1
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Hoffmann KM, Hernandez JD, Goncuian EG, March NL. ITC-based kinetics assay for NIS synthetases. Methods Enzymol 2024; 702:75-87. [PMID: 39155121 DOI: 10.1016/bs.mie.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
NIS Synthetases are a widely distributed, novel superfamily of enzymes critical to stealth siderophore production-small molecules increasingly associated with virulence. Study of these enzymes for inhibition or utilization in biosynthesis of new antibiotics has been hindered by multiple kinetics assays utilizing different limiting reporters or relying on product dissociation as a precursor to signal. We present a label free, continuous readout assay optimized for NIS Synthetase systems utilizing an isothermal titration calorimetry instrument. This assay has been tested in an iterative system comparing multiple turnovers on a single substrate to a single bond formation event and is able to delineate these complex kinetics well. The ITC-based kinetic assay is the first label-free assay for the NIS field, which may allow for more detailed kinetic comparisons in the future, and may also have broader use for iterative enzymes in general.
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Affiliation(s)
- Katherine M Hoffmann
- Department of Chemistry, California Lutheran University, Thousand Oaks, CA, United States.
| | - Jocelin D Hernandez
- Department of Chemistry, California Lutheran University, Thousand Oaks, CA, United States
| | - Eliana G Goncuian
- Department of Chemistry, California Lutheran University, Thousand Oaks, CA, United States
| | - Nathan L March
- Department of Chemistry, California Lutheran University, Thousand Oaks, CA, United States
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2
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Gulick AM, Mydy LS, Patel KD. Kinetic analysis of the three-substrate reaction mechanism of an NRPS-independent siderophore (NIS) synthetase. Methods Enzymol 2024; 702:1-19. [PMID: 39155107 PMCID: PMC11331036 DOI: 10.1016/bs.mie.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
The biosynthesis of many bacterial siderophores employs a member of a family of ligases that have been defined as NRPS-independent siderophore (NIS) synthetases. These NIS synthetases use a molecule of ATP to produce an amide linkage between a carboxylate and an amine. Commonly used carboxylate substrates include citrate or α-ketoglutarate, or derivatives thereof, while the amines are often hydroxamate derivatives of lysine or ornithine, or their decarboxylated forms cadaverine and putrescine. Enzymes that employ three substrates to catalyze a reaction may proceed through alternate mechanisms. Some enzymes use sequential mechanisms in which all three substrates bind prior to any chemical steps. In such mechanisms, substrates can bind in a random, ordered, or mixed fashion. Alternately, other enzymes employ a ping-pong mechanism in which a chemical step occurs prior to the binding of all three substrates. Here we describe an enzyme assay that will distinguish among these different mechanisms for the NIS synthetase, using IucA, an enzyme involved in the production of aerobactin, as the model system.
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Affiliation(s)
- Andrew M Gulick
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, United States.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Ketan D Patel
- Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, United States
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3
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Su L, Souaibou Y, Hôtel L, Paris C, Weissman KJ, Aigle B. Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways. Appl Environ Microbiol 2024; 90:e0211523. [PMID: 38323847 PMCID: PMC10952394 DOI: 10.1128/aem.02115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.
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Affiliation(s)
- Li Su
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Yaouba Souaibou
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
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4
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae. G3 (BETHESDA, MD.) 2023; 13:jkad205. [PMID: 37843963 PMCID: PMC10700112 DOI: 10.1093/g3journal/jkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/18/2023]
Abstract
Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
- CSIR—Food Research Institute, Microbiology and Mushroom Research Division, P. O. Box, M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
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5
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Blanco Nouche C, Paris C, Dhalleine T, Oger P, Turpault MP, Uroz S. The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals. Appl Environ Microbiol 2023; 89:e0045323. [PMID: 37800940 PMCID: PMC10617554 DOI: 10.1128/aem.00453-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain Caballeronia mineralivorans PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.
