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Helbrecht I, Heiter D, Yang W, Vincze T, Hanneman A, Lutz T, Ettwiller L, Bochtler M, Xu SY. Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems. Front Microbiol 2024; 15:1286822. [PMID: 38655080 PMCID: PMC11037411 DOI: 10.3389/fmicb.2024.1286822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/08/2024] [Indexed: 04/26/2024] Open
Abstract
Winged helix (wH) domains, also termed winged helix-turn-helix (wHTH) domains, are widespread in all kingdoms of life and have diverse roles. In the context of DNA binding and DNA modification sensing, some eukaryotic wH domains are known as sensors of non-methylated CpG. In contrast, the prokaryotic wH domains in DpnI and HhiV4I act as sensors of adenine methylation in the 6mApT (N6-methyladenine, 6mA, or N6mA) context. DNA-binding modes and interactions with the probed dinucleotide are vastly different in the two cases. Here, we show that the role of the wH domain as a sensor of adenine methylation is widespread in prokaryotes. We present previously uncharacterized examples of PD-(D/E)XK-wH (FcyTI, Psp4BI), PUA-wH-HNH (HtuIII), wH-GIY-YIG (Ahi29725I, Apa233I), and PLD-wH (Aba4572I, CbaI) fusion endonucleases that sense adenine methylation in the Dam+ Gm6ATC sequence contexts. Representatives of the wH domain endonuclease fusion families with the exception of the PLD-wH family could be purified, and an in vitro preference for adenine methylation in the Dam context could be demonstrated. Like most other modification-dependent restriction endonucleases (MDREs, also called type IV restriction systems), the new fusion endonucleases except those in the PD-(D/E)XK-wH family cleave close to but outside the recognition sequence. Taken together, our data illustrate the widespread combinatorial use of prokaryotic wH domains as adenine methylation readers. Other potential 6mA sensors in modified DNA are also discussed.
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Affiliation(s)
- Igor Helbrecht
- New England Biolabs, Inc., Ipswich, MA, United States
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Daniel Heiter
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Weiwei Yang
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Tamas Vincze
- New England Biolabs, Inc., Ipswich, MA, United States
| | | | - Thomas Lutz
- New England Biolabs, Inc., Ipswich, MA, United States
| | | | - Matthias Bochtler
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- International Institute of Molecular and Cell Biology, Warsaw, Poland
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2
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Zhou J, Chen Q, Ren R, Yang J, Liu B, Horton JR, Chang C, Li C, Maksoud L, Yang Y, Rotili D, Zhang X, Blumenthal RM, Chen T, Gao Y, Valente S, Mai A, Cheng X. Quinoline-based compounds can inhibit diverse enzymes that act on DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587980. [PMID: 38617249 PMCID: PMC11014617 DOI: 10.1101/2024.04.03.587980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation, as exemplified by cytosine-C5 methylation in mammals and adenine-N6 methylation in bacteria, is a crucial epigenetic mechanism driving numerous vital biological processes. Developing non-nucleoside inhibitors to cause DNA hypomethylation is a high priority, in order to treat a variety of significant medical conditions without the toxicities associated with existing cytidine-based hypomethylating agents. In this study, we have characterized fifteen quinoline-based analogs. Notably, compounds with additions like a methylamine ( 9 ) or methylpiperazine ( 11 ) demonstrate similar low micromolar inhibitory potency against both human DNMT1 (which generates C5-methylcytosine) and Clostridioides difficile CamA (which generates N6-methyladenine). Structurally, compounds 9 and 11 specifically intercalate into CamA-bound DNA via the minor groove, adjacent to the target adenine, leading to a substantial conformational shift that moves the catalytic domain away from the DNA. This study adds to the limited examples of DNA methyltransferases being inhibited by non-nucleotide compounds through DNA intercalation, following the discovery of dicyanopyridine-based inhibitors for DNMT1. Furthermore, our study shows that some of these quinoline-based analogs inhibit other enzymes that act on DNA, such as polymerases and base excision repair glycosylases. Finally, in cancer cells compound 11 elicits DNA damage response via p53 activation. Abstract Figure Highlights Six of fifteen quinoline-based derivatives demonstrated comparable low micromolar inhibitory effects on human cytosine methyltransferase DNMT1, and the bacterial adenine methyltransferases Clostridioides difficile CamA and Caulobacter crescentus CcrM. Compounds 9 and 11 were found to intercalate into a DNA substrate bound by CamA. These quinoline-based derivatives also showed inhibitory activity against various base excision repair DNA glycosylases, and DNA and RNA polymerases. Compound 11 provokes DNA damage response via p53 activation in cancer cells.
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3
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov B. Examining DNA breathing with pyDNA-EPBD. Bioinformatics 2023; 39:btad699. [PMID: 37991847 PMCID: PMC10681863 DOI: 10.1093/bioinformatics/btad699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/23/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
MOTIVATION The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA 22030, United States
| | - Anny Usheva
- Department of Surgery, Brown University, Providence, RI 02912, United States
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
| | - Boian Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87544, United States
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4
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Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov BS. Examining DNA Breathing with pyDNA-EPBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557010. [PMID: 37745370 PMCID: PMC10515784 DOI: 10.1101/2023.09.09.557010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Motivation The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. Results We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.
