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Islam A, Chakraborty A, Gambardella S, Campopiano R, Sarker AH, Boldogh I, Hazra T. Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans. J Biol Chem 2023; 299:104714. [PMID: 37061005 PMCID: PMC10197107 DOI: 10.1016/j.jbc.2023.104714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells-a potential cause of neurodegeneration in AOA4 patients.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Stefano Gambardella
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Rosa Campopiano
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.
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2
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Hoggard T, Hollatz AJ, Cherney RE, Seman MR, Fox CA. The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast. Nucleic Acids Res 2021; 49:10207-10220. [PMID: 34095951 PMCID: PMC8501964 DOI: 10.1093/nar/gkab450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
The pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognitioncomplex (ORC). The ORC-DNA complex directs the formation of origins, the specific chromosomal regions where DNA synthesis initiates. In all eukaryotes, incompletely understood features of chromatin promote ORC-DNA binding. Here, we uncover a role for the Fkh1 (Forkhead homolog) protein and its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins in Saccharomyces cerevisiae. Several of the FHA-dependent origins examined required a distinct Fkh1 binding site located 5′ of and proximal to their ORC sites (5′-FKH-T site). Genetic and molecular experiments provided evidence that the Fkh1-FHA domain promoted origin activity directly through Fkh1 binding to this 5′ FKH-T site. Nucleotide substitutions within two relevant origins that enhanced their ORC-DNA affinity bypassed the requirement for their 5′ FKH-T sites and for the Fkh1-FHA domain. Significantly, assessment of ORC-origin binding by ChIPSeq provided evidence that this mechanism was relevant at ∼25% of yeast origins. Thus, the FHA domain of the conserved cell-cycle transcription factor Fkh1 enhanced origin selection in yeast at the level of ORC-origin binding.
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Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Rachel E Cherney
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Melissa R Seman
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Catherine A Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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3
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Zhang CF, Wang HM, Wu A, Li Y, Tian XL. FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1884-1894. [PMID: 33471274 DOI: 10.1007/s11427-020-1844-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Angiogenic factor with G-patch and FHA domains 1 (AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechanism of this nucleocytoplasmic transport remains unknown. Here, we demonstrate that the dynamic distribution is essential for AGGF1 to execute its angiogenic function. To search the structural bases for this nucleocytoplasmic transport, we characterized three potential nuclear localization regions, one potential nuclear export region, forkhead-associated (FHA), and G-patch domains to determine their effects on nucleocytoplasmic transport and angiogenesis, and we show that AGGF1 remains intact during the dynamic subcellular distribution and the region from 260 to 288 amino acids acts as a signal for its nuclear localization. The distribution of AGGF1 in cytoplasm needs both FHA domain and 14-3-3α/β. Binding of AGGF1 via FHA domain to 14-3-3α/β is required to complete the transport. Thus, we for the first time established structural bases for the nucleocytoplasmic transport of AGGF1 and revealed that the FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis.
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Affiliation(s)
- Cui-Fang Zhang
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Han-Ming Wang
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Andong Wu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China
| | - Yang Li
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China.
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4
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Xie C, He C, Jiang Y, Yu H, Cheng L, Nshogoza G, Ala MS, Tian C, Wu J, Shi Y, Li F. Structural insights into the recognition of phosphorylated Hop1 by Mek1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1027-1038. [PMID: 30289413 DOI: 10.1107/s2059798318011993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022]
Abstract
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition. It was further found that in Schizosaccharomyces pombe Mek1 FHA binds both pT15 in its N-terminal SQ/TQ cluster domain (SCD) and pT270 in the Hop1 SCD. The results revealed the structural basis for the preferential recognition of phosphorylated Hop1 by Mek1 in S. cerevisiae and facilitate the understanding of the interaction between the S. pombe Mek1 FHA domain and its binding targets.
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Affiliation(s)
- Changlin Xie
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Hailong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Lin Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Moududee Sayed Ala
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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5
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Cherry AL, Nott TJ, Kelly G, Rulten SL, Caldecott KW, Smerdon SJ. Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains. DNA Repair (Amst) 2015; 35:116-25. [PMID: 26519825 PMCID: PMC4655838 DOI: 10.1016/j.dnarep.2015.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/05/2015] [Accepted: 10/05/2015] [Indexed: 11/11/2022]
Abstract
Aprataxin, aprataxin and PNKP-like factor (APLF) and polynucleotide kinase phosphatase (PNKP) are key DNA-repair proteins with diverse functions but which all contain a homologous forkhead-associated (FHA) domain. Their primary binding targets are casein kinase 2-phosphorylated forms of the XRCC1 and XRCC4 scaffold molecules which respectively coordinate single-stranded and double-stranded DNA break repair pathways. Here, we present the high-resolution X-ray structure of a complex of phosphorylated XRCC4 with APLF, the most divergent of the three FHA domain family members. This, combined with NMR and biochemical analysis of aprataxin and APLF binding to singly and multiply-phosphorylated forms of XRCC1 and XRCC4, and comparison with PNKP reveals a pattern of distinct but overlapping binding specificities that are differentially modulated by multi-site phosphorylation. Together, our data illuminate important differences between activities of the three phospho-binding domains, in spite of a close evolutionary relationship between them.
