DOCSLIB.ORG

Biosynthesis of Natural Products

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biosynthesis of Natural Products Biosynthesis of Natural Products Biosynthesis of Fatty Acids & Polyketides Alan C. Spivey [email protected] Nov 2015 Format & Scope of Lectures • What are fatty acids? – 1° metabolites: fatty acids; 2° metabolites: their derivatives – biosynthesis of the building blocks: acetyl CoA & malonyl CoA • Fatty acid synthesis by Fatty Acid Synthases (FASs) – the chemistry involved – the FAS protein complex & the dynamics of the iterative synthesis process • Fatty acid secondary metabolites – eiconasiods: prostaglandins, thromboxanes & leukotrienes • What are polyketides? – definitions & variety • Polyketide synthesis by PolyKetide Synthases (PKSs) – the chemistry involved – the PKS protein complexes & the dynamics of the iterative synthesis process • Polyketide secondary metabolites – Type I modular metabolites: macrolides – e.g. erythromycin – Type I iterative metabolites: e.g. mevinolin (=lovastatin®) – Type II iterative metabolites: aromatic compounds and polyphenols: e.g. actinorhodin Fatty Acid Primary Metabolites OH OH • Primary metabolites: OH glycerol – fully saturated, linear carboxylic acids & derived (poly)unsaturated derivatives: 3x fatty acids • constituents of essential natural waxes, seed oils, glycerides (fats) & phospholipids • structural role – glycerides & phospholipids are essential constituents of cell membranes OCOR1 • energy storage – glycerides (fats) can also be catabolised into acetate → citric acid cycle OCOR2 OCOR3 • biosynthetic precursors – for elaboration to secondary metabolites glycerides SATURATED ACIDS [MeCH2(CH2CH2)nCH2CO2H (n=2-8)] e.g. CO2H caprylic acid (C8, n = 2) CO2H myristic acid (C14, n = 5) 8 1 14 1 CO H CO2H capric acid (C8, n = 3) 2 palmitic acid (C16, n = 6) 1 10 1 16 CO2H lauric acid (C12, n = 4) CO2H stearic acid (C18, n = 7) 12 1 18 1 MONO-UNSATURATED ACID DERIVATIVES (MUFAs) e.g. 9 9 CO H CO2H 2 1 1 9 oleic acid (C18, Z-9) palmitoleic acid (C16, Z - ) 18 16 (>80% of fat in olive oil ) POLY-UNSATURATED ACID DERIVATIVES (PUFAs) e.g. 8 5 8 5 CO2H eicosapentaenoic acid (EPA) CO2H arachidonic acid (AA) 1 5 8 11 14, 17 1 (C20, Z -5, Z -8, Z -11, Z -14) (C20, Z- , Z - , Z- , Z - Z - ) 20 11 14 17 20 (in cod liver oil) 11 14 Fatty Acids Derivatives – Secondary Metabolites • Secondary metabolites – further elaborated derivatives of polyunsaturated fatty acids (PUFAs) • e.g. polyacetylenes & ‘eicosanoids’ (prostaglandins, thromboxanes & leukotrienes) Primary Metabolism - Overview Primary metabolism Primary metabolites Secondary metabolites CO2 +H2O 1) 'light reactions': hv -> ATP and NADPH PHOTOSYNTHESIS 2) 'dark reactions': CO2 -> sugars (Calvin cycle) HO O oligosaccharides HOHO polysaccharides HO nucleic acids (RNA, DNA) OH glycolysis glucose & other 4,5,6 & 7 carbon sugars CO2 SHIKIMATE METABOLITES PO cinnamic acid derivatives CO2 aromatic compounds + HO HO OH lignans, flavinoids PO O OH OH phosphoenol pyruvate erythrose-4-phosphate shikimate ALKALOIDS aromatic amino acids peptides penicillins CO 2 proteins cephalosporins aliphatic amino acids cyclic peptides O pyruvate tetrapyrroles (porphyrins) Citric acid cycle (Krebs cycle) saturated f atty acids FATTY ACIDS & POLYKETIDES SCoA