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Joosten, Han M.L.J.; Herst, Patricia M.; Drift, Chris Van Der
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Groningen University of Groningen Characterization of Glutamine-Requiring Mutants of Pseudomonas aeruginosa Janssen, Dick B.; Joosten, Han M.L.J.; Herst, Patricia M.; Drift, Chris van der Published in: Archives of Microbiology IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 1982 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Janssen, D. B., Joosten, H. M. L. J., Herst, P. M., & Drift, C. V. D. (1982). Characterization of Glutamine- Requiring Mutants of Pseudomonas aeruginosa. Archives of Microbiology, 131(4). Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 12-11-2019 JOURNAL OF BACTERIOLOGY, Sept. 1982, p. 1176-1183 Vol. 151, No. -
Genome-Wide Transcriptional Changes and Lipid Profile
G C A T T A C G G C A T genes Article Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti Chiara Santi 1, Barbara Molesini 1, Flavia Guzzo 1, Youry Pii 2 ID , Nicola Vitulo 1 and Tiziana Pandolfini 1,* ID 1 Department of Biotechnology, University of Verona, 37134 Verona, Italy; [email protected] (C.S.); [email protected] (B.M.); fl[email protected] (F.G.); [email protected] (N.V.) 2 Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bolzano BZ, Italy; [email protected] * Correspondence: tiziana.pandolfi[email protected]; Tel.: +39-045-8027918 Received: 30 October 2017; Accepted: 11 December 2017; Published: 19 December 2017 Abstract: Plant lipid-transfer proteins (LTPs) are small basic secreted proteins, which are characterized by lipid-binding capacity and are putatively involved in lipid trafficking. LTPs play a role in several biological processes, including the root nodule symbiosis. In this regard, the Medicago truncatula nodulin 5 (MtN5) LTP has been proved to positively regulate the nodulation capacity, controlling rhizobial infection and nodule primordia invasion. To better define the lipid transfer protein MtN5 function during the symbiosis, we produced MtN5-downregulated and -overexpressing plants, and we analysed the transcriptomic changes occurring in the roots at an early stage of Sinorhizobium meliloti infection. We also carried out the lipid profile analysis of wild type (WT) and MtN5-overexpressing roots after rhizobia infection. The downregulation of MtN5 increased the root hair curling, an early event of rhizobia infection, and concomitantly induced changes in the expression of defence-related genes. -
Transcripts of the Adeno-Associated Virus Genome: Mapping of the Major Rnas MICHAEL R
JOURNAL OF VIROLOGY, Oct. 1980, p. 79-92 Vol. 36, No. 1 0022-538X/80/10-0079/14$02.00/0 Transcripts of the Adeno-Associated Virus Genome: Mapping of the Major RNAs MICHAEL R. GREEN AND ROBERT G. ROEDER Departments ofBiological Chemistry and Genetics, Division ofBiology and Biomedical Sciences, Washington University School ofMedicine, St. Louis, Missouri 63110 The four major adeno-associated virus type 2 (AAV2)-specific RNAs were mapped on the linear viral genome by a variety of biochemical techniques, including Si nuclease and exonuclease VII mapping, RNA gel-transfer hybridi- zation, and analysis of reverse transcriptase extension products. All the major AAV2 RNAs were derived from the minus DNA strand and had 3' termini at position 96. The nucleus-specific 4.3- and 3.6-kilobase (kb) RNAs had 5' termini at positions 6 and 19, respectively. The 5' terminus of the 2.6-kb RNA mapped to position 38.5. The predominant 2.3-kb AAV2 mRNA was spliced and contained a short leader sequence (approximately 50 nucleotides) which mapped to position 38.5, coincident with the 5' terminus of the 2.6-kb RNA. The 5' end of the body of the 2.3-kb RNA mapped to position 46.5. These results are discussed in terms of the involvement of single versus multiple promoters (for transcription) and RNA splicing mechanisms in the generation of the AAV2 RNAs. Mammalian DNA viruses have provided pow- In our earlier studies ofAAV2 (19), we defined erful models for the analysis and formulation of and partially characterized four predominant mechaisms of gene expression in eucaryotic AAV2 RNAs in virus-infected cells, indicating cells. -
Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo -
Part One Amino Acids As Building Blocks
Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials. -
Pseudouridine Synthase 1: a Site-Specific Synthase Without Strict Sequence Recognition Requirements Bryan S
