201
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Tomilova JE, Kuznetsov VV, Abdurashitov MA, Netesova NA, Degtyarev SK. Recombinant DNA-methyltransferase M1.Bst19I from Bacillus stearothermophilus 19: Purification, properties, and amino acid sequence analysis. Mol Biol 2010. [DOI: 10.1134/s0026893310040163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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202
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Madhusoodanan UK, Rao DN. Diversity of DNA methyltransferases that recognize asymmetric target sequences. Crit Rev Biochem Mol Biol 2010; 45:125-45. [PMID: 20184512 DOI: 10.3109/10409231003628007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.
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203
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Li W, Liu Z, Lin H, Nie Z, Chen J, Xu X, Yao S. Label-free colorimetric assay for methyltransferase activity based on a novel methylation-responsive DNAzyme strategy. Anal Chem 2010; 82:1935-41. [PMID: 20148579 DOI: 10.1021/ac902670c] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation catalyzed by methyltransferase (MTase) is a significant epigenetic process for modulating gene expression. Traditional methods to study MTase activity require a laborious and costly DNA labeling process. In this article, we report a simple, colorimetric, and label-free methylation-responsive DNAzyme (MR-DNAzyme) strategy for MTase activity analysis. This new strategy relies on horseradish peroxidase (HRP) mimicking DNAzyme and the methylation-responsive sequence (MRS) of DNA which can be methylated and cleaved by the MTase/endonuclease coupling reaction. Methylation-induced scission of MRS would activate the DNAzyme that can catalyze the generation of a color signal for the amplified detection of methylation events. Taking Dam MTase and DpnI endonuclease as examples, we have developed two colorimetric methods based on the MR-DNAzyme strategy. The first method is to utilize an engineered hairpin-DNAzyme hybrid probe for facile turn-on detection of Dam MTase activity, with a wide linear range (6-100 U/mL) and a low detection limit (6 U/mL). Furthermore, this method could be easily expanded to profile the activity and inhibition of restriction endonuclease. The second method involves a methylation-triggered DNAzyme-based DNA machine, which achieves the ultrahigh sensitive detection of Dam MTase activity (detection limit = 0.25 U/mL) by a two-step signal amplification cascade.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
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204
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Rapti Z. Stationary solutions for a modified Peyrard-Bishop DNA model with up to third-neighbor interactions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2010; 32:209-216. [PMID: 20556463 DOI: 10.1140/epje/i2010-10618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 05/10/2010] [Indexed: 05/29/2023]
Abstract
We investigate a DNA model that takes into account stacking interactions with neighbors up to three bases away. The model is a generalization of the well-known Peyrard-Bishop (PB) model and is motivated by studies that suggest that nearest-neighbor models for base-pair interaction in a DNA chain might not be enough to capture the mechanism and dynamics of DNA base-pair opening. We study stationary solutions of the modified model and investigate their stability. A comparison with the PB model reveals that under a wide range of parameter values the main characteristics of the original model --such as the hyperbolicity of the equilibrium at the origin-- are preserved, but new types of stationary solutions emerge.
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Affiliation(s)
- Z Rapti
- Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL 61801-2975, USA.
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205
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Rodríguez López CM, Wetten AC, Wilkinson MJ. Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. THE NEW PHYTOLOGIST 2010; 186:856-868. [PMID: 20406408 DOI: 10.1111/j.1469-8137.2010.03242.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
*Relatively little is known about the timing of genetic and epigenetic forms of somaclonal variation arising from callus growth. We surveyed for both types of change in cocoa (Theobroma cacao) plants regenerated from calli of various ages, and also between tissues from the source trees. *For genetic change, we used 15 single sequence repeat (SSR) markers from four source trees and from 233 regenerated plants. For epigenetic change, we used 386 methylation-sensitive amplified polymorphism (MSAP) markers on leaf and explant (staminode) DNA from two source trees and on leaf DNA from 114 regenerants. *Genetic variation within source trees was limited to one slippage mutation in one leaf. Regenerants were far more variable, with 35% exhibiting at least one mutation. Genetic variation initially accumulated with culture age but subsequently declined. MSAP (epigenetic) profiles diverged between leaf and staminode samples from source trees. Multivariate analysis revealed that leaves from regenerants occupied intermediate eigenspace between leaves and staminodes of source plants but became progressively more similar to source tree leaves with culture age. *Statistical analysis confirmed this rather counterintuitive finding that leaves of 'late regenerants' exhibited significantly less genetic and epigenetic divergence from source leaves than those exposed to short periods of callus growth.
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Affiliation(s)
- Carlos M Rodríguez López
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University Penglais, Aberystwyth, Wales, UK, SY23 3DA
| | - Andrew C Wetten
- School of Biological Sciences, Harborne Building, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AS, UK
| | - Michael J Wilkinson
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University Penglais, Aberystwyth, Wales, UK, SY23 3DA
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206
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Hoffmann MH, Trembleau S, Muller S, Steiner G. Nucleic acid-associated autoantigens: pathogenic involvement and therapeutic potential. J Autoimmun 2009; 34:J178-206. [PMID: 20031372 DOI: 10.1016/j.jaut.2009.11.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Autoimmunity to ubiquitously expressed macromolecular nucleic acid-protein complexes such as the nucleosome or the spliceosome is a characteristic feature of systemic autoimmune diseases. Disease-specificity and/or association with clinical features of some of these autoimmune responses suggest pathogenic involvement which, however, has been proven in only a few cases so far. Although the mechanisms leading to autoimmunity against nucleic acid-containing complexes are still far from being fully understood, there is increasing experimental evidence that the nucleic acid component may act as a co-stimulator or adjuvans via activation of nucleic acid-binding receptor systems such as Toll-like receptors in antigen-presenting cells. Dysregulated apoptosis and inappropriate stimulation of nucleic acid-sensing receptors may lead to loss of tolerance against the protein components of such complexes, activation of autoreactive T cells and formation of autoantibodies. This has been demonstrated to occur in systemic lupus erythematosus and seems to represent a general mechanism that may be crucial for the development of systemic autoimmune diseases. This review provides a comprehensive overview of the most thoroughly-characterized nucleic acid-associated autoantigens, describing their structure and biological function, as well as the nature and pathogenic importance of the reactivities directed against them. Furthermore, recent advances in immunotherapy such as antigen-specific approaches targeted at nucleic acid-binding antigens are discussed.
