Short-range translocation by a restriction enzyme motor triggers diffusion along DNA

Martin Göse; Emma E Magill; Alex Hughes-Games; Steven J Shaw; Fiona M Diffin; Tara Rawson; Zsofia Nagy; Ralf Seidel; Mark D Szczelkun

doi:10.1038/s41589-023-01504-1

Short-range translocation by a restriction enzyme motor triggers diffusion along DNA

Martin Göse, Emma E Magill, Alex Hughes-Games, Steven J Shaw, Fiona M Diffin, Tara Rawson, Zsofia Nagy, Ralf Seidel^*, Mark D Szczelkun^*

^*Corresponding author for this work

School of Biochemistry

Research output: Contribution to journal › Article (Academic Journal) › peer-review

1 Citation (Scopus)

Abstract

Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion ('DNA sliding') initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8-15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.

Original language	English
Pages (from-to)	689-698
Number of pages	10
Journal	Nature Chemical Biology
Volume	20
Issue number	6
Early online date	2 Jan 2024
DOIs	https://doi.org/10.1038/s41589-023-01504-1
Publication status	Published - 1 Jun 2024

Bibliographical note

Funding Information:
This work was supported by the EPSRC and BBSRC Centre for Doctoral Training in Synthetic Biology (EP/L016494/1 to E.E.M.), by the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC-2017-ADG-788405 to M.D.S. and ERC-2016-CoG-724863 to R.S.), by the European Social Fund (ESF to R.S.) and the Free State of Saxony (Junior Research Group UniDyn, project no. SAB 100382164 to R.S.) and by BBSRC (21ALERT BB/W019337/1 to M.D.S.). For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) license to any author accepted manuscript version arising. We thank N. Savery for Mfd suggestions, Y. Tsai (University of Cardiff, UK) for advice on orthogonal amino acid labeling and for providing pCDF PylST, R. Smith (University of Bristol, UK) for supplying LlaGI, and K. van Aelst (University of Bristol, UK), M. Bird (University of Bristol, UK) and N. Nabila Roslan (University of Bristol, UK) for preliminary experiments.

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© 2024, The Author(s).

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title = "Short-range translocation by a restriction enzyme motor triggers diffusion along DNA",

abstract = "Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion ('DNA sliding') initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8-15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.",

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note = "Funding Information: This work was supported by the EPSRC and BBSRC Centre for Doctoral Training in Synthetic Biology (EP/L016494/1 to E.E.M.), by the European Research Council under the European Union{\textquoteright}s Horizon 2020 research and innovation program (ERC-2017-ADG-788405 to M.D.S. and ERC-2016-CoG-724863 to R.S.), by the European Social Fund (ESF to R.S.) and the Free State of Saxony (Junior Research Group UniDyn, project no. SAB 100382164 to R.S.) and by BBSRC (21ALERT BB/W019337/1 to M.D.S.). For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) license to any author accepted manuscript version arising. We thank N. Savery for Mfd suggestions, Y. Tsai (University of Cardiff, UK) for advice on orthogonal amino acid labeling and for providing pCDF PylST, R. Smith (University of Bristol, UK) for supplying LlaGI, and K. van Aelst (University of Bristol, UK), M. Bird (University of Bristol, UK) and N. Nabila Roslan (University of Bristol, UK) for preliminary experiments. Publisher Copyright: {\textcopyright} 2024, The Author(s).",

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doi = "10.1038/s41589-023-01504-1",

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AU - Göse, Martin

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AU - Shaw, Steven J

AU - Diffin, Fiona M

AU - Rawson, Tara

AU - Nagy, Zsofia

AU - Seidel, Ralf

AU - Szczelkun, Mark D

N1 - Funding Information: This work was supported by the EPSRC and BBSRC Centre for Doctoral Training in Synthetic Biology (EP/L016494/1 to E.E.M.), by the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC-2017-ADG-788405 to M.D.S. and ERC-2016-CoG-724863 to R.S.), by the European Social Fund (ESF to R.S.) and the Free State of Saxony (Junior Research Group UniDyn, project no. SAB 100382164 to R.S.) and by BBSRC (21ALERT BB/W019337/1 to M.D.S.). For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) license to any author accepted manuscript version arising. We thank N. Savery for Mfd suggestions, Y. Tsai (University of Cardiff, UK) for advice on orthogonal amino acid labeling and for providing pCDF PylST, R. Smith (University of Bristol, UK) for supplying LlaGI, and K. van Aelst (University of Bristol, UK), M. Bird (University of Bristol, UK) and N. Nabila Roslan (University of Bristol, UK) for preliminary experiments. Publisher Copyright: © 2024, The Author(s).

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N2 - Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion ('DNA sliding') initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8-15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.

AB - Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion ('DNA sliding') initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8-15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.

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DO - 10.1038/s41589-023-01504-1

M3 - Article (Academic Journal)

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SN - 1552-4450

VL - 20

SP - 689

EP - 698

JO - Nature Chemical Biology

JF - Nature Chemical Biology

IS - 6

ER -

Short-range translocation by a restriction enzyme motor triggers diffusion along DNA

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