Complete Genome Sequence of Producer of the Glycopeptide
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Selective Isolation, Characterisation and Identification of Streptosporangia
SELECTIVE ISOLATION, CHARACTERISATION AND IDENTIFICATION OF STREPTOSPORANGIA Thesissubmitted in accordancewith the requirementsof theUniversity of Newcastleupon Tyne for the Degreeof Doctor of Philosophy by Hong-Joong Kim B. Sc. NEWCASTLE UNIVERSITY LIBRARY ____________________________ 093 51117 X ------------------------------- fn L:L, Iýý:, - L. 51-ý CJ - Departmentof Microbiology, The Medical School,University of Newcastleupon Tyne December1993 CONTENTS ACKNOWLEDGEMENTS Page Number PUBLICATIONS SUMMARY INTRODUCTION A. AIMS 1 B. AN HISTORICAL SURVEY OF THE GENUS STREPTOSPORANGIUM 5 C. NUMERICAL SYSTEMATICS 17 D. MOLECULAR SYSTEMATICS 35 E. CHARACTERISATION OF STREPTOSPORANGIA 41 F. SELECTIVE ISOLATION OF STREPTOSPORANGIA 62 MATERIALS AND METHODS A. SELECTIVE ISOLATION, ENUMERATION AND 75 CHARACTERISATION OF STREPTOSPORANGIA B. NUMERICAL IDENTIFICATION 85 C. SEQUENCING OF 5S RIBOSOMAL RNA 101 D. PYROLYSIS MASS SPECTROMETRY 103 E. RAPID ENZYME TESTS 113 RESULTS A. SELECTIVE ISOLATION, ENUMERATION AND 122 CHARACTERISATION OF STREPTOSPORANGIA B. NUMERICAL IDENTIFICATION OF STREPTOSPORANGIA 142 C. PYROLYSIS MASS SPECTROMETRY 178 D. 5S RIBOSOMAL RNA SEQUENCING 185 E. RAPID ENZYME TESTS 190 DISCUSSION A. SELECTIVE ISOLATION 197 B. CLASSIFICATION 202 C. IDENTIFICATION 208 D. FUTURE STUDIES 215 REFERENCES 220 APPENDICES A. TAXON PROGRAM 286 B. MEDIA AND REAGENTS 292 C. RAW DATA OF PRACTICAL EVALUATION 295 D. RAW DATA OF IDENTIFICATION 297 E. RAW DATA OF RAPID ENZYME TESTS 300 ACKNOWLEDGEMENTS I would like to sincerely thank my supervisor, Professor Michael Goodfellow for his assistance,guidance and patienceduring the course of this study. I am greatly indebted to Dr. Yong-Ha Park of the Genetic Engineering Research Institute in Daejon, Korea for his encouragement, for giving me the opportunity to extend my taxonomic experience and for carrying out the 5S rRNA sequencing studies. -
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Kent Academic Repository Full text document (pdf) Citation for published version Wichner, Dominik and Idris, Hamidah and Houssen, Wael E and McEwan, Andrew R and Bull, Alan T. and Asenjo, Juan A and Goodfellow, Michael and Jaspars, Marcel and Ebel, Rainer and Rateb, Mostafa E (2016) Isolation and anti-HIV-1 integrase activity of lentzeosides A–F from extremotolerant lentzea sp. H45, a strain isolated from a high-altitude Atacama Desert soil. The DOI https://doi.org/10.1038/ja.2016.78 Link to record in KAR https://kar.kent.ac.uk/61946/ Document Version Author's Accepted Manuscript Copyright & reuse Content in the Kent Academic Repository is made available for research purposes. Unless otherwise stated all content is protected by copyright and in the absence of an open licence (eg Creative Commons), permissions for further reuse of content should be sought from the publisher, author or other copyright holder. Versions of research The version in the Kent Academic Repository may differ from the final published version. Users are advised to check http://kar.kent.ac.uk for the status of the paper. Users should always cite the published version of record. Enquiries For any further enquiries regarding the licence status of this document, please contact: [email protected] If you believe this document infringes copyright then please contact the KAR admin team with the take-down information provided at http://kar.kent.ac.uk/contact.html 1 Isolation and Anti-HIV-1 Integrase Activity of Lentzeosides A-F from Extremotolerant 2 Lentzea sp. H45, a strain isolated from a high altitude Atacama Desert soil 3 Running head: Lentzeosides A-F from Extremotolerant Lentzea sp. -
Rare Actinobacteria: a Possible Solution for Antimicrobial Drug Resistance in Egypt
Mini Review JOJ Nurse Health Care Volume 6 Issue 4 - March 2018 Copyright © All rights are reserved by Dina Hatem Amin DOI: 10.19080/JOJNHC.2018.06.555695 Rare Actinobacteria: A Possible Solution for Antimicrobial Drug Resistance in Egypt Dina Hatem Amin* Department of Microbiology, Ain shams University, Egypt Submission: December 04, 2017; Published: March 15, 2018 *Corresponding author: Dina Hatem Amin, Department of Microbiology, Faculty of Science, Ain shams University, Cairo, Egypt, Email: Mini Review rare actinobacteria. Currently, it is fundamental to discover new “For every action, there is an equal and opposite reaction” antibiotics from distinct strains against multidrug resistant Newton’s Third Law of Motion. We can apply this rule on the pathogens. Since unusual natural products with new structures overuse of antibiotics and