DOCSLIB.ORG

Streptomyces Coelicolor: DNA Cytosine Methylation and Differentiation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Streptomyces Coelicolor: DNA Cytosine Methylation and Differentiation University of Palermo Department of Biological Chemical and Pharmaceutical Sciences and Technology (STEBICEF) Streptomyces coelicolor: DNA cytosine methylation and differentiation Doctoral Thesis of Annalisa Pisciotta PhD in Cellular Biology XXVI cycle Scientific area code BIO 19 Supervisor: PhD coordinator: Dr. Rosa Alduina Prof. Maria Carmela Roccheri Acknowledgment I would like to express my sincere gratitude to my supervisor Dr. Rosa Alduina for the continuous support of my Ph.D study and related research, for her patience, motivation, and knowledge. Her guidance helped me in all the time of research and writing of this thesis. My sincere thank also goes to Prof. Anna Maria Puglia, for funding the BS sequencing of MG medium. My honest thank also goes to Dr. Angel Manteca, who provided me an opportunity to join his team, who gave access to the laboratory and research facilities and for funding part of this research project. I thank my lab mates in Oviedo, Dr. Maria Teresa Lopez, Dr Paula Yagüe, Beatriz Gutierrez Beatriz Rioseras, Nathaly Gonzalez and my lab mates in Palermo, Dr. Letizia Lo Grasso for the stimulating discussions and for the help in the progress of this research, and Federica Attardo for the passion with which contributed to development of this project. ABSTRACT ........................................................................................................................................... - 6 - INTRODUCTION ................................................................................................................................ - 9 - 1. DNA METHYLATION ........................................................................................................................- 10 - 1.1 DNA METHYLATION IN EUKARYOTES .............................................................................................- 10 - 1.2 DNA METHYLATION IN PROKARYOTES ...........................................................................................- 11 - 1.2.1 Restriction-modification system .................................................................................................. - 12 - 1.2.2 Gene expression .......................................................................................................................... - 14 - 1.2.3 DNA repair .................................................................................................................................. - 15 - 1.2.4 Coordination of replication and cell division ............................................................................... - 16 - 1.2.5 Cytosine methylation ................................................................................................................... - 17 - 1.3 BACTERIAL METHYLOMES ...............................................................................................................- 18 - 2. STREPTOMYCETES ...........................................................................................................................- 21 - 2.1 STREPTOMYCES COELICOLOR TRANSCRIPTOME ON SOLID GYM AND IN LIQUID R5A .......................- 25 - 3. METHYLATION IN STREPTOMYCETEAE ..........................................................................................- 27 - AIM ..................................................................................................................................................... - 29 - RESULTS ........................................................................................................................................... - 32 - 1. DNA CYTOSINE AND ADENINE METHYLATION IN THE DEFINED LIQUID MG ................................- 33 - 1.1 CHARACTERIZATION OF S. COELICOLOR CYTOSINE METHYLOME ....................................................- 34 - 1.2 OPTIMIZATION OF THE USE OF 5-AZA-2’-DEOXYCYTIDINE (AZA-DC) ..............................................- 39 - 1.3 EFFECT OF CYTOSINE DEMETHYLATION ON GROWTH (TREATMENT EVERY 24H).............................- 40 - 1.3.1 Effect of cytosine demethylation on physiological differentiation (treatment every 24h)............ - 41 - 1.4 EFFECT OF CYTOSINE DEMETHYLATION ON GROWTH (TREATMENT EVERY 12H).............................- 42 - 1.4.1 Effect of cytosine demethylation on physiological differentiation (treatment every 12h)............ - 43 - 1.5 DNA CYTOSINE METHYLATION AND GENE EXPRESSION ..................................................................- 44 - 2. DNA CYTOSINE METHYLATION IN THE RICH LIQUID R5A.............................................................- 48 - 2.1 DNA CYTOSINE METHYLATION DURING DEVELOPMENT .................................................................- 48 - 2.2 CHARACTERIZATION OF S. COELICOLOR CYTOSINE METHYLOME ....................................................- 49 - 2.3 EFFECT OF CYTOSINE DEMETHYLATION ON GROWTH ......................................................................- 53 - 2.4 EFFECT OF CYTOSINE DEMETHYLATION ON PHYSIOLOGICAL DIFFERENTIATION .............................- 53 - 2.5 DNA CYTOSINE METHYLATION AND GENE EXPRESSION ..................................................................- 54 - 2.5.1 GGCmCGG consensus sequence .................................................................................................. - 54 - 2.5.2 GCCmCG consensus sequence ..................................................................................................... - 56 - 2.5.3 CmGGGC consensus sequence .................................................................................................... - 58 - 3. DNA CYTOSINE METHYLATION ON SOLID RICH GYM .......................................................................- 60 - 3.1 DNA CYTOSINE METHYLATION DURING DEVELOPMENT .................................................................