1
|
Nishikubo K, Izumi Y, Matsumoto Y, Fujii K, Matsuo K, Yokoya A. STRUCTURAL ANALYSIS OF DNA REPAIR PROTEIN XRCC4 APPLYING CIRCULAR DICHROISM IN AN AQUEOUS SOLUTION. RADIATION PROTECTION DOSIMETRY 2019; 183:36-39. [PMID: 30561720 DOI: 10.1093/rpd/ncy275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
We applied circular dichroism (CD) spectral analysis to obtain the secondary structure of the DNA repair protein XRCC4, with a focus on its C-terminus. Using synchrotron radiation as a light source across a wide range of wavelengths, including vacuum ultraviolet (UV) light from 180 to 200 nm and UV light from 200 to 240 nm, we determined the secondary structure composition of the full-length protein, including its C-terminus, which had not yet been -the focus of crystallography studies, though it contains several phosphorylation sites. The secondary structures inferred using the obtained CD spectra indicate that the C-terminus is composed of a substantial fraction of turns with a few unordered and alpha-helix structures and almost no beta-strands. The C-terminus is likely to form a characteristic secondary structure with turns as a main component, and its DNA repair function is likely regulated by the structural change induced by phosphorylation of the terminus.
Collapse
Affiliation(s)
- Kai Nishikubo
- Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, Japan
- Tokai Quantum Beam Science Center, National Institutes for Quantum and Radiological Science and Technology (QST), 2-4 Shirakata-Oaza, Tokai, Ibaraki, Japan
| | - Yudai Izumi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313, Kagamiyama, Higashihiroshima-shi, Hiroshima, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, ookayama, meguro-ku, Tokyo, Japan
| | - Kentaro Fujii
- Tokai Quantum Beam Science Center, National Institutes for Quantum and Radiological Science and Technology (QST), 2-4 Shirakata-Oaza, Tokai, Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313, Kagamiyama, Higashihiroshima-shi, Hiroshima, Japan
| | - Akinari Yokoya
- Tokai Quantum Beam Science Center, National Institutes for Quantum and Radiological Science and Technology (QST), 2-4 Shirakata-Oaza, Tokai, Ibaraki, Japan
| |
Collapse
|
2
|
Quezada Urban R, Díaz Velásquez CE, Gitler R, Rojo Castillo MP, Sirota Toporek M, Figueroa Morales A, Moreno García O, García Esquivel L, Torres Mejía G, Dean M, Delgado Enciso I, Ochoa Díaz López H, Rodríguez León F, Jan V, Garzón Barrientos VH, Ruiz Flores P, Espino Silva PK, Haro Santa Cruz J, Martínez Gregorio H, Rojas Jiménez EA, Romero Cruz LE, Méndez Catalá CF, Álvarez Gómez RM, Fragoso Ontiveros V, Herrera LA, Romieu I, Terrazas LI, Chirino YI, Frecha C, Oliver J, Perdomo S, Vaca Paniagua F. Comprehensive Analysis of Germline Variants in Mexican Patients with Hereditary Breast and Ovarian Cancer Susceptibility. Cancers (Basel) 2018; 10:E361. [PMID: 30262796 PMCID: PMC6211045 DOI: 10.3390/cancers10100361] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/05/2018] [Accepted: 09/15/2018] [Indexed: 12/11/2022] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) represents 5⁻10% of all patients with breast cancer and is associated with high-risk pathogenic alleles in BRCA1/2 genes, but only for 25% of cases. We aimed to find new pathogenic alleles in a panel of 143 cancer-predisposing genes in 300 Mexican cancer patients with suspicion of HBOC and 27 high-risk patients with a severe family history of cancer, using massive parallel sequencing. We found pathogenic variants in 23 genes, including BRCA1/2. In the group of cancer patients 15% (46/300) had a pathogenic variant; 11% (33/300) harbored variants with unknown clinical significance (VUS) and 74% (221/300) were negative. The high-risk group had 22% (6/27) of patients with pathogenic variants, 4% (1/27) had VUS and 74% (20/27) were negative. The most recurrent mutations were the Mexican founder deletion of exons 9-12 and the variant p.G228fs in BRCA1, each found in 5 of 17 patients with alterations in this gene. Rare VUS with potential impact at the protein level were found in 21 genes. Our results show for the first time in the Mexican population a higher contribution of pathogenic alleles in other susceptibility cancer genes (54%) than in BRCA1/2 (46%), highlighting the high locus heterogeneity of HBOC and the necessity of expanding genetic tests for this disease to include broader gene panels.
