151
|
Akhoon BA, Gupta SK, Dhaliwal G, Srivastava M, Gupta SK. Virtual screening of specific chemical compounds by exploring E.coli NAD+-dependent DNA ligase as a target for antibacterial drug discovery. J Mol Model 2010; 17:265-73. [PMID: 20443037 DOI: 10.1007/s00894-010-0713-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 03/18/2010] [Indexed: 11/26/2022]
Abstract
Unique substrate specificity compared with ATP-dependent human DNA ligases recommends E.coli NAD(+)-ligases as potential targets. A plausible strategy is to identify the structural components of bacterial DNA ligase that interact with NAD(+) and then to isolate small molecules that recognize these components and thereby block the binding of NAD(+) to the ligase. This work describes a molecular modeling approach to detect the 3D structure of NAD(+)-dependent DNA ligase in E. coli whose partial structure was determined by wet lab experiments and rest structure was left as such on the road for repairment. We applied protein-drug docking approach to detect the binding affinity of this enzyme with Quinacrine and some of its virtual derivatives. In silico docking results predict that the virtual derivative of Quinacrine (C21H26ClN3O2) has greater binding affinity than Quinacrine. Drug likeness value of 0.833 was observed for this derivative without showing any toxicity risk.
Collapse
Affiliation(s)
- Bashir Akhlaq Akhoon
- Department of Bioinformatics, Dolphin Post Graduate College of Life Sciences, Punjabi University, Patiala, Punjab, India.
| | | | | | | | | |
Collapse
|
152
|
Becherel OJ, Jakob B, Cherry AL, Gueven N, Fusser M, Kijas AW, Peng C, Katyal S, McKinnon PJ, Chen J, Epe B, Smerdon SJ, Taucher-Scholz G, Lavin MF. CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response. Nucleic Acids Res 2010; 38:1489-503. [PMID: 20008512 PMCID: PMC2836575 DOI: 10.1093/nar/gkp1149] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/26/2009] [Accepted: 11/20/2009] [Indexed: 11/13/2022] Open
Abstract
Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1, resolves abortive DNA ligation intermediates during DNA repair. Here, we demonstrate that aprataxin localizes at sites of DNA damage induced by high LET radiation and binds to mediator of DNA-damage checkpoint protein 1 (MDC1/NFBD1) through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin FHA domain and multiple casein kinase 2 di-phosphorylated S-D-T-D motifs in MDC1. X-ray structural and mutagenic analysis of aprataxin FHA domain, combined with modelling of the pSDpTD peptide interaction suggest an unusual FHA binding mechanism mediated by a cluster of basic residues at and around the canonical pT-docking site. Mutation of aprataxin FHA Arg29 prevented its interaction with MDC1 and recruitment to sites of DNA damage. These results indicate that aprataxin is involved not only in single strand break repair but also in the processing of a subset of double strand breaks presumably through its interaction with MDC1.
Collapse
Affiliation(s)
- Olivier J. Becherel
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Burkhard Jakob
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Amy L. Cherry
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Nuri Gueven
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Markus Fusser
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Amanda W. Kijas
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Cheng Peng
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Sachin Katyal
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Peter J. McKinnon
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Junjie Chen
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Bernd Epe
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Stephen J. Smerdon
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Gisela Taucher-Scholz
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| | - Martin F. Lavin
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia, GSI Helmholtzzentrum Schwerionenforschung GmBH, Planckstr. 1, 64291 Darmstadt, Germany, The MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK, Institute of Pharmacy, University of Mainz, Mainz, Germany, Department of Genetics and Tumor Cell Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA and Central Clinical Division, University of Queensland, Brisbane, Australia
| |
Collapse
|
153
|
Balakrishnan L, Gloor JW, Bambara RA. Reconstitution of eukaryotic lagging strand DNA replication. Methods 2010; 51:347-57. [PMID: 20178844 DOI: 10.1016/j.ymeth.2010.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/15/2010] [Accepted: 02/17/2010] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic DNA replication is a complex process requiring the proper functioning of a multitude of proteins to create error-free daughter DNA strands and maintain genome integrity. Even though synthesis and joining of Okazaki fragments on the lagging strand involves only half the DNA in the nucleus, the complexity associated with processing these fragments is about twice that needed for leading strand synthesis. Flap endonuclease 1 (FEN1) is the central component of the Okazaki fragment maturation pathway. FEN1 cleaves flaps that are displaced by DNA polymerase delta (pol delta), to create a nick that is effectively joined by DNA ligase I. The Pif1 helicase and Dna2 helicase/nuclease contribute to the maturation process by elongating the flap displaced by pol delta. Though the reason for generating long flaps is still a matter of debate, genetic studies have shown that Dna2 and Pif1 are both important components of DNA replication. Our current knowledge of the exact enzymatic steps that govern Okazaki fragment maturation has heavily derived from reconstitution reactions in vitro, which have augmented genetic information, to yield current mechanistic models. In this review, we describe both the design of specific DNA substrates that simulate intermediates of fragment maturation and protocols for reconstituting partial and complete lagging strand replication.
Collapse
Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | | | | |
Collapse
|
154
|
Properties of an NAD+-dependent DNA ligase from the hyperthermophile Thermotoga maritima and its application in PCR amplification of long DNA fragments. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
155
|
Luan Q, Xue Y, Yao X, Lu W. Hairpin DNA probe based surface plasmon resonance biosensor used for the activity assay of E. coli DNA ligase. Analyst 2009; 135:414-8. [PMID: 20098778 DOI: 10.1039/b920228e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Using hairpin DNA probe self-structure change during DNA ligation process, a sensitive, label-free and simple method of E. coli DNA ligase assay via a home-built high-resolution surface plasmon resonance (SPR) instrument was developed. The DNA ligation process was monitored in real-time and the effects of single-base mutation on the DNA ligation process were investigated. Then an assay of E. coli DNA ligase was completed with a lower detection limit (0.6 nM), wider concentration range and better reproducibility. Moreover, the influence of Quinacrine on the activity of E. coli DNA ligase was also studied, which demonstrated that our method was useful for drug screening.
Collapse
Affiliation(s)
- Qingfen Luan
- College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | | | | |
Collapse
|
156
|
Andersen FF, Stougaard M, Jørgensen HL, Bendsen S, Juul S, Hald K, Andersen AH, Koch J, Knudsen BR. Multiplexed detection of site specific recombinase and DNA topoisomerase activities at the single molecule level. ACS NANO 2009; 3:4043-4054. [PMID: 19950974 DOI: 10.1021/nn9012912] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We previously demonstrated the conversion of a single human topoisomerase I mediated DNA cleavage-ligation event happening within nanometer dimensions to a micrometer-sized DNA molecule, readily detectable using standard fluorescence microscopy. This conversion was achieved by topoisomerase I mediated closure of a nicked DNA circle followed by rolling circle amplification leading to an anchored product that was visualized at the single molecule level by hybridization to fluorescently labeled probes (Stougaard et al. ACS Nano 2009, 3, 223-33). An important inherent property of the presented setup is, at least in theory, the easy adaptability to multiplexed enzyme detection simply by using differently labeled probes for the detection of rolling circle products of different circularized substrates. In the present study we demonstrate the specific detection of three different enzyme activities, human topoisomerase I, and Flp and Cre recombinase in nuclear extracts from human cells one at a time or multiplexed using the rolling circle amplification based single-molecule detection system. Besides serving as a proof-of-principle for the feasibility of the presented assay for multiplexed enzyme detection in crude human cell extracts, the simultaneous detection of Flp and Cre activities in a single sample may find immediate practical use since these enzymes are often used in combination to control mammalian gene expression.