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Affiliation(s)
- Amy L Cherry
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Timothy J Nott
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoffrey Kelly
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stuart L Rulten
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stephen J Smerdon
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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6
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Zhang F, Shi J, Chen SH, Bian C, Yu X. The PIN domain of EXO1 recognizes poly(ADP-ribose) in DNA damage response. Nucleic Acids Res 2015; 43:10782-94. [PMID: 26400172 PMCID: PMC4678857 DOI: 10.1093/nar/gkv939] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/08/2015] [Indexed: 11/14/2022] Open
Abstract
Following DNA double-strand breaks, poly(ADP-ribose) (PAR) is quickly and heavily synthesized to mediate fast and early recruitment of a number of DNA damage response factors to the sites of DNA lesions and facilitates DNA damage repair. Here, we found that EXO1, an exonuclease for DNA damage repair, is quickly recruited to the sites of DNA damage via PAR-binding. With further dissection of the functional domains of EXO1, we report that the PIN domain of EXO1 recognizes PAR both in vitro and in vivo and the interaction between the PIN domain and PAR is sufficient for the recruitment. We also found that the R93G variant of EXO1, generated by a single nucleotide polymorphism, abolishes the interaction and the early recruitment. Moreover, our study suggests that the PAR-mediated fast recruitment of EXO1 facilities early DNA end resection, the first step of homologous recombination repair. We observed that other PIN domains could also recognize DNA damage-induced PAR. Taken together, our study demonstrates a novel class of PAR-binding module that plays an important role in DNA damage response.
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Affiliation(s)
- Feng Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA
| | - Jiazhong Shi
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA Department of Cell Biology, the Third Military Medical University, Chongqing, 400038, China
| | - Shih-Hsun Chen
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91773, USA
| | - Chunjing Bian
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91773, USA
| | - Xiaochun Yu
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91773, USA
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7
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Xu H, Zhang H, Yang W, Yadav R, Morrison AC, Qian M, Devidas M, Liu Y, Perez-Andreu V, Zhao X, Gastier-Foster JM, Lupo PJ, Neale G, Raetz E, Larsen E, Bowman WP, Carroll WL, Winick N, Williams R, Hansen T, Holm JC, Mardis E, Fulton R, Pui CH, Zhang J, Mullighan CG, Evans WE, Hunger SP, Gupta R, Schmiegelow K, Loh ML, Relling MV, Yang JJ. Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children. Nat Commun 2015; 6:7553. [PMID: 26104880 PMCID: PMC4544058 DOI: 10.1038/ncomms8553] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/20/2015] [Indexed: 02/05/2023] Open
Abstract
There is increasing evidence from genome-wide association studies for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children, yet the effects of protein-coding variants on ALL risk have not been systematically evaluated. Here we show a missense variant in CDKN2A associated with the development of ALL at genome-wide significance (rs3731249, P=9.4 × 10−23, odds ratio=2.23). Functional studies indicate that this hypomorphic variant results in reduced tumour suppressor function of p16INK4A, increases the susceptibility to leukaemic transformation of haematopoietic progenitor cells, and is preferentially retained in ALL tumour cells. Resequencing the CDKN2A–CDKN2B locus in 2,407 childhood ALL cases reveals 19 additional putative functional germline variants. These results provide direct functional evidence for the influence of inherited genetic variation on ALL risk, highlighting the important and complex roles of CDKN2A–CDKN2B tumour suppressors in leukaemogenesis. Genome-wide association studies indicate a strong genetic susceptibility to acute lymphoblastic leukaemia in children, though the effect on protein-coding genes is not fully understood. Here Xu and Zhang et al. identify a missense variant in CDKN2A which reduces tumour suppression.
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Affiliation(s)
- Heng Xu
- 1] Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Department of Laboratory Medicine, National Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hui Zhang
- 1] Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Department of Pediatrics, The first affiliated hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Rachita Yadav
- Centre for Biological Sequence Analysis, The Technical University of Denmark, Kgs, Lyngby DK-2800, Denmark
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Meenakshi Devidas
- Department of Biostatistics, Epidemiology and Health Policy Research, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Julie M Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, and Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, Ohio 43205, USA
| | - Philip J Lupo
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Geoff Neale
- Hartwell Center for Bioinformatics &Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elizabeth Raetz
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Eric Larsen
- Maine Children's Cancer Program, Scarborough, Maine 04074, USA
| | - W Paul Bowman
- Cook Children's Medical Center, Ft. Worth, Texas 38754, USA
| | - William L Carroll
- Pediatric Oncology, Cancer Institute New York University, New York City, New York 10016, USA
| | - Naomi Winick
- Pediatric Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | | | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Jens-Christian Holm
- Department of Pediatrics, The Children's Obesity Clinic, Copenhagen University Hospital Holbaek, Holbaek DK-4300, Denmark
| | - Elaine Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Ching-Hon Pui
- 1] Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Charles G Mullighan
- 1] Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - William E Evans
- 1] Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ramneek Gupta
- Centre for Biological Sequence Analysis, The Technical University of Denmark, Kgs, Lyngby DK-2800, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, The Juliane Marie Centre, The University Hospital Rigshospitalet, and the Institute of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94115, USA
| | - Mary V Relling
- 1] Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jun J Yang
- 1] Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [2] Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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8
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Schellenberg MJ, Tumbale PP, Williams RS. Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:157-165. [PMID: 25637650 DOI: 10.1016/j.pbiomolbio.2015.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/12/2015] [Accepted: 01/18/2015] [Indexed: 11/30/2022]
Abstract
Eukaryotic DNA ligases seal DNA breaks in the final step of DNA replication and repair transactions via a three-step reaction mechanism that can abort if DNA ligases encounter modified DNA termini, such as the products and repair intermediates of DNA oxidation, alkylation, or the aberrant incorporation of ribonucleotides into genomic DNA. Such abortive DNA ligation reactions act as molecular checkpoint for DNA damage and create 5'-adenylated nucleic acid termini in the context of DNA and RNA-DNA substrates in DNA single strand break repair (SSBR) and ribonucleotide excision repair (RER). Aprataxin (APTX), a protein altered in the heritable neurological disorder Ataxia with Oculomotor Apraxia 1 (AOA1), acts as a DNA ligase "proofreader" to directly reverse AMP-modified nucleic acid termini in DNA- and RNA-DNA damage responses. Herein, we survey APTX function and the emerging cell biological, structural and biochemical data that has established a molecular foundation for understanding the APTX mediated deadenylation reaction, and is providing insights into the molecular bases of APTX deficiency in AOA1.