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Affiliation(s)
- Cintia Blanco Nouche
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
| | - Cédric Paris
- Université de Lorraine, EA 4367 Laboratoire d’Ingénierie des Biomolécules, Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Vandœuvre-lès-Nancy, France
| | - Tiphaine Dhalleine
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Villeurbanne, France
| | | | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 Interactions Arbres-Microorganismes, Nancy, France
- INRAE, UR1138 Biogéochimie des Ecosystèmes Forestiers, Champenoux, France
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6
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Yang J, Banas VS, Rivera GSM, Wencewicz TA. Siderophore Synthetase DesD Catalyzes N-to-C Condensation in Desferrioxamine Biosynthesis. ACS Chem Biol 2023; 18:1266-1270. [PMID: 37207292 DOI: 10.1021/acschembio.3c00167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Desferrioxamine siderophores are assembled by the nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase enzyme DesD via ATP-dependent iterative condensation of three N1-hydroxy-N1-succinyl-cadaverine (HSC) units. Current knowledge of NIS enzymology and the desferrioxamine biosynthetic pathway does not account for the existence of most known members of this natural product family, which differ in substitution patterns of the N- and C-termini. The directionality of desferrioxamine biosynthetic assembly, N-to-C versus C-to-N, is a longstanding knowledge gap that is limiting further progress in understanding the origins of natural products in this structural family. Here, we establish the directionality of desferrioxamine biosynthesis using a chemoenzymatic approach with stable isotope incorporation and dimeric substrates. We propose a mechanism where DesD catalyzes the N-to-C condensation of HSC units to establish a unifying biosynthetic paradigm for desferrioxamine natural products in Streptomyces.
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Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Victoria S Banas
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Gerry S M Rivera
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
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7
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Timofeeva AM, Galyamova MR, Sedykh SE. Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223065. [PMID: 36432794 PMCID: PMC9694258 DOI: 10.3390/plants11223065] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/07/2023]
Abstract
Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
| | - Maria R. Galyamova
- Center for Entrepreneurial Initiatives, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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8
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Hoffmann KM, Kingsbury JS, March NL, Jang Y, Nguyen JH, Hutt MM. Chemoenzymatic Synthesis of Select Intermediates and Natural Products of the Desferrioxamine E Siderophore Pathway. Molecules 2022; 27:molecules27196144. [PMID: 36234688 PMCID: PMC9571020 DOI: 10.3390/molecules27196144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The NIS synthetase family of enzymes responsible for the biosynthesis of siderophores is increasingly associated with bacterial virulence. Proteins in this class represent outstanding potential drug targets, assuming that basic biochemical and structural characterizations can be completed. Towards this goal, we have mated an improved synthesis of the non-commercial amino acid N-hydroxy-N-succinylcadaverine (HSC, 6) with an isothermal titration calorimetry (ITC) assay that profiles the iterative stages of HSC trimerization and macrocyclization by NIS synthetase DesD from Streptomyces coelicolor. HSC synthesis begins with multigram-scale Gabrielle and tert-butyl N-(benzyloxy)carbamate alkylations of 1-bromo-5-chloropentane following prior literature, but the end-game reported herein has two advantages for greater material throughput: (1) hydrogenolysis of benzyl ether and Cbz blocking groups is best accomplished with Pearlman’s catalyst at 40 psi of H2 and (2) purification of neutral (zwitterionic) HSC is effected by simple flash chromatography over silica gel in MeOH. HSC is subsequently shown to be a substrate for NIS synthetase DesD, which catalyzes three successive amide bond syntheses via adenyl monophosphate ester intermediates. We quantify and present the iterative and overall enzyme kinetic constants associated with formation of the cyclotrimeric siderophore desferrioxamine E (dfoE, 1).
