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Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A. RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res 2024; 52:5195-5208. [PMID: 38567730 PMCID: PMC11109961 DOI: 10.1093/nar/gkae243] [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: 09/19/2023] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria Yanovskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Olga Musharova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Piscataway, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Manzer HS, Doran KS. Complete m6A and m4C methylomes for group B streptococcal clinical isolates CJB111, A909, COH1, and NEM316. Microbiol Resour Announc 2024; 13:e0073323. [PMID: 38099685 PMCID: PMC10793328 DOI: 10.1128/mra.00733-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 01/18/2024] Open
Abstract
Group B Streptococcus (GBS) is known to colonize the female reproductive tract and causes adverse pregnancy outcomes and neonatal disease. DNA methylation is a common mechanism for both phage defense and transcriptional regulation. Here, we report the m6A and m4C methylomes of four clinical GBS isolates, CJB111, A909, COH1, and NEM316.
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Affiliation(s)
- Haider S. Manzer
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelly S. Doran
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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3
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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4
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Wang J, Huang C, Guo K, Ma L, Meng X, Wang N, Huo YX. Converting Escherichia coli MG1655 into a chemical overproducer through inactivating defense system against exogenous DNA. Synth Syst Biotechnol 2020; 5:333-342. [PMID: 33102829 PMCID: PMC7568196 DOI: 10.1016/j.synbio.2020.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli strain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency and plasmid instability. Herein, we conducted genetic modifications at a serial of loci of MG1655 genome, generating a robust and universal host strain JW128 with higher transformation efficiency and plasmid stability that can be used to efficiently produce desired chemicals after introducing the corresponding synthetic pathways. Using JW128 as the host, the titer of isobutanol reached 5.76 g/L in shake-flask fermentation, and the titer of lycopene reached 1.91 g/L in test-tube fermentation, 40-fold and 5-fold higher than that of original MG1655, respectively. These results demonstrated JW128 is a promising chassis for high-level production of value-added chemicals.
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Affiliation(s)
- Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Kai Guo
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiangyu Meng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- Corresponding author.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
- Corresponding author. Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.
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5
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Isolation and characterization of spontaneous phage-resistant mutants of Lactobacillus paracasei. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Structural basis underlying complex assembly and conformational transition of the type I R-M system. Proc Natl Acad Sci U S A 2017; 114:11151-11156. [PMID: 28973912 DOI: 10.1073/pnas.1711754114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type I restriction-modification (R-M) systems are multisubunit enzymes with separate DNA-recognition (S), methylation (M), and restriction (R) subunits. Despite extensive studies spanning five decades, the detailed molecular mechanisms underlying subunit assembly and conformational transition are still unclear due to the lack of high-resolution structural information. Here, we report the atomic structure of a type I MTase complex (2M+1S) bound to DNA and cofactor S-adenosyl methionine in the "open" form. The intermolecular interactions between M and S subunits are mediated by a four-helix bundle motif, which also determines the specificity of the interaction. Structural comparison between open and previously reported low-resolution "closed" structures identifies the huge conformational changes within the MTase complex. Furthermore, biochemical results show that R subunits prefer to load onto the closed form MTase. Based on our results, we proposed an updated model for the complex assembly. The work reported here provides guidelines for future applications in molecular biology.
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7
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Jeong H, Sim YM, Kim HJ, Lee SJ. Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA +). Front Microbiol 2017; 8:585. [PMID: 28421066 PMCID: PMC5379014 DOI: 10.3389/fmicb.2017.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/21/2017] [Indexed: 01/26/2023] Open
Abstract
There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang UniversityAnseong, South Korea
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8
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Youell J, Sikora AE, Vejsadová Š, Weiserova M, Smith JR, Firman K. Cofactor induced dissociation of the multifunctional multisubunit EcoR124I investigated using electromobility shift assays, AFM and SPR. RSC Adv 2017. [DOI: 10.1039/c7ra07505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have applied three techniques to the study of subunit assembly of the Type IC Restriction–Modification enzyme EcoR124I.
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Affiliation(s)
- James Youell
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Aneta E. Sikora
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Štěpánka Vejsadová
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Marie Weiserova
- Institute of Microbiology
- ASCR, v.v.i
- 142 20 Prague 4
- Czech Republic
| | - James R. Smith
- School of Pharmacy and Biomedical Sciences
- University of Portsmouth
- Portsmouth PO1 2DT
- UK
| | - Keith Firman
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
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9
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Ershova AS, Rusinov IS, Spirin SA, Karyagina AS, Alexeevski AV. Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology. BIOCHEMISTRY (MOSCOW) 2016; 80:1373-86. [PMID: 26567582 DOI: 10.1134/s0006297915100193] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on methylation status of their recognition site. It allows them to protect bacterial cells from invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in adaptation of bacteria to change in their environmental conditions. R-M systems can be essential for host colonization by pathogenic bacteria. Phase variation and intragenomic recombinations are sources of the fast evolution of the specificity of R-M systems. This review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.
