201
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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.
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Affiliation(s)
- Delphine Benarroch
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
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202
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Nishida H, Kiyonari S, Ishino Y, Morikawa K. The closed structure of an archaeal DNA ligase from Pyrococcus furiosus. J Mol Biol 2006; 360:956-67. [PMID: 16820169 DOI: 10.1016/j.jmb.2006.05.062] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 05/25/2006] [Accepted: 05/26/2006] [Indexed: 11/21/2022]
Abstract
DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 A resolution structure of Pyrococcus furiosus DNA ligase (PfuLig), which represents the first full-length atomic view of an ATP-dependent eukaryotic-type DNA ligase. The enzyme comprises the N-terminal DNA-binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architecture of each domain resembles those of human DNA ligase I, but the domain arrangements differ strikingly between the two enzymes. The closed conformation of the two "catalytic core" domains at the carboxyl terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP molecule. This domain rearrangement results from the "domain-connecting" role of the helical extension conserved at the C termini in archaeal and eukaryotic DNA ligases. The DNA substrate in the human open-ligase is replaced by motif VI in the Pfu closed-ligase. Both the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. Two basic residues (R531 and K534) in motif VI reside within the active site pocket and interact with the phosphate group of the bound AMP. The crystallographic and functional analyses of mutant enzymes revealed that these two residues within the RxDK sequence play essential and complementary roles in ATP processing. This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini.
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Affiliation(s)
- Hirokazu Nishida
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), Osaka 565-0874, Japan
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203
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Abstract
I am a member of what has been called, perhaps too grandiosely, "The Greatest Generation." I grew up during the Great Depression and served in the U.S. Army during World War II. Because of my military service and the benefits of the GI Bill, I was able to attend college and, later, graduate school. Early in my graduate studies, I became fascinated with enzymes and the biochemical reactions that they catalyze. This fascination has never left me during the 50 years I have been a "DNA enzymologist." I was fortunate to have had as a mentor Arthur Kornberg, one of the great biochemists of the twentieth century, and a splendid group of postdocs and graduate students. I have studied DNA polymerases, DNA nucleases, DNA ligases, and DNA recombinases, enzymes that are critical to our understanding of DNA replication, repair, and recombination. Most recently, I have been studying herpes virus replication and inadvertently wandered into an entirely new area-viral latency.
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Affiliation(s)
- I Robert Lehman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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204
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Showalter AK, Lamarche BJ, Bakhtina M, Su MI, Tang KH, Tsai MD. Mechanistic comparison of high-fidelity and error-prone DNA polymerases and ligases involved in DNA repair. Chem Rev 2006; 106:340-60. [PMID: 16464009 DOI: 10.1021/cr040487k] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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205
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Affiliation(s)
- Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, 48109-0606, USA.
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206
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Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T. DNA ligases: structure, reaction mechanism, and function. Chem Rev 2006; 106:687-99. [PMID: 16464020 DOI: 10.1021/cr040498d] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Alan E Tomkinson
- Radiation Oncology Research Laboratory and Marlene and Stewart Greenebaum Cancer Center, Molecular and Cellular Biology Graduate Program, University of Maryland School of Medicine, Baltimore, 21201, USA.
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207
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Sinha KM, Hines JC, Ray DS. Cell cycle-dependent localization and properties of a second mitochondrial DNA ligase in Crithidia fasciculata. EUKARYOTIC CELL 2006; 5:54-61. [PMID: 16400168 PMCID: PMC1360255 DOI: 10.1128/ec.5.1.54-61.2006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mitochondrial DNA in kinetoplastid protozoa is contained in a single highly condensed structure consisting of thousands of minicircles and approximately 25 maxicircles. The disk-shaped structure is termed kinetoplast DNA (kDNA) and is located in the mitochondrial matrix near the basal body. We have previously identified a mitochondrial DNA ligase (LIG kbeta) in the trypanosomatid Crithidia fasciculata that localizes to antipodal sites flanking the kDNA disk where several other replication proteins are localized. We describe here a second mitochondrial DNA ligase (LIG kalpha). LIG kalpha localizes to the kinetoplast primarily in cells that have completed mitosis and contain either a dividing kinetoplast or two newly divided kinetoplasts. Essentially all dividing or newly divided kinetoplasts show localization of LIG kalpha. The ligase is present on both faces of the kDNA disk and at a high level in the kinetoflagellar zone of the mitochondrial matrix. Cells containing a single nucleus show localization of the LIG kalpha to the kDNA but at a much lower frequency. The mRNA level of LIG kalpha varies during the cell cycle out of phase with that of LIG kbeta. LIG kalpha transcript levels are maximal during the phase when cells contain two nuclei, whereas LIG kbeta transcript levels are maximal during S phase. The LIG kalpha protein decays with a half-life of 100 min in the absence of protein synthesis. The periodic expression of the LIG kalpha transcript and the instability of the LIG kalpha protein suggest a possible role of the ligase in regulating minicircle replication.
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Affiliation(s)
- Krishna Murari Sinha
- Molecular Biology Institute and Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, 301A Paul D. Boyer Hall, 611 Charles Young Dr. East, Los Angeles, California 90095-1570, USA
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208
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Akey D, Martins A, Aniukwu J, Glickman MS, Shuman S, Berger JM. Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D. J Biol Chem 2006; 281:13412-13423. [PMID: 16476729 DOI: 10.1074/jbc.m513550200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligase D (LigD) is a large polyfunctional enzyme involved in nonhomologous end-joining (NHEJ) in mycobacteria. LigD consists of a C-terminal ATP-dependent ligase domain fused to upstream polymerase and phosphoesterase modules. Here we report the 2.4 angstroms crystal structure of the ligase domain of Mycobacterium LigD, captured as the covalent ligase-AMP intermediate with a divalent metal in the active site. A chloride anion on the protein surface coordinated by the ribose 3'-OH and caged by arginine and lysine side chains is a putative mimetic of the 5'-phosphate at a DNA nick. Structure-guided mutational analysis revealed distinct requirements for the adenylylation and end-sealing reactions catalyzed by LigD. We found that a mutation of Mycobacterium LigD that ablates only ligase activity results in decreased fidelity of NHEJ in vivo and a strong bias of mutagenic events toward deletions instead of insertions at the sealed DNA ends. This phenotype contrasts with the increased fidelity of double-strand break repair in deltaligD cells or in a strain in which only the polymerase function of LigD is defective. We surmise that the signature error-prone quality of bacterial NHEJ in vivo arises from a dynamic balance between the end-remodeling and end-sealing steps.
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Affiliation(s)
- David Akey
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720
| | - Alexandra Martins
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Jideofor Aniukwu
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Michael S Glickman
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021; Division of Infectious Diseases, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021.
| | - James M Berger
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720.
