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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401150. [PMID: 38582512 PMCID: PMC11220639 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325011China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Haihong Li
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
| | - Ximiao Hou
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
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2
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Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
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Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
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3
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Abbas Q, Muhammad MA, Shakir NA, Aslam M, Rashid N. Molecular cloning and characterization of Pcal_0039, an ATP-/NAD +-independent DNA ligase from hyperthermophilic archaeon Pyrobaculum calidifontis. Int J Biol Macromol 2023; 253:126711. [PMID: 37673141 DOI: 10.1016/j.ijbiomac.2023.126711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/25/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
The genome sequence of hyperthermophilic archaeon Pyrobaculum calidifontis contains an open reading frame, Pcal_0039, which encodes a putative DNA ligase. Structural analysis disclosed the presence of signature sequences of ATP-dependent DNA ligases. We have heterologously expressed Pcal_0039 gene in Escherichia coli. The recombinant protein, majorly produced in soluble form, was purified and functionally characterized. Recombinant Pcal_0039 displayed nick-joining activity between 40 and 85 °C. Optimal activity was observed at 70 °C and pH 5.5. Nick-joining activity was retained even after heating for 1 h at 90 °C, indicating highly thermostable nature of Pcal_0039. The nick-joining activity, displayed by Pcal_0039, was metal ion dependent and Mg2+ was the most preferred. NaCl and KCl inhibited the nick-joining activity at or above 200 mmol/L. The activity catalyzed by recombinant Pcal_0039 was independent of addition of ATP or NAD+ or any other nucleotide cofactor. A mismatch adjacent to the nick, either at 3'- or 5'-end, abolished the nick-joining activity. These characteristics make Pcal_0039 a potential candidate for applications in DNA diagnostics. To the best of our knowledge, Pcal_0039 is the only DNA ligase, characterized from genus Pyrobaculum, which exhibits optimum nick-joining activity at pH below 6.0 and independent of any nucleotide cofactor.
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Affiliation(s)
- Qamar Abbas
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Nisar Ahmad Shakir
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Mehwish Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
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4
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Arrías PN, Monzon AM, Clementel D, Mozaffari S, Piovesan D, Kajava AV, Tosatto SCE. The repetitive structure of DNA clamps: An overlooked protein tandem repeat. J Struct Biol 2023; 215:108001. [PMID: 37467824 DOI: 10.1016/j.jsb.2023.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe "Box repeats", an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V "beads-on-a-string" type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses.
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Affiliation(s)
- Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Damiano Clementel
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Soroush Mozaffari
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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5
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Shao Z, Yang J, Gao Y, Zhang Y, Zhao X, Shao Q, Zhang W, Cao C, Liu H, Gan J. Structural and functional studies of PCNA from African swine fever virus. J Virol 2023; 97:e0074823. [PMID: 37534905 PMCID: PMC10506467 DOI: 10.1128/jvi.00748-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) belongs to the DNA sliding clamp family. Via interacting with various partner proteins, PCNA plays critical roles in DNA replication, DNA repair, chromatin assembly, epigenetic inheritance, chromatin remodeling, and many other fundamental biological processes. Although PCNA and PCNA-interacting partner networks are conserved across species, PCNA of a given species is rarely functional in heterologous systems, emphasizing the importance of more representative PCNA studies. Here, we report two crystal structures of PCNA from African swine fever virus (ASFV), which is the only member of the Asfarviridae family. Compared to the eukaryotic and archaeal PCNAs and the sliding clamp structural homologs from other viruses, AsfvPCNA possesses unique sequences and/or conformations at several regions, such as the J-loop, interdomain-connecting loop (IDCL), P-loop, and C-tail, which are involved in partner recognition or modification of sliding clamps. In addition to double-stranded DNA binding, we also demonstrate that AsfvPCNA can modestly enhance the ligation activity of the AsfvLIG protein. The unique structural features of AsfvPCNA can serve as a potential target for the development of ASFV-specific inhibitors and help combat the deadly virus. IMPORTANCE Two high-resolution crystal structures of African swine fever virus proliferating cell nuclear antigen (AsfvPCNA) are presented here. Structural comparison revealed that AsfvPCNA is unique at several regions, such as the J-loop, the interdomain-connecting loop linker, and the P-loop, which may play important roles in ASFV-specific partner selection of AsfvPCNA. Unlike eukaryotic and archaeal PCNAs, AsfvPCNA possesses high double-stranded DNA-binding affinity. Besides DNA binding, AsfvPCNA can also modestly enhance the ligation activity of the AsfvLIG protein, which is essential for the replication and repair of ASFV genome. The unique structural features make AsfvPCNA a potential target for drug development, which will help combat the deadly virus.
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Affiliation(s)
- Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weizhen Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chulei Cao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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6
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Shi J, Oger PM, Cao P, Zhang L. Thermostable DNA ligases from hyperthermophiles in biotechnology. Front Microbiol 2023; 14:1198784. [PMID: 37293226 PMCID: PMC10244674 DOI: 10.3389/fmicb.2023.1198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.