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9
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Yang J, Banas VS, Patel KD, Rivera GSM, Mydy LS, Gulick AM, Wencewicz TA. An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD. J Biol Chem 2022; 298:102166. [PMID: 35750210 PMCID: PMC9356276 DOI: 10.1016/j.jbc.2022.102166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N1-hydroxy-cadaverine (or N1-hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (Vmax = 0.9–2.5 μM⋅min−1) and produced the macrocyclic trimer DFOE as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of N1-hydroxy-N1-succinyl-cadaverine (HSC)-acyl-adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PPi-bound, and HSC-AMS/Pi-bound forms. We found HSC-AMS inhibited DesD orthologs (IC50 values = 48–53 μM) leading to accumulation of linear trimeric DFOG and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PPi enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD–HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PPi remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bisubstrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.
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Affiliation(s)
- Jinping Yang
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Victoria S Banas
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
| | - Gerry S M Rivera
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Lisa S Mydy
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo, Buffalo, New York, USA.
| | - Timothy A Wencewicz
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA.
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10
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Cavas L, Kirkiz I. Characterization of siderophores from Escherichia coli strains through genome mining tools: an antiSMASH study. AMB Express 2022; 12:74. [PMID: 35704153 PMCID: PMC9200922 DOI: 10.1186/s13568-022-01421-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Although urinary tract infections (UTIs) affect many people, they are usually a disease observed in women. UTIs happen when exogenous and endogenous bacteria enter the urinary tract and colonize there. Cystitis and pyelonephritis occur when bacteria infect the bladder and the kidneys, respectively. UTIs become much serious if the bacteria causing the infection are antibiotic resistant. Since the pathogenic microorganisms have been adopted to current antibiotics via genetic variations, UTIs have become an even more severe health problem. Therefore, there is a great need for the discovery of novel antibiotics. Genome mining of nonpathogenic and pathogenic Escherichia coli strains for investigating secondary metabolites were conducted by the antiSMASH analysis. When the resulting secondary metabolites were examined, it was found that some of the siderophores are effective in UTIs. In conclusion, since the siderophore production in E. coli is directly related to UTIs, these molecules can be a good target for development of future pharmaceutical approaches and compounds. Siderophores can also be used in industrial studies due to their higher chelating affinity for iron. ![]()
Genome mining on nonpathogenic and pathogenic E. coli was studied. Comprehensive and comparative analysis of siderophores were investigated. The results may open a new gate on the development of new drugs on pathogenic E. coli-based diseases.
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Affiliation(s)
- Levent Cavas
- The Graduate School of Natural and Applied Sciences, Department of Biotechnology, Dokuz Eylül University, Kaynaklar Campus, 35390, İzmir, Türkiye. .,Dokuz Eylül University, Faculty of Science, Department of Chemistry, 35390, Kaynaklar Campus, İzmir, Türkiye.
| | - Ibrahim Kirkiz
- The Graduate School of Natural and Applied Sciences, Department of Biotechnology, Dokuz Eylül University, Kaynaklar Campus, 35390, İzmir, Türkiye
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11
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Teta R, Esposito G, Kundu K, Stornaiuolo M, Scarpato S, Pollio A, Costantino V. A Glimpse at Siderophores Production by Anabaena flos-aquae UTEX 1444. Mar Drugs 2022; 20:md20040256. [PMID: 35447929 PMCID: PMC9025534 DOI: 10.3390/md20040256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, a strain of Anabaena flos-aquae UTEX 1444 was cultivated in six different concentrations of iron (III). Cultures were extracted with organic solvents and analyzed using our dereplication strategy, based on the combined use of high-resolution tandem mass spectrometry and molecular networking. The analysis showed the presence of the siderophores’ family, named synechobactins, only in the zero iron (III) treatment culture. Seven unknown synechobactin variants were present in the extract, and their structures have been determined by a careful HRMS/MS analysis. This study unveils the capability of Anabaena flos-aquae UTEX 1444 to produce a large array of siderophores and may be a suitable model organism for a sustainable scale-up exploitation of such bioactive molecules, for the bioremediation of contaminated ecosystems, as well as in drug discovery.
