A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element
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Catalytic Domain of Plasmid Pad1 Relaxase Trax Defines a Group Of
Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases María Victoria Franciaa,1, Don B. Clewellb,c, Fernando de la Cruzd, and Gabriel Moncaliánd aServicio de Microbiología, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla, Santander 39008, Spain; bDepartment of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, MI 48109; cDepartment of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109; and dDepartamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria–Consejo Superior de Investigaciones Científicas–Sociedad para el Desarrollo Regional de Cantabria, Santander 39011, Spain Edited by Roy Curtiss III, Arizona State University, Tempe, AZ, and approved July 9, 2013 (received for review May 30, 2013) Plasmid pAD1 is a 60-kb conjugative element commonly found in known relaxases show two characteristic sequence motifs, motif I clinical isolates of Enterococcus faecalis. The relaxase TraX and the containing the catalytic Tyr residue (which covalently attaches to primary origin of transfer oriT2 are located close to each other and the 5′ end of the cleaved DNA) and motif III with the His-triad have been shown to be essential for conjugation. The oriT2 site essential for relaxase activity (facilitating the cleavage reaction contains a large inverted repeat (where the nic site is located) by activation of the catalytic Tyr). This His-triad has been used as adjacent to a series of short direct repeats. TraX does not show a relaxase diagnostic signature (12). fi any of the typical relaxase sequence motifs but is the prototype of Plasmid pAD1 relaxase, TraX, was identi ed (9) and shown to oriT2 a unique family of relaxases (MOB ). -
Processivity of DNA Polymerases: Two Mechanisms, One Goal Zvi Kelman1*, Jerard Hurwitz1 and Mike O’Donnell2
Minireview 121 Processivity of DNA polymerases: two mechanisms, one goal Zvi Kelman1*, Jerard Hurwitz1 and Mike O’Donnell2 Replicative DNA polymerases are highly processive Processive DNA synthesis by cellular replicases and the enzymes that polymerize thousands of nucleotides without bacteriophage T4 replicase dissociating from the DNA template. The recently Until recently, the only mechanism for high processivity determined structure of the Escherichia coli bacteriophage that was understood in detail was that utilized by cellular T7 DNA polymerase suggests a unique mechanism that replicases and the replicase of bacteriophage T4. This underlies processivity, and this mechanism may generalize mechanism involves a ring-shaped protein called a ‘DNA to other replicative polymerases. sliding clamp’ that encircles the DNA and tethers the polymerase catalytic unit to the DNA [3,4]. The three- Addresses: 1Department of Molecular Biology, Memorial Sloan- dimensional structures of several sliding clamps have been Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, 2 determined: the eukaryotic proliferating cell nuclear USA and Laboratory of DNA Replication, Howard Hughes Medical β Institute, The Rockefeller University, 1230 York Avenue, New York, NY antigen (PCNA) [5,6]; the subunit of the prokaryotic 10021, USA. DNA polymerase III [7]; and the bacteriophage T4 gene 45 protein (gp45) (J Kuriyan, personal communication) *Corresponding author. (Figure 1). The overall structure of these clamps is very E-mail: [email protected] similar; the PCNA, β subunit and gp45 rings are super- Structure 15 February 1998, 6:121–125 imposable [8]. Each ring has similar dimensions and a http://biomednet.com/elecref/0969212600600121 central cavity large enough to accommodate duplex DNA (Figure 1). -
The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
The Bacterial Conjugation Protein Trwb Resembles Ring Helicases And
letters to nature metabolically labelled with BrdU (10 mM, 4 h), trypsinized, and ®xed with 70% ethanol. 17. Stampfer, M. R. et al. Gradual phenotypic conversion associated with immortalization of cultured Nuclei were isolated and stained with propidium iodide and FITC-conjugated anti-BrdU human mammary epithelial cells. Mol. Biol. Cell 8, 2391±2405 (1997). antibodies (Becton Dickinson, USA), as described7. Flow cytometry was performed on a 18. Karlseder, J., Broccoli, D., Dai, Y., Hardy, S. & de Lange, T. p53- and ATM-dependent apoptosis FACS Sorter (Becton Dickinson). All analysed events were gated to remove debris and induced by telomeres lacking TRF2. Science 283, 1321±1325 (1999). aggregates. 19. Artandi, S. E. et al. Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice. Nature 406, 641±645 (2000). Cell death assays 20. Chin, L. et al. p53 De®ciency rescues the adverse effects of telomere loss and cooperates with telomere dysfunction to accelerate carcinogenesis. Cell 97, 527±538 (1999). TUNEL assay for DNA fragmentation was done using an In Situ Cell Death Detection kit 21. Alcorta, D. A. et al. Involvement of the cyclin-dependent kinase inhibitor p16 (INK4A) in replicative (BMB), according to manufacturer's protocol. Alternatively, cells were stained with senescence of normal human ®broblasts. Proc. Natl Acad. Sci. USA 92, 13742±13747 (1996). Annexin-V-FLUOR (BMB) and propidium iodide, and analysed by ¯uorescence 22. Hara, E. et al. Regulation of p16CDKN2 expression and its implications for cell immortalization and microscopy. senescence. Mol. Cell. Biol. 16, 859±867 (1996). 23. Burbano, R. R. et al. -