Collapse
Affiliation(s)
- Rosalía Quezada Urban
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | | | | | | | | | | | | | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | | | - Héctor Ochoa Díaz López
- Department of Health, El Colegio de la Frontera Sur (ECOSUR), San Cristóbal de Las Casas 29290, Chiapas, Mexico.
| | - Fernando Rodríguez León
- Department of Health, El Colegio de la Frontera Sur (ECOSUR), San Cristóbal de Las Casas 29290, Chiapas, Mexico.
| | - Virginia Jan
- Internal Medicine, Hospital de Especialidades Vida Mejor, ISSTECH, Tuxtla Gutiérrez 29040, Chiapas, Mexico.
| | | | - Pablo Ruiz Flores
- Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón 27000, Coahuila, Mexico.
| | - Perla Karina Espino Silva
- Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón 27000, Coahuila, Mexico.
| | - Jorge Haro Santa Cruz
- Centro de Investigación Biomédica, Universidad Autónoma de Coahuila, Torreón 27000, Coahuila, Mexico.
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | - Luis Enrique Romero Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | - Claudia Fabiola Méndez Catalá
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
| | | | | | - Luis Alonso Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas-Instituto Nacional de Cancerología, CDMX 14080, Mexico.
| | - Isabelle Romieu
- Center for Center for Research on Population Health, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico.
- Hubert Department of Global Health, Emory University, Atlanta, GA 30322, USA.
| | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, 54090 Tlalnepantla, Estado de México, Mexico.
| | - Yolanda Irasema Chirino
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, 54090 Tlalnepantla, Estado de México, Mexico.
| | | | - Javier Oliver
- Hospital Italiano, Buenos Aires C1199ABB, Argentina.
| | - Sandra Perdomo
- Investigación en Nutrición, Genética y Metabolismo, Facultad de Medicina, Universidad El Bosque, Bogotá 110121, Colombia.
- Department of Pathology and Laboratories, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá 110100, Colombia.
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
- Instituto Nacional de Cancerología, CDMX 14080, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, 54090 Tlalnepantla, Estado de México, Mexico.
| |
Collapse
|
3
|
Saito S, Maeda R, Adachi N. Dual loss of human POLQ and LIG4 abolishes random integration. Nat Commun 2017; 8:16112. [PMID: 28695890 PMCID: PMC5508229 DOI: 10.1038/ncomms16112] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/30/2017] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination-mediated gene targeting has greatly contributed to genetic analysis in a wide range of species, but is highly inefficient in human cells because of overwhelmingly frequent random integration events, whose molecular mechanism remains elusive. Here we show that DNA polymerase θ, despite its minor role in chromosomal DNA repair, substantially contributes to random integration, and that cells lacking both DNA polymerase θ and DNA ligase IV, which is essential for non-homologous end joining (NHEJ), exhibit 100% efficiency of spontaneous gene targeting by virtue of undetectable levels of random integration. Thus, DNA polymerase θ-mediated end joining is the sole homology-independent repair route in the absence of NHEJ and, intriguingly, their combined absence reveals rare Alu-Alu recombination events utilizing a stretch of homology. Our findings provide new insights into the mechanics of foreign DNA integration and the role of DNA polymerase θ in human genome maintenance.
