DOCSLIB.ORG

Row Labels Gene Name GLU 1 GLU 2 GLU 3 RF 1 RF 2 RF 3

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Row Labels Gene Name GLU 1 GLU 2 GLU 3 RF 1 RF 2 RF 3 Ga0073285_102189 S-layer homology domain-containing protein 1549 1805 1683 1214 1230 1364 Ga0073285_10263 pyruvate-ferredoxin/flavodoxin oxidoreductase 901 1003 950 757 754 738 Ga0073285_14010 acetaldehyde dehydrogenase /alcohol 774 880 805 751 771 823 dehydrogenase AdhE Ga0073285_1166 chaperonin GroEL 663 798 645 563 703 716 Ga0073285_11916 enolase 486 378 459 422 454 412 Ga0073285_11684 elongation factor Tu 426 390 479 453 396 361 Ga0073285_11912 glyceraldehyde 3-phosphate dehydrogenase 443 382 352 417 381 367 Ga0073285_101203 ketol-acid reductoisomerase 465 555 441 251 251 280 Ga0073285_10199 4-hydroxy-3-methylbut-2-enyl diphosphate 361 382 343 314 358 372 reductase Ga0073285_102163 ATP synthase F1 subcomplex beta subunit 256 228 255 241 272 295 Ga0073285_1376 DNA-directed RNA polymerase subunit beta' 195 227 186 155 161 171 Ga0073285_12917 D-3-phosphoglycerate dehydrogenase 237 195 192 142 147 138 Ga0073285_10829 pyruvate carboxylase 185 226 195 141 148 151 Ga0073285_1377 DNA-directed RNA polymerase subunit beta 185 212 179 144 145 157 Ga0073285_11620 NAD(P)-dependent iron-only hydrogenase catalytic 98 91 93 233 227 248 subunit Contaminant_TRYP_BOVIN #N/A 157 200 188 130 150 149 Ga0073285_11681 LSU ribosomal protein L4P 198 217 190 108 122 131 Ga0073285_11561 carbamoyl-phosphate synthase large subunit 184 186 149 141 147 142 Ga0073285_101306 polyribonucleotide nucleotidyltransferase 165 164 147 128 146 162 Ga0073285_102105 inosine-5'-monophosphate dehydrogenase 221 178 182 95 116 118 Ga0073285_1372 elongation factor G 154 109 161 173 147 128 Ga0073285_11913 phosphoglycerate kinase 146 91 144 184 144 144 Ga0073285_11417 molecular chaperone DnaK 129 146 125 145 151 139 Ga0073285_10712 xylose ABC transporter ATP-binding protein 101 124 111 142 161 172 Ga0073285_1018 phosphoenolpyruvate--protein phosphotransferase 133 125 137 135 120 117 Ga0073285_1164 pyruvate phosphate dikinase 93 115 116 134 152 137 Ga0073285_101106 ferritin 122 147 133 96 109 108 Ga0073285_11679 LSU ribosomal protein L2P 123 149 131 90 110 111 Ga0073285_1483 glycerol dehydratase, cobalamin-independent, large 176 161 172 68 66 70 subunit Ga0073285_101200 dihydroxyacid dehydratase 144 173 131 79 77 70 Ga0073285_1378 LSU ribosomal protein L12P 131 148 102 85 74 100 Ga0073285_10815 glutamate dehydrogenase (NADP+) 106 108 109 106 94 105 Ga0073285_10738 Uncharacterized protein, linocin/CFP29 family 91 87 87 110 113 130 Ga0073285_11222 NADPH-dependent 2,4-dienoyl-CoA reductase, sulfur 217 214 167 1 1 reductase Ga0073285_1379 LSU ribosomal protein L10P 105 113 95 101 85 99 Ga0073285_12932 cell division protease FtsH 95 121 93 92 100 94 Ga0073285_13416 Alcohol dehydrogenase, class IV 202 152 233 1 Ga0073285_102161 ATP synthase F1 subcomplex alpha subunit 91 85 94 95 110 112 Ga0073285_12031 ribonucleoside-diphosphate reductase alpha chain 90 96 78 108 104 111 Ga0073285_10747 starch synthase 106 114 102 71 85 103 Ga0073285_10523 pyruvate kinase 96 93 88 92 95 104 Ga0073285_10188 acetate kinase 69 50 88 121 136 103 Ga0073285_10636 aconitase 99 81 92 99 94 80 Ga0073285_11063 electron