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Affiliation(s)
- Anowarul Kabir
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Manish Bhattarai
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Kim Ø. Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Amarda Shehu
- George Mason University, 4400 University Dr, Fairfax, VA 22030
| | - Anny Usheva
- Brown University, 69 Brown St Box 1822, Providence, RI 02912
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, 87544, NM, 87102
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5
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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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Gao Q, Lu S, Wang Y, He L, Wang M, Jia R, Chen S, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Sun D, Tian B, Cheng A. Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria. Front Microbiol 2023; 14:1129437. [PMID: 37032876 PMCID: PMC10073500 DOI: 10.3389/fmicb.2023.1129437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Shuwei Lu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuwei Wang
- Key Laboratory of Livestock and Poultry Provenance Disease Research in Mianyang, Sichuan, China
| | - Longgui He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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7
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Chen LQ, Zhang Z, Chen HX, Xi JF, Liu XH, Ma DZ, Zhong YH, Ng WH, Chen T, Mak DW, Chen Q, Chen YQ, Luo GZ. High-precision mapping reveals rare N 6-deoxyadenosine methylation in the mammalian genome. Cell Discov 2022; 8:138. [PMID: 36575183 PMCID: PMC9794812 DOI: 10.1038/s41421-022-00484-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/16/2022] [Indexed: 12/28/2022] Open
Abstract
N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.
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Affiliation(s)
- Li-Qian Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China ,grid.410643.4Guangdong Cardiovascular Institute, Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong China
| | - Zhang Zhang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Hong-Xuan Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jian-Fei Xi
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xue-Hong Liu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Dong-Zhao Ma
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yu-Hao Zhong
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Wen Hui Ng
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tao Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Daniel W. Mak
- grid.194645.b0000000121742757School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qi Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Yao-Qing Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Guan-Zheng Luo
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
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8
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Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res 2022; 50:8290-8301. [PMID: 35801916 DOI: 10.1093/nar/gkac589] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/13/2023] Open
Abstract
Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
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Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Kevin John Butay
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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9
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Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X. Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure 2022; 30:793-802.e5. [PMID: 35395178 PMCID: PMC9177618 DOI: 10.1016/j.str.2022.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 12/21/2022]
Abstract
DNMT1 maintains the parental DNA methylation pattern on newly replicated hemimethylated DNA. The failure of this maintenance process causes aberrant DNA methylation that affects transcription and contributes to the development and progression of cancers such as acute myeloid leukemia. Here, we structurally characterized a set of newly discovered DNMT1-selective, reversible, non-nucleoside inhibitors that bear a core 3,5-dicyanopyridine moiety, as exemplified by GSK3735967, to better understand their mechanism of inhibition. All of the dicyanopydridine-containing inhibitors examined intercalate into the hemimethylated DNA between two CpG base pairs through the DNA minor groove, resulting in conformational movement of the DNMT1 active-site loop. In addition, GSK3735967 introduces two new binding sites, where it interacts with and stabilizes the displaced DNMT1 active-site loop and it occupies an open aromatic cage in which trimethylated histone H4 lysine 20 is expected to bind. Our work represents a substantial step in generating potent, selective, and non-nucleoside inhibitors of DNMT1.
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Affiliation(s)
- John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarath Pathuri
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kristen Wong
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lourdes Rueda
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - David T Fosbenner
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Dirk A Heerding
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Michael T McCabe
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Melissa B Pappalardi
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bryan W King
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA 19426, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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10
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Advances in the Structural Biology, Mechanism, and Physiology of Cyclopropane Fatty Acid Modifications of Bacterial Membranes. Microbiol Mol Biol Rev 2022; 86:e0001322. [PMID: 35435731 PMCID: PMC9199407 DOI: 10.1128/mmbr.00013-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclopropane fatty acid (CFA) synthase catalyzes a remarkable reaction. The
cis
double bonds of unsaturated fatty acyl chains of phospholipid bilayers are converted to cyclopropane rings by transfer of a methylene moiety from S-adenosyl-L-methionine (SAM).
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11
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Abstract
![]()
We
explore the process of base-flipping for four central bases,
adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid
(DNA) duplex using the energy landscape perspective. NMR imino-proton
exchange and fluorescence correlation spectroscopy studies have been
used in previous experiments to obtain lifetimes for bases in paired
and extrahelical states. However, the difference of almost 4 orders
of magnitude in the base-flipping rates obtained by the two methods
implies that they are exploring different pathways and possibly different
open states. Our results support the previous suggestion that minor
groove opening may be favored by distortions in the DNA backbone and
reveal links between sequence effects and the direction of opening,
i.e., whether the base flips toward the major or the minor groove
side. In particular, base flipping along the minor groove pathway
was found to align toward the 5′ side of the backbone. We find
that bases align toward the 3′ side of the backbone when flipping
along the major groove pathway. However, in some cases for cytosine
and thymine, the base flipping along the major groove pathway also
aligns toward the 5′ side. The sequence effect may be caused
by the polar interactions between the flipping-base and its neighboring
bases on either of the strands. For guanine flipping toward the minor
groove side, we find that the equilibrium constant for opening is
large compared to flipping via the major groove. We find that the
estimated rates of base opening, and hence the lifetimes of the closed
state, obtained for thymine flipping through small and large angles
along the major groove differ by 6 orders of magnitude, whereas for
thymine flipping through small angles along the minor groove and large
angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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12
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Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.02.480688. [PMID: 35262076 PMCID: PMC8902873 DOI: 10.1101/2022.03.02.480688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
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Affiliation(s)
- Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M. Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Kevin John Butay
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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13
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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15
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Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
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16
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Nehzati S, Summers AO, Dolgova NV, Zhu J, Sokaras D, Kroll T, Pickering IJ, George GN. Hg(II) Binding to Thymine Bases in DNA. Inorg Chem 2021; 60:7442-7452. [PMID: 33938732 DOI: 10.1021/acs.inorgchem.1c00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The compounds of mercury can be highly toxic and can interfere with a range of biological processes, although many aspects of the mechanism of toxicity are still obscure or unknown. One especially intriguing property of Hg(II) is its ability to bind DNA directly, making interstrand cross-links between thymine nucleobases in AT-rich sequences. We have used a combination of small molecule X-ray diffraction, X-ray spectroscopies, and computational chemistry to study the interactions of Hg(II) with thymine. We find that the energetically preferred mode of thymine binding in DNA is to the N3 and predict only minor distortions of the DNA structure on binding one Hg(II) to two cross-adjacent thymine nucleotides. The preferred geometry is predicted to be twisted away from coplanar through a torsion angle of between 32 and 43°. Using 1-methylthymine as a model, the bis-thymine coordination of Hg(II) is found to give a highly characteristic X-ray spectroscopic signature that is quite distinct from other previously described biological modes of binding of Hg(II). This work enlarges and deepens our view of significant biological targets of Hg(II) and demonstrates tools that can provide a characteristic signature for the binding of Hg(II) to DNA in more complex matrices including intact cells and tissues, laying the foundation for future studies of mechanisms of mercury toxicity.
