DOCSLIB.ORG

Hyper Ammonia Producing Bacteria and Bacteriophages in the Rumen Microbiome

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

STUDYING THE UNDERSTUDIED: HYPER AMMONIA PRODUCING BACTERIA AND BACTERIOPHAGES IN THE RUMEN MICROBIOME by Jessica Charlotte Abigail Friedersdorff A thesis submitted in partial fulfillment of the requirements for the degree of PhD in Biological Sciences Aberystwyth University 2020 Preface I. Mandatory Layout of Declaration/Statements Word Count of thesis: 62,288 DECLARATION This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Candidate name Jessica Charlotte Abigail Friedersdorff Signature: Date 15/09/2020 STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where *correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signature: Date 15/09/2020 [*this refers to the extent to which the text has been corrected by others] STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signature: Date 15/09/2020 NB: Candidates on whose behalf a bar on access (hard copy) has been approved by the University should use the following version of Statement 2: I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loans after expiry of a bar on access approved by Aberystwyth University. Signature: Date 15/09/2020 1 Preface II. Summary Candidate’s Surname/Family Name Friedersdorff Candidate’s Forenames (in full) Jessica Charlotte Abigail Candidate for the Degree of PhD Academic year the work submitted for examination 2020 Summary: Greenhouse gas emissions and feed efficiency in ruminant livestock are pertinent and important topics, ones which have not suffered from lack of attention as ample research has endeavoured to further our understanding of the complex rumen microbial ecosystem. Despite this, some populations remain understudied. This is the key motivation behind the studies herein, which contribute to the understanding of the niche bacterial population of hyper ammonia producers (HAP) and bacteriophages (viruses that infect bacteria). HAP species degrade amino acids and peptides for energy, in the process producing hydrogen, carbon dioxide, and excessive amounts of ammonia. Hydrogen and carbon dioxide feed into methane production by archaea present in the rumen, whilst excess ammonia is removed from the animal host. This makes the HAPs an ideal target for potential population control, but firstly it was imperative to better understand them. This study first characterised the ammonia production phenotypes of bacterial cultures, then compared their genomes and transcriptomes to identify a signature that indicates the HAP phenotype. The work presented here has demonstrated the complexity and variability underlying the seemingly simple HAP phenotype, warranting further investigation in future work and isolation of novel HAPs in order to better understand this group before controlling the population. Phage therapy is one approach to population control that has been relatively little explored to date in the rumen. Despite phages being abundant in the rumen, there were only five genomes available of phages isolated from rumen-associated samples. This study isolated and characterised a further five novel phages that infect Butyrivibrio fibrisolvens. While the work presented here did not identify phages active against HAPs, these five Butyrivibrio phages contribute valuable information about the structure and function of the rumen ecosystem. It is suggested that continuation of this line of enquiry in future work would complement ongoing research utilising metagenomics, metatranscriptomics and metaproteomics aimed at understanding and improving rumen efficiency. 2 Preface III. Funding Knowledge Economy Skills Scholarships (KESS 2) is a pan-Wales higher level skills initiative led by Bangor University on behalf of the HE sector in Wales. It is part funded by the Welsh Government’s European Social Fund (ESF) convergence programme for West Wales and the Valleys. The supporting company partner was Dr David Rooke, director of Dynamic Extractions LTD. 3 Preface IV. Contents I. MANDATORY LAYOUT OF DECLARATION/STATEMENTS ...................................... 1 II. SUMMARY ............................................................................................................................... 2 III. FUNDING ................................................................................................................................. 3 IV. CONTENTS .............................................................................................................................. 4 V. ACKNOWLEDGMENTS ...................................................................................................... 10 VI. LIST OF PUBLICATIONS ................................................................................................... 11 VII. FIGURE LEGENDS .............................................................................................................. 12 VIII. TABLE LEGENDS ................................................................................................................ 21 IX. ABBREVIATIONS ................................................................................................................ 24 X. ABSTRACT ............................................................................................................................ 25 1. BACKGROUND AND INTRODUCTION .......................................................................... 27 1.1. RUMINANTS AND THEIR IMPORTANCE ................................................................................. 27 1.2. STRUCTURE AND FUNCTION OF THE RUMINANT STOMACH ................................................ 27 1.2.1. The Rumen and its Specialised Function ........................................................................ 28 1.3. DIGESTION IN RUMINANTS .................................................................................................. 29 1.3.1. Feed and Diet ................................................................................................................... 29 1.3.2. Mechanical Digestion ...................................................................................................... 29 1.3.3. Fermentation .................................................................................................................... 30 1.3.4. Carbohydrate Metabolism ............................................................................................... 32 1.3.5. Nitrogen Metabolism ....................................................................................................... 32 1.3.5.1. Ammonia in the Rumen; Sources, Transport and Fate ........................................... 33 1.4. THE RUMEN MICROBIOME ................................................................................................... 36 1.4.1. Bacteria ............................................................................................................................ 36 1.4.1.1. Fibrolytic Bacteria .................................................................................................. 37 1.4.1.2. Proteolytic Bacteria ................................................................................................ 39 1.4.1.3. Deaminating Bacteria ............................................................................................. 40 1.4.1.4. Hyper Ammonia Producing (HAP) bacteria........................................................... 43 1.4.2. Archaea ............................................................................................................................ 50 1.4.3. Viruses ............................................................................................................................. 50 1.4.3.1. Bacteriophages ....................................................................................................... 50 1.4.3.2. Archaeal phages ..................................................................................................... 55 1.4.4. Fungi ................................................................................................................................ 55 1.4.5. Protozoa ........................................................................................................................... 55 4 Preface 1.4.6. Understanding the Rumen Microbiome .......................................................................... 56 1.5. FEED EFFICIENCY AND METHANE PRODUCTION IN THE RUMEN ......................................... 57 1.5.1. Methane Production in the Rumen .................................................................................. 58 1.5.2. Ammonia Production in the Rumen ................................................................................ 58 1.5.3. Methods Considered to Mitigate Methane Emissions and Increase Feed Efficiency ...... 59 1.6. AIMS AND OBJECTIVES ........................................................................................................ 61 2. MATERIALS AND METHODS ........................................................................................... 62 2.1. RUMEN FLUID .....................................................................................................................
Recommended publications
  • Microbial Biochemistry, 2Nd Edition

    Microbial Biochemistry, 2Nd Edition

    Microbial Biochemistry . G.N. Cohen Microbial Biochemistry Second Edition Prof. G.N. Cohen Institut Pasteur rue du Docteur Roux 28 75724 Paris France [email protected] ISBN 978-90-481-9436-0 e-ISBN 978-90-481-9437-7 DOI 10.1007/978-90-481-9437-7 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2010938472 # Springer Science+Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Foreword This book originates from almost 60 years of living in the company of micro- organisms, mainly with Escherichia coli. My scientific life has taken place almost exclusively at the Institut Pasteur in Paris, where many concepts of modern molecular biology were born or developed. The present work emphasizes the interest of microbial physiology, biochemistry and genetics. It takes into account the considerable advances which have been made in the field in the last 30 years by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallog- raphy of proteins. The younger generation of biochemists is legitimately interested in the problems raised by differentiation and development in higher organisms, and also in neuros- ciences.
  • SI Appendix Index 1

    SI Appendix Index 1

    SI Appendix Index Calculating chemical attributes using EC-BLAST ................................................................................ 2 Chemical attributes in isomerase reactions ............................................................................................ 3 Bond changes …..................................................................................................................................... 3 Reaction centres …................................................................................................................................. 5 Substrates and products …..................................................................................................................... 6 Comparative analysis …........................................................................................................................ 7 Racemases and epimerases (EC 5.1) ….................................................................................................. 7 Intramolecular oxidoreductases (EC 5.3) …........................................................................................... 8 Intramolecular transferases (EC 5.4) ….................................................................................................. 9 Supporting references …....................................................................................................................... 10 Fig. S1. Overview …............................................................................................................................
  • Natural Occurrence and Industrial Applications of D-Amino Acids: an Overview

    Natural Occurrence and Industrial Applications of D-Amino Acids: an Overview

    CHEMISTRY & BIODIVERSITY – Vol. 7 (2010) 1531 REVIEW Natural Occurrence and Industrial Applications of d-Amino Acids: An Overview by Sergio Martnez-Rodrguez*, Ana Isabel Martnez-Go´ mez, Felipe Rodrguez-Vico, Josefa Mara Clemente-Jime´nez, Francisco Javier Las Heras-Va´zquez* Dpto. Qumica Fsica, Bioqumica y Qumica Inorga´nica, Universidad de Almera, Edificio CITE I, Carretera de Sacramento s/n, 04120 La Can˜ ada de San Urbano, Almera, Spain (S. M.-R.: phone: þ34950015850; fax: þ34950015615; F. J. H.-V.: phone: þ34950015055; fax: þ34950015615) Interest in d-amino acids has increased in recent decades with the development of new analytical methods highlighting their presence in all kingdoms of life. Their involvement in physiological functions, and the presence of metabolic routes for their synthesis and degradation have been shown. Furthermore, d-amino acids are gaining considerable importance in the pharmaceutical industry. The immense amount of information scattered throughout the literature makes it difficult to achieve a general overview of their applications. This review summarizes the state-of-the-art on d-amino acid applications and occurrence, providing both established and neophyte researchers with a comprehensive introduction to this topic. Introduction. – Since Miller established in 1953 that amino acids were most probably present in the primitive Earths atmosphere [1], one of the largest mysteries in science has been why evolution chose the l-isomer of a-amino acids for the emergence of life. While, from the chemical-physical point of view, enantiomeric enhancement in the prebiotic scenario of l-amino acids is plausible [2][3], the most broadly accepted theory is that primitive life acquired polymers by an as yet unknown mechanism.
  • 12) United States Patent (10