Collapse
Affiliation(s)
- Felicie Faucon Andersen
- Department of Molecular Biology and Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
157
|
Kim J, Mrksich M. Profiling the selectivity of DNA ligases in an array format with mass spectrometry. Nucleic Acids Res 2009; 38:e2. [PMID: 19854942 PMCID: PMC2800213 DOI: 10.1093/nar/gkp827] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This article describes a method for the global profiling of the substrate specificities of DNA ligases and illustrates examples using the Taq and T4 DNA ligases. The method combines oligonucleotide arrays, which offer the benefits of high throughput and multiplexed assays, with mass spectrometry to permit label-free assays of ligase activity. Arrays were prepared by immobilizing ternary biotin-tagged DNA substrates to a self-assembled monolayer presenting a layer of streptavidin protein. The array represented complexes having all possible matched and mismatched base pairs at the 3′ side of the nick site and also included a number of deletions and insertions at this site. The arrays were treated with ligases and adenosine triphosphate or analogs of the nucleotide triphosphate and then analyzed by matrix-assisted laser desorption-ionization mass spectrometry to determine the yields for both adenylation of the 5′-probe strand and joining of the two probe strands. The resulting activity profiles reveal the basis for specificity of the ligases and also point to strategies that use ATP analogs to improve specificity. This work introduces a method that can be applied to profile a broad range of enzymes that operate on nucleic acid substrates.
Collapse
Affiliation(s)
- Joohoon Kim
- Department of Chemistry, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | | |
Collapse
|
158
|
Abstract
DNA ligases seal 5'-PO4 and 3'-OH polynucleotide ends via three nucleotidyl transfer steps involving ligase-adenylate and DNA-adenylate intermediates. DNA ligases are essential guardians of genomic integrity, and ligase dysfunction underlies human genetic disease syndromes. Crystal structures of DNA ligases bound to nucleotide and nucleic acid substrates have illuminated how ligase reaction chemistry is catalyzed, how ligases recognize damaged DNA ends, and how protein domain movements and active-site remodeling are used to choreograph the end-joining pathway. Although a shared feature of DNA ligases is their envelopment of the nicked duplex as a C-shaped protein clamp, they accomplish this feat by using remarkably different accessory structural modules and domain topologies. As structural, biochemical, and phylogenetic insights coalesce, we can expect advances on several fronts, including (i) pharmacological targeting of ligases for antibacterial and anticancer therapies and (ii) the discovery and design of new strand-sealing enzymes with unique substrate specificities.
Collapse
Affiliation(s)
- Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA.
| |
Collapse
|
159
|
Bezsudnova EY, Kovalchuk MV, Mardanov AV, Poliakov KM, Popov VO, Ravin NV, Skryabin KG, Smagin VA, Stekhanova TN, Tikhonova TV. Overexpression, purification and crystallization of a thermostable DNA ligase from the archaeon Thermococcus sp. 1519. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:368-71. [PMID: 19342782 PMCID: PMC2664762 DOI: 10.1107/s1744309109007799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/03/2009] [Indexed: 11/11/2022]
Abstract
DNA ligases catalyze the sealing of 5'-phosphate and 3'-hydroxyl termini at single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome in DNA metabolism. An ATP-dependent DNA ligase from the archaeon Thermococcus sp. 1519 was overexpressed, purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion method employing 35%(v/v) Tacsimate pH 7.0 as a precipitant and diffracted X-rays to 3.09 A resolution. They belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 79.7, c = 182.6 A.
Collapse
Affiliation(s)
- E Y Bezsudnova
- Bach Institute of Biochemistry RAS, Leninsky Prospect 33, 119071 Moscow, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
160
|
Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc Natl Acad Sci U S A 2009; 106:4647-52. [PMID: 19255439 DOI: 10.1073/pnas.0811196106] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring.
Collapse
|
161
|
Vigneault F, Sismour AM, Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods 2009; 5:777-9. [PMID: 19160512 DOI: 10.1038/nmeth.1244] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we report a highly efficient and simplified strategy to preadenylate bar-coded oligonucleotides designed for microRNA (miRNA) capture and multiplex analysis. Using this approach, we enzymatically preadenylated bar-coded oligonucleotides with high efficiency when compared to the chemical method currently used by miRNA investigators. As a case study, we used these oligonucleotides in an ATP-independent ligation to miRNAs, suggesting the utility of our method in end-capture protocols and high-throughput sequencing applications.
Collapse
Affiliation(s)
- Francois Vigneault
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
| | | | | |
Collapse
|
162
|
Stougaard M, Lohmann JS, Mancino A, Celik S, Andersen FF, Koch J, Knudsen BR. Single-molecule detection of human topoisomerase I cleavage-ligation activity. ACS NANO 2009; 3:223-233. [PMID: 19206270 DOI: 10.1021/nn800509b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the present study, we demonstrate the conversion of a single human topoisomerase I mediated DNA cleavage-ligation event happening within nanometer dimensions to a micrometer-sized DNA molecule, readily detectable using standard fluorescence microscopy. This conversion is achieved by topoisomerase I mediated closure of a nicked DNA dumbbell structure, followed by rolling circle amplification. The resulting product consists of multiple tandem repeats of the DNA dumbbell and can subsequently be visualized by annealing to fluorescently labeled probes. Since amplification involves no thermal cycling, each fluorescent rolling circle product, which gives rise to an individual signal upon microscopic analysis, will correspond to a single human topoisomerase I mediated cleavage-ligation event. Regarding sensitivity, speed, and ease of performance, the presented activity assay based on single-molecule product detection is superior to current state of the art assays using supercoiled plasmids or radiolabeled oligonucleotides as the substrate for topoisomerase I activity. Moreover, inherent in the experimental design is the easy adaptation to multiplexed and/or high-throughput systems. Human topoisomerase I is the cellular target of clinically important anticancer drugs, and the effect of such drugs corresponds directly to the intracellular topoisomerase I cleavage-ligation activity level. We therefore believe that the presented setup, measuring directly the number of cleavage-ligation events in a given sample, has great diagnostic potential, adding considerably to the possibilities of accurate prognosis before treatment with topoisomerase I directed chemotherapeutics.
