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Thermodynamics of DNA Binding by DNA Polymerase I and Reca
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2014 Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans Jaycob Dalton Warfel Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Warfel, Jaycob Dalton, "Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans" (2014). LSU Doctoral Dissertations. 2382. https://digitalcommons.lsu.edu/gradschool_dissertations/2382 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THERMODYNAMICS OF DNA BINDING BY DNA POLYMERASE I AND RECA RECOMBINASE FROM DEINOCOCCUS RADIODURANS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Jaycob Dalton Warfel B.S. Louisiana State University, 2006 May 2015 ACKNOWLEDGEMENTS I would like to express my utmost gratitude to the myriad of individuals who have lent their support during the time it has taken to complete this dissertation. First and foremost is due glory to God, The Father, The Son and The Holy Spirit, through whom all is accomplished. It is with extreme thankfulness for the blessings bestowed upon me, and with vast appreciation for the beauty of God’s creation that I have pursued a scientific education. -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. -
In Vivo Interactions of Archaeal Cdc6 Orc1 and Minichromosome
In vivo interactions of archaeal Cdc6͞Orc1 and minichromosome maintenance proteins with the replication origin Fujihiko Matsunaga*, Patrick Forterre*, Yoshizumi Ishino†, and Hannu Myllykallio*§ *Institut de Ge´ne´ tique et Microbiologie, Universite´de Paris-Sud, 91405 Orsay, France; and †Department of Molecular Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan Communicated by Bruce W. Stillman, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, July 25, 2001 (received for review May 25, 2001) Although genome analyses have suggested parallels between basis of asymmetry in base composition between leading and archaeal and eukaryotic replication systems, little is known about lagging strands (10, 11). In Pyrococcus abyssi, the location of the the DNA replication mechanism in Archaea. By two-dimensional predicted origin coincides with an early replicating chromosomal gel electrophoreses we positioned a replication origin (oriC) within segment of 80 kb identified by radioactive labeling of chromo- 1 kb in the chromosomal DNA of Pyrococcus abyssi, an anaerobic somal DNA in cultures released from a replication block (12). hyperthermophile, and demonstrated that the oriC is physically Our in silico and labeling data also allowed us to conclude that linked to the cdc6 gene. Our chromatin immunoprecipitation as- the hyperthermophilic archaeon P. abyssi uses a single bidirec- says indicated that P. abyssi Cdc6 and minichromosome mainte- tional origin to replicate its genome. We proposed that this origin nance (MCM) proteins bind preferentially to the oriC region in the would correspond to the long intergenic region conserved in all exponentially growing cells. Whereas the oriC association of MCM three known Pyrococcus sp. -
Tackling the Methanopyrus Kandleri Paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo†
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Open Access Research2004BrochieretVolume al. 5, Issue 3, Article R17 Archaeal phylogeny based on proteins of the transcription and comment translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo† Addresses: *Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France. †Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Céline Brochier. E-mail: [email protected] Published: 26 February 2004 Received: 14 November 2003 Revised: 5 January 2004 Genome Biology 2004, 5:R17 Accepted: 21 January 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/3/R17 reports © 2004 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. ArchaealPhylogeneticsequencedusingrespectively). two phylogeny concatenated genomes, analysis based it of is datasetsthe now on Archaea proteinspossible consisting has ofto been thetest of transcription alternative mainly14 proteins established approach involv and translationed byes in 16S bytranscription rRNAusing machineries: largesequence andsequence 53comparison.tackling ribosomal datasets. the Methanopyrus Withproteins We theanalyzed accumulation(3,275 archaealkandleri and 6,377 of phyparadox comp positions,logenyletely Abstract deposited research Background: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. -
