1
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Konttinen O, Carmody J, Kurnik M, Johnson KA, Reich N. High fidelity DNA strand-separation is the major specificity determinant in DNA methyltransferase CcrM's catalytic mechanism. Nucleic Acids Res 2023; 51:6883-6898. [PMID: 37326016 PMCID: PMC10359602 DOI: 10.1093/nar/gkad443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/29/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
Strand-separation is emerging as a novel DNA recognition mechanism but the underlying mechanisms and quantitative contribution of strand-separation to fidelity remain obscure. The bacterial DNA adenine methyltransferase, CcrM, recognizes 5'GANTC'3 sequences through a DNA strand-separation mechanism with unusually high selectivity. To explore this novel recognition mechanism, we incorporated Pyrrolo-dC into cognate and noncognate DNA to monitor the kinetics of strand-separation and used tryptophan fluorescence to follow protein conformational changes. Both signals are biphasic and global fitting showed that the faster phase of DNA strand-separation was coincident with the protein conformational transition. Non-cognate sequences did not display strand-separation and methylation was reduced > 300-fold, providing evidence that strand-separation is a major determinant of selectivity. Analysis of an R350A mutant showed that the enzyme conformational step can occur without strand-separation, so the two events are uncoupled. A stabilizing role for the methyl-donor (SAM) is proposed; the cofactor interacts with a critical loop which is inserted between the DNA strands, thereby stabilizing the strand-separated conformation. The results presented here are broadly applicable to the study of other N6-adenine methyltransferases that contain the structural features implicated in strand-separation, which are found widely dispersed across many bacterial phyla, including human and animal pathogens, and some Eukaryotes.
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Affiliation(s)
- Olivia Konttinen
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jason Carmody
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Martin Kurnik
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Kenneth A Johnson
- Life Sciences Interdisciplinary Graduate Program, Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Norbert Reich
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
- Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
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2
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Kouidou S, Malousi A, Andreou AZ. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: Triggering a Lethal Fight to Keep Control of the Ten-Eleven Translocase (TET)-Associated DNA Demethylation? Pathogens 2020; 9:E1006. [PMID: 33266135 PMCID: PMC7760189 DOI: 10.3390/pathogens9121006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/15/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
The extended and diverse interference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in multiple host functions and the diverse associated symptoms implicate its involvement in fundamental cellular regulatory processes. The activity of ten-eleven translocase 2 (TET2) responsible for selective DNA demethylation, has been recently identified as a regulator of endogenous virus inactivation and viral invasion, possibly by proteasomal deregulation of the TET2/TET3 activities. In a recent report, we presented a detailed list of factors that can be affected by TET activity, including recognition of zinc finger protein binding sites and bimodal promoters, by enhancing the flexibility of adjacent sequences. In this review, we summarize the TET-associated processes and factors that could account for SARS-CoV-2 diverse symptoms. Moreover, we provide a correlation for the observed virus-induced symptoms that have been previously associated with TET activities by in vitro and in vitro studies. These include early hypoxia, neuronal regulation, smell and taste development, liver, intestinal, and cardiomyocyte differentiation. Finally, we propose that the high mortality of SARS-CoV-2 among adult patients, the different clinical symptoms of adults compared to children, the higher risk of patients with metabolic deregulation, and the low mortality rates among women can all be accounted for by the complex balance of the three enzymes with TET activity, which is developmentally regulated. This activity is age-dependent, related to telomere homeostasis and integrity, and associated with X chromosome inactivation via (de)regulation of the responsible XIST gene expression.
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Affiliation(s)
- Sofia Kouidou
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Andigoni Malousi
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
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3
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Malousi A, Andreou AZ, Kouidou S. In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors. Epigenetics 2020; 16:503-518. [PMID: 32752914 DOI: 10.1080/15592294.2020.1805693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (p < 2.2x10-16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY6TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA 'springs' and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
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Affiliation(s)
- Andigoni Malousi
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Sofia Kouidou
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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4
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Fossépré M, Trévisan ME, Cyriaque V, Wattiez R, Beljonne D, Richeter S, Clément S, Surin M. Detection of the Enzymatic Cleavage of DNA through Supramolecular Chiral Induction to a Cationic Polythiophene. ACS APPLIED BIO MATERIALS 2019; 2:2125-2136. [DOI: 10.1021/acsabm.9b00123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Marie E. Trévisan
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Sébastien Richeter
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Sébastien Clément
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
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5
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Liu L, Shi T, Houk KN, Zhao YL. Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations. RSC Adv 2019; 9:31425-31434. [PMID: 35527972 PMCID: PMC9072302 DOI: 10.1039/c9ra06791d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme forde novoepigenetic methylation in human beings, was characterized by a disturbing conformation ofS-adenosylmethionine (SAM).
