One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism

Abstract Several DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional...

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Autores principales:	Takashi Kinebuchi, Nobuo Shimamoto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4eca2dec88a64cbd952c2513c9843ae3
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spelling	oai:doaj.org-article:4eca2dec88a64cbd952c2513c9843ae32021-12-02T10:54:06ZOne-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism10.1038/s41598-021-83156-62045-2322https://doaj.org/article/4eca2dec88a64cbd952c2513c9843ae32021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83156-6https://doaj.org/toc/2045-2322Abstract Several DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional diffusion also has been suggested to cause the effect for proteins with single DNA sites, the diffusion mechanism, which could violate detailed balance. We addressed which mechanism is possible for E. coli TrpR showing 104-fold antenna effect with a single DNA binding site. When a trpO-harboring DNA fragment was connected to a nonspecific DNA with biotin-avidin connection, the otherwise sevenfold antenna effect disappeared. This result denies the looping mechanism with an unknown second DNA binding site. The 3.5-fold repression by TrpR in vivo disappeared when a tight LexA binding site was introduced at various sites near the trpO, suggesting that the binding of LexA blocks one-dimensional diffusion causing the antenna effect. These results are consistent with the chemical ratchet recently proposed for TrpR-trpO binding to solve the deviation from detailed balance, and evidence that the antenna effect due to one-dimensional diffusion exists in cells.Takashi KinebuchiNobuo ShimamotoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Takashi Kinebuchi Nobuo Shimamoto One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
description	Abstract Several DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional diffusion also has been suggested to cause the effect for proteins with single DNA sites, the diffusion mechanism, which could violate detailed balance. We addressed which mechanism is possible for E. coli TrpR showing 104-fold antenna effect with a single DNA binding site. When a trpO-harboring DNA fragment was connected to a nonspecific DNA with biotin-avidin connection, the otherwise sevenfold antenna effect disappeared. This result denies the looping mechanism with an unknown second DNA binding site. The 3.5-fold repression by TrpR in vivo disappeared when a tight LexA binding site was introduced at various sites near the trpO, suggesting that the binding of LexA blocks one-dimensional diffusion causing the antenna effect. These results are consistent with the chemical ratchet recently proposed for TrpR-trpO binding to solve the deviation from detailed balance, and evidence that the antenna effect due to one-dimensional diffusion exists in cells.
format	article
author	Takashi Kinebuchi Nobuo Shimamoto
author_facet	Takashi Kinebuchi Nobuo Shimamoto
author_sort	Takashi Kinebuchi
title	One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
title_short	One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
title_full	One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
title_fullStr	One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
title_full_unstemmed	One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism
title_sort	one-dimensional diffusion of trpr along dna enhances its affinity for the operator by chemical ratchet mechanism
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4eca2dec88a64cbd952c2513c9843ae3
work_keys_str_mv	AT takashikinebuchi onedimensionaldiffusionoftrpralongdnaenhancesitsaffinityfortheoperatorbychemicalratchetmechanism AT nobuoshimamoto onedimensionaldiffusionoftrpralongdnaenhancesitsaffinityfortheoperatorbychemicalratchetmechanism
_version_	1718396468467859456

One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism

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