Microorganisms
microorganisms Article Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans Lihua Gao, Zhengfu Zhou, Xiaonan Chen, Wei Zhang, Min Lin and Ming Chen * Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; [email protected] (L.G.); [email protected] (Z.Z.); [email protected] (X.C.); [email protected] (W.Z.); [email protected] (M.L.) * Correspondence: [email protected] Received: 20 February 2020; Accepted: 19 March 2020; Published: 23 March 2020 Abstract: Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. -
DNA Protection Mechanisms Are Not Involved in the Radioresistance of the Hyper Thermophilic Archaea P Yrococcus Abyssi and P
Mol Genet Genomics 62001) 266: 72±78 DOI 10.1007/s004380100520 ORIGINAL PAPER E. Ge rard á E. Jolivet á D. Prieur á P. Forterre DNA protection mechanisms are not involved in the radioresistance of the hyper thermophilic archaea P yrococcus abyssi and P. furiosus Received: 1 February 2001 / Accepted: 4 May 2001 / Published online: 20 June 2001 Ó Springer-Verlag 2001 Abstract Hyperthermophilic archaea of the genus environments. They are able to grow at low pH, in high Pyrococcus are resistant to gamma radiation, suggesting salt concentrations or at high temperatures 6Woese et al. that ecient mechanisms for DNA repair exist in these 1990). Pyrococcus abyssi and P. furiosus are two hyper- organisms. To determine whether protective mechanisms thermophilic archaea that are found in geothermal might also be implicated in this radioresistance, we have habitats. They grow optimally at 100°C and 95°C, estimated the linear density of DNA double-stranded respectively 6Fiala and Stetter 1986; Erauso 1993). These breaks caused by gamma irradiation in the genomic extremely high temperatures accelerate the spontaneous DNA of two Pyrococcus species, using Escherichia coli degradation of DNA. The main problem with respect to and the radioresistant bacterium Deinococcus radiodu- DNA stability at high temperatures is thermal degrada- rans as controls. The linear density of double-stranded tion via depurination and subsequent breakage of the breaks was essentially the same in all four microorgan- phosphodiester bonds 6Marguet and Forterre 1994). This isms when irradiation was carried under similar suggests that speci®c mechanisms might exist in hyper- anaerobic conditions, indicating that no speci®c DNA thermophilic archaea that protect and repair DNA. -
Phylogenomic Analysis of Proteins That Are Distinctive of Archaea and Its Main Subgroups and the Origin of Methanogenesis Beile Gao and Radhey S Gupta*
BMC Genomics BioMed Central Research article Open Access Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis Beile Gao and Radhey S Gupta* Address: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, L8N3Z5, Canada Email: Beile Gao - [email protected]; Radhey S Gupta* - [email protected] * Corresponding author Published: 29 March 2007 Received: 26 July 2006 Accepted: 29 March 2007 BMC Genomics 2007, 8:86 doi:10.1186/1471-2164-8-86 This article is available from: http://www.biomedcentral.com/1471-2164/8/86 © 2007 Gao and Gupta; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood. Results: We have carried out comprehensive analyses on each open reading frame (ORFs) in the genomes of 11 archaea (3 Crenarchaeota – Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota – Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus) to search for proteins that are unique to either all Archaea or for its main subgroups. -
Genome Analysis and Genome-Wide Proteomics
Open Access Research2009ZivanovicetVolume al. 10, Issue 6, Article R70 Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic¤*, Jean Armengaud¤†, Arnaud Lagorce*, Christophe Leplat*, Philippe Guérin†, Murielle Dutertre*, Véronique Anthouard‡, Patrick Forterre§, Patrick Wincker‡ and Fabrice Confalonieri* Addresses: *Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France. †CEA, DSV, IBEB Laboratoire de Biochimie des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France. ‡CEA, DSV, Institut de Génomique, Genoscope, rue Gaston Crémieux CP5706, F-91057 Evry Cedex, France. §Laboratoire de Biologie moléculaire du gène chez les extrêmophiles, Université Paris-Sud 11, CNRS, UMR8621, Bât 409, F-91405 Orsay, France. ¤ These authors contributed equally to this work. Correspondence: Fabrice Confalonieri. Email: [email protected] Published: 26 June 2009 Received: 24 March 2009 Revised: 29 May 2009 Genome Biology 2009, 10:R70 (doi:10.1186/gb-2009-10-6-r70) Accepted: 26 June 2009 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2009/10/6/R70 © 2009 Zivanovic et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Thermococcus<p>Theoresistance genome may gammatole besequence due to ransunknownof Thermococcus proteogenomics DNA repair gammatolerans, enzymes.