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209
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Abstract
T4 DNA ligase is one of the workhorses of molecular biology and used in various biotechnological applications. Here we report that this ligase, unlike Escherichia coli DNA ligase, Taq DNA ligase and Ampligase, is able to join the ends of single-stranded DNA in the absence of any duplex DNA structure at the ligation site. Such nontemplated ligation of DNA oligomers catalyzed by T4 DNA ligase occurs with a very low yield, as assessed by quantitative competitive PCR, between 10(-6) and 10(-4) at oligonucleotide concentrations in the range 0.1-10 nm, and thus is insignificant in many molecular biological applications of T4 DNA ligase. However, this side reaction may be of paramount importance for diagnostic detection methods that rely on template-dependent or target-dependent DNA probe ligation in combination with amplification techniques, such as PCR or rolling-circle amplification, because it can lead to nonspecific background signals or false positives. Comparison of ligation yields obtained with substrates differing in their strandedness at the terminal segments involved in ligation shows that an acceptor duplex DNA segment bearing a 3'-hydroxy end, but lacking a 5'-phosphate end, is sufficient to play a role as a cofactor in blunt-end ligation.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, MA 02215, USA.
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210
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Chen X, Pascal J, Vijayakumar S, Wilson GM, Ellenberger T, Tomkinson AE. Human DNA ligases I, III, and IV-purification and new specific assays for these enzymes. Methods Enzymol 2006; 409:39-52. [PMID: 16793394 DOI: 10.1016/s0076-6879(05)09003-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The joining of DNA strand breaks by DNA ligases is required to seal Okazaki fragments during DNA replication and to complete almost all DNA repair pathways. In human cells, there are multiple species of DNA ligase encoded by the LIG1, LIG3, and LIG4 genes. Here we describe protocols to overexpress and purify recombinant DNA ligase I, DNA ligase IIIbeta, and DNA ligase IV/XRCC4 and the assays used to purify and distinguish between these enzymes. In addition, we describe a fluorescence-based ligation assay that can be used for high throughput screening of chemical libraries.
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Affiliation(s)
- Xi Chen
- Radiation Oncology, Research Laboratory and the Marlene and Stewart Greenebaum Cancer Center, Universtiy of Maryland School of Medicine, Baltimore, USA
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211
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Nishida H, Tsuchiya D, Ishino Y, Morikawa K. Overexpression, purification and crystallization of an archaeal DNA ligase from Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1100-2. [PMID: 16511246 PMCID: PMC1978145 DOI: 10.1107/s1744309105038649] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 11/22/2005] [Indexed: 11/10/2022]
Abstract
DNA ligases seal single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome during various aspects of DNA metabolism, such as replication, excision repair and recombination. DNA-strand breaks are frequently generated as reaction intermediates in these events and the sealing of these breaks depends solely on the proper function of DNA ligase. Crystals of the archaeal DNA ligase from Pyrococcus furiosus were obtained using 6.6%(v/v) ethanol as a precipitant and diffracted X-rays to 1.7 A resolution. They belong to the monoclinic space group P2(1), with unit-cell parameters a = 61.1, b = 88.3, c = 63.4 A, beta = 108.9 degrees. The asymmetric unit contains one ligase molecule.
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Affiliation(s)
- Hirokazu Nishida
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Daisuke Tsuchiya
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshizumi Ishino
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan
| | - Kosuke Morikawa
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Correspondence e-mail:
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212
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Keppetipola N, Shuman S. Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J Bacteriol 2005; 187:6902-8. [PMID: 16199559 PMCID: PMC1251619 DOI: 10.1128/jb.187.20.6902-6908.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Accepted: 06/24/2005] [Indexed: 11/20/2022] Open
Abstract
Archaea encode a DNA ligase composed of a C-terminal catalytic domain typical of ATP-dependent ligases plus an N-terminal domain similar to that found in eukaryotic cellular and poxvirus DNA ligases. All archaeal DNA ligases characterized to date have ATP-dependent adenylyltransferase and nick-joining activities. However, recent reports of dual-specificity ATP/NAD+ ligases in two Thermococcus species and Pyrococcus abyssi and an ATP/ADP ligase in Aeropyrum pernix raise the prospect that certain archaeal enzymes might exemplify an undifferentiated ancestral stage in the evolution of ligase substrate specificity. Here we analyze the biochemical properties of Pyrococcus horikoshii DNA ligase. P. horikoshii ligase catalyzes auto-adenylylation and nick sealing in the presence of a divalent cation and ATP; it is unable to utilize NAD+ or ADP to promote ligation in lieu of ATP. P. horikoshii ligase is thermophilic in vitro, with optimal adenylyltransferase activity at 90 degrees C and nick-joining activity at 70 to 90 degrees C. P. horikoshii ligase resembles the ligases of Methanobacterium thermautotrophicum and Sulfolobus shibatae in its strict specificity for ATP.
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213
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Wilkinson A, Smith A, Bullard D, Lavesa-Curto M, Sayer H, Bonner A, Hemmings A, Bowater R. Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:113-22. [PMID: 15848142 DOI: 10.1016/j.bbapap.2005.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/03/2005] [Accepted: 03/03/2005] [Indexed: 01/05/2023]
Abstract
NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. NAD(+)-dependent DNA ligases comprise several discrete structural domains, including a BRCT domain at the C-terminus that is highly-conserved in this group of proteins. The over-expression and purification of various fragments of E. coli LigA allowed the investigation of the different domains in DNA-binding and ligation by this enzyme. Compared to the full-length protein, the deletion of the BRCT domain from LigA reduced in vitro ligation activity by 3-fold and also reduced DNA binding. Using an E. coli strain harbouring a temperature-sensitive mutation of ligA, the over-expression of protein with its BRCT domain deleted enabled growth at the non-permissive temperature. In gel-mobility shift experiments, the isolated BRCT domain bound DNA in a stable manner and to a wider range of DNA molecules compared to full LigA. Thus, the BRCT domain of E. coli LigA can bind DNA, but it is not essential for DNA nick-joining activity in vitro or in vivo.
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Affiliation(s)
- Adam Wilkinson
- Phico Therapeutics Ltd, Babraham Hall, Babraham, Cambridge, CB2 4AT, UK
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214
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Chandra PK, Wikel SK. Analyzing ligation mixtures using a PCR based method. Biol Proced Online 2005; 7:93-100. [PMID: 16136227 PMCID: PMC1190383 DOI: 10.1251/bpo108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 03/22/2005] [Accepted: 05/20/2005] [Indexed: 11/23/2022] Open
Abstract
We have developed a simple and effective method (Lig-PCR) for monitoring ligation reactions using PCR and primers that are common to many cloning vectors. Ligation mixtures can directly be used as templates and the results can be analyzed by conventional gel electrophoresis. The PCR products are representative of the recombinant molecules created during ligation and the corresponding transformants. Orientation of inserts can also be determined using an internal primer. The usefulness of this method has been demonstrated using ligation mixtures of two cDNA's derived from the salivary glands of Aedes aegypti mosquitoes. The method described here is sensitive and easy to perform compared to currently available methods.