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Affiliation(s)
- A S Ershova
- Belozerksy Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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10
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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11
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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12
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Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev 2013; 77:53-72. [PMID: 23471617 PMCID: PMC3591985 DOI: 10.1128/mmbr.00044-12] [Citation(s) in RCA: 376] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.
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Affiliation(s)
- Kommireddy Vasu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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13
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Roberts GA, Stephanou AS, Kanwar N, Dawson A, Cooper LP, Chen K, Nutley M, Cooper A, Blakely GW, Dryden DTF. Exploring the DNA mimicry of the Ocr protein of phage T7. Nucleic Acids Res 2012; 40:8129-43. [PMID: 22684506 PMCID: PMC3439906 DOI: 10.1093/nar/gks516] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 11/30/2022] Open
Abstract
DNA mimic proteins have evolved to control DNA-binding proteins by competing with the target DNA for binding to the protein. The Ocr protein of bacteriophage T7 is the most studied DNA mimic and functions to block the DNA-binding groove of Type I DNA restriction/modification enzymes. This binding prevents the enzyme from cleaving invading phage DNA. Each 116 amino acid monomer of the Ocr dimer has an unusual amino acid composition with 34 negatively charged side chains but only 6 positively charged side chains. Extensive mutagenesis of the charges of Ocr revealed a regression of Ocr activity from wild-type activity to partial activity then to variants inactive in antirestriction but deleterious for cell viability and lastly to totally inactive variants with no deleterious effect on cell viability. Throughout the mutagenesis the Ocr mutant proteins retained their folding. Our results show that the extreme bias in charged amino acids is not necessary for antirestriction activity but that less charged variants can affect cell viability by leading to restriction proficient but modification deficient cell phenotypes.
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Affiliation(s)
- Gareth A. Roberts
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Augoustinos S. Stephanou
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Nisha Kanwar
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Angela Dawson
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Laurie P. Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Kai Chen
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Margaret Nutley
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Alan Cooper
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - Garry W. Blakely
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
| | - David T. F. Dryden
- EastChem School of Chemistry, School of Physics and Astronomy, The University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JZ, School of Chemistry, The University of Glasgow, Glasgow G12 8QQ and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK
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14
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Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DT. Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes Dev 2012; 26:92-104. [PMID: 22215814 PMCID: PMC3258970 DOI: 10.1101/gad.179085.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/14/2011] [Indexed: 11/24/2022]
Abstract
Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.
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Affiliation(s)
- Christopher K. Kennaway
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James E. Taylor
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Chun Feng Song
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Wojciech Potrzebowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
| | - William Nicholson
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - John H. White
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Anna Swiderska
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Agnieszka Obarska-Kosinska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
| | - Philip Callow
- Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France
| | - Laurie P. Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Gareth A. Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Jean-Baptiste Artero
- Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France
- EPSAM and ISTM, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, PL-61-614 Poznan, Poland
| | - John Trinick
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - G. Geoff Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - David T.F. Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
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15
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Amarir-Bouhram J, Goin M, Petit MA. Low efficiency of homology-facilitated illegitimate recombination during conjugation in Escherichia coli. PLoS One 2011; 6:e28876. [PMID: 22194937 PMCID: PMC3240628 DOI: 10.1371/journal.pone.0028876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/16/2011] [Indexed: 12/01/2022] Open
Abstract
Homology-facilitated illegitimate recombination has been described in three naturally competent bacterial species. It permits integration of small linear DNA molecules into the chromosome by homologous recombination at one end of the linear DNA substrate, and illegitimate recombination at the other end. We report that homology-facilitated illegitimate recombination also occurs in Escherichia coli during conjugation with small non-replicative plasmids, but at a low frequency of 3×10−10 per recipient cell. The fate of linear DNA in E. coli is either RecBCD-dependent degradation, or circularisation by ligation, and integration into the chromosome by single crossing-over. We also report that the observed single crossing-overs are recA-dependent, but essentially recBCD, and recFOR independent. This suggests that other, still unknown, proteins may act as mediator for the loading of RecA on DNA during single crossing-over recombination in E. coli.