transport complex protein RnfC 97 104 84 88 80 90 Ga0073285_101285 elongation factor Ts 78 57 93 132 96 83 Ga0073285_11067 transketolase 111 66 89 113 86 69 Ga0073285_11621 NADP-reducing hydrogenase subunit HndC 18 23 43 168 134 147 Ga0073285_101163 alanyl-tRNA synthetase 99 111 101 71 76 74 Ga0073285_101204 2-isopropylmalate synthase 115 110 85 73 76 65 Ga0073285_101300 translation initiation factor IF-2 97 115 79 80 75 74 Ga0073285_13421 Threonine dehydrogenase 168 170 167 5 2 Ga0073285_11945 trigger factor 94 106 89 77 69 76 Ga0073285_10670 propionyl-CoA carboxylase carboxyltransferase 82 75 86 79 90 93 subunit Ga0073285_11616 PTS system D-glucosamine-specific IIA component, 112 135 112 27 53 64 Glc family /PTS system D-glucosamine-specific IIB component, Glc family /PTS system D-glucosamine- specific IIC component, Glc family Ga0073285_11680 LSU ribosomal protein L23P 89 93 87 73 83 77 Ga0073285_11722 Outer membrane protein TolC 32 35 42 132 121 126 Ga0073285_11656 SSU ribosomal protein S4P 89 107 89 61 65 75 Ga0073285_10133 Isoleucyl-tRNA synthetase 71 59 68 113 87 82 Ga0073285_11573 formate C-acetyltransferase 90 108 91 73 56 61 Ga0073285_11466 aspartyl-tRNA synthetase 92 90 75 79 67 66 Ga0073285_102114 methionyl-tRNA synthetase 93 78 70 80 77 69 Ga0073285_11676 SSU ribosomal protein S3P 77 76 86 70 80 78 Ga0073285_13711 large subunit ribosomal protein L1 83 68 67 83 80 79 Ga0073285_1174 conserved repeat domain-containing protein 83 80 83 68 73 69 Ga0073285_101284 SSU ribosomal protein S2P 71 87 90 64 64 68 Ga0073285_11338 ribonucrease Y 78 85 77 67 60 69 Ga0073285_1163 GMP synthase (glutamine-hydrolyzing) 83 75 66 72 78 61 Ga0073285_101305 small subunit ribosomal protein S15 77 85 62 56 67 87 Ga0073285_101156 phenylalanyl-tRNA synthetase beta subunit 68 91 81 63 64 65 Ga0073285_101205 3-isopropylmalate/(R)-2-methylmalate dehydratase 105 83 78 63 55 48 large subunit Ga0073285_11667 LSU ribosomal protein L6P 90 86 72 53 60 69 Ga0073285_10646 hydrophobic/amphiphilic exporter-1, HAE1 family 82 87 72 56 60 68 Ga0073285_10187 phosphate acetyltransferase 55 32 67 107 88 68 Ga0073285_11915 phosphoglycerate mutase 81 37 70 75 84 70 Ga0073285_11368 tryptophan synthase, beta chain 59 42 54 99 75 87 Ga0073285_11456 preprotein translocase subunit SecD 70 87 56 62 69 71 Ga0073285_10658 phosphoribosylformylglycinamidine synthase 79 74 70 66 62 54 Ga0073285_101104 bacterial nucleoid protein Hbs 64 31 57 100 86 64 Ga0073285_1021 DNA gyrase subunit A 72 73 68 54 69 65 Ga0073285_11347 S-layer homology domain-containing protein 69 82 71 64 44 61 Ga0073285_10756 starch phosphorylase 76 42 62 82 61 67 Ga0073285_102159 ATP synthase F0 subcomplex B subunit 59 73 68 53 57 77 Ga0073285_11735 serine protease, S1-C subfamily, contains C-terminal 43 49 48 88 75 84 PDZ domain Ga0073285_11918 K(+)-stimulated pyrophosphate-energized sodium 68 88 82 32 55 58 pump Ga0073285_11437 glycyl-tRNA synthetase beta chain 64 54 56 78 65 64 Ga0073285_11655 DNA-directed RNA polymerase subunit alpha 63 82 74 50 56 53 Ga0073285_101148 threonyl-tRNA synthetase 64 68 54 57 65 66 Ga0073285_11464 Tetratricopeptide repeat-containing protein 59 80 68 49 50 66 Ga0073285_12519 preprotein translocase subunit SecA 66 57 53 66 63 65 Ga0073285_10788 argininosuccinate