</p> a radioresistant archaeon, is described; a proteomic analysis reveals that radi- Abstract Background: Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. -
Thermophiles and Thermozymes
Thermophiles and Thermozymes Edited by María-Isabel González-Siso Printed Edition of the Special Issue Published in Microorganisms www.mdpi.com/journal/microorganisms Thermophiles and Thermozymes Thermophiles and Thermozymes Special Issue Editor Mar´ıa-Isabel Gonz´alez-Siso MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editor Mar´ıa-Isabel Gonzalez-Siso´ Universidade da Coruna˜ Spain Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Microorganisms (ISSN 2076-2607) from 2018 to 2019 (available at: https://www.mdpi.com/journal/ microorganisms/special issues/thermophiles) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-816-9 (Pbk) ISBN 978-3-03897-817-6 (PDF) c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editor ...................................... vii Mar´ıa-Isabel Gonz´alez-Siso Editorial for the Special Issue: Thermophiles and Thermozymes Reprinted from: Microorganisms 2019, 7, 62, doi:10.3390/microorganisms7030062 ........ -
Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus Pacificus DY20341T from Deep-Sea Hydrothermal Sediments
International Journal of Molecular Sciences Article Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments Xiang Zeng 1, Xiaobo Zhang 1,2 and Zongze Shao 1,* 1 Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No.178 Daxue Road, Xiamen 361005, China; [email protected] (X.Z.); [email protected] (X.Z.) 2 School of public health, Xinjiang Medical University, No.393 Xinyi Road, Urumchi 830011, China * Correspondence: [email protected]; Tel.: +86-592-2195321 Received: 4 December 2019; Accepted: 29 December 2019; Published: 6 January 2020 Abstract: The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. -
When Contemporary Aminoacyl-Trna Synthetases Invent Their Cognate Amino Acid Metabolism
When contemporary aminoacyl-tRNA synthetases SEE COMMENTARY invent their cognate amino acid metabolism Herve´ Roy, Hubert Dominique Becker, Joseph Reinbolt, and Daniel Kern* De´partement Me´canismes et Macromole´cules de la Synthe`se Prote´ique et Cristallogene`se, Unite´Propre de Recherche 9002, Institut de Biologie Mole´culaire et Cellulaire du Centre National de la Recherche Scientifique, 15 Rue Rene´Descartes, F-67084 Strasbourg Ce´dex, France Edited by Paul R. Schimmel, The Scripps Research Institute, La Jolla, CA, and approved June 9, 2003 (received for review April 14, 2003) Faithful protein synthesis relies on a family of essential enzymes genomes drew our attention to the fact that all archaea that called aminoacyl-tRNA synthetases, assembled in a piecewise fash- possess AsnRS (7 of 13) display a second ORF highly homolo- ion. Analysis of the completed archaeal genomes reveals that all gous to the catalytic core of AsnRS (AsnRS2) but lacking the archaea that possess asparaginyl-tRNA synthetase (AsnRS) also anticodon-binding domain. We analyzed the functional proper- display a second ORF encoding an AsnRS truncated from its ties of AsnRS2 from Pyrococcus abyssi, a hyperthermophilic anticodon binding-domain (AsnRS2). We show herein that Pyro- archaeon. The results show that this truncated AsnRS does not coccus abyssi AsnRS2, in contrast to AsnRS, does not sustain form Asn-tRNAAsn but produces Asn by amidation of Asp. asparaginyl-tRNAAsn synthesis but is instead capable of converting Phylogeny suggests this asparagine synthetase (AS) appeared aspartic acid into asparagine. Functional analysis and complemen- recently in archaea and allowed emergence of a direct and tation of an Escherichia coli asparagine auxotrophic strain show autonomous pathway of tRNA asparaginylation.