1
|
Sholder G, Creech A, Loechler EL. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene. DNA Repair (Amst) 2015; 35:144-53. [PMID: 26523515 DOI: 10.1016/j.dnarep.2015.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022]
Abstract
To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal to the active site) to suppress dATP/dGTP/dTTP misinsertions; collectively these four structural features enhance DNAP IV's dNTP insertion fidelity opposite a BP-N(2)-dG adduct compared to Dpo4.
Collapse
Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, USA
| | | | | |
Collapse
|
2
|
Sholder G, Loechler EL. A method to accurately quantitate intensities of (32)P-DNA bands when multiple bands appear in a single lane of a gel is used to study dNTP insertion opposite a benzo[a]pyrene-dG adduct by Sulfolobus DNA polymerases Dpo4 and Dbh. DNA Repair (Amst) 2014; 25:97-103. [PMID: 25497330 DOI: 10.1016/j.dnarep.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 11/27/2022]
Abstract
Quantitating relative (32)P-band intensity in gels is desired, e.g., to study primer-extension kinetics of DNA polymerases (DNAPs). Following imaging, multiple (32)P-bands are often present in lanes. Though individual bands appear by eye to be simple and well-resolved, scanning reveals they are actually skewed-Gaussian in shape and neighboring bands are overlapping, which complicates quantitation, because slower migrating bands often have considerable contributions from the trailing edges of faster migrating bands. A method is described to accurately quantitate adjacent (32)P-bands, which relies on having a standard: a simple skewed-Gaussian curve from an analogous pure, single-component band (e.g., primer alone). This single-component scan/curve is superimposed on its corresponding band in an experimentally determined scan/curve containing multiple bands (e.g., generated in a primer-extension reaction); intensity exceeding the single-component scan/curve is attributed to other components (e.g., insertion products). Relative areas/intensities are determined via pixel analysis, from which relative molarity of components is computed. Common software is used. Commonly used alternative methods (e.g., drawing boxes around bands) are shown to be less accurate. Our method was used to study kinetics of dNTP primer-extension opposite a benzo[a]pyrene-N(2)-dG-adduct with four DNAPs, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (∼20-fold), dGTP (∼110-fold) and dTTP (∼6-fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNAP class as eukaryotic DNAP κ and bacterial DNAP IV, which accurately bypass N(2)-dG adducts, as well as establish the scan-method described herein as an accurate method to quantitate relative intensity of overlapping bands in a single lane, whether generated from (32)P-signals or by other means (e.g., staining).
Collapse
Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, United States
| | - Edward L Loechler
- Biology Department, Boston University, Boston, MA 02215, United States.
| |
Collapse
|
3
|
Ishii Y, Takasu S, Kuroda K, Matsushita K, Kijima A, Nohmi T, Ogawa K, Umemura T. Combined application of comprehensive analysis for DNA modification and reporter gene mutation assay to evaluate kidneys of gpt delta rats given madder color or its constituents. Anal Bioanal Chem 2014; 406:2467-75. [DOI: 10.1007/s00216-014-7621-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 12/13/2022]
|
4
|
Ishii Y, Inoue K, Takasu S, Jin M, Matsushita K, Kuroda K, Fukuhara K, Nishikawa A, Umemura T. Determination of Lucidin-Specific DNA Adducts by Liquid Chromatography with Tandem Mass Spectrometry in the Livers and Kidneys of Rats Given Lucidin-3-O-primeveroside. Chem Res Toxicol 2012; 25:1112-8. [DOI: 10.1021/tx300084p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuji Ishii
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kaoru Inoue
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Shinji Takasu