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Affiliation(s)
- Roberta Teta
- “TheBlueChemistryLab”, Department of Pharmacy, Task Force “BIGFED2”, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.T.); (G.E.); (K.K.); (S.S.)
| | - Germana Esposito
- “TheBlueChemistryLab”, Department of Pharmacy, Task Force “BIGFED2”, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.T.); (G.E.); (K.K.); (S.S.)
| | - Karishma Kundu
- “TheBlueChemistryLab”, Department of Pharmacy, Task Force “BIGFED2”, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.T.); (G.E.); (K.K.); (S.S.)
| | - Mariano Stornaiuolo
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy;
| | - Silvia Scarpato
- “TheBlueChemistryLab”, Department of Pharmacy, Task Force “BIGFED2”, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.T.); (G.E.); (K.K.); (S.S.)
| | - Antonino Pollio
- Department of Biology, Complesso Universitario Monte Sant’Angelo via Cinthia–Edificio 7, University of Naples Federico II, 80126 Napoli, Italy;
| | - Valeria Costantino
- “TheBlueChemistryLab”, Department of Pharmacy, Task Force “BIGFED2”, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.T.); (G.E.); (K.K.); (S.S.)
- Correspondence:
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12
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Nolan KP, Font J, Sresutharsan A, Gotsbacher MP, Brown CJM, Ryan RM, Codd R. Acetyl-CoA-Mediated Post-Biosynthetic Modification of Desferrioxamine B Generates N- and N- O-Acetylated Isomers Controlled by a pH Switch. ACS Chem Biol 2022; 17:426-437. [PMID: 35015506 DOI: 10.1021/acschembio.1c00879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Biosynthesis of the hydroxamic acid siderophore desferrioxamine D1 (DFOD1, 6), which is the N-acetylated analogue of desferrioxamine B (DFOB, 5), has been delineated. Enzyme-independent Ac-CoA-mediated N-acetylation of 5 produced 6, in addition to three constitutional isomers containing an N-O-acetyl group installed at either one of the three hydroxamic acid groups of 5. The formation of N-Ac-DFOB (DFOD1, 6) and the composite of N-O-acetylated isomers N-O-Ac-DFOB[001] (6a), N-O-Ac-DFOB[010] (6b), and N-O-Ac-DFOB[100] (6c) (defined as the N-O-Ac motif positioned within the terminal amine, internal, or N-acetylated region of 5, respectively), was pH-dependent, with 6a-6c dominant at pH < 8.5 and 6 dominant at pH > 8.5. The trend in the pH dependence was consistent with the pKa values of the NH3+ (pKa ∼ 10) and N-OH (pKa ∼ 8.5-9) groups in 5. The N- and N-O-acetyl motifs can be conceived as a post-biosynthetic modification (PBM) of a nonproteinaceous secondary metabolite, akin to a post-translational modification (PTM) of a protein. The pH-labile N-O-acetyl group could act as a reversible switch to modulate the properties and functions of secondary metabolites, including hydroxamic acid siderophores. An alternative (most likely minor) biosynthetic pathway for 6 showed that the nonribosomal peptide synthetase-independent siderophore synthetase DesD was competent in condensing N'-acetyl-N-succinyl-N-hydroxy-1,5-diaminopentane (N'-Ac-SHDP, 7) with the dimeric hydroxamic acid precursor (AHDP-SHDP, 4) native to 5 biosynthesis to generate 6. The strategy of diversifying protein structure and function using PTMs could be paralleled in secondary metabolites with the use of PBMs.