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Affiliation(s)
- Markus H Hoffmann
- Division of Rheumatology, Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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207
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The physiological and pathophysiological role of PRMT1-mediated protein arginine methylation. Pharmacol Res 2009; 60:466-74. [DOI: 10.1016/j.phrs.2009.07.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 07/20/2009] [Accepted: 07/21/2009] [Indexed: 11/22/2022]
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208
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Kirsanova OV, Cherepanova NA, Gromova ES. Inhibition of C5-cytosine-DNA-methyltransferases. BIOCHEMISTRY (MOSCOW) 2009; 74:1175-86. [DOI: 10.1134/s0006297909110017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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209
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Coffin SR, Reich NO. Escherichia coli DNA adenine methyltransferase: intrasite processivity and substrate-induced dimerization and activation. Biochemistry 2009; 48:7399-410. [PMID: 19580332 DOI: 10.1021/bi9008006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylation of GATC sites in Escherichia coli by DNA adenine methyltransferase (EcoDam) is essential for proper DNA replication timing, gene regulation, and mismatch repair. The low cellular concentration of EcoDam and the high number of GATC sites in the genome (approximately 20000) support the reliance on methylation efficiency-enhancing strategies such as extensive intersite processivity. Here, we present evidence that EcoDam has evolved other unique mechanisms of activation not commonly observed with restriction-modification methyltransferases. EcoDam dimerizes on short, synthetic DNA, resulting in enhanced catalysis; however, dimerization is not observed on large genomic DNA where the potential for intersite processive methylation precludes any dimerization-dependent activation. An activated form of the enzyme is apparent on large genomic DNA and can also be achieved with high concentrations of short, synthetic substrates. We suggest that this activation is inherent on polymeric DNA where either multiple GATC sites are available for methylation or the partitioning of the enzyme onto nonspecific DNA is favored. Unlike other restriction-modification methyltransferases, EcoDam carries out intrasite processive catalysis whereby the enzyme-DNA complex methylates both strands of an unmethylated GATC site prior to dissociation from the DNA. This occurs with short 21 bp oligonucleotides and is highly dependent upon salt concentrations. Kinetic modeling which invokes enzyme activation by both dimerization and excess substrate provides mechanistic insights into key regulatory checkpoints for an enzyme involved in multiple, diverse biological pathways.
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Affiliation(s)
- Stephanie R Coffin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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210
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Sufrin JR, Finckbeiner S, Oliver CM. Marine-derived metabolites of S-adenosylmethionine as templates for new anti-infectives. Mar Drugs 2009; 7:401-34. [PMID: 19841722 PMCID: PMC2763108 DOI: 10.3390/md7030401] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/20/2009] [Accepted: 08/24/2009] [Indexed: 12/24/2022] Open
Abstract
S-Adenosylmethionine (AdoMet) is a key biochemical co-factor whose proximate metabolites include methylated macromolecules (e.g., nucleic acids, proteins, phospholipids), methylated small molecules (e.g., sterols, biogenic amines), polyamines (e.g., spermidine, spermine), ethylene, and N-acyl-homoserine lactones. Marine organisms produce numerous AdoMet metabolites whose novel structures can be regarded as lead compounds for anti-infective drug design.
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Affiliation(s)
- Janice R. Sufrin
- Department of Pharmacology and Therapeutics, Grace Cancer Drug Center, Roswell Park Cancer Institute, Buffalo, New York, NY, USA; E-Mails: (S.F.); (C.O.)
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211
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Randall GL, Zechiedrich L, Pettitt BM. In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Res 2009; 37:5568-77. [PMID: 19586933 PMCID: PMC2760789 DOI: 10.1093/nar/gkp556] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from single-molecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress.
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212
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Cytosine-5-methyltransferases add aldehydes to DNA. Nat Chem Biol 2009; 5:400-2. [PMID: 19430486 DOI: 10.1038/nchembio.172] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 04/03/2009] [Indexed: 12/31/2022]
Abstract
Targeted methylation of cytosine residues by S-adenosylmethionine-dependent DNA methyltransferases modulates gene expression in vertebrates. Here we show that cytosine-5-methyltransferases catalyze reversible covalent addition of exogenous aliphatic aldehydes to their target residues in DNA, thus yielding corresponding 5-hydroxyalkylcytosines. Such atypical enzymatic reactions with non-cofactor-like substrates open new ways for sequence-specific derivatization of DNA and demonstrate enzymatic exchange of 5-hydroxymethyl groups on cytosine in support of an oxidative mechanism of DNA demethylation.
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213
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Liu B, Gu LP, Xing CP, Ha YD, Gao ZF, Su QJ, Zhang JH, Qian Z, Dong L. Clinical significance and association of caveolin-1 and Dnmt1 gene with carcinogenesis, development of gastric carcinomas. Shijie Huaren Xiaohua Zazhi 2009; 17:1561-1566. [DOI: 10.11569/wcjd.v17.i15.1561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of caveolin-1and Dnmt1 genes in normal gastric mucosa and gastric carcinoma, and to detect methylation status of CpG island of caveolin-1 gene promoter region located in exon 1 and its clinical significance in gastric carcinoma.