the emergence of antimicrobial will have valuable biological activities Koehn and Carter, Baltz, drug resistance. In the meantime, the uncontrolled practices of Amin et al. [6-8]. antibiotics mainly triggered this problem in both developed and developing countries. The intensity of antimicrobial resistance Rare Actinobacteria has a great potential to produce novel in developing countries is generally higher because of the excess antibiotics [8-12]. My previous work focused on exploring an antibiotics usage. unordinary group of Actinobacteria, which is known as Rare Antibiotics resistant pathogens are recognized as a gigantic actinomycetes isolates from Egyptian soils and antimicrobial worldwide public health threat, and they have vital effects Actinobacteria [13]. I successfully isolated and identified rare potential of this unique group against some food and blood borne concerning morbidity, mortality and elevation of healthcare costs Yong et al. -
Downloaded from Genbank
bioRxiv preprint doi: https://doi.org/10.1101/036087; this version posted January 7, 2016. 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 4.0 International license. 1 Automating Assessment of the Undiscovered 2 Biosynthetic Potential of Actinobacteria 3 Bogdan Tokovenko1*, Yuriy Rebets1, Andriy Luzhetskyy1,2* 4 1 Actinomycetes Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research 5 Saarland, Saarbrücken, Germany 6 2 Department of Pharmaceutical Biotechnology, Faculty of Natural Sciences and Technology, University of 7 Saarland, Saarbrücken, Germany 8 * Corresponding author 9 E-mail: [email protected] (AL), [email protected] (BT) 1 bioRxiv preprint doi: https://doi.org/10.1101/036087; this version posted January 7, 2016. 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 4.0 International license. 1 Abstract 2 Background. Biosynthetic potential of Actinobacteria has long been the subject of theoretical estimates. 3 Such an estimate is indeed important as a test of further exploitability of a taxon or group of taxa for new 4 therapeutics. As neither a set of available genomes nor a set of bacterial cultivation methods are static, it 5 makes sense to simplify as much as possible and to improve reproducibility of biosynthetic gene clusters 6 similarity, diversity, and abundance estimations. -
The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid
microorganisms Article The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid Francesca Decorosi 1,2, Maria Luna Exana 1,2, Francesco Pini 1,2, Alessandra Adessi 1 , Anna Messini 1, Luciana Giovannetti 1,2 and Carlo Viti 1,2,* 1 Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Piazzale delle Cascine 18, I50144 Florence, Italy; francesca.decorosi@unifi.it (F.D.); [email protected] (M.L.E.); francesco.pini@unifi.it (F.P.); alessandra.adessi@unifi.it (A.A.); anna.messini@unifi.it (A.M.); luciana.giovannetti@unifi.it (L.G.) 2 Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Via della Lastruccia 14, I50019 Sesto Fiorentino, Italy * Correspondence: carlo.viti@unifi.it; Tel.: +39-05-5457-3224 Received: 15 October 2019; Accepted: 18 November 2019; Published: 20 November 2019 Abstract: Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis. -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. 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. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Exploring the Potential of Antibiotic Production from Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis
fmicb-11-01540 July 27, 2020 Time: 14:51 # 1 ORIGINAL RESEARCH published: 15 July 2020 doi: 10.3389/fmicb.2020.01540 Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis Dini Hu1,2, Chenghang Sun3, Tao Jin4, Guangyi Fan4, Kai Meng Mok2, Kai Li1* and Simon Ming-Yuen Lee5* 1 School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China, 2 Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China, 3 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, 4 Beijing Genomics Institute, Shenzhen, China, 5 State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China Actinobacteria are well recognized for their production of structurally diverse bioactive Edited by: secondary metabolites, but the rare actinobacterial genera have been underexploited Sukhwan Yoon, for such potential. To search for new sources of active compounds, an experiment Korea Advanced Institute of Science combining genomic analysis and tandem mass spectrometry (MS/MS) screening and Technology, South Korea was designed to isolate and characterize actinobacterial strains from a mangrove Reviewed by: Hui Li, environment in Macau. Fourteen actinobacterial strains were isolated from the collected Jinan University, China samples. Partial 16S sequences indicated that they were from six genera, including Baogang Zhang, China University of Geosciences, Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and China Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference *Correspondence: rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for Kai Li whole genome sequencing. -