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Affiliation(s)
- Kate P. Nolan
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Josep Font
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Athavan Sresutharsan
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michael P. Gotsbacher
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christopher J. M. Brown
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Renae M. Ryan
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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13
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Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain. Nat Commun 2022; 13:592. [PMID: 35105906 PMCID: PMC8807600 DOI: 10.1038/s41467-022-28284-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The structural dynamics of synthetic elongation has remained unclear. Here, we present cryo-EM structures of PchE, an NRPS elongation module, in distinct conformations. The domain organization reveals a unique “H”-shaped head-to-tail dimeric architecture. The capture of both aryl and peptidyl carrier protein-tethered substrates and intermediates inside the heterocyclization domain and l-cysteinyl adenylate in the adenylation domain illustrates the catalytic and recognition residues. The multilevel structural transitions guided by the adenylation C-terminal subdomain in combination with the inserted epimerase and the conformational changes of the heterocyclization tunnel are controlled by two residues. Moreover, we visualized the direct structural dynamics of the full catalytic cycle from thiolation to epimerization. This study establishes the catalytic trajectory of PchE and sheds light on the rational re-engineering of domain-inserted dimeric NRPSs for the production of novel pharmaceutical agents. The catalytic domains in nonribosomal peptide synthetases (NRPSs) are responsible for a choreography of events that elongates substrates into natural products. Here, the authors present cryo-EM structures of a siderophore-producing dimeric NRPS elongation module in multiple distinct conformations, which provides insight into the mechanisms of catalytic trajectory.
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Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
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15
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Sora VM, Meroni G, Martino PA, Soggiu A, Bonizzi L, Zecconi A. Extraintestinal Pathogenic Escherichia coli: Virulence Factors and Antibiotic Resistance. Pathogens 2021; 10:pathogens10111355. [PMID: 34832511 PMCID: PMC8618662 DOI: 10.3390/pathogens10111355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/29/2022] Open
Abstract
The One Health approach emphasizes the importance of antimicrobial resistance (AMR) as a major concern both in public health and in food animal production systems. As a general classification, E. coli can be distinguished based on the ability to cause infection of the gastrointestinal system (IPEC) or outside of it (ExPEC). Among the different pathogens, E. coli are becoming of great importance, and it has been suggested that ExPEC may harbor resistance genes that may be transferred to pathogenic or opportunistic bacteria. ExPEC strains are versatile bacteria that can cause urinary tract, bloodstream, prostate, and other infections at non-intestinal sites. In this context of rapidly increasing multidrug-resistance worldwide and a diminishingly effective antimicrobial arsenal to tackle resistant strains. ExPEC infections are now a serious public health threat worldwide. However, the clinical and economic impact of these infections and their optimal management are challenging, and consequently, there is an increasing awareness of the importance of ExPECs amongst healthcare professionals and the general public alike. This review aims to describe pathotype characteristics of ExPEC to increase our knowledge of these bacteria and, consequently, to increase our chances to control them and reduce the risk for AMR, following a One Health approach.
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16
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Jones CV, Jarboe BG, Majer HM, Ma AT, Beld J. Escherichia coli Nissle 1917 secondary metabolism: aryl polyene biosynthesis and phosphopantetheinyl transferase crosstalk. Appl Microbiol Biotechnol 2021; 105:7785-7799. [PMID: 34546406 DOI: 10.1007/s00253-021-11546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
Escherichia coli Nissle 1917 (EcN) is a Gram-negative bacterium that is used to treat inflammatory bowel diseases. The probiotic character of EcN is not well-understood, but its ability to produce secondary metabolites plays an important role in its activity. The EcN genome encodes for an aryl polyene (APE) biosynthetic gene cluster (BGC), and APE products have a role in biofilm formation. We show here that this unusual polyketide assembly line synthase produces four APE molecules which are likely cis/trans isomers. Within the APE BGC, two acyl carrier proteins are involved in biosynthesis. Acyl carrier proteins require activation by post-translational modification with a phosphopantetheinyl transferase (PPTase). Through analysis of single, double, and triple mutants of three PPTases, the PPTase-BGC crosstalk relationship in EcN was characterized. Understanding PPTase-BGC crosstalk is important for the engineering of secondary metabolite production hosts and for targeting of PPTases with new antibiotics. KEY POINTS: • Escherichia coli Nissle 1917 biosynthesizes four aryl polyene isoforms. • Phosphopantetheinyl transferase crosstalk is important for biosynthesis.