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Affiliation(s)
- Prafulla K Chandra
- Center for Microbial Pathogenesis, MC3710, School of Medicine, University of Connecticut Health Center, Farmington, CT 06030-3710, USA.
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215
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Nandakumar J, Shuman S. Dual Mechanisms whereby a Broken RNA End Assists the Catalysis of Its Repair by T4 RNA Ligase 2. J Biol Chem 2005; 280:23484-9. [PMID: 15851476 DOI: 10.1074/jbc.m500831200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
T4 RNA ligase 2 (Rnl2) efficiently seals 3'-OH/5'-PO4 RNA nicks via three nucleotidyl transfer steps. Here we show that the terminal 3'-OH at the nick accelerates the second step of the ligase pathway (adenylylation of the 5'-PO4 strand) by a factor of 1000, even though the 3'-OH is not chemically transformed during the reaction. Also, the terminal 2'-OH at the nick accelerates the third step (attack of the 3'-OH on the 5'-adenylated strand to form a phosphodiester) by a factor of 25-35, even though the 2'-OH is not chemically reactive. His-37 of Rnl2 is uniquely required for step 3, providing a approximately 10(2) rate acceleration. Biochemical epistasis experiments show that His-37 and the RNA 2'-OH act independently. We conclude that the broken RNA end promotes catalysis of its own repair by Rnl2 via two mechanisms, one of which (enhancement of step 3 by the 2'-OH) is specific to RNA ligation. Substrate-assisted catalysis provides a potential biochemical checkpoint during nucleic acid repair.
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216
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Srivastava SK, Tripathi RP, Ramachandran R. NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors. J Biol Chem 2005; 280:30273-81. [PMID: 15901723 DOI: 10.1074/jbc.m503780200] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents.
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Affiliation(s)
- Sandeep Kumar Srivastava
- Division Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil, Mahatma Gandhi Marg, Lucknow-226001, India
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217
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Gul S, Brown R, May E, Mazzulla M, Smyth MG, Berry C, Morby A, Powell DJ. Staphylococcus aureus DNA ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay. Biochem J 2005; 383:551-9. [PMID: 15283677 PMCID: PMC1133749 DOI: 10.1042/bj20040054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA ligases are key enzymes involved in the repair and replication of DNA. Prokaryotic DNA ligases uniquely use NAD+ as the adenylate donor during catalysis, whereas eukaryotic enzymes use ATP. This difference in substrate specificity makes the bacterial enzymes potential targets for therapeutic intervention. We have developed a homogeneous chemiluminescence-based hybridization protection assay for Staphylococcus aureus DNA ligase that uses novel acridinium ester technology and demonstrate that it is an alternative to the commonly used radiometric assays for ligases. The assay has been used to determine a number of kinetic constants for S. aureus DNA ligase catalysis. These included the K(m) values for NAD+ (2.75+/-0.1 microM) and the acridinium-ester-labelled DNA substrate (2.5+/-0.2 nM). A study of the pH-dependencies of kcat, K(m) and kcat/K(m) has revealed values of kinetically influential ionizations within the enzyme-substrate complexes (kcat) and free enzyme (kcat/K(m)). In each case, the curves were shown to be composed of one kinetically influential ionization, for k(cat), pK(a)=6.6+/-0.1 and kcat/K(m), pK(a)=7.1+/-0.1. Inhibition characteristics of the enzyme against two Escherichia coli DNA ligase inhibitors have also been determined with IC50 values for these being 3.30+/-0.86 microM for doxorubicin and 1.40+/-0.07 microM for chloroquine diphosphate. The assay has also been successfully miniaturized to a sufficiently low volume to allow it to be utilized in a high-throughput screen (384-well format; 20 microl reaction volume), enabling the assay to be used in screening campaigns against libraries of compounds to discover leads for further drug development.
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Affiliation(s)
- Sheraz Gul
- Assay Development and Compound Profiling, GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park (North), Third Avenue, Harlow, Essex CM19 4AW, UK.
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218
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Bakht S, Qi X. Ligation-mediated rolling-circle amplification-based approaches to single nucleotide polymorphism detection. Expert Rev Mol Diagn 2005; 5:111-6. [PMID: 15723597 DOI: 10.1586/14737159.5.1.111] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ligation-mediated single nucleotide polymorphism detection coupled with an efficient method of signal enhancement, such as rolling-circle amplification, hyperbranched rolling-circle amplification or PCR, has provided the foundation for the development of variable single nucleotide polymorphism genotyping and analyzing methods for different applications. Several methods based on the above approaches have been developed, enabling rapid genotyping of a large number of single nucleotide polymorphisms directly from a small amount of genomic DNA and large-scale multiplex single nucleotide polymorphism (>1000 single nucleotide polymorphisms per assay) analysis on microarrays. This review categorizes different approaches and describes the principles of each approach for single nucleotide polymorphism detection. Possible future research directions including the development of optimized methods for analysis of cytologic samples and other applications are also discussed.
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Affiliation(s)
- Saleha Bakht
- John Innes Centre, Sainsbury Laboratory, Norwich Research Park, Colney, Norwich NR47UH, UK.
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219
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Abstract
The crystal structure of human DNA ligase I catches the enzyme just before the last step of ligation and shows that the protein wraps completely around nicked DNA. The elegant structure explains how ligase attains fidelity for the sealing operation.
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Affiliation(s)
- Aaron Johnson
- The Rockefeller University 1230 York Avenue, Box 228, New York, New York 10021-6399, USA.
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220
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Sun D, Urrabaz R. Development of non-electrophoretic assay method for DNA ligases and its application to screening of chemical inhibitors of DNA ligase I. ACTA ACUST UNITED AC 2005; 59:49-59. [PMID: 15134906 DOI: 10.1016/s0165-022x(02)00071-4] [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] [Received: 01/19/2002] [Revised: 05/13/2002] [Accepted: 08/02/2002] [Indexed: 11/24/2022]
Abstract
A new rapid assay method for DNA ligases has been developed, which allows direct quantification of enzyme activity without using the traditional polyacrylamide gel electrophoretic technique. In this method, the 5'-biotinylated nicked duplex was used as a substrate for the ligase reaction, in which the 5'-end of the first oligonucleotide (19-mer) on the nicked strand is biotinylated and the second oligonucleotide (20-mer) on the same strand is labeled with radioactive 32P at the 5'-end. After ligation of the biotinylated 19-mer oligonucleotide into the second oligonucleotide with the reaction of DNA ligases, the biotinylated 19-mer oligonucleotide is converted into the radioactive 39-mer oligonucleotide. The ligase reaction products were heat-denatured to release both ligated and unligated biotinylated oligonucleotides. The biotinylated oligonucleotides were then captured on a streptavidin-coated microtiter plate and counted. The results obtained using this method correlated very well with those from the standard assay method using electrophoresis. Using this assay method, we were able to screen a chemical library and identify new DNA ligase inhibitors structurally related to resorcinol, which has growth inhibitory effects on the human breast cancer cell, MCF-7. The method described here is anticipated to be very useful for screening DNA ligase inhibitors from chemical libraries.