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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6
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Wons E, Mruk I, Kaczorowski T. Isospecific adenine DNA methyltransferases show distinct preferences towards DNA substrates. Sci Rep 2018; 8:8243. [PMID: 29844340 PMCID: PMC5974420 DOI: 10.1038/s41598-018-26434-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/09/2018] [Indexed: 11/09/2022] Open
Abstract
Here, we report results on systematic analysis of DNA substrate preferences of three N6-adenine β-class DNA methyltransferases that are part of the type II restriction-modification systems. The studied enzymes were: M.EcoVIII, M.HindIII and M.LlaCI, which although found in phylogenetically distant bacteria (γ-proteobacteria and low-GC Gram-positive bacteria), recognize the same palindromic specific sequence 5′-AAGCTT-3′ and catalyze formation of N6-methyladenine at the first A-residue. As expected overall the enzymes share the most analyzed features, but they show also some distinct differences in substrate recognition. Therefore DNA methylation reactions were carried out not only under standard, but also under relaxed conditions using DMSO or glycerol. We found that all of these enzymes preferred DNA containing a hemimethylated target site, but differ in modification of ssDNA, especially more pronounced for M.EcoVIII under relaxed conditions. In these conditions they also have shown varied preferences toward secondary sites, which differ by one nucleotide from specific sequence. They preferred sequences with substitutions at the 1st (A1 → G/C) and at the 2nd position (A2 → C), while sites with substitutions at the 3rd position (G3 → A/C) were modified less efficiently. Kinetic parameters of the methylation reaction carried out by M.EcoVIII were determined. Methylation efficiency (kcat/Km) of secondary sites was 4.5–10 times lower when compared to the unmethylated specific sequences, whilst efficiency observed for the hemimethylated substrate was almost 4.5 times greater. We also observed a distinct effect of analyzed enzymes on unspecific interaction with DNA phosphate backbone. We concluded that for all three enzymes the most critical is the phosphodiester bond between G3-C4 nucleotides at the center of the target site.
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Affiliation(s)
- Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland. .,Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland.
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7
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S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells. Oncotarget 2017; 8:111866-111881. [PMID: 29340097 PMCID: PMC5762365 DOI: 10.18632/oncotarget.22942] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/29/2017] [Indexed: 12/17/2022] Open
Abstract
S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM is unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated liver cancer cell lines HepG2 and SKhep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and are downregulated by SAM. Analysis of the methylome using bisulfite mapping of captured promoters and enhancers reveals that SAM hyper-methylates and downregulates genes in pathways of growth and metastasis that are upregulated in liver cancer cells. Depletion of two SAM downregulated genes STMN1 and TAF15 reduces cellular transformation and invasiveness, providing evidence that SAM targets are genes important for cancer growth and invasiveness. Taken together these data provide a molecular rationale for SAM as an anticancer agent.
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8
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Environmental triggers in systemic lupus erythematosus. Semin Arthritis Rheum 2017; 47:710-717. [PMID: 29169635 DOI: 10.1016/j.semarthrit.2017.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/20/2017] [Accepted: 10/02/2017] [Indexed: 12/25/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that can affect almost any organ in the human body. Despite significant advancements in our understanding of SLE over the recent years, its exact mode of onset and disease progression remains elusive. Low concordance rates among monozygotic twins with SLE (as low as 24%), clustering of disease prevalence around polluted regions and an urban-rural difference in prevalence all highlight the importance of environmental influences in SLE. Experimental data strongly suggests a complex interaction between the exposome (or environmental influences) and genome (genetic material) to produce epigenetic changes (epigenome) that can alter the expression of genetic material and lead to development of disease in the susceptible individual. In this review, we focus on the available literature to explore the role of environmental factors in SLE disease onset and progression and to better understand the role of exposome-epigenome-genome interactions in this dreaded disease.