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Affiliation(s)
- Courtney V Jones
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Brianna G Jarboe
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Haley M Majer
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Amy T Ma
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA.
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17
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Torres Salazar BO, Heilbronner S, Peschel A, Krismer B. Secondary Metabolites Governing Microbiome Interaction of Staphylococcal Pathogens and Commensals. Microb Physiol 2021; 31:198-216. [PMID: 34325424 DOI: 10.1159/000517082] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/03/2021] [Indexed: 11/19/2022]
Abstract
Various Staphylococcus species colonize skin and upper airways of warm-blooded animals. They compete successfully with many other microorganisms under the hostile and nutrient-poor conditions of these habitats using mechanisms that we are only beginning to appreciate. Small-molecule mediators, whose biosynthesis requires complex enzymatic cascades, so-called secondary metabolites, have emerged as crucial components of staphylococcal microbiome interactions. Such mediators belong to a large variety of compound classes and several of them have attractive properties for future drug development. They include, for instance, bacteriocins such as lanthipeptides, thiopeptides, and fibupeptides that inhibit bacterial competitor species; signaling molecules such as thiolactone peptides that induce or inhibit sensory cascades in other bacteria; or metallophores such as staphyloferrins and staphylopine that scavenge scant transition metal ions. For some secondary metabolites such as the aureusimines, the exact function remains to be elucidated. How secondary metabolites shape the fitness of Staphylococcus species in the complex context of other microbial and host defense factors remains a challenging field of future research. A detailed understanding will help to harness staphylococcal secondary metabolites for excluding the pathogenic species Staphylococcus aureus from the nasal microbiomes of at-risk patients, and it will be instrumental for the development of advanced anti-infective interventions.
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Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon Heilbronner
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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18
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Butler A, Harder T, Ostrowski AD, Carrano CJ. Photoactive siderophores: Structure, function and biology. J Inorg Biochem 2021; 221:111457. [PMID: 34010741 DOI: 10.1016/j.jinorgbio.2021.111457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/17/2022]
Abstract
It is well known that bacteria and fungi have evolved sophisticated systems for acquiring the abundant but biologically inaccessible trace element iron. These systems are based on high affinity Fe(III)-specific binding compounds called siderophores which function to acquire, transport, and process this essential metal ion. Many hundreds of siderophores are now known and their numbers continue to grow. Extensive studies of their isolation, structure, transport, and molecular genetics have been undertaken in the last three decades and have been comprehensively reviewed many times. In this review we focus on a unique subset of siderophores that has only been recognized in the last 20 years, namely those whose iron complexes display photoactivity. This photoactivity, which typically results in the photooxidation of the siderophore ligand with concomitant reduction of Fe(III) to Fe(II), seemingly upsets the siderophore paradigm of forming and transporting only extremely stable Fe(III) complexes into microbial cells. Here we review their structure, synthesis, photochemistry, photoproduct coordination chemistry and explore the potential biological and ecological consequences of this photoactivity.
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Affiliation(s)
- Alison Butler
- Department of Chemistry and Biochemistry University of California, Santa Barbara, CA 93106 United States
| | - Tilmann Harder
- Department of Biology and Chemistry, University of Bremen, and Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Germany
| | | | - Carl J Carrano
- Department of Chemistry and Biochemistry, San Diego State University, United States.
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19
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Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ. Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin. J Biol Chem 2020; 296:100146. [PMID: 33277357 PMCID: PMC7857480 DOI: 10.1074/jbc.ra120.016738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
The siderophore rhizoferrin (N1,N4-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyi Deng
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sok Ho Kim
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Leann Buhrow
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Diana R Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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20
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Tang J, