DOCSLIB.ORG

Bacterial Natural Product Gene Biomining in Polar

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bacterial Natural Product Gene Biomining in Polar BACTERIAL NATURAL PRODUCT GENE BIOMINING IN POLAR DESERT SOILS A DISSERTATION SUBMITTED BY NICOLE BENAUD IN FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY SCHOOL OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES UNIVERSITY OF NEW SOUTH WALES, SYDNEY AUSTRALIA SUPERVISOR: ASSOCIATE PROFESSOR BELINDA C. FERRARI CO- SUPERVISOR: DR JOHN A. KALAITZIS June, 2019 THESIS ABSTRACT New antimicrobial agents are urgently required to address a global antibiotic resistance crisis. Natural products, biosynthesised through secondary metabolite pathways, remain at the forefront of drug discovery. Extreme environments are attractive targets for microbial biomining, due to their potential as reservoirs for novel metabolites. In polar regions, environmental conditions are some of Earth's most severe, and microbes dominate the biosphere. Moreover, arid polar soils comprise high relative abundances of Actinobacteria and Proteobacteria, prolific producers of natural products. This research had three main objectives: to identify polar soil bacterial communities with novel biosynthetic potential; to establish a culture collection of Antarctic isolates with demonstrated bioactive capabilities; and to perform whole genome sequencing (WGS) on biotechnologically promising isolates for biosynthetic gene cluster (BGC) mining. Third generation long-read PacBio sequencing was employed to survey > 200 Antarctic and high Arctic soils for non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) domain amplicons. Significant negative relationships were observed between natural product genes and soil fertility factors carbon, nitrogen and moisture. Sequences primarily aligned to domains encoding antifungal, antitumour and antimicrobial/surfactant compounds, but with low sequence similarity (< 70%) to known genes. Using novel culturing approaches, 19 bacterial genera across 4 phyla were isolated from Antarctic soils, including 32 Actinomycetales species. Extended oligotrophic incubation times were related to the recovery of novel and rare strains. In in situ antimicrobial assays, Streptomyces was the only genus to produce measurable activity. WGS was performed for 17 Antarctic isolates using PacBio technology. Genomes predominantly returned high-quality assemblies, and BGC analysis revealed an abundance of terpene, i NRPS, PKS, bacteriocin and siderophore clusters, with minimal gene similarity (< 70%) to known BGC. In accordance with amplicon sequencing results, many NRPS and PKS domains aligned most closely to antifungal, antitumour and antimicrobial/surfactant- encoding genes. These findings indicate that Antarctic desert soils are excellent candidates for novel natural product bioprospecting and gives further insight into the functional and ecological relevance of natural products in terms of competition between microbiota for scarce resources. ii PUBLICATIONS Peer reviewed journal article Benaud, N., Zhang, E., van Dorst, J., Brown, M.V., Kalaitzis, J.A., Neilan, B.A., Ferrari, B.C. (2019). Harnessing Long-Read Amplicon Sequencing to Uncover NRPS and Type I PKS Gene Sequence Diversity in Polar Desert Soils. FEMS Microbiology Ecology, doi.org/10.1093/femsec/fiz031 iii TABLE OF CONTENTS ABSTRACT....................................................................................... ...................... i PUBLICATIONS..................................................................................................... iii TABLE OF CONTENTS......................................................................................... iv ACKNOWLEDGEMENTS...................................................................................... x LIST OF FIGURES.................................................................................................. xi LIST OF TABLES................................................................................................... xvi ABBREVIATIONS.................................................................................................. xix CHAPTER 1 1 INTRODUCTION..............................................…………........................ 1 1.1 Antibiotic resistance drives the need for novel bioactive compounds......... 1 1.2 Microbial natural products............................................................................ 3 1.3 Natural product biosynthesis......................................................................... 6 1.3.1 Polyketide synthases (PKS).............................................................. 8 1.3.1.1 Type I PKS........................................................................... 9 1.3.1.2 Type II PKS......................................................................... 13 1.3.1.3 Type III PKS......................................................................... 13 1.3.2 Non-ribosomal peptide synthetases (NRPS)...................................... 15 1.4 Dominant natural product-producing bacterial phyla.................................... 16 1.4.1 The Actinobacteria............................................................................. 17 1.4.2 The Proteobacteria............................................................................ 19 1.4.3 The Cyanobacteria............................................................................ 