synthase 65 71 62 56 60 55 Ga0073285_11071 3-oxoacyl-[acyl-carrier-protein] synthase II 49 31 47 103 73 65 Ga0073285_11914 triosephosphate isomerase 72 32 48 79 80 55 Ga0073285_102143 fructose-bisphosphate aldolase 64 60 60 63 59 59 Ga0073285_11665 small subunit ribosomal protein S5 60 62 56 68 57 61 Ga0073285_1173 hypothetical protein 49 57 52 68 70 67 Ga0073285_10175 hypothetical protein 68 79 62 57 42 52 Ga0073285_1143 hypothetical protein 67 71 56 57 52 56 Ga0073285_103118 adenylosuccinate lyase 67 62 69 53 52 55 Ga0073285_101162 tyrosyl-tRNA synthetase 59 51 50 70 60 65 Ga0073285_13313 ATP-dependent Clp protease ATP-binding subunit 64 70 62 59 49 49 ClpC Ga0073285_102134 Aspartyl aminopeptidase 68 79 63 34 50 56 Ga0073285_103124 pyridoxal phosphate synthase yaaD subunit 62 36 49 70 71 60 Ga0073285_101207 3-isopropylmalate dehydrogenase 75 77 62 45 48 40 Ga0073285_101208 2-isopropylmalate synthase 81 94 56 38 37 39 Ga0073285_12040 PTS system D-fructose-specific IIB component (F1P- 96 123 99 5 7 11 forming), Frc family /PTS system D-fructose-specific IIC component (F1P-forming), Frc family Ga0073285_11658 small subunit ribosomal protein S13 65 86 65 48 33 43 Ga0073285_11154 bifunctional enzyme CysN/CysC 61 53 54 46 61 64 Ga0073285_11668 small subunit ribosomal protein S8 59 60 53 55 57 55 Ga0073285_11947 ATP-dependent Clp protease ATP-binding subunit 67 67 61 47 48 48 ClpX Ga0073285_102173 Beta-barrel assembly machine subunit BamA 47 50 42 63 70 65 Ga0073285_103144 Predicted oxidoreductase 54 45 47 50 71 66 Ga0073285_11312 ribonuclease J 57 73 58 45 50 50 Ga0073285_1059 CoA-disulfide reductase 53 72 62 40 50 52 Ga0073285_10645 RND family efflux transporter, MFP subunit 49 52 49 62 59 56 Ga0073285_10971 molecular chaperone DnaK 62 61 52 47 50 55 Ga0073285_10454 leucyl-tRNA synthetase 60 49 61 63 43 46 Ga0073285_12039 foldase protein PrsA 110 112 89 4 4 3 Ga0073285_10644 Outer membrane protein TolC 54 62 51 56 48 49 Ga0073285_11682 large subunit ribosomal protein L3 60 72 57 43 45 43 Ga0073285_10228 small subunit ribosomal protein S6 51 42 45 49 66 65 Ga0073285_1335 glutamyl-tRNA synthetase /glutamate--tRNA(Gln) 53 37 52 75 51 50 ligase Ga0073285_1373 small subunit ribosomal protein S7 54 45 61 50 54 50 Ga0073285_11648 small subunit ribosomal protein S9 56 57 55 43 53 49 Ga0073285_101274 hypothetical protein 46 56 55 47 55 53 Ga0073285_10539 CoA:oxalate CoA-transferase 46 34 49 76 57 50 Ga0073285_101201 acetolactate synthase, large subunit 64 78 54 44 32 32 Ga0073285_101110 hypothetical protein 57 65 54 40 38 48 Ga0073285_101199 branched-chain amino acid aminotransferase 60 70 61 36 35 37 Ga0073285_11613 glutamate-5-semialdehyde dehydrogenase 51 43 52 51 52 46 Ga0073285_1055 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase 47 38 36 70 53 49 subunit A Ga0073285_10713 xylose-binding protein 21 16 25 85 75 70 Ga0073285_10156 peptide/nickel transport system substrate-binding 61 38 63 52 41 34 protein Ga0073285_11657 SSU ribosomal protein S11P 59 48 51 40 50 41 Ga0073285_1256 PRC-barrel domain-containing protein 26 12 34 79 76 62 Ga0073285_11948 ATP-dependent proteinase. Serine peptidase. 47 72 48 43 39 39 MEROPS family
Recommended publications
  • METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase

    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.
  • Phospholipid:Diacylglycerol Acyltransferase: an Enzyme That Catalyzes the Acyl-Coa-Independent Formation of Triacylglycerol in Yeast and Plants

    Phospholipid:Diacylglycerol Acyltransferase: an Enzyme That Catalyzes the Acyl-Coa-Independent Formation of Triacylglycerol in Yeast and Plants

    Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants Anders Dahlqvist*†‡, Ulf Ståhl†§, Marit Lenman*, Antoni Banas*, Michael Lee*, Line Sandager¶, Hans Ronne§, and Sten Stymne¶ *Scandinavian Biotechnology Research (ScanBi) AB, Herman Ehles Va¨g 2 S-26831 Svaloˆv, Sweden; ¶Department of Plant Breeding Research, Swedish University of Agricultural Sciences, Herman Ehles va¨g 2–4, S-268 31 Svalo¨v, Sweden; and §Department of Plant Biology, Uppsala Genetic Center, Swedish University of Agricultural Sciences, Box 7080, S-750 07 Uppsala, Sweden Edited by Christopher R. Somerville, Carnegie Institution of Washington, Stanford, CA, and approved March 31, 2000 (received for review February 15, 2000) Triacylglycerol (TAG) is known to be synthesized in a reaction that acid) and epoxidated fatty acid (vernolic acid) in TAG in castor uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, bean (Ricinus communis) and the hawk’s-beard Crepis palaestina, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol respectively. Furthermore, a similar enzyme is shown to be acyltransferase. We have found that some plants and yeast also present in the yeast Saccharomyces cerevisiae, and the gene have an acyl-CoA-independent mechanism for TAG synthesis, encoding this enzyme, YNR008w, is identified. which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:dia- Materials and Methods cylglycerol acyltransferase, or PDAT. PDAT was characterized in Yeast Strains and Plasmids. The wild-type yeast strains used were microsomal preparations from three different oil seeds: sunflower, either FY1679 (MAT␣ his3-⌬200 leu2-⌬1 trp1-⌬6 ura3-52) (9) or castor bean, and Crepis palaestina.
  • The World of Cyclic Dinucleotides in Bacterial Behavior