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Affiliation(s)
- Susan Nehzati
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Natalia V Dolgova
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Jianfeng Zhu
- Saskatchewan Structural Sciences Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ingrid J Pickering
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Graham N George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
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17
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Mondal M, Yang L, Cai Z, Patra P, Gao YQ. A perspective on the molecular simulation of DNA from structural and functional aspects. Chem Sci 2021; 12:5390-5409. [PMID: 34168783 PMCID: PMC8179617 DOI: 10.1039/d0sc05329e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Accordingly, molecular simulations can provide atomistic details of interactions and conformational dynamics involved in different biological processes of DNA, including those inaccessible by current experimental methods. In this perspective, which is mainly based on our recent studies, we provide a brief overview of the atomistic simulations on how the hierarchical structure and dynamics of DNA can be influenced by its sequences, base modifications, environmental factors and protein binding in the context of the protein-DNA interactions, gene regulation and structural organization of chromatin. We try to connect the DNA sequence, the hierarchical structures of DNA and gene regulation.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China.,Beijing Advanced Innovation Center for Genomics, Peking University 100871 Beijing China
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18
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Westwood MN, Ljunggren KD, Boyd B, Becker J, Dwyer TJ, Meints GA. Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA. Biochemistry 2021; 60:873-885. [PMID: 33689312 DOI: 10.1021/acs.biochem.0c00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions and mismatches in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Altered local dynamics and conformational properties in damaged DNAs have previously been suggested to assist in recognition and specificity. Herein, we use solution nuclear magnetic resonance to quantify changes in BI-BII backbone conformational dynamics due to the presence of single-base lesions in DNA, including uracil, dihydrouracil, 1,N6-ethenoadenine, and T:G mismatches. Stepwise changes to the %BII and ΔG of the BI-BII dynamic equilibrium compared to those of unmodified sequences were observed. Additionally, the equilibrium skews toward endothermicity for the phosphates nearest the lesion/mismatched base pair. Finally, the phosphates with the greatest alterations correlate with those most relevant to the repair of enzyme binding. All of these results suggest local conformational rearrangement of the DNA backbone may play a role in lesion recognition by repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - K D Ljunggren
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Benjamin Boyd
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Jaclyn Becker
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Tammy J Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States
| | - Gary A Meints
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
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19
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Levintov L, Paul S, Vashisth H. Reaction Coordinate and Thermodynamics of Base Flipping in RNA. J Chem Theory Comput 2021; 17:1914-1921. [PMID: 33594886 DOI: 10.1021/acs.jctc.0c01199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Sanjib Paul
- Department of Chemistry, New York University, New York 10003, New York, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
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20
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Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J. Molecular mechanism for vitamin C-derived C 5-glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1. Nat Commun 2021; 12:744. [PMID: 33531488 PMCID: PMC7854593 DOI: 10.1038/s41467-021-21061-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 01/07/2023] Open
Abstract
C5-glyceryl-methylcytosine (5gmC) is a novel DNA modification catalyzed by algal TET homologue CMD1 using vitamin C (VC) as co-substrate. Here, we report the structures of CMD1 in apo form and in complexes with VC or/and dsDNA. CMD1 exhibits comparable binding affinities for DNAs of different lengths, structures, and 5mC levels, and displays a moderate substrate preference for 5mCpG-containing DNA. CMD1 adopts the typical DSBH fold of Fe2+/2-OG-dependent dioxygenases. The lactone form of VC binds to the active site and mono-coordinates the Fe2+ in a manner different from 2-OG. The dsDNA binds to a positively charged cleft of CMD1 and the 5mC/C is inserted into the active site and recognized by CMD1 in a similar manner as the TET proteins. The functions of key residues are validated by mutagenesis and activity assay. Our structural and biochemical data together reveal the molecular mechanism for the VC-derived 5gmC DNA modification by CMD1.