Sequence-Specific DNA Nicking Endonucleases
BioMol Concepts 2015; 6(4): 253–267 Review Open Access Shuang-yong Xu* Sequence-specific DNA nicking endonucleases DOI 10.1515/bmc-2015-0016 Received May 20, 2015; accepted June 24, 2015 Introduction In this article, I will discuss natural DNA nicking endo- nucleases (NEases or nickases) with 3- to 7-bp specificities, Abstract: A group of small HNH nicking endonucleases e.g. Nt.CviPII (↓CCD, the down arrow indicates the nicked (NEases) was discovered recently from phage or prophage strand as shown) originally found in chlorella virus (1), genomes that nick double-stranded DNA sites ranging engineered NEases such as Nt.BspQI (GCTCTTCN↓), and from 3 to 5 bp in the presence of Mg2+ or Mn2+. The cosN site Nt.BbvCI (CC↓TCAGC) engineered from BspQI and BbvCI of phage HK97 contains a gp74 nicking site AC↑CGC, which restriction endonucleases (REases) (2, 3). The other group is similar to AC↑CGR (R = A/G) of N.φGamma encoded by of DNA NEases contains natural or engineered enzymes Bacillus phage Gamma. A minimal nicking domain of 76 with more than 8-bp target sites, which includes group I amino acid residues from N.φGamma could be fused to intron-encoded homing endonucleases (HEs) (4, 5), other DNA binding partners to generate chimeric NEases engineered nicking variants from LAGLIDAG HEs (6–8), with new specificities. The biological roles of a few small engineered TALE nucleases (TALENs) by fusion of tran- HNH endonucleases (HNHE, gp74 of HK97, gp37 of φSLT, scription activator-like effector (TALE) repeat domain with φ12 HNHE) have been demonstrated in phage and patho- FokI nuclease domain or a MutH nicking variant (9–11), ZF genicity island DNA packaging. -
Plasmid Replication-Associated Single-Strand-Specific
12858–12873 Nucleic Acids Research, 2020, Vol. 48, No. 22 Published online 3 December 2020 doi: 10.1093/nar/gkaa1163 Plasmid replication-associated single-strand-specific methyltransferases Alexey Fomenkov 1,*, Zhiyi Sun1, Iain A. Murray 1, Cristian Ruse1, Colleen McClung1, Yoshiharu Yamaichi 2, Elisabeth A. Raleigh 1,* and Richard J. Roberts1,* 1New England Biolabs Inc., 240 County Road, Ipswich, MA, USA and 2Universite´ Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Downloaded from https://academic.oup.com/nar/article/48/22/12858/6018438 by guest on 24 September 2021 Received August 06, 2020; Revised November 10, 2020; Editorial Decision November 11, 2020; Accepted November 12, 2020 ABSTRACT RM-associated modification and the diversity of associ- ated functions remains incompletely understood (3). Long- Analysis of genomic DNA from pathogenic strains read, modification-sensitive SMRT sequencing technology of Burkholderia cenocepacia J2315 and Escherichia has facilitated sequencing and assembly of a wide variety coli O104:H4 revealed the presence of two unusual of genomes and also clarified the modification repertoire. MTase genes. Both are plasmid-borne ORFs, carried Detection of the modification status of bases is possible by pBCA072 for B. cenocepacia J2315 and pESBL for for m6A, m4C and oxidized forms of m5C modified bases E. coli O104:H4. Pacific Biosciences SMRT sequenc- (m5hC and 5caC) (4). Recently, high throughput analy- ing was used to investigate DNA methyltransferases sis of 230 diverse bacterial and archaeal methylomes strik- M.BceJIII and M.EcoGIX, using artificial constructs. ingly revealed that almost 50% of organisms harbor Type Mating properties of engineered pESBL derivatives II DNA methyltransferases (MTase) homologs with no ap- were also investigated. -
Structural Basis of a Histidine-DNA Nicking/Joining Mechanism for Gene Transfer and Promiscuous Spread of Antibiotic Resistance
Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance Radoslaw Plutaa,b,1,2, D. Roeland Boera,b,1,3, Fabián Lorenzo-Díazc,4, Silvia Russia,b,5, Hansel Gómeza,d, Cris Fernández-Lópezc, Rosa Pérez-Luquea,b, Modesto Orozcoa,d,e, Manuel Espinosac, and Miquel Colla,b,6 aInstitute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; bMolecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain; cBiological Research Center, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain; dJoint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; and eDepartment of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain Edited by Nancy L. Craig, Johns Hopkins University School of Medicine, Baltimore, MD, and approved June 28, 2017 (received for review February 23, 2017) Relaxases are metal-dependent nucleases that break and join DNA the relaxase assembles with other proteins participating in HGT, for the initiation and completion of conjugative bacterial gene namely the coupling protein and the proteins that constitute the transfer. Conjugation is the main process through which antibiotic type IV secretion system (T4SS). To date, relaxase-mediated nu- resistance spreads among bacteria, with multidrug-resistant staph- cleophilic attack at the nic site has been shown to generate a co- ylococci and streptococci infections posing major threats to human valent linkage between a tyrosine residue and the 5′-phosphate health. The MOBV family of relaxases accounts for approximately DNA of the cleaved dinucleotide (8). -