SCoA unsaturated f atty acids prostaglandins lipids CO2 polyacetylenes O O aromatic compounds, polyphenols acetyl coenzyme A malonyl coenzyme A macrolides CoAS O HO ISOPRENOIDS terpenoids CO2 O HO steroids carotenoids acetoacetyl coenzyme A mevalonate For interesting animations’ of e.g. photosynthesis see: http://www.johnkyrk.com/index.html Biosynthesis of Malonyl Coenzyme A • Malonyl coenzyme A is the key ‘extender unit’ for the biosynthesis of fatty acids (& polyketides): – is formed by the carboxylation of acetyl coenzyme A mediated by a biotin-dependent enzyme – this is the first committed step of fatty acid/polyketide biosynthesis (& is a rate controlling step) Primary metabolism Secondary metabolism CO2 pyruvate GLYCOLYSIS O CoASH CO2 oxidative decarboxylation NAD NADH SCoA acetyl CoA CITRIC ACID CYCLE O SCoA acetyl CoA carboxylase CO O CoASH 2 (biotin-dependent) CoAS O saturated fatty acids O SCoA FATTY ACIDS & POLYKETIDES acetoacetyl CoA unsaturated fatty acids prostaglandins CO O 2 lipids polyacetylenes 2x CoASH 2x NADPH SCoA malonyl CoA aromatic compounds, polyphenols macrolides O 2x NADP HO ISOPRENOIDS CO2 terpenoids HO steroids mevalonate (MVA) carotenoids Biosynthesis of Malonyl Coenzyme A • Bicarbonate is the source of the CO2: – the bicarbonate is first activated via phosphorylation by ATP – then the phosphorylated bicarbonate carboxylates biotin to give carboxybiotin – then the carboxybiotin carboxylates the enolate of acetyl CoA to give malonyl CoA: O bicarbonate HO O Mg Nu O O Pi O N NH ATP H H O NHEnz CoAS S O enolate of acetyl CoA = Nu O Nu O O HN NH O O ADP P H H HO O OH O NHEnz CoAS O biotin S transcarboxylase carboxylase O malonyl CoA biotin=Nu – the carboxylation of biotin & acetyl CoA are mediated by a single biotin-dependent enzyme (complex) having both biotin carboxylase and transcarboxylase active sites – NB. coupling to ATP ‘hydrolysis’ provides energy to drive carboxylation processes Biosynthesis of Fatty Acids – Iterative Oligomerisation • fatty acids are biosynthesised from acetyl CoA as a starter unit by iterative ‘head-to-tail’ oligomerisation involving: – condensation with malonyl CoA as an extender unit (with loss of CO2) – a decarboxylative Claisen condensation – 3-step reduction of the resulting ketone → methylene •after n = 2-8 iterations the C8-20 saturated fatty acid is released from the enzyme(s): Malonyl CoA O O SEnz O O 2x NADPH O O EnzS OO O O CoAS EnzS EnzS EnzS EnzS CO 2x NADP 2 EnzS + H2O decarboxylative #1 #1 dCc reduction [R] #2 Claisen condensation dCc [R]#3 #3 [R]#2 fatty O OO dCc O OO acids EnzS EnzS EnzS EnzS The Decarboxylative Claisen Condensation (dCc) • in vitro – the classical Claisen condensation: EtO O O O O OEt O O H OEt OEt EtO EtO + O EtO EtO • in vivo - the decarboxylative Claisen condensation catalysed by a ketosynthase (KS) O O OO SEnz O O O EnzS EnzS O + EnzS EnzS EnzS CO2 – the energy released upon loss of CO2 provides a driving force for the condensation – thioesters are also particularly reactive partners in this type of condensation... The Claisen Condensation - Why Thioesters? • recall the chemistry of coenzyme A (1st lecture) – properties of alkyl thioesters (cf. alkyl esters) – highly electrophilic carbonyl (~ ketone) – high acidity of protons to the carbonyl of thioesters (cf. ester) – weak C-S bond (cf. C-O bond): • due to poor orbital overlap between the p-orbital lone pair on sulfur (nS) [cf. nO] and the carbonyl anti bonding orbital *C=O; (i.e. minimal ‘resonance’ nS → *C=O) polarised reacive carbonyl weak C-S bond O O O O H R cf . H R H R H R S O S less ef f ective O 3p 2p pKa = 20 pKa = 25 – good leaving group ability of RS- (cf. RO-) • due to pKa (RSH) ~10 cf. pKa (ROH) ~16 Nu: Nu: O O Nu O O O Nu O cf. SR SR Nu OR OR Nu SR OR a good leaving group a poorer leaving group Ketone → Methylene - Reduction • ketone → methylene reduction is achieved via a 3-step process: 1. NADPH-mediated ketone → alcohol reduction catalysed by a keto reductase (KR) 2. syn-eliminataion of water catalysed by a dehydratase (DH) 3. NADPH-mediated hydrogenation of the double bond catalysed by an enoyl reductase (ER) ketone -> alcohol syn- OO alkene reduction OOH elimination O hydrogenation O O EnzS EnzS EnzS EnzS EnzS HS H O O H O O O HS H 2 H HR NH2 NH NH2 NH2 2 N N N N NADPH NADP NADPH NADP • all steps are generally stereospecific but stereospecificity varies from organism to organism – indicated specificities are for human FAS Biosynthesis of Fatty Acids – Overview of FAS • The in vivo process by which all this takes place involves a ‘molecular machine’ - Fatty Acid Synthase (FAS) – Type I FAS: single multifunctional protein complex (e.g. in mammals incl. humans) – Type II FAS: set of discrete, dissociable single-function proteins (e.g. in bacteria) – All FASs comprise 8 components (ACP & 7× catalytic activities): ACP, KS, AT, MT, KR, DH, ER & [TE] : O O O O O decarboxylative SHS O O S SH OOS S CoAS O Claisen condensation O AT MT KS ACP KS ACP CoAS KS ACP 1) KR reduction 2) DH SH SH 3) ER n = 2-8 cycles KS ACP n O S SH O S SH SHS O O translocation TE n OH KS ACP KS ACP KS ACP KS = keto synthase (also known as CE = condensing enzyme); AT = acetyl transferase; MT = malonyl transferase; KR = keto reductase; DH = dehydratase; ER = enoyl reductase; TE = thioesterase; ACP = acyl carrier protein The Acyl Carrier Protein (ACP) • the Acyl Carrier Protein (ACP) is the key protein that allows the growing oligomer to access the appropriate active sites • The ACP is first primed by the post-translational modification of one of its serine hydroxyl groups: – the introduction of a phosphopantetheine ‘swinging-arm’ by reaction with acetyl coenzyme A: NH2 N N O O N N HS N N O P O P O H H O HO H O O O O coenzyme A (CoASH) pantetheinate chain HO P O OH O O ACP OH phpsphopantetheinyl transferase (ACP synthase) O O Me Me HS O O ACP N N P primed acyl carrier protein H H - OH O O phosphopantetheine chain ~ 20Å – this swinging-arm provides flexibility for module-module acyl transfer & provides binding energy for catalysis – the ACP is inactive prior to priming Human Fatty Acid Synthase (FAS) • the first three-dimensional structure of human fatty acid synthase (272 kDa) at 4.5 Å resolution by X- ray crystallography: – Maier, Jenni & Ban Science 2006, 311, 1258 (DOI) ; also Fungal FAS @ 3.1 Å resolution see: Jenni et al. Science 2007, 316, 254 & 288 Structural overview. (A) Front view: FAS consists of a lower part comprising the KS (lower body) and MAT domains (legs) connected at the waist with an upper part formed by the DH, ER (upper body), and KR domains (arms).