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Affiliation(s)
- Wenjing Li
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tianlong Zhang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Mingliang Sun
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Shi
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiao-Jie Zhang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Guo-Liang Xu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jianping Ding
- grid.410726.60000 0004 1797 8419State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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21
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Menssen RJ, Kimmel GJ, Tokmakoff A. Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations. J Chem Phys 2021; 154:045101. [PMID: 33514113 DOI: 10.1063/5.0035187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The model is designed to be accessible to experimental researchers in terms of both computational simplicity and expense while providing detailed insights beyond those provided by experimental methods. The model is an extension of a thermodynamic lattice model for DNA hybridization utilizing the formalism of the nucleation-zipper mechanism. Association and dissociation trajectories were generated utilizing the Gillespie algorithm and parameters determined via fitting the association and dissociation timescales to previously published experimental data. Terminal end fraying, experimentally observed following a rapid T-jump, in the sequence 5'-ATATGCATAT-3' was replicated by the model that also demonstrated that experimentally observed fast dynamics in the sequences 5'-C(AT)nG-3', where n = 2-6, were also due to terminal end fraying. The dominant association pathways, isolated by transition pathway theory, showed two primary motifs: initiating at or next to a G:C base pair, which is enthalpically favorable and related to the increased strength of G:C base pairs, and initiating in the center of the sequence, which is entropically favorable and related to minimizing the penalty associated with the decrease in configurational entropy due to hybridization.
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Affiliation(s)
- Ryan J Menssen
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gregory J Kimmel
- Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida 33612, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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22
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Woodcock CB, Horton JR, Zhang X, Blumenthal RM, Cheng X. Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. Nucleic Acids Res 2020; 48:10034-10044. [PMID: 32453412 PMCID: PMC7544214 DOI: 10.1093/nar/gkaa446] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
S-adenosyl-l-methionine dependent methyltransferases catalyze methyl transfers onto a wide variety of target molecules, including DNA and RNA. We discuss a family of methyltransferases, those that act on the amino groups of adenine or cytosine in DNA, have conserved motifs in a particular order in their amino acid sequence, and are referred to as class beta MTases. Members of this class include M.EcoGII and M.EcoP15I from Escherichia coli, Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM), the MTA1-MTA9 complex from the ciliate Oxytricha, and the mammalian MettL3-MettL14 complex. These methyltransferases all generate N6-methyladenine in DNA, with some members having activity on single-stranded DNA as well as RNA. The beta class of methyltransferases has a unique multimeric feature, forming either homo- or hetero-dimers, allowing the enzyme to use division of labor between two subunits in terms of substrate recognition and methylation. We suggest that M.EcoGII may represent an ancestral form of these enzymes, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).
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Affiliation(s)
- Clayton B Woodcock
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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23
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DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nat Commun 2020; 11:3723. [PMID: 32709850 PMCID: PMC7381644 DOI: 10.1038/s41467-020-17531-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.
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24
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Dumesic PA, Stoddard CI, Catania S, Narlikar GJ, Madhani HD. ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA. Mol Cell 2020; 79:127-139.e4. [PMID: 32437639 DOI: 10.1016/j.molcel.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]
Abstract
C.neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5's ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a "flipped-out" conformation of the target cytosine bypass the SNF2 domain's requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain's substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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25
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The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun 2019; 10:4600. [PMID: 31601797 PMCID: PMC6787082 DOI: 10.1038/s41467-019-12498-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
The Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM) methylates the adenine of hemimethylated GANTC after replication. Here we present the structure of CcrM in complex with double-stranded DNA containing the recognition sequence. CcrM contains an N-terminal methyltransferase domain and a C-terminal nonspecific DNA-binding domain. CcrM is a dimer, with each monomer contacting primarily one DNA strand: the methyltransferase domain of one molecule binds the target strand, recognizes the target sequence, and catalyzes methyl transfer, while the C-terminal domain of the second molecule binds the non-target strand. The DNA contacts at the 5-base pair recognition site results in dramatic DNA distortions including bending, unwinding and base flipping. The two DNA strands are pulled apart, creating a bubble comprising four recognized base pairs. The five bases of the target strand are recognized meticulously by stacking contacts, van der Waals interactions and specific Watson–Crick polar hydrogen bonds to ensure high enzymatic specificity. CcrM is a cell cycle-regulated DNA methyltransferase that methylates an adenine within a specific sequence following replication in the gram negative bacterium Caulobacter crescentus. Here the authors present a crystal structure of DNA-bound CcrM that reveals the molecular mechanism leading to sequence-specific methylation.
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26
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Da LT, Yu J. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Nucleic Acids Res 2019; 46:5410-5425. [PMID: 29762710 PMCID: PMC6009601 DOI: 10.1093/nar/gky386] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive. Here, we employ the Markov State Model (MSM) constructed from extensive all-atom molecular dynamics (MD) simulations to reveal the complete base-flipping process for a G.T mispair at a tens of microsecond timescale. Our studies identify critical intermediates of the mispaired dT during its extrusion process and reveal the key TDG residues involved in the inter-state transitions. Notably, we find an active role of TDG in promoting the intrahelical nt eversion, sculpturing the DNA backbone, and penetrating into the DNA minor groove. Three additional TDG substrates, namely dU, 5fC, and 5caC, are further tested to evaluate the substituent effects of various chemical modifications of the pyrimidine ring on base-flipping dynamics.