Synergy of Topoisomerase and Structural-Maintenance
Synergy of topoisomerase and structural-maintenance- of-chromosomes proteins creates a universal pathway to simplify genome topology Enzo Orlandinia, Davide Marenduzzob, and Davide Michielettob,1 aDipartimento di Fisica e Astronomia “Galileo Galilei,” Sezione Istituto Nazionale di Fisica Nucleare, Universita` degli Studi di Padova, I-35131 Padova, Italy; and bSchool of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom Edited by Michael L. Klein, Institute of Computational Molecular Science, Temple University, Philadelphia, PA, and approved March 14, 2019 (received for review September 6, 2018) Topological entanglements severely interfere with important bio- cal simplification. Our simulations reveal that this mechanism is logical processes. For this reason, genomes must be kept unknot- independent of either substrate condensation or crowding and is ted and unlinked during most of a cell cycle. Type II topoisomerase therefore likely to lead to unknotting and unlinking even under (TopoII) enzymes play an important role in this process but the extreme conditions such as those in the cell nucleus. Finally, we precise mechanisms yielding systematic disentanglement of DNA discuss our model in the context of recent experiments report- in vivo are not clear. Here we report computational evidence that ing that SMC proteins are essential to achieve correct sister structural-maintenance-of-chromosomes (SMC) proteins—such as chromatid decatenation in metaphase (23), that DNA damage cohesins and condensins—can cooperate with TopoII to establish is frequently found in front of cohesin motion (24), and that a synergistic mechanism to resolve topological entanglements. there is a remarkable low frequency of knots in intracellular SMC-driven loop extrusion (or diffusion) induces the spatial local- chromatin (17). -
Bacterial Type 1A Topoisomerases Maintain the Stability of the Genome
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.10.451908; this version posted July 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Bacterial type 1A topoisomerases maintain the stability of the genome by preventing and dealing with R-loop-and nucleotide excision repair-dependent topological stress. Julien Brochu, Emilie Vlachos-Breton and Marc Drolet*. Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, P. Québec, Canada, H3C 3J7. *To whom correspondence should be addressed. Tel: 1-514-343-5796. Email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.07.10.451908; this version posted July 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT E. coli type 1A topoisomerases (topos), topo I (topA) and topo III (topB) have both relaxation and decatenation activities. B. subtilis and E. coli topA topB null cells can survive owing to DNA amplifications allowing overproduction of topo IV, the main cellular decatenase that can also relax supercoiling. We show that overproducing human topo IB, a relaxase but not a decatenase, can substitute for topo IV in allowing E. coli topA null but not topA topB null cells to survive. Deleting topB exacerbates phenotypes of topA null mutants including hypernegative supercoiling, R-loop formation, and RNase HI-sensitive replication, phenotypes that are not corrected by topo IV overproduction. These phenotypes lead to Ter DNA amplification causing a chromosome segregation defect that is corrected by topo IV overproduction. -
Group II Intron Rnps and Reverse Transcriptases: from Retroelements to Research Tools
Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools Marlene Belfort1 and Alan M. Lambowitz2 1Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222 2Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 Correspondence: [email protected]; [email protected] SUMMARY Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA anal- ysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8–4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processiv- ity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed. Outline 1 Introduction 5 Technique 4. RTs with novel enzymatic properties as potent research tools 2 Technique 1. -
DNA Structure at the Plasmid Origin-Of-Transfer Indicates Its
www.nature.com/scientificreports OPEN DNA structure at the plasmid origin-of-transfer indicates its potential transfer range Received: 12 May 2016 Jan Zrimec1,2,3 & Aleš Lapanje1,4,5 Accepted: 10 January 2018 Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread Published: xx xx xxxx among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efciently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.html. Antimicrobial resistance (AMR) is a pressing global issue, as it diminishes the activity of 29 antibiotics and conse- quently leads to over 25,000 deaths each year in Europe alone1,2. Te development of AMR in microbial commu- nities is facilitated by horizontal gene transfer (HGT) of conjugative elements (including plasmids and integrative elements)3 carrying antibiotic resistance genes along with virulence genes4,5.