20 1.4.4 The Firmicutes.................................................................................. 20 1.5 Microbial natural product diversity............................................................... 21 1.6 Cold-adapted bacteria as a source of novel natural products........................ 23 1.7 Polar terrestrial environments and their microbial diversity......................... 29 1.8 Molecular technologies for natural products discovery................................ 34 1.9 Thesis scope and aims……………............................................................... 37 iv CHAPTER 2 2 HARNESSING LONG-READ AMPLICON SEQUENCING TO UNCOVER NRPS AND TYPE I PKS GENE SEQUENCE DIVERSITY IN POLAR DESERT SOILS............................................. 40 2.1 INTRODUCTION…………………………................................................ 40 2.1.1 The polar deserts of East Antarctica and the High Arctic............... 40 2.1.2 Surveying polar desert soils for natural product genes................... 44 2.2 MATERIALS AND METHODS……………….......................................... 45 2.2.1 Polar locations and soil collection.................................................. 45 2.2.2 DNA extraction and 16S rDNA gene sequencing............................ 47 2.2.3 Soil physical and chemical properties............................................. 48 2.2.4 PKS PCR amplification, gel extraction and barcoding................... 48 2.2.5 NRPS PCR amplification and barcoding......................................... 51 2.2.6 Natural product amplicon library preparation for SMRT sequencing…………………………………………………. 52 2.2.7 Processing PacBio SMRT sequencing data..................................... 52 2.2.8 Taxonomic classification of sequences using the BLAST database.. 53 2.2.9 Multivariate data analysis................................................................ 53 2.2.10 Statistical analysis............................................................................ 54 2.2.11 Construction of phylogenetic trees................................................... 55 2.3 RESULTS………………………………...................................................... 56 2.3.1 PKS and NRPS gene sequences compared across polar soils.......... 56 2.3.2 PKS and NRPS biosynthetic diversity in polar soils......................... 57 2.3.3 Classification and distribution of natural product gene cluster families…………………………………………………………….. 58 2.3.4 Phylogenetic analysis of NP domain sequences………………........ 64 2.3.5 Bacterial and Actinobacterial diversity of polar soils....................... 67 2.3.6 Relationships between polar natural product genes, microbiomes and soil fertility parameters……………………………………….. 69 2.3.7 NP domain sequence novelty............................................................. 75 2.4 DISCUSSION………………….................................................................... 76 v CHAPTER 3 3 CULTURING COLD ADAPTED BACTERIA FROM MAJOR NATURAL PRODUCT PRODUCING PHYLA USING NOVEL APPROACHES............................................................................ 80 3.1 INTRODUCTION…………………………................................................. 80 3.2 MATERIALS AND METHODS……………………….............................. 84 3.2.1 Site description and soil characteristics........................................... 84 3.2.1.1 Herring Island ....................................................................... 85 3.2.1.2 Mitchell Peninsula................................................................. 86 3.2.1.3 Rookery Lake........................................................................ 87 3.2.1.4 Wilkes Tip............................................................................. 87 3.2.2 Direct soil culturing methods........................................................... 88 3.2.2.1 Herring Island and Mitchell Peninsula DSC......................... 88 3.2.2.2 Rookery Lake and Wilkes Tip DSC...................................... 90 3.2.2.3 Isolation and purification of bacteria from DSC................... 91 3.2.3 SSMS culturing at cold temperatures................................................ 91 3.2.3.1 Assessing microcolony growth and bacterial viability on the SSMS.........................................................................
Load more

Recommended publications
  • Table S1. Bacterial Otus from 16S Rrna
    Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria
    [Show full text]
  • Estimation of Antimicrobial Activities and Fatty Acid Composition Of
    Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia Irina V. Voytsekhovskaya1,*, Denis V. Axenov-Gribanov1,2,*, Svetlana A. Murzina3, Svetlana N. Pekkoeva3, Eugeniy S. Protasov1, Stanislav V. Gamaiunov2 and Maxim A. Timofeyev1 1 Irkutsk State University, Irkutsk, Russia 2 Baikal Research Centre, Irkutsk, Russia 3 Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Karelia, Russia * These authors contributed equally to this work. ABSTRACT Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Acti- nobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against Submitted 23 May 2018 bacteria and fungi. It was shown that representatives of the genera Nocardia and Accepted 24 September 2018 Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic Published 25 October 2018 properties. However, despite the lack of antimicrobial and fungicidal activity of Corresponding author Nocardia extracts, those strains are specific in terms of their fatty acid spectrum.