Collapse
Affiliation(s)
- Magnus Stougaard
- Department of Pathology and Interdisciplinary Nanoscience Center (iNano), Aarhus University Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark
| | | | | | | | | | | | | |
Collapse
|
163
|
Dwivedi N, Dube D, Pandey J, Singh B, Kukshal V, Ramachandran R, Tripathi RP. NAD(+)-dependent DNA ligase: a novel target waiting for the right inhibitor. Med Res Rev 2009; 28:545-68. [PMID: 18080330 DOI: 10.1002/med.20114] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA ligases (EC.6.5.1.1) are key enzymes that catalyze the formation of phosphodiester bonds at single stranded or double stranded breaks between adjacent 5' phosphoryl and 3' hydroxyl groups of DNA. These enzymes are important for survival because they are involved in major cellular processes like DNA replication/repair and recombination. DNA ligases can be classified into two groups on the basis of their cofactor specificities. NAD(+)-dependent DNA ligases are present in bacteria, some entomopox viruses and mimi virus while ATP-dependent DNA ligases are ubiquitous. The former have recently been drawing a lot of attention as novel targets for antibiotics to overcome current drug resistance issues. Currently a diverse range of inhibitors have been identified. There are several issues to be addressed in the quest for optimized inhibitors of the enzyme. In the first part of the review we summarize current structural work on these enzymes. Subsequently we describe the currently available classes of inhibitors. We also address modalities to improve the specificity and potencies of new inhibitors identified using protein structure based rational approaches. In conclusion, NAD(+)-dependent ligases show great promise and represent a novel drug target whose time has come.
Collapse
Affiliation(s)
- Namrata Dwivedi
- Medicinal & Process Chemistry Division, Central Drug Research Institute, Chattar Manzil, P.O. Box 173, Mahatma Gandhi Marg, Lucknow-226001, India
| | | | | | | | | | | | | |
Collapse
|
164
|
Conze T, Shetye A, Tanaka Y, Gu J, Larsson C, Göransson J, Tavoosidana G, Söderberg O, Nilsson M, Landegren U. Analysis of genes, transcripts, and proteins via DNA ligation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:215-239. [PMID: 20636060 DOI: 10.1146/annurev-anchem-060908-155239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Analytical reactions in which short DNA strands are used in combination with DNA ligases have proven useful for measuring, decoding, and locating most classes of macromolecules. Given the need to accumulate large amounts of precise molecular information from biological systems in research and in diagnostics, ligation reactions will continue to offer valuable strategies for advanced analytical reactions. Here, we provide a basis for further development of methods by reviewing the history of analytical ligation reactions, discussing the properties of ligation reactions that render them suitable for engineering novel assays, describing a wide range of successful ligase-based assays, and briefly considering future directions.
Collapse
Affiliation(s)
- Tim Conze
- Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
165
|
Smagin VA, Mardanov AV, Bonch-Osmolovskaya EA, Ravin NV. Isolation and characteristics of new thermostable DNA ligase from archaea of the genus Thermococcus. APPL BIOCHEM MICRO+ 2008. [DOI: 10.1134/s0003683808050037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
166
|
Rittié L, Perbal B. Enzymes used in molecular biology: a useful guide. J Cell Commun Signal 2008; 2:25-45. [PMID: 18766469 DOI: 10.1007/s12079-008-0026-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 08/13/2008] [Indexed: 12/31/2022] Open
Abstract
Since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments.
Collapse
Affiliation(s)
- Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA,
| | | |
Collapse
|
167
|
Abstract
DNA ligases are required for DNA replication, repair, and recombination. In eukaryotes, there are three families of ATP-dependent DNA ligases. Members of the DNA ligase I and IV families are found in all eukaryotes, whereas DNA ligase III family members are restricted to vertebrates. These enzymes share a common catalytic region comprising a DNA-binding domain, a nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The catalytic region encircles nicked DNA with each of the domains contacting the DNA duplex. The unique segments adjacent to the catalytic region of eukaryotic DNA ligases are involved in specific protein-protein interactions with a growing number of DNA replication and repair proteins. These interactions determine the specific cellular functions of the DNA ligase isozymes. In mammals, defects in DNA ligation have been linked with an increased incidence of cancer and neurodegeneration.
Collapse
Affiliation(s)
- Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | | |
Collapse
|
168
|
Sun Y, Seo MS, Kim JH, Kim YJ, Kim GA, Lee JI, Lee JH, Kwon ST. Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization. Environ Microbiol 2008; 10:3212-24. [PMID: 18647334 DOI: 10.1111/j.1462-2920.2008.01710.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
DNA ligases are divided into two groups according to their cofactor requirement to form ligase-adenylate, ATP-dependent DNA ligases and NAD(+)-dependent DNA ligases. The conventional view that archaeal DNA ligases only utilize ATP has recently been disputed with discoveries of dual-specificity DNA ligases (ATP/ADP or ATP/NAD(+)) from the orders Desulfurococcales and Thermococcales. Here, we studied DNA ligase encoded by the hyperthermophilic crenarchaeon Sulfophobococcus zilligii. The ligase exhibited multiple cofactor specificity utilizing ADP and GTP in addition to ATP. The unusual cofactor specificity was confirmed via a DNA ligase nick-closing activity assay using a fluorescein/biotin-labelled oligonucleotide and a radiolabelled oligonucleotide. The exploitation of GTP as a catalytic energy source has not to date been reported in any known DNA ligase. This phenomenon may provide evolutionary evidence of the nucleotide cofactor utilization by DNA ligases. To bolster this hypothesis, we summarize and evaluate previous assertions. We contend that DNA ligase evolution likely started from crenarchaeotal DNA ligases and diverged to eukaryal DNA ligases and euryarchaeotal DNA ligases. Subsequently, the NAD(+)-utilizing property of some euryarchaeotal DNA ligases may have successfully differentiated to bacterial NAD(+)-dependent DNA ligases.
Collapse
Affiliation(s)
- Younguk Sun
- Department of Genetic Engineering, Sungkyunkwan University, 300 Chunchun-dong, Jangan-gu, Suwon 440-746, Korea
| | | | | | | | | | | | | | | |
Collapse
|
169
|
Tougan T, Okuzaki D, Nojima H. Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification. Nucleic Acids Res 2008; 36:e92. [PMID: 18603591 PMCID: PMC2528176 DOI: 10.1093/nar/gkn420] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Linear RNA amplification using T7 RNA polymerase is useful in genome-wide analysis of gene expression using DNA microarrays, but exponential amplification using polymerase chain reaction (PCR) is still required for cDNA library preparation from single-cell quantities of RNA. We have designed a small RNA molecule called chum-RNA that has enabled us to prepare a single-cell cDNA library after four rounds of T7-based linear amplification, without using PCR amplification. Chum-RNA drove cDNA synthesis from only 0.49 femtograms of mRNA (730 mRNA molecules) as a substrate, a quantity that corresponds to a minor population of mRNA molecules in a single mammalian cell. Analysis of the independent cDNA clone of this library (6.6 × 105 cfu) suggests that 30-fold RNA amplification occurred in each round of the amplification process. The size distribution and representation of mRNAs in the resulting one-cell cDNA library retained its similarity to that of the million-cell cDNA library. The use of chum-RNA might also facilitate reactions involving other DNA/RNA modifying enzymes whose Michaelis constant (Km) values are around 1 mM, allowing them to be activated in the presence of only small quantities of substrate.