METHODS: Methylation status of caveolin-1 gene in 60 gastric carcinoma cases and 14 normal gastric tissues was detected using Methylation-specific PCR (MSP). SP immunohistochemcal method and in site hybridization (ISH) were used to detect the expression of caveolin-1 protein and Dnmt1 protein and mRNA.
RESULTS: The methylation rate of the 5' CpG island of caveolin-1 gene was 0% in 14 normal gastric tissues, and 73.3% in 60 gastric carcinoma cases. There was significant difference between two groups (P < 0.005). Methylation status of caveolin-1 gene was related to the patient's age. The positive rates of caveolin-1 protein, Dnmt1 protein and mRNA were 30%, 63.3% and 53.3% in 60 gastric carcinoma cases.
CONCLUSION: The methylation and inactivation of caveolin-1 gene leads to carcinogenesis and development of gastric carcinomas by the function of Dnmt1 gene.
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214
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Yang CG, Garcia K, He C. Damage detection and base flipping in direct DNA alkylation repair. Chembiochem 2009; 10:417-23. [PMID: 19145606 DOI: 10.1002/cbic.200800580] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
THE FOREIGN LESION: The mechanistic questions for DNA base damage detection by repair proteins are discussed in this Minireview. Repair proteins could either probe and locate a weakened base pair that results from base damage, or passively capture an extrahelical base lesion in the first step of damage searching on double-stranded DNA. How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood.To remove a few damaged bases efficiently from the context of the entire genome, the DNA base repair proteins rely on remarkably specific detection mechanisms to locate base lesions. This efficient molecular recognition event inside cells has been extensively studied with various structural and biochemical tools. These studies suggest that DNA base damage can be located by repair proteins by using two mechanisms: a repair protein can probe and detect a weakened base pair that results from mutagenic or cytotoxic base damage; alternatively, a protein can passively capture and stabilize an extrahelical base lesion. Our chemical and structural studies on the direct DNA repair proteins hAGT, C-Ada and ABH2 suggest that these proteins search for weakened base pairs in their first step of damage searching. We have also discovered a very unique base-flipping mechanism used by the DNA repair protein AlkB. This protein distorts DNA and favors single stranded DNA (ssDNA) substrates over double-stranded (dsDNA) ones. Potentially, it locates base lesions in dsDNA by imposing a constraint that targets less rigid regions of the duplex DNA. The exact mechanism of how AlkB and related proteins search for damage in ssDNA and dsDNA still awaits further studies.
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Affiliation(s)
- Cai-Guang Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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215
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Theoretical analysis of disruptions in DNA minicircles. Biophys J 2009; 96:1341-9. [PMID: 19217852 DOI: 10.1016/j.bpj.2008.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 11/13/2008] [Indexed: 11/20/2022] Open
Abstract
Under sufficient bending stress, which appears in DNA minicircles and small DNA loops, the double helix experiences local disruptions of its regular structure. We developed a statistical-mechanical treatment of the disruptions in DNA minicircles, studied experimentally by Du et al. The model of disruptions used in our Monte Carlo simulation of minicircle conformations specifies these conformations by three parameters: DNA bend angle at the disruption, theta(d); local DNA unwinding caused by the disruption; and the free energy associated with the disruption in the unstressed double helix, G(d). The model is applicable to any structural type of disruption, kinks or opening of single basepairs. The simulation shows that accounting for both torsional and bending deformation associated with the disruptions is very important for proper analysis. We obtained a relationship between values of G(d) and theta(d) under which the simulation results are compatible with the experimental data. The relationship suggests that the free energy of basepair opening, which includes flipping out both bases, is significantly higher than the generally accepted value. The model is also applied to the analysis of j-factors of very short DNA fragments.
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216
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Mallajosyula SS, Gupta A, Pati SK. Fluctuations at the Base Pair Level Effecting Charge Transfer in DNA. J Phys Chem A 2009; 113:3955-62. [DOI: 10.1021/jp8101942] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sairam S. Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Ashutosh Gupta
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Swapan K. Pati
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
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217
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Hashimoto H, Horton JR, Zhang X, Cheng X. UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics 2009; 4:8-14. [PMID: 19077538 DOI: 10.4161/epi.4.1.7370] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying appropriate markers (on the tails of H3 and hemimethylated CpG sites) ready to be assembled into a nucleosome after replication.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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218
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de Marco G, Várnai P. Molecular simulation of conformational transitions in biomolecules using a combination of structure-based potential and empirical valence bond theory. Phys Chem Chem Phys 2009; 11:10694-700. [DOI: 10.1039/b917109f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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219
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Abreu PA, Dellamora-Ortiz G, Leão-Ferreira LR, Gouveia M, Braggio E, Zalcberg I, Santos DO, Bourguinhon S, Cabral LM, Rodrigues CR, Castro HC. DNA methylation: a promising target for the twenty-first century. Expert Opin Ther Targets 2008; 12:1035-47. [PMID: 18620524 DOI: 10.1517/14728222.12.8.1035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Over the last few years DNA methylation and its involvement in diseases such as cancer has become of great interest for applied research. Since reversal of aberrant DNA methylation may influence the behavior of tumors, the methylation of DNA CpG sites is a potential target for the development of inhibitors for use in cancer treatment. OBJECTIVE/METHODS We briefly review the structural and mechanistic features of DNA methylation, including a structural analysis of the three main human DNA methyltransferases and some (pre)clinical results. RESULTS/CONCLUSION Despite side effects, data obtained to date still support the vision that DNA-methylation, possibly associated with the use of histone deacetylases (HDACs) and/or artificial transcription factors (ATFs), is a promising target for improving anticancer therapy in the 21st century.
