A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Amer Bralić; Muhammad Tehseen; Mohamed A. Sobhy; Chi Lin Tsai; Lubna Alhudhali; Gang Yi; Jina Yu; Chunli Yan; Ivaylo Ivanov; Susan E. Tsutakawa; John A. Tainer; Samir M. Hamdan

doi:10.1093/nar/gkac1095

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Amer Bralić, Muhammad Tehseen, Mohamed A. Sobhy, Chi Lin Tsai, Lubna Alhudhali, Gang Yi, Jina Yu, Chunli Yan, Ivaylo Ivanov, Susan E. Tsutakawa, John A. Tainer^*, Samir M. Hamdan^*

^*Corresponding author for this work

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

14 Scopus citations

Abstract

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5′-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5′-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

Original language	English (US)
Pages (from-to)	1019-1033
Number of pages	15
Journal	NUCLEIC ACIDS RESEARCH
Volume	51
Issue number	3
DOIs	https://doi.org/10.1093/nar/gkac1095
State	Published - Feb 22 2023

Bibliographical note

Funding Information:
King Abdullah University of Science and Technology through Competitive Research Award [URF/1/3764-01-01 (CRG7) to S.M.H. and J.A.T.]; NCI [P01 CA092584 to J.A.T., S.T., I.I., in part]; NCI [R35 CA220430 to J.A.T.]; CPRIT [RP180813 to J.A.T.]; NIEHS [R01ES032786 to S.T., I.I.]; Robert A. Welch Chemistry Chair (to J.A.T.); NSF MCB (to I.I.) Funding for open access charges were provided by the King Abdullah University of Science and Technology through URF/1/3764-01-01 (CRG7).

Publisher Copyright:
© 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkac1095

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@article{7892f70a79c74f9e9bf1b070b5731b3b,

title = "A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair",

abstract = "Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5′-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5′-ssDNA, ensuring the correct ssDNA bubble size before cleavage.",

author = "Amer Brali{\'c} and Muhammad Tehseen and Sobhy, {Mohamed A.} and Tsai, {Chi Lin} and Lubna Alhudhali and Gang Yi and Jina Yu and Chunli Yan and Ivaylo Ivanov and Tsutakawa, {Susan E.} and Tainer, {John A.} and Hamdan, {Samir M.}",

note = "Funding Information: King Abdullah University of Science and Technology through Competitive Research Award [URF/1/3764-01-01 (CRG7) to S.M.H. and J.A.T.]; NCI [P01 CA092584 to J.A.T., S.T., I.I., in part]; NCI [R35 CA220430 to J.A.T.]; CPRIT [RP180813 to J.A.T.]; NIEHS [R01ES032786 to S.T., I.I.]; Robert A. Welch Chemistry Chair (to J.A.T.); NSF MCB (to I.I.) Funding for open access charges were provided by the King Abdullah University of Science and Technology through URF/1/3764-01-01 (CRG7). Publisher Copyright: {\textcopyright} 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2023",

month = feb,

day = "22",

doi = "10.1093/nar/gkac1095",

language = "English (US)",

volume = "51",

pages = "1019--1033",

journal = "NUCLEIC ACIDS RESEARCH",

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publisher = "OXFORD UNIV PRESS",

number = "3",

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TY - JOUR

T1 - A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

AU - Bralić, Amer

AU - Tehseen, Muhammad

AU - Sobhy, Mohamed A.

AU - Tsai, Chi Lin

AU - Alhudhali, Lubna

AU - Yi, Gang

AU - Yu, Jina

AU - Yan, Chunli

AU - Ivanov, Ivaylo

AU - Tsutakawa, Susan E.

AU - Tainer, John A.

AU - Hamdan, Samir M.

N1 - Funding Information: King Abdullah University of Science and Technology through Competitive Research Award [URF/1/3764-01-01 (CRG7) to S.M.H. and J.A.T.]; NCI [P01 CA092584 to J.A.T., S.T., I.I., in part]; NCI [R35 CA220430 to J.A.T.]; CPRIT [RP180813 to J.A.T.]; NIEHS [R01ES032786 to S.T., I.I.]; Robert A. Welch Chemistry Chair (to J.A.T.); NSF MCB (to I.I.) Funding for open access charges were provided by the King Abdullah University of Science and Technology through URF/1/3764-01-01 (CRG7). Publisher Copyright: © 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2023/2/22

Y1 - 2023/2/22

N2 - Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5′-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5′-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

AB - Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5′-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5′-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

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U2 - 10.1093/nar/gkac1095

DO - 10.1093/nar/gkac1095

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ER -

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

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