Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability

Handle URI:
http://hdl.handle.net/10754/625186
Title:
Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability
Authors:
Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.; Neil, Alexander J.; Shaw, Steven J.; Algasaier, Sana I.; Kim, Jane C.; Finger, L. David; Jardine, Emma; Gotham, Victoria J.B.; Sarker, Altaf H.; Her, Mai Z.; Rashid, Fahad; Hamdan, Samir ( 0000-0001-5192-1852 ) ; Mirkin, Sergei M.; Grasby, Jane A.; Tainer, John A.
Abstract:
DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, et al. (2017) Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability. Nature Communications 8: 15855. Available: http://dx.doi.org/10.1038/ncomms15855.
Publisher:
Springer Nature
Journal:
Nature Communications
Issue Date:
27-Jun-2017
DOI:
10.1038/ncomms15855
Type:
Article
ISSN:
2041-1723
Sponsors:
For financial support, we thank NCI (PO1CA92584 to J.A.T.); BBSRC (grants BB/K009079/1 and BB/M00404X/1 to J.A.G.); the Ministry of Higher Education Libya, EPSRC and the University of Sheffield (studentships to S.I.A., S.J.S. and E.J., respectively); NIH (R01GM060987 to S.M. and R01GM110387 to S.T.); and KAUST for core and CRG3 funding to S.M.H. and J.A.T. J.A.T. acknowledges support by a Robert A. Welch Chemistry Chair, the Cancer Prevention and Research Institute of Texas, and the University of Texas System Science and Technology Acquisition and Retention. The tumour mutation analysis includes data generated by the TCGA Research Network: http://cancergenome.nih.gov/. We thank the ALS, SSRL, the IDAT program, the DOE BER and the NIH project MINOS (R01GM105404) for X-ray data facilities. We thank James Holton for aiding X-ray data analysis.
Additional Links:
https://www.nature.com/articles/ncomms15855
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorTsutakawa, Susan E.en
dc.contributor.authorThompson, Mark J.en
dc.contributor.authorArvai, Andrew S.en
dc.contributor.authorNeil, Alexander J.en
dc.contributor.authorShaw, Steven J.en
dc.contributor.authorAlgasaier, Sana I.en
dc.contributor.authorKim, Jane C.en
dc.contributor.authorFinger, L. Daviden
dc.contributor.authorJardine, Emmaen
dc.contributor.authorGotham, Victoria J.B.en
dc.contributor.authorSarker, Altaf H.en
dc.contributor.authorHer, Mai Z.en
dc.contributor.authorRashid, Fahaden
dc.contributor.authorHamdan, Samiren
dc.contributor.authorMirkin, Sergei M.en
dc.contributor.authorGrasby, Jane A.en
dc.contributor.authorTainer, John A.en
dc.date.accessioned2017-07-12T07:20:55Z-
dc.date.available2017-07-12T07:20:55Z-
dc.date.issued2017-06-27en
dc.identifier.citationTsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, et al. (2017) Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability. Nature Communications 8: 15855. Available: http://dx.doi.org/10.1038/ncomms15855.en
dc.identifier.issn2041-1723en
dc.identifier.doi10.1038/ncomms15855en
dc.identifier.urihttp://hdl.handle.net/10754/625186-
dc.description.abstractDNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.en
dc.description.sponsorshipFor financial support, we thank NCI (PO1CA92584 to J.A.T.); BBSRC (grants BB/K009079/1 and BB/M00404X/1 to J.A.G.); the Ministry of Higher Education Libya, EPSRC and the University of Sheffield (studentships to S.I.A., S.J.S. and E.J., respectively); NIH (R01GM060987 to S.M. and R01GM110387 to S.T.); and KAUST for core and CRG3 funding to S.M.H. and J.A.T. J.A.T. acknowledges support by a Robert A. Welch Chemistry Chair, the Cancer Prevention and Research Institute of Texas, and the University of Texas System Science and Technology Acquisition and Retention. The tumour mutation analysis includes data generated by the TCGA Research Network: http://cancergenome.nih.gov/. We thank the ALS, SSRL, the IDAT program, the DOE BER and the NIH project MINOS (R01GM105404) for X-ray data facilities. We thank James Holton for aiding X-ray data analysis.en
dc.publisherSpringer Natureen
dc.relation.urlhttps://www.nature.com/articles/ncomms15855en
dc.rightsThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titlePhosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instabilityen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalNature Communicationsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionMolecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, , United Statesen
dc.contributor.institutionCentre for Chemical Biology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Chemistry, University of Sheffield, Sheffield, S37HF, , United Kingdomen
dc.contributor.institutionDepartment of Molecular Biology, Scripps Research Institute, San Diego, CA, 92037, , United Statesen
dc.contributor.institutionDepartment of Biology, Tufts University, Medford, MA, 02155, , United Statesen
dc.contributor.institutionBiological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, , United Statesen
dc.contributor.institutionDepartment of Molecular and Cellular Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX, 77030, , , United Statesen
kaust.authorRashid, Fahaden
kaust.authorHamdan, Samiren
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