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Affiliation(s)
- Matthew J Schellenberg
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
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9
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Abbruzzese G, Cousin H, Salicioni AM, Alfandari D. GSK3 and Polo-like kinase regulate ADAM13 function during cranial neural crest cell migration. Mol Biol Cell 2014; 25:4072-82. [PMID: 25298404 PMCID: PMC4263450 DOI: 10.1091/mbc.e14-05-0970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 12/28/2022] Open
Abstract
ADAMs are cell surface metalloproteases that control multiple biological processes by cleaving signaling and adhesion molecules. ADAM13 controls cranial neural crest (CNC) cell migration both by cleaving cadherin-11 to release a promigratory extracellular fragment and by controlling expression of multiple genes via its cytoplasmic domain. The latter activity is regulated by γ-secretase cleavage and the translocation of the cytoplasmic domain into the nucleus. One of the genes regulated by ADAM13, the protease calpain8, is essential for CNC migration. Although the nuclear function of ADAM13 is evolutionarily conserved, it is unclear whether the transcriptional regulation is also performed by other ADAMs and how this process may be regulated. We show that ADAM13 function to promote CNC migration is regulated by two phosphorylation events involving GSK3 and Polo-like kinase (Plk). We further show that inhibition of either kinase blocks CNC migration and that the respective phosphomimetic forms of ADAM13 can rescue these inhibitions. However, these phosphorylations are not required for ADAM13 proteolysis of its substrates, γ-secretase cleavage, or nuclear translocation of its cytoplasmic domain. Of significance, migration of the CNC can be restored in the absence of Plk phosphorylation by expression of calpain-8a, pointing to impaired nuclear activity of ADAM13.
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Affiliation(s)
- Genevieve Abbruzzese
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003
| | - Hélène Cousin
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003
| | - Ana Maria Salicioni
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003
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10
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O'Donnell V, Pacheco JM, Larocco M, Gladue DP, Pauszek SJ, Smoliga G, Krug PW, Baxt B, Borca MV, Rodriguez L. Virus-host interactions in persistently FMDV-infected cells derived from bovine pharynx. Virology 2014; 468-470:185-196. [PMID: 25216088 DOI: 10.1016/j.virol.2014.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/07/2014] [Accepted: 08/04/2014] [Indexed: 11/26/2022]
Abstract
Foot-and-mouth disease virus (FMDV) produces a disease in cattle characterized by vesicular lesions and a persistent infection with asymptomatic low-level production of virus in pharyngeal tissues. Here we describe the establishment of a persistently infected primary cell culture derived from bovine pharynx tissue (PBPT) infected with FMDV serotype O1 Manisa, where surviving cells were serially passed until a persistently infected culture was generated. Characterization of the persistent virus demonstrated changes in its plaque size, ability to grow in different cell lines, and change in the use of integrins as receptors, when compared with the parental virus. These results demonstrate the establishment of persistently infected PBPT cell cultures where co-adaptation has taken place between the virus and host cells. This in vitro model for FMDV persistence may help further understanding of the molecular mechanisms of the cattle carrier state.