Collapse
Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
| | - Ryo Maeda
- Department of Biology, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| |
Collapse
|
4
|
McKay MJ, Goh SK, McKay JN, Chao M, McKay TM. Non-homologous end-joining protein expression screen from radiosensitive cancer patients yields a novel DNA double strand break repair phenotype. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:96. [PMID: 28361061 DOI: 10.21037/atm.2017.03.04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Clinical radiosensitivity is a significant impediment to tumour control and cure, in that it restricts the total doses which can safely be delivered to the whole radiotherapy population, within the tissue tolerance of potentially radiosensitive (RS) individuals. Understanding its causes could lead to personalization of radiotherapy. METHODS We screened tissues from a unique bank of RS cancer patients for expression defects in major DNA double-strand break repair proteins, using Western blot analysis and subsequently reverse-transcriptase polymerase chain reaction and pulsed-field gel electrophoresis. RESULTS We hypothesized that abnormalities in expression of these proteins may explain the radiosensitivity of some of our cancer patients. The cells from one patient showed a reproducibly consistent expression reduction in two complex-forming DNA double-strand break repair protein components (DNA Ligase IV and XRCC4). We also showed a corresponding reduction in both gene products at the mRNA level. Additionally, the mRNA inducibility by ionizing radiation was increased for one of the proteins in the patient's cells. We confirmed the likely functional significance of the non-homologous end-joining (NHEJ) expression abnormalities with a DNA double strand break (DNA DSB) repair assay. CONCLUSIONS We have identified a novel biological phenotype linked to clinical radiosensitivity. This is important in that very few molecular defects are known in human radiotherapy subjects. Such knowledge may contribute to the understanding of radiation response mechanisms in cancer patients and to personalization of radiotherapy.
Collapse
Affiliation(s)
- Michael J McKay
- University of Sydney, Department of Medicine, Camperdown, 2050 NSW, Australia
| | - Su Kak Goh
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Michael Chao
- Genesis Cancer Care, Melbourne, 3001 VIC, Australia
| | | |
Collapse
|
5
|
Williamson A, Hjerde E, Kahlke T. Analysis of the distribution and evolution of the ATP-dependent DNA ligases of bacteria delineates a distinct phylogenetic group 'Lig E'. Mol Microbiol 2015; 99:274-90. [PMID: 26412580 DOI: 10.1111/mmi.13229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 12/01/2022]
Abstract
Prior to the discovery of a minimal ATP-dependent DNA ligase in Haemophilus influenzae, bacteria were thought to only possess a NAD-dependent ligase, which was involved in sealing of Okazaki fragments. We now know that a diverse range of bacterial species possess up to six of these accessory bacterial ATP-dependent DNA ligases (b-ADLs), which vary in size and enzymatic domain associations. Here we compare the domain structure of different types of b-ADLs and investigate their distribution among the bacterial domain to describe possible evolutionary trajectories that gave rise to the sequence and structural diversity of these enzymes. Previous biochemical and genetic analyses have delineated three main classes of these enzymes: Lig B, Lig C and Lig D, which appear to have descended from a common ancestor within the bacterial domain. In the present study, we delineate a fourth group of b-ADLs, Lig E, which possesses a number of unique features at the primary and tertiary structural levels. The biochemical characteristics, domain structure and inferred extracellular location sets this group apart from the other b-ADLs. The results presented here indicate that the Lig E type ligases were horizontally transferred into bacteria in a separate event from other b-ADLs possibly from a bacteriophage.