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Affiliation(s)
- Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing 100193, China
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27
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Endutkin AV, Zharkov DO. Critical Sites of DNA Backbone Integrity for Damaged Base Removal by Formamidopyrimidine-DNA Glycosylase. Biochemistry 2019; 58:2740-2749. [PMID: 31120733 DOI: 10.1021/acs.biochem.9b00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA glycosylases, the enzymes that initiate base excision DNA repair, recognize damaged bases through a series of precisely orchestrated movements. Most glycosylases sharply kink the DNA axis at the lesion site and extrude the target base from the DNA double helix into the enzyme's active site. Little attention has been paid so far to the role of the physical continuity of the DNA backbone in allowing the required conformational distortion. Here, we analyze base excision by formamidopyrimidine-DNA glycosylase (Fpg) from substrates keeping all phosphates but containing a nick within three nucleotides of the lesion in either DNA strand. Four phosphoester linkages at the damaged nucleotide and two nucleotides 3' to it were essential for Fpg activity, while the breakage of the others, even at the same critical phosphates, had no effect or even stimulated the reaction. Reduction of the likelihood of hydrogen bonding at the nicks by using dideoxynucleotides as their 3'-terminal groups was more detrimental for the activity. All phosphoester bonds in the complementary strand were dispensable for base excision, but nicks close to the orphaned nucleotide caused early termination of damaged strand cleavage. Elastic network analysis of Fpg-DNA structures showed that the vibrational motions of the critical phosphates are strongly correlated, in part due to the presence of the protein. Overall, our results suggest that mechanical forces propagating along the DNA backbone play a critical role in the correct conformational distortion of DNA by Fpg and possibly by other target base-everting DNA glycosylases.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue , Novosibirsk 630090 , Russia.,Novosibirsk State University , 2 Pirogova Street , Novosibirsk 630090 , Russia
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28
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Mullins EA, Rodriguez AA, Bradley NP, Eichman BF. Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway. Trends Biochem Sci 2019; 44:765-781. [PMID: 31078398 DOI: 10.1016/j.tibs.2019.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases - enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alyssa A Rodriguez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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29
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Berg MD, Genereaux J, Zhu Y, Mian S, Gloor GB, Brandl CJ. Acceptor Stem Differences Contribute to Species-Specific Use of Yeast and Human tRNA Ser. Genes (Basel) 2018; 9:E612. [PMID: 30544642 PMCID: PMC6316282 DOI: 10.3390/genes9120612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 01/01/2023] Open
Abstract
The molecular mechanisms of translation are highly conserved in all organisms indicative of a single evolutionary origin. This includes the molecular interactions of tRNAs with their cognate aminoacyl-tRNA synthetase, which must be precise to ensure the specificity of the process. For many tRNAs, the anticodon is a major component of the specificity. This is not the case for the aminoacylation of alanine and serine to their cognate tRNAs. Rather, aminoacylation relies on other features of the tRNA. For tRNASer, a key specificity feature is the variable arm, which is positioned between the anticodon arm and the T-arm. The variable arm is conserved from yeast to human. This work was initiated to determine if the structure/function of tRNASer has been conserved from Saccharomyces cerevisiae to human. We did this by detecting mistranslation in yeast cells with tRNASer derivatives having the UGA anticodon converted to UGG for proline. Despite being nearly identical in everything except the acceptor stem, human tRNASer is less active than yeast tRNASer. A chimeric tRNA with the human acceptor stem and other sequences from the yeast molecule acts similarly to the human tRNASer. The 3:70 base pair in the acceptor stem (C:G in yeast and A:U in humans) is a prime determinant of the specificity. Consistent with the functional difference of yeast and human tRNASer resulting from subtle changes in the specificity of their respective SerRS enzymes, the functionality of the human and chimeric tRNASerUGG molecules was enhanced when human SerRS was introduced into yeast. Residues in motif 2 of the aminoacylation domain of SerRS likely participated in the species-specific differences. Trp290 in yeast SerRS (Arg313 in humans) found in motif 2 is proximal to base 70 in models of the tRNA-synthetase interaction. Altering this motif 2 sequence of hSerRS to the yeast sequence decreases the activity of the human enzyme with human tRNASer, supporting the coadaptation of motif 2 loop⁻acceptor stem interactions.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Safee Mian
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
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30
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Reich NO, Dang E, Kurnik M, Pathuri S, Woodcock CB. The highly specific, cell cycle-regulated methyltransferase from Caulobacter crescentus relies on a novel DNA recognition mechanism. J Biol Chem 2018; 293:19038-19046. [PMID: 30323065 DOI: 10.1074/jbc.ra118.005212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/09/2018] [Indexed: 12/15/2022] Open
Abstract
Two DNA methyltransferases, Dam and β-class cell cycle-regulated DNA methyltransferase (CcrM), are key mediators of bacterial epigenetics. CcrM from the bacterium Caulobacter crescentus (CcrM C. crescentus, methylates adenine at 5'-GANTC-3') displays 105-107-fold sequence discrimination against noncognate sequences. However, the underlying recognition mechanism is unclear. Here, CcrM C. crescentus activity was either improved or mildly attenuated with substrates having one to three mismatched bp within or adjacent to the recognition site, but only if the strand undergoing methylation is left unchanged. By comparison, single-mismatched substrates resulted in up to 106-fold losses of activity with α (Dam) and γ-class (M.HhaI) DNA methyltransferases. We found that CcrM C. crescentus has a greatly expanded DNA-interaction surface, covering six nucleotides on the 5' side and eight nucleotides on the 3' side of its recognition site. Such a large interface may contribute to the enzyme's high sequence fidelity. CcrM C. crescentus displayed the same sequence discrimination with single-stranded substrates, and a surprisingly large (>107-fold) discrimination against ssRNA was largely due to the presence of two or more riboses within the cognate (DNA) site but not outside the site. Results from C-terminal truncations and point mutants supported our hypothesis that the recently identified C-terminal, 80-residue segment is essential for dsDNA recognition but is not required for single-stranded substrates. CcrM orthologs from Agrobacterium tumefaciens and Brucella abortus share some of these newly discovered features of the C. crescentus enzyme, suggesting that the recognition mechanism is conserved. In summary, CcrM C. crescentus uses a previously unknown DNA recognition mechanism.