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9
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Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. J Chem Inf Model 2017; 57:2020-2026. [PMID: 28696686 DOI: 10.1021/acs.jcim.7b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Free energy simulations are presented to probe the energetic coupling between DNA bending and the flipping of a central thymine in double stranded DNA 13mers. The energetics are shown to depend on the neighboring base pairs, and upstream C or T or downstream C tended to make flipping more costly. Flipping to the major groove side was generally preferred. Bending aids flipping, by pushing the system up in free energy, but for small and intermediate bending angles the two were uncorrelated. At higher bending angles, bending and flipping became correlated, and bending primed the system for base flipping toward the major groove. Flipping of the 6-4 pyrimidine-pyrimidone and pyrimidine dimer photoproducts is shown to be more facile than for undamaged DNA. For the damages, major groove flipping was preferred, and DNA bending was much facilitated in the 6-4 pyrimidine-pyrimidone damaged system. Aspects of the calculations were verified by structural analyses of protein-DNA complexes with flipped bases.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States
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10
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Abstract
Rheumatoid arthritis (RA) is an immune-mediated disease of unknown cause that primarily affects the joints and ultimately leads to joint destruction. In recent years, the potential role of DNA methylation in the development of RA is raising great expectations among clinicians and researchers. DNA methylation influences diverse aspects of the disease and regulates epigenetic silencing of genes and behavior of several cell types, especially fibroblast-like synoviocytes (FLS), the most resident cells in joints. The activation of FLS is generally regarded as a key process in the development of RA that actively results in the promotion of ongoing inflammation and joint damage. It has also been shown that aberrant DNA methylation occurs in the pathogenesis of RA and contributes to the development of the disease. Recently, there has been an impressive increase in studies involving DNA methylation in RA. In this paper, we consider the role of DNA methylation in the development of RA.
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Affiliation(s)
- Feng-Lai Yuan
- Department of Orthopaedics and Central Laboratory, The Third Hospital Affiliated to Nantong University, Wuxi, 214041, Jiangsu, China
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11
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Cloning, purification and characterization of translationally fused protein DNA methyltransferase M•HhaI-EGFP. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Miao CG, Yang JT, Yang YY, Du CL, Huang C, Huang Y, Zhang L, Lv XW, Jin Y, Li J. Critical role of DNA methylation in the pathogenesis of systemic lupus erythematosus: new advances and future challenges. Lupus 2014; 23:730-42. [PMID: 24644011 DOI: 10.1177/0961203314527365] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/10/2014] [Indexed: 01/12/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic multi-organ autoimmune disease with different immunological characteristics and clinical manifestations characterized by an autoantibody response to nuclear and cytoplasmic antigens; the etiology of this disease remains largely unknown. Most recent genome-wide association studies demonstrate that genetics significantly predispose to SLE onset, but the incomplete disease concordance rates between monozygotic twins indicates a role for other complementary factors in SLE pathogenesis. Recently, much evidence strongly supports other molecular mechanisms involved in the regulation of gene expression ultimately causing autoimmune disease, and several studies, both in clinical settings and experimental models, have demonstrated that epigenetic modifications may hold the key to a better understanding of SLE initiation and development. DNA methylation changes the structure of chromatin, being typically able to modulate the fine interactions between promoter-transcription factors and encoding genes within the transcription machinery. Alteration in DNA methylation has been confirmed as a major epigenetic mechanism that may potentially cause a breakdown of immune tolerance and perpetuation of SLE. Based on recent findings, DNA methylation treatments already being used in oncology may soon prove beneficial to patients with SLE. We herein discuss what we currently know, and what we expect in the future.