    12) United States Patent (10

    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
  • Supplementary Figure 1. Rpod Sequence Alignment. Protein Sequence Alignment Was Performed for Rpod from Three Species, Pseudoruegeria Sp

    Supplementary Figure 1. Rpod Sequence Alignment. Protein Sequence Alignment Was Performed for Rpod from Three Species, Pseudoruegeria Sp

    J. Microbiol. Biotechnol. https://doi.org/10.4014/jmb.1911.11006 J. Microbiol. Biotechnol. https://doi.org/10.4014/jmb.2003.03025 Supplementary Figure 1. RpoD sequence alignment. Protein sequence alignment was performed for RpoD from three species, Pseudoruegeria sp. M32A2M (FPS10_24745, this study), Ruegeria pomeroyi (NCBI RefSeq: WP_011047484.1), and Escherichia coli (NCBI RefSeq: NP_417539.1). Multalin version 5.4.1 was used for the analysis. Subregion 2 and 4 are represented in a rectangle, and the helix-turn-helix motif in subregion 4 is highlighted in red. The amino acid degeneration from any of the three was highlighted in light gray and the sequence degeneration between Pseudoruegeria sp. M32A2M and R. pomeroyi is highlighted in dark gray. The substituted two amino acids into HTH motif (K578Q and D581S) against E. coli were marked as asterisk. Supplementary Table 1. Genome assembly statistics Categories Pseudoruegeria sp. M32A2M Number of scaffolds less than 1,000 bp 0 Number of scaffolds between 1,000 bp –10,000 bp 39 Number of scaffolds between 10,000 bp – 100,000 bp 38 Number of scaffolds larger than 100,000 bp 14 Number of scaffolds 91 Total assembled length (bp) 5,466,515 G+C contents (%) 62.4 N50 (bp) 249,384 Minimum length of scaffold (bp) 1,015 Maximum length of scaffold (bp) 733,566 Total Ns included in the draft genome 2,158 Supplementary Table 2. The list of gene annotation and its functional categorization in Pseudoruegeria sp.
  • Lawrence Berkeley National Laboratory Recent Work

    Lawrence Berkeley National Laboratory Recent Work

    Lawrence Berkeley National Laboratory Recent Work Title PROTONATED AMINO ACID PRECURSOR STUDIES OH RHODOTORULIC ACID BIOSYNTHESIS IN DEUTERIUM OXIDE MEDIA Permalink https://escholarship.org/uc/item/0w01t99f Author Akers, Hugh A. Publication Date 1972-06-01 eScholarship.org Powered by the California Digital Library University of California ., ~ " .... ,) Submitted to Biochemistry LBL-957 Preprint:· - PROTONATED AMINO ACID PRECURSOR STUDIES ON RHODOTORU LIC ACID BIOSYNTHESIS IN DEUTERIUM OXIDE MEDIA Hugh A. Akers, Miguel Llincrs and J. B. Neilands June 1972 AEC Contract No. W-7405-eng-48 -For Reference Not to be taken from this room DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California. -\ ·.1 ~ -~ ,,} U ~, ( . J Protonatcd Amino Acid Precursor Studies on Rhodotorulic Acid Biosynthesis in Deuterium Oxide Media* t ~ t I~gh A.
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al

    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System

    All Enzymes in BRENDA™ the Comprehensive Enzyme Information System

    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
  • (12) Patent Application Publication (10) Pub. No.: US 2017/0159083 A1 Valgepea Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2017/0159083 A1 Valgepea Et Al