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Affiliation(s)
- Norbert O Reich
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Eric Dang
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Martin Kurnik
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Sarath Pathuri
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Clayton B Woodcock
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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31
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Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays 2018; 40:e1800133. [PMID: 30264543 DOI: 10.1002/bies.201800133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/27/2018] [Indexed: 11/08/2022]
Abstract
DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
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32
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Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018; 193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Rukshan T Perera
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Henry S White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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33
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Chen W, Yang H, Feng P, Ding H, Lin H. iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties. Bioinformatics 2018; 33:3518-3523. [PMID: 28961687 DOI: 10.1093/bioinformatics/btx479] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022] Open
Abstract
Motivation DNA N4-methylcytosine (4mC) is an epigenetic modification. The knowledge about the distribution of 4mC is helpful for understanding its biological functions. Although experimental methods have been proposed to detect 4mC sites, they are expensive for performing genome-wide detections. Thus, it is necessary to develop computational methods for predicting 4mC sites. Results In this work, we developed iDNA4mC, the first webserver to identify 4mC sites, in which DNA sequences are encoded with both nucleotide chemical properties and nucleotide frequency. The predictive results of the rigorous jackknife test and cross species test demonstrated that the performance of iDNA4mC is quite promising and holds high potential to become a useful tool for identifying 4mC sites. Availability and implementation The user-friendly web-server, iDNA4mC, is freely accessible at http://lin.uestc.edu.cn/server/iDNA4mC. Contact chenweiimu@gmail.com or hlin@uestc.edu.cn.
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Affiliation(s)
- Wei Chen
- Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Pengmian Feng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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34
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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35
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Grell TJ, Young AP, Drennan CL, Bandarian V. Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. J Am Chem Soc 2018; 140:6842-6852. [PMID: 29792696 PMCID: PMC5994729 DOI: 10.1021/jacs.8b01493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 12/03/2022]
Abstract
TYW1 is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine to form the posttranscriptional modification, 4-demethylwyosine, in situ on transfer RNA (tRNA). Two mechanisms have been proposed for this transformation, with one of the possible mechanisms invoking a Schiff base intermediate formed between a conserved lysine residue and pyruvate. Utilizing a combination of mass spectrometry and X-ray crystallography, we have obtained evidence to support the formation of a Schiff base lysine adduct in TYW1. When 13C labeled pyruvate is used, the mass shift of the adduct matches that of the labeled pyruvate, indicating that pyruvate is the source of the adduct. Furthermore, a crystal structure of TYW1 provides visualization of the Schiff base lysine-pyruvate adduct, which is positioned directly adjacent to the auxiliary [4Fe-4S] cluster. The adduct coordinates the unique iron of the auxiliary cluster through the lysine nitrogen and a carboxylate oxygen, reminiscent of how the radical SAM [4Fe-4S] cluster is coordinated by SAM. The structure provides insight into the binding site for tRNA and further suggests how radical SAM chemistry can be combined with Schiff base chemistry for RNA modification.
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Affiliation(s)
- Tsehai
A. J. Grell
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony P. Young
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vahe Bandarian
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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36
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Herzon SB. DNA Repair: Unconventional Lesions Require Unconventional Repair. Biochemistry 2018; 57:1057-1058. [PMID: 29406697 DOI: 10.1021/acs.biochem.7b01241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seth B Herzon
- Department of Chemistry, Yale University , New Haven, Connecticut 06511, United States.,Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06511, United States
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37
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Roy NS, Debnath S, Chakraborty A, Chakraborty P, Bera I, Ghosh R, Ghoshal N, Chakrabarti S, Roy S. Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation. Phys Chem Chem Phys 2018; 20:9449-9459. [DOI: 10.1039/c8cp01119b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.
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Affiliation(s)
- Neeladri Sekhar Roy
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Subrata Debnath
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Abhijit Chakraborty
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | | | - Indrani Bera
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Raka Ghosh
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Nanda Ghoshal
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Saikat Chakrabarti
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Siddhartha Roy
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
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38
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Ba X, Boldogh I. 8-Oxoguanine DNA glycosylase 1: Beyond repair of the oxidatively modified base lesions. Redox Biol 2017; 14:669-678. [PMID: 29175754 PMCID: PMC5975208 DOI: 10.1016/j.redox.2017.11.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/08/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress and the resulting damage to genomic DNA are inevitable consequences of endogenous physiological processes, and they are amplified by cellular responses to environmental exposures. One of the most frequent reactions of reactive oxygen species with DNA is the oxidation of guanine to pre-mutagenic 8-oxo-7,8-dihydroguanine (8-oxoG). Despite the vulnerability of guanine to oxidation, vertebrate genes are primarily embedded in GC-rich genomic regions, and over 72% of the promoters of human genes belong to a class with a high GC content. In the promoter, 8-oxoG may serve as an epigenetic mark, and when complexed with the oxidatively inactivated repair enzyme 8-oxoguanine DNA glycosylase 1, provide a platform for the coordination of the initial steps of DNA repair and the assembly of the transcriptional machinery to launch the prompt and preferential expression of redox-regulated genes. Deviations/variations from this artful coordination may be the etiological links between guanine oxidation and various cellular pathologies and diseases during ageing processes.