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Affiliation(s)
- Jingru Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Philippe M. Oger
- University of Lyon, INSA de Lyon, CNRS UMR, Villeurbanne, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
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7
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Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Crehuet R, Hamdan SM, De Biasio A. Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing. Nat Commun 2022; 13:7833. [PMID: 36539424 PMCID: PMC9767926 DOI: 10.1038/s41467-022-35475-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIPN-term) and DNA binding domain (PIPDBD). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIPN-term is released from PCNA and only PIPDBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.
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Affiliation(s)
- Kerry Blair
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Taha Shahid
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Fahad Rashid
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Ramon Crehuet
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC) C/ Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK.
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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8
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Kaczmarczyk AP, Déclais AC, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nat Commun 2022; 13:5921. [PMID: 36207294 PMCID: PMC9547003 DOI: 10.1038/s41467-022-33503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
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Affiliation(s)
- Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
| | | | - Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David M J Lilley
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK.
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9
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Abstract
In this issue of Structure, Sverzhinsky et al. (2022) report structures of archaeal DNA ligase bound to the proliferating cell nuclear antigen (PCNA) sliding clamp and a nicked DNA substrate. The structures provide snapshots of ligation intermediates, which reveal a dynamic nature of the complex and explain how PCNA stimulates the DNA ligase activity.
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Affiliation(s)
- Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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10
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Sverzhinsky A, Tomkinson AE, Pascal JM. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure 2022; 30:371-385.e5. [PMID: 34838188 PMCID: PMC8897274 DOI: 10.1016/j.str.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break. The cryo-EM structures highlight a continuous DNA-binding surface formed between DNA ligase and PCNA that supports the distorted conformation of the DNA break undergoing repair and contributes to PCNA stimulation of DNA ligation. DNA ligase is conformationally flexible within the complex, with its domains fully ordered only when encircling the repaired DNA to form a stacked ring structure with PCNA. The structures highlight DNA ligase structural transitions while docked on PCNA, changes in DNA conformation during ligation, and the potential for DNA ligase domains to regulate PCNA accessibility to other repair factors.
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Affiliation(s)
- Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology, and University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada.
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11
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Krakowska-Sieprawska A, Kiełbasa A, Rafińska K, Ligor M, Buszewski B. Modern Methods of Pre-Treatment of Plant Material for the Extraction of Bioactive Compounds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030730. [PMID: 35163995 PMCID: PMC8840492 DOI: 10.3390/molecules27030730] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 12/22/2022]
Abstract
In this review, recent advances in the methods of pre-treatment of plant material for the extraction of secondary metabolites with high biological activity are presented. The correct preparation of the material for extraction is as important as the selection of the extraction method. This step should prevent the degradation of bioactive compounds as well as the development of fungi and bacteria. Currently, the methods of preparation are expected to modify the particles of the plant material in such a way that will contribute to the release of bioactive compounds loosely bonded to cell wall polymers. This review presents a wide range of methods of preparing plant material, including drying, freeze-drying, convection drying, microwave vacuum drying, enzymatic processes, and fermentation. The influence of the particular methods on the structure of plant material particles, the level of preserved bioactive compounds, and the possibility of their release during the extraction were highlighted. The plant material pre-treatment techniques used were discussed with respect to the amount of compounds released during extraction as well their application in various industries interested in products with a high content of biologically active compounds, such as the pharmaceutical, cosmetics, and food industries.
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Affiliation(s)
- Aneta Krakowska-Sieprawska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 St., PL-87100 Torun, Poland; (A.K.-S.); (A.K.); (K.R.); (M.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, Wileńska 4 St., PL-87100 Torun, Poland
| | - Anna Kiełbasa
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 St., PL-87100 Torun, Poland; (A.K.-S.); (A.K.); (K.R.); (M.L.)
| | - Katarzyna Rafińska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 St., PL-87100 Torun, Poland; (A.K.-S.); (A.K.); (K.R.); (M.L.)
| | - Magdalena Ligor
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 St., PL-87100 Torun, Poland; (A.K.-S.); (A.K.); (K.R.); (M.L.)
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 St., PL-87100 Torun, Poland; (A.K.-S.); (A.K.); (K.R.); (M.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, Wileńska 4 St., PL-87100 Torun, Poland
- Correspondence: ; Tel.: +49-56-611-4308; Fax: +49-56-611-4837
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12
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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13
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Hammel M, Tainer JA. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci 2021; 30:1735-1756. [PMID: 34056803 PMCID: PMC8376411 DOI: 10.1002/pro.4133] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIVBRCT–Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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14
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Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. FEBS Lett 2021; 595:1328-1349. [PMID: 33544878 DOI: 10.1002/1873-3468.14055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/11/2023]
Abstract
An assembly of multiprotein complexes achieves chromosomal DNA replication at the replication fork. In eukaryotes, proliferating cell nuclear antigen (PCNA) plays a vital role in the assembly of multiprotein complexes at the replication fork and is essential for cell viability. PCNA from several organisms, including Saccharomyces cerevisiae, has been structurally characterised. However, the structural analyses of PCNA from fungal pathogens are limited. Recently, we have reported that PCNA from the opportunistic fungal pathogen Candida albicans complements the essential functions of ScPCNA in S. cerevisiae. Still, it only partially rescues the loss of ScPCNA when the yeast cells are under genotoxic stress. To understand this further, herein, we have determined the crystal structure of CaPCNA and compared that with the existing structures of other fungal and human PCNA. Our comparative structural and in-solution small-angle X-ray scattering (SAXS) analyses reveal that CaPCNA forms a stable homotrimer, both in crystal and in solution. It displays noticeable structural alterations in the oligomerisation interface, P-loop and hydrophobic pocket regions, suggesting its differential function in a heterologous system and avenues for developing specific therapeutics. DATABASES: The PDB and SASBDB accession codes for CaPCNA are 7BUP and SASDHQ9, respectively.