- 60 - 3.2 CHARACTERIZATION OF S. COELICOLOR CYTOSINE METHYLOME ....................................................- 62 - 3.3 EFFECT OF CYTOSINE DEMETHYLATION ON GROWTH ......................................................................- 66 - 3.4 EFFECT OF CYTOSINE DEMETHYLATION ON MORPHOLOGICAL DIFFERENTIATION ...........................- 66 - 3.5 EFFECT OF DEMETHYLATION ON PHYSIOLOGICAL DIFFERENTIATION ..............................................- 69 - 3.6 DNA CYTOSINE METHYLATION AND GENE EXPRESSION ..................................................................- 69 - 3.6.1 GGCmCGG consensus sequence .................................................................................................. - 69 - 3.6.2 GCCmCG consensus sequence ..................................................................................................... - 72 - 3.6.3 CmGGGC consensus sequence .................................................................................................... - 74 - 4. ANALYSIS OF S. COELICOLOR CYTOSINE METHYLOME ...................................................................- 76 - 4.1 SIMILARITIES AND DIFFERENCES BETWEEN CYTOSINE METHYLOME IN LIQUID AND SOLID MEDIUM- 76 - 5. ROLE OF THE DNA METHYLTRANSFERASE SCO1731 ....................................................................- 79 - 5.1 CONSTRUCTION OF A KNOCK OUT MUTANT IN SCO1731 GENE .......................................................- 79 - 5.2 EFFECT OF THE INACTIVATION OF SCO1731 GENE ..........................................................................- 81 - 5.3 COMPLEMENTATION OF MUTANT ΔSCO1731 AND CONSTRUCTION OF A STRAIN EXPRESSING TWO COPIES OF THE SCO1731 GENE ..............................................................................................................- 83 - 6. ROLE OF THE DNA METHYLTRANSFERASE SCO0995 ....................................................................- 88 - 6.1 CONSTRUCTION OF A KNOCK OUT MUTANT IN SC0995 GENE ...........................................................- 88 - 6.2 EFFECT OF THE INACTIVATION OF SCO0995 GENE ..........................................................................- 90 - 6.3 COMPLEMENTATION OF MUTANT ΔSCO0995 ..................................................................................- 90 - 7. DNA CYTOSINE METHYLATION IN SEVERAL STREPTOMYCETES ...................................................- 93 - DISCUSSION ..................................................................................................................................... - 96 - 1. DNA CYTOSINE METHYLATION ALONG THE GROWTH ...................................................................- 97 - 2. CYTOSINE METHYLOMES .................................................................................................................- 98 - 3. CORRELATION BETWEEN CYTOSINE METHYLOME AND TRANSCRIPTOMIC ANALYSIS ...............- 100 - 4. EFFECT OF CYTOSINE DEMETHYLATION BY ADDING AZA-DC .....................................................- 101 - 5. ROLE OF A PUTATIVE DNA(5-CYTOSINE)-METHYLTRANSFERASE ..............................................- 102 - MATERIAL AND METHODS ....................................................................................................... - 105 - 1. STRAINS AND MEDIA.......................................................................................................................- 106 - 2. PLASMIDS AND COSMIDS ................................................................................................................- 107 - 3. TREATMENT OF S. COELICOLOR WITH AZA-DC .............................................................................- 107 - 4. DOT BLOT ASSAY ...........................................................................................................................-
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]
  • 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]
  • 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]
  • Ultrafast Dynamics of Energy and Electron Transfer in Dna-Photolyase
    ULTRAFAST DYNAMICS OF ENERGY AND ELECTRON TRANSFER IN DNA-PHOTOLYASE DISSERTATION Presented in Partial Fulfillment of the Requirements for The Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Chaitanya Saxena, M.Phil. ****** The Ohio State University 2007 Dissertation Committee: Professor Dongping Zhong, Advisor Approved by Professor Richard P. Swenson Professor Zucai Suo Professor Michael G. Poirier Advisor Biophysics Graduate Studies Program ABSTRACT One of the detrimental effects of UV radiation on the biosphere is the formation of cyclobutane pyrimidine dimers (Pyr<>Pyr) between two adjacent thymine bases in DNA. Pyr<>Pyr dimers can not be repaired by normal DNA repair machinery and may result in gene mutation or cell death. Photolyase, a photoenzyme harnesses blue or near- UV light energy to cleave the cyclobutane ring of the Pyr<>Pyr and thus protects against the harmful effects of UV radiation. In the proposed hypothesis for the catalysis, the enzyme binds a Pyr<>Pyr in DNA, independent of light. The photoantenna, a photolyase cofactor methenyltetrahydrofolate (MTHF) harvests a UV/blue-light photon, and transfers the excitation energy (dipole-dipole interaction) to another photolyase cofactor, a fully reduced flavin (FADH−). Excited FADH−* then transfers an electron to the Pyr<>Pyr, which consequently splits the Pyr<>Pyr into two pyrimidine moieties and hence repairs the damaged DNA. As proposed, the repair cycle ends when the excess electron from the repaired pyrimidine moieties is transferred back to the nascent-formed neutral FADH• species and regenerates the active FADH− form. The complex mechanism of energy and electron transfer in photolyase enzyme involved in performing its DNA repair function was investigated using femtosecond-resolved fluorescence up- conversion and transient absorption methods.
