DOCSLIB.ORG

Modelling of Metabolic Pathways of Saccharopolyspora Erythraea Using Flux Balance Analysis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Modelling of Metabolic Pathways of Saccharopolyspora Erythraea Using Flux Balance Analysis PhD Thesis Modelling of Metabolic Pathways of Saccharopolyspora erythraea Using Flux Balance Analysis A Thesis submitted to the University of London for the degree of Doctor of Philosophy By Colin Mark Jaques March 2004 The Advanced Centre for Biochemical Engineering Department of Biochemical Engineering University College London Torrington Place London WC1E 7JE United Kingdom Colin Jaques 1 UMI Number: U602593 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U602593 Published by ProQuest LLC 2014. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 PhD Thesis Soli Deo Gloria Colin Jaques 2 PhD Thesis Abstract The objective of this thesis is to use metabolic modelling techniques to investigate primary and secondary metabolism in S. erythraea and from this to identify key factors controlling flux distribution during secondary metabolism. S. erythraea is a member of the actinomycetes a group of bacteria responsible for the production of a number of commercially important small molecules. Actinomycete physiology is considerably more complicated than that seen in "simple" bacteria such as E. coli. The conjecture investigated in this thesis is that metabolic modelling techniques that take into account this extra complexity should be more useful in designing strategies for overproduction of desired metabolites than simpler models. The thesis gives the first detailed description of the dynamic changes in biomass composition seen during the batch cultivation of S. erythraea. It further shows that incorporation of this information into a flux balance model of the organism’s metabolism significantly improves the flux distributions generated especially in the stationary phase. Using this improved technique growth phase and stationary phase metabolism are investigated. Some of the unusual stationary phase behaviour is shown to be the result of glucose uptake being independent of demand. Rigid control of branch points in the metabolic network is not found suggesting that the organism’s metabolism is flexible. A reverse metabolic engineering strategy is applied, two variants of the wild type organism are compared with an industrial strain. The industrial strain is found to have a considerably lower glucose uptake rate than the parental strain. The relationship between TCA cycle flux, oxidative phosphorylation and organic acid secretion is investigated using an uncoupler. This project demonstrates that applied correctly flux balance analysis is a powerful tool for investigating actinomycete physiology. The insights gained are of direct relevance to the commercial production of secondary metabolites in S. erythraea. Colin Jaques 3 PhD Thesis Acknowledgements It is impossible in this day and age to pursue cutting edge science and engineering without a large amount of help. I have received financial, material, intellectual and practical support from many sources and I wish to take this opportunity to thank those who supported me. I am indebted to my supervisors, Yuhong Zhou, Frank Baganz and John Ward for setting up the opportunity for me to study S. erythraea in this way. All their time, thoughts and direction over the course of the project have proved invaluable. I also have much to be thankful for in the officemates I have had in the cloisters office over my time at UCL, with them I have batted back and forth many of the ideas developed in this thesis. Particular thanks go to Misti Ushio for help with modelling and physiology, to Preben Krabben for his willingness to share his huge knowledge of the biochemistry of actinomycetes and to help out with the practical work, to Helen Irvine for help with identifying fumarate and to Jake Hodgson for his general enthusiasm for discussion. Unseen but not unappreciated were James Jameson’s all night sampling efforts when he could have been enjoying his holidays. I am extremely grateful for the financial support I have received from the BBSRC without which the project could not have taken place. Their generous provision has enabled me to live comfortably and has provided me access to first class biochemical engineering research facilities. The quality of these facilities is also in no small part due to the continued determination of the department and the academic staff in pursuing cutting edge research. Thanks are also due to Clive Osborne, Billy Doyle and Ian Buchanan who maintain these facilities. On a more personal note thanks are due to my parents who brought me up to be interested in and to think about the world around me, who taught me to fear the Lord and spoke to me the words of eternal life. More recently they have had to put up with my absent presence as I spent several months with them writing at my desk in the attic. Finally I would like to thank my fiancee Grace who will shortly become my helper, ally, encourager, confidant and companion and who has provided great motivation to finish writing quickly before our wedding. Colin Jaques 4 PhD Thesis Table of Contents 1 INTRODUCTION............................................................................................................................................... 