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Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Manipal Academy of Higher Education, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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15
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Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res 2021; 49:306-321. [PMID: 33330937 PMCID: PMC7797052 DOI: 10.1093/nar/gkaa1188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/21/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tom Ellenberger
- Department of Biochemistry, Washington University, St. Louis, MO, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular & Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
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16
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Matsumoto Y, Brooks RC, Sverzhinsky A, Pascal JM, Tomkinson AE. Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation. J Mol Biol 2020; 432:166698. [PMID: 33157085 DOI: 10.1016/j.jmb.2020.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/07/2020] [Accepted: 10/27/2020] [Indexed: 11/28/2022]
Abstract
More than a million Okazaki fragments are synthesized, processed and joined during replication of the human genome. After synthesis of an RNA-DNA oligonucleotide by DNA polymerase α holoenzyme, proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp and polymerase processivity factor, is loaded onto the primer-template junction by replication factor C (RFC). Although PCNA interacts with the enzymes DNA polymerase δ (Pol δ), flap endonuclease 1 (FEN1) and DNA ligase I (LigI) that complete Okazaki fragment processing and joining, it is not known how the activities of these enzymes are coordinated. Here we describe a novel interaction between Pol δ and LigI that is critical for Okazaki fragment joining in vitro. Both LigI and FEN1 associate with PCNA-Pol δ during gap-filling synthesis, suggesting that gap-filling synthesis is carried out by a complex of PCNA, Pol δ, FEN1 and LigI. Following ligation, PCNA and LigI remain on the DNA, indicating that Pol δ and FEN1 dissociate during 5' end processing and that LigI engages PCNA at the DNA nick generated by FEN1 and Pol δ. Thus, dynamic PCNA complexes coordinate Okazaki fragment synthesis and processing with PCNA and LigI forming a terminal structure of two linked protein rings encircling the ligated DNA.
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Affiliation(s)
- Yoshihiro Matsumoto
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Rhys C Brooks
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States.
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17
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Binding-Induced Conformational Changes Involved in Sliding Clamp PCNA and DNA Polymerase DPO4. iScience 2020; 23:101117. [PMID: 32422591 PMCID: PMC7229285 DOI: 10.1016/j.isci.2020.101117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/22/2020] [Accepted: 04/26/2020] [Indexed: 11/29/2022] Open
Abstract
Cooperation between DNA polymerases and DNA sliding clamp proteins is essential for DNA replication and repair. However, it is still challenging to clarify the binding mechanism and the movements of Y-family DNA polymerase IV (DPO4) on the proliferating cell nuclear antigen (PCNA) ring. Here we develop the simulation models of DPO4–PCNA123 and DPO4–PCNA12 complexes and uncover the underlying dynamics of DPO4 during binding and the binding order of the DPO4 domains. Two important intermediate states are found on the free energy surface before reaching the final bound state. Our results suggest that both PCNA3 and DPO4 can influence the PCNA12 planar conformation, whereas the impact of PCNA3 on PCNA12 is more significant than DPO4. These findings provide the crucial information of the conformational dynamics of DPO4 and PCNA, as well as the clue of the underlying mechanism of the cooperation between DPO4 and PCNA during DNA replication. The mechanism of DPO4 binding to PCNA ring and PCNA dimer is investigated Two important intermediate states are found before reaching the final bound state Both PCNA3 and DPO4 can influence the PCNA12 planar conformation
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18
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Williamson A, Leiros HKS. Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation. Nucleic Acids Res 2019; 47:7147-7162. [PMID: 31312841 PMCID: PMC6698739 DOI: 10.1093/nar/gkz596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/05/2019] [Indexed: 01/17/2023] Open
Abstract
DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
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Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway.,School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
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19
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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20
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Unciuleac MC, Goldgur Y, Shuman S. Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. J Biol Chem 2019; 294:5094-5104. [PMID: 30718283 PMCID: PMC6442053 DOI: 10.1074/jbc.ra119.007445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD+ to form a covalent ligase-(lysyl-Nζ)-AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide. In step 2, AMP is transferred from ligase-adenylate to the 5'-PO4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.8 Å resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to nonhomologous end joining, in complexes with ATP that highlight large movements of the OB domain (∼50 Å), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD·ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg2+ that engages the ATP α phosphate and a second metal that bridges the ATP β and γ phosphates.