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Affiliation(s)
- C-G Miao
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - J-T Yang
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China
| | - Y-Y Yang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - C-L Du
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China
| | - C Huang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - Y Huang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - L Zhang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - X-W Lv
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - Y Jin
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - J Li
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
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13
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Smith RM, Pernstich C, Halford SE. TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide. Nucleic Acids Res 2014; 42:5809-22. [PMID: 24634443 PMCID: PMC4027205 DOI: 10.1093/nar/gku187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Type II restriction–modification systems cleave and methylate DNA at specific sequences. However, the Type IIB systems look more like Type I than conventional Type II schemes as they employ the same protein for both restriction and modification and for DNA recognition. Several Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB proteins express all three functions from separate segments of a single polypeptide. This study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one- and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI, TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually cutting the DNA in both strands on both sides of the sites, but at each site the first double-strand break is made long before the second. In contrast, BcgI cuts all eight target bonds at two sites in a single step. TstI also differs from BcgI in either methylating or cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make the second double-strand break. TstI MTase acts best at hemi-methylated sites.
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Affiliation(s)
- Rachel M Smith
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Christian Pernstich
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen E Halford
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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14
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Butterer A, Pernstich C, Smith RM, Sobott F, Szczelkun MD, Tóth J. Type III restriction endonucleases are heterotrimeric: comprising one helicase-nuclease subunit and a dimeric methyltransferase that binds only one specific DNA. Nucleic Acids Res 2014; 42:5139-50. [PMID: 24510100 PMCID: PMC4005696 DOI: 10.1093/nar/gku122] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mechanism. In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI. Our data are also consistent with a model where ATP hydrolysis activated by recognition site binding leads to release of the enzyme from the site, dissociation from the substrate via a free DNA end and cleavage of the DNA. These results are discussed critically in the light of the published literature, aiming to resolve controversies and discuss consequences in terms of the reaction mechanism.
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Affiliation(s)
- Annika Butterer
- Biomolecular & Analytical Mass Spectrometry and Center for Proteomics (CFP-CeProMa), Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium and DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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15
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Miao CG, Yang YY, He X, Li J. New advances of DNA methylation and histone modifications in rheumatoid arthritis, with special emphasis on MeCP2. Cell Signal 2013; 25:875-82. [DOI: 10.1016/j.cellsig.2012.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 12/21/2012] [Indexed: 01/04/2023]
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16
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Doyle OM, Tsaneva-Atansaova K, Harte J, Tiffin PA, Tino P, Díaz-Zuccarini V. Bridging paradigms: hybrid mechanistic-discriminative predictive models. IEEE Trans Biomed Eng 2013; 60:735-42. [PMID: 23392334 DOI: 10.1109/tbme.2013.2244598] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Many disease processes are extremely complex and characterized by multiple stochastic processes interacting simultaneously. Current analytical approaches have included mechanistic models and machine learning (ML), which are often treated as orthogonal viewpoints. However, to facilitate truly personalized medicine, new perspectives may be required. This paper reviews the use of both mechanistic models and ML in healthcare as well as emerging hybrid methods, which are an exciting and promising approach for biologically based, yet data-driven advanced intelligent systems.
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Affiliation(s)
- Orla M Doyle
- Department of Neuroimaging, Institute of Psychiatry, King's College London, London, UK.
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17
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Smith RM, Jacklin AJ, Marshall JJT, Sobott F, Halford SE. Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA. Nucleic Acids Res 2012; 41:405-17. [PMID: 23147004 PMCID: PMC3592466 DOI: 10.1093/nar/gks1000] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Type IIB restriction–modification protein BcgI contains A and B subunits in a
2:1 ratio: A has the active sites for both endonuclease and methyltransferase functions
while B recognizes the DNA. Like almost all Type IIB systems, BcgI needs two unmethylated
sites for nuclease activity; it cuts both sites upstream and downstream of the recognition
sequence, hydrolyzing eight phosphodiester bonds in a single synaptic complex. This
complex may incorporate four A2B protomers to give the eight catalytic centres
(one per A subunit) needed to cut all eight bonds. The BcgI recognition sequence contains
one adenine in each strand that can be N6-methylated. Although most DNA
methyltransferases operate at both unmethylated and hemi-methylated sites, BcgI
methyltransferase is only effective at hemi-methylated sites, where the nuclease component
is inactive. Unlike the nuclease, the methyltransferase acts at solitary sites,
functioning catalytically rather than stoichiometrically. Though it transfers one methyl
group at a time, presumably through a single A subunit, BcgI methyltransferase can be
activated by adding extra A subunits, either individually or as part of A2B
protomers, which indicates that it requires an assembly containing at least two
A2B units.
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Affiliation(s)
- Rachel M Smith
- The DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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