12 1.1 System U nder Investigation ....................................................................................................................13 1.1.1 Introduction............................................................................................................................................. 13 1.1.2 Saccharopolyspora erythraea ............................................................................................................. 14 1.1.3 Polyketides .............................................................................................................................................16 1.2 Synthesis of Erythromycin .................................................................................................................... 18 1.2.1 Macrolactone Biosynthesis ................................................................................................................. 18 1.2.2 Deoxysugar Biosynthesis .....................................................................................................................23 1.2.3 Synthesis of the Red Pigment ...................................... 27 1.3 M etabolic Engineering of P olyketide Biosynthesis .................................................................... 28 1.3.1 Introduction............................................................................................................................................. 28 1.3.2 Manipulating Chain Length................................................................................................................29 1.3.3 Changing the Priming Unit ..................................................................................................................29 1.3.4 Changing the Extender Unit. ............................................................................................................... 29 1.3.5 Changing the Reduction Level............................................................................................................30 1.3.6 Manipulating the Stereochemistry.................................................................................................... 30 1.3.7 Hybrid PKS and Nonribosomal Peptide Systems ...........................................................................31 1.3.8 Post PKS Modifications .......................................................................................................................31 1.3.9 Changing Deoxysugar Groups............................................................................................................31 1.3.10 Combinatorial Biosynthesis ................................................................................................................ 32 1.3.11 Problems with Fusing Proteins .......................................................................................................... 32 1.3.12 Interspecies PKS Transfer................................................................................................................... 33 1.3.13 Conclusions.............................................................................................................................................33 1.4 M etabolic M o d e l l in g ;................................................................................................................... 34 1.4.1 Introduction to Metabolic Modelling ................................................................................................34 1.4.2 Kinetic Models ....................................................................................................................................... 34 1.4.3 Flux balance Analysis ...........................................................................................................................36 1.4.4 Metabolic Network Analysis ................................................................................................................41
Load more

Recommended publications
  • Successful Drug Discovery Informed by Actinobacterial Systematics
    Successful Drug Discovery Informed by Actinobacterial Systematics Verrucosispora HPLC-DAD analysis of culture filtrate Structures of Abyssomicins Biological activity T DAD1, 7.382 (196 mAU,Up2) of 002-0101.D V. maris AB-18-032 mAU CH3 CH3 T extract H3C H3C Antibacterial activity (MIC): S. leeuwenhoekii C34 maris AB-18-032 175 mAU DAD1 A, Sig=210,10 150 C DAD1 B, Sig=230,10 O O DAD1 C, Sig=260,20 125 7 7 500 Rt 7.4 min DAD1 D, Sig=280,20 O O O O Growth inhibition of Gram-positive bacteria DAD1 , Sig=310,20 100 Abyssomicins DAD1 F, Sig=360,40 C 75 DAD1 G, Sig=435,40 Staphylococcus aureus (MRSA) 4 µg/ml DAD1 H, Sig=500,40 50 400 O O 25 O O Staphylococcus aureus (iVRSA) 13 µg/ml 0 CH CH3 300 400 500 nm 3 DAD1, 7.446 (300 mAU,Dn1) of 002-0101.D 300 mAU Mode of action: C HO atrop-C HO 250 atrop-C CH3 CH3 CH3 CH3 200 H C H C H C inhibitior of pABA biosynthesis 200 Rt 7.5 min H3C 3 3 3 Proximicin A Proximicin 150 HO O HO O O O O O O O O O A 100 O covalent binding to Cys263 of PabB 100 N 50 O O HO O O Sea of Japan B O O N O O (4-amino-4-deoxychorismate synthase) by 0 CH CH3 CH3 CH3 3 300 400 500 nm HO HO HO HO Michael addition -289 m 0 B D G H 2 4 6 8 10 12 14 16 min Newcastle Michael Goodfellow, School of Biology, University Newcastle University, Newcastle upon Tyne Atacama Desert In This Talk I will Consider: • Actinobacteria as a key group in the search for new therapeutic drugs.