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Affiliation(s)
| | - Yehuda Goldgur
- Structural Biology Programs, Sloan Kettering Institute, New York, New York 10065
| | - Stewart Shuman
- From the Molecular Biology and , To whom correspondence should be addressed:
Molecular Biology Program, Sloan Kettering Institute, 1275 York Ave., New York, NY 10065. E-mail:
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21
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Berg K, Leiros I, Williamson A. Temperature adaptation of DNA ligases from psychrophilic organisms. Extremophiles 2019; 23:305-317. [DOI: 10.1007/s00792-019-01082-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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22
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Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J. Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues. Nat Commun 2019; 10:387. [PMID: 30674878 PMCID: PMC6344480 DOI: 10.1038/s41467-019-08296-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
African swine fever virus (ASFV) is contagious and can cause highly lethal disease in pigs. ASFV DNA ligase (AsfvLIG) is one of the most error-prone ligases identified to date; it catalyzes DNA joining reaction during DNA repair process of ASFV and plays important roles in mutagenesis of the viral genome. Here, we report four AsfvLIG:DNA complex structures and demonstrate that AsfvLIG has a unique N-terminal domain (NTD) that plays critical roles in substrate binding and catalytic complex assembly. In combination with mutagenesis, in vitro binding and catalytic assays, our study reveals that four unique active site residues (Asn153 and Leu211 of the AD domain; Leu402 and Gln403 of the OB domain) are crucial for the catalytic efficiency of AsfvLIG. These unique structural features can serve as potential targets for small molecule design, which could impair genome repair in ASFV and help combat this virus in the future.
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Affiliation(s)
- Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xiang Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Suhua Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Xuhang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Zhen Huang
- College of Life Sciences, Sichuan University, 610041, Chengdu, China. .,Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China. .,Department of Neurology, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200433, Shanghai, China.
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23
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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24
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Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara H. T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res 2018; 46:10474-10488. [PMID: 30169742 PMCID: PMC6212786 DOI: 10.1093/nar/gky776] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/18/2018] [Indexed: 01/07/2023] Open
Abstract
DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Thomas E Bohl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Jeonghyun Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Andrew Zasada
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Shray Malik
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, 60439, USA
| | - Vincent Tran
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Na Li
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Zhiqi Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Fredy Kurniawan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Kayo Orellana
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA,To whom correspondence should be addressed. Tel: +1 612 624 1491;
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25
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Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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26
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Cordeiro TN, Chen PC, De Biasio A, Sibille N, Blanco FJ, Hub JS, Crehuet R, Bernadó P. Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly. Nucleic Acids Res 2017; 45:1501-1515. [PMID: 28180305 PMCID: PMC5388412 DOI: 10.1093/nar/gkw1183] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
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Affiliation(s)
- Tiago N Cordeiro
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | | | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Francisco J Blanco
- CIC-bioGUNE, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia, CSIC, Barcelona 08034, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
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27
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Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017; 12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.
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Affiliation(s)
- Ibrahim Koç
- Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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28
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Prakash A, Moharana K, Wallace SS, Doublié S. Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 2017; 45:2897-2909. [PMID: 27994037 PMCID: PMC5389659 DOI: 10.1093/nar/gkw1282] [Citation(s) in RCA: 7] [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: 07/27/2016] [Revised: 11/11/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis and mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.
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Affiliation(s)
- Aishwarya Prakash
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Kedar Moharana
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Susan S. Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
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29
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Trasviña-Arenas CH, Cardona-Felix CS, Azuara-Liceaga E, Díaz-Quezada C, Brieba LG. Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding. FEBS Open Bio 2017; 7:659-674. [PMID: 28469979 PMCID: PMC5407892 DOI: 10.1002/2211-5463.12209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) coordinates multienzymatic reactions by interacting with a variety of protein partners. Family I DNA ligases are multidomain proteins involved in sealing of DNA nicks during Okazaki fragment maturation and DNA repair. The interaction of DNA ligases with the interdomain connector loop (IDCL) of PCNA through its PCNA‐interacting peptide (PIP box) is well studied but the role of the interacting surface between both proteins is not well characterized. In this work, we used a minimal DNA ligase I and two N‐terminal deletions to establish that DNA binding and nick‐sealing stimulation of DNA ligase I by PCNA are not solely dependent on the PIP box–IDCL interaction. We found that a truncated DNA ligase I with a deleted PIP box is stimulated by PCNA. Furthermore, the activity of a DNA ligase defective in DNA binding is rescued upon PCNA addition. As the rate constants for single‐turnover ligation for the full‐length and truncated DNA ligases are not affected by PCNA, our data suggest that PCNA stimulation is achieved by increasing the affinity for nicked DNA substrate and not by increasing catalytic efficiency. Surprisingly C‐terminal mutants of PCNA are not able to stimulate nick‐sealing activity of Entamoeba histolytica DNA ligase I. Our data support the notion that the C‐terminal region of PCNA may be involved in promoting an allosteric transition in E. histolytica DNA ligase I from a spread‐shaped to a ring‐shaped structure. This study suggests that the ring‐shaped PCNA is a binding platform able to stabilize coevolved protein–protein interactions, in this case an interaction with DNA ligase I.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
| | - Cesar S Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México.,Present address: Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN) Av. Instituto Politécnico Nacional. s/n.La Paz Baja California Sur 23096 Mexico.,Present address: Cátedras CONACyT Dirección Adjunta de Desarrollo Científico Consejo Nacional de Ciencia y Tecnología Av. Insurgentes Sur 1582 Ciudad de Mexico 03940 Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas Universidad Autónoma de la Ciudad de México México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad Centro de Investigación y de Estudios Avanzados Irapuato Guanajuato México
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30
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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31
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Pandey P, Tarique KF, Mazumder M, Rehman SAA, Kumari N, Gourinath S. Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori. Sci Rep 2016; 6:31181. [PMID: 27499105 PMCID: PMC4976356 DOI: 10.1038/srep31181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/14/2016] [Indexed: 12/30/2022] Open
Abstract
Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of β-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of β-clamp binding regions in them and validated by SPR studies. Hpβ-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of β-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with β-clamp.