Collapse
Affiliation(s)
- Takahiro Tougan
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | |
Collapse
|
170
|
The associative nature of adenylyl transfer catalyzed by T4 DNA ligase. Proc Natl Acad Sci U S A 2008; 105:8563-8. [PMID: 18562298 DOI: 10.1073/pnas.0709140105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA ligase seals nicks in dsDNA using chemical energy of the phosphoanhydride bond in ATP or NAD(+) and assistance of a divalent metal cofactor Mg(2+). Molecular details of ligase catalysis are essential for understanding the mechanism of metal-promoted phosphoryl transfer reactions in the living cell responsible for a wide range of processes, e.g., DNA replication and transcription, signaling and differentiation, energy coupling and metabolism. Here we report a single-turnover (31)P solid-state NMR study of adenylyl transfer catalyzed by DNA ligase from bacteriophage T4. Formation of a high-energy covalent ligase-nucleotide complex is triggered in situ by the photo release of caged Mg(2+), and sequentially formed intermediates are monitored by NMR. Analyses of reaction kinetics and chemical-shift changes indicate that the pentacoordinated phosphorane intermediate builds up to 35% of the total reacting species after 4-5 h of reaction. This is direct experimental evidence of the associative nature of adenylyl transfer catalyzed by DNA ligase. NMR spectroscopy in rotating solids is introduced as an analytical tool for recording molecular movies of reaction processes. Presented work pioneers a promising direction in structural studies of biochemical transformations.
Collapse
|
171
|
Lavin MF, Gueven N, Grattan-Smith P. Defective responses to DNA single- and double-strand breaks in spinocerebellar ataxia. DNA Repair (Amst) 2008; 7:1061-76. [PMID: 18467193 DOI: 10.1016/j.dnarep.2008.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Failure to maintain the integrity of DNA/chromatin can result in genome instability and an increased risk of cancer. The description of a number of human genetic disorders characterised not only by cancer predisposition but by a broader phenotype including neurodegeneration suggests that maintaining genome stability is also important for preserving post-mitotic neurons. The identification of genes associated with other neurodegenerative disorders provides further evidence for the importance of DNA damage response and DNA repair genes in protecting against neurodegeneration. This theme is further developed in this review.
Collapse
Affiliation(s)
- Martin F Lavin
- Radiation Biology and Oncology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia.
| | | | | |
Collapse
|
172
|
Abstract
Ligases are essential actors in DNA replication, recombination, and repair by virtue of their ability to seal breaks in the phosphodiester backbone. Ligation proceeds through a nicked DNA-adenylate intermediate (AppDNA), which must be sealed quickly to avoid creating a potentially toxic lesion. Here, we take advantage of ligase-catalyzed AMP-dependent incision of a single supercoiled DNA molecule to observe the step of phosphodiester synthesis in real time. An exponentially distributed number of supercoils was relaxed per successful incision-resealing event, from which we deduce the torque-dependent ligation probability per DNA swivel. Premature dissociation of ligase from nicked DNA-adenylate accounted for approximately 10% of the observed events. The ability of ligase to form a C-shaped protein clamp around DNA is a key determinant of ligation probability per turn and the stability of the ligase-AppDNA intermediate. The estimated rate of phosphodiester synthesis by DNA ligase (400 s(-1)) is similar to the high rates of phosphodiester synthesis by replicative DNA polymerases.
Collapse
|
173
|
Girigoswami A, Jung C, Mun HY, Park HG. PCR-free mutation detection of BRCA1 on a zip-code microarray using ligase chain reaction. ACTA ACUST UNITED AC 2008; 70:897-902. [DOI: 10.1016/j.jprot.2008.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/07/2007] [Accepted: 01/09/2008] [Indexed: 01/16/2023]
|
174
|
Pascal JM. DNA and RNA ligases: structural variations and shared mechanisms. Curr Opin Struct Biol 2008; 18:96-105. [PMID: 18262407 DOI: 10.1016/j.sbi.2007.12.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 12/12/2022]
Abstract
DNA and RNA ligases join 3' OH and 5' PO4 ends in polynucleotide substrates using a three-step reaction mechanism that involves covalent modification of both the ligase enzyme and the polynucleotide substrate with AMP. In the past three years, several polynucleotide ligases have been crystallized in complex with nucleic acid, providing the introductory views of ligase enzymes engaging their substrates. Crystal structures for two ATP-dependent DNA ligases, an NAD+-dependent DNA ligase, and an ATP-dependent RNA ligase demonstrate how ligases utilize the AMP group and their multi-domain architectures to manipulate nucleic acid structure and catalyze the end-joining reaction. Together with unliganded crystal structures of DNA and RNA ligases, a more comprehensive and dynamic understanding of the multi-step ligation reaction mechanism has emerged.
Collapse
Affiliation(s)
- John M Pascal
- Department of Biochemistry & Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.
| |
Collapse
|
175
|
Zhu H, Shuman S. Bacterial nonhomologous end joining ligases preferentially seal breaks with a 3'-OH monoribonucleotide. J Biol Chem 2008; 283:8331-9. [PMID: 18203718 DOI: 10.1074/jbc.m705476200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Many bacterial species have a nonhomologous end joining system of DNA repair driven by dedicated DNA ligases (LigD and LigC). LigD is a multifunctional enzyme composed of a ligase domain fused to two other catalytic modules: a polymerase that preferentially adds ribonucleotides to double-strand break ends and a phosphoesterase that trims 3'-oligoribonucleotide tracts until only a single 3'-ribonucleotide remains. LigD and LigC have a feeble capacity to seal 3'-OH/5'-PO(4) DNA nicks. Here, we report that nick sealing by LigD and LigC enzymes is stimulated by the presence of a single ribonucleotide at the broken 3'-OH end. The ribonucleotide effect on LigD and LigC is specific for the 3'-terminal nucleotide and is either diminished or abolished when additional vicinal ribonucleotides are present. No such 3'-ribonucleotide effect is observed for bacterial LigA or Chlorella virus ligase. We found that in vitro repair of a double-strand break by Pseudomonas LigD requires the polymerase module and results in incorporation of an alkali-labile ribonucleotide at the repair junction. These results illuminate an underlying logic for the domain organization of LigD, whereby the polymerase and phosphoesterase domains can heal the broken 3'-end to generate the monoribonucleotide terminus favored by the nonhomologous end joining ligases.
Collapse
Affiliation(s)
- Hui Zhu
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
| | | |
Collapse
|
176
|
Abstract
ADP-ribosylation using nicotinamide adenine dinucleotide (NAD+) is an important type of enzymatic reaction that affects many biological processes. A brief introductory review is given here to various ADP-ribosyltransferases, including poly(ADP-ribose) polymerase (PARPs), mono(ADP-ribosyl)-transferases (ARTs), NAD(+)-dependent deacetylases (sirtuins), tRNA 2'-phosphotransferases, and ADP-ribosyl cyclases (CD38 and CD157). Focus is given to the enzymatic reactions, mechanisms, structures, and biological functions.