Load more

Recommended publications
  • Polyketide Biosynthesis Beyond the Type I, II and III Polyketide Synthase Paradigms Ben Shen
    285 Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms Ben Shen Recent literature on polyketide biosynthesis suggests that Three types of bacterial PKSs are known to date. First, polyketide synthases have much greater diversity in both type I PKSs are multifunctional enzymes that are orga- mechanism and structure than the current type I, II and III nized into modules, each of which harbors a set of distinct, paradigms. These examples serve as an inspiration for searching non-iteratively acting activities responsible for the cata- novel polyketide synthases to give new insights into polyketide lysis of one cycle of polyketide chain elongation, as biosynthesis and to provide new opportunities for combinatorial exemplified by the 6-deoxyerythromycin B synthase biosynthesis. (DEBS) for the biosynthesis of reduced polyketides (i.e. macrolides, polyethers and polyene) such as erythro- Addresses mycin A (1)(Figure 1a) [1]. Second, type II PKSs are Division of Pharmaceutical Sciences and Department of Chemistry, multienzyme complexes that carry a single set of iteratively University of Wisconsin, Madison, WI 53705, USA acting activities, as exemplified by the tetracenomycin e-mail: [email protected] PKS for the biosynthesis of aromatic polyketides (often polycyclic) such as tetracenomycin C (2)(Figure 1b) [2]. Current Opinion in Chemical Biology 2003, 7:285–295 Third, type III PKSs, also known as chalcone synthase- like PKSs, are homodimeric enzymes that essentially are This review comes from a themed section on iteratively acting condensing enzymes, as exemplified by Biocatalysis and biotransformation Edited by Tadhg Begley and Ming-Daw Tsai the RppA synthase for the biosynthesis of aromatic poly- ketides (often monocyclic or bicyclic), such as flavolin (3) 1367-5931/03/$ – see front matter (Figure 1c) [3].
    [Show full text]
  • Keto Acid Dehydrogenase Gene Cluster
    JOURNAL OF BACTERIOLOGY, June 1995, p. 3504–3511 Vol. 177, No. 12 0021-9193/95/$04.0010 Copyright q 1995, American Society for Microbiology A Second Branched-Chain a-Keto Acid Dehydrogenase Gene Cluster (bkdFGH) from Streptomyces avermitilis: Its Relationship to Avermectin Biosynthesis and the Construction of a bkdF Mutant Suitable for the Production of Novel Antiparasitic Avermectins CLAUDIO D. DENOYA,* RONALD W. FEDECHKO, EDMUND W. HAFNER, HAMISH A. I. MCARTHUR, MARGARET R. MORGENSTERN, DEBORAH D. SKINNER, KIM STUTZMAN-ENGWALL, RICHARD G. WAX, AND WILLIAM C. WERNAU Bioprocess Research, Central Research Division, Pfizer Inc., Groton, Connecticut 06340 Received 22 February 1995/Accepted 10 April 1995 A second cluster of genes encoding the E1a,E1b, and E2 subunits of branched-chain a-keto acid dehydro- genase (BCDH), bkdFGH, has been cloned and characterized from Streptomyces avermitilis, the soil microor- ganism which produces anthelmintic avermectins. Open reading frame 1 (ORF1) (bkdF, encoding E1a), would encode a polypeptide of 44,394 Da (406 amino acids). The putative start codon of the incompletely sequenced ORF2 (bkdG, encoding E1b) is located 83 bp downstream from the end of ORF1. The deduced amino acid sequence of bkdF resembled the corresponding E1a subunit of several prokaryotic and eukaryotic BCDH complexes. An S. avermitilis bkd mutant constructed by deletion of a genomic region comprising the 5* end of bkdF is also described. The mutant exhibited a typical Bkd2 phenotype: it lacked E1 BCDH activity and had lost the ability to grow on solid minimal medium containing isoleucine, leucine, and valine as sole carbon sources. Since BCDH provides an a-branched-chain fatty acid starter unit, either S(1)-a-methylbutyryl coenzyme A or isobutyryl coenzyme A, which is essential to initiate the synthesis of the avermectin polyketide backbone in S.