    The World of Cyclic Dinucleotides in Bacterial Behavior

    molecules Review The World of Cyclic Dinucleotides in Bacterial Behavior Aline Dias da Purificação, Nathalia Marins de Azevedo, Gabriel Guarany de Araujo , Robson Francisco de Souza and Cristiane Rodrigues Guzzo * Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 01000-000, Brazil * Correspondence: [email protected] or [email protected]; Tel.: +55-11-3091-7298 Received: 27 December 2019; Accepted: 17 March 2020; Published: 25 May 2020 Abstract: The regulation of multiple bacterial phenotypes was found to depend on different cyclic dinucleotides (CDNs) that constitute intracellular signaling second messenger systems. Most notably, c-di-GMP, along with proteins related to its synthesis, sensing, and degradation, was identified as playing a central role in the switching from biofilm to planktonic modes of growth. Recently, this research topic has been under expansion, with the discoveries of new CDNs, novel classes of CDN receptors, and the numerous functions regulated by these molecules. In this review, we comprehensively describe the three main bacterial enzymes involved in the synthesis of c-di-GMP, c-di-AMP, and cGAMP focusing on description of their three-dimensional structures and their structural similarities with other protein families, as well as the essential residues for catalysis. The diversity of CDN receptors is described in detail along with the residues important for the interaction with the ligand. Interestingly, genomic data strongly suggest that there is a tendency for bacterial cells to use both c-di-AMP and c-di-GMP signaling networks simultaneously, raising the question of whether there is crosstalk between different signaling systems. In summary, the large amount of sequence and structural data available allows a broad view of the complexity and the importance of these CDNs in the regulation of different bacterial behaviors.
  • Peroxisomal Fatty Acid Beta-Oxidation in Relation to the Accumulation Of

    Peroxisomal Fatty Acid Beta-Oxidation in Relation to the Accumulation Of

    Peroxisomal fatty acid beta-oxidation in relation to the accumulation of very long chain fatty acids in cultured skin fibroblasts from patients with Zellweger syndrome and other peroxisomal disorders. R J Wanders, … , A W Schram, J M Tager J Clin Invest. 1987;80(6):1778-1783. https://doi.org/10.1172/JCI113271. Research Article The peroxisomal oxidation of the long chain fatty acid palmitate (C16:0) and the very long chain fatty acids lignocerate (C24:0) and cerotate (C26:0) was studied in freshly prepared homogenates of cultured skin fibroblasts from control individuals and patients with peroxisomal disorders. The peroxisomal oxidation of the fatty acids is almost completely dependent on the addition of ATP, coenzyme A (CoA), Mg2+ and NAD+. However, the dependency of the oxidation of palmitate on the concentration of the cofactors differs markedly from that of the oxidation of lignocerate and cerotate. The peroxisomal oxidation of all three fatty acid substrates is markedly deficient in fibroblasts from patients with the Zellweger syndrome, the neonatal form of adrenoleukodystrophy and the infantile form of Refsum disease, in accordance with the deficiency of peroxisomes in these patients. In fibroblasts from patients with X-linked adrenoleukodystrophy the peroxisomal oxidation of lignocerate and cerotate is impaired, but not that of palmitate. Competition experiments indicate that in fibroblasts, as in rat liver, distinct enzyme systems are responsible for the oxidation of palmitate on the one hand and lignocerate and cerotate on the other hand. Fractionation studies indicate that in rat liver activation of cerotate and lignocerate to cerotoyl-CoA and lignoceroyl-CoA, respectively, occurs in two subcellular fractions, the endoplasmic reticulum and the peroxisomes but not in the mitochondria.
  • Adaptive Responses by Transcriptional Regulators to Small Molecules in Prokaryotes

    Adaptive Responses by Transcriptional Regulators to Small Molecules in Prokaryotes

    Adaptive Responses by Transcriptional Regulators to small molecules in Prokaryotes Structural studies of two bacterial one-component signal transduction systems DntR and HpNikR Cyril Dian Stockholm University Doctoral thesis © Cyril Dian, Stockholm 2007 ISBN 978-91-7155-500-7 Department of Biochemistry and Biophysics The Arrhenius Laboratories for Natural Sciences Stockholm University SE-106 91 Stockholm Sweden All previously published papers are reprinted With permission from the publishers Intellecta Docusys, Stockholm 2007 Abstract Prokaryotes are continually exposed to environmental changes in their physiological conditions. In order to survive such unstable conditions, or to compete with others species for the same environmental niche, prokaryotes must monitor signals about both their extracellular environment and intracellular physiological status and provide rapid and appropriate responses to variations in their surroundings. This adaptive response to environmental signals is triggered mainly by transcriptional regulators via two components, the one- and two-component signal transduction systems. These scan intra- and extracellular small-molecule mixtures and modulate gene expression to provide the appropriate physiological response to the prevailing conditions. Most prokaryotic one component regulators are simple transcription factors comprising of a small-molecule binding domain (SMBD) and a DNA binding domain (DBD). Although the effects of transcription factors on the transcription machinery are well understood, the exact location
  • Structure of Human Aspartyl Aminopeptidase Complexed With

    Structure of Human Aspartyl Aminopeptidase Complexed With

    Chaikuad et al. BMC Structural Biology 2012, 12:14 http://www.biomedcentral.com/1472-6807/12/14 RESEARCH ARTICLE Open Access Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family Apirat Chaikuad1, Ewa S Pilka1, Antonio De Riso2, Frank von Delft1, Kathryn L Kavanagh1, Catherine Vénien-Bryan2, Udo Oppermann1,3 and Wyatt W Yue1* Abstract Backround: Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results: The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β- hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions: The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference.
  • Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes

    Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes

    Sulfite dehydrogenases in organotrophic bacteria: enzymes, genes and regulation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sabine Lehmann Tag der mündlichen Prüfung: 10. April 2013 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Andrew W. B. Johnston So eine Arbeit wird eigentlich nie fertig, man muss sie für fertig erklären, wenn man nach Zeit und Umständen das möglichste getan hat. (Johann Wolfgang von Goethe, Italienische Reise, 1787) DANKSAGUNG An dieser Stelle möchte ich mich herzlich bei folgenden Personen bedanken: . Prof. Dr. Alasdair M. Cook (Universität Konstanz, Deutschland), der mir dieses Thema und seine Laboratorien zur Verfügung stellte, . Prof. Dr. Bernhard Schink (Universität Konstanz, Deutschland), für seine spontane und engagierte Übernahme der Betreuung, . Prof. Dr. Andrew W. B. Johnston (University of East Anglia, UK), für seine herzliche und bereitwillige Aufnahme in seiner Arbeitsgruppe, seiner engagierten Unter- stützung, sowie für die Übernahme des Koreferates, . Prof. Dr. Frithjof C. Küpper (University of Aberdeen, UK), für seine große Hilfsbereitschaft bei der vorliegenden Arbeit und geplanter Manuskripte, als auch für die mentale Unterstützung während der letzten Jahre! Desweiteren möchte ich herzlichst Dr. David Schleheck für die Übernahme des Koreferates der mündlichen Prüfung sowie Prof. Dr. Alexander Bürkle, für die Übernahme des Prüfungsvorsitzes sowie für seine vielen hilfreichen Ratschläge danken! Ein herzliches Dankeschön geht an alle beteiligten Arbeitsgruppen der Universität Konstanz, der UEA und des SAMS, ganz besonders möchte ich dabei folgenden Personen danken: . Dr. David Schleheck und Karin Denger, für die kritische Durchsicht dieser Arbeit, der durch und durch sehr engagierten Hilfsbereitschaft bei Problemen, den zahlreichen wissenschaftlichen Diskussionen und für die aufbauenden Worte, .
  • Regulation of Stringent Factor by Branched-Chain Amino Acids

    Regulation of Stringent Factor by Branched-Chain Amino Acids

    Regulation of stringent factor by branched-chain amino acids Mingxu Fanga and Carl E. Bauera,1 aMolecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405 Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved May 9, 2018 (received for review February 21, 2018) When faced with amino acid starvation, prokaryotic cells induce a Under normal growth conditions, the synthetase activity of Rel is stringent response that modulates their physiology. The stringent thought to be self-inhibited; however, during times of amino acid response is manifested by production of signaling molecules starvation, Rel interacts with stalled ribosomes, which activates guanosine 5′-diphosphate,3′-diphosphate (ppGpp) and guanosine synthetase activity to produce (p)ppGpp. The regulation of hy- 5′-triphosphate,3′-diphosphate (pppGpp) that are also called drolase activity is less understood but may involve one or more alarmones. In many species, alarmone levels are regulated by a downstream domains called the TGS and ACT domains. The TGS multidomain bifunctional alarmone synthetase/hydrolase called domain of SpoT has been shown to interact with an acyl carrier Rel. In this enzyme, there is an ACT domain at the carboxyl region protein, so it is presumed to sense the status of fatty acid metab- that has an unknown function; however, similar ACT domains are olism in E. coli (4). The function of the ACT domain is not as clear; present in other enzymes that have roles in controlling amino acid however, recent cryo-EM structures of E. coli RelA show that this metabolism. In many cases, these other ACT domains have been domain is involved in binding deacyl-tRNA as well as the ribosome shown to allosterically regulate enzyme activity through the bind- (5–7).
  • Two-Step Synthesis and Hydrolysis of Cyclic Di-AMP in Mycobacterium Tuberculosis