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Affiliation(s)
- Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, China; School of Life Science, Northeast Normal University, Changchun, Jilin 130024, China.
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
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39
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Hendershot JM, O'Brien PJ. Search for DNA damage by human alkyladenine DNA glycosylase involves early intercalation by an aromatic residue. J Biol Chem 2017; 292:16070-16080. [PMID: 28747435 PMCID: PMC5625039 DOI: 10.1074/jbc.m117.782813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/19/2017] [Indexed: 01/22/2023] Open
Abstract
DNA repair enzymes recognize and remove damaged bases that are embedded in the duplex. To gain access, most enzymes use nucleotide flipping, whereby the target nucleotide is rotated 180° into the active site. In human alkyladenine DNA glycosylase (AAG), the enzyme that initiates base excision repair of alkylated bases, the flipped-out nucleotide is stabilized by intercalation of the side chain of tyrosine 162 that replaces the lesion nucleobase. Previous kinetic studies provided evidence for the formation of a transient complex that precedes the stable flipped-out complex, but it is not clear how this complex differs from nonspecific complexes. We used site-directed mutagenesis and transient-kinetic approaches to investigate the timing of Tyr162 intercalation for AAG. The tryptophan substitution (Y162W) appeared to be conservative, because the mutant protein retained a highly favorable equilibrium constant for flipping the 1,N6-ethenoadenine (ϵA) lesion, and the rate of N-glycosidic bond cleavage was identical to that of the wild-type enzyme. We assigned the tryptophan fluorescence signal from Y162W by removing two native tryptophan residues (W270A/W284A). Stopped-flow experiments then demonstrated that the change in tryptophan fluorescence of the Y162W mutant is extremely rapid upon binding to either damaged or undamaged DNA, much faster than the lesion-recognition and nucleotide flipping steps that were independently determined by monitoring the ϵA fluorescence. These observations suggest that intercalation by this aromatic residue is one of the earliest steps in the search for DNA damage and that this interaction is important for the progression of AAG from nonspecific searching to specific-recognition complexes.
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Affiliation(s)
- Jenna M Hendershot
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Patrick J O'Brien
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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40
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Adrian M, Winnerdy FR, Heddi B, Phan AT. Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding. Biophys J 2017; 113:775-784. [PMID: 28834714 DOI: 10.1016/j.bpj.2017.05.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.
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Affiliation(s)
- Michael Adrian
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
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41
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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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42
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Hendershot JM, O'Brien PJ. Transient Kinetic Methods for Mechanistic Characterization of DNA Binding and Nucleotide Flipping. Methods Enzymol 2017; 592:377-415. [PMID: 28668128 DOI: 10.1016/bs.mie.2017.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Enzymes that modify nucleobases in double-stranded genomic DNA, either as part of a DNA repair pathway or as an epigenetic modifying pathway, adopt a multistep pathway to locate target sites and reconfigure the DNA to gain access. Work on several different enzymes has shown that in almost all cases base flipping, also known as nucleotide flipping, is a key feature of specific site recognition. In this chapter, we discuss some of the strategies that can be used to perform a kinetic characterization for DNA binding and nucleotide flipping. The resulting kinetic and thermodynamic framework provides a platform for understanding substrate specificity, mechanisms of inhibition, and the roles of important amino acids. We use a human DNA repair glycosylase called alkyladenine DNA glycosylase as a case study, because this is one of the best-characterized nucleotide-flipping enzymes. However, the approaches that are described can be readily adapted to study other enzymes, and future studies are needed to understand the mechanism of substrate recognition in each individual case. As more enzymes are characterized, we can hope to uncover which features of DNA searching and nucleotide flipping are fundamental features shared by many different families of DNA modifying enzymes, and which features are specific to a particular enzyme. Such an understanding provides reasonable models for less characterized enzymes that are important for epigenetic DNA modification and DNA repair pathways.
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Affiliation(s)
| | - Patrick J O'Brien
- University of Michigan Medical School, Ann Arbor, MI, United States.
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43
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Kirsanova OV, Sergeev AV, Yasko IS, Gromova ES. The impact of 6-thioguanine incorporation into DNA on the function of DNA methyltransferase Dnmt3a. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:392-405. [PMID: 28498075 DOI: 10.1080/15257770.2017.1287921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The incorporation of chemotherapeutic agent 6-thioguanine (SG) into DNA is a prerequisite for its cytotoxic action. This modification of DNA impedes the activity of enzymes involved in DNA repair and replication. Here, using hemimethylated DNA substrates we demonstrated that DNA methylation by Dnmt3a-CD is reduced if DNA is damaged by the incorporation of SG into one or two CpG sites separated by nine base pairs. An increase in the number of SG substitutions did not enhance the effect. Dnmt3a-CD binding to either of SG-containing DNA substrates was not distorted. Our results suggest that SG incorporation into DNA may influence epigenetic regulation via DNA methylation.