    [Show full text]
  • 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]
  • Genome-Based Classification of The
    Antonie van Leeuwenhoek https://doi.org/10.1007/s10482-021-01564-0 (0123456789().,-volV)( 0123456789().,-volV) ORIGINAL PAPER Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune Ali B. Kusuma . Imen Nouioui . Michael Goodfellow Received: 26 January 2021 / Accepted: 18 March 2021 Ó The Author(s) 2021 Abstract A polyphasic study was designed to fatty acids. Whole-genome sequences generated for determine the taxonomic provenance of a strain, the isolate and Streptomyces albiflaviniger DSM isolate PRKS01-29T, recovered from an Indonesian 41598T and Streptomyces javensis DSM 41764T were sand dune and provisionally assigned to the Strepto- compared with phylogenetically closely related myces violaceusniger clade. Genomic, genotypic and strains, the isolate formed a branch within the S. phenotypic data confirmed this classification. The violaceusniger clade in the resultant phylogenomic isolate formed an extensively branched substrate tree. Whole-genome sequences data showed that mycelium which carried aerial hyphae that differen- isolate PRKS01-29T was most closely related to the tiated into spiral chains of rugose ornamented spores, S. albiflaviniger strain but was distinguished from the contained LL-as the wall diaminopimelic acid, MK-9 latter and from other members of the clade using (H6,H8) as predominant isoprenologues, phos- combinations of phenotypic properties and average phatidylethanolamine as the diagnostic phospholipid nucleotide identity and digital DNA:DNA hybridiza- and major proportions of saturated, iso- and anteiso- tion scores. Consequently, it is proposed that isolate PRKS01-29T (= CCMM B1303T = ICEBB-02T- = NCIMB 15210T) should be classified in the genus Supplementary Information The online version contains Streptomyces as Streptomyces sabulosicollis sp.
    [Show full text]
  • Corynebacterium Sp.|NML98-0116
    1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • Multi-Locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level11
    CHAPTER Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level11 Xiaoying Rong, Ying Huang1 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China 1Corresponding author: e-mail address: [email protected] 1 INTRODUCTION The study of genetic variation among prokaryotes is fundamental for understanding their evolution, and untangling their ecology and evolutionary theory-based system- atics. Recently, advances in DNA sequencing technology, the exploration of neglected habitats and the discovery of new species and products have forced micro- bial systematists to undertake comprehensive analyses of genetic variation within and between species and determine its impact on evolutionary relationships. 16S rRNA gene sequence analyses have enhanced our understanding of prokaryotic diversity and phylogeny, including that of non-culturable microorganisms (Doolittle, 1999; Head, Saunders, & Pickup, 1998; Mason et al., 2009). However, 16S rRNA gene phy- logenetic analyses have major drawbacks, notably providing insufficient resolution, especially for distinguishing between closely related species. In addition, there are well-documented cases in which individual prokaryotic organisms have been found to contain divergent 16S rRNA genes, thereby suggesting the potential for horizontal exchange of rRNA genes; such problems pose a challenge for reconstructing the evolutionary history of prokaryotic species and complicate efforts to classify them (Acinas, Marcelino, Klepac-Ceraj, & Polz, 2004; Cilia, Lafay, & Christen, 1996; Michon et al., 2010; Pei et al., 2010; Rokas, Williams, King, & Carroll, 2003). Multi-locus sequence analysis/typing (MLSA/MLST) is a nucleotide sequence- based approach for the unambiguous characterization of prokaryotes via the Internet, which directly characterizes DNA sequence variations in a set of housekeeping genes and evaluates relationships between strains based on their unique allelic profiles or sequences (Maiden, 2006).
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO the Genus Salinispora As A
    UNIVERSITY OF CALIFORNIA, SAN DIEGO The genus Salinispora as a model organism for species concepts and natural products discovery A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Natalie Millán Aguiñaga Committee in charge: Paul R. Jensen, Chair Eric E. Allen William Fenical Joseph Pogliano Gregory W. Rouse 2016 Copyright Natalie Millán Aguiñaga, 2016 All rights reserved The dissertation of Natalie Millán Aguiñaga is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2016 iii DEDICATION To my parents Roberto and Yolanda. Thanks for sharing this dream come true and for continuing to support me in the dreams I still want to achieve. iv TABLE OF CONTENTS Signature Page ...................................................................................................... iii Dedication ............................................................................................................. iv Table of Contents ................................................................................................ v List of Figures .....................................................................................................