    [Show full text]
  • Metabolic Engineering for Unusual Lipid Production in Yarrowia Lipolytica
    microorganisms Review Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica Young-Kyoung Park * and Jean-Marc Nicaud Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78352 Jouy-en-Josas, France; [email protected] * Correspondence: [email protected]; Tel.: +33-(0)1-74-07-16-92 Received: 14 November 2020; Accepted: 2 December 2020; Published: 6 December 2020 Abstract: Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica. Keywords: Yarrowia lipolytica; oleochemicals; lipids; unusual lipids; metabolic engineering 1. Introduction Microbial lipids are promising alternative fuel sources given growing concerns about climate change and environmental pollution [1–4]. They offer multiple advantages over plant oils and animal fats. For example, the production of microbial lipids does not result in resource competition with food production systems; is largely independent of environmental conditions; can be based on diverse substrates; and allows product composition to be customized based on the desired application [3,4].
    [Show full text]
  • Synthesis and Biosynthesis of Polyketide Natural Products
    Syracuse University SURFACE Chemistry - Dissertations College of Arts and Sciences 12-2011 Synthesis and Biosynthesis of Polyketide Natural Products Atahualpa Pinto Syracuse University Follow this and additional works at: https://surface.syr.edu/che_etd Part of the Chemistry Commons Recommended Citation Pinto, Atahualpa, "Synthesis and Biosynthesis of Polyketide Natural Products" (2011). Chemistry - Dissertations. 181. https://surface.syr.edu/che_etd/181 This Dissertation is brought to you for free and open access by the College of Arts and Sciences at SURFACE. It has been accepted for inclusion in Chemistry - Dissertations by an authorized administrator of SURFACE. For more information, please contact [email protected]. Abstract Traditionally separate disciplines of a large and broad chemical spectrum, synthetic organic chemistry and biochemistry have found in the last two decades a fertile common ground in the area pertaining to the biosynthesis of natural products. Both disciplines remain indispensable in providing unique solutions on numerous questions populating the field. Our contributions to this interdisciplinary pursuit have been confined to the biosynthesis of polyketides, a therapeutically and structurally diverse class of natural products, where we employed both synthetic chemistry and biochemical techniques to validate complex metabolic processes. One such example pertained to the uncertainty surrounding the regiochemistry of dehydration and cyclization in the biosynthetic pathway of the marine polyketide spiculoic acid A. The molecule's key intramolecular cyclization was proposed to occur through a linear chain containing an abnormally dehydrated polyene system. We synthesized a putative advanced polyketide intermediate and tested its viability to undergo a mild chemical transformation to spiculoic acid A. In addition, we applied a synthetic and biochemical approach to elucidate the biosynthetic details of thioesterase-catalyzed macrocyclizations in polyketide natural products.