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Affiliation(s)
- Daekyu Sun
- Institute for Drug Development, Cancer Therapy and Research Center, 14960 Omicron Drive, San Antonio, TX 78245-3217, USA.
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221
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Zhu H, Shuman S. Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA). J Biol Chem 2005; 280:12137-44. [PMID: 15671015 DOI: 10.1074/jbc.m413685200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NAD+-dependent DNA ligase (LigA) is essential for bacterial growth and a potential target for antimicrobial drug discovery. Here we queried the role of 14 conserved amino acids of Escherichia coli LigA by alanine scanning and thereby identified five new residues within the nucleotidyltransferase domain as being essential for LigA function in vitro and in vivo. Structure activity relationships were determined by conservative mutagenesis for the Glu-173, Arg-200, Arg-208, and Arg-277 side chains, as well as four other essential side chains that had been identified previously (Lys-115, Asp-117, Asp-285, and Lys-314). In addition, we identified Lys-290 as important for LigA activity. Reference to the structure of Enterococcus faecalis LigA allowed us to discriminate three classes of essential/important side chains that: (i) contact NAD+ directly (Lys-115, Glu-173, Lys-290, and Lys-314); (ii) comprise the interface between the NMN-binding domain (domain Ia) and the nucleotidyltransferase domain or comprise part of a nick-binding site on the surface of the nucleotidyltransferase domain (Arg-200 and Arg-208); or (iii) stabilize the active site fold of the nucleotidyltransferase domain (Arg-277). Analysis of mutational effects on the isolated ligase adenylylation and phosphodiester formation reactions revealed different functions for essential side chains at different steps of the DNA ligase pathway, consistent with the proposal that the active site is serially remodeled as the reaction proceeds.
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Affiliation(s)
- Hui Zhu
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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222
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Gajiwala KS, Pinko C. Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. Structure 2005; 12:1449-59. [PMID: 15296738 DOI: 10.1016/j.str.2004.05.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 05/14/2004] [Accepted: 05/17/2004] [Indexed: 10/26/2022]
Abstract
DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction.
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Affiliation(s)
- Ketan S Gajiwala
- Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad, California 92008, USA.
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223
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Liu L, Tang Z, Wang K, Tan W, Li J, Guo Q, Meng X, Ma C. Using molecular beacon to monitor activity of E. coli DNA ligase. Analyst 2005; 130:350-7. [PMID: 15724164 DOI: 10.1039/b413959c] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
NAD(+)-dependent DNA ligase has been widely used in gene diagnostics for disease-associated mutation detection and has proved to be necessary for screening bactericidal drugs targeted to DNA ligases. However, further research has been restricted since conventional ligase assay technology is limited to gel electrophoresis, which is discontinuous, time-consuming and laborious. An innovative approach is developed for monitoring the activity of E. coli DNA ligase catalyzing nucleic acid ligation in the report. This approach utilizes a molecular beacon hybridized with two single-stranded DNA (ssDNA) segments to be ligated to form a hybrid with a nick, and could therefore be recognized by the enzyme. Ligation of the two ssDNA segments would cause conformation changes of the molecular beacon, leading to significant fluorescence enhancement. Compared to gel electrophoresis, this approach can provide real time information about ligase, is more time efficient, and is easier to use. The effect of quinacrine, a drug for malaria, on the activity of the ligase is detected, thereby certifying the capability of the method for developing novel antibacterial drugs targeted at NAD(+)-dependent ligase. The fidelity of strand joining by the ligase is examined based on this approach. The effects of external factors on activity of the ligase are analyzed, and then an assay of E. coli DNA ligase is performed with a broad linear range of 4.0 x 10(-4) Weiss Unit mL(-1) to 0.4 Weiss Unit mL(-1) and the detection limit of 4.0 x 10(-4) Weiss Unit mL(-1).
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Affiliation(s)
- Lingfeng Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Biological Technology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R.China
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224
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Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 2004; 432:473-8. [PMID: 15565146 DOI: 10.1038/nature03082] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 10/06/2004] [Indexed: 11/09/2022]
Abstract
The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication. Here we report the crystal structure of human DNA ligase I (residues 233 to 919) in complex with a nicked, 5' adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein-protein interface that may coordinate the joining of Okazaki fragments.
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Affiliation(s)
- John M Pascal
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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225
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Tiemann B, Depping R, Gineikiene E, Kaliniene L, Nivinskas R, Rüger W. ModA and ModB, two ADP-ribosyltransferases encoded by bacteriophage T4: catalytic properties and mutation analysis. J Bacteriol 2004; 186:7262-72. [PMID: 15489438 PMCID: PMC523198 DOI: 10.1128/jb.186.21.7262-7272.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage T4 encodes three ADP-ribosyltransferases, Alt, ModA, and ModB. These enzymes participate in the regulation of the T4 replication cycle by ADP-ribosylating a defined set of host proteins. In order to obtain a better understanding of the phage-host interactions and their consequences for regulating the T4 replication cycle, we studied cloning, overexpression, and characterization of purified ModA and ModB enzymes. Site-directed mutagenesis confirmed that amino acids, as deduced from secondary structure alignments, are indeed decisive for the activity of the enzymes, implying that the transfer reaction follows the Sn1-type reaction scheme proposed for this class of enzymes. In vitro transcription assays performed with Alt- and ModA-modified RNA polymerases demonstrated that the Alt-ribosylated polymerase enhances transcription from T4 early promoters on a T4 DNA template, whereas the transcriptional activity of ModA-modified polymerase, without the participation of T4-encoded auxiliary proteins for middle mode or late transcription, is reduced. The results presented here support the conclusion that ADP-ribosylation of RNA polymerase and of other host proteins allows initial phage-directed mRNA synthesis reactions to escape from host control. In contrast, subsequent modification of the other cellular target proteins limits transcription from phage early genes and participates in redirecting transcription to phage middle and late genes.
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Affiliation(s)
- Bernd Tiemann
- Ruhr Universität Bochum, Fakultät für Biologie, Arbeitsgruppe Molekulare Genetik, 44780 Bochum, Germany.
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226
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Zhu H, Shuman S. A primer-dependent polymerase function of pseudomonas aeruginosa ATP-dependent DNA ligase (LigD). J Biol Chem 2004; 280:418-27. [PMID: 15520014 DOI: 10.1074/jbc.m410110200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Pseudomonas aeruginosa encodes two putative DNA ligases: a classical NAD(+)-dependent DNA ligase (LigA) plus an ATP-dependent DNA ligase (LigD). LigD exemplifies a family of bacterial proteins that consist of a ligase domain fused to flanking domains that resemble nucleases and/or polymerases. Here we purify LigD and show that it possesses an intrinsic polymerase function resident within an autonomous C-terminal polymerase domain, LigD-(533-840), that flanks an autonomous DNA ligase domain, LigD-(188-527). Native LigD and the polymerase domain are both monomeric proteins. The polymerase activity is manifest in three ways: (i) non-templated nucleotide addition to a blunt-ended duplex DNA primer; (ii) non-templated addition to a single-stranded DNA primer; and (iii) templated extension of a 5'-tailed duplex DNA primer-template. The divalent cation cofactor requirement for non-templated and templated polymerase activity is satisfied by manganese or cobalt. rNTPs are preferred over dNTPs as substrates for non-templated blunt-end addition, which typically entails the incorporation of only 1 or 2 nucleotides at the primer terminus. Templated dNMP addition to a 5'-tailed substrate is efficient with respect to dNTP utilization; the primer is elongated to the end of the template strand and is then further extended with a non-templated nucleotide. The polymerase activity is abolished by alanine substitution for two aspartates (Asp-669 and Asp-671) within the putative metal-binding site. We speculate that polymerase activity is relevant to LigD function in nonhomologous end-joining.