    [Show full text]
  • Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead
    1 Supplementary Material 2 Genomic and phylogenomic insights into the family Streptomycetaceae lead 3 to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera with 4 emended descriptions of Streptomyces calvus 5 Munusamy Madhaiyan1, †, *, Venkatakrishnan Sivaraj Saravanan2, †, Wah-Seng See-Too3, † 6 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 7 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 8 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 9 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 10 Malaysia 1 11 Table S3. List of the core genes in the genome used for phylogenomic analysis. NCBI Protein Accession Gene WP_074993204.1 NUDIX hydrolase WP_070028582.1 YggS family pyridoxal phosphate-dependent enzyme WP_074992763.1 ParB/RepB/Spo0J family partition protein WP_070022023.1 lipoyl(octanoyl) transferase LipB WP_070025151.1 FABP family protein WP_070027039.1 heat-inducible transcriptional repressor HrcA WP_074992865.1 folate-binding protein YgfZ WP_074992658.1 recombination protein RecR WP_074991826.1 HIT domain-containing protein WP_070024163.1 adenylosuccinate synthase WP_009190566.1 anti-sigma regulatory factor WP_071828679.1 preprotein translocase subunit SecG WP_070026304.1 50S ribosomal protein L13 WP_009190144.1 30S ribosomal protein S5 WP_014674378.1 30S ribosomal protein S8 WP_070026314.1 50S ribosomal protein L5 WP_009300593.1 30S ribosomal protein S13 WP_003998809.1
    [Show full text]
  • Pseudonocardia Parietis Sp. Nov., from the Indoor Environment
    This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of ‘Fair Use of Copyrighted Materials’ (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://ijs.sgmjournals.org, and is freely available without a subscription 24 months after publication. First published in: Int J Syst Evol Microbiol, 2009. 59(10) 2449-52. doi:10.1099/ijs.0.009993-0 Pseudonocardia parietis sp. nov., from the indoor environment J. Scha¨fer,1 H.-J. Busse2 and P. Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, P. Ka¨mpfer Germany [email protected] 2Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, giessen.de Austria A Gram-positive, rod-shaped, non-endospore-forming, mycelium-forming actinobacterium (04- St-002T) was isolated from the wall of an indoor environment colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 04-St-002T was shown to belong to the family Pseudonocardiaceae, and to be most closely related to Pseudonocardia antarctica (99.2 %) and Pseudonocardia alni (99.1 %).
    [Show full text]
  • Saccharopolyspora Flava Sp. Nov. and Saccharopolyspora Thermophila Sp
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 319–325 Printed in Great Britain Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil Zhitang Lu,1† Zhiheng Liu,1 Liming Wang,1 Yamei Zhang,1 Weihong Qi1 and Michael Goodfellow2 Author for correspondence: Zhiheng Liu. Tel: j86 10 6255 3628. Fax: j86 10 6256 0912. e-mail: zhliu!sun.im.ac.cn 1 Institute of Microbiology, The generic position of two aerobic, Gram-positive, non-acid–alcohol-fast Chinese Academy of actinomycetes was established following the isolation of their PCR-amplified Sciences, Beijing 100080, People’s Republic of China 16S rRNA genes and alignment of the resultant sequences with the corresponding sequences from representatives of the families 2 Department of Agricultural and Actinosynnemataceae and Pseudonocardiaceae. The assignment of the Environmental Science, organisms to the genus Saccharopolyspora was strongly supported by University of Newcastle, chemotaxonomic and morphological data. The strains were distinguished both Newcastle upon Tyne NE1 7RU, UK from one another and from representatives of validly described Saccharopolyspora species on the basis of a number of phenotypic properties. It is proposed that the organisms, strains 07T (l AS4.1520T l IFO 16345T l JCM 10665T) and 216T (l AS4.1511T l IFO 16346T l JCM 10664T), be classified in the genus Saccharopolyspora as Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., respectively. Keywords: Saccharopolyspora flava sp. nov., Saccharopolyspora thermophila sp. nov., polyphasic taxonomy INTRODUCTION these taxa were excluded from the family by Warwick et al. (1994), who considered that they might form a The application of the polyphasic taxonomic approach ‘sister’ group to the Pseudonocardiaceae clade.
