A DNA-translocating Snf2 Molecular Motor: Saccharomyces cerevisiae Rdh54 Displays Processive Translocation and Extrudes DNA Loops

Tekkatte Krishnamurthy Prasad; Ragan B. Robertson; Mari Liis Visnapuu; Peter Chi; Patrick Sung; Eric C. Greene

doi:10.1016/j.jmb.2007.04.005

A DNA-translocating Snf2 Molecular Motor: Saccharomyces cerevisiae Rdh54 Displays Processive Translocation and Extrudes DNA Loops

Tekkatte Krishnamurthy Prasad, Ragan B. Robertson, Mari Liis Visnapuu, Peter Chi, Patrick Sung, Eric C. Greene

Research output: Contribution to journal › Article › peer-review

65 Scopus citations

Abstract

We have used total internal reflection fluorescence microscopy (TIRFM) to investigate the characteristics of the yeast homologous recombination factor Rdh54 on DNA. Our results demonstrate translocation of Rdh54 on DNA and extrusion of DNA loops by Rdh54 in an ATP hydrolysis-dependent manner. The translocating Rdh54 was highly processive and displayed a variety of behavior, including variations in translocation rate and distance, pauses, and reversals. We provide evidence that the DNA loops generated encompass an average of 6 kb, and Rdh54 often abruptly releases the extruded DNA. Rdh54 forms a multimeric complex, which we speculate has at least two functionally distinct DNA-binding sites, one of which enables translocation while the other remains anchored to another DNA locale. Our work, together with other recent studies, suggests that translocation-coupled DNA loop extrusion is a common mechanistic feature among the Snf2-family of chromatin-remodeling proteins.

Original language	English (US)
Pages (from-to)	940-953
Number of pages	14
Journal	Journal of Molecular Biology
Volume	369
Issue number	4
DOIs	https://doi.org/10.1016/j.jmb.2007.04.005
State	Published - Jun 15 2007
Externally published	Yes

Keywords

DNA curtain
Rdh54
TIRFM
homologous recombination
single-molecule

ASJC Scopus subject areas

Molecular Biology
Structural Biology

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10.1016/j.jmb.2007.04.005

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title = "A DNA-translocating Snf2 Molecular Motor: Saccharomyces cerevisiae Rdh54 Displays Processive Translocation and Extrudes DNA Loops",

abstract = "We have used total internal reflection fluorescence microscopy (TIRFM) to investigate the characteristics of the yeast homologous recombination factor Rdh54 on DNA. Our results demonstrate translocation of Rdh54 on DNA and extrusion of DNA loops by Rdh54 in an ATP hydrolysis-dependent manner. The translocating Rdh54 was highly processive and displayed a variety of behavior, including variations in translocation rate and distance, pauses, and reversals. We provide evidence that the DNA loops generated encompass an average of 6 kb, and Rdh54 often abruptly releases the extruded DNA. Rdh54 forms a multimeric complex, which we speculate has at least two functionally distinct DNA-binding sites, one of which enables translocation while the other remains anchored to another DNA locale. Our work, together with other recent studies, suggests that translocation-coupled DNA loop extrusion is a common mechanistic feature among the Snf2-family of chromatin-remodeling proteins.",

keywords = "DNA curtain, Rdh54, TIRFM, homologous recombination, single-molecule",

author = "Prasad, {Tekkatte Krishnamurthy} and Robertson, {Ragan B.} and Visnapuu, {Mari Liis} and Peter Chi and Patrick Sung and Greene, {Eric C.}",

note = "Funding Information: This work was supported, in part, by a March of Dimes Basil O'Connor Starter Scholar Research Award (to E.C.G.) and National Institutes of Health grants GM074739 (to E.C.G.) and GM57814 (to P.S.). R.B.R. was supported by an NIH Biophysics training grant (5T32GM008281). We thank Goran Ahlsen for assistance with analytical ultracentrifugation. We thank Ruben Gonzalez, Lorraine Symington, Rodney Rothstein and members of our laboratories for discussion and comments on the manuscript. ",

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AU - Visnapuu, Mari Liis

AU - Chi, Peter

AU - Sung, Patrick

AU - Greene, Eric C.

N1 - Funding Information: This work was supported, in part, by a March of Dimes Basil O'Connor Starter Scholar Research Award (to E.C.G.) and National Institutes of Health grants GM074739 (to E.C.G.) and GM57814 (to P.S.). R.B.R. was supported by an NIH Biophysics training grant (5T32GM008281). We thank Goran Ahlsen for assistance with analytical ultracentrifugation. We thank Ruben Gonzalez, Lorraine Symington, Rodney Rothstein and members of our laboratories for discussion and comments on the manuscript.

PY - 2007/6/15

Y1 - 2007/6/15

N2 - We have used total internal reflection fluorescence microscopy (TIRFM) to investigate the characteristics of the yeast homologous recombination factor Rdh54 on DNA. Our results demonstrate translocation of Rdh54 on DNA and extrusion of DNA loops by Rdh54 in an ATP hydrolysis-dependent manner. The translocating Rdh54 was highly processive and displayed a variety of behavior, including variations in translocation rate and distance, pauses, and reversals. We provide evidence that the DNA loops generated encompass an average of 6 kb, and Rdh54 often abruptly releases the extruded DNA. Rdh54 forms a multimeric complex, which we speculate has at least two functionally distinct DNA-binding sites, one of which enables translocation while the other remains anchored to another DNA locale. Our work, together with other recent studies, suggests that translocation-coupled DNA loop extrusion is a common mechanistic feature among the Snf2-family of chromatin-remodeling proteins.

AB - We have used total internal reflection fluorescence microscopy (TIRFM) to investigate the characteristics of the yeast homologous recombination factor Rdh54 on DNA. Our results demonstrate translocation of Rdh54 on DNA and extrusion of DNA loops by Rdh54 in an ATP hydrolysis-dependent manner. The translocating Rdh54 was highly processive and displayed a variety of behavior, including variations in translocation rate and distance, pauses, and reversals. We provide evidence that the DNA loops generated encompass an average of 6 kb, and Rdh54 often abruptly releases the extruded DNA. Rdh54 forms a multimeric complex, which we speculate has at least two functionally distinct DNA-binding sites, one of which enables translocation while the other remains anchored to another DNA locale. Our work, together with other recent studies, suggests that translocation-coupled DNA loop extrusion is a common mechanistic feature among the Snf2-family of chromatin-remodeling proteins.

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A DNA-translocating Snf2 Molecular Motor: Saccharomyces cerevisiae Rdh54 Displays Processive Translocation and Extrudes DNA Loops

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