    [Show full text]
  • Bio-Based Production of Fuels and Industrial Chemicals by Repurposing Antibiotic-Producing Type I Modular Polyketide Synthases: Opportunities and Challenges
    The Journal of Antibiotics (2017) 70, 378–385 & 2017 Japan Antibiotics Research Association All rights reserved 0021-8820/17 www.nature.com/ja REVIEW ARTICLE Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges Satoshi Yuzawa1, Jay D Keasling1,2,3,4,5,6 and Leonard Katz2 Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. We have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals. The Journal of Antibiotics (2017) 70, 378–385; doi:10.1038/ja.2016.136; published online 16 November 2016 INTRODUCTION complex polyketide is programmed by its cognate PKS, by the number Complex polyketides represent a family of natural products that and composition of modules. possess a wide variety of pharmacological or biological activities. Since the concept of modular polyketide biosynthesis was initially Numerous polyketides and their semisynthetic derivatives have been report by Katz and colleagues2 more than 25 years
    [Show full text]
  • Investigation and Engineering of Polyketide Biosynthetic Pathways
    Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 12-2017 Investigation and Engineering of Polyketide Biosynthetic Pathways Lei Sun Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biological Engineering Commons Recommended Citation Sun, Lei, "Investigation and Engineering of Polyketide Biosynthetic Pathways" (2017). All Graduate Theses and Dissertations. 6903. https://digitalcommons.usu.edu/etd/6903 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. INVESTIGATION AND ENGINEERING OF POLYKETIDE BIOSYNTHETIC PATHWAYS by Lei Sun A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPHY in Biological Engineering Approved: ______________________ ____________________ Jixun Zhan, Ph.D. David W. Britt, Ph.D. Major Professor Committee Member ______________________ ____________________ Dong Chen, Ph.D. Jon Takemoto, Ph.D. Committee Member Committee Member ______________________ ____________________ Elizabeth Vargis, Ph.D. Mark R. McLellan, Ph.D. Committee Member Vice President for Research and Dean of the School of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2017 ii Copyright© Lei Sun 2017 All Rights Reserved iii ABSTRACT Investigation and engineering of polyketide biosynthetic pathways by Lei Sun, Doctor of Philosophy Utah State University, 2017 Major Professor: Jixun Zhan Department: Biological Engineering Polyketides are a large family of natural products widely found in bacteria, fungi and plants, which include many clinically important drugs such as tetracycline, chromomycin, spirolaxine, endocrocin and emodin.
    [Show full text]
  • An Iterative Type I Polyketide Synthase Initiates the Biosynthesis of the Antimycoplasma Agent Micacocidin
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Chemistry & Biology Article An Iterative Type I Polyketide Synthase Initiates the Biosynthesis of the Antimycoplasma Agent Micacocidin Hirokazu Kage,1 Martin F. Kreutzer,1 Barbara Wackler,2 Dirk Hoffmeister,2 and Markus Nett1,* 1Junior Research Group ‘‘Secondary Metabolism of Predatory Bacteria’’, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Kno¨ ll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany 2Department of Pharmaceutical Biology at the Hans-Kno¨ ll-Institute, Friedrich Schiller Universita¨ t Jena, 07745 Jena, Germany *Correspondence: [email protected] http://dx.doi.org/10.1016/j.chembiol.2013.04.010 SUMMARY under macrolide therapy have been described (Averbuch et al., 2011; Cardinale et al., 2011; Itagaki et al., 2013). Micacocidin is a thiazoline-containing natural pro- Micacocidin is a new antibiotic that exerts strong inhibitory duct from the bacterium Ralstonia solanacearum effects in the nanomolar range against several Mycoplasma that shows significant activity against Mycoplasma species, including M. pneumoniae (Kobayashi et al., 1998). pneumoniae. The presence of a pentylphenol moiety In vivo efficacy after oral administration was demonstrated in distinguishes micacocidin from the structurally chicken that had been infected with M. gallisepticum (Kobayashi related siderophore yersiniabactin, and this residue et al., 2000). The thiazoline-containing natural product micaco- cidin is structurally closely related to the siderophore yersinia- also contributes to the potent antimycoplasma bactin (Drechsel et al., 1995), and cellular uptake studies effects. The biosynthesis of the pentylphenol moiety, suggest that it might also be involved in iron acquisition of the as deduced from bioinformatic analysis and stable producing bacterium Ralstonia solanacearum (Kreutzer et al., isotope feeding experiments, involves an iterative 2011).
