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He X, Hull V, Thomas JA, Fu X, Gidwani S, Gupta YK, Black LW, Xu SY. Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference. Sci Rep 2015; 5:9747. [PMID: 25988532 PMCID: PMC4437046 DOI: 10.1038/srep09747] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 03/06/2015] [Indexed: 01/30/2023] Open
Abstract
The first reported Type IV restriction endonuclease (REase) GmrSD consists of GmrS
and GmrD subunits. In most bacteria, however, the gmrS and gmrD genes
are fused together to encode a single-chain protein. The fused coding sequence for
ECSTEC94C_1402 from E. coli strain STEC_94C was expressed in T7 Express. The
protein designated as Eco94GmrSD displays modification-dependent ATP-stimulated
REase activity on T4 DNA with glucosyl-5-hydroxymethyl-cytosines (glc-5hmC) and T4gt
DNA with 5-hydroxymethyl-cytosines (5hmC). A C-terminal 6xHis-tagged protein was
purified by two-column chromatography. The enzyme is active in Mg2+
and Mn2+ buffer. It prefers to cleave large glc-5hmC- or
5hmC-modified DNA. In phage restriction assays, Eco94GmrSD weakly restricted T4 and
T4gt, whereas T4 IPI*-deficient phage (Δip1) were restricted more
than 106-fold, consistent with IPI* protection of E. coli
DH10B from lethal expression of the closely homologous E. coli CT596 GmrSD.
Eco94GmrSD is proposed to belong to the His-Asn-His (HNH)-nuclease family by the
identification of a putative C-terminal REase catalytic site D507-H508-N522.
Supporting this, GmrSD variants D507A, H508A, and N522A displayed no endonuclease
activity. The presence of a large number of fused GmrSD homologs suggests that GmrSD
is an effective phage exclusion protein that provides a mechanism to thwart T-even
phage infection.
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Affiliation(s)
- Xinyi He
- 1] New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA [2] State Key Laboratory of Microbial Metabolism, and School of Life Sciences &Biotechnology Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
| | - Victoria Hull
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Julie A Thomas
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Green St, Baltimore, MD 21201-1503, USA
| | - Xiaoqing Fu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Sonal Gidwani
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Yogesh K Gupta
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Green St, Baltimore, MD 21201-1503, USA
| | - Shuang-yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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102
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Ouellette M, Jackson L, Chimileski S, Papke RT. Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Front Microbiol 2015; 6:251. [PMID: 25904898 PMCID: PMC4389544 DOI: 10.3389/fmicb.2015.00251] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/13/2015] [Indexed: 01/16/2023] Open
Abstract
Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis of H. volcanii strain H26 was performed using PacBio single molecule real-time (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the ΔHVO_A0006 strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria. It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s). Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Laura Jackson
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Scott Chimileski
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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103
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Sánchez-Romero MA, Cota I, Casadesús J. DNA methylation in bacteria: from the methyl group to the methylome. Curr Opin Microbiol 2015; 25:9-16. [PMID: 25818841 DOI: 10.1016/j.mib.2015.03.004] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine in bacterial genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the interaction of DNA-binding proteins with their cognate sites, and controls chromosome replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in bacterial physiology have been investigated by analyzing the contribution of individual methyl groups or small methyl group clusters to the control of DNA-protein interactions. Nowadays, single-molecule real-time sequencing can analyze the DNA methylation of the entire genome (the 'methylome'). Bacterial methylomes provide a wealth of information on the methylation marks present in bacterial genomes, and may open a new era in bacterial epigenomics.
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Affiliation(s)
| | - Ignacio Cota
- Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080 Seville, Spain
| | - Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080 Seville, Spain.