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Meilan Jin
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kohei Matsushita
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Ken Kuroda
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kiyoshi Fukuhara
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Akiyoshi Nishikawa
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Takashi Umemura
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| |
Collapse
|
5
|
Chandani S, Jacobs C, Loechler EL. Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies. J Nucleic Acids 2010; 2010. [PMID: 20936174 PMCID: PMC2945684 DOI: 10.4061/2010/784081] [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] [Received: 07/06/2010] [Accepted: 07/26/2010] [Indexed: 12/22/2022] Open
Abstract
DNA adducts, which block replicative DNA polymerases (DNAPs), are often bypassed by lesion-bypass DNAPs, which are mostly in the Y-Family. Y-Family DNAPs can do non-mutagenic or mutagenic dNTP insertion, and understanding this difference is important, because mutations transform normal into tumorigenic cells. Y-Family DNAP architecture that dictates mechanism, as revealed in structural and modeling studies, is considered. Steps from adduct blockage of replicative DNAPs, to bypass by a lesion-bypass DNAP, to resumption of synthesis by a replicative DNAP are described. Catalytic steps and protein conformational changes are considered. One adduct is analyzed in greater detail: the major benzo[a]pyrene adduct (B[a]P-N2-dG), which is bypassed non-mutagenically (dCTP insertion) by Y-family DNAPs in the IV/κ-class and mutagenically (dATP insertion) by V/η-class Y-Family DNAPs. Important architectural differences between IV/κ-class versus V/η-class DNAPs are discussed, including insights gained by analyzing ~400 sequences each for bacterial DNAPs IV and V, along with sequences from eukaryotic DNAPs kappa, eta and iota. The little finger domains of Y-Family DNAPs do not show sequence conservation; however, their structures are remarkably similar due to the presence of a core of hydrophobic amino acids, whose exact identity is less important than the hydrophobic amino acid spacing.
Collapse
Affiliation(s)
- Sushil Chandani
- Biology Department, Boston University, Boston, MA 02215, USA
| | | | | |
Collapse
|
6
|
Cai Y, Patel DJ, Broyde S, Geacintov NE. Base sequence context effects on nucleotide excision repair. J Nucleic Acids 2010; 2010. [PMID: 20871811 PMCID: PMC2943111 DOI: 10.4061/2010/174252] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 06/16/2010] [Indexed: 01/10/2023] Open
Abstract
Nucleotide excision repair (NER) plays a critical role in maintaining the integrity of the genome when damaged by bulky DNA lesions, since inefficient repair can cause mutations and human diseases notably cancer. The structural properties of DNA lesions that determine their relative susceptibilities to NER are therefore of great interest. As a model system, we have investigated the major mutagenic lesion derived from the environmental carcinogen benzo[a]pyrene (B[a]P),
10S (+)-trans-anti-B[a]P-N2-dG in six different sequence contexts that differ in how the lesion is positioned in relation to nearby guanine amino groups. We have obtained molecular structural data by NMR and MD simulations, bending properties from gel electrophoresis studies, and NER data obtained from human HeLa cell extracts for our six investigated sequence contexts. This model system suggests that disturbed Watson-Crick base pairing is a better recognition signal than a flexible bend, and that these can act in concert to provide an enhanced signal. Steric hinderance between the minor groove-aligned lesion and nearby guanine amino groups determines the exact nature of the disturbances. Both nearest neighbor and more distant neighbor sequence contexts have an impact. Regardless of the exact distortions, we hypothesize that they provide a local thermodynamic destabilization signal for repair.