    Two-Step Synthesis and Hydrolysis of Cyclic Di-AMP in Mycobacterium Tuberculosis

    Two-Step Synthesis and Hydrolysis of Cyclic di-AMP in Mycobacterium tuberculosis Kasi Manikandan1, Varatharajan Sabareesh2¤, Nirpendra Singh3, Kashyap Saigal1, Undine Mechold4, Krishna Murari Sinha1* 1 Institute of Molecular Medicine, New Delhi, India, 2 Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology, Delhi and IGIB Extension Centre (Naraina), New Delhi, India, 3 Central Instrument Facility, University of Delhi South Campus, New Delhi, India, 4 Institut Pasteur, CNRS UMR 3528, Unite´ de Biochimie des Interactions macromole´culaires, Paris, France Abstract Cyclic di-AMP is a recently discovered signaling molecule which regulates various aspects of bacterial physiology and virulence. Here we report the characterization of c-di-AMP synthesizing and hydrolyzing proteins from Mycobacterium tuberculosis. Recombinant Rv3586 (MtbDisA) can synthesize c-di-AMP from ATP through the diadenylate cyclase activity. Detailed biochemical characterization of the protein revealed that the diadenylate cyclase (DAC) activity is allosterically regulated by ATP. We have identified the intermediates of the DAC reaction and propose a two-step synthesis of c-di-AMP from ATP/ADP. MtbDisA also possesses ATPase activity which is suppressed in the presence of the DAC activity. Investigations by liquid chromatography -electrospray ionization mass spectrometry have detected multimeric forms of c- di-AMP which have implications for the regulation of c-di-AMP cellular concentration and various pathways regulated by the dinucleotide. We have identified Rv2837c (MtbPDE) to have c-di-AMP specific phosphodiesterase activity. It hydrolyzes c-di- AMP to 59-AMP in two steps. First, it linearizes c-di-AMP into pApA which is further hydrolyzed to 59-AMP.
  • Characterization of Nudix Hydrolases: a Utilitarian

    Characterization of Nudix Hydrolases: a Utilitarian

    CHARACTERIZATION OF NUDIX HYDROLASES: A UTILITARIAN SUPERFAMILY OF ENZYMES By Andres Hernandez de la Peña A dissertation submitted to the Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland August, 2015 Abstract The present work details the structural and enzymatic characterization of Nudix hydrolases from three different organisms – Bdellovibrio bacteriovorus, Mycobacterium tuberculosis, and Tetrahymena thermophila. Each of these Nudix enzymes presents unique questions about their physiological function within their organism which are answered with a combination of structural biology, genetic manipulation, enzyme kinetics, and a wide range of protein assays. We demonstrate that RenU, from M. tuberculosis, is part of Redox Homeostasis Control System (RHOCS), which senses and regulates NADH concentrations. This control systems involves two other proteins, the serine/threonine protein kinase G (pknG) and the L13 ribosomal subunits, without which the bacterium fails to evade lysosomal delivery and falls prey to the oxidative arsenal of the macrophage host. Bd-NDPSase, a Nudix enzyme encoded by the B. bacteriovorus gene BD3179, localizes to the periplasmic space of the bacterium and hydrolyses at least four nucleoside diphosphate sugars in vitro. Through atomic-resolution models from X-ray diffraction, we identified a motif that differentiates this hydrolase from the similar, but more substrate specific, ADP- ribose hydrolase from E. coli. Lastly, we show that Nud1p from T. thermophila is a member of the Ezl1p complex, the histone methyltransferase Polycomb Group homologue of this protozoan. With the use of in vitro enzymatic assays we show, in addition, that Nu1dp hydrolyses CoA preferentially over acetyl-CoA and other nucleoside derivatives.
  • Ribonuclease and Deoxyribonuclease Activities in Experimental and Human Tumors by the Histochemical Substrate Film Method*