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Affiliation(s)
- Jihane Amarir-Bouhram
- INRA, UMR 1319, Micalis, Jouy en Josas, France
- AgroParisTech, UMR 1319, Micalis, Jouy en Josas, France
| | - Mélodie Goin
- INRA, UMR 1319, Micalis, Jouy en Josas, France
- AgroParisTech, UMR 1319, Micalis, Jouy en Josas, France
| | - Marie-Agnès Petit
- INRA, UMR 1319, Micalis, Jouy en Josas, France
- AgroParisTech, UMR 1319, Micalis, Jouy en Josas, France
- * E-mail:
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16
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Roberts GA, Cooper LP, White JH, Su TJ, Zipprich JT, Geary P, Kennedy C, Dryden DTF. An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme. Nucleic Acids Res 2011; 39:7667-76. [PMID: 21685455 PMCID: PMC3177214 DOI: 10.1093/nar/gkr480] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Type I DNA restriction/modification systems are oligomeric enzymes capable of switching between a methyltransferase function on hemimethylated host DNA and an endonuclease function on unmethylated foreign DNA. They have long been believed to not turnover as endonucleases with the enzyme becoming inactive after cleavage. Cleavage is preceded and followed by extensive ATP hydrolysis and DNA translocation. A role for dissociation of subunits to allow their reuse has been proposed for the EcoR124I enzyme. The EcoKI enzyme is a stable assembly in the absence of DNA, so recycling was thought impossible. Here, we demonstrate that EcoKI becomes unstable on long unmethylated DNA; reuse of the methyltransferase subunits is possible so that restriction proceeds until the restriction subunits have been depleted. We observed that RecBCD exonuclease halts restriction and does not assist recycling. We examined the DNA structure required to initiate ATP hydrolysis by EcoKI and find that a 21-bp duplex with single-stranded extensions of 12 bases on either side of the target sequence is sufficient to support hydrolysis. Lastly, we discuss whether turnover is an evolutionary requirement for restriction, show that the ATP hydrolysis is not deleterious to the host cell and discuss how foreign DNA occasionally becomes fully methylated by these systems.
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17
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Zavilgelsky GB, Rastorguev SM. Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes. Mol Biol 2009. [DOI: 10.1134/s0026893309020071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 2009; 37:762-70. [PMID: 19074193 PMCID: PMC2647291 DOI: 10.1093/nar/gkn988] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 11/20/2008] [Accepted: 11/21/2008] [Indexed: 12/25/2022] Open
Abstract
Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.
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Affiliation(s)
- Christopher K. Kennaway
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Agnieszka Obarska-Kosinska
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - John H. White
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Irina Tuszynska
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Laurie P. Cooper
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Janusz M. Bujnicki
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - John Trinick
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - David T. F. Dryden
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
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19
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Hobman JL, Penn CW, Pallen MJ. Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully? Mol Microbiol 2007; 64:881-5. [PMID: 17501914 DOI: 10.1111/j.1365-2958.2007.05710.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Escherichia coli stands unchallenged as biology's premier model organism. However, we propose, equipped with insights from the post-genomic era, a contrary view: that microbiology's chief idol has feet of clay. E. coli laboratory strains, particularly E. coli K-12, are far from model citizens, but instead degenerate and deceitful delinquents growing old disgracefully in our scientific institutions. E. coli K-12 is neither archetype nor ancestor. In addition, it has a far from optimal provenance for a model organism, with strong grounds for believing that current versions of the strain are quite distinct from any original wild-type free-living ancestor. In addition, it is usually studied under conditions far removed from its natural habitats and in ignorance of the selective pressures that have shaped its evolution. Fortunately, a flood of information from high-throughput genome sequencing, together with a new 'eco-evo' view of this model organism, promises to help put K-12 better into context.
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Affiliation(s)
- Jon L Hobman
- School of Biosciences, The Medical School, The University of Birmingham, Edgbaston, Birmingham, UK
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20
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Dryden DTF. DNA mimicry by proteins and the control of enzymatic activity on DNA. Trends Biotechnol 2006; 24:378-82. [PMID: 16815576 DOI: 10.1016/j.tibtech.2006.06.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 05/03/2006] [Accepted: 06/14/2006] [Indexed: 11/18/2022]
Abstract
Cells are unable to perform any function on their DNA in the absence of proteins, and it is of vital importance that these proteins only perform their function at appropriate times during the cell cycle. Thus, DNA-binding proteins are always controlled by a wide range of other factors, primarily other proteins. These controlling factors usually block access of the protein to the DNA, often operating by simple competitive inhibition. However, it has recently been demonstrated that DNA-binding proteins can be controlled by the direct binding of the control protein to the DNA-binding site on the first protein. The structures of these control proteins have revealed that they mimic the structure and electrostatics of DNA. This review highlights the roles of DNA mimics in the control of DNA-binding proteins, suggests other possible candidate proteins using DNA mimicry, and puts forward a range of potential uses of DNA mimics.
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Affiliation(s)
- David T F Dryden
- School of Chemistry, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK.
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21
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Obarska A, Blundell A, Feder M, Vejsadová Š, Šišáková E, Weiserová M, Bujnicki JM, Firman K. Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res 2006; 34:1992-2005. [PMID: 16614449 PMCID: PMC1435980 DOI: 10.1093/nar/gkl132] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restriction–modification (R-M) enzymes MjaXIP and MgeORF438 have provided a convenient structural template for analysis of the more extensively characterized members of this interesting family of multisubunit molecular motors. Here, we present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative modelling, followed by optimization of inter-subunit contacts by energy minimization. The model of M.EcoR124I has allowed identification of a number of functionally important residues that appear to be involved in DNA-binding. In addition, we have mapped onto the model the location of several new mutations of the hsdS gene of M.EcoR124I that were produced by misincorporation mutagenesis within the central conserved region of hsdS, we have mapped all previously identified DNA-binding mutants of TRD2 and produced a detailed analysis of the location of surface-modifiable lysines. The model structure, together with location of the mutant residues, provides a better background on which to study protein–protein and protein–DNA interactions in Type I R-M systems.
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Affiliation(s)
| | - Alex Blundell
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
| | | | - Štěpánka Vejsadová
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | - Eva Šišáková
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | - Marie Weiserová
- Institute of Microbiology, Czech Academy of SciencesVidenska 1083, 142 20 Prague 4, Czech Republic
| | | | - Keith Firman
- IBBS Biophysics Laboratories, School of Biological Sciences, University of PortsmouthKing Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
- To whom all correspondence should be addressed. Tel: +44 2392 842059; Fax: +44 2392 842070;
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22
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Abstract
SAM (S-adenosylmethionine, also known as AdoMet) is well known as the methyl donor for the majority of methyltransferases that modify DNA, RNA, histones and other proteins, dictating replicational, transcriptional and translational fidelity, mismatch repair, chromatin modelling, epigenetic modifications and imprinting, which are all topics of great interest and importance in cancer research and aging. In total, 15 superfamilies of SAM-binding proteins have been identified, with many additional functions varying from methylation of phospholipids and small molecules such as arsenic to synthesis of polyamines or radical formation. SAM is regenerated from demethylated SAM via the methionine cycle, which involves folate. Imbalance of this cycle in humans, e.g. through folate shortage via dietary insufficiency, alcohol abuse, arsenic poisoning or hereditary factors, leads to depletion of SAM and human disease. In addition to its role as a methyl donor to modification enzymes that protect bacterial DNA against cognate restriction, SAM also serves as a co-factor for nucleases such as the type I restriction enzyme EcoKI, which is unable to restrict DNA in the absence of SAM. Finally, on a completely different tack, SAM can bind to certain RNA structures called riboswitches that control transcription or translation. In this way, expression of multiple genes can be regulated in a SAM-dependent manner, an unexpected finding that opens up new avenues into gene control. This minireview discusses some of these diverse and amazing roles of this small metabolite.
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23
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Zavilgelsky GB, Letuchaya TA, Rastorguev SM. Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406030045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Abstract
Bacteriophages possess attributes that appear to be attractive to those searching for novel ways to control foodborne pathogens and spoilage organisms. These phages have a history of safe use, can be highly host specific, and replicate in the presence of a host. Campylobacter, Salmonella, and Listeria monocytogenes and various spoilage organisms have responded to phage control on some foods. However, the use of phages as biocontrol agents is complicated by factors such as an apparent requirement for a threshold level of host before replication can proceed and by suboptimal performance, at best, at temperatures beneath the optimum for the host. This review is a summary of the information on these issues and includes brief descriptions of alternative phage-based strategies for control of foodborne pathogens.
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Affiliation(s)
- J A Hudson
- Food Safety Programme, ESR Ltd., P.O. Box 29-181, Ilam, Christchurch, New Zealand.
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25
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Su TJ, Connolly BA, Darlington C, Mallin R, Dryden DTF. Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase. Nucleic Acids Res 2004; 32:2223-30. [PMID: 15107490 PMCID: PMC407817 DOI: 10.1093/nar/gkh531] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2-aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2-aminopurine.
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Affiliation(s)
- T-J Su
- School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
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