research Flagship Project NANOMAX.
KeyWords: diffusion-driven mechanisms; facilitated target location; operator interaction; optical tweezers; nucleic-acids
DOI: 10.1093/nar/gky208

Citations: 17
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