DOCSLIB.ORG

Discrimination of Class I Cyclobutane Pyrimidine Dimer Photolyase from Blue Light Photoreceptors by Single Methionine Residue

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Discrimination of Class I Cyclobutane Pyrimidine Dimer Photolyase from Blue Light Photoreceptors by Single Methionine Residue View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector 2194 Biophysical Journal Volume 94 March 2008 2194–2203 Discrimination of Class I Cyclobutane Pyrimidine Dimer Photolyase from Blue Light Photoreceptors by Single Methionine Residue Yuji Miyazawa,* Hirotaka Nishioka,y Kei Yura,z§ and Takahisa Yamato*{ *Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; yGraduate School of Environmental and Human Science, Meijo University, Nagoya 468-8502, Japan; zQuantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency, Kyoto 619-0215, Japan; §Research Unit for Quantum Beam Life Science Initiative, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto 619-0215, Japan; and {CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan ABSTRACT DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. Theoretical analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met-353, where busy trafficking of electron-tunneling currents is observed. The amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met-353 in the biological function of DNA photolyase. INTRODUCTION Ultraviolet (UV) light creates cyclobutane pyrimidine dimers Various methods for computation of the electronic factor (CPDs) in a DNA chain and causes skin cancer. DNA pho- in electron transfer reactions have been presented (9–11). tolyase, containing a flavin cofactor, absorbs light and repairs Three major computational methods have been developed for the UV-damaged DNA using the electron transfer reaction the long-range electron transfer reactions in biological sys- between the electron donor (flavin adenine dinucleotide, tems, namely, the extended Hu¨ckel approach used by Marcus FADHÀ) and the electron acceptor (CPD) (1). Improperly and Stuchebrukhov (12) and expanded by Kakitani and co- formed covalent bonds in CPD are broken as a result of the workers (13–15), the pathway approach by Beratan and electron transfer reaction, which is completed within 170 ps. Onuchic (16), the square barrier model of Hopfield (17) To analyze the spatial pattern of electron-tunneling path- promoted by Dutton (18), and the more intensive self-con- ways, Medvedev and Stuchebrukhov proposed an electron- sistent field molecular orbital methods (19,20). In this study, tunneling current and studied the electron transfer reaction of we employed the extended Hu¨ckel approach to analyze the the computationally predicted complex structure of Escherichia thermal fluctuation of electron-tunneling pathways for a large coli DNA photolyase and CPD (2). They proposed a scheme number of protein structures extracted from a molecular of indirect electron transfer via the adenine of FADHÀ as a dynamics simulation trajectory. mediator of electron tunneling from the donor to the acceptor It is widely accepted that the electronic factor for the in their pioneering work on the CPD photolyase complex electron transfer reaction fluctuates significantly along with model. In 2004, Mees et al. reported the complex structure of the thermal fluctuation of the protein environment (15,21– the DNA photolyase derived from Anacystis nidulans and the 24). Troisi et al. have made important contributions to the CPD analog by x-ray crystallography (3). The isoalloxazine analysis of the effects of thermal fluctuations on the donor- ring of the FADHÀ in the crystal structure is located close to acceptor couplings (25,26). Skourtis et al. have explicitly the CPD, indicating the possibility of direct electron transfer analyzed how thermal fluctuations affect the protein electron from the FADHÀ to the CPD (4,5), and recent theoretical transfer (27). Recently, Nishioka et al. proposed a non- analyses support the direct transfer (6). An active role of the Condon theory for the electron transfer of thermally fluctu- protein environment in electron transfer from the FADHÀ*to ating protein media (28), and another study has analyzed the the CPD has not been supported (1,7,8), but the possibility electron-tunneling pathways in a fixed protein environment of protein-mediated electron transfer is not completely ex- (2). In this study, we used molecular dynamics simulation cluded. and quantum mechanical calculations to study the electron transfer reaction from the excited flavin cofactor to the thy- mine dimer in the explicit protein environment of a thermally Submitted August 7, 2007, and accepted for publication November 5, 2007. fluctuating CPD photolyase complex (3). These calculations Address reprint requests to Takahisa Yamato, E-mail: yamato@phys. turned out to be