    [Show full text]
  • Transition from Unclassified Ktedonobacterales to Actinobacteria During Amorphous Silica Precipitation in a Quartzite Cave Envir
    www.nature.com/scientificreports OPEN Transition from unclassifed Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment D. Ghezzi1,2, F. Sauro3,4,5, A. Columbu3, C. Carbone6, P.‑Y. Hong7, F. Vergara4,5, J. De Waele3 & M. Cappelletti1* The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The frst stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the fnal coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves. Silicon is one of the most abundant elements in the Earth’s crust and can be broadly found in the form of silicates, aluminosilicates and silicon dioxide (e.g., quartz, amorphous silica).
    [Show full text]
  • Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
    Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
    [Show full text]
  • 1 Supplementary Material a Major Clade of Prokaryotes with Ancient
    Supplementary Material A major clade of prokaryotes with ancient adaptations to life on land Fabia U. Battistuzzi and S. Blair Hedges Data assembly and phylogenetic analyses Protein data set: Amino acid sequences of 25 protein-coding genes (“proteins”) were concatenated in an alignment of 18,586 amino acid sites and 283 species. These proteins included: 15 ribosomal proteins (RPL1, 2, 3, 5, 6, 11, 13, 16; RPS2, 3, 4, 5, 7, 9, 11), four genes (RNA polymerase alpha, beta, and gamma subunits, Transcription antitermination factor NusG) from the functional category of Transcription, three proteins (Elongation factor G, Elongation factor Tu, Translation initiation factor IF2) of the Translation, Ribosomal Structure and Biogenesis functional category, one protein (DNA polymerase III, beta subunit) of the DNA Replication, Recombination and repair category, one protein (Preprotein translocase SecY) of the Cell Motility and Secretion category, and one protein (O-sialoglycoprotein endopeptidase) of the Posttranslational Modification, Protein Turnover, Chaperones category, as annotated in the Cluster of Orthologous Groups (COG) (Tatusov et al. 2001). After removal of multiple strains of the same species, GBlocks 0.91b (Castresana 2000) was applied to each protein in the concatenation to delete poorly aligned sites (i.e., sites with gaps in more than 50% of the species and conserved in less than 50% of the species) with the following parameters: minimum number of sequences for a conserved position: 110, minimum number of sequences for a flank position: 110, maximum number of contiguous non-conserved positions: 32000, allowed gap positions: with half. The signal-to-noise ratio was determined by altering the “minimum length of a block” parameter.
    [Show full text]
  • Complete Genome Sequence of Jiangella Gansuensis Strain YIM 002T (DSM 44835T), the Type Species of the Genus Jiangella and Source of New Antibiotic Compounds
    UC Davis UC Davis Previously Published Works Title Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. Permalink https://escholarship.org/uc/item/34s6p01n Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Jiao, Jian-Yu Carro, Lorena Liu, Lan et al. Publication Date 2017 DOI 10.1186/s40793-017-0226-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Jiao et al. Standards in Genomic Sciences (2017) 12:21 DOI 10.1186/s40793-017-0226-6 SHORTGENOMEREPORT Open Access Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds Jian-Yu Jiao1, Lorena Carro2, Lan Liu1, Xiao-Yang Gao3, Xiao-Tong Zhang1, Wael N. Hozzein4,12, Alla Lapidus5,6, Marcel Huntemann7, T. B. K. Reddy7, Neha Varghese7, Michalis Hadjithomas7, Natalia N. Ivanova7, Markus Göker8, Manoj Pillay9, Jonathan A. Eisen10, Tanja Woyke7, Hans-Peter Klenk2,8*, Nikos C. Kyrpides7,11 and Wen-Jun Li1,13* Abstract Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon.