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Affiliation(s)
- Preeti Pandey
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India
| | | | - Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Nilima Kumari
- Department of Bioscience and Biotechnology, Banasthali University, Rajasthan, India
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32
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Iwata F, Hirakawa H, Nagamune T. Three proliferating cell nuclear antigen homologues from Metallosphaera sedula form a head-to-tail heterotrimer. Sci Rep 2016; 6:26588. [PMID: 27228945 PMCID: PMC4894655 DOI: 10.1038/srep26588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp that plays a key role in
DNA metabolism. Genome sequence analysis has revealed that some crenarchaea possess
three PCNA genes in their genome, but it has been reported that three PCNAs
do not always form a unique heterotrimer composed of one of each molecule. The
thermoacidophilic archaeon, Metallosphaera sedula, has three PCNA
homologue genes. Here, we demonstrated that the three PCNA homologues, MsePCNA1,
MsePCNA2 and MsePCNA3, exclusively form a heterotrimer in a stepwise fashion;
MsePCNA1 and MsePCNA2 form a heterodimer, and then MsePCNA3 binds to the
heterodimer. We determined that the dissociation constants between MsePCNA1 and
MsePCNA2, and between MsePCNA3 and the MsePCNA1:MsePCNA2 heterodimer are 0.29 and
43 nM, respectively. Moreover, the MsePCNA1, MsePCNA2 and MsePCNA3
heterotrimer stimulated M. sedula DNA ligase 1 activity, suggesting that the
heterotrimer works as a DNA sliding clamp in the organism. The stable and stepwise
heterotrimerization of M. sedula PCNA homologues would be useful to generate
functional protein-based materials such as artificial multi-enzyme complexes,
functional hydrogels and protein fibres, which have recently been achieved by
protein self-assembly.
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Affiliation(s)
- Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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33
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The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase. PLoS One 2016; 11:e0150802. [PMID: 26954034 PMCID: PMC4782999 DOI: 10.1371/journal.pone.0150802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/19/2016] [Indexed: 02/02/2023] Open
Abstract
DNA ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. Prior characterization of DNA ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsDNA substrate, with no interaction evident on dsDNA lacking a nick. In the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation and nick-sealing steps of T4 DNA ligase by non-nicked, non-substrate dsDNA. Inhibition by non-substrate DNA was dependent only on the total DNA concentration rather than the structure; with 1 μg/mL of 40-mers, 75-mers, or circular plasmid DNA all inhibiting ligation equally. A >15-fold reduction in T4 DNA ligase self-adenylylation rate when in the presence of high non-nicked dsDNA concentrations was observed. Finally, EMSAs were utilized to demonstrate that non-substrate dsDNA can compete with nicked dsDNA substrates for enzyme binding. Based upon these data, we hypothesize the inhibition of T4 DNA ligase by non-nicked dsDNA is direct evidence for a two-step nick-binding mechanism, with an initial, nick-independent, transient dsDNA-binding event preceding a transition to a stable binding complex in the presence of a nick site.
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Smith SJ, Hickey RJ, Malkas LH. Validating the disruption of proliferating cell nuclear antigen interactions in the development of targeted cancer therapeutics. Cancer Biol Ther 2016; 17:310-9. [PMID: 26889573 DOI: 10.1080/15384047.2016.1139247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human DNA replication and repair is a highly coordinated process involving the specifically timed actions of numerous proteins and enzymes. Many of these proteins require interaction with proliferating cell nuclear antigen (PCNA) for activation within the process. The interdomain connector loop (IDCL) of PCNA provides a docking site for many of those proteins, suggesting that this region is critically important in the regulation of cellular function. Previous work in this laboratory has demonstrated that a peptide mimicking a specific region of the IDCL (caPeptide) has the ability to disrupt key protein-protein interactions between PCNA and its binding partners, thereby inhibiting DNA replication within the cells. In this study, we confirm the ability of the caPeptide to disrupt DNA replication function using both intact cell and in vitro DNA replication assays. Further, we were able to demonstrate that treatment with caPeptide results in a decrease of polymerase δ activity that correlates with the observed decrease in DNA replication. We have also successfully developed a surface plasmon resonance (SPR) assay to validate the disruption of the PCNA-pol δ interaction with caPeptide.