Actinopolyspora Egyptensis Sp. Nov., a New Halophilic Actinomycete
African Journal of Microbiology Research Vol. 5(2) pp. 100-105, 18 January, 2011 Available online http://www.academicjournals.org/ajmr DOI: 10.5897/AJMR10.667 ISSN 1996-0808 ©2011 Academic Journals Full Length Research Paper Actinopolyspora egyptensis sp. nov., a new halophilic actinomycete Wael N. Hozzein1,2* and Michael Goodfellow3 1Chair of Advanced Proteomics and Cytomics Research, College of Science, King Saud University, Riyadh, Saudi Arabia. 2Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt. 3Division of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK. Accepted 22 December, 2010 A halophilic actinomycete, designated HT371T, was isolated from a soil sample collected from the shore of the salty Lake Qaroun, Egypt, and was the subject of a polyphasic study. Analysis of 16S rRNA indicated that the isolate belonged to the genus Actinopolyspora and constituted a separate clade in the Actinopolyspora 16S rRNA gene tree with similarity values of 96.5 and 96.2% with Actinopolyspora halophila DSM43834T and Actinopolyspora mortivallis DSM44261T, respectively. Isolate HT371T had chemotaxonomic and morphological properties consistent with its classification in the genus Actinopolyspora and could grow on agar plates at NaCl concentrations of up to 25% (w/v). The isolate was readily differentiated from the type strains of genus Actinopolyspora using a range of phenotypic characters. On the basis of polyphasic evidence, the strain HT371T represents a novel species for which the name Actinopolyspora egyptensis sp. nov. is proposed. The type strain is HT371T (=CGMCC 4.2041T). Key words: Actinopolyspora egyptensis sp. nov., halophilic isolate, polyphasic taxonomy. INTRODUCTION The genus Actinopolyspora was created by Gochnauer et taxonomic status, which showed that it merited al. -
Isolation and Anti-HIV-1 Integrase Activity of Lentzeosides A–F from Extremotolerant Lentzea Sp
The Journal of Antibiotics (2017) 70, 448–453 & 2017 Japan Antibiotics Research Association All rights reserved 0021-8820/17 www.nature.com/ja ORIGINAL ARTICLE Isolation and anti-HIV-1 integrase activity of lentzeosides A–F from extremotolerant lentzea sp. H45, a strain isolated from a high-altitude Atacama Desert soil Dominik Wichner1,2, Hamidah Idris3, Wael E Houssen1,4,5, Andrew R McEwan1,4, Alan T Bull6, Juan A Asenjo7, Michael Goodfellow3, Marcel Jaspars1, Rainer Ebel1 and Mostafa E Rateb1,8,9 The extremotolerant isolate H45 was one of several actinomycetes isolated from a high-altitude Atacama Desert soil collected in northwest Chile. The isolate was identified as a new Lentzea sp. using a combination of chemotaxonomic, morphological and phylogenetic properties. Large scale fermentation of the strain in two different media followed by chromatographic purification led to the isolation of six new diene and monoene glycosides named lentzeosides A–F, together with the known compound (Z)-3-hexenyl glucoside. The structures of the new compounds were confirmed by HRESIMS and NMR analyses. Compounds 1–6 displayed moderate inhibitory activity against HIV integrase. The Journal of Antibiotics (2017) 70, 448–453; doi:10.1038/ja.2016.78; published online 29 June 2016 INTRODUCTION extreme hyper-arid soils.8,9 Biological and genome-guided screening of Natural products are known to be a rich source of diverse chemical some of these actinomycetes has led to the isolation and characteriza- scaffolds for drug discovery. However, their use has diminished in the tion of new natural products belonging to diverse structural classes past two decades, mainly due to technical barriers when screening and exhibiting various biological activities, as exemplified by the natural products in high-throughput assays against molecular targets antimicrobial chaxamycins and chaxalactins isolated from Streptomyces and to their limited availability for clinical trials.1 In addition, the leeuwenhoekii C34T, the abenquines from Streptomyces sp. -
Pairwise Testing of Lentzea Strains Against Mycobacterium Smegmatis to Search for and Identify New Anti-Tuberculosis Compounds