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Affiliation(s)
- Paula A Abreu
- Federal Fluminense University, Biology Institute, Department of Celular and Molecular Biology, CEP 24020-150 Niterói, Rio de Janeiro, Brazil
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220
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The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 2008; 455:826-9. [PMID: 18772888 DOI: 10.1038/nature07280] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 07/23/2008] [Indexed: 12/11/2022]
Abstract
Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for maintenance methylation by interacting with DNA nucleotide methyltransferase 1 (DNMT1), the maintenance methyltransferase, and with hemimethylated CpG, the substrate for DNMT1 (refs 1 and 2). Here we present the crystal structure of the SET and RING-associated (SRA) domain of mouse UHRF1 in complex with DNA containing a hemimethylated CpG site. The DNA is contacted in both the major and minor grooves by two loops that penetrate into the middle of the DNA helix. The 5-methylcytosine has flipped completely out of the DNA helix and is positioned in a binding pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5-methylcytosine. Hence, UHRF1 contains a previously unknown DNA-binding module and is the first example of a non-enzymatic, sequence-specific DNA-binding protein domain to use the base flipping mechanism to interact with DNA.
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221
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Carpenter MA, Bhagwat AS. DNA base flipping by both members of the PspGI restriction-modification system. Nucleic Acids Res 2008; 36:5417-25. [PMID: 18718929 PMCID: PMC2532716 DOI: 10.1093/nar/gkn528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The PspGI restriction–modification system recognizes the sequence CCWGG. R.PspGI cuts DNA before the first C in the cognate sequence and M.PspGI is thought to methylate N4 of one of the cytosines in the sequence. M.PspGI enhances fluorescence of 2-aminopurine in DNA if it replaces the second C in the sequence, while R.PspGI enhances fluorescence when the fluorophore replaces adenine in the central base pair. This strongly suggests that the methyltransferase flips the second C in the recognition sequence, while the endonuclease flips both bases in the central base pair out of the duplex. M.PspGI is the first N4-cytosine MTase for which biochemical evidence for base flipping has been presented. It is also the first type IIP methyltransferase whose catalytic activity is strongly stimulated by divalent metal ions. However, divalent metal ions are not required for its base-flipping activity. In contrast, these ions are required for both base flipping and catalysis by the endonuclease. The two enzymes have similar temperature profiles for base flipping and optimal flipping occurs at temperatures substantially below the growth temperature of the source organism for PspGI and for the catalytic activity of endonuclease. We discuss the implications of these results for DNA binding by these enzymes and their evolutionary origin.
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Affiliation(s)
- Michael A Carpenter
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
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222
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Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36:4941-55. [PMID: 18653524 PMCID: PMC2528173 DOI: 10.1093/nar/gkn473] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein···DNA recognition in the ‘κB’ family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate κB site recognized by the proto-oncogenic ‘c-Rel’ subfamily of NF-κB transcription factors. Simulations of the κB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation—including a peculiar state arising at ≈0.7 μs and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at ≈1 μs) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-κB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
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Affiliation(s)
- Cameron Mura
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093-0365, USA.
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223
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Morita R, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R. Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8. Proteins 2008; 73:259-64. [DOI: 10.1002/prot.22158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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224
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Pederson K, Meints GA, Shajani Z, Miller PA, Drobny GP. Backbone dynamics in the DNA HhaI protein binding site. J Am Chem Soc 2008; 130:9072-9. [PMID: 18570423 DOI: 10.1021/ja801243d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dynamics of the phosphodiester backbone in the [5'-GCGC-3'] 2 moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5' methylene group of nucleotides within the [5'-GCGC-3'] 2 moiety indicated that all of these positions are structurally flexible. Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone and furanose ring of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through not only a loss of mobility but also a change of direction of motion. These NMR data indicate that the [5'-GCGC-3'] 2 moiety is dynamic, with the largest amplitude motions occurring nearest the methylation site. The change of orientation of this moiety in DNA upon methylation may make the molecule less amenable to binding to the HhaI endonuclease.
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Affiliation(s)
- Kari Pederson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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225
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Rutherford K, Le Trong I, Stenkamp R, Parson W. Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase. J Mol Biol 2008; 380:120-30. [DOI: 10.1016/j.jmb.2008.04.040] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 04/14/2008] [Accepted: 04/16/2008] [Indexed: 11/29/2022]
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226
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Subcellular localization and RNA interference of an RNA methyltransferase gene from silkworm, Bombyx mori. Comp Funct Genomics 2008:571023. [PMID: 18509492 PMCID: PMC2396236 DOI: 10.1155/2008/571023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 03/17/2008] [Indexed: 11/24/2022] Open
Abstract
RNA methylation, which is a form of posttranscriptional modification, is catalyzed by S-adenosyl-L-methionone-dependent RNA methyltransterases (RNA MTases). We have identified a novel silkworm gene, BmRNAMTase, containing a 369-bp open reading frame that encodes a putative protein containing 122 amino acid residues and having a molecular weight of 13.88 kd. We expressed a recombinant His-tagged BmRNAMTase in E. coli BL21 (DE3), purified the fusion protein by metal-chelation affinity chromatography, and injected a New Zealand rabbit with the purified protein to generate anti-BmRNAMTase polyclonal antibodies. Immunohistochemistry revealed that BmRNAMTase is abundant in the cytoplasm of Bm5 cells. In addition, using RNA interference to reduce the intracellular activity and content of BmRNAMTase, we determined that this cytoplasmic RNA methyltransferase may be involved in preventing cell death in the silkworm.