Collapse
Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University, New York, NY 10003, USA
| | | | | | | |
Collapse
|
7
|
Sun YW, Guttenplan JB, Khmelnitsky M, Krzeminski J, Boyiri T, Amin S, El-Bayoumy K. Stereoselective metabolism of the environmental mammary carcinogen 6-nitrochrysene to trans-1,2-dihydroxy-1,2-dihydro-6-nitrochrysene by aroclor 1254-treated rat liver microsomes and their comparative mutation profiles in a laci mammary epithelial cell line. Chem Res Toxicol 2010; 22:1992-7. [PMID: 19886636 DOI: 10.1021/tx9002897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The environmental pollutant 6-nitrochrysene (6-NC) is a powerful mammary carcinogen and mutagen in rats. Our previous studies have shown that 6-NC is metabolized to trans-1,2-dihydroxy-1,2-dihydro-6-nitrochrysene (1,2-DHD-6-NC) in rats and in several in vitro systems, including human breast tissue, and the latter is the proximate carcinogenic form in the rat mammary gland. Because optically active enantiomers of numerous polynuclear aromatic hydrocarbon (PAH) metabolites including chrysene have different biological activities, we hypothesized that the stereochemical course of 6-NC metabolism might play a significant role in the carcinogenic/mutagenic activities of the parent 6-NC. The goal of this study is to evaluate the effect of stereochemistry on the mutagenicity of 1,2-DHD-6-NC using the cII gene of lacI mammary epithelial cells in vitro. Resolution of (+/-)-1,2-DHD-6-NC was obtained by either nonchiral or chiral stationary phase HPLC methods. We determined that the ratio of (-)-[R,R]- and (+)-[S,S]-1,2-DHD-6-NC formed in the metabolism of 6-NC by rat liver microsomes is 88:12. The mutation fractions and mutation spectra of [R,R] and [S,S]-enantiomers were examined. Our results showed that the [R,R]-isomer is a significantly (p < 0.01) more potent mutagen than the [S,S]-isomer. The major types of mutation induced by the [R,R]-enantiomer are AT > GC, AT > TA, and GC > TA substitutions, and these are similar to those obtained from 6-NC in vivo in the mammary glands of rats treated with 6-NC. The mutation spectra of the [S,S]-isomer were similar to the [R,R]-isomer, but a higher percentage of AT > GC substitutions in the [R,R]-isomer was noted. On the basis of the results of the present study, we hypothesize that [R,R]-1,2-DHD-6-NC is the proximate carcinogen of 6-NC in the rat mammary gland in vivo and will test this hypothesis in a future study.
Collapse
Affiliation(s)
- Yuan-Wan Sun
- Department of Biochemistry and Molecular Biology and Department of Pharmacology, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania 17033, USA
| | | | | | | | | | | | | |
Collapse
|
8
|
Ishii Y, Okamura T, Inoue T, Fukuhara K, Umemura T, Nishikawa A. Chemical Structure Determination of DNA Bases Modified by Active Metabolites of Lucidin-3-O-primeveroside. Chem Res Toxicol 2009; 23:134-41. [DOI: 10.1021/tx900314c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yuji Ishii
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| | - Toshiya Okamura
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| | - Tomoki Inoue
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| | - Kiyoshi Fukuhara
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| | - Takashi Umemura
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| | - Akiyoshi Nishikawa
- Division of Pathology, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, and Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1 Kamiyoga Setagaya-ku, Tokyo 158-8501, Japan
| |
Collapse
|
9
|
Seo KY, Yin J, Donthamsetti P, Chandani S, Lee CH, Loechler EL. Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli. J Mol Biol 2009; 392:270-82. [PMID: 19607844 DOI: 10.1016/j.jmb.2009.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 07/03/2009] [Accepted: 07/07/2009] [Indexed: 11/19/2022]
Abstract
Y-family DNA polymerases (DNAPs) are often required in cells to synthesize past DNA-containing lesions, such as [+ta]-B[a]P-N(2)-dG, which is the major adduct of the potent mutagen/carcinogen benzo[a]pyrene. The current model for the non-mutagenic pathway in Escherichia coli involves DNAP IV inserting deoxycytidine triphosphate opposite [+ta]-B[a]P-N(2)-dG and DNAP V doing the next step(s), extension. We are investigating what structural differences in these related Y-family DNAPs dictate their functional differences. X-ray structures of Y-family DNAPs reveal a number of interesting features in the vicinity of the active site, including (1) the "roof-amino acid" (roof-aa), which is the amino acid that lies above the nucleobase of the deoxynucleotide triphosphate (dNTP) and is expected to play a role in dNTP insertion efficiency, and (2) a cluster of three amino acids, including the roof-aa, which anchors the base of a loop, whose detailed structure dictates several important mechanistic functions. Since no X-ray structures existed for UmuC (the polymerase subunit of DNAP V) or DNAP IV, we previously built molecular models. Herein, we test the accuracy of our UmuC(V) model by investigating how amino acid replacement mutants affect lesion bypass efficiency. A ssM13 vector containing a single [+ta]-B[a]P-N(2)-dG is transformed into E. coli carrying mutations at I38, which is the roof-aa in our UmuC(V) model, and output progeny vector yield is monitored as a measure of the relative efficiency of the non-mutagenic pathway. Findings show that (1) the roof-aa is almost certainly I38, whose beta-carbon branching R-group is key for optimal activity, and (2) I38/A39/V29 form a hydrophobic cluster that anchors an important mechanistic loop, aa29-39. In addition, bypass efficiency is significantly lower both for the I38A mutation of the roof-aa and for the adjacent A39T mutation; however, the I38A/A39T double mutant is almost as active as wild-type UmuC(V), which probably reflects the following. Y-family DNAPs fall into several classes with respect to the [roof-aa/next amino acid]: one class has [isoleucine/alanine] and includes UmuC(V) and DNAP eta (from many species), while the second class has [alanine (or serine)/threonine] and includes DNAP IV, DNAP kappa (from many species), and Dpo4. Thus, the high activity of the I38A/A39T double mutant probably arises because UmuC(V) was converted from the V/eta class to the IV/kappa class with respect to the [roof-aa/next amino acid]. Structural and mechanistic aspects of these two classes of Y-family DNAPs are discussed.