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Affiliation(s)
- Hui Zhu
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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227
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Lu J, Tong J, Feng H, Huang J, Afonso CL, Rock DL, Barany F, Cao W. Unique ligation properties of eukaryotic NAD+-dependent DNA ligase from Melanoplus sanguinipes entomopoxvirus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1701:37-48. [PMID: 15450174 DOI: 10.1016/j.bbapap.2004.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 05/26/2004] [Accepted: 06/04/2004] [Indexed: 10/26/2022]
Abstract
The eukaryotic Melanoplus sanguinipes entomopoxvirus (MsEPV) genome reveals a homologous sequence to eubacterial nicotinamide adenine dinucleotide (NAD(+))-dependent DNA ligases [J. Virol. 73 (1999) 533]. This 522-amino acid open reading frame (ORF) contains all conserved nucleotidyl transferase motifs but lacks the zinc finger motif and BRCT domain found in conventional eubacterial NAD(+) ligases. Nevertheless, cloned MsEPV ligase seals DNA nicks in a NAD(+)-dependent fashion, while adenosine 5'-monophosphate (ATP) cannot serve as an adenylation cofactor. The ligation activity of MsEPV ligase requires Mg(2+) or Mn(2+). MsEPV ligase seals sticky ends efficiently, but has little activity on 1-nucleotide gap or blunt-ended DNA substrates even in the presence of polyethylene glycol. In comparison, bacterial NAD(+)-dependent ligases seal blunt-ended DNA substrates in the presence of polyethylene glycol. MsEPV DNA ligase readily joins DNA nicks with mismatches at either side of the nick junction, except for mismatches at the nick junction containing an A base in the template strand (A/A, G/A, and C/A). MsEPV NAD(+)-dependent DNA ligase can join DNA probes on RNA templates, a unique property that distinguishes this enzyme from other conventional bacterial NAD(+) DNA ligases. T4 ATP-dependent DNA ligase shows no detectable mismatch ligation at the 3' side of the nick but substantial 5' T/G mismatch ligation on an RNA template. In contrast, MsEPV ligase joins mismatches at the 3' side of the nick more frequently than at the 5' side of the nick on an RNA template. The complementary specificities of these two enzymes suggest alternative primer design for genomic profiling approaches that use allele-specific detection directly from RNA transcripts.
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Affiliation(s)
- Jing Lu
- Department of Genetics, Biochemistry and Life Science Studies, South Carolina Experiment Station, Clemson University, Room 219, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
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228
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Affiliation(s)
- Vuokko Jansson
- CSI Biotech Ltd., Lyseonkatu 2, FIN-40100 Jyväskylä, Finland.
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229
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Drake TJ, Tan W. Molecular beacon DNA probes and their bioanalytical applications. APPLIED SPECTROSCOPY 2004; 58:269A-280A. [PMID: 15479516 DOI: 10.1366/0003702041959406] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Timothy J Drake
- Center for Research at the Bio/Nano Interface, Department of Chemistry and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA
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230
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Liu P, Burdzy A, Sowers LC. DNA ligases ensure fidelity by interrogating minor groove contacts. Nucleic Acids Res 2004; 32:4503-11. [PMID: 15328364 PMCID: PMC516055 DOI: 10.1093/nar/gkh781] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA ligases, found in both prokaryotes and eukaryotes, covalently link the 3'-hydroxyl and 5'-phosphate ends of duplex DNA segments. This reaction represents a completion step for DNA replication, repair and recombination. It is well established that ligases are sensitive to mispairs present on the 3' side of the ligase junction, but tolerant of mispairs on the 5' side. While such discrimination would increase the overall accuracy of DNA replication and repair, the mechanisms by which this fidelity is accomplished are as yet unknown. In this paper, we present the results of experiments with Tth ligase from Thermus thermophilus HB8 and a series of nucleoside analogs in which the mechanism of discrimination has been probed. Using a series of purine analogs substituted in the 2 and 6 positions, we establish that the apparent base pair geometry is much more important than relative base pair stability and that major groove contacts are of little importance. This result is further confirmed using 5-fluorouracil (FU) mispaired with guanine. At neutral pH, the FU:G mispair on the 3' side of a ligase junction is predominantly in a neutral wobble configuration and is poorly ligated. Increasing the solution pH increases the proportion of an ionized base pair approximating Watson-Crick geometry, substantially increasing the relative ligation efficiency. These results suggest that the ligase could distinguish Watson-Crick from mispaired geometry by probing the hydrogen bond acceptors present in the minor groove as has been proposed for DNA polymerases. The significance of minor groove hydrogen bonding interactions is confirmed with both Tth and T4 DNA ligases upon examination of base pairs containing the pyrimidine shape analog, difluorotoluene (DFT). Although DFT paired with adenine approximates Watson-Crick geometry, a minor groove hydrogen bond acceptor is lost. Consistent with this hypothesis, we observe that DFT-containing base pairs inhibit ligation when on the 3' side of the ligase junction. The NAD+-dependent ligase, Tth, is more sensitive to the DFT analog on the unligated strand whereas the ATP-dependent T4 ligase is more sensitive to substitutions in the template strand. Electrophoretic gel mobility-shift assays demonstrate that the Tth ligase binds poorly to oligonucleotide substrates containing analogs with altered minor groove contacts.
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Affiliation(s)
- Pingfang Liu
- Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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231
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Jeon HJ, Shin HJ, Choi JJ, Hoe HS, Kim HK, Suh SW, Kwon ST. Mutational analyses of the thermostable NAD+-dependent DNA ligase fromThermus filiformis. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09685.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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232
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Ng PS, Bergstrom DE. Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides. Nucleic Acids Res 2004; 32:e107. [PMID: 15263063 PMCID: PMC506826 DOI: 10.1093/nar/gnh103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 06/25/2004] [Accepted: 06/25/2004] [Indexed: 11/12/2022] Open
Abstract
Oligodeoxyribonucleotides (5'-phosphorylated) of varying lengths were capped using a polyamide linker to form thermodynamically stable, endcapped DNA duplexes containing 8-14 bp. We have employed these endcapped DNA duplexes as tools to determine the DNA footprint of T4 DNA ligase. By high-performance liquid chromatography and PAGE analysis of the ligation mixtures of the endcapped DNA duplexes, we have found that by varying the lengths and the position of the nick, we can determine the minimal DNA-binding site as well as the mode of binding (symmetrical or asymmetrical binding) by the enzyme. The results of the study revealed that a 11 bp endcapped duplex was the shortest duplex effectively ligated. Dependence of ligation efficiency on nick position demonstrates that T4 DNA ligase bound asymmetrically to its DNA substrate. The use of a set of thermodynamically stable endcapped deoxyribonucleoside duplexes as a tool to elucidate the DNA footprint provides an efficient strategy for footprinting, which avoids ambiguities associated with chemical and biochemical footprinting methods.