Collapse
Affiliation(s)
- Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
177
|
|
178
|
Banin S, Wilson S, Stanley C. The LiMA technology: measurement of ATP on a nucleic acid testing platform. Clin Chem 2007; 53:2034-6. [PMID: 18035597 DOI: 10.1373/clinchem.2007.09113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
179
|
One-base excess adaptor ligation method for walking uncloned genomic DNA. Appl Microbiol Biotechnol 2007; 78:173-80. [PMID: 18071644 DOI: 10.1007/s00253-007-1289-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 11/14/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
This report describes a novel and efficient method for walking the sequence of a genomic deoxyribonucleic acid (DNA) from a known region to an unknown region based on an oligodeoxynucleotide (oligo) cassette-mediated polymerase chain reaction technique. In this method, genomic DNA is digested by a restriction enzyme that generates a sticky 5'-end, followed by ligation of a one-base excess oligo-adaptor using T4 DNA ligase. The adaptor consists of two complementary oligos that form the same sticky end as the digested genomic DNA fragments, except that the 5'-overhang base overlaps the corresponding 3'-end base of the restriction site. This overhanging terminal base prevents ligation between the adaptors, and the appropriate molar ratio of adaptor to genomic DNA enables specific amplification of the target sequence. T4 DNA ligase catalyzes both the ligation of the phosphorylated overhang base of the adaptor to genomic DNA and the excision of the corresponding 3'-terminal base of the genomic DNA. This sequence-specific exonuclease activity of T4 DNA ligase was confirmed by ligation of an alternative adaptor in which the 5'-terminal base was not consistent with the corresponding 3'-terminal base. Using this technique, the 3'- and 5'-flanking sequences of the catalase gene of the ciliate Paramecium bursaria were determined.
Collapse
|
180
|
Patel MP, Baum DA, Silverman SK. Improvement of DNA adenylation using T4 DNA ligase with a template strand and a strategically mismatched acceptor strand. Bioorg Chem 2007; 36:46-56. [PMID: 18022669 DOI: 10.1016/j.bioorg.2007.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 10/04/2007] [Accepted: 10/05/2007] [Indexed: 11/18/2022]
Abstract
DNA with a 5'-adenylpyrophosphoryl cap (5'-adenylated DNA; AppDNA) is an activated form of DNA that is the biochemical intermediate of the reactions catalyzed by DNA ligase, RNA ligase, polynucleotide kinase, and other nucleic acid modifying enzymes. 5'-Adenylated DNA is also useful for in vitro selection experiments. Efficient preparation of 5'-adenylated DNA is therefore desirable for several biochemical applications. Here we have developed a DNA adenylation procedure that uses T4 DNA ligase and is more reliable than a previously reported approach that used the 5'-phosphorylated donor DNA substrate to be adenylated, a DNA template, and ATP but no acceptor strand. Our improved DNA adenylation procedure uses the above components as well as an acceptor strand that has a strategically chosen C-T acceptor-template mismatch directly adjacent to the adenylation site. This mismatch permits adenylation of the donor DNA substrate but largely suppresses subsequent ligation of the donor with the acceptor, as assayed on nine different DNA substrates that collectively have all four DNA nucleotides represented at each of the first two positions. The new DNA adenylation procedure is successful using either laboratory-prepared or commercial T4 DNA ligase and works well on the preparative (2 nmol) scale for all nine of the test DNA substrates.
Collapse
Affiliation(s)
- Maha P Patel
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
181
|
Abstract
The capacity to rectify DNA double-strand breaks (DSBs) is crucial for the survival of all species. DSBs can be repaired either by homologous recombination (HR) or non-homologous end joining (NHEJ). The long-standing notion that bacteria rely solely on HR for DSB repair has been overturned by evidence that mycobacteria and other genera have an NHEJ system that depends on a dedicated DNA ligase, LigD, and the DNA-end-binding protein Ku. Recent studies have illuminated the role of NHEJ in protecting the bacterial chromosome against DSBs and other clastogenic stresses. There is also emerging evidence of functional crosstalk between bacterial NHEJ proteins and components of other DNA-repair pathways. Although still a young field, bacterial NHEJ promises to teach us a great deal about the nexus of DNA repair and bacterial pathogenesis.
Collapse
Affiliation(s)
- Stewart Shuman
- Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.
| | | |
Collapse
|
182
|
A simple and rapid strategy for the molecular cloning and monitoring of mouse HtrA2 serine protease. Biotechnol Lett 2007; 30:397-403. [DOI: 10.1007/s10529-007-9556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 09/10/2007] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
|
183
|
Yuan C, Lou XW, Rhoades E, Chen H, Archer LA. T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res 2007; 35:5294-302. [PMID: 17686784 PMCID: PMC2018621 DOI: 10.1093/nar/gkm582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.
Collapse
Affiliation(s)
- Chongli Yuan
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Xiong Wen Lou
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth Rhoades
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Huimin Chen
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Lynden A. Archer
- School of Chemical and Biomolecular Engineering, and Department of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- *To whom correspondence should be addressed. +1 607 254 8825+1 607 255 9166
| |
Collapse
|
184
|
Feng H. Mutational analysis of bacterial NAD+-dependent DNA ligase: role of motif IV in ligation catalysis. Acta Biochim Biophys Sin (Shanghai) 2007; 39:608-16. [PMID: 17687496 DOI: 10.1111/j.1745-7270.2007.00313.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The bacterial DNA ligase as a multiple domain protein is involved in DNA replication, repair and recombination. Its catalysis of ligation can be divided into three steps. To delineate the roles of amino acid residues in motif IV in ligation catalysis, site-directed mutants were constructed in a bacterial NAD+-dependent DNA ligase from Thermus sp. TAK16D. It was shown that four conserved residues (D286, G287, V289 and K291) in motif IV had significant roles on the overall ligation. Under single turnover conditions, the observed apparent rates of D286E, G287A, V289I and K291R mutants were clearly reduced compared with that of WT ligase on both match and mismatch nicked substrates. The effects of D286E mutation on overall ligation may not only be ascribed to the third step. The G287A mutation has a major effect on the second step. The effects of V289I and K291R mutation on overall ligation are not on the third step, perhaps other aspects, such as conformation change of ligase protein in ligation catalysis, are involved. Moreover, the amino acid substitutions of above four residues were more sensitive on mismatch nicked substrate, indicating an enhanced ligation fidelity.