Collapse
Affiliation(s)
- Kwang Young Seo
- Biology Department, Boston University, Boston, MA 02215, USA
| | | | | | | | | | | |
Collapse
|
10
|
Kropachev K, Kolbanovskii M, Cai Y, Rodríguez F, Kolbanovskii A, Liu Y, Zhang L, Amin S, Patel D, Broyde S, Geacintov NE. The sequence dependence of human nucleotide excision repair efficiencies of benzo[a]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions. J Mol Biol 2009; 386:1193-203. [PMID: 19162041 DOI: 10.1016/j.jmb.2008.12.082] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/17/2008] [Accepted: 12/22/2008] [Indexed: 10/21/2022]
Abstract
Nucleotide excision repair (NER) is a vital cellular defense system against carcinogen-DNA adducts, which, if not repaired, can initiate cancer development. The structural features of bulky DNA lesions that account for differences in NER efficiencies in mammalian cells are not well understood. In vivo, the predominant DNA adduct derived from metabolically activated benzo[a]pyrene (BP), a prominent environmental carcinogen, is the 10S (+)-trans-anti-[BP]-N(2)-dG adduct (G*), which resides in the B-DNA minor groove 5'-oriented along the modified strand. We have compared the structural distortions in double-stranded DNA, imposed by this adduct, in the different sequence contexts 5'-...CGG*C..., 5'-...CG*GC..., 5'-...CIG*C... (I is 2'-deoxyinosine), and 5'-...CG*C.... On the basis of electrophoretic mobilities, all duplexes manifest moderate bends, except the 5'-...CGG*C...duplex, which exhibits an anomalous, slow mobility attributed to a pronounced flexible kink at the site of the lesion. This kink, resulting from steric hindrance between the 5'-flanking guanine amino group and the BP aromatic rings, both positioned in the minor groove, is abolished in the 5'-...CIG*C...duplex (the 2'-deoxyinosine group, I, lacks this amino group). In contrast, the sequence-isomeric 5'-...CG*GC...duplex exhibits only a moderate bend, but displays a remarkably increased opening rate at the 5'-flanking base pair of G*, indicating a significant destabilization of Watson-Crick hydrogen bonding. The NER dual incision product yields were compared for these different sequences embedded in otherwise identical 135-mer duplexes in cell-free human HeLa extracts. The yields of excision products varied by a factor of as much as approximately 4 in the order 5'-...CG*GC...>5'...CGG*C...>or=5'...CIG*C...>or=5'-...CG*C.... Overall, destabilized Watson-Crick hydrogen bonding, manifested in the 5'-...CG*GC...duplex, elicits the most significant NER response, while the flexible kink displayed in the sequence-isomeric 5'-...CGG*C...duplex represents a less significant signal in this series of substrates. These results demonstrate that the identical lesion can be repaired with markedly variable efficiency in different local sequence contexts that differentially alter the structural features of the DNA duplex around the lesion site.