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Affiliation(s)
- Pei-Sze Ng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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233
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Rolland JL, Gueguen Y, Persillon CÃ, Masson JM, Dietrich J. Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09657.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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234
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Silverman SK. Practical and general synthesis of 5'-adenylated RNA (5'-AppRNA). RNA (NEW YORK, N.Y.) 2004; 10:731-46. [PMID: 15037782 PMCID: PMC1370563 DOI: 10.1261/rna.5247704] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Accepted: 01/12/2004] [Indexed: 05/22/2023]
Abstract
A simple strategy is reported for 5'-adenylation of nearly any RNA sequence of indefinite length. The 5'-adenylated product (5'-AppRNA) is an activated RNA that is structurally similar to 5'-triphosphorylated RNA, which is usually prepared by in vitro transcription using T7 RNA polymerase. In the new 5'-adenylation strategy, the RNA substrate is first 5'-monophosphorylated either by T4 polynucleotide kinase, by in vitro transcription in the presence of excess GMP, or by appropriate derivatization during solid-phase synthesis. The RNA is then 5'-adenylated using ATP and T4 RNA ligase, in an interrupted version of the natural adenylation-ligation mechanism by which T4 RNA ligase joins two RNA substrates. Here, the final ligation step of the mechanism is inhibited with complementary DNA blocking oligonucleotide(s) that permit adenylation to occur with good yield. The 5'-AppRNA products of this approach should be valuable as activated RNAs for in vitro selection experiments as an alternative to 5'-triphosphorylated RNAs, among other likely applications. The 5'-terminal nucleotide of an RNA substrate to be adenylated using the new method is not restricted to guanosine, in contrast to 5'-triphosphorylated RNA prepared by in vitro transcription. Therefore, using the new approach, essentially any RNA obtained from solid-phase synthesis or other means can be activated by 5'-adenylation in a practical manner.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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235
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Gong C, Martins A, Bongiorno P, Glickman M, Shuman S. Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 2004; 279:20594-606. [PMID: 14985346 DOI: 10.1074/jbc.m401841200] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis encodes an NAD(+)-dependent DNA ligase (LigA) plus three distinct ATP-dependent ligase homologs (LigB, LigC, and LigD). Here we purify and characterize the multiple DNA ligase enzymes of mycobacteria and probe genetically whether the ATP-dependent ligases are required for growth of M. tuberculosis. We find significant differences in the reactivity of mycobacterial ligases with a nicked DNA substrate, whereby LigA and LigB display vigorous nick sealing activity in the presence of NAD(+) and ATP, respectively, whereas LigC and LigD, which have ATP-specific adenylyltransferase activity, display weak nick joining activity and generate high levels of the DNA-adenylate intermediate. All four of the mycobacterial ligases are monomeric enzymes. LigA has a low K(m) for NAD(+) (1 microm) and is sensitive to a recently described pyridochromanone inhibitor of NAD(+)-dependent ligases. LigA is able to sustain growth of Saccharomyces cerevisiae in lieu of the essential yeast ligase Cdc9, but LigB, LigC, and LigD are not. LigB is distinguished by its relatively high K(m) for ATP (0.34 mm) and its dependence on a distinctive N-terminal domain for nick joining. None of the three ATP-dependent ligases are essential for mycobacterial growth. M. tuberculosis ligDDelta cells are defective in nonhomologous DNA end joining.
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Affiliation(s)
- Chunling Gong
- Molecular Biology and Immunology Programs, Sloan-Kettering Institute, and Infectious Disease Division, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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236
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Georlette D, Blaise V, Bouillenne F, Damien B, Thorbjarnardóttir SH, Depiereux E, Gerday C, Uversky VN, Feller G. Adenylation-dependent conformation and unfolding pathways of the NAD+-dependent DNA ligase from the thermophile Thermus scotoductus. Biophys J 2004; 86:1089-104. [PMID: 14747344 PMCID: PMC1303902 DOI: 10.1016/s0006-3495(04)74184-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Accepted: 09/22/2003] [Indexed: 10/21/2022] Open
Abstract
In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD(+)-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD(+)-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor binding induces conformational rearrangement within the active site and promotes a compaction of the enzyme. These data support an induced "open-closure" process upon adenylation, leading to the formation of the catalytically active enzyme that is able to bind DNA. These conformational changes are likely to be associated with the protein function, preventing the formation of nonproductive complexes between deadenylated ligases and DNA. In addition, enzyme adenylation significantly increases resistance of the protein to thermal denaturation and GdmCl-induced unfolding, establishing a thermodynamic link between ligand binding and increased conformational stability. Finally, chemical unfolding of deadenylated and adenylated enzyme is accompanied by accumulation of at least two equilibrium intermediates, the molten globule and premolten globule states. Maximal populations of these intermediates are shifted toward higher GdmCl concentrations in the case of the adenylated ligase. These data provide further insights into the properties of partially folded intermediates.
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Affiliation(s)
- Daphné Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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237
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Mendel-Hartvig M, Kumar A, Landegren U. Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase. Nucleic Acids Res 2004; 32:e2. [PMID: 14704359 PMCID: PMC373312 DOI: 10.1093/nar/gnh011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Branched nucleic acid strands exist as intermediates in certain biological reactions, and bifurcating DNA also presents interesting opportunities in biotechnological applications. We describe here how T4 DNA ligase can be used for efficient construction of DNA molecules having one 5' end but two distinct 3' ends that extend from the 2' and 3' carbons, respectively, of an internal nucleotide. The nature of the reaction products is investigated, and optimal reaction conditions are reported for the construction of branched oligonucleotides. We discuss the utility of these branched DNA nanostructures for gene detection.
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238
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Benson EL, Tomich PK, Wolfe ML, Choi GH, Hagadorn JC, Mutchler VT, Garlick RL. A high-throughput resonance energy transfer assay for Staphylococcus aureus DNA ligase. Anal Biochem 2004; 324:298-300. [PMID: 14690695 DOI: 10.1016/j.ab.2003.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ericka L Benson
- Infectious Diseases Biology, Pharmacia Corp., 301 Henrietta St., Kalamazoo, MI 49007, USA.