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104
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Barnes HE, Liu G, Weston CQ, King P, Pham LK, Waltz S, Helzer KT, Day L, Sphar D, Yamamoto RT, Forsyth RA. Selective microbial genomic DNA isolation using restriction endonucleases. PLoS One 2014; 9:e109061. [PMID: 25279840 PMCID: PMC4184833 DOI: 10.1371/journal.pone.0109061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/28/2014] [Indexed: 11/25/2022] Open
Abstract
To improve the metagenomic analysis of complex microbiomes, we have repurposed restriction endonucleases as methyl specific DNA binding proteins. As an example, we use DpnI immobilized on magnetic beads. The ten minute extraction technique allows specific binding of genomes containing the DpnI Gm6ATC motif common in the genomic DNA of many bacteria including γ-proteobacteria. Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background. Binding is very specific with less than 0.5% of human DNA bound. Next Generation Sequencing of input and enriched synthetic mixtures results in over 100-fold enrichment of target genomes relative to human and plant DNA. We also show comparable enrichment when sequencing complex microbiomes such as those from creek water and human saliva. The technique can be broadened to other restriction enzymes allowing for the selective enrichment of trace and unculturable organisms from complex microbiomes and the stratification of organisms according to restriction enzyme enrichment.
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Affiliation(s)
- Helen E. Barnes
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Guohong Liu
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Paula King
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Long K. Pham
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Shannon Waltz
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Laura Day
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Dan Sphar
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - R. Allyn Forsyth
- FLIR Systems, Inc., La Jolla, California, United States of America
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105
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Abstract
ABSTRACT
Since the discovery of restriction enzymes and the generation of the first recombinant DNA molecule over 40 years ago, molecular biology has evolved into a multidisciplinary field that has democratized the conversion of a digitized DNA sequence stored in a computer into its biological counterpart, usually as a plasmid, stored in a living cell. In this article, we summarize the most relevant tools that allow the swift assembly of DNA sequences into useful plasmids for biotechnological purposes. We cover the main components and stages in a typical DNA assembly workflow, namely
in silico
design,
de novo
gene synthesis, and
in vitro
and
in vivo
sequence assembly methodologies.
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106
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Shao C, Wang C, Zang J. Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2477-86. [PMID: 25195760 PMCID: PMC4157451 DOI: 10.1107/s139900471401606x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/10/2014] [Indexed: 11/13/2022]
Abstract
5-Hydroxymethylation is a curious modification of cytosine that was discovered some decades ago, but its functional role in eukaryotes still awaits elucidation. 5-Hydroxymethylcytosine is an epigenetic marker that is crucial for multiple biological processes. The profile is altered under certain disease conditions such as cancer, Huntington's disease and Alzheimer's disease. Using the DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq), the hydroxymethylome can be deciphered at the resolution of individual bases. The method is based on the enzymatic properties of AbaSI, a member of the PvuRts1I family of endonucleases. PvuRts1I is a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine over 5-methylcytosine and cytosine. In this study, the crystal structure of PvuRts1I was determined in order to understand and improve the substrate selectivity. A nuclease domain and an SRA-like domain are located at the N- and C-termini, respectively. Through comparison with other SRA-domain structures, the SRA-like domain was proposed to be the 5-hmC recognition module. Several mutants of PvuRts1I with enzymatic activity restricted to 5-hydroxymethylcytosine only were generated based on the structural analysis, and these enzyme variants are appropriate for separating the hydroxymethylome from the wider methylome.
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Affiliation(s)
- Chen Shao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Chengliang Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
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107
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Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains. Gut Pathog 2014; 6:36. [PMID: 25349631 PMCID: PMC4209512 DOI: 10.1186/s13099-014-0036-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/18/2014] [Indexed: 02/06/2023] Open
Abstract
Background Strains of Pediococcus pentosaceus from food and the human gastrointestinal tract have been widely identified, and some have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, we sequenced the whole genome of P. pentosaceus LI05 (CGMCC 7049), which was isolated from the fecal samples of healthy volunteers, and determined its ability to reduce acute liver injury. No other genomic information for gut-borne P. pentosaceus is currently available in the public domain. Results We obtained the draft genome of P. pentosaceus LI05, which was 1,751,578 bp in size and possessed a mean G + C content of 37.3%. This genome encoded an abundance of proteins that were protective against acids, bile salts, heat, oxidative stresses, enterocin A, arsenate and universal stresses. Important adhesion proteins were also encoded by the genome. Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate. A comparison of P. pentosaceus LI05 with all known genomes of food-borne P. pentosaceus strains (ATCC 25745, SL4 and IE-3) revealed that it possessed four novel exopolysaccharide biosynthesis proteins, additional putative environmental stress tolerance proteins and phage-related proteins. Conclusions This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses. We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties.