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227
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Coffin SR, Reich NO. Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences. J Biol Chem 2008; 283:20106-16. [PMID: 18502761 DOI: 10.1074/jbc.m802502200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli DNA adenine methyltransferase (EcoDam) methylates the N-6 position of the adenine in the sequence 5'-GATC-3' and plays vital roles in gene regulation, mismatch repair, and DNA replication. It remains unclear how the small number of critical GATC sites involved in the regulation of replication and gene expression are differentially methylated, whereas the approximately 20,000 GATCs important for mismatch repair and dispersed throughout the genome are extensively methylated. Our prior work, limited to the pap regulon, showed that methylation efficiency is controlled by sequences immediately flanking the GATC sites. We extend these studies to include GATC sites involved in diverse gene regulatory and DNA replication pathways as well as sites previously shown to undergo differential in vivo methylation but whose function remains to be assigned. EcoDam shows no change in affinity with variations in flanking sequences derived from these sources, but methylation kinetics varied 12-fold. A-tracts immediately adjacent to the GATC site contribute significantly to these differences in methylation kinetics. Interestingly, only when the poly(A) is located 5' of the GATC are the changes in methylation kinetics revealed. Preferential methylation is obscured when two GATC sites are positioned on the same DNA molecule, unless both sites are surrounded by large amounts of nonspecific DNA. Thus, facilitated diffusion and sequences immediately flanking target sites contribute to higher order specificity for EcoDam; we suggest that the diverse biological roles of the enzyme are in part regulated by these two factors, which may be important for other enzymes that sequence-specifically modify DNA.
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Affiliation(s)
- Stephanie R Coffin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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228
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Daujotyte D, Liutkeviciūte Z, Tamulaitis G, Klimasauskas S. Chemical mapping of cytosines enzymatically flipped out of the DNA helix. Nucleic Acids Res 2008; 36:e57. [PMID: 18450817 PMCID: PMC2425465 DOI: 10.1093/nar/gkn200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in protein-DNA complexes. The generality of this method was verified with two other DNA cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein-DNA complexes.
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Affiliation(s)
- Dalia Daujotyte
- Institute of Biotechnology, Graiciūno 8, LT-02241 Vilnius, Lithuania
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229
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Abstract
The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural and mechanistic approaches have provided glimpses into this enigmatic molecular recognition event in several systems. A ubiquitous feature of these essential reactions is the binding of the damaged base in an extrahelical binding mode. The reaction pathway by which this remarkable extrahelical state is achieved is of great interest and even more debate.
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Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe St., WBS 314, Baltimore, MD 21205, USA.
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230
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Youngblood B, Bonnist E, Dryden DTF, Jones AC, Reich NO. Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies. Nucleic Acids Res 2008; 36:2917-25. [PMID: 18385156 PMCID: PMC2396439 DOI: 10.1093/nar/gkn131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
M.EcoRI, a bacterial sequence-specific S-adenosyl-l-methionine-dependent DNA methyltransferase, relies on a complex conformational mechanism to achieve its remarkable specificity, including DNA bending, base flipping and intercalation into the DNA. Using transient fluorescence and fluorescence lifetime studies with cognate and noncognate DNA, we have characterized several reaction intermediates involving the WT enzyme. Similar studies with a bending-impaired, enhanced-specificity M.EcoRI mutant show minimal differences with the cognate DNA, but significant differences with noncognate DNA. These results provide a plausible explanation of the way in which destabilization of reaction intermediates can lead to changes in substrate specificity.
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Affiliation(s)
- Ben Youngblood
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106-9510, USA
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231
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Orozco M, Noy A, Pérez A. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr Opin Struct Biol 2008; 18:185-93. [PMID: 18304803 DOI: 10.1016/j.sbi.2008.01.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 12/05/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
Abstract
The recent use of molecular dynamics (MD) simulations to study flexibility of nucleic acids has been reviewed from an analysis of the publications appearing in the past two years (from 2005 till date). Despite the existence of some unsolved problems in the methodologies, these years have been witness to major advances in the field. Based on a critical review of the most recent contributions, excitement exists on the expected evolution of the field in the next years.
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Affiliation(s)
- Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
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232
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Cheng X, Blumenthal RM. Mammalian DNA methyltransferases: a structural perspective. Structure 2008; 16:341-50. [PMID: 18334209 PMCID: PMC2597194 DOI: 10.1016/j.str.2008.01.004] [Citation(s) in RCA: 269] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 01/15/2008] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
The methylation of mammalian DNA, primarily at CpG dinucleotides, has long been recognized to play a major role in controlling gene expression, among other functions. Given their importance, it is surprising how many basic questions remain to be answered about the proteins responsible for this methylation and for coordination with the parallel chromatin-marking system that operates at the level of histone modification. This article reviews recent studies on, and discusses the resulting biochemical and structural insights into, the DNA nucleotide methyltransferase (Dnmt) proteins 1, 3a, 3a2, 3b, and 3L.
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Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence: (X.C.), (R.M.B.)
| | - Robert M. Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics and Proteomics/Genomics, University of Toledo Health Science Campus, Toledo, OH 43614, USA
- Correspondence: (X.C.), (R.M.B.)