helpful in identifying residues that are im- nagoya-u.ac.jp. portant in the electron transfer reaction. Furthermore, we Editor: David P. Millar. Ó 2008 by the Biophysical Society 0006-3495/08/03/2194/10 $2.00 doi: 10.1529/biophysj.107.119248 Theoretical Study on DNA Photolyase 2195 used sequence database search techniques to evaluate the ¼ + ; ¼ 1 ð i f À f i Þð À Þ; biological conservation of the key residues found by the Jab Jmn Jmn - CmCn CmCn Hmn ESmn (2) m2a;n2b h analysis. As a result of the combined use of multiple disci- i i where Cm; Cn are the coefficients of atomic orbitals fm; fn in Ci; and plines of computational biology, we discovered that the f f Cm; Cnare the coefficients of atomic orbitals fm; fn in Cf . The total electron methionine residue located at site 353 of A. nidulans CPD population should be conserved throughout the reaction from the initial state photolyase is a likely determinant for the function of class I i to the final state. To impose this conservationpffiffiffiffiffiffiffiffiffi condition,pffiffiffiffiffiffiffiffiffiffi we scale the Cm f i f i CPD photolyase in the blue light photoreceptor superfamily. inCi (Cmin Cf ) by multiplying 1/ Pop (1/ Pop ), where Pop ¼ + i i ; f ¼ + f f n;m2all atomic orbital CnSnmCm Pop n;m2all atomic orbital CnSnmCm. To find the important region for long-range intramolecular electron tunneling, MATERIALS AND METHODS analysis of the interatomic-tunneling current Jab is helpful. However, since the value of T fluctuates as the thermal fluctuation of the protein, direct Molecular dynamics simulations and electronic DA comparison of Jab for different protein structures is not useful. To compare structure calculations the significance of Jab among different protein structures, we introduce the normalized tunneling current K as K ¼ h- J =T . In the mediator region, The initial conformation of the complex of CPD analog and the DNA pho- ab ab ab DA the summation of the normalized tunneling current is always zero for a given tolyase of A. nidulans was extracted from the Protein Data Bank (PDB code atom, a, because the annihilation and creation of electrons do not take place. 1TEZ) (3). Crystallographic water molecules within the DNA photolyase and Therefore, the significance of electron tunneling cannot be evaluated for between the DNA photolyase and the CPD fragment were incorporated into each atom with the normalized tunneling current. To evaluate the amount of the system. This system was then immersed in an octahedral box of water the electron-tunneling current traffic, we introduce the electron-tunneling molecules. The total number of water molecules was 25,268. The AMBER99 count (35) as N ¼ h- +9 J =jT j; where the summation +9 is taken over force field (29) and the TIP3P model (30) were employed for the polypeptide a b ab DA À all positive tunneling currents J . The electronic states of the donor, accep- chain and water molecules, respectively. The force field for the FADH , ab tor, protein, and the crystallographic waters are solved at the extended CPD analog, and 8-hydroxy-5-deazaflavin (8-HDF) were developed based Hu¨ckel level. The extended Hu¨ckel parameters were taken from the litera- on FADH(À), thymine dimer, and flavin mononucleotide (FMN) in the ture (36), which are similar to those adopted by Stuchebrukhov et al. (37) in AMBER Parameter Database (http://pharmacy.man.ac.uk/amber), respec- their previous work (2). We confirmed that the extended Hu¨ckel calcula- tively. The atomic partial charges for these cofactors were calculated with the tion with this parameterization reproduced a result similar to that of the RESP scheme using the GAMESS (31) and AMBER8 (32) program pack- previous work (2) for the fixed environment of the protein medium directly ages. The 4-31G basis set was employed for this purpose. The bond lengths derived from x-ray crystallography (3). The value of T is calculated by of the equilibrium conformation were adopted from the x-ray crystallo- DA the pseudo-Green function technique (14,38) for each MD snapshot. The graphic values. The spring constants for the bond stretching and angles and electron-tunneling pathways are analyzed by drawing the map of interatomic- dihedral torsional barriers were obtained from the AMBER parameter da- tunneling currents (24). tabase. To construct the force field of the CPD analog, the structure of CPD To obtain the electron-tunneling pathways of CPD photolyase, we cal- was extracted from the PDB entry, 1SNH (33), and the ÀO–P –O– part was 2 culated electron-tunneling matrix elements and the interatomic electron- replaced with ÀO–CH –O–. Structure optimization of the system was per- 2 tunneling current for each of the instantaneous structures derived from the formed using the AMBER8 program with the harmonic restraints imposed molecular dynamics simulation.