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Published online 18 November 2011 Nucleic Acids Research, 2012, Vol. 40, No. 5 2107–2118 doi:10.1093/nar/gkr1017 Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements Bryan S. Sibert and Jeffrey R. Patton* Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC 29208 USA Received May 20, 2011; Revised October 19, 2011; Accepted October 22, 2011 ABSTRACT rRNA and snRNA and requires Dyskerin or its homologs Pseudouridine synthase 1 (Pus1p) is an unusual (Cbf5p in yeast for example) and RNP cofactors [most site-specific modification enzyme in that it can often H/ACA small nucleolar ribonucleoprotein particles modify a number of positions in tRNAs and can rec- (snoRNPs)] that enable one enzyme to recognize many ognize several other types of RNA. No consensus different sites for modification on different substrates recognition sequence or structure has been identi- (17–25). The other pathway for É formation employs fied for Pus1p. Human Pus1p was used to determine site-specific É synthases that require no cofactors to rec- which structural or sequence elements of human ognize and modify the RNA substrate. A number of en- tRNASer are necessary for pseudouridine ()) forma- zymes have been identified in this pathway and are grouped in six families that all share a common basic tion at position 28 in the anticodon stem-loop (ASL). Ser structure (4). It is safe to say the cofactor ‘guided’ pathway Some point mutations in the ASL stem of tRNA has received a great deal of attention because of its simi- had significant effects on the levels of modification larity to aspects of RNA editing, but the site-specific and compensatory mutation, to reform the base pseudouridine synthases accomplish the same task, on pair, restored a wild-type level of ) formation. -
Ubc 2008 Spring Li Alice.Pdf
IDENTIFICATION OF VIRULENCE DETERMINANTS OF MYCOBACTERIUM TUBERCULOSIS VIA GENETIC COMPARISONS OF A VIRULENT AND AN ATTENUATED STRAIN OF MYCOBACTERIUM TUBERCULOSIS. by ALICE HOY LAM LI B.Sc., The University of British Columbia, 2001 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIRMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Pathology) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) MARCH 2008 Alice Hoy Lam Li, 2008 i ABSTRACT Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. -
Reduction of Pectinesterase Activity in a Commercial Enzyme Preparation
Journal of the Science of Food and Agriculture J Sci Food Agric 85:1613–1621 (2005) DOI: 10.1002/jsfa.2154 Reduction of pectinesterase activity in a commercial enzyme preparation by pulsed electric fields: comparison of inactivation kinetic models Joaquın´ Giner, Pascal Grouberman, Vicente Gimeno and Olga Martın´ ∗ Department of Food Technology, University of Lleida, CeRTA-UTPV, ETSEA, Avda Alcalde Rovira Roure 191, 25198-Lleida, Spain Abstract: The inactivation of pectinesterase (PE) in a commercial enzyme preparation (CEP) under high intensity pulsed electric fields (HIPEF) was studied. After desalting and water dilution of the raw CEP, samples were exposed to exponentially decay waveform pulses for up to 463 µs at electric field intensities ranging from 19 to 38 kV cm−1. Pulses were applied in monopolar mode. Experimental data were fitted to a first-order kinetic model as well as to models based on Fermi, Hulsheger¨ or Weibull equations to describe PE inactivation kinetics. Characteristic parameters for each model were calculated. Relationships between some of the parameters and process variables were obtained. The Weibull model yielded the best accuracy factor. The relationship between residual PE and input of electrical energy density was found to be that of exponential decay. 2005 Society of Chemical Industry Keywords: pulsed electric fields; kinetics; pectinesterase; model; inactivation INTRODUCTION It has become customary to use CEPs in fruit and Pectinesterase (PE; EC 3.1.1.11) is a pectic enzyme vegetable juice technology. Depending -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Production of Muconic Acid in Plants T ⁎ Aymerick Eudesa,B, , Roland Berthomieua,C, Zhangying Haoa,B, Nanxia Zhaoa,D, ⁎ Veronica Teixeira Benitesa,E, Edward E.K
Metabolic Engineering 46 (2018) 13–19 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Production of muconic acid in plants T ⁎ Aymerick Eudesa,b, , Roland Berthomieua,c, Zhangying Haoa,b, Nanxia Zhaoa,d, ⁎ Veronica Teixeira Benitesa,e, Edward E.K. Baidooa,e, Dominique Loquéa,b,f,g, a Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA b Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA c Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France d Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA e Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA f Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA g Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France ARTICLE INFO ABSTRACT Keywords: Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as Muconic acid adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates Salicylic acid toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of al- Catechol ternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic Shikimate carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous Plastid hosts for engineered metabolic pathways towards the manufacturing of chemicals. -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.