Collapse
Affiliation(s)
- Adele Williamson
- Department of Chemistry, University of Tromsø, N-9019, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, University of Tromsø, N-9019, Tromsø, Norway
| | - Tim Kahlke
- CSIRO Oceans and Atmosphere Flagship, Castray Esplanade, Hobart, TAS, 7000, Australia
| |
Collapse
|
6
|
Yeast DNA ligase IV mutations reveal a nonhomologous end joining function of BRCT1 distinct from XRCC4/Lif1 binding. DNA Repair (Amst) 2015; 24:37-45. [PMID: 25457772 DOI: 10.1016/j.dnarep.2014.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 08/23/2014] [Accepted: 10/02/2014] [Indexed: 02/03/2023]
Abstract
LIG4/Dnl4 is the DNA ligase that (re)joins DNA double-strand breaks (DSBs) via nonhomologous end joining (NHEJ), an activity supported by binding of its tandem BRCT domains to the ligase accessory protein XRCC4/Lif1. We screened a panel of 88 distinct ligase mutants to explore the structure–function relationships of the yeast Dnl4 BRCT domains and inter-BRCT linker in NHEJ. Screen results suggested two distinct classes of BRCT mutations with differential effects on Lif1 interaction as compared to NHEJ completion. Validated constructs confirmed that D800K and GG(868:869)AA mutations, which target the Lif1 binding interface, showed a severely defective Dnl4–Lif1 interaction but a less consistent and often small decrease in NHEJ activity in some assays, as well as nearly normal levels of Dnl4 accumulation at DSBs. In contrast, mutants K742A and KTT(742:744)ATA, which target the β3-α2 region of the first BRCT domain, substantially decreased NHEJ function commensurate with a large defect in Dnl4 recruitment to DSBs, despite a comparatively greater preservation of the Lif1 interaction. Together, these separation-of-function mutants indicate that Dnl4 BRCT1 supports DSB recruitment and NHEJ in a manner distinct from Lif1 binding and reveal a complexity of Dnl4 BRCT domain functions in support of stable DSB association.
Collapse
|
7
|
Fukuchi M, Wanotayan R, Liu S, Imamichi S, Sharma MK, Matsumoto Y. Lysine 271 but not lysine 210 of XRCC4 is required for the nuclear localization of XRCC4 and DNA ligase IV. Biochem Biophys Res Commun 2015; 461:687-94. [PMID: 25934149 DOI: 10.1016/j.bbrc.2015.04.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/18/2015] [Indexed: 11/16/2022]
Abstract
XRCC4 and DNA Ligase IV (LIG4) cooperate to join two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). However, it is not fully understood how these proteins are localized to the nucleus. Here we created XRCC4(K271R) mutant, as Lys271 lies within the putative nuclear localization signal (NLS), and XRCC4(K210R) mutant, as Lys210 was reported to undergo SUMOylation, implicated in the nuclear localization of XRCC4. Wild-type and mutated XRCC4 with EGFP tag were introduced into HeLa cell, in which endogenous XRCC4 had been knocked down using siRNA directed to 3'-untranslated region, and tested for the nuclear localization function by fluorescence microscopy. XRCC4(K271R) was defective in the nuclear localization of itself and LIG4, whereas XRCC4(K210R) was competent for the nuclear localization with LIG4. To examine DSB repair function, wild-type and mutated XRCC4 were introduced into XRCC4-deficient M10. M10-XRCC4(K271R), but not M10-XRCC4(K210R), showed significantly reduced surviving fraction after 2 Gy γ-ray irradiation as compared to M10-XRCC4(WT). The number of γ-H2AX foci remaining 2 h after 2 Gy γ-ray irradiation was significantly greater in M10-XRCC4(K271R) than in M10-XRCC4(WT), whereas it was only marginally increased in M10-XRCC4(K210R) as compared to M10-XRCC4(WT). The present results collectively indicated that Lys271, but not Lys210, of XRCC4 is required for the nuclear localization of XRCC4 and LIG4 and that the nuclear localizing ability is essential for DSB repair function of XRCC4.