Load more

Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
    Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
    [Show full text]
  • Intraprotein Radical Transfer During Photoactivation of DNA Photolyase
    letters to nature tri-NaCitrate and 20% PEG 3350, at a ®nal pH of 7.4 (PEG/Ion Screen, Hampton (Daresbury Laboratory, Warrington, 1992). Research, San Diego, California) within two weeks at 4 8C. Intact complex was veri®ed by 25. Evans P. R. in Proceedings of the CCP4 Study Weekend. Data Collection and Processing (eds Sawyer, L., SDS±polyacrylamide gel electrophoresis of washed crystals (see Supplementary Infor- Isaacs, N. & Bailey, S.) 114±122 (Daresbury Laboratory, 1993). mation). Data were collected from a single frozen crystal, cryoprotected in 28.5% PEG 26. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystal- 4000 and 10% PEG 400, at beamline 9.6 at the SRS Daresbury, UK. lography. Acta Crystallogr. 50, 760±763 (1994). The data were processed using MOSFLM24 and merged using SCALA25 from the CCP4 27. Navaza, J. AMORE - An automated package for molecular replacement. Acta Cryst. A 50, 157±163 26 (1994). package (Table 1) The molecular replacement solution for a1-antitrypsin in the complex 27 28 28. Engh, R. et al. The S variant of human alpha 1-antitrypsin, structure and implications for function and was obtained using AMORE and the structure of cleaved a1-antitrypsin as the search model. Conventional molecular replacement searches failed to place a model of intact metabolism. Protein Eng. 2, 407±415 (1989). 29 29. Lee, S. L. New inhibitors of thrombin and other trypsin-like proteases: hydrogen bonding of an trypsin in the complex, although maps calculated with phases from a1-antitrypsin alone showed clear density for the ordered portion of trypsin (Fig.
    [Show full text]
  • Copyright by Christopher James Thibodeaux 2010
    Copyright by Christopher James Thibodeaux 2010 The Dissertation Committee for Christopher James Thibodeaux Certifies that this is the approved version of the following dissertation: Mechanistic Studies of Two Enzymes that Employ Common Coenzymes in Uncommon Ways Committee: Hung-wen Liu, Supervisor Eric Anslyn Walter Fast Kenneth A. Johnson Christian P. Whitman Mechanistic Studies of Two Enzymes that Employ Common Coenzymes in Uncommon Ways by Christopher James Thibodeaux, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August, 2010 Dedication To all whom have made significant contributions to my life: I am eternally grateful. Acknowledgements First and foremost, I would like to thank Dr. Liu for providing me with the opportunity to work at the cutting edge of biochemical research, and for allowing me the freedom to explore and develop my scientific interests. In addition, I would like to thank the numerous other members of the Liu group (both past and present) for their helpful insights, stimulating conversations, and jovial personalities. They have all helped to immeasurably enrich my experience as a graduate student, and I would consider myself lucky to ever have another group of coworkers as friendly and as helpful as they all have been. Special thanks need to be attributed to Drs. Mark Ruszczycky, Chad Melançon, Yasushi Ogasawara, and Svetlana Borisova for their helpful suggestions and discussions at various points throughout my research, to Dr. Steven Mansoorabadi for performing the DFT calculations and for the many interesting conversations we have had over the years, and to Mr.