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233
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Feder M, Purta E, Koscinski L, Čubrilo S, Maravic Vlahovicek G, Bujnicki J. Virtual Screening and Experimental Verification to Identify Potential Inhibitors of the ErmC Methyltransferase Responsible for Bacterial Resistance against Macrolide Antibiotics. ChemMedChem 2008; 3:316-22. [DOI: 10.1002/cmdc.200700201] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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234
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Shigdel U, Zhang J, He C. Diazirine-Based DNA Photo-Cross-Linking Probes for the Study of Protein–DNA Interactions. Angew Chem Int Ed Engl 2008; 47:90-3. [DOI: 10.1002/anie.200703625] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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235
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Shigdel U, Zhang J, He C. Diazirine-Based DNA Photo-Cross-Linking Probes for the Study of Protein–DNA Interactions. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200703625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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236
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A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 2007; 5:69-74. [PMID: 18084297 DOI: 10.1038/nmeth1148] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 11/16/2007] [Indexed: 11/08/2022]
Abstract
Despite the fact that many genomes have been decoded, proteome chips comprising individually purified proteins have been reported only for budding yeast, mainly because of the complexity and difficulty of high-throughput protein purification. To facilitate proteomics studies in prokaryotes, we have developed a high-throughput protein purification protocol that allowed us to purify 4,256 proteins encoded by the Escherichia coli K12 strain within 10 h. The purified proteins were then spotted onto glass slides to create E. coli proteome chips. We used these chips to develop assays for identifying proteins involved in the recognition of potential base damage in DNA. By using a group of DNA probes, each containing a mismatched base pair or an abasic site, we found a small number of proteins that could recognize each type of probe with high affinity and specificity. We further evaluated two of these proteins, YbaZ and YbcN, by biochemical analyses. The assembly of libraries containing DNA probes with specific modifications and the availability of E. coli proteome chips have the potential to reveal important interactions between proteins and nucleic acids that are time-consuming and difficult to detect using other techniques.
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237
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Jurkowski TP, Anspach N, Kulishova L, Nellen W, Jeltsch A. The M.EcoRV DNA-(Adenine N6)-methyltransferase Uses DNA Bending for Recognition of an Expanded EcoDam Recognition Site. J Biol Chem 2007; 282:36942-52. [DOI: 10.1074/jbc.m706933200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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238
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Shieh FK, Reich NO. AdoMet-dependent Methyl-transfer: Glu119 Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI. J Mol Biol 2007; 373:1157-68. [PMID: 17897676 DOI: 10.1016/j.jmb.2007.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Revised: 07/17/2007] [Accepted: 08/03/2007] [Indexed: 11/21/2022]
Abstract
The role of Glu119 in S-adenosyl-L-methionine-dependent DNA methyltransferase M.HhaI-catalyzed DNA methylation was studied. Glu119 belongs to the highly conserved Glu/Asn/Val motif found in all DNA C5-cytosine methyltransferases, and its importance for M.HhaI function remains untested. We show that formation of the covalent intermediate between Cys81 and the target cytosine requires Glu119, since conversion to Ala, Asp or Gln lowers the rate of methyl transfer 10(2)-10(6) fold. Further, unlike the wild-type M.HhaI, these mutants are not trapped by the substrate in which the target cytosine is replaced with the mechanism-based inhibitor 5-fluorocytosine. The DNA binding affinity for the Glu119Asp mutant is decreased 10(3)-fold. Thus, the ability of the enzyme to stabilize the extrahelical cytosine is coupled directly to tight DNA binding. The structures of the ternary protein/DNA/AdoHcy complexes for both the Glu119Ala and Glu119Gln mutants (2.70 A and 2.75 A, respectively) show that the flipped base is positioned nearly identically with that observed in the wild-type M.HhaI complex. A single water molecule in the Glu119Ala structure between Ala119 and the extrahelical cytosine N3 is lacking in the Glu119Gln and wild-type M.HhaI structures, and most likely accounts for this mutant's partial activity. Glu119 has essential roles in activating the target cytosine for nucleophilic attack and contributes to tight DNA binding.
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Affiliation(s)
- Fa-Kuen Shieh
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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239
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Walbott H, Auxilien S, Grosjean H, Golinelli-Pimpaneau B. The Carboxyl-terminal Extension of Yeast tRNA m5C Methyltransferase Enhances the Catalytic Efficiency of the Amino-terminal Domain. J Biol Chem 2007; 282:23663-71. [PMID: 17567576 DOI: 10.1074/jbc.m703818200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The human tRNA m(5)C methyltransferase is a potential target for anticancer drugs because it is a novel downstream target of the proto-oncogene myc, mediating Myc-induced cell proliferation. Sequence comparisons of RNA m(5)C methyltransferases indicate that the eukaryotic enzymes possess, in addition to a conserved catalytic domain, a large characteristic carboxyl-terminal extension. To gain insight into the function of this additional domain, the modular architecture of the yeast tRNA m(5)C methyltransferase orthologue, Trm4p, was studied. The yeast enzyme catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to carbon 5 of cytosine at different positions depending on the tRNAs. By limited proteolysis, Trm4p was shown to be composed of two domains that have been separately produced and purified. Here we demonstrate that the aminoterminal domain, encompassing the active site, binds tRNA with similar affinity as the whole enzyme but shows low catalytic efficiency. The carboxyl-terminal domain displays only weak affinity for tRNA. It is not required for m(5)C formation and does not appear to contribute to substrate specificity. However, it enhances considerably the catalytic efficiency of the amino-terminal domain.
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Affiliation(s)
- Hélène Walbott
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS Bâtiment 34, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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240
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Oruganti S, Zhang Y, Li H, Robinson H, Terns MP, Terns RM, Yang W, Li H. Alternative Conformations of the Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility in Box C/D RNPs. J Mol Biol 2007; 371:1141-50. [PMID: 17617422 DOI: 10.1016/j.jmb.2007.06.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 06/05/2007] [Accepted: 06/12/2007] [Indexed: 12/31/2022]
Abstract
The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.
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Affiliation(s)
- Sri Oruganti
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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241
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Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V. Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res 2007; 35:4792-9. [PMID: 17617640 PMCID: PMC1950555 DOI: 10.1093/nar/gkm513] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI–DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.