Collapse
Affiliation(s)
- Hong Feng
- Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
| |
Collapse
|
185
|
Srivastava SK, Dube D, Kukshal V, Jha AK, Hajela K, Ramachandran R. NAD+-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: Novel structure-function relationship and identification of a specific inhibitor. Proteins 2007; 69:97-111. [PMID: 17557328 DOI: 10.1002/prot.21457] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mycobacterium tuberculosis codes for an essential NAD+-dependent DNA ligase (MtuLigA) which is a novel, validated, and attractive drug target. We created mutants of the enzyme by systematically deleting domains from the C-terminal end of the enzyme to probe for their functional roles in the DNA nick joining reaction. Deletion of just the BRCT domain from MtuLigA resulted in total loss of activity in in vitro assays. However, the mutant could form an AMP-ligase intermediate that suggests that the defects caused by deletion of the BRCT domain occur primarily at steps after enzyme adenylation. Furthermore, genetic complementation experiments using a LigA deficient E. coli strain demonstrates that the BRCT domain of MtuLigA is necessary for bacterial survival in contrast to E. coli and T. filiformis LigA, respectively. We also report the identification, through virtual screening, of a novel N-substituted tetracyclic indole that competes with NAD+ and inhibits the enzyme with IC50 in the low muM range. It exhibits approximately 15-fold better affinity for MtuLigA compared to human DNA ligase I. In vivo assays using LigA deficient S. typhimurium and E. coli strains suggest that the observed antibacterial activity of the inhibitor arises from specific inhibition of LigA over ATP ligases in the bacteria. In silico ligand-docking studies suggest that the exquisite specificity of the inhibitor arises on account of its mimicking the interactions of NAD+ with MtuLigA. An analysis of conserved water in the binding site of the enzyme suggests strategies for synthesis of improved inhibitors with better specificity and potency.
Collapse
Affiliation(s)
- Sandeep Kumar Srivastava
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow 226001, Uttar Pradesh, India
| | | | | | | | | | | |
Collapse
|
186
|
Korycka-Machala M, Rychta E, Brzostek A, Sayer HR, Rumijowska-Galewicz A, Bowater RP, Dziadek J. Evaluation of NAD(+) -dependent DNA ligase of mycobacteria as a potential target for antibiotics. Antimicrob Agents Chemother 2007; 51:2888-97. [PMID: 17548501 PMCID: PMC1932498 DOI: 10.1128/aac.00254-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacteria contain genes for several DNA ligases, including ligA, which encodes a NAD(+)-dependent enzyme that has been postulated to be a target for novel antibacterial compounds. Using a homologous recombination system, direct evidence is presented that wild-type ligA cannot be deleted from the chromosome of Mycobacterium smegmatis. Deletions of native ligA in M. smegmatis could be obtained only after the integration of an extra copy of M. smegmatis or Mycobacterium tuberculosis ligA into the attB site of the chromosome, with expression controlled by chemically inducible promoters. The four ATP-dependent DNA ligases encoded by the M. smegmatis chromosome were unable to replace the function of LigA. Interestingly, the LigA protein from M. smegmatis could be substituted with the NAD(+)-dependent DNA ligase of Escherichia coli or the ATP-dependent ligase of bacteriophage T4. The conditional mutant strains allowed the analysis of the effect of LigA depletion on the growth of M. smegmatis. The protein level of the conditional mutants was estimated by Western blot analysis using antibodies raised against LigA of M. tuberculosis. This revealed that a strong overproduction or depletion of LigA did not affect the growth or survival of mycobacteria under standard laboratory conditions. In conclusion, although NAD(+)-dependent DNA ligase is essential for mycobacterial viability, only low levels of protein are required for growth. These findings suggest that very efficient inhibition of enzyme activity would be required if NAD(+)-dependent DNA ligase is to be useful as an antibiotic target in mycobacteria. The strains developed here will provide useful tools for the evaluation of the efficacy of any appropriate compounds in mycobacteria.
Collapse
|
187
|
Abstract
Agrobacterium tumefaciens encodes a single NAD+-dependent DNA ligase and six putative ATP-dependent ligases. Two of the ligases are homologs of LigD, a bacterial enzyme that catalyzes end-healing and end-sealing steps during nonhomologous end joining (NHEJ). Agrobacterium LigD1 and AtuLigD2 are composed of a central ligase domain fused to a C-terminal polymerase-like (POL) domain and an N-terminal 3′-phosphoesterase (PE) module. Both LigD proteins seal DNA nicks, albeit inefficiently. The LigD2 POL domain adds ribonucleotides or deoxyribonucleotides to a DNA primer-template, with rNTPs being the preferred substrates. The LigD1 POL domain has no detectable polymerase activity. The PE domains catalyze metal-dependent phosphodiesterase and phosphomonoesterase reactions at a primer-template with a 3′-terminal diribonucleotide to yield a primer-template with a monoribonucleotide 3′-OH end. The PE domains also have a 3′-phosphatase activity on an all-DNA primer-template that yields a 3′-OH DNA end. Agrobacterium ligases C2 and C3 are composed of a minimal ligase core domain, analogous to Mycobacterium LigC (another NHEJ ligase), and they display feeble nick-sealing activity. Ligation at DNA double-strand breaks in vitro by LigD2, LigC2 and LigC3 is stimulated by bacterial Ku, consistent with their proposed function in NHEJ.
Collapse
Affiliation(s)
| | - Stewart Shuman
- *To whom correspondence should be addressed. 212 639 7145212 717 3623
| |
Collapse
|
188
|
Miesel L, Kravec C, Xin AT, McMonagle P, Ma S, Pichardo J, Feld B, Barrabee E, Palermo R. A high-throughput assay for the adenylation reaction of bacterial DNA ligase. Anal Biochem 2007; 366:9-17. [PMID: 17493575 DOI: 10.1016/j.ab.2007.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 03/21/2007] [Accepted: 03/26/2007] [Indexed: 11/23/2022]
Abstract
DNA ligase catalyzes the closure of single-strand nicks in double-stranded DNA that arise during replication and recombination. Inhibition of bacterial ligase is expected to cause chromosome degradation and cell death, making it an attractive target for new antibacterials. The prototypical bacterial ligase couples the hydrolysis of NAD(+) to phosphodiester bond formation between an adjacent 3'OH and 5'-terminal phosphate of nicked duplex DNA. The first step is the reversible formation of a ligase-adenylate from the reaction between apoenzyme and NAD(+). Inhibitors that compete with NAD(+) are expected to be bacterial specific because eukaryotic DNA ligases use ATP and differ in the sequence composition of their adenylation domain. We report here a high-throughput assay that measures the adenylation reaction specifically by monitoring ligase-AMP formation via scintillation proximity technologies. Escherichia coli DNA ligase was biotinylated in vivo; after reaction with radiolabeled NAD(+), ligase-[(3)H]AMP could be captured onto the streptavidin-coated surface of the solid scintillant. The method was ideal for high-throughput screening because it required minimal manipulations and generated a robust signal with minimal scatter. Certain adenosine analogs were found to inhibit the adenylation assay and had similar potency of inhibition in a DNA ligation assay.