    [Show full text]
  • ATP-Citrate Lyase Has an Essential Role in Cytosolic Acetyl-Coa Production in Arabidopsis Beth Leann Fatland Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2002 ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis Beth LeAnn Fatland Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Molecular Biology Commons, and the Plant Sciences Commons Recommended Citation Fatland, Beth LeAnn, "ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis " (2002). Retrospective Theses and Dissertations. 1218. https://lib.dr.iastate.edu/rtd/1218 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis by Beth LeAnn Fatland A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Eve Syrkin Wurtele (Major Professor) James Colbert Harry Homer Basil Nikolau Martin Spalding Iowa State University Ames, Iowa 2002 UMI Number: 3158393 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted.
    [Show full text]
  • The Structure of an Authentic Spore Photoproduct Lesion in DNA Suggests a Basis for Recognition
    addenda and errata Acta Crystallographica Section D Biological addenda and errata Crystallography ISSN 1399-0047 The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. Corrigendum Isha Singh,a Yajun Jian,b Lei Lia,b and Millie M. Georgiadisa,b* aDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA, and bDepartment of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA Correspondence e-mail: [email protected] The article by Singh et al. [ (2014). Acta Cryst. D70, 752–759] is corrected. In the article by Singh et al. (2014) the name of one of the authors was given incorrectly. The correct name is Yajun Jian as given above. References Singh, I., Lian, Y., Li, L. & Georgiadis, M. M. (2014). Acta Cryst. D70, 752–759. Acta Cryst. (2014). D70, 1173 doi:10.1107/S1399004714006130 # 2014 International Union of Crystallography 1173 research papers Acta Crystallographica Section D Biological The structure of an authentic spore photoproduct Crystallography lesion in DNA suggests a basis for recognition ISSN 1399-0047 Isha Singh,a Yajun Lian,b Lei Lia,b The spore photoproduct lesion (SP; 5-thymine-5,6-dihydro- Received 12 September 2013 and Millie M. Georgiadisa,b* thymine) is the dominant photoproduct found in UV- Accepted 5 December 2013 irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light- PDB references: N-terminal aDepartment of Biochemistry and Molecular independent manner by a specific repair enzyme: the spore fragment of MMLV RT, SP Biology, Indiana University School of Medicine, DNA complex, 4m94; non-SP Indianapolis, IN 46202, USA, and bDepartment photoproduct lyase (SP lyase).
    [Show full text]
  • Genetic and Phylogenetic Characterization of the Type II Cyclobutane Pyrimidine Dimer Photolyases Encoded by Leporipoxviruses
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com R Virology 315 (2003) 10–19 www.elsevier.com/locate/yviro Genetic and phylogenetic characterization of the type II cyclobutane pyrimidine dimer photolyases encoded by Leporipoxviruses C. James Bennett, Melissa Webb, David O. Willer,1 and David H. Evans2,* Department of Molecular Biology and Genetics, The University of Guelph, Guelph, Ontario, N1G 2W1, Canada Received 2 May 2003; returned to author for revision 21 May 2003; accepted 23 June 2003 Abstract Shope fibroma virus and myxoma virus encode proteins predicted to be Type II photolyases. These are enzymes that catalyze light-dependent repair of cyclobutane pyrimidine dimers (CPDs). When the Shope fibroma virus S127L gene was expressed in an Escherichia coli strain lacking functional CPD repair pathways, the expressed gene protected the bacteria from 70–75% of the ultraviolet (UV) light-induced cytotoxic DNA damage. This proportion suggests that Leporipoxvirus photolyases can only repair CPDs, which typically comprise ϳ70% of the damage caused by short wavelength UV light. To test whether these enzymes can protect virus genomes from UV, we exposed virus suspensions to UV-C light followed by graded exposure to filtered visible light. Viruses encoding a deletion of the putative photolyase gene were unable to photoreactivate UV damage while this treatment again eliminated 70–90% of the lethal photoproducts in wild-type viruses. Western blotting detected photolyase protein in extracts prepared from purified virions and it can be deduced that the poxvirion interior must be fluid enough to permit diffusion of this ϳ50-kDa DNA-binding protein to the sites where it catalyzes photoreactivation.