    Ribonuclease and Deoxyribonuclease Activities in Experimental and Human Tumors by the Histochemical Substrate Film Method*

    Ribonuclease and Deoxyribonuclease Activities in Experimental and Human Tumors by the Histochemical Substrate Film Method* R. DAOUSTJANDHARUKOAMANOÕ (Laboratoires de Recherche, Institut du Cancer de Montréal,Hôpital Notre-Dame et Universitéde Montréal,Montréal,Canada) SUMMARY The ribonuclease and deoxyribonuclease activities of 65 experimental and human tu mors (32 different types) have been examined by histochemical substrate film methods. A same general pattern was obtained for the distribution of both nucleases in the various types of experimental and human tumors. The connective tissue stroma and the necrotic regions of the tumor masses showed various levels of nuclease activity, whereas the neoplastic cells showed no demonstrable activity. It appears that deficien cies in ribonuclease and deoxyribonuclease activities represent general properties of cancer cells. The possible significance of the losses of nuclease activities in carcinogenesis is dis cussed. Studies on nucleases by histochemical methods MATERIALS AND METHODS have shown that losses of ribonuclease (RNase) The experimental tumors used in the present and deoxyribonuclease (DNase) activities take study were mostly rat, mouse, and hamster trans- place in rat liver during azo-dye carcinogenesis (1, plantable tumors (see Table 1). The tumor-bearing 6). The loss of RNase activity is progressive and animals were obtained from commercial or private occurs before parenchymal cells become cancerous, sources, and the tumors were used as supplied or whereas the loss of DNase activity is abrupt and closely associated with the neoplastic transforma TABLE1 tion of parenchymal cells. EXPERIMENTALTUMORS If a loss of RNase or DNase activity plays an important role in tumor formation, the lack of SpeciesRat"""MouseHamsterTumorPrimary demonstrable nuclease activity observed in rat hepatomaNovikoff primary hepatomas should also be observed in a hepatomaWalker variety of tumors.
  • Crystallographic Snapshots of Sulfur Insertion by Lipoyl Synthase

    Crystallographic Snapshots of Sulfur Insertion by Lipoyl Synthase

    Crystallographic snapshots of sulfur insertion by lipoyl synthase Martin I. McLaughlina,b,1, Nicholas D. Lanzc, Peter J. Goldmana, Kyung-Hoon Leeb, Squire J. Bookerb,c,d, and Catherine L. Drennana,e,f,2 aDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; bDepartment of Chemistry, The Pennsylvania State University, University Park, PA 16802; cDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802; dHoward Hughes Medical Institute, The Pennsylvania State University, University Park, PA 16802; eDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and fHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Vern L. Schramm, Albert Einstein College of Medicine, Bronx, NY, and approved July 5, 2016 (received for review March 8, 2016) Lipoyl synthase (LipA) catalyzes the insertion of two sulfur atoms substrate and at an intermediate stage in the reaction, just after at the unactivated C6 and C8 positions of a protein-bound octanoyl insertion of the C6 sulfur atom but before sulfur insertion at C8. chain to produce the lipoyl cofactor. To activate its substrate for sulfur insertion, LipA uses a [4Fe-4S] cluster and S-adenosylmethio- Results nine (AdoMet) radical chemistry; the remainder of the reaction The crystal structure of LipA from M. tuberculosis was de- mechanism, especially the source of the sulfur, has been less clear. termined to 1.64-Å resolution by iron multiwavelength anoma- One controversial proposal involves the removal of sulfur from a lous dispersion phasing (Table S1). The overall fold of LipA consists second (auxiliary) [4Fe-4S] cluster on the enzyme, resulting in de- of a (β/α)6 partial barrel common to most AdoMet radical enzymes struction of the cluster during each round of catalysis.