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Affiliation(s)
- Shanna J Smith
- a Beckman Research Institute at City of Hope , Department of Molecular and Cellular Biology , Duarte , CA , USA
| | - Robert J Hickey
- b Beckman Research Institute at City of Hope , Department of Molecular Pharmacology , Duarte , CA , USA
| | - Linda H Malkas
- a Beckman Research Institute at City of Hope , Department of Molecular and Cellular Biology , Duarte , CA , USA
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Dynamic structures in DNA damage responses & cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 117:129-133. [PMID: 25934179 DOI: 10.1016/j.pbiomolbio.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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.
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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
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From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:267570. [PMID: 26508902 PMCID: PMC4609770 DOI: 10.1155/2015/267570] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 01/03/2023]
Abstract
DNA ligases are indispensable in all living cells and ubiquitous in all organs. DNA ligases are broadly utilized in molecular biology research fields, such as genetic engineering and DNA sequencing technologies. Here we review the utilization of DNA ligases in a variety of in vitro gene manipulations, developed over the past several decades. During this period, fewer protein engineering attempts for DNA ligases have been made, as compared to those for DNA polymerases. We summarize the recent progress in the elucidation of the DNA ligation mechanisms obtained from the tertiary structures solved thus far, in each step of the ligation reaction scheme. We also present some examples of engineered DNA ligases, developed from the viewpoint of their three-dimensional structures.
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Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:170571. [PMID: 26494982 PMCID: PMC4606414 DOI: 10.1155/2015/170571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.
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Abstract
DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.
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Affiliation(s)
- Lori M Kelman
- Program in Biotechnology, Montgomery College, Germantown, Maryland 20876;
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Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Nucleic Acids Res 2015; 43:7021-31. [PMID: 26130724 PMCID: PMC4538836 DOI: 10.1093/nar/gkv652] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022] Open
Abstract
Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation.
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Affiliation(s)
- Vandna Kukshal
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Kwon Kim
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gregory L Hura
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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The architecture of an Okazaki fragment-processing holoenzyme from the archaeon Sulfolobus solfataricus. Biochem J 2015; 465:239-45. [PMID: 25299633 DOI: 10.1042/bj20141120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA replication on the lagging strand occurs via the synthesis and maturation of Okazaki fragments. In archaea and eukaryotes, the enzymatic activities required for this process are supplied by a replicative DNA polymerase, Flap endonuclease 1 (Fen1) and DNA ligase 1 (Lig1). These factors interact with the sliding clamp PCNA (proliferating cell nuclear antigen) providing a potential means of co-ordinating their sequential actions within a higher order assembly. In hyperthermophilic archaea of the Sulfolobus genus, PCNA is a defined heterotrimeric assembly and each subunit interacts preferentially with specific client proteins. We have exploited this inherent asymmetry to assemble a PCNA-polymerase-Fen1-ligase complex on DNA and have visualized it by electron microscopy. Our studies reveal the structural basis of co-occupancy of a single PCNA ring by the three distinct client proteins.
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Lafrance-Vanasse J, Williams GJ, Tainer JA. Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:182-193. [PMID: 25576492 PMCID: PMC4417436 DOI: 10.1016/j.pbiomolbio.2014.12.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/20/2014] [Accepted: 12/28/2014] [Indexed: 12/23/2022]
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex is a dynamic macromolecular machine that acts in the first steps of DNA double strand break repair, and each of its components has intrinsic dynamics and flexibility properties that are directly linked with their functions. As a result, deciphering the functional structural biology of the MRN complex is driving novel and integrated technologies to define the dynamic structural biology of protein machinery interacting with DNA. Rad50 promotes dramatic long-range allostery through its coiled-coil and zinc-hook domains. Its ATPase activity drives dynamic transitions between monomeric and dimeric forms that can be modulated with mutants modifying the ATPase rate to control end joining versus resection activities. The biological functions of Mre11's dual endo- and exonuclease activities in repair pathway choice were enigmatic until recently, when they were unveiled by the development of specific nuclease inhibitors. Mre11 dimer flexibility, which may be regulated in cells to control MRN function, suggests new inhibitor design strategies for cancer intervention. Nbs1 has FHA and BRCT domains to bind multiple interaction partners that further regulate MRN. One of them, CtIP, modulates the Mre11 excision activity for homologous recombination repair. Overall, these combined properties suggest novel therapeutic strategies. Furthermore, they collectively help to explain how MRN regulates DNA repair pathway choice with implications for improving the design and analysis of cancer clinical trials that employ DNA damaging agents or target the DNA damage response.