    [Show full text]
  • UV-B Induced Stress Responses in Three Rice Cultivars
    BIOLOGIA PLANTARUM 54 (3): 571-574, 2010 BRIEF COMMUNICATION UV-B induced stress responses in three rice cultivars I. FEDINA1*, J. HIDEMA2, M. VELITCHKOVA3, K. GEORGIEVA1 and D. NEDEVA1 Institute of Plant Physiology1 and Institute of Biophysics3, Bulgarian Academy of Sciences, Academic Georgi Bonchev Street, Building 21, Sofia 1113, Bulgaria Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan2 Abstract UV-B responses of three rice (Oryza sativa L.) cultivars (Sasanishiki, Norin 1 and Surjamkhi) with different photolyase activity were investigated. Carbon dioxide assimilation data support that Sasanishiki was less sensitive to UV-B than Norin 1 and Surjamkhi. UV-B radiation sharply decreased the content of Rubisco protein in Surjamkhi and has no effect in Sasanishiki. The photochemical activities of photosystem (PS) 1 and PS 2 was slightly affected by UV-B treatment. The content of H2O2 and the activities of antioxidant enzymes, catalase (CAT), peroxides (POX) and superoxide dismutase (SOD) were enhanced after UV-B treatment. The activities of CAT and POX isoenzymes in Sasanishiki were more enhanced by UV-B radiation than those in Norin 1 and Surjamkhi. 14 Additional key words: catalase, CO2 fixation, hydrogen peroxide, peroxidase, Rubisco, superoxide dismutase. ⎯⎯⎯⎯ UV-B sensitivity of plants is determined by the balance of Furthermore, transgenic rice plants in which the CPD damage incurred and by the efficiency of repair processes photolyase was overexpressed had higher CPD photolyase that can restore the impaired functions. This balance is activity and showed significantly greater resistance to influenced by several factors, including the genetic UV-B than wild plants (Hidema et al.
    [Show full text]
  • Identification and Characterization of a DNA Photolyase-Containing Baculovirus from Chrysodeixis Chalcites $
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Virology 330 (2004) 460–470 www.elsevier.com/locate/yviro Identification and characterization of a DNA photolyase-containing baculovirus from Chrysodeixis chalcites $ Monique M. van Oersa,*, Elisabeth A. Hernioub, Magda Usmanya, Gerben J. Messelinkc, Just M. Vlaka aLaboratory of Virology, Wageningen University, 6709 PD Wageningen, The Netherlands bDepartment of Biological Sciences, Imperial College London, Ascot Berkshire SL5 7PY, United Kingdom cApplied Plant Research, Business Unit Glasshouse Horticulture, 2670 AA Naaldwijk, The Netherlands Received 27 August 2004; returned to author for revision 20 September 2004; accepted 22 September 2004 Abstract A hitherto unknown single nucleocapsid nucleopolyhedrovirus (SNPV) with a unique property was isolated from larvae of the looper Chrysodeixis chalcites (Lepidoptera, Noctuidae, Plusiinae). Polyhedrin, lef-8, and pif-2 gene sequences were obtained by PCR with degenerate primers and used for phylogenetic analysis. ChchNPV belonged to class II NPVs and its polyhedrin sequence was most similar to that of class II NPVs of other members of the subfamily Plusiinae. Further genetic characterization involved the random cloning of HindIII fragments into a plasmid vector and analysis by end-in sequencing. A gene so far unique to baculoviruses was identified, which encodes a putative DNA repair enzyme: cyclobutane pyrimidine dimer (CPD) DNA photolyase (dpl). The transcriptional activity of this gene was demonstrated in both ChchNPV-infected C. chalcites larvae and infected Trichoplusia ni High Five cells by RT-PCR and 5Vand 3VRACE analysis. The possible role of this gene in the biology of the virus is discussed.