Collapse
|
11
|
Chandani S, Loechler EL. Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications. J Mol Graph Model 2008; 27:759-69. [PMID: 19188081 DOI: 10.1016/j.jmgm.2008.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/30/2008] [Accepted: 11/01/2008] [Indexed: 01/14/2023]
Abstract
Chemicals and radiation can damage DNA leading to the formation of adducts/lesions, which - if not removed by DNA repair pathways - usually block replicative DNA polymerases (DNAPs). To overcome such potentially lethal blockage, cells have lesion bypass DNAPs, which are often in the Y-Family and include several classes. One class includes human DNAP kappa and E. coli DNAP IV, and they insert dCTP in the non-mutagenic pathway opposite [+ta]-B[a]P-N(2)-dG, which is the major adduct formed by the environmental carcinogen benzo[a]pyrene. Another class includes hDNAP eta and ecDNAP V, and they insert dATP opposite [+ta]-B[a]P-N(2)-dG in the dominant G-->T mutagenic pathway. Herein we develop a hypothesis for why the IV/kappa-class preferentially does cellular dCTP insertion. On the minor groove side of the active site, Y-Family DNAPs have a cleft/hole that can be analyzed based on an analogy to a "chimney." Our models of DNAP IV show a large chimney opening from which the pyrene of [+ta]-B[a]P-N(2)-dG can protrude, which allows canonical adduct-dG:dCTP pairing. In contrast, our models of DNAP V have small chimney openings that forces adduct-dG downward in the active site such that canonical adduct-dG:dCTP pairing is not possible. Based on X-ray structures, sequence alignment and our modeled structures of Y-Family DNAPs, chimney opening size seems primarily controlled by one amino acid ("flue-handle"), which dictates whether nearby amino acids ("flue") plug the chimney or not. Based on this analysis, a correlation is apparent: the flue is closed in V/eta-class DNAPs giving small chimney openings, while the flue is open for the IV/kappa-class giving large chimney openings. Secondarily, a hypothesis is developed for why the V/eta-class might preferentially do cellular dATP insertion opposite [+ta]-B[a]P-N(2)-dG: the small chimney forces adduct-dG lower in the active site, possibly leading to catalysis using a non-canonical dNTP shape that permits syn-adenine:adduct-dG base pairing. In summary, a hypothesize is developed that the pyrene moiety of [+ta]-B[a]P-N(2)-dG protrudes from the large chimney opening of DNAP IV, thus permitting canonical dCTP:adduct-dG pairing, while the small chimney opening of DNAP V forces [+ta]-B[a]P-N(2)-dG lower down in the active site, in which syn-adenine can pair with adduct-dG via a non-canonical dNTP shape.
Collapse
Affiliation(s)
- Sushil Chandani
- Biology Department, Boston University, Boston, MA 02215, USA
| | | |
Collapse
|
12
|
Delaney JC, Essigmann JM. Biological properties of single chemical-DNA adducts: a twenty year perspective. Chem Res Toxicol 2008; 21:232-52. [PMID: 18072751 PMCID: PMC2821157 DOI: 10.1021/tx700292a] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The genome and its nucleotide precursor pool are under sustained attack by radiation, reactive oxygen and nitrogen species, chemical carcinogens, hydrolytic reactions, and certain drugs. As a result, a large and heterogeneous population of damaged nucleotides forms in all cells. Some of the lesions are repaired, but for those that remain, there can be serious biological consequences. For example, lesions that form in DNA can lead to altered gene expression, mutation, and death. This perspective examines systems developed over the past 20 years to study the biological properties of single DNA lesions.