    [Show full text]
  • Impact of Solar Radiation on Gene Expression in Bacteria
    Proteomes 2013, 1, 70-86; doi:10.3390/proteomes1020070 OPEN ACCESS proteomes ISSN 2227-7382 www.mdpi.com/journal/proteomes Review Impact of Solar Radiation on Gene Expression in Bacteria Sabine Matallana-Surget 1,2,* and Ruddy Wattiez 3 1 UPMC Univ Paris 06, UMR7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer F-66650, France 2 CNRS, UMR7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer F-66650, France 3 Department of Proteomics and Microbiology, Research Institute for Biosciences, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons B-7000, Belgium; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +33-4-68-88-73-18. Received: 2 May 2013; in revised form: 21 June 2013 / Accepted: 2 July 2013 / Published: 16 July 2013 Abstract: Microorganisms often regulate their gene expression at the level of transcription and/or translation in response to solar radiation. In this review, we present the use of both transcriptomics and proteomics to advance knowledge in the field of bacterial response to damaging radiation. Those studies pertain to diverse application areas such as fundamental microbiology, water treatment, microbial ecology and astrobiology. Even though it has been demonstrated that mRNA abundance is not always consistent with the protein regulation, we present here an exhaustive review on how bacteria regulate their gene expression at both transcription and translation levels to enable biomarkers identification and comparison of gene regulation from one bacterial species to another. Keywords: transcriptomic; proteomic; gene regulation; radiation; bacteria 1. Introduction Bacteria present a wide diversity of tolerances to damaging radiation and are the simplest model organisms for studying their response and strategies of defense in terms of gene regulation.
    [Show full text]
  • Generate Metabolic Map Poster
    Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical
    [Show full text]
  • Structural Insights Into Recognition and Repair of UV-DNA Damage by Spore Photoproduct Lyase, a Radical SAM Enzyme Alhosna Benjdia1,*, Korbinian Heil2, Thomas R
    9308–9318 Nucleic Acids Research, 2012, Vol. 40, No. 18 Published online 2 July 2012 doi:10.1093/nar/gks603 Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme Alhosna Benjdia1,*, Korbinian Heil2, Thomas R. M. Barends1, Thomas Carell2,* and Ilme Schlichting1,* 1Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg and 2Department of Chemistry, Center for Integrated Protein Science (CiPSM), Ludwig-Maximilians University, Butenandtstrasse 5-13, 81377 Munich, Germany Received April 2, 2012; Revised May 26, 2012; Accepted May 29, 2012 ABSTRACT INTRODUCTION Bacterial spores possess an enormous resistance Given the myriad of DNA-damaging agents, bacteria have to ultraviolet (UV) radiation. This is largely due to a evolved diverse DNA repair pathways to resist and survive unique DNA repair enzyme, Spore Photoproduct up to thousands of years in the extreme case of spores. Lyase (SP lyase) that repairs a specific UV-induced This tremendous resistance is achieved by a combination DNA lesion, the spore photoproduct (SP), through of several factors including DNA packing assisted by an unprecedented radical-based mechanism. small acid-soluble spore proteins, dehydration and the Unlike DNA photolyases, SP lyase belongs to the high content of dipicolinic acid (2,6-pyridinedicarboxylic emerging superfamily of radical S-adenosyl-L-me- acid) (1). Under these conditions, ultraviolet (UV) radi- thionine (SAM) enzymes and uses a [4Fe–4S]1+ ation results in the formation of one major DNA lesion, cluster and SAM to initiate the repair reaction. We the so-called spore photoproduct (SP or 5-(R-thyminyl)- report here the first crystal structure of this enig- 5,6-dihydrothymine) (2,3).
    [Show full text]