    [Show full text]
  • Dynamics and Mechanism of Cyclobutane Pyrimidine Dimer Repair by DNA Photolyase
    Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase Zheyun Liua, Chuang Tana, Xunmin Guoa, Ya-Ting Kaoa, Jiang Lia, Lijuan Wanga, Aziz Sancarb,1, and Dongping Zhonga,1 aDepartments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210; and bDepartment of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599 Contributed by Aziz Sancar, July 7, 2011 (sent for review June 28, 2011) Photolyase uses blue light to restore the major ultraviolet (UV)- induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultra- fast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox poten- tials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the com- plete spatio-temporal molecular picture of CPD repair by photo- lyase and elucidate the underlying molecular mechanism of the enzyme’s high repair efficiency. Fig. 1. Enzyme-substrate complex structure and one sequential repair me- DNA repair photocycle ∣ ultrafast enzyme dynamics ∣ thymine dimer chanism with all elementary reactions.
    [Show full text]
  • Supplementary Information
    Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
    [Show full text]
  • Download Author Version (PDF)
    Environmental Science: Water Research & Technology Elimination of transforming activity and gene degradation during UV and UV/H2O2 treatment of plasmid-encoded antibiotic resistance genes Journal: Environmental Science: Water Research & Technology Manuscript ID EW-ART-03-2018-000200.R2 Article Type: Paper Date Submitted by the Author: 27-May-2018 Complete List of Authors: Yoon, Younggun; Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering Dodd, Michael; University of Washington, Civil and Environmental Engineering Lee, Yunho; Gwangju Institute of Science and Technology, Environmental Science and Engineering Page 1 of 40 Environmental Science: Water Research & Technology Water Impact Statement The efficiency and mode of actions for deactivating and degrading antibiotic resistance genes (ARGs) during water treatment with UV (254 nm) and UV/H2O2 have been poorly understood. Here, we show that efficiency of elimination of the transforming activity for a plasmid-encoded ARG during the UV-based treatments depends on the rate of formation of cyclobutane-pyrimidine dimers (CPDs) in the plasmid and the repair of such DNA damage during the transformation process in host cells. This work has important contributions to optimizing the monitoring and operation of UV-based water disinfection and oxidation processes for removing ARGs. Environmental Science: Water Research & Technology Page 2 of 40 1 Elimination of transforming activity and gene degradation during 2 UV and UV/H2O2 treatment of plasmid-encoded
    [Show full text]
  • A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring
    Cell Reports Resource A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring Rohith Srivas,1,6 Thomas Costelloe,2,6 Anne-Ruxandra Carvunis,1 Sovan Sarkar,3 Erik Malta,2 Su Ming Sun,2 Marijke Pool,2 Katherine Licon,1,5 Tibor van Welsem,4 Fred van Leeuwen,4 Peter J. McHugh,3 Haico van Attikum,2,* and Trey Ideker1,5,* 1Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA 2Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands 3Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK 4Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands 5Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA 6These authors contributed equally to this work *Correspondence: [email protected] (H.v.A.), [email protected] (T.I.) http://dx.doi.org/10.1016/j.celrep.2013.11.035 This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. SUMMARY nick is sealed by a DNA ligase (Prakash and Prakash, 2000). The NER machinery, however, does not work in isolation. Increasing Efficient repair of UV-induced DNA damage requires evidence points to the precise coordination of NER with several the precise coordination of nucleotide excision repair other biological processes, such as the cell-cycle checkpoint (NER) with numerous other biological processes.
    [Show full text]