Collapse
Affiliation(s)
- James C. Delaney
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - John M. Essigmann
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| |
Collapse
|
13
|
Chakravarti D, Venugopal D, Mailander PC, Meza JL, Higginbotham S, Cavalieri EL, Rogan EG. The role of polycyclic aromatic hydrocarbon-DNA adducts in inducing mutations in mouse skin. Mutat Res 2007; 649:161-78. [PMID: 17931959 DOI: 10.1016/j.mrgentox.2007.08.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 08/17/2007] [Accepted: 08/31/2007] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAH) form stable and depurinating DNA adducts in mouse skin to induce preneoplastic mutations. Some mutations transform cells, which then clonally expand to establish tumors. Strong clues about the mutagenic mechanism can be obtained if the PAH-DNA adducts can be correlated with both preneoplastic and tumor mutations. To this end, we studied mutagenesis in PAH-treated early preneoplastic skin (1 day after exposure) and in the induced papillomas in SENCAR mice. Papillomas were studied by PCR amplification of the H-ras gene and sequencing. For benzo[a]pyrene (BP), BP-7,8-dihydrodiol (BPDHD), 7,12-dimethylbenz[a]anthracene (DMBA) and dibenzo[a,l]pyrene (DB[a,l]P), the codon 13 (GGC to GTC) and codon 61 (CAA to CTA) mutations in papillomas corresponded to the relative levels of Gua and Ade-depurinating adducts, despite BP and BPDHD forming significant amounts of stable DNA adducts. Such a relationship was expected for DMBA and DB[a,l]P, as they formed primarily depurinating adducts. These results suggest that depurinating adducts play a major role in forming the tumorigenic mutations. To validate this correlation, preneoplastic skin mutations were studied by cloning H-ras PCR products and sequencing individual clones. DMBA- and DB[a,l]P-treated skin showed primarily A.T to G.C mutations, which correlated with the high ratio of the Ade/Gua-depurinating adducts. Incubation of skin DNA with T.G-DNA glycosylase eliminated most of these A.T to G.C mutations, indicating that they existed as G.T heteroduplexes, as would be expected if they were formed by errors in the repair of abasic sites generated by the depurinating adducts. BP and its metabolites induced mainly G.C to T.A mutations in preneoplastic skin. However, PCR over unrepaired anti-BPDE-N(2)dG adducts can generate similar mutations as artifacts of the study protocol, making it difficult to establish an adduct-mutation correlation for determining which BP-DNA adducts induce the early preneoplastic mutations. In conclusion, this study suggests that depurinating adducts play a major role in PAH mutagenesis.
Collapse
|
14
|
Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Nucleic Acids Res 2007; 35:4275-88. [PMID: 17576677 PMCID: PMC1934992 DOI: 10.1093/nar/gkm416] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We have investigated how a benzo[a]pyrene-derived N2-dG adduct, 10S(+)-trans-anti-[BP]-N2-dG ([BP]G*), is processed in a well-characterized Pol I family model replicative DNA polymerase, Bacillus fragment (BF). Experimental results are presented that reveal relatively facile nucleotide incorporation opposite the lesion, but very inefficient further extension. Computational studies follow the possible bypass of [BP]G* through the pre-insertion, insertion and post-insertion sites as BF alternates between open and closed conformations. With dG* in the normal B-DNA anti conformation, BP seriously disturbs the polymerase structure, positioning itself either deeply in the pre-insertion site or on the crowded evolving minor groove side of the modified template, consistent with a polymerase-blocking conformation. With dG* in the less prevalent syn conformation, BP causes less distortion: it is either out of the pre-insertion site or in the major groove open pocket of the polymerase. Thus, the syn conformation can account for the observed relatively easy incorporation of nucleotides, with mutagenic purines favored, opposite the [BP]G* adduct. However, with the lesion in the BF post-insertion site, more serious distortions caused by the adduct even in the syn conformation explain the very inefficient extension observed experimentally. In vivo, a switch to a potentially error-prone bypass polymerase likely dominates translesion bypass.