Collapse
Affiliation(s)
- Mikoto Fukuchi
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Rujira Wanotayan
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sicheng Liu
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Shoji Imamichi
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mukesh Kumar Sharma
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshihisa Matsumoto
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| |
Collapse
|
8
|
Wanotayan R, Fukuchi M, Imamichi S, Sharma MK, Matsumoto Y. Asparagine 326 in the extremely C-terminal region of XRCC4 is essential for the cell survival after irradiation. Biochem Biophys Res Commun 2015; 457:526-31. [PMID: 25597996 DOI: 10.1016/j.bbrc.2015.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/07/2015] [Indexed: 12/25/2022]
Abstract
XRCC4 is one of the crucial proteins in the repair of DNA double-strand break (DSB) through non-homologous end-joining (NHEJ). As XRCC4 consists of 336 amino acids, N-terminal 200 amino acids include domains for dimerization and for association with DNA ligase IV and XLF and shown to be essential for XRCC4 function in DSB repair and V(D)J recombination. On the other hand, the role of the remaining C-terminal region of XRCC4 is not well understood. In the present study, we noticed that a stretch of ∼20 amino acids located at the extreme C-terminus of XRCC4 is highly conserved among vertebrate species. To explore its possible importance, series of mutants in this region were constructed and assessed for the functionality in terms of ability to rescue radiosensitivity of M10 cells lacking XRCC4. Among 13 mutants, M10 transfectant with N326L mutant (M10-XRCC4(N326L)) showed elevated radiosensitivity. N326L protein showed defective nuclear localization. N326L sequence matched the consensus sequence of nuclear export signal. Leptomycin B treatment accumulated XRCC4(N326L) in the nucleus but only partially rescued radiosensitivity of M10-XRCC4(N326L). These results collectively indicated that the functional defects of XRCC4(N326L) might be partially, but not solely, due to its exclusion from nucleus by synthetic nuclear export signal. Further mutation of XRCC4 Asn326 to other amino acids, i.e., alanine, aspartic acid or glutamine did not affect the nuclear localization but still exhibited radiosensitivity. The present results indicated the importance of the extremely C-terminal region of XRCC4 and, especially, Asn326 therein.
Collapse
Affiliation(s)
- Rujira Wanotayan
- Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mikoto Fukuchi
- Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Shoji Imamichi
- Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mukesh Kumar Sharma
- Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshihisa Matsumoto
- Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| |
Collapse
|
9
|
Williamson A, Rothweiler U, Leiros HKS. Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface. ACTA ACUST UNITED AC 2014; 70:3043-56. [PMID: 25372693 PMCID: PMC4220977 DOI: 10.1107/s1399004714021099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022]
Abstract
The enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase (ADL), which does not have any additional DNA-binding domains, is similar to minimal viral ADLs that comprise only the core catalytic domains. The bacterial ADL also lacks the unstructured loops which are involved in DNA binding in the viral ADLs, implying that it must instead use short well structured motifs of the core domains to engage its substrate. DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. strain SP041 is described. This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. The 1.65 Å resolution crystal structure of the enzyme–adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. This is in contrast to previously characterized minimal DNA ligases from viruses, which use flexible loop regions for DNA interaction. The Psychromonas sp. enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date.
Collapse
Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ulli Rothweiler
- NorStruct, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | | |
Collapse
|
10
|
Francis DB, Kozlov M, Chavez J, Chu J, Malu S, Hanna M, Cortes P. DNA Ligase IV regulates XRCC4 nuclear localization. DNA Repair (Amst) 2014; 21:36-42. [PMID: 24984242 DOI: 10.1016/j.dnarep.2014.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/22/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022]
Abstract
DNA Ligase IV, along with its interacting partner XRCC4, are essential for repairing DNA double strand breaks by non-homologous end joining (NHEJ). Together, they complete the final ligation step resolving the DNA break. Ligase IV is regulated by XRCC4 and XLF. However, the mechanism(s) by which Ligase IV control the NHEJ reaction and other NHEJ factor(s) remains poorly characterized. Here, we show that a C-terminal region of Ligase IV (aa 620-800), which encompasses a NLS, the BRCT I, and the XRCC4 interacting region (XIR), is essential for nuclear localization of its co-factor XRCC4. In Ligase IV deficient cells, XRCC4 showed deregulated localization remaining in the cytosol even after induction of DNA double strand breaks. DNA Ligase IV was also required for efficient localization of XLF into the nucleus. Additionally, human fibroblasts that harbor hypomorphic mutations within the Ligase IV gene displayed decreased levels of XRCC4 protein, implicating that DNA Ligase IV is also regulating XRCC4 stability. Our results provide evidence for a role of DNA Ligase IV in controlling the cellular localization and protein levels of XRCC4.
Collapse
Affiliation(s)
- Dailia B Francis
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mikhail Kozlov
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jose Chavez
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jennifer Chu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Shruti Malu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Mary Hanna
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Patricia Cortes
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| |
Collapse
|