    [Show full text]
  • Pseudonocardia Asaccharolytica Sp. Nov. and Pseudonocardia Sulfidoxydans Sp
    International Journal of Systematic Bacteriology (1998), 48, 441-449 Printed in Great Britain Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulf ide-degrading actinomycetes and emended description of the genus Pseudonocardia Katrin Reichert,’ Andre Lipski,’ Silke Pradella,2 Erko Stackebrandt2 and Karlheinz Altendorf’ Author for correspondence: Andre Lipski. Fax: +49 541 969 2870. e-mail : Lipski@sfbbiol .biologie.uni-osnabrueck.de 1 Abteilung Mikrobiologie, Seven bacterial strains capable of oxidizing methyl sulfides were isolated from Universitat Osnabruck, experimental biofilters filled with tree-bark compost. The isolates could be Fachbereich BiologieKhemie, D-49069 divided into two groups according to their method of methyl sulfide Osnabruck, Germany degradation. Four isolates could use only dimethyl disulfide as the sole source * Deutsche Sammlung von of energy and three strains were able to use dimethyl sulfide and dimethyl Mikroorganismen und disulfide. Oxidation of the methyl sulfides by both groups led to the Zellkulturen GmbH, stoichiometric formation of sulfate. Chemotaxonomic, morphological, Mascheroder Weg 1b, D-38124 Braunschweig, physiological and phylogenetic properties identified all isolates as members of Germany the genus Pseudonocardia. The absence of phosphatidylcholine from the polar lipid pattern, as well as results of 16s rDNA analyses, led to the proposal of two new species, Pseudonocadia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov.
    [Show full text]
  • Microbiome and Metagenome Analysis Reveals Huanglongbing Affects the Abundance of Citrus Rhizosphere Bacteria Associated with Resistance and Energy Metabolism
    horticulturae Article Microbiome and Metagenome Analysis Reveals Huanglongbing Affects the Abundance of Citrus Rhizosphere Bacteria Associated with Resistance and Energy Metabolism Hongfei Li 1, Fang Song 1 , Xiaoxiao Wu 2, Chongling Deng 2, Qiang Xu 1 , Shu’ang Peng 1 and Zhiyong Pan 1,* 1 Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; [email protected] (H.L.); [email protected] (F.S.); [email protected] (Q.X.); [email protected] (S.P.) 2 Guangxi Academy of Specialty Crops/Guangxi Citrus Breeding and Cultivation Research Center of Engineering Technology, Guilin 541004, China; [email protected] (X.W.); [email protected] (C.D.) * Correspondence: [email protected] Abstract: The plant rhizosphere microbiome is known to play a vital role in plant health by com- peting with pathogens or inducing plant resistance. This study aims to investigate rhizosphere microorganisms responsive to a devastating citrus disease caused by ‘Candidatus Liberibacter asiaticus’ (CLas) infection, by using 16S rRNA sequencing and metagenome technologies. The results show that 30 rhizosphere and 14 root bacterial genera were significantly affected by CLas infection, including 9 plant resistance-associated bacterial genera. Among these, Amycolatopsis, Sphingopyxis, Chryseobac- terium, Flavobacterium, Ralstonia, Stenotrophomonas, Duganella, and Streptacidiphilus were considerably Citation: Li, H.; Song, F.; Xu, Q.; enriched in CLas-infected roots, while Rhizobium was significantly decreased. Metagenome analysis Peng, S.; Pan, Z.; Wu, X.; Deng, C. revealed that the abundance of genes involved in carbohydrate metabolism, such as glycolysis, starch Microbiome and Metagenome and sucrose metabolism, amino sugar and nucleotide sugar metabolism, was significantly reduced Analysis Reveals Huanglongbing in the CLas-infected citrus rhizosphere microbial community.