Pairwise testing of Lentzea strains against Mycobacterium smegmatis to search for and identify new anti-tuberculosis compounds By: Julie Anne Dayrit A Thesis Submitted to Saint Mary’s University, Halifax, Nova Scotia In Partial Fulfilment of the Requirements for the Degree of Bachelor of Science with Honours in Chemistry April 2020, Halifax, Nova Scotia Copyright Julie Anne Dayrit, 2020 ___________________ Approved: Dr. Clarissa Sit Supervisor ___________________ Approved: Dr. Jason Masuda Department Chair Date: April 2020 1 | P a g e Pairwise testing of Lentzea strains against Mycobacterium smegmatis to search for and identify new anti-tuberculosis compounds By Julie Anne Dayrit Abstract Tuberculosis remains one of the top ten causes of death worldwide. Therefore, immediate discovery of new antibiotic compounds is crucial for counteracting the evolving antibiotic resistance in strains of Mycobacterium tuberculosis and related species. Previous studies have shown that a soil bacterium, Lentzea kentuckyensis, can biosynthesize lassomycin, a peptide that has the ability to kill multi-drug resistant M. tuberculosis. Two Lentzea strains were grown and observed to exhibit inhibitory activity against M. smegmatis. The active compounds were extracted and analyzed by mass spectrometry. Structure elucidation of the molecules by NMR spectroscopy is ongoing. Further studies will focus on determining the mechanism of action of the active compounds. Characterizing these metabolites will provide a better understanding of how Lentzea strains both interact with and defend themselves against competing microbes, such as mycobacteria. March 2020 2 | P a g e Acknowledgements I would like to thank my amazing research supervisor, Dr. Clarissa Sit, for her support and guidance during this research project. -
Streptosporangium Roseum Type Strain (NI 9100T)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Permalink https://escholarship.org/uc/item/7g79w47k Journal Standards in genomic sciences, 2(1) ISSN 1944-3277 Authors Nolan, Matt Sikorski, Johannes Jando, Marlen et al. Publication Date 2010-01-28 DOI 10.4056/sigs.631049 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:29-37 DOI:10.4056/sigs.631049 Complete genome sequence of Streptosporangium T roseum type strain (NI 9100 ) Matt Nolan1, Johannes Sikorski2, Marlen Jando2, Susan Lucas1, Alla Lapidus1, Tijana Glavina Del Rio1, Feng Chen1, Hope Tice1, Sam Pitluck1, Jan-Fang Cheng1, Olga Chertkov1,3, David Sims1,3, Linda Meincke1,3, Thomas Brettin1,3, Cliff Han1,3, John C. Detter1,3, David Bruce1,3, Lynne Goodwin1,3, Miriam Land1,4, Loren Hauser1,4, Yun-Juan Chang1,4, Cynthia D. Jeffries1,4, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amy Chen5, Krishna Pala- niappan5, Patrick Chain1,3, Manfred Rohde6, Markus Göker2, Jim Bristow1, Jonathan A. Ei- sen1,7, Victor Markowitz5, Philip Hugenholtz1, Nikos C. Kyrpides1, and Hans-Peter Klenk2* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: sporangia, vegetative and aerial mycelia, aerobic, non-motile, non-motile spores, Gram-positive, Streptosporangiaceae, S. -
Lentzea Kentuckyensis Sp. Nov., of Equine Origin
9583 International Journal of Systematic and Evolutionary Microbiology (2007), 57, 1780-1783 DOl 10.1 099/ijs.0.64245-0 Lentzea kentuckyensis sp. nov., of equine origin D. P. Labeda, 1 J. M. Donahue,2 S. F. Sells2 and R. M. Kroppenstedt3 Correspondence Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization D. P. Labeda Research, USDA - Agricultural Research Service, Peoria, IL 61604, USA [email protected] 2Livestock Disease Diagnostic Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40511, USA I 3DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany A novel actinomycete, designated strain LDDC 287605T was isolated from an equine placenta during the course of routine diagnostic tests for nocardioform placentitis. In a preliminary study, the strain was observed to be phylogenetically distinct from the genera Crossiella and Amycolatopsis and probably a member of the genus Lentzea. A polyphasic study of strain LDDC 287605T confirmed its identification as a member of Lentzea on the basis of its chemotaxonomic and morphological similarity to all of the known species of the genus. Moreover, the strain could be distinguished from other species with validly published names on the basis of its phylogenetic and physiological characteristics and its fatty acid profile. Therefore strain LDDC 287605T represents a novel species of the genus Lentzea, for which the name Lentzea ken fuckyensis sp. nov. is proposed. The type strain is LDDC 287605T (=NRRL B24416T =DSM 44909T) Nocardioform placentitis is a distinctive type of placentitis UltraClean microbial DNA isolation kits (Mc, Bio I.abora- in horses, in which lesions observed on the chorionic tories), amplified, sequenced according to previously surface of the placenta are associated with Gram-positive, described procedures (Labeda & Kroppenstedt, 2000) and branching micro-organisms that can be recovered upon then deposited in GenBank.