Collapse
Affiliation(s)
- Pingna Xu
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lida Oum
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lorena S. Beese
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Nicholas E. Geacintov
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Suse Broyde
- Department of Biology and Department of Chemistry, New York University, New York, NY and Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- *To whom correspondence should be addressed. (212)998-8231(212)995-4015
| |
Collapse
|
15
|
Meneni S, Shell SM, Zou Y, Cho BP. Conformation-specific recognition of carcinogen-DNA adduct in escherichia coli nucleotide excision repair. Chem Res Toxicol 2007; 20:6-10. [PMID: 17226921 DOI: 10.1021/tx600273h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a systematic and quantitative structure-function relationship study of the major N-[deoxyguanosin-8-yl]-2-aminofluorene adduct (AF) derived from the prototype carcinogen 2-aminofluorene and its derivatives. The AF adduct is known to exist in two distinct conformational motifs, depending upon the location of the hydrophobic fluorine moiety: major groove binding "B type" (B) conformation (AF-dGanti) and base-displaced "stacked" (S) conformation (AF-dGsyn). The AF-induced S/B conformational heterogeneity is sequence-dependent and follows a typical two-site dynamic chemical exchange. The population of S conformation decreases in the order of 3'-G > A > C > T, indicating the importance of the purine flanking bases in promoting the stacking structure. Line-shape analysis showed that the S/B interconversion energy barriers (DeltaG) are in the narrow 14-16 kcal/mol range. The energy differences of the two conformers are relatively small (<0.5 kcal/mol), suggesting a possibility for a facile adduct conformation switch in the active site of a polymerase. The S/B equilibrium modulates the efficiency of Escherichia coli UvrABC-based nucleotide excision repair (NER) in a conformation-specific manner. The 19F NMR/NER results indicate greater repair susceptibility for the base-displaced S conformer, which lacks a Watson-Crick base pair at the lesion site. These findings represent the first of its kind quantitative structure-function work relating NER activity to a specific adduct conformer and will lead to a better understanding of how bulky DNA adducts are accommodated by the repair protein.
Collapse
Affiliation(s)
- Srinivasarao Meneni
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, Rhode Island 02881, USA
| | | | | | | |
Collapse
|
16
|
Chandani S, Loechler EL. Molecular modeling benzo[a]pyrene N2-dG adducts in the two overlapping active sites of the Y-family DNA polymerase Dpo4. J Mol Graph Model 2007; 25:658-70. [PMID: 16782374 DOI: 10.1016/j.jmgm.2006.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 05/03/2006] [Accepted: 05/03/2006] [Indexed: 11/18/2022]
Abstract
The potent, ubiquitous environmental mutagen/carcinogen benzo[a]pyrene (B[a]P) induces a single major adduct [+ta]-B[a]P-N2-dG, whose bypass in most cases results in either no mutation (dCTP insertion) or a G-->T mutation (dATP insertion). Translesion synthesis (TLS) of [+ta]-B[a]P-N2-dG generally requires DNA polymerases (DNAPs) in the Y-family, which exist in cells to bypass DNA damage caused by chemicals and radiation. A molecular dynamics (MD) study is described with dCTP opposite [+ta]-B[a]P-N2-dG in Dpo4, which is the best studied Y-family DNAP from a structural point of view. Two orientations of B[a]P-N2-dG (BPmi5 and BPmi3) are considered, along with two orientations of the dCTP (AS1 and AS2), as outlined next. Based on NMR studies, the pyrene moiety of B[a]P-N2-dG is in the minor groove, when paired with dC, and can point toward either the base on the 5'-side (BPmi5) or the 3'-side (BPmi3). Based on published X-ray structures, Dpo4 appears to have two partially overlapping active sites. The architecture of active site 1 (AS1) is similar to all other families of DNAPs (e.g., the shape of the dNTP). Active site 2 (AS2), however, is non-canonical (e.g., the beta- and gamma-phosphates in AS2 are approximately where the alpha- and beta-phosphates are in AS1). In the Dpo4 models generated herein, using the BPmi3 orientation the pyrene moiety of [+ta]-B[a]P-N2-dG points toward the duplex region of the DNA, and is accommodated without distortions in AS1, but with distortions in AS2. Considering the BPmi5 orientation, the pyrene moiety points toward the ss-region of DNA in Dpo4, and sits in a hole defined by the fingers and little fingers domain ("chimney"); BPmi5 is accommodated in AS2 without significant distortions, but poorly in AS1. In summary, when dCTP is paired with [+ta]-B[a]P-N2-dG in the two overlapping active sites in Dpo4, the pyrene in the BPmi3 orientation is accommodated better in active site 1 (AS1), while the pyrene in the BPmi5 orientation is accommodated better in AS2. Finally, we discuss why Y-family DNAPs might have two catalytic active sites.