    [Show full text]
  • Chapter 4 Erythronolide B and the Erythromycins
    124 Chapter 4 Erythronolide B and the Erythromycins Isolation and Structure Isolated in 1952 from the soil bacteria actinomycetes,1 the erythromycins are a distinguished family of natural products by virtue of their clinically useful antibacterial properties and complex structures. Soon after their discovery, scientists elucidated the structure of erythromycin A (1),2 and then erythromycin B (2),3,4 through extensive degradation studies (Figure 1).5 X-ray crystallography studies have established the three dimensional structure of these natural products.6 The erythromycins are characterized by 14-membered macrolactones with glycosidic linkages at C(3) and C(5) to 6-deoxysugars, L-cladinose and D-desosamine, respectively. The name “erythronolide” refers to the polyketide derived-aglycone (e.g., 3 and 4, Figure 1), while the letter codes (i.e., A, B, etc.) reflect each isomer and its order of discovery. In contrast to erythronolide A (3), erythronolide B (4) is a natural product and more importantly, the biogenic precursor of all the erythromycin isomers. 125 O O Me Me Me Me 9 Me Me Me 11 7 OH Me OH R OH R OH NMe 13 Me 5 HO 2 Me O O O Me O OH Me 1 3 Me O O OMe O OH Me Me Me O OH Me 1 R = OH erythromycin A 3 R = OH erythronolide A 2 R = H erythromycin B 4 R = H erythronolide B Figure 1. Representative members of the erythromycin macrolide family of antibiotics Biosynthesis of Erythronolide B Our understanding on the biosynthesis of polyketides derives mainly from extensive studies conducted on the biosynthetic mechanism of the erythromycins.7 The first polyketide synthase genome sequenced was that of 6-deoxyerythronolide B synthase (DEBS).8 Many Streptomyces polyketide synthases sequenced thereafter proved similar in structure and function to DEBS.
    [Show full text]
  • Forazoline A: Marine-Derived Polyketide with Antifungal in Vivo Efficacy** Thomas P
    Angewandte Chemie DOI: 10.1002/anie.201405990 Natural Products Hot Paper Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy** Thomas P. Wyche, Jeff S. Piotrowski, Yanpeng Hou, Doug Braun, Raamesh Deshpande, Sean McIlwain, Irene M. Ong, Chad L. Myers, Ilia A. Guzei, William M. Westler, David R. Andes, and Tim S. Bugni* Abstract: Forazoline A, a novel antifungal polyketide with The high mortality rate[2] combined with the continued rise in in vivo efficacy against Candida albicans, was discovered using fungal resistance to current therapeutics[4] demonstrates the LCMS-based metabolomics to investigate marine-invertebrate- ever-present need for new therapeutics. associated bacteria. Forazoline A had a highly unusual and As part of a drug discovery program to discover novel unprecedented skeleton. Acquisition of 13C–13C gCOSY and antifungal therapeutics, we analyzed a collection of marine- 13C–15N HMQC NMR data provided the direct carbon–carbon invertebrate-associated bacteria using LCMS-based metab- and carbon–nitrogen connectivity, respectively. This approach olomics in conjunction with disc diffusion assays. Metabolo- represents the first example of determining direct 13C–15N mics methodology has shown great promise for streamlining connectivity for a natural product. Using yeast chemical the discovery of novel natural products[5] and overcoming genomics, we propose that forazoline A operated through historic barriers such as the high rate of rediscovery of known a new mechanism of action with a phenotypic outcome of compounds.[6] disrupting membrane integrity. Using metabolomics-based strategies which we previously published,[5] we analyzed LCMS profiles of 34 marine-derived Fungal infections result in over 1.5 million deaths annually bacterial extracts by principal component analysis (PCA) and worldwide and cost $12 billion to treat.[1] Candida spp.
    [Show full text]
  • Comparative Genome-Centric Analysis Reveals Seasonal Variation in the Function of Coral Reef Microbiomes
    The ISME Journal (2020) 14:1435–1450 https://doi.org/10.1038/s41396-020-0622-6 ARTICLE Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes 1,2,3 4 5 1,2,3 1 Bettina Glasl ● Steven Robbins ● Pedro R. Frade ● Emma Marangon ● Patrick W. Laffy ● 1,2,3 1,3,4 David G. Bourne ● Nicole S. Webster Received: 8 October 2019 / Revised: 16 February 2020 / Accepted: 19 February 2020 / Published online: 2 March 2020 © The Author(s) 2020. This article is published with open access Abstract Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in fl 1234567890();,: 1234567890();,: relation to seasonal environmental uctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes.