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Affiliation(s)
- V O'Donnell
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA; Department of Pathobiology and Veterinary Science, University of Connecticut at Storrs, Storrs, CT 06269, USA
| | - J M Pacheco
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - Michael Larocco
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - D P Gladue
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - S J Pauszek
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - G Smoliga
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - P W Krug
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - B Baxt
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - M V Borca
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
| | - L Rodriguez
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY 11944, USA
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11
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Wang H, Shi LZ, Wong CCL, Han X, Hwang PYH, Truong LN, Zhu Q, Shao Z, Chen DJ, Berns MW, Yates JR, Chen L, Wu X. The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair. PLoS Genet 2013; 9:e1003277. [PMID: 23468639 PMCID: PMC3585124 DOI: 10.1371/journal.pgen.1003277] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/12/2012] [Indexed: 11/19/2022] Open
Abstract
CtIP plays an important role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair and interacts with Nbs1 and BRCA1, which are linked to Nijmegen breakage syndrome (NBS) and familial breast cancer, respectively. We identified new CDK phosphorylation sites on CtIP and found that phosphorylation of these newly identified CDK sites induces association of CtIP with the N-terminus FHA and BRCT domains of Nbs1. We further showed that these CDK-dependent phosphorylation events are a prerequisite for ATM to phosphorylate CtIP upon DNA damage, which is important for end resection to activate HR by promoting recruitment of BLM and Exo1 to DSBs. Most notably, this CDK-dependent CtIP and Nbs1 interaction facilitates ATM to phosphorylate CtIP in a substrate-specific manner. These studies reveal one important mechanism to regulate cell-cycle-dependent activation of HR upon DNA damage by coupling CDK- and ATM-mediated phosphorylation of CtIP through modulating the interaction of CtIP with Nbs1, which significantly helps to understand how DSB repair is regulated in mammalian cells to maintain genome stability.
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Affiliation(s)
- Hailong Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Linda Z. Shi
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Catherine C. L. Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patty Yi-Hwa Hwang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lan N. Truong
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Qingyuan Zhu
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Zhengping Shao
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - David J. Chen
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael W. Berns
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Longchuan Chen
- Department of Pathology, Veterans Affairs Medical Center, Long Beach, California, United States of America
| | - Xiaohua Wu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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12
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Neumayer G, Helfricht A, Shim SY, Le HT, Lundin C, Belzil C, Chansard M, Yu Y, Lees-Miller SP, Gruss OJ, van Attikum H, Helleday T, Nguyen MD. Targeting protein for xenopus kinesin-like protein 2 (TPX2) regulates γ-histone 2AX (γ-H2AX) levels upon ionizing radiation. J Biol Chem 2012; 287:42206-22. [PMID: 23045526 DOI: 10.1074/jbc.m112.385674] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The microtubule-associated protein targeting protein for Xenopus kinesin-like protein 2 (TPX2) plays a key role in spindle assembly and is required for mitosis in human cells. In interphase, TPX2 is actively imported into the nucleus to prevent its premature activity in microtubule organization. To date, no function has been assigned to nuclear TPX2. We now report that TPX2 plays a role in the cellular response to DNA double strand breaks induced by ionizing radiation. Loss of TPX2 leads to inordinately strong and transient accumulation of ionizing radiation-dependent Ser-139-phosphorylated Histone 2AX (γ-H2AX) at G(0) and G(1) phases of the cell cycle. This is accompanied by the formation of increased numbers of high intensity γ-H2AX ionizing radiation-induced foci. Conversely, cells overexpressing TPX2 have reduced levels of γ-H2AX after ionizing radiation. Consistent with a role for TPX2 in the DNA damage response, we found that the protein accumulates at DNA double strand breaks and associates with the mediator of DNA damage checkpoint 1 (MDC1) and the ataxia telangiectasia mutated (ATM) kinase, both key regulators of γ-H2AX amplification. Pharmacologic inhibition or depletion of ATM or MDC1, but not of DNA-dependent protein kinase (DNA-PK), antagonizes the γ-H2AX phenotype caused by TPX2 depletion. Importantly, the regulation of γ-H2AX signals by TPX2 is not associated with apoptosis or the mitotic functions of TPX2. In sum, our study identifies a novel and the first nuclear function for TPX2 in the cellular responses to DNA damage.
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Affiliation(s)
- Gernot Neumayer
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary T2N4N1, Canada
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13
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Molle V, Kremer L. Division and cell envelope regulation by Ser/Thr phosphorylation: Mycobacterium shows the way. Mol Microbiol 2010; 75:1064-77. [PMID: 20487298 DOI: 10.1111/j.1365-2958.2009.07041.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (M. tb) has a complex lifestyle in different environments and involving several developmental stages. The success of M. tb results from its remarkable capacity to survive within the infected host, where it can persist in a non-replicating state for several decades. The survival strategies developed by M. tb are linked to the presence of an unusual cell envelope. However, little is known regarding its capacity to modulate and adapt production of cell wall components in response to environmental conditions or to changes in cell shape and cell division. Signal sensing leading to cellular responses must be tightly regulated to allow survival under variable conditions. Although prokaryotes generally control their signal transduction processes through two-component systems, signalling through Ser/Thr phosphorylation has recently emerged as a critical regulatory mechanism in bacteria. The genome of M. tb possesses a large family of eukaryotic-like Ser/Thr protein kinases (STPKs). The physiological roles of several mycobacterial STPK substrates are connected to cell shape/division and cell envelope biosynthesis. Although these regulatory mechanisms have mostly been studied in Mycobacterium, Ser/Thr phosphorylation appears also to regulate cell division and peptidoglycan synthesis in Corynebacterium and Streptomyces. This review focuses on the proteins which have been identified as STPK substrates and involved in the synthesis of major cell envelope components and cell shape/division in actinomycetes. It is also intended to describe how phosphorylation affects the activity of peptidoglycan biosynthetic enzymes or cell division proteins.