Collapse
Affiliation(s)
- Sushil Chandani
- Biology Department, Boston University, Boston, MA 02215, USA
| | | |
Collapse
|
17
|
Perlow-Poehnelt RA, Likhterov I, Wang L, Scicchitano DA, Geacintov NE, Broyde S. Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase. J Biol Chem 2006; 282:1397-408. [PMID: 17090533 DOI: 10.1074/jbc.m606769200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Y-family DNA polymerase Dpo4, from the thermophilic crenarchaeon Sulfolobus solfataricus P2, offers a valuable opportunity to investigate the effect of conformational flexibility on the bypass of bulky lesions because of its ability to function efficiently at a wide range of temperatures. Combined molecular modeling and experimental kinetic studies have been carried out for 10S-(+)-trans-anti-[BP]-N2-dG ((+)-ta-[BP]G), a lesion derived from the covalent reaction of a benzo[a]pyrene metabolite with guanine in DNA, at 55 degrees C and results compared with an earlier study at 37 degrees C (Perlow-Poehnelt, R. A., Likhterov, I., Scicchitano, D. A., Geacintov, N. E., and Broyde, S. (2004) J. Biol. Chem. 279, 36951-36961). The experimental results show that there is more overall nucleotide insertion opposite (+)-ta-[BP]G due to particularly enhanced mismatch incorporation at 55 degrees C compared with 37 degrees C. The molecular dynamics simulations suggest that mismatched nucleotide insertion opposite (+)-ta-[BP]G is increased at 55 degrees C compared with 37 degrees C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. However, with the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite (+)-ta-[BP]G by Dpo4.
Collapse
|
18
|
Meneni SR, D'Mello R, Norigian G, Baker G, Gao L, Chiarelli MP, Cho BP. Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties. Nucleic Acids Res 2006; 34:755-63. [PMID: 16449208 PMCID: PMC1356535 DOI: 10.1093/nar/gkj480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/14/2005] [Accepted: 01/14/2005] [Indexed: 11/12/2022] Open
Abstract
Circular dichroism (CD) and UV-melting experiments were conducted with 16 oligodeoxynucleotides modified by the carcinogen 2-aminofluorene, whose sequence around the lesion was varied systematically [d(CTTCTNG[AF]NCCTC), N = G, A, C, T], to gain insight into the factors that determine the equilibrium between base-displaced stacked (S) and external B-type (B) duplex conformers. Differing stabilities among the duplexes can be attributed to different populations of S and B conformers. The AF modification always resulted in sequence-dependent thermal (T(m)) and thermodynamic (-DeltaG degrees ) destabilization. The population of B-type conformers derived from eight selected duplexes (i.e. -AG*N- and -CG*N-) was inversely proportional to the -DeltaG degrees and T(m) values, which highlights the importance of carcinogen/base stacking in duplex stabilization even in the face of disrupted Watson-Crick base pairing in S-conformation. CD studies showed that the extent of the adduct-induced negative ellipticities in the 290-350 nm range is correlated linearly with -DeltaG degrees and T(m), but inversely with the population of B-type conformations. Taken together, these results revealed a unique interplay between the extent of carcinogenic interaction with neighboring base pairs and the thermodynamic properties of the AF-modified duplexes. The sequence-dependent S/B heterogeneities have important implications in understanding how arylamine-DNA adducts are recognized in nucleotide excision repair.
Collapse
Affiliation(s)
- Srinivasa Rao Meneni
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Rhijuta D'Mello
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Gregory Norigian
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Gregory Baker
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode IslandKingston, RI 02881, USA
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | - Lan Gao
- Department of Chemistry, Loyola UniversityChicago, IL 60626, USA
| | | | - Bongsup P. Cho
- To whom correspondence should be addressed at Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA. Tel: +1 401 874 5024; Fax: +1 401 874 5766;
| |
Collapse
|