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239
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Abstract
T4 DNA ligase is an Mg2+-dependent and ATP-dependent enzyme that seals DNA nicks in three steps: it covalently binds AMP, transadenylates the nick phosphate, and catalyses formation of the phosphodiester bond releasing AMP. In this kinetic study, we further detail the reaction mechanism, showing that the overall ligation reaction is a superimposition of two parallel processes: a 'processive' ligation, in which the enzyme transadenylates and seals the nick without dissociating from dsDNA, and a 'nonprocessive' ligation, in which the enzyme takes part in the abortive adenylation cycle (covalent binding of AMP, transadenylation of the nick, and dissociation). At low concentrations of ATP (<10 microM) and when the DNA nick is sealed with mismatching base pairs (e.g. five adjacent), this superimposition resolves into two kinetic phases, a burst ligation (approximately 0.2 min(-1)) and a subsequent slow ligation (approximately 2x10(-3) min(-1)). The relative rate and extent of each phase depend on the concentrations of ATP and Mg2+. The activation energies of self-adenylation (16.2 kcal.mol(-1)), transadenylation of the nick (0.9 kcal.mol(-1)), and nick-sealing (16.3-18.8 kcal.mol(-1)) were determined for several DNA substrates. The low activation energy of transadenylation implies that the transfer of AMP to the terminal DNA phosphate is a spontaneous reaction, and that the T4 DNA ligase-AMP complex is a high-energy intermediate. To summarize current findings in the DNA ligation field, we delineate a kinetic mechanism of T4 DNA ligase catalysis.
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Affiliation(s)
- Alexey V Cherepanov
- Kluyver Department of Biotechnology, Delft University of Technology, The Netherlands
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240
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Tang Z, Wang K, Tan W, Li J, Liu L, Guo Q, Meng X, Ma C, Huang S. Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons. Nucleic Acids Res 2003; 31:e148. [PMID: 14627838 PMCID: PMC290283 DOI: 10.1093/nar/gng146] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2003] [Revised: 08/28/2003] [Accepted: 09/26/2003] [Indexed: 11/14/2022] Open
Abstract
Nucleic acids ligation is a vital process in the repair, replication and recombination of nucleic acids. Traditionally, it is assayed by denatured gel electrophoresis and autoradiography, which are not sensitive, and are complex and discontinuous. Here we report a new approach for ligation monitoring using molecular beacon DNA probes. The molecular beacon, designed in such a way that its sequence is complementary with the product of the ligation process, is used to monitor the nucleic acid ligation in a homogeneous solution and in real-time. Our method is fast and simple. We are able to study nucleic acids ligation kinetics conveniently and to determine the activity of DNA ligase accurately. We have studied different factors that influence DNA ligation catalyzed by T4 DNA ligase. The major advantages of our method are its ultrasensitivity, excellent specificity, convenience and real-time monitoring in homogeneous solution. This method will be widely useful for studying nucleic acids ligation process and other nucleic acid interactions.
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Affiliation(s)
- Zhiwen Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Biological Technology, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
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241
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Brötz-Oesterhelt H, Knezevic I, Bartel S, Lampe T, Warnecke-Eberz U, Ziegelbauer K, Häbich D, Labischinski H. Specific and potent inhibition of NAD+-dependent DNA ligase by pyridochromanones. J Biol Chem 2003; 278:39435-42. [PMID: 12867414 DOI: 10.1074/jbc.m306479200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyridochromanones were identified by high throughput screening as potent inhibitors of NAD+-dependent DNA ligase from Escherichia coli. Further characterization revealed that eubacterial DNA ligases from Gram-negative and Gram-positive sources were inhibited at nanomolar concentrations. In contrast, purified human DNA ligase I was not affected (IC50 > 75 microm), demonstrating remarkable specificity for the prokaryotic target. The binding mode is competitive with the eubacteria-specific cofactor NAD+, and no intercalation into DNA was detected. Accordingly, the compounds were bactericidal for the prominent human pathogen Staphylococcus aureus in the low microg/ml range, whereas eukaryotic cells were not affected up to 60 microg/ml. The hypothesis that inhibition of DNA ligase is the antibacterial principle was proven in studies with a temperature-sensitive ligase-deficient E. coli strain. This mutant was highly susceptible for pyridochromanones at elevated temperatures but was rescued by heterologous expression of human DNA ligase I. A physiological consequence of ligase inhibition in bacteria was massive DNA degradation, as visualized by fluorescence microscopy of labeled DNA. In summary, the pyridochromanones demonstrate that diverse eubacterial DNA ligases can be addressed by a single inhibitor without affecting eukaryotic ligases or other DNA-binding enzymes, which proves the value of DNA ligase as a novel target in antibacterial therapy.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- Department of Anti-infectives, Bayer AG, Bayer Health Care, Pharma Research, Aprather Weg 18a, D-42096 Wuppertal, Germany. heike.broetz-oesterhelt.hb@bayer-ag
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242
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Georlette D, Blaise V, Dohmen C, Bouillenne F, Damien B, Depiereux E, Gerday C, Uversky VN, Feller G. Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus. J Biol Chem 2003; 278:49945-53. [PMID: 14523019 DOI: 10.1074/jbc.m307761200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA ligases are important enzymes required for cellular processes such as DNA replication, recombination, and repair. NAD(+)-dependent DNA ligases are essentially restricted to eubacteria, thus constituting an attractive target in the development of novel antibiotics. Although such a project might involve the systematic testing of a vast number of chemical compounds, it can essentially gain from the preliminary deciphering of the conformational stability and structural perturbations associated with the formation of the catalytically active adenylated enzyme. We have, therefore, investigated the adenylation-induced conformational changes in the mesophilic Escherichia coli and thermophilic Thermus scotoductus NAD(+)-DNA ligases, and the resistance of these enzymes to thermal and chemical (guanidine hydrochloride) denaturation. Our results clearly demonstrate that anchoring of the cofactor induces a conformational rearrangement within the active site of both mesophilic and thermophilic enzymes accompanied by their partial compaction. Furthermore, the adenylation of enzymes increases their resistance to thermal and chemical denaturation, establishing a thermodynamic link between cofactor binding and conformational stability enhancement. Finally, guanidine hydrochloride-induced unfolding of NAD(+)-dependent DNA ligases is shown to be a complex process that involves accumulation of at least two equilibrium intermediates, the molten globule and its precursor.
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Affiliation(s)
- Daphné Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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243
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Moser MJ, Prudent JR. Enzymatic repair of an expanded genetic information system. Nucleic Acids Res 2003; 31:5048-53. [PMID: 12930955 PMCID: PMC212808 DOI: 10.1093/nar/gkg709] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The excision repair machinery of a thermophilic bacterium has been shown to recognize and repair an expanded genetic base pair. Native Thermus aquaticus DNA polymerase will remove a mispaired natural base and replace it with a non-natural base to form an expanded base pair. In addition, DNA ligase will recognize a nick formed by polymerase between two non-natural base pairs and covalently attach the two strands, thus demonstrating complete repair of a bifurcated base-paired model duplex. These results add evidence to the idea that the cellular replication and repair machinery of an organism containing an expanded genetic alphabet could recognize and properly repair a site containing consecutive unnatural bases.