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Affiliation(s)
| | | | - John A Tainer
- Life Science Division, 1 Cyclotron Road, Berkeley, CA 94720, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Tajedin L, Anwar M, Gupta D, Tuteja R. Comparative insight into nucleotide excision repair components of Plasmodium falciparum. DNA Repair (Amst) 2015; 28:60-72. [PMID: 25757193 DOI: 10.1016/j.dnarep.2015.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 01/27/2015] [Accepted: 02/10/2015] [Indexed: 12/19/2022]
Abstract
Nucleotide excision repair (NER) is one of the DNA repair pathways crucial for maintenance of genome integrity and deals with repair of DNA damages arising due to exogenous and endogenous factors. The multi-protein transcription initiation factor TFIIH plays a critical role in NER and transcription and is highly conserved throughout evolution. The malaria parasite Plasmodium falciparum has been a challenge for the researchers for a long time because of emergence of drug resistance. The availability of its genome sequence has opened new avenues for research. Antimalarial drugs like chloroquine and mefloquine have been reported to inhibit NER pathway mediated repair reactions and thus promote mutagenesis. Previous studies have validated existence and implied possible association of defective or altered DNA repair pathways with development of drug resistant phenotype in certain P. falciparum strains. We conjecture that a compromised NER pathway in combination with other DNA repair pathways might be conducive for the emergence and sustenance of drug resistance in P. falciparum. Therefore we decided to unravel the components of NER pathway in P. falciparum and using bioinformatics based approaches here we report a genome wide in silico analysis of NER components from P. falciparum and their comparison with the human host. Our results reveal that P. falciparum genome contains almost all the components of NER but we were unable to find clear homologue for p62 and XPC in its genome. The structure modeling of all the components further suggests that their structures are significantly conserved. Furthermore this study lays a foundation to perform similar comparative studies between drug resistant and drug sensitive strains of parasite in order to understand DNA repair-related mechanisms of drug resistance.
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Affiliation(s)
- Leila Tajedin
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Masroor Anwar
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dinesh Gupta
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India.
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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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Smith SJ, Gu L, Phipps EA, Dobrolecki LE, Mabrey KS, Gulley P, Dillehay KL, Dong Z, Fields GB, Chen YR, Ann D, Hickey RJ, Malkas LH. A Peptide mimicking a region in proliferating cell nuclear antigen specific to key protein interactions is cytotoxic to breast cancer. Mol Pharmacol 2014; 87:263-76. [PMID: 25480843 DOI: 10.1124/mol.114.093211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a highly conserved protein necessary for proper component loading during the DNA replication and repair process. Proteins make a connection within the interdomain connector loop of PCNA, and much of the regulation is a result of the inherent competition for this docking site. If this target region of PCNA is modified, the DNA replication and repair process in cancer cells is potentially altered. Exploitation of this cancer-associated region has implications for targeted breast cancer therapy. In the present communication, we characterize a novel peptide (caPeptide) that has been synthesized to mimic the sequence identified as critical to the cancer-associated isoform of PCNA. This peptide is delivered into cells using a nine-arginine linking mechanism, and the resulting peptide (R9-cc-caPeptide) exhibits cytotoxicity in a triple-negative breast cancer cell line, MDA-MB-436, while having less of an effect on the normal counterparts (MCF10A and primary breast epithelial cells). The novel peptide was then evaluated for cytotoxicity using various in vivo techniques, including ATP activity assays, flow cytometry, and clonogenetic assays. This cytotoxicity has been observed in other breast cancer cell lines (MCF7 and HCC1937) and other forms of cancer (pancreatic and lymphoma). R9-cc-caPeptide has also been shown to block the association of PCNA with chromatin. Alanine scanning of the peptide sequence, combined with preliminary in silico modeling, gives insight to the disruptive ability and the molecular mechanism of action of the therapeutic peptide in vivo.
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Affiliation(s)
- Shanna J Smith
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Long Gu
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Elizabeth A Phipps
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Lacey E Dobrolecki
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Karla S Mabrey
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Pattie Gulley
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Kelsey L Dillehay
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Zhongyun Dong
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Gregg B Fields
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Yun-Ru Chen
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - David Ann
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Robert J Hickey
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
| | - Linda H Malkas
- Department of Molecular and Cellular Biology (S.J.S., L.G., L.H.M.), Department of Molecular Medicine (R.J.H.), and Department of Diabetes and Metabolic Diseases Research (Y.-R.C., D.A.), Beckman Research Institute at City of Hope, Duarte, California; Department of Medical and Molecular Genetics (E.A.P.) and Department of Medicine (K.S.M., P.G.), Indiana University School of Medicine, Indianapolis, Indiana; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas (L.E.D.); Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio (K.L.D., Z.D.); and Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida (G.B.F.)
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46
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De Biasio A, Ibáñez de Opakua A, Cordeiro TN, Villate M, Merino N, Sibille N, Lelli M, Diercks T, Bernadó P, Blanco FJ. p15PAF is an intrinsically disordered protein with nonrandom structural preferences at sites of interaction with other proteins. Biophys J 2014; 106:865-74. [PMID: 24559989 DOI: 10.1016/j.bpj.2013.12.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/18/2013] [Accepted: 12/27/2013] [Indexed: 11/16/2022] Open
Abstract
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15(PAF) is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15(PAF) gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15(PAF) allowed us to measure 86 N-H(N) residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15(PAF) for degradation). In accordance with these findings, analysis of the (15)N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15(PAF) and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15(PAF). The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15(PAF).