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108
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Oliveira PH, Touchon M, Rocha EPC. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 2014; 42:10618-31. [PMID: 25120263 PMCID: PMC4176335 DOI: 10.1093/nar/gku734] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/29/2014] [Accepted: 07/30/2014] [Indexed: 01/21/2023] Open
Abstract
The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
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Affiliation(s)
- Pedro H Oliveira
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
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109
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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110
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Gutjahr A, Xu SY. Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA. Nucleic Acids Res 2014; 42:e77. [PMID: 24609382 PMCID: PMC4027164 DOI: 10.1093/nar/gku192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
N.ϕGamma is a strand-specific and site-specific DNA nicking enzyme (YCG↓GT or AC↑CGR). Here we describe the isolation of single and double mutants of N.ϕGamma with attenuated activity. The nicking domains (NDs) of E59A and 11 double mutants were fused to the 5mCG-binding domain of MBD2 and generated fusion enzymes that preferentially nick 5mCG-modified DNA. The CG dinucleotide can be modified by C5 methyltransferases (MTases) such as M.SssI, M.HhaI or M.HpaII to create composite sites AC↑YGG N(8-15) 5mCG. We also constructed a fusion enzyme 2xMBD2-ND(N.BceSVIII) targeting more frequent composite sites AS↑YS N(5-12) 5mCG in Mn2+ buffer. 5mCG-dependent nicking requires special digestion conditions in high salt (0.3 M KCl) or in Ni2+ buffer. The fusion enzyme can be used to nick and label 5mCG-modified plasmid and genomic DNAs with fluorescently labeled Cy3-dUTP and potentially be useful for diagnostic applications, DNA sequencing and optical mapping of epigenetic markers. The importance of the predicted catalytic residues D89, H90, N106 and H115 in N.ϕGamma was confirmed by mutagenesis. We found that the wild-type enzyme N.ϕGamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking activity is sub-optimal compared to the activity in Mg2+ buffer.
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Affiliation(s)
- Alice Gutjahr
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shuang-yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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111
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Dynan W, Fox K, Stoddard B. Editorial: NAR surveys the past, present and future of restriction endonucleases. Nucleic Acids Res 2014; 42:1-2. [PMID: 24376271 PMCID: PMC3874147 DOI: 10.1093/nar/gkt1324] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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112
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Ghosh A, Passaris I, Tesfazgi Mebrhatu M, Rocha S, Vanoirbeek K, Hofkens J, Aertsen A. Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli. Nucleic Acids Res 2014; 42:3908-18. [PMID: 24423871 PMCID: PMC3973329 DOI: 10.1093/nar/gkt1370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction endonuclease of Escherichia coli K12, in response to different conditions. In absence of stimuli triggering its activity, Mrr was found to be strongly associated with the nucleoid as a number of discrete foci, suggesting the presence of Mrr hotspots on the chromosome. Previously established elicitors of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or expression of the HhaII methyltransferase, both caused nucleoid condensation and an unexpected coalescence of Mrr foci. However, although the resulting Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr typically led to cellular blebbing, suggesting a link between chromosome and cellular integrity. Interestingly, Mrr variants could be isolated that were specifically compromised in either HhaII- or HP-dependent activation, underscoring a mechanistic difference in the way both triggers activate Mrr. In general, our results reveal that Mrr can take part in complex spatial distributions on the nucleoid and can be engaged in distinct modes of activity.
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Affiliation(s)
- Anirban Ghosh
- Department of Microbial and Molecular Systems (M2S), Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium and Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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113
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Restriction-Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus. Methods Mol Biol 2014; 1373:9-23. [PMID: 25646604 DOI: 10.1007/7651_2014_180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic manipulation is a powerful approach to study fundamental aspects of bacterial physiology, metabolism, and pathogenesis. Most Staphylococcus aureus strains are remarkably difficult to genetically manipulate as they possess strong host defense mechanisms that protect bacteria from cellular invasion by foreign DNA. In S. aureus these bacterial "immunity" mechanisms against invading genomes are mainly associated with restriction-modification systems. To date, prokaryotic restriction-modification systems are classified into four different types (Type I-IV), all of which have been found in the sequenced S. aureus genomes. This chapter describes the roles, classification, mechanisms of action of different types of restriction-modification systems and the recent advances in the biology of restriction and modification in S. aureus.
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