    [Show full text]
  • Polyketide Synthases
    ACTA SCIENTIFIC MICROBIOLOGY (ISSN: 2581-3226) Volume 2 Issue 11 November 2019 Short Communication Polyketide Synthases Sulagna Roy* R and D Microbiologist, CBL, Ahmedabad, Gujarat, India *Corresponding Author: Sulagna Roy, R and D Microbiologist, CBL, Ahmedabad, Gujarat, India. Received: October 09, 2019; Published: October 16, 2019 DOI: 10.31080/ASMI.2019.02.0403 Introduction Polyketide Biosynthesis Antibiotics are substances produced by microorganisms, which The biosynthesis of polyketides is modular at many levels and inhibit the growth of or kill other microorganisms at very low con- closely resembles fatty acid biosynthesis. First, the genes respon- centrations [1]. Amongst these substances, polyketides are a large sible for polyketide biosynthesis are typically clustered in the class of secondary metabolites, in bacteria, fungi, plants, and a few genome, forming a biosynthetic gene cluster (BGC). Each BGC en- animal lineages. They are used in medicine mainly as immunosup- codes the Polyketide Synthases (PKS) responsible for the forma- pressants, antibiotics and cholesterol-lowering, antitumour or tion of the carbon backbone, together with the tailoring enzymes anti-parasitic agents, and they are primarily derived from acetic required for primary tailoring events, for example cyclization and acid, one of the simplest building blocks available in nature. Their biosynthesis shares with fatty acids, not only the chemical mecha- - dimerization of the β-keto-acyl carbon chain, subsequent tailoring nisms involved in chain extension but also the pool of precursors coding the regulation of the BGC and resistance to the end prod- events to form the final polyketide structure as well as genes en used as acetyl coenzyme A and malonyl-CoA [2].
    [Show full text]
  • Combinatorial Biosynthesis of Reduced Polyketides
    REVIEWS COMBINATORIAL BIOSYNTHESIS OF REDUCED POLYKETIDES Kira J. Weissman and Peter F. Leadlay Abstract | The bacterial multienzyme polyketide synthases (PKSs) produce a diverse array of products that have been developed into medicines, including antibiotics and anticancer agents. The modular genetic architecture of these PKSs suggests that it might be possible to engineer the enzymes to produce novel drug candidates, a strategy known as ‘combinatorial biosynthesis’. So far, directed engineering of modular PKSs has resulted in the production of more than 200 new polyketides, but key challenges remain before the potential of combinatorial biosynthesis can be fully realized. 3,4 SCAFFOLD Polyketide natural products are among the most polyketide antibiotic erythromycin A . By mixing The backbone atoms of a important microbial metabolites in human medicine, and matching some of the actinorhodin PKS genes molecule, on which targeting both acute and degenerative diseases. They with their counterparts from other aromatic-antibiotic functionality is displayed. are in clinical use as antibiotics (erythromycin A, gene clusters, hybrid molecules were often produced5,6, rifamycin S), anticancer drugs (doxorubicin, epothi- giving rise to the concept now known as ‘combinatorial lone), cholesterol-lowering agents (lovastatin), anti- biosynthesis’7. Given the modular organization within parasitics (avermectin), antifungals (amphotericin B), the giant PKS proteins that catalyse erythro mycin insecticides (spinosyn A) and immunosuppressants biosynthesis, simple mixing and matching of these (rapamycin) (FIG. 1). Polyketide-derived pharma- intact proteins would be of limited interest. However, ceuticals comprise 20% of the top-selling drugs, with once methods were devised to ‘cut and paste’ portions combined worldwide revenues of over UK£10 billion of these giant genes to produce chimaeric genes, in a per year.
    [Show full text]