Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein

被引：7

作者：

Yadav, Indresh ^{[1
]}

Basak, Rajib ^{[1
]}

Yan, Peiyan ^{[1
]}

van Kan, Jeroen A. ^{[1
]}

Arluison, Veronique ^{[2
,3
]}

van der Maarel, Johan R. C. ^{[1
]}

机构：

[1] Natl Univ Singapore, Dept Phys, Singapore 117542, Singapore

[2] Univ Paris, UFR SDV, F-75006 Paris, France

[3] Univ Paris Saclay, Lab Leon Brillouin, CNRS, CEA, F-91191 Gif Sur Yvette, France

来源：

JOURNAL OF PHYSICAL CHEMISTRY LETTERS | 2020年 / 11卷 / 19期

关键词：

SINGLE DNA; FACILITATED DIFFUSION; RNA-POLYMERASE; HFQ; COMPACTION; ELONGATION; MOLECULES; DYNAMICS; BINDING; SEARCH;

D O I：

10.1021/acs.jpclett.0c02251

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.

引用

页码：8424 / 8429

页数：6

共 40 条

[1] Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid [J].

Azam, TA ;

Iwata, A ;

Nishimura, A ;

Ueda, S ;

Ishihama, A .

JOURNAL OF BACTERIOLOGY, 1999, 181 (20) :6361-6370

[2] Short Residence Times of DNA-Bound Transcription Factors Can Reduce Gene Expression Noise and Increase the Transmission of Information in a Gene Regulation System [J].

Azpeitia, Eugenio ;

Wagner, Andreas .

FRONTIERS IN MOLECULAR BIOSCIENCES, 2020, 7

[3] A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA [J].

Blainey, PC ;

van Oijent, AM ;

Banerjee, A ;

Verdine, GL ;

Xie, XS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (15) :5752-5757

[4] Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA [J].

Bonnet, Isabelle ;

Biebricher, Andreas ;

Porte, Pierre-Louis ;

Loverdo, Claude ;

Benichou, Olivier ;

Voituriez, Raphael ;

Escude, Christophe ;

Wende, Wolfgang ;

Pingoud, Alfred ;

Desbiolles, Pierre .

NUCLEIC ACIDS RESEARCH, 2008, 36 (12) :4118-4127

[5] Hopping Diffusion of Nanoparticles in Polymer Matrices [J].

Cai, Li-Heng ;

Panyukov, Sergey ;

Rubinstein, Michael .

MACROMOLECULES, 2015, 48 (03) :847-862

[6] The Escherichia Coli Hfq Protein: An Unattended DNA-Transactions Regulator [J].

Cech, Grzegorz M. ;

Szalewska-Palasz, Agnieszka ;

Kubiak, Krzysztof ;

Malabirade, Antoine ;

Grange, Wilfried ;

Ailuison, Veronique ;

Wegrzyn, Grzegorz .

FRONTIERS IN MOLECULAR BIOSCIENCES, 2016, 3

[7] Hfq protein deficiency in Escherichia coli affects ColE1-like but not λ plasmid DNA replication [J].

Cech, Grzegorz M. ;

Pakula, Bartosz ;

Kamrowska, Dominika ;

Wegrzyn, Grzegorz ;

Arluison, Veronique ;

Szalewska-Palasz, Agnieszka .

PLASMID, 2014, 73 :10-15

[8] DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid [J].

Chow, Edmond ;

Skolnick, Jeffrey .

BIOPHYSICAL JOURNAL, 2017, 112 (11) :2261-2270

[9] The polymer physics of single DNA confined in nanochannels [J].

Dai, Liang ;

Renner, C. Benjamin ;

Doyle, Patrick S. .

ADVANCES IN COLLOID AND INTERFACE SCIENCE, 2016, 232 :80-100

[10] Rapid movement and transcriptional re-localization of human cohesin on DNA [J].

Davidson, Iain F. ;

Goetz, Daniela ;

Zaczek, Maciej P. ;

Molodtsov, Maxim I. ;

in't Veld, Pim J. Huis ;

Weissmann, Florian ;

Litos, Gabriele ;

Cisneros, David A. ;

Ocampo-Hafalla, Maria ;

Ladurner, Rene ;

Uhlmann, Frank ;

Vaziri, Alipasha ;

Peters, Jan-Michael .

EMBO JOURNAL, 2016, 35 (24) :2671-2685

← 1 2 3 4 →