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Affiliation(s)
- Olga V Kirsanova
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Alexander V Sergeev
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Ivan S Yasko
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Elizaveta S Gromova
- a Department of Chemistry , M. V. Lomonosov Moscow State University , Moscow , Russia
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44
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Hong T, Wu F, Fu B, Yuan Y, Xu J, Wang T, Zhou X. 5-Formylcytosine and 5-Carboxylcytosine Significantly Reduce the Catalytic Activity of Hhal DNA Methyltransferase. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tingting Hong
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Yushu Yuan
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Tianlu Wang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
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45
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Methyltransferase-Directed Labeling of Biomolecules and its Applications. Angew Chem Int Ed Engl 2017; 56:5182-5200. [PMID: 27943567 PMCID: PMC5502580 DOI: 10.1002/anie.201608625] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 01/01/2023]
Abstract
Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.
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Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale BiologySchool of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM)Station 17CH-1015LausanneSwitzerland
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Robert K. Neely
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
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46
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Die Methyltransferase-gesteuerte Markierung von Biomolekülen und ihre Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale Biology; School of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM); Station 17 CH-1015 Lausanne Schweiz
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Robert K. Neely
- School of Chemistry; University of Birmingham; Edgbaston Birmingham B15 2TT Großbritannien
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
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47
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Lindahl V, Villa A, Hess B. Sequence dependency of canonical base pair opening in the DNA double helix. PLoS Comput Biol 2017; 13:e1005463. [PMID: 28369121 PMCID: PMC5393899 DOI: 10.1371/journal.pcbi.1005463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/17/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair. The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.
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Affiliation(s)
- Viveca Lindahl
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Berk Hess
- Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm and Uppsala, Stockholm, Sweden
- * E-mail:
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48
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Kilin V, Gavvala K, Barthes NPF, Michel BY, Shin D, Boudier C, Mauffret O, Yashchuk V, Mousli M, Ruff M, Granger F, Eiler S, Bronner C, Tor Y, Burger A, Mély Y. Dynamics of Methylated Cytosine Flipping by UHRF1. J Am Chem Soc 2017; 139:2520-2528. [PMID: 28112929 PMCID: PMC5335914 DOI: 10.1021/jacs.7b00154] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation patterns, which are critical for gene expression, are replicated by DNA methyltransferase 1 (DNMT1) and ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) proteins. This replication is initiated by the recognition of hemimethylated CpG sites and further flipping of methylated cytosines (mC) by the Set and Ring Associated (SRA) domain of UHRF1. Although crystallography has shed light on the mechanism of mC flipping by SRA, tools are required to monitor in real time how SRA reads DNA and flips the modified nucleobase. To accomplish this aim, we have utilized two distinct fluorescent nucleobase surrogates, 2-thienyl-3-hydroxychromone nucleoside (3HCnt) and thienoguanosine (thG), incorporated at different positions into hemimethylated (HM) and nonmethylated (NM) DNA duplexes. Large fluorescence changes were associated with mC flipping in HM duplexes, showing the outstanding sensitivity of both nucleobase surrogates to the small structural changes accompanying base flipping. Importantly, the nucleobase surrogates marginally affected the structure of the duplex and its affinity for SRA at positions where they were responsive to base flipping, illustrating their promise as nonperturbing probes for monitoring such events. Stopped-flow studies using these two distinct tools revealed the fast kinetics of SRA binding and sliding to NM duplexes, consistent with its reader role. In contrast, the kinetics of mC flipping was found to be much slower in HM duplexes, substantially increasing the lifetime of CpG-bound UHRF1, and thus the probability of recruiting DNMT1 to faithfully duplicate the DNA methylation profile. The fluorescence-based approach using these two different fluorescent nucleoside surrogates advances the mechanistic understanding of the UHRF1/DNMT1 tandem and the development of assays for the identification of base flipping inhibitors.
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Affiliation(s)
- Vasyl Kilin
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas P. F. Barthes
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Benoît Y. Michel
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Dongwon Shin
- TriLink BioTechnologies, LLC., San Diego, California 92121, United States
| | - Christian Boudier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Olivier Mauffret
- LBPA, UMR 8113 CNRS, ENS Paris-Saclay, Université Paris Saclay, 94235 Cachan Cedex, France
| | - Valeriy Yashchuk
- Department of Physics, Kiev National Taras Shevchenko University, Kiev 01601, Ukraine
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Florence Granger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
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49
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Yang L, Adhikari J, Gross ML, Li L. Kinetic Isotope Effects and Hydrogen/Deuterium Exchange Reveal Large Conformational Changes During the Catalysis of the Clostridium acetobutylicum Spore Photoproduct Lyase. Photochem Photobiol 2017; 93:331-342. [PMID: 27992649 PMCID: PMC5315627 DOI: 10.1111/php.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e. the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical-transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium Clostridium acetobutylicum (Ca), the cysteine (at position 74) and the tyrosine are located on the opposite sides of a substrate-binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) . To test this hypothesis, we adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to show that C74(Ca) is located at a highly flexible region. The repair of dinucleotide SP TpT by SPL(Ca) is eight-fold to 10-fold slower than that by SPL(Bs) ; the process also generates a large portion of the aborted product TpTSO2- . SPL(Ca) exhibits apparent (D V) kinetic isotope effects (KIEs) of ~6 and abnormally large competitive (D V/K) KIEs (~20), both of which are much larger than the KIEs observed for SPL(Bs) . All these observations indicate that SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Davis MC, Kesthely CA, Franklin EA, MacLellan SR. The essential activities of the bacterial sigma factor. Can J Microbiol 2016; 63:89-99. [PMID: 28117604 DOI: 10.1139/cjm-2016-0576] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.
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Affiliation(s)
- Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Christopher A Kesthely
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Emily A Franklin
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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