    US 201701.59083A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0159083 A1 Valgepea et al. (43) Pub. Date: Jun. 8, 2017 (54) ARGININE SUPPLEMENTATION TO CI2N L/20 (2006.01) IMPROVE EFFICIENCY IN GAS CI2N 9/12 (2006.01) FERMENTING ACETOGENS CI2N 9/90 (2006.01) CI2N 9/06 (2006.01) (71) Applicant: LanzaTech New Zealand Limited, CI2N I/38 (2006.01) Skokie, IL (US) CI2N 9/78 (2006.01) CI2N 9/10 (2006.01) (72) Inventors: Kaspar Valgepea, Brisbane (AU): (52) U.S. Cl. Michael Koepke, Skokie, IL (US); CPC .................. CI2P 7/56 (2013.01); CI2N 9/78 James Bruce Yarnton Haycock (2013.01); C12Y305/03006 (2013.01); C12P Behrendorf, Skokie, IL (US); Esteban 7/54 (2013.01); C12P 7/065 (2013.01): CI2P Marcellin, Brisbane (AU), Lars K. 7/18 (2013.01); C12N 9/1018 (2013.01); C12Y Nielsen, Brisbane (AU); Renato de S.P. 201/03003 (2013.01); C12N 9/1217 (2013.01); Lemgruber, Brisbane (AU) CI2Y 207/02002 (2013.01); C12N 9/90 (2013.01); C12Y501/01012 (2013.01); C12Y (21) Appl. No.: 15/368,521 504/03005 (2013.01); C12N 9/0016 (2013.01); 1-1. CI2Y 104/01012 (2013.01); C12N 9/1029 (22) Filed: Dec. 2, 2016 (2013.01); C12N 1/38 (2013.01); C12N I/20 Related U.S. Application Data (2013.01) (60) Provisional application No. 62/262,886, filed on Dec. 57 ABSTRACT 3, 2015, provisional application No. 62/262,888, filed (57) on Dec. 3, 2015. The invention provides methods for improving efficiency of O O fermentation by arginine Supplementation, and genetically Publication Classification modified bacterium for use therefor.
  • (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al

    US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006.

  • Detection of D-Ornithine Extracellularly Produced by Corynebacterium Glutamicum ATCC 13032::Argf

    Biosci. Biotechnol. Biochem., 74 (12), 2507–2510, 2010 Note Detection of D-Ornithine Extracellularly Produced by Corynebacterium glutamicum ATCC 13032::argF y Daisuke MATSUI and Tadao OIKAWA Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan Received July 21, 2010; Accepted September 7, 2010; Online Publication, December 23, 2010 [doi:10.1271/bbb.100523] We found that Corynebacterium glutamicum ATCC the method of Hwang et al. using Escherichia coli 13032::argF extracellularly produced a large amount of JM110 instead of E. coli DH5 for non-methylation of a D-ornithine when cultivated in a CGXII medium vector transformed into C. glutamicum ATCC 13032.2) containing 1 mML-arginine. This is the first report that C. glutamicum ATCC 13032::argF was pre-cultivated C. glutamicum ATCC 13032 or its mutant produces a on a brain-heart infusion (BHI) agar medium (Difco, D-amino acid extracellularly. C. glutamicum ATCC BD, France), and then a single colony on the medium 13032::argF produced 13 mMD-ornithine in 45 h of was inoculated into 50 ml of a BHI medium in a 500-ml cultivation. Erlenmeyer flask with a baffle and cultivated at 30 C for 24 h with shaking (150 rpm) until the growth of the Key words: Corynebacterium glutamicum ATCC microorganism reached stationary phase. After centrifu- 13032; D-ornithine; ornithine carbamoyl- gation at 5;500 Â g for 15 min at 4 C, the collected cells transferase; ornithine racemase were washed with an ice-chilled CGXII medium plus 1mML-arginine,7) and inoculated into 50 ml of the same Corynebacterium glutamicum ATCC 13032 is a facul- medium at an A600 of 1.0.
  • Engineering Aminotransferases for the Biocatalytic Production of Aromatic D-Amino Acids

    Engineering Aminotransferases for the Biocatalytic Production of Aromatic D-Amino Acids

    ENGINEERING AMINOTRANSFERASES FOR THE BIOCATALYTIC PRODUCTION OF AROMATIC D-AMINO ACIDS. CURTIS JAMES WILLIAM WALTON Thesis submitted to the University of Ottawa in partial fulfillment of the requirements for the Doctorate in Philosophy Chemistry Department of Chemistry and Biomolecular Sciences Ottawa-Carleton Chemistry Institute Faculty of Science University of Ottawa © Curtis James William Walton, Ottawa, Canada, 2018 Table of Contents Abstract .......................................................................................................................................... ii Acknowledgements ...................................................................................................................... iii Dedication ..................................................................................................................................... iv Table of Contents ...........................................................................................................................v List of Figures .................................................................................................................................x List of Tables .............................................................................................................................. xiii List of