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Affiliation(s)
- Michael J Moser
- Eragen Biosciences, Inc., 918 Deming Way, Madison, WI 53717-1944, USA
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244
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Abstract
A gene encoding a putative ATP-dependent DNA ligase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1 was cloned and the biochemical characteristics of the resulting recombinant protein were examined. The gene (accession no. APE1094) from A. pernix encoding a 69-kDa protein showed a 39-61% identity with other ATP-dependent DNA ligases from the archaea. Normally DNA ligase is activated by NAD(+) or ATP. There has been no report about the other activators for DNA ligase. The recombinant ligase was a monomeric protein and catalyzed strand joining on a singly nicked DNA substrate in the presence of ADP and a divalent cation (Mg(2+), Mn(2+), Ca(2+) and Co(2+)) at high temperature. The optimum temperature and pH for nick-closing activity were above 70 degrees C and 7.5 degrees C, respectively. The ligase remained stable for 60 min of treatment at 100 degrees C, and the half-life was about 25 min at 110 degrees C. This is the first report of a novel hyperthermostable DNA ligase that can utilize ADP to activate the enzyme.
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Affiliation(s)
- Sung-Jong Jeon
- The Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology (AIST Kansai), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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245
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Alexander RC, Johnson AK, Thorpe JA, Gevedon T, Testa SM. Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions. Nucleic Acids Res 2003; 31:3208-16. [PMID: 12799448 PMCID: PMC162249 DOI: 10.1093/nar/gkg415] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
T4 DNA ligase catalyzes the template-dependent ligation of DNA. Using T4 DNA ligase under specific experimental conditions, we demonstrate that each of the four canonical nucleosides, centrally located on a template molecule such that they flank the site of ligation, can direct the ligation of nucleic acids regardless of the identity of the terminal nucleosides being covalently joined. This universal templating capability extends to those positions adjacent to the ligation junction. This is the first report, irrespective of the ligation method used or the identity of the template nucleosides (including analogs), which shows that nucleosides can act essentially as universal templates at ligation junctions in vitro. The canonical nucleosides do, however, differ in their ability to template sequence- independent ligations, with thymidine and guanosine being equally effective, yet more effective than adenosine and cytidine. Results indicate that hybridization strength surrounding the ligation junction is an important factor. The implications of this previously undiscovered property of T4 DNA ligase with canonical nucleosides are discussed.
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246
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Abstract
The availability of genome sequences is revolutionizing the field of microbiology. Genetic methods are being modified to facilitate rapid analysis at a genome-wide level and are blossoming for human pathogens that were previously considered intractable. This revolution coincided with a growing concern about the emergence of microbial drug resistance, compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of the new technologies, combined with many genetic strategies, has changed the way that researchers approach antibacterial drug discovery.
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Affiliation(s)
- Lynn Miesel
- Department of Antimicrobial Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-0530, USA.
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247
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248
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Du Y, Arvidson CG. Identification of ZipA, a signal recognition particle-dependent protein from Neisseria gonorrhoeae. J Bacteriol 2003; 185:2122-30. [PMID: 12644481 PMCID: PMC151515 DOI: 10.1128/jb.185.7.2122-2130.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A genetic screen designed to identify proteins that utilize the signal recognition particle (SRP) for targeting in Escherichia coli was used to screen a Neisseria gonorrhoeae plasmid library. Six plasmids were identified in this screen, and each is predicted to encode one or more putative cytoplasmic membrane (CM) proteins. One of these, pSLO7, has three open reading frames (ORFs), two of which have no similarity to known proteins in GenBank other than sequences from the closely related N. meningitidis. Further analyses showed that one of these, SLO7ORF3, encodes a protein that is dependent on the SRP for localization. This gene also appears to be essential in N. gonorrhoeae since it was not possible to generate null mutations in the gene. Although appearing unique to Neisseria at the DNA sequence level, SLO7ORF3 was found to share some features with the cell division gene zipA of E. coli. These features included similar chromosomal locations (with respect to linked genes) as well as similarities in the predicted protein domain structures. Here, we show that SLO7ORF3 can complement an E. coli conditional zipA mutant and therefore encodes a functional ZipA homolog in N. gonorrhoeae. This observation is significant in that it is the first ZipA homolog identified in a non-rod-shaped organism. Also interesting is that this is the fourth cell division protein (the others are FtsE, FtsX, and FtsQ) shown to utilize the SRP for localization, which may in part explain why the genes encoding the three SRP components are essential in bacteria.
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Affiliation(s)
- Ying Du
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-1101, USA
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249
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Cherepanov AV, de Vries S. Dynamic mechanism of nick recognition by DNA ligase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:5993-9. [PMID: 12473094 DOI: 10.1046/j.1432-1033.2002.03309.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA ligases are the enzymes responsible for the repair of single-stranded and double-stranded nicks in dsDNA. DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNA has yet to be solved. DNA ligases share common structural elements with DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase-dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase. According to this mechanism, ligase induces a B-to-A DNA helix transition of the enzyme-bound dsDNA motif, which results in DNA contraction, bending and unwinding. For non-nicked dsDNA, this transition is reversible, leading to dissociation of the enzyme. For a nicked dsDNA substrate, the contraction of the enzyme-bound DNA motif (a) triggers an opened-closed conformational change of the enzyme, and (b) forces the motif to accommodate the strained A/B-form hybrid conformation, in which the nicked strand tends to retain a B-type helix, while the non-nicked strand tends to form a shortened A-type helix. We propose that this conformation is the catalytically competent transition state, which leads to the formation of the DNA-AMP intermediate and to the subsequent sealing of the nick.
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Affiliation(s)
- Alexei V Cherepanov
- Kluyver Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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250
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Abstract
5('),5(')-Adenylyl pyrophosphoryl DNA (AppDNA) contains a high-energy pyrophosphate linkage and can be exploited as an activated DNA substrate to derive new DNA enzymes for carrying out various DNA modification reactions. For this reason, enzymatic synthesis of AppDNA is highly desirable. AppDNA is a known intermediate in DNA ligase mediated DNA ligation reactions, but rarely accumulates under normal reaction conditions. Here we report that T4 DNA ligase can quantitatively convert 5(')-phosphoryl DNA donor into AppDNA in the absence of acceptor DNA but in the presence of a template DNA that contains at least one unpaired nucleotide opposite the 5(')-phosphoryl DNA donor site. This adenylylation behavior of T4 DNA ligase is not observed with Thermus aquaticus (Taq) and Escherichia coli DNA ligases. We further found that a donor-template duplex of 11-bp in length is required by T4 DNA ligase for the formation of AppDNA.
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Affiliation(s)
- William Chiuman
- Department of Biochemistry/Department of Chemistry, Health Sciences Centre, McMaster University, 1200 Main Street West, Hamilton, Ont., Canada L8N 3Z5
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