    [Show full text]
  • Biosynthetic Origin of Anthracimycin: a Tricyclic Macrolide from Streptomyces Sp
    The Journal of Antibiotics (2016) 69, 403–405 & 2016 Japan Antibiotics Research Association All rights reserved 0021-8820/16 www.nature.com/ja NOTE Biosynthetic origin of anthracimycin: a tricyclic macrolide from Streptomyces sp. Enjuro Harunari1, Hisayuki Komaki2 and Yasuhiro Igarashi1 The Journal of Antibiotics (2016) 69, 403–405; doi:10.1038/ja.2015.118; published online 2 December 2015 Anthracimycin (1) is a decalin-fused tricyclic macrolide isolated from signals arising from the 13C–13C coupling were clearly observed for all terrestrial and marine Streptomyces species (Figure 1).1–3 1 shows the carbons except for three methyl groups (C-23, C-24 and C-25) strong activity against Gram-stain-positive bacteria including Bacillus and C-11 and C-12 (Supplementary Figure S1). The outer split peaks anthracis and methicillin-resistant Staphylococcus aureus (MRSA).3,4 were invisible owing to the roof effect7 caused by the close chemical The most intriguing feature of this molecule is its enantiomerism to shifts between C-11 and C-12 (Δ 0.11 p.p.m.) although these carbons chlorotonil A (2), a secondary metabolite of a myxobacterium are likely derived from a single acetate unit. In the 2D-INADEQUATE 5 1 Sorangium cellulosum (Figure 1). Except for a methyl substitution at spectrum measured with a parameter set optimized for JCC 45 Hz, 13 C-8 in 2, the absolute configurations of the remaining chiral centers at cross peaks derived from the intact C2 acetate units were observed C-2, C-6, C-7, C-12, C-15 and C-16 are opposite between 1 and 2 for C-1/C-2, C-3/C-4, C-5/C-6, C-7/C-8, C-9/C-10, C-13/C-14, C-15/ although the dichrorination at C-4 in 2 is an additional difference C-16, C-17/C-18, C-19/C-20 and C-21/C-22 (Table 1, Supplementary between these compounds.
    [Show full text]
  • Towards the Total Synthesis of Anthracimycin
    Towards the Total Synthesis of Anthracimycin Giacomo Lodovici Doctor of Philosophy University of York Chemistry January 2019 1. Abstract In 2013 W. Fenical et al. reported the isolation of a natural product from a marine microorganism of streptomyces species, which possessed significant activity against Gram-positive pathogens Bacillus anthracis, methicillin-resistant and vancomycin resistant Staphylococcus aureus (MRSA).15 The compound responsible for the antibiotic activity was found to be the 14-membered macrolide named anthracimycin. The research detailed in this thesis describes the efforts towards the total synthesis of this natural product and specifically the formation of the core of anthracimycin in 12-steps. Direct palladium catalysed oxidation formed the enone used as a dienophile in a stereo- and regio-selective Diels‒Alder/epimerisation sequence, which afforded the trans-decalin. A facial and stereoselective Hosomi‒Sakurai 1,4-addition reaction, followed by a selective borylation/dihydroxylation sequence on the exocyclic alkene, allowed the formation of the core of anthracimycin (Scheme 1). Scheme 1. The formation of the decalin core of anthracimcyin. 1 2. Contents 1. Abstract ............................................................................................................................................... 1 2. Contents .............................................................................................................................................. 2 3. List of Figures .....................................................................................................................................
    [Show full text]
  • Cryobacterium Psychrophilum Gen. Nov., Sp. Nov., Nom. Rev., Comb. Nov
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1997, p. 474-478 Vol. 47, No. 2 0020-7713/97/$04.00+0 Copyright 0 1997, International Union of Microbiological Societies Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an Obligately Psychrophilic Actinomycete To Accommodate “Curtobacteriumpsychrophilum” Inoue and Komagata 1976 KEN-ICHIRO SUZUKI,l* JUNK0 SASAKI,’ MASAKAZU URAMOT0,2 TAKASHI NAKASE,’ AND KAZUO KOMAGATA3 Japan Collection of Microorganisms, The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama 351 -01, Department of Agriculture, Tamagawa University, Machida, Tokyo 192, and Tokyo University of Agn’culture, Setagaya-ku, Tokyo 156, Japan “Curtobacteriumpsychrophilum,” proposed by Inoue and Komagata in 1976, is a psychrophilic gram-positive irregular rod isolated from Antarctic soil. This organism grew optimally at 9 to 12°C and did not grow at higher than 18°C. Chemotaxonomic characteristics of this organism were the presence of 2,4-diaminobutyricacid in the cell wall and menaquinone-10as the predominant respiratory quinone. The cellular fatty acid profile, which contained a significant amount of an anteiso-branched monounsaturated acid, 12-methyl tetradecenoic acid, was a distinctive characteristic of this organism and was reasonable for adaptation to low temperature. Phylogenetic analysis based on 16s ribosomal DNA sequences revealed that this organism was positioned at a separate branch in the family Microbacteriaceae, actinomycetes with group B peptidoglycan. We propose the name Cryobacterium psychrophilum gen. nov., sp. nov. for this organism. The type strain is JCM 1463 (=IAM 12024 =ATCC 43563 =IF0 15735 =NCIMB 2068). In the course of an ecological study of microorganisms in albidurn JCM 1344T, Curtobacterium citreum JCM 134fiT, and Curtobacterium Antarctica, Inoue isolated some obligately psychrophilic bac- pusillurn JCM 1350T were cultivated at 10 and 17°C on R agar for comparison of the cellular fatty acid compositions.
    [Show full text]