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Affiliation(s)
- Virginie Molle
- Institut de Biologie et Chimie des Protéines (IBCP UMR 5086), CNRS, Université Lyon1, IFR128 BioSciences, Lyon-Gerland, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
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14
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Flynn RL, Zou L. Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Crit Rev Biochem Mol Biol 2010; 45:266-75. [PMID: 20515430 DOI: 10.3109/10409238.2010.488216] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The maintenance of genomic stability relies on the coordinated action of a number of cellular processes, including activation of the DNA-damage checkpoint, DNA replication, DNA repair, and telomere homeostasis. Many proteins involved in these cellular processes use different types of functional modules to regulate and execute their functions. Recent studies have revealed that many DNA-damage checkpoint and DNA repair proteins in human cells possess the oligonucleotide/oligosaccharide-binding (OB) fold domains, which are known to bind single-stranded DNA in both prokaryotes and eukaryotes. Furthermore, during the DNA damage response, the OB folds of the human checkpoint and DNA repair proteins play critical roles in DNA binding, protein complex assembly, and regulating protein-protein interactions. These findings suggest that the OB fold is an evolutionarily conserved functional module that is widely used by genome guardians. In this review, we will highlight the functions of several well-characterized or newly discovered eukaryotic OB-fold proteins in the DNA damage response.
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Affiliation(s)
- Rachel Litman Flynn
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
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15
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Usui T, Foster SS, Petrini JHJ. Maintenance of the DNA-damage checkpoint requires DNA-damage-induced mediator protein oligomerization. Mol Cell 2009; 33:147-59. [PMID: 19187758 DOI: 10.1016/j.molcel.2008.12.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 11/17/2008] [Accepted: 12/16/2008] [Indexed: 12/30/2022]
Abstract
Oligomeric assembly of Brca1 C-terminal (BRCT) domain-containing mediator proteins occurs at sites of DNA damage. However, the functional significance and regulation of such assemblies are not well understood. In this study, we defined the molecular mechanism of DNA-damage-induced oligomerization of the S. cerevisiae BRCT protein Rad9. Our data suggest that Rad9's tandem BRCT domain mediates Rad9 oligomerization via its interaction with its own Mec1/Tel1-phosphorylated SQ/TQ cluster domain (SCD). Rad53 activation is unaffected by mutations that impair Rad9 oligomerization, but checkpoint maintenance is lost, indicating that oligomerization is required to sustain checkpoint signaling. Once activated, Rad53 phosphorylates the Rad9 BRCT domain, which attenuates the BRCT-SCD interaction. Failure to phosphorylate the Rad9 BRCT results in cytologically visible Rad9 foci. This suggests a feedback loop wherein Rad53 activity and Rad9 oligomerization are regulated to tune the DNA-damage response.
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Affiliation(s)
- Takehiko Usui
- Laboratory of Chromosome Biology, Sloan-Kettering Institute, New York, NY 10065, USA
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16
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Ali AAE, Jukes RM, Pearl LH, Oliver AW. Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK. Nucleic Acids Res 2009; 37:1701-12. [PMID: 19155274 PMCID: PMC2655680 DOI: 10.1093/nar/gkn1086] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Short-patch repair of DNA single-strand breaks and gaps (SSB) is coordinated by XRCC1, a scaffold protein that recruits the DNA polymerase and DNA ligase required for filling and sealing the damaged strand. XRCC1 can also recruit end-processing enzymes, such as PNK (polynucleotide kinase 3'-phosphatase), Aprataxin and APLF (aprataxin/PNK-like factor), which ensure the availability of a free 3'-hydroxyl on one side of the gap, and a 5'-phosphate group on the other, for the polymerase and ligase reactions respectively. PNK binds to a phosphorylated segment of XRCC1 (between its two C-terminal BRCT domains) via its Forkhead-associated (FHA) domain. We show here, contrary to previous studies, that the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex. The high-resolution crystal structure of a PNK-FHA-XRCC1 phosphopeptide complex reveals the basis for this unusual bis-phosphopeptide recognition, which is probably a common feature of the known XRCC1-associating end-processing enzymes.
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Affiliation(s)
- Ammar A E Ali
- Cancer Research UK DNA Repair Enzyme Group, Section of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK
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17
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Xu C, Wu L, Cui G, Botuyan MV, Chen J, Mer G. Structure of a second BRCT domain identified in the nijmegen breakage syndrome protein Nbs1 and its function in an MDC1-dependent localization of Nbs1 to DNA damage sites. J Mol Biol 2008; 381:361-72. [PMID: 18582474 DOI: 10.1016/j.jmb.2008.05.087] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 05/27/2008] [Indexed: 12/23/2022]
Abstract
The Nijmegen breakage syndrome protein Nbs1 is a component of the MRN (Mre11-Rad50-Nbs1) complex, central to the DNA damage response. While Nbs1 is generally believed to encompass a forkhead-associated domain linked to a breast cancer C-terminal (BRCT) domain, to date there is no experimental information on its three-dimensional structure. Through nuclear magnetic resonance (NMR) three-dimensional structure determination, we demonstrate that there is a second BRCT domain (BRCT2) in Nbs1. The domain has the characteristic BRCT topology, but with a long insertion shown to be flexible by NMR relaxation measurements. In the absence of sequence similarity to other proteins, a search for structural analogs of BRCT2 returned the second BRCT domain of the tandem BRCT repeats of cell cycle checkpoint proteins MDC1 (mediator of DNA damage checkpoint protein 1) and BRCA1 (breast cancer protein 1), suggesting that like MDC1 and BRCA1, Nbs1 also possesses tandem BRCT domains with phosphoprotein binding ability. Structure-based single point mutations in human Nbs1 were evaluated in vivo and revealed that BRCT2 is essential for an MDC1-dependent relocalization of Nbs1 to DNA damage sites, most likely through a direct interaction of Nbs1 tandem BRCT domains with phosphorylated MDC1.
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Affiliation(s)
- Chao Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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18
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Loring GL, Christensen KC, Gerber SA, Brenner C. Yeast Chfr homologs retard cell cycle at G1 and G2/M via Ubc4 and Ubc13/Mms2-dependent ubiquitination. Cell Cycle 2007; 7:96-105. [PMID: 18202552 DOI: 10.4161/cc.7.1.5113] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Checkpoint with forkhead-associated and RING (Chfr) is a ubiquitin ligase (E3) that establishes an antephase or prometaphase checkpoint in response to mitotic stress. Though ubiquitination is essential for checkpoint function, the sites, linkages and ubiquitin conjugating enzyme (E2) specificity are controversial. Here we dissect the function of the two Chfr homologs in S. cerevisiae, Chf1 and Chf2, overexpression of which retard cell cycle at both G(1) and G(2). Using a genetic assay, we establish that Ubc4 is required for Chf2-dependent G(1) cell cycle delay and Chf protein turnover. In contrast, Ubc13/Mms2 is required for G(2) delay and does not contribute to Chf protein turnover. By reconstituting cis and trans-ubiquitination activities of Chf proteins in purified systems and characterizing sites modified and linkages formed by tandem mass spectrometry, we discovered that Ubc13/Mms2- dependent modifications are a distinct subset of those catalyzed by Ubc4. Mutagenesis of Lys residues identified in vitro indicates that site-specific Ubc4-dependent Chf protein autoubiquitination is responsible for Chf protein turnover. Thus, combined genetic and biochemical analyses indicate that Chf proteins have dual E2 specificity accounting for different functions in the cell cycle.
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Affiliation(s)
- Greta L Loring
- Department of Genetics and Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
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19
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Woolstencroft RN, Beilharz TH, Cook MA, Preiss T, Durocher D, Tyers M. Ccr4 contributes to tolerance of replication stress through control of CRT1 mRNA poly(A) tail length. J Cell Sci 2007; 119:5178-92. [PMID: 17158920 DOI: 10.1242/jcs.03221] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, DNA replication stress activates the replication checkpoint, which slows S-phase progression, stabilizes slowed or stalled replication forks, and relieves inhibition of the ribonucleotide reductase (RNR) complex. To identify novel genes that promote cellular viability after replication stress, the S. cerevisiae non-essential haploid gene deletion set (4812 strains) was screened for sensitivity to the RNR inhibitor hydroxyurea (HU). Strains bearing deletions in either CCR4 or CAF1/POP2, which encode components of the cytoplasmic mRNA deadenylase complex, were particularly sensitive to HU. We found that Ccr4 cooperated with the Dun1 branch of the replication checkpoint, such that ccr4Delta dun1Delta strains exhibited irreversible hypersensitivity to HU and persistent activation of Rad53. Moreover, because ccr4Delta and chk1Delta exhibited epistasis in several genetic contexts, we infer that Ccr4 and Chk1 act in the same pathway to overcome replication stress. A counterscreen for suppressors of ccr4Delta HU sensitivity uncovered mutations in CRT1, which encodes the transcriptional repressor of the DNA-damage-induced gene regulon. Whereas Dun1 is known to inhibit Crt1 repressor activity, we found that Ccr4 regulates CRT1 mRNA poly(A) tail length and may subtly influence Crt1 protein abundance. Simultaneous overexpression of RNR2, RNR3 and RNR4 partially rescued the HU hypersensitivity of a ccr4Delta dun1Delta strain, consistent with the notion that the RNR genes are key targets of Crt1. These results implicate the coordinated regulation of Crt1 via Ccr4 and Dun1 as a crucial nodal point in the response to DNA replication stress.
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20
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The transcriptome analysis of early morphogenesis in Paracoccidioides brasiliensis mycelium reveals novel and induced genes potentially associated to the dimorphic process. BMC Microbiol 2007; 7:29. [PMID: 17425801 PMCID: PMC1855332 DOI: 10.1186/1471-2180-7-29] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 04/10/2007] [Indexed: 11/10/2022] Open
Abstract
Background Paracoccidioides brasiliensis is a human pathogen with a broad distribution in Latin America. The fungus is thermally dimorphic with two distinct forms corresponding to completely different lifestyles. Upon elevation of the temperature to that of the mammalian body, the fungus adopts a yeast-like form that is exclusively associated with its pathogenic lifestyle. We describe expressed sequence tags (ESTs) analysis to assess the expression profile of the mycelium to yeast transition. To identify P. brasiliensis differentially expressed sequences during conversion we performed a large-scale comparative analysis between P. brasiliensis ESTs identified in the transition transcriptome and databases. Results Our analysis was based on 1107 ESTs from a transition cDNA library of P. brasiliensis. A total of 639 consensus sequences were assembled. Genes of primary metabolism, energy, protein synthesis and fate, cellular transport, biogenesis of cellular components were represented in the transition cDNA library. A considerable number of genes (7.51%) had not been previously reported for P. brasiliensis in public databases. Gene expression analysis using in silico EST subtraction revealed that numerous genes were more expressed during the transition phase when compared to the mycelial ESTs [1]. Classes of differentially expressed sequences were selected for further analysis including: genes related to the synthesis/remodeling of the cell wall/membrane. Thirty four genes from this family were induced. Ten genes related to signal transduction were increased. Twelve genes encoding putative virulence factors manifested increased expression. The in silico approach was validated by northern blot and semi-quantitative RT-PCR. Conclusion The developmental program of P. brasiliensis is characterized by significant differential positive modulation of the cell wall/membrane related transcripts, and signal transduction proteins, suggesting the related processes important contributors to dimorphism. Also, putative virulence factors are more expressed in the transition process suggesting adaptation to the host of the yeast incoming parasitic phase. Those genes provide ideal candidates for further studies directed at understanding fungal morphogenesis and its regulation.
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Abstract
c-Myc regulates target genes by engaging a number of transcriptional cofactors. In a recent issue of Molecular Cell, Fujii et al. (2006) showed that the FHA-domain protein SNIP1 is an important c-Myc coactivator that regulates c-Myc stability and is overexpressed in many tumors.
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Affiliation(s)
- Lars-Gunnar Larsson
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden
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22
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Henderson MJ, Munoz MA, Saunders DN, Clancy JL, Russell AJ, Williams B, Pappin D, Khanna KK, Jackson SP, Sutherland RL, Watts CKW. EDD mediates DNA damage-induced activation of CHK2. J Biol Chem 2006; 281:39990-40000. [PMID: 17074762 DOI: 10.1074/jbc.m602818200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
EDD, the human orthologue of Drosophila melanogaster "hyperplastic discs," is overexpressed or mutated in a number of common human cancers. Although EDD has been implicated in DNA damage signaling, a definitive role has yet to be demonstrated. Here we report a novel interaction between EDD and the DNA damage checkpoint kinase CHK2. EDD and CHK2 associate through a phospho-dependent interaction involving the CHK2 Forkhead-associated domain and a region of EDD spanning a number of putative Forkhead-associated domain-binding threonines. Using RNA interference, we demonstrate a critical role for EDD upstream of CHK2 in the DNA damage signaling pathway. EDD is necessary for the efficient activating phosphorylation of CHK2 in response to DNA damage following exposure to ionizing radiation or the radiomimetic, phleomycin. Cells depleted of EDD display impaired CHK2 kinase activity and an inability to respond to DNA damage. These results identify EDD as a novel mediator in DNA damage signal transduction via CHK2 and emphasize the potential importance of EDD in cancer.
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Affiliation(s)
- Michelle J Henderson
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, New South Wales 2010, Australia
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23
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Stucki M, Jackson SP. gammaH2AX and MDC1: anchoring the DNA-damage-response machinery to broken chromosomes. DNA Repair (Amst) 2006; 5:534-43. [PMID: 16531125 DOI: 10.1016/j.dnarep.2006.01.012] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 01/27/2006] [Indexed: 01/27/2023]
Abstract
Higher-order chromatin structure presents a barrier to the recognition and repair of DNA lesions. Thus, cells must be equipped with mechanisms to surpass this natural obstacle. DNA damage induces histone H2AX phosphorylation by the phosphoinositide 3-kinase like kinases ATM, ATR and DNA-PKcs. H2AX phosphorylation contributes to DNA double-strand break repair but the mechanisms involved are not yet fully understood. In this review, we discuss recent advances in our understanding of how cells use the epigenetic mark of H2AX phosphorylation to dynamically link the DNA-damage-response machinery to broken chromosomes. In addition, we highlight potential regulatory mechanisms of H2AX phosphorylation and speculate about a central functional role of this post-translational histone modification at the interface of DNA repair, chromatin-structure modulation and cell-cycle checkpoint activation.
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Affiliation(s)
- Manuel Stucki
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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24
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Lydall D, Whitehall S. Chromatin and the DNA damage response. DNA Repair (Amst) 2005; 4:1195-207. [PMID: 16046284 DOI: 10.1016/j.dnarep.2005.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 06/07/2005] [Accepted: 06/10/2005] [Indexed: 12/25/2022]
Abstract
The impact of chromatin structure upon the DNA damage response is becoming increasingly apparent. We can reasonably expect many more papers showing how chromatin and chromatin modifications impact upon aspects of the DNA damage response. Here, we present our perspective on some recent developments in this exciting area of cell biology. We aim that this review will be of interest to those who study the DNA damage response, but not usually in the context of chromatin, and equally to those who study chromatin, but not the DNA damage response. It seems likely that these two communities will increasingly share common questions and interests.
