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Genest PA, Baugh L, Taipale A, Zhao W, Jan S, van Luenen HGAM, Korlach J, Clark T, Luong K, Boitano M, Turner S, Myler PJ, Borst P. Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing. Nucleic Acids Res 2015; 43:2102-15. [PMID: 25662217 PMCID: PMC4344527 DOI: 10.1093/nar/gkv095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication.
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Affiliation(s)
- Paul-Andre Genest
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Loren Baugh
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA
| | - Alex Taipale
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA
| | - Wanqi Zhao
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sabrina Jan
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Henri G A M van Luenen
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jonas Korlach
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Tyson Clark
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Khai Luong
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Matthew Boitano
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Steve Turner
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
| | - Peter J Myler
- Seattle Biomedical Research Institute, 307 Westlake Avenue, Seattle, WA 98109-5219, USA Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Piet Borst
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Yu Z, Genest PA, ter Riet B, Sweeney K, DiPaolo C, Kieft R, Christodoulou E, Perrakis A, Simmons JM, Hausinger RP, van Luenen HG, Rigden DJ, Sabatini R, Borst P. The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res 2007; 35:2107-15. [PMID: 17389644 PMCID: PMC1874643 DOI: 10.1093/nar/gkm049] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trypanosomatids contain an unusual DNA base J (beta-d-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe(2+) and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe(2+) and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
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Affiliation(s)
- Zhong Yu
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Paul-André Genest
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bas ter Riet
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Kate Sweeney
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Courtney DiPaolo
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rudo Kieft
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Evangelos Christodoulou
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Anastassis Perrakis
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jana M. Simmons
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert P. Hausinger
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Henri G.A.M. van Luenen
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Daniel J. Rigden
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert Sabatini
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Piet Borst
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
- *To whom correspondence should be addressed. +31 20 512 2880+31 20 669 1383
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