Collapse
Affiliation(s)
- Lynn Miesel
- Schering-Plough Research Institute, Kneilworth, NJ 07033, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
189
|
Cost GJ, Cozzarelli NR. Directed assembly of DNA molecules via simultaneous ligation and digestion. Biotechniques 2007; 42:84, 86-9. [PMID: 17269489 DOI: 10.2144/000112283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA ligation is a routine laboratory practice, yet the yield of the desired product is often very low due to competing off-pathway reactions. The sensitivity of subsequent manipulations (e.g., selection via bacterial transformation) often obviates the need for a high yield of correctly ligated products. However the ability to perform high-yield, preparative-scale DNA ligations would benefit a number of downstream applications ranging from standard molecular cloning to biophysics and DNA computing. We describe here a ligation technique that specifically converts off-pathway ligation products back into substrate. We term this second-chance strategy enzymatic ligation assisted by nucleases (ELAN) and demonstrate the ordered assembly of four DNA fragments via simultaneous ligation and digestion in the presence of eight restriction enzymes. Use of ELAN increased the yield of the desired product by more than 30-fold.
Collapse
Affiliation(s)
- Gregory J Cost
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
| | | |
Collapse
|
190
|
Zhao X, Muller JG, Halasyam M, David SS, Burrows CJ. In vitro ligation of oligodeoxynucleotides containing C8-oxidized purine lesions using bacteriophage T4 DNA ligase. Biochemistry 2007; 46:3734-44. [PMID: 17323928 PMCID: PMC2442820 DOI: 10.1021/bi062214k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ligases conduct the final stage of repair of DNA damage by sealing a single-stranded nick after excision of damaged nucleotides and reinsertion of correct nucleotides. Depending upon the circumstances and the success of the repair process, lesions may remain at the ligation site, either in the template or at the oligomer termini to be joined. Ligation experiments using bacteriophage T4 DNA ligase were carried out with purine lesions in four positions surrounding the nick site in a total of 96 different duplexes. The oxidized lesion 8-oxo-7,8-dihydroguanosine (OG) showed, as expected, that the enzyme is most sensitive to lesions on the 3' end of the nick compared to the 5' end and to lesions located in the intact template strand. In general, substrates containing the OG.A mismatch were more readily ligated than those with the OG.C mismatch. Ligations of duplexes containing the OA.T base pair (OA = 8-oxo-7,8-dihydroadenosine) that could adopt an anti-anti conformation proceeded with high efficiencies. An OI.A mismatch-containing duplex (OI = 8-oxo-7,8-dihydroinosine) behaved like OG.A. Due to its low reduction potential, OG is readily oxidized to secondary oxidation products, such as the guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) nucleosides; these lesions also contain an oxo group at the original C8 position of the purine. Ligation of oligomers containing Gh and Sp occurred when opposite A and G, although the overall ligation efficiencies were much lower than those of most OG base pairs. Steady-state kinetic studies were carried out for representative examples of lesions in the template. Km increased by 90-100-fold for OG.C-, OI.C-, OI.A-, and OA.T-containing duplexes compared to that of a G.C-containing duplex. Substrates containing Gh.A, Gh.G, Sp.A, and Sp.G base pairs exhibited Km values 20-70-fold higher than that of the substrate containing a G.C base pair, while the Km value for OG.A was 5 times lower than that for G.C.
Collapse
Affiliation(s)
| | | | | | | | - Cynthia J. Burrows
- *To whom correspondence should be addressed. Phone: (801) 585-7290. Fax: (801) 585-0024. E-mail:
| |
Collapse
|
191
|
|
192
|
Juodka BA. Covalent Interaction of Proteins and Nucleic Acids. Synthetic and Natural Nucleotide-Peptides. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328318408081283] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
193
|
Nandakumar J, Shuman S, Lima CD. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell 2006; 127:71-84. [PMID: 17018278 DOI: 10.1016/j.cell.2006.08.038] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 07/20/2006] [Accepted: 08/04/2006] [Indexed: 11/24/2022]
Abstract
T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.
Collapse
|
194
|
Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 2006; 24:279-91. [PMID: 17052461 DOI: 10.1016/j.molcel.2006.08.015] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 08/01/2006] [Accepted: 08/10/2006] [Indexed: 10/24/2022]
Abstract
DNA sliding clamps encircle DNA and provide binding sites for many DNA-processing enzymes. However, it is largely unknown how sliding clamps like proliferating cell nuclear antigen (PCNA) coordinate multistep DNA transactions. We have determined structures of Sulfolobus solfataricus DNA ligase and heterotrimeric PCNA separately by X-ray diffraction and in complex by small-angle X-ray scattering (SAXS). Three distinct PCNA subunits assemble into a protein ring resembling the homotrimeric PCNA of humans but with three unique protein-binding sites. In the absence of nicked DNA, the Sulfolobus solfataricus DNA ligase has an open, extended conformation. When complexed with heterotrimeric PCNA, the DNA ligase binds to the PCNA3 subunit and ligase retains an open, extended conformation. A closed, ring-shaped conformation of ligase catalyzes a DNA end-joining reaction that is strongly stimulated by PCNA. This open-to-closed switch in the conformation of DNA ligase is accommodated by a malleable interface with PCNA that serves as an efficient platform for DNA ligation.
Collapse
Affiliation(s)
- John M Pascal
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
195
|
Jackson BR, Noble C, Lavesa-Curto M, Bond PL, Bowater RP. Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon "Ferroplasma acidarmanus" Fer1. Extremophiles 2006; 11:315-27. [PMID: 17136487 DOI: 10.1007/s00792-006-0041-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 10/17/2006] [Indexed: 01/05/2023]
Abstract
Analysis of the genome of "Ferroplasma acidarmanus" Fer1, an archaeon that is an extreme acidophile, identified an open reading frame encoding a putative ATP-dependent DNA ligase, which we termed FaLig. The deduced amino acid sequence of FaLig contains 595 amino acids, with a predicted molecular mass of 67.8 kDa. "F. acidarmanus" Fer1 is classified as a Euryarchaeote, but phylogenetic analysis using amino acid sequences showed that FaLig is more similar to DNA ligases from Crenarchaeota, suggesting that lateral transfer of these genes has occurred among archaea. The gene sequence encoding FaLig was cloned into a bacterial expression vector harbouring an upstream His-tag to aid purification. Conditions for expression and purification from Escherichia coli were identified and recombinant FaLig was confirmed to be an ATP-dependent DNA ligase. Optimal conditions for nick-joining by the protein were pH 6-7, 0.5 mM ATP, in the presence of either Mg(2+) or Mn(2+). Using a range of nicked, double-stranded nucleic acids, ligation was detected with the same substrates as previously determined for other DNA ligases. Although FaLig is the DNA ligase from one of the most extreme acidophilic organism yet studied, this characterization suggests that its biochemical mechanism is analogous to that of enzymes from other cellular systems.