    [Show full text]
  • Faenia Rectivirgula Kurup and Agre 1983 to the Genus Saccharopolyspora Lacey and Goodfellow 1975, Elevation of Saccharopolyspora Hirsuta Subsp
    INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY,OCt. 1989, p. 430441 Vol. 39, No. 4 0020-7713/89/04043 0- 12$02.00/0 Copyright 0 1989, International Union of Microbiological Societies Transfer of Faenia rectivirgula Kurup and Agre 1983 to the Genus Saccharopolyspora Lacey and Goodfellow 1975, Elevation of Saccharopolyspora hirsuta subsp. taberi Labeda 1987 to Species Level, and Emended Description of the Genus Saccharopolyspora F. KORN-WENDISCH,’” A. KEMPF,’ E. GRUND,’ R. M. KROPPENSTEDT,2 AND H. J. KUTZNER’ Institut fur Mikrobiologie der Technischen Hochschule Darmstadt, 0-6100 Darmstadt, ’ and Deutsche Sammlung von Mikroorganismen, 0-3300 Braunschweig,2 Federal Republic of Germany A thorough taxonomic study of the genera Succhuropolysporu and Fueniu showed that both of these taxa can be included in one genus. We propose that Fueniu rectivirgula be transferred to the genus Saccharopolysporu Lacey and Goodfellow 1975 as Sacchuropolyspora rectivirgula (Kurup and Agre 1983) comb. nov. A description of the new SucchuropoZysporu species is presented. The type strain is strain DSM 43 747 (= ATCC 33 515). In addition, we propose that Sacchuropolysporu hirsuta subsp. tuberi Labeda 1987 strain NRRL B-16 173T (T = type strain) be given species status as Succharopolysporu tuben sp. nov. In 1987 Labeda (30) transferred Streptomyces erythraeus MATERIALS AND METHODS to the genus Saccharopolyspora as Saccharopolyspora Organisms. The origins of the 24 strains used in this study, erythraea Labeda 1987 comb. nov. on the basis of its cell as well as three reference strains, are shown in Table 1. wall chemistry. Our studies of the genus Streptomyces also Cultural characteristics were observed on Trypticase soy indicated that Streptomyces erythraeus did not belong in the agar (TSA) (BBL Microbiology Systems, Cockeysville, Md.) genus Streptomyces, since the cell walls contained meso- and GYM agar (29), each prepared with and without 5% diaminopimelic acid (DAP) and because of phage typing NaCl, and on inorganic salts starch agar (48).
    [Show full text]
  • A Genome Compendium Reveals Diverse Metabolic Adaptations of Antarctic Soil Microorganisms
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. August 3, 2020 A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms Maximiliano Ortiz1 #, Pok Man Leung2 # *, Guy Shelley3, Marc W. Van Goethem1,4, Sean K. Bay2, Karen Jordaan1,5, Surendra Vikram1, Ian D. Hogg1,7,8, Thulani P. Makhalanyane1, Steven L. Chown6, Rhys Grinter2, Don A. Cowan1 *, Chris Greening2,3 * 1 Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0002, South Africa 2 Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia 3 School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 4 Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 6 Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia 7 School of Science, University of Waikato, Hamilton 3240, New Zealand 8 Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay, NU X0B 0C0, Canada # These authors contributed equally to this work. * Correspondence may be addressed to: A/Prof Chris Greening ([email protected]) Prof Don A. Cowan ([email protected]) Pok Man Leung ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.06.239558; this version posted August 6, 2020.
    [Show full text]