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Affiliation(s)
- David Lydall
- Institute of Cell and Molecular Biosciences, University of Newcastle, Henry Wellcome Building, Newcastle General Hospital, Newcastle upon Tyne NE4 6BE, UK
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25
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Bekker-Jensen S, Lukas C, Melander F, Bartek J, Lukas J. Dynamic assembly and sustained retention of 53BP1 at the sites of DNA damage are controlled by Mdc1/NFBD1. ACTA ACUST UNITED AC 2005; 170:201-11. [PMID: 16009723 PMCID: PMC2171401 DOI: 10.1083/jcb.200503043] [Citation(s) in RCA: 222] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
53BP1 is a key component of the genome surveillance network activated by DNA double strand breaks (DSBs). Despite its known accumulation at the DSB sites, the spatiotemporal aspects of 53BP1 interaction with DSBs and the role of other DSB regulators in this process remain unclear. Here, we used real-time microscopy to study the DSB-induced redistribution of 53BP1 in living cells. We show that within minutes after DNA damage, 53BP1 becomes progressively, yet transiently, immobilized around the DSB-flanking chromatin. Quantitative imaging of single cells revealed that the assembly of 53BP1 at DSBs significantly lagged behind Mdc1/NFBD1, another DSB-interacting checkpoint mediator. Furthermore, short interfering RNA-mediated ablation of Mdc1/NFBD1 drastically impaired 53BP1 redistribution to DSBs and triggered premature dissociation of 53BP1 from these regions. Collectively, these in vivo measurements identify Mdc1/NFBD1 as a key upstream determinant of 53BP1's interaction with DSBs from its dynamic assembly at the DSB sites through sustained retention within the DSB-flanking chromatin up to the recovery from the checkpoint.
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Affiliation(s)
- Simon Bekker-Jensen
- Institute of Cancer Biology and Centre for Genotoxic Stress Research, Danish Cancer Society, DK-2100, Copenhagen, Denmark
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26
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Pawson T, Linding R. Synthetic modular systems--reverse engineering of signal transduction. FEBS Lett 2005; 579:1808-14. [PMID: 15763556 DOI: 10.1016/j.febslet.2005.02.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 02/08/2005] [Accepted: 02/08/2005] [Indexed: 12/31/2022]
Abstract
During the last decades, biology has decomposed cellular systems into genetic, functional and molecular networks. It has become evident that these networks consist of components with specific functions (e.g., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization. The idea discussed here is to test the extent of this knowledge by reconstructing, or reverse engineering, new synthetic biological systems from known components. We will discuss how integration of computational methods with proteomics and engineering concepts might lead us to a deeper and more abstract understanding of signal transduction systems. Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways.
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Affiliation(s)
- Tony Pawson
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5.
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Abstract
Left unrepaired, the myriad types of damage that can occur in genomic DNA pose a serious threat to the faithful transmission of the correct complement of genetic material. Defects in DNA damage signaling and repair result in genomic instability, a hallmark of cancer, and often cause lethality, underlining the importance of these processes in the cell and whole organism. The past decade has seen huge advances in our understanding of how the signal transduction pathways triggered by DNA damage radically alter cell behavior. In contrast, it is still unclear how primary DNA damage is detected and how this interfaces with signal transduction and DNA repair proteins.
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Affiliation(s)
- John Rouse
- The Wellcome Trust/Cancer Research UK Institute (of Cancer and Developmental Biology), University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
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28
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Stavridi ES, Huyen Y, Loreto IR, Scolnick DM, Halazonetis TD, Pavletich NP, Jeffrey PD. Crystal structure of the FHA domain of the Chfr mitotic checkpoint protein and its complex with tungstate. Structure 2002; 10:891-9. [PMID: 12121644 DOI: 10.1016/s0969-2126(02)00776-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Chfr mitotic checkpoint protein is frequently inactivated in human cancer. We determined the three-dimensional structure of its FHA domain in its native form and in complex with tungstate, an analog of phosphate. The structures revealed a beta sandwich fold similar to the previously determined folds of the Rad53 N- and C-terminal FHA domains, except that the Rad53 domains were monomeric, whereas the Chfr FHA domain crystallized as a segment-swapped dimer. The ability of the Chfr FHA domain to recognize tungstate suggests that it shares the ability with other FHA domains to bind phosphoproteins. Nevertheless, differences in the sequence and structure of the Chfr and Rad53 FHA domains suggest that FHA domains can be divided into families with distinct binding properties.
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Affiliation(s)
- Elena S Stavridi
- Molecular Genetics Program, Structural Biology Program, Wistar Institute, Philadelphia, PA 19104, USA
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Abstract
The forkhead-associated (FHA) domain is a small protein module recently shown to recognize phosphothreonine epitopes on proteins. It is present in a diverse range of proteins in eukaryotic cells, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins, and metabolic enzymes. It is also found in a number of bacterial proteins. This suggests that FHA domain-mediated phospho-dependent assembly of protein complexes is an ancient and widespread regulatory mechanism.
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Affiliation(s)
- Daniel Durocher
- Samuel Lumenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada M5G 1 X5.
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