Collapse
Affiliation(s)
- Brian R Jackson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | | | | | | |
Collapse
|
196
|
Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations. BMC Mol Biol 2006; 7:44. [PMID: 17132163 PMCID: PMC1684257 DOI: 10.1186/1471-2199-7-44] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 11/28/2006] [Indexed: 11/10/2022] Open
Abstract
Background DNA ligases are required for DNA strand joining in all forms of cellular life. NAD+-dependent DNA ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. Among the archaeal NAD+-dependent DNA ligases is the LigN enzyme of the halophilic euryarchaeon Haloferax volcanii, the gene for which was apparently acquired by Hfx.volcanii through lateral gene transfer (LGT) from a halophilic eubacterium. Genetic studies show that the LGT-acquired LigN enzyme shares an essential function with the native Hfx.volcanii ATP-dependent DNA ligase protein LigA. Results To characterise the enzymatic properties of the LigN protein, wild-type and three mutant forms of the LigN protein were separately expressed in recombinant form in E.coli and purified to apparent homogeneity by immobilised metal ion affinity chromatography (IMAC). Non-isotopic DNA ligase activity assays using λ DNA restriction fragments with 12 bp cos cohesive ends were used to show that LigN activity was dependent on addition of divalent cations and salt. No activity was detected in the absence of KCl, whereas maximum activity could be detected at 3.2 M KCl, close to the intracellular KCl concentration of Hfx.volcanii cells. Conclusion LigN is unique amongst characterised DNA ligase enzymes in displaying maximal DNA strand joining activity at high (> 3 M) salt levels. As such the LigN enzyme has potential both as a novel tool for biotechnology and as a model enzyme for studying the adaptation of proteins to high intracellular salt levels.
Collapse
|
197
|
Scott BOS, Lavesa-Curto M, Bullard DR, Butt JN, Bowater RP. Immobilized DNA hairpins for assay of sequential breaking and joining of DNA backbones. Anal Biochem 2006; 358:90-8. [PMID: 16996469 DOI: 10.1016/j.ab.2006.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 07/21/2006] [Accepted: 08/05/2006] [Indexed: 10/24/2022]
Abstract
Immobilized DNA hairpins are exploited in a novel approach to assay DNA ligases and nucleases. A fundamental characteristic of the assay is that a fluorophore at the remote terminus of the hairpin reports on the integrity of the DNA backbone. The functionality of the protocol is confirmed using ATP- and NAD+-dependent DNA ligases and the nicking enzyme N.BbvCIA. The assay format is amenable to high-throughput analysis and quantitation of enzyme activity, and it is shown to be in excellent agreement with the more laborious electrophoretic approaches that are widely used for such analyses. Significantly, the assay is used to demonstrate sequential breaking and rejoining of a specific nucleic acid. Thus, a simple platform for biochemically innovative studies of pathways in cellular nucleic acid metabolism is demonstrated.
Collapse
Affiliation(s)
- Benjamin O S Scott
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | | | | | | |
Collapse
|
198
|
Bullard D, Bowater R. Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4. Biochem J 2006; 398:135-44. [PMID: 16671895 PMCID: PMC1525015 DOI: 10.1042/bj20060313] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-stranded oligonucleotides containing a single-strand break was determined. Between 4 and 37 degrees C, all proteins ligated substrates containing various combinations of DNA and RNA. The RNA ligases ligated a more diverse set of substrates than T4Dnl and, generally, T4Rnl1 had 50-1000-fold lower activity than T4Rnl2. In assays using identical conditions, optimal ligation of all substrates was at pH 8 for T4Dnl and T4Rnl1 and pH 7 for T4Rnl2, demonstrating that the protein dictates the pH optimum for ligation. All proteins ligated a substrate containing DNA as the unbroken strand, with the nucleotides at the nick of the broken strand being RNA at the 3'-hydroxy group and DNA at the 5'-phosphate. Since this RNA-DNA hybrid was joined at a similar maximal rate by T4Dnl and T4Rnl2 at 37 degrees C, we consider the possibility that this could be an unexpected physiological substrate used during some pathways of 'DNA repair'.
Collapse
Affiliation(s)
- Desmond R. Bullard
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
- To whom correspondence should be addressed (email )
| |
Collapse
|
199
|
Kim YJ, Lee HS, Bae SS, Jeon JH, Yang SH, Lim JK, Kang SG, Kwon ST, Lee JH. Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp. Biotechnol Lett 2006; 28:401-7. [PMID: 16614906 DOI: 10.1007/s10529-005-6070-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 12/14/2005] [Indexed: 11/24/2022]
Abstract
Genomic analysis of a hyperthermophilic archaeon, Thermococcus sp. NA1, revealed an ORF of 1689 bases encoding 562 amino acids that showed a high similarity to DNA ligases from other hyperthermophilic archaea. The ligase, which was designated TNA1_lig (Thermococcus sp. NA1 ligase), was cloned and expressed in Escherichia coli. The recombinant TNA1_lig was purified by metal affinity chromatography. The optimum ligase activity of the recombinant TNA1_lig occurred at 80 degrees C and pH 7.5. The enzyme was activated by MgCl2 and ZnCl2 but was inhibited by MnCl2 and NiCl2. Additionally, the enzyme was activated by either ATP or NAD+.
Collapse
Affiliation(s)
- Yun Jae Kim
- Korean Ocean Research & Development Institute, Ansan P.O. Box 29, Seoul, 425-600, Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
200
|
Benarroch D, Shuman S. Characterization of mimivirus NAD+-dependent DNA ligase. Virology 2006; 353:133-43. [PMID: 16844179 DOI: 10.1016/j.virol.2006.04.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 04/06/2006] [Accepted: 04/07/2006] [Indexed: 10/24/2022]
Abstract
Mimivirus, a parasite of Acanthamoeba polyphaga, is the largest DNA virus known; it encodes a cornucopia of proteins with imputed functions in DNA replication, modification, and repair. Here we produced, purified, and characterized mimivirus DNA ligase (MimiLIG), an NAD+-dependent nick joining enzyme homologous to bacterial LigA and entomopoxvirus DNA ligase. MimiLIG is a 636-aa polypeptide composed of an N-terminal NAD+ specificity module (domain Ia), linked to nucleotidyltransferase, OB-fold, helix-hairpin-helix, and BRCT domains, but it lacks the tetracysteine Zn-binding module found in all bacterial LigA enzymes. MimiLIG requires conserved domain Ia residues Tyr36, Asp46, Tyr49, and Asp50 for its initial reaction with NAD+ to form the ligase-AMP intermediate, but not for the third step of phosphodiester formation at a preadenylylated nick. MimiLIG differs from bacterial LigA enzymes in that its activity is strongly dependent on the C-terminal BRCT domain, deletion of which reduced its specific activity in nick joining by 75-fold without affecting the ligase adenylylation step. The DeltaBRCT mutant of MimiLIG was impaired in sealing at a preadenylylated nick. We propose that eukaryal DNA viruses acquired the NAD+-dependent ligases by horizontal transfer from a bacterium and that MimiLIG predates entomopoxvirus ligase, which lacks both the tetracysteine and BRCT domains. We speculate that the dissemination of NAD+-dependent ligase from bacterium to eukaryotic virus might have occurred within an amoebal host.
Collapse
Affiliation(s)
- Delphine Benarroch
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
| | | |
Collapse
|