1
|
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proc Natl Acad Sci U S A 2020; 117:14322-14330. [PMID: 32518115 DOI: 10.1073/pnas.2002933117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Phosphorothioate (PT) DNA modifications-in which a nonbonding phosphate oxygen is replaced with sulfur-represent a widespread, horizontally transferred epigenetic system in prokaryotes and have a highly unusual property of occupying only a small fraction of available consensus sequences in a genome. Using Salmonella enterica as a model, we asked a question of fundamental importance: How do the PT-modifying DndA-E proteins select their GPSAAC/GPSTTC targets? Here, we applied innovative analytical, sequencing, and computational tools to discover a novel behavior for DNA-binding proteins: The Dnd proteins are "parked" at the G6mATC Dam methyltransferase consensus sequence instead of the expected GAAC/GTTC motif, with removal of the 6mA permitting extensive PT modification of GATC sites. This shift in modification sites further revealed a surprising constancy in the density of PT modifications across the genome. Computational analysis showed that GAAC, GTTC, and GATC share common features of DNA shape, which suggests that PT epigenetics are regulated in a density-dependent manner partly by DNA shape-driven target selection in the genome.
Collapse
|
2
|
Crouzier L, Dubois C, Wengel J, Veedu RN. Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases. Bioorg Med Chem Lett 2012; 22:4836-8. [PMID: 22727669 DOI: 10.1016/j.bmcl.2012.05.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/10/2012] [Accepted: 05/10/2012] [Indexed: 01/30/2023]
Abstract
Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far. We herein for the first time report cleavage by restriction endonuclease of LNA-modified DNA oligonucleotides. The experiments revealed that RsaI is an efficient enzyme capable of recognizing and cleaving LNA-modified DNA oligonucleotides. Furthermore, introduction of LNA nucleotides protects against cleavage by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI.
Collapse
Affiliation(s)
- Lucile Crouzier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | | | | |
Collapse
|
3
|
Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A 2011; 108:2963-8. [PMID: 21285367 PMCID: PMC3041111 DOI: 10.1073/pnas.1017261108] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
Collapse
Affiliation(s)
- Lianrong Wang
- Department of Biological Engineering
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Shi Chen
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Kevin L. Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR 97331; and
| | | | | | | | | | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael Cutler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Eric J. Alm
- Department of Biological Engineering
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jarone Pinhassi
- Marine Microbiology, School of Natural Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
- College of Pharmacy, Wuhan University, Wuhan 430071, China
| | - Peter C. Dedon
- Department of Biological Engineering
- Center for Environmental Health Sciences, and
| |
Collapse
|
4
|
Kuznetsova SA, Blumenfeld M, Vasseur M, Shabarova ZA. Synthesis and Properties of DNA Dumbbells Containing Chemically Active Substituted Pyrophosphate Internucleotide Groups. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608007390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
6
|
Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)35836-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
7
|
Iyengar R, Bhat M, Riser M, Birnbaumer L. Receptor-specific desensitization of the S49 lymphoma cell adenylyl cyclase. Unaltered behavior of the regulatory component. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69325-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|