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Affiliation(s)
- Alfredo De Biasio
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Alain Ibáñez de Opakua
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Tiago N Cordeiro
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France
| | - Maider Villate
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Nekane Merino
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Nathalie Sibille
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France
| | - Moreno Lelli
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Institut de Sciences Analytiques (CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Villeurbanne, France
| | - Tammo Diercks
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France
| | - Francisco J Blanco
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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47
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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.
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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
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48
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Base excision repair in Archaea: back to the future in DNA repair. DNA Repair (Amst) 2014; 21:148-57. [PMID: 25012975 DOI: 10.1016/j.dnarep.2014.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/24/2014] [Indexed: 11/22/2022]
Abstract
Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account.
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49
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De-Donatis GM, Zhao Z, Wang S, Huang LP, Schwartz C, Tsodikov OV, Zhang H, Haque F, Guo P. Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell Biosci 2014; 4:30. [PMID: 24940480 PMCID: PMC4060578 DOI: 10.1186/2045-3701-4-30] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022] Open
Abstract
Background Double-stranded DNA translocation is ubiquitous in living systems. Cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging and cell entry all involve biomotor-driven dsDNA translocation. Previously, biomotors have been primarily classified into linear and rotational motors. We recently discovered a third class of dsDNA translocation motors in Phi29 utilizing revolution mechanism without rotation. Analogically, the Earth rotates around its own axis every 24 hours, but revolves around the Sun every 365 days. Results Single-channel DNA translocation conductance assay combined with structure inspections of motor channels on bacteriophages P22, SPP1, HK97, T7, T4, Phi29, and other dsDNA translocation motors such as bacterial FtsK and eukaryotic mimiviruses or vaccinia viruses showed that revolution motor is widespread. The force generation mechanism for revolution motors is elucidated. Revolution motors can be differentiated from rotation motors by their channel size and chirality. Crystal structure inspection revealed that revolution motors commonly exhibit channel diameters larger than 3 nm, while rotation motors that rotate around one of the two separated DNA strands feature a diameter smaller than 2 nm. Phi29 revolution motor translocated double- and tetra-stranded DNA that occupied 32% and 64% of the narrowest channel cross-section, respectively, evidencing that revolution motors exhibit channel diameters significantly wider than the dsDNA. Left-handed oriented channels found in revolution motors drive the right-handed dsDNA via anti-chiral interaction, while right-handed channels observed in rotation motors drive the right-handed dsDNA via parallel threads. Tethering both the motor and the dsDNA distal-end of the revolution motor does not block DNA packaging, indicating that no rotation is required for motors of dsDNA phages, while a small-angle left-handed twist of dsDNA that is aligned with the channel could occur due to the conformational change of the phage motor channels from a left-handed configuration for DNA entry to a right-handed configuration for DNA ejection for host cell infection. Conclusions The revolution motor is widespread among biological systems, and can be distinguished from rotation motors by channel size and chirality. The revolution mechanism renders dsDNA void of coiling and torque during translocation of the lengthy helical chromosome, thus resulting in more efficient motor energy conversion.
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Affiliation(s)
- Gian Marco De-Donatis
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhengyi Zhao
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Lisa P Huang
- Current address: Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., Hamilton, NJ 08690, USA
| | - Chad Schwartz
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,William Farish Endowed Chair in Nanobiotechnology, School of Pharmacy, University of Kentucky, 565 Biopharmaceutical Complex, 789 S. Limestone Street, Lexington, KY 40536, USA
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50
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Binder JK, Douma LG, Ranjit S, Kanno DM, Chakraborty M, Bloom LB, Levitus M. Intrinsic stability and oligomerization dynamics of DNA processivity clamps. Nucleic Acids Res 2014; 42:6476-86. [PMID: 24728995 PMCID: PMC4041429 DOI: 10.1093/nar/gku255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/29/2022] Open
Abstract
Sliding clamps are ring-shaped oligomeric proteins that are essential for processive deoxyribonucleic acid replication. Although crystallographic structures of several clamps have been determined, much less is known about clamp structure and dynamics in solution. Here, we characterized the intrinsic solution stability and oligomerization dynamics of the homodimeric Escherichia coli β and the homotrimeric Saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA) clamps using single-molecule approaches. We show that E. coli β is stable in solution as a closed ring at concentrations three orders of magnitude lower than PCNA. The trimeric structure of PCNA results in slow subunit association rates and is largely responsible for the lower solution stability. Despite this large difference, the intrinsic lifetimes of the rings differ by only one order of magnitude. Our results show that the longer lifetime of the E. coli β dimer is due to more prominent electrostatic interactions that stabilize the subunit interfaces.
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Affiliation(s)
- Jennifer K Binder
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Suman Ranjit
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - David M Kanno
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Manas Chakraborty
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Marcia Levitus
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
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