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Affiliation(s)
- Gintautas Tamulaitis
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Mindaugas Zaremba
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Roman H. Szczepanowski
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Matthias Bochtler
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
- *To whom correspondence should be addressed.+370 5 2602108+370 5 2602116
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242
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Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res 2007; 35:4264-74. [PMID: 17576679 PMCID: PMC1934991 DOI: 10.1093/nar/gkm411] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA methyltransferases (MTases) are important players in the biogenesis and regulation of the ribosome, the cellular machine for protein synthesis. RsmC is a MTase that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to G1207 of 16S rRNA. Mutations of G1207 have dominant lethal phenotypes in Escherichia coli, underscoring the significance of this modified nucleotide for ribosome function. Here we report the crystal structure of E. coli RsmC refined to 2.1 A resolution, which reveals two homologous domains tandemly duplicated within a single polypeptide. We characterized the function of the individual domains and identified key residues involved in binding of rRNA and SAM, and in catalysis. We also discovered that one of the domains is important for the folding of the other. Domain duplication and subfunctionalization by complementary degeneration of redundant functions (in particular substrate binding versus catalysis) has been reported for many enzymes, including those involved in RNA metabolism. Thus, RsmC can be regarded as a model system for functional streamlining of domains accompanied by the development of dependencies concerning folding and stability.
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Affiliation(s)
- S. Sunita
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Elzbieta Purta
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Malgorzata Durawa
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Karolina L. Tkaczuk
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - J. Swaathi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Janusz M. Bujnicki
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - J. Sivaraman
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
- *To whom correspondence should be addressed. +65 65161163+65 67792486
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243
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Schubert HL, Blumenthal RM, Cheng X. 1 Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases. Enzymes 2007; 24:3-28. [PMID: 26718035 DOI: 10.1016/s1874-6047(06)80003-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
S-adenosyl-l-methionine (AdoMet) dependent methyltransferases (MTases) are involved in biosynthesis, signal transduction, protein repair, chromatin regulation, and gene silencing. Five different structural folds (designated I through V) have been described that bind AdoMet and catalyze methyltransfer to diverse substrates, although the great majority of known MTases have the Class I fold. Even within a particular MTase class the amino-acid sequence similarity can be as low as 10%. Thus, the structural and catalytic requirements for methyltransfer from AdoMet appear to be remarkably flexible. MTases that act on protein substrates have been found to date among three of the five structural classes (I, the classical fold; III, the corrin MTase fold; and V, the SET fold). "There are many paths to the top of the mountain, but the view is always the same."-Chinese proverb The Columbia World of Quotations, New York, Columbia University Press, 1996.
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Affiliation(s)
- Heidi L Schubert
- Department of Biochemistry University of Utah 15 North Medical DriveEast Salt Lake City, UT 84112, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics and Proteomics/Genomics Medical University of Ohio 3000 Arlington Avenue Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry Emory University School of Medicine 1510 Clifton Road Northeast Atlanta, GA 30322, USA
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244
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Liebert K, Horton JR, Chahar S, Orwick M, Cheng X, Jeltsch A. Two alternative conformations of S-adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle. J Biol Chem 2007; 282:22848-55. [PMID: 17545164 DOI: 10.1074/jbc.m700926200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the Escherichia coli DNA adenine methyltransferase (EcoDam) in a binary complex with the cofactor product S-adenosyl-L-homocysteine (AdoHcy) unexpectedly showed the bound AdoHcy in two alternative conformations, extended or folded. The extended conformation represents the catalytically competent conformation, identical to that of EcoDam-DNA-AdoHcy ternary complex. The folded conformation prevents catalysis, because the homocysteine moiety occupies the target Ade binding pocket. The largest difference between the binary and ternary structures is in the conformation of the N-terminal hexapeptide ((9)KWAGGK(14)). Cofactor binding leads to a strong change in the fluorescence of Trp(10), whose indole ring approaches the cofactor by 3.3A(.) Stopped-flow kinetics and AdoMet cross-linking studies indicate that the cofactor prefers binding to the enzyme after preincubation with DNA. In the presence of DNA, AdoMet binding is approximately 2-fold stronger than AdoHcy binding. In the binary complex the side chain of Lys(14) is disordered, whereas Lys(14) stabilizes the active site in the ternary complex. Fluorescence stopped-flow experiments indicate that Lys(14) is important for EcoDam binding of the extrahelical target base into the active site pocket. This suggests that the hexapeptide couples specific DNA binding (Lys(9)), AdoMet binding (Trp(10)), and insertion of the flipped target base into the active site pocket (Lys(14)).
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Affiliation(s)
- Kirsten Liebert
- Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
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245
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Lenz T, Bonnist EYM, Pljevaljcić G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E. 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence. J Am Chem Soc 2007; 129:6240-8. [PMID: 17455934 DOI: 10.1021/ja069366n] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.
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Affiliation(s)
- Thomas Lenz
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
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246
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Jeltsch A, Jurkowska RZ, Jurkowski TP, Liebert K, Rathert P, Schlickenrieder M. Application of DNA methyltransferases in targeted DNA methylation. Appl Microbiol Biotechnol 2007; 75:1233-40. [PMID: 17431611 DOI: 10.1007/s00253-007-0966-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 03/21/2007] [Accepted: 03/21/2007] [Indexed: 12/31/2022]
Abstract
DNA methylation is an essential epigenetic modification. In bacteria, it is involved in gene regulation, DNA repair, and control of cell cycle. In eukaryotes, it acts in concert with other epigenetic modifications to regulate gene expression and chromatin structure. In addition to these biological roles, DNA methyltransferases have several interesting applications in biotechnology, which are the main focus of this review, namely, (1) in vivo footprinting: as several bacterial DNA methyltransferases cannot methylate DNA bound to histone proteins, the pattern of DNA methylation after expression of DNA methyltransferases in the cell allows determining nucleosome positioning; (2) mapping the binding specificity of DNA binding proteins: after fusion of a DNA methyltransferase to a DNA-binding protein and expression of the fusion protein in a cell, the DNA methylation pattern reflects the DNA-binding specificity of the DNA-binding protein; and (3) targeted gene silencing: after fusion of a DNA methyltransferase to a suitable DNA-binding domain, DNA methylation can be directed to promoter regions of target genes. Thereby, gene expression can be switched off specifically, efficiently, and stably, which has a number of potential medical applications.
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Affiliation(s)
- Albert Jeltsch
- Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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247
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Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem 2007; 282:5880-7. [PMID: 17189261 PMCID: PMC2885967 DOI: 10.1074/jbc.m608214200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.
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Affiliation(s)
- Dmitry V. Lesnyak
- Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119992, Russia
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Tatiana Skarina
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Petr V. Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G IL6, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Olga A. Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
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248
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Reichow SL, Hamma T, Ferré-D'Amaré AR, Varani G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 2007; 35:1452-64. [PMID: 17284456 PMCID: PMC1865073 DOI: 10.1093/nar/gkl1172] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequence-specific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose-2′-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the core archaeal sRNP proteins have been determined and their assembly pathways delineated. Furthermore, the recent structure of an H/ACA complex has revealed the organization of a complete sRNP. Combined with current biochemical data, these structures offer insight into the highly homologous eukaryotic snoRNPs.
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Affiliation(s)
- Steve L. Reichow
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Tomoko Hamma
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Adrian R. Ferré-D'Amaré
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
- *To whom correspondence should be addressed. +(206) 543 1610+(206) 685 8665
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249
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Li J, Yan H, Wang K, Tan W, Zhou X. Hairpin Fluorescence DNA Probe for Real-Time Monitoring of DNA Methylation. Anal Chem 2007; 79:1050-6. [PMID: 17263334 DOI: 10.1021/ac061694i] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA methylation catalyzed by methylase plays an important role in many biological events. However, traditional methods of methylase activity analysis by gel electrophoresis were laborious and discontinuous. In this paper, we report a new strategy to study methylase activity using fluorescent probes coupled with enzyme-linkage reactions. A hairpin DNA probe is prepared with a fluorophore and a quencher linked at the 5'- and 3'-terminus of the probe. A disturbance of the stem sequence by DNA methylation would cause the separation of the fluorophore and the quencher, resulting in the restoration of the fluorescence. We used DNA adenine methylation (Dam) methyltransferase (MTase) and Dpn I endonuclease, both having a 5'-G-A-T-C-3' recognition sequence. Dam MTase catalyzed the methylation of the sequence of 5'-GATC-3', and Dpn I cut the sequence of 5'-G-Am-T-C-3'. The fluorescence of the hairpin probe was restored when it was cleaved by Dpn I endonuclease during the course of methylation. Unlike traditional methods, this assay was done in real time and could be used to monitor the dynamic process of methylation. Our method is easy, simple, and nonradioactive, yet as efficient as gel electrophoresis in detecting the activity of methylase. It also had the potential to screen suitable inhibitor drugs for Dam methylase.
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Affiliation(s)
- Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha 410082, P R China
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250
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Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry 2006; 45:11776-89. [PMID: 17002278 PMCID: PMC4070884 DOI: 10.1021/bi0605787] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Internal loops play an important role in structure and folding of RNA and in recognition of RNA by other molecules such as proteins and ligands. An understanding of internal loops with propensities to form a particular structure will help predict RNA structure, recognition, and function. The structures of internal loops 5' 1009CUAAG1013 3'/3' 1168GAAGC1164 5' and 5' 998CUAAG1002 3'/3' 1157GAAGC1153 5' from helix 40 of the large subunit rRNA in Deinococcus radiodurans and Escherichia coli, respectively, are phylogenetically conserved, suggesting functional relevance. The energetics and NMR solution structure of the loop were determined in the duplex 5' 1GGCUAAGAC9 3'/3' 18CCGAAGCUG10 5'. The internal loop forms a different structure in solution and in the crystal structures of the ribosomal subunits. In particular, the crystal structures have a bulged out adenine at the equivalent of position A15 and a reverse Hoogsteen UA pair (trans Watson-Crick/Hoogsteen UA) at the equivalent of U4 and A14, whereas the solution structure has a single hydrogen bond UA pair (cis Watson-Crick/sugar edge A15U4) between U4 and A15 and a sheared AA pair (trans Hoogsteen/sugar edge A14A5) between A5 and A14. There is cross-strand stacking between A6 and A14 (A6/A14/A15 stacking pattern) in the NMR structure. All three structures have a sheared GA pair (trans Hoogsteen/sugar edge A6G13) at the equivalent of A6 and G13. The internal loop has contacts with ribosomal protein L20 and other parts of the RNA in the crystal structures. These contacts presumably provide the free energy to rearrange the base pairing in the loop. Evidently, molecular recognition of this internal loop involves induced fit binding, which could confer several advantages. The predicted thermodynamic stability of the loop agrees with the experimental value, even though the thermodynamic model assumes a Watson-Crick UA pair.
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Affiliation(s)
- Neelaabh Shankar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Gang Chen
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Thomas R. Krugh
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
- Center for Pediatric Biomedical Research and Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642
- To whom correspondence should be addressed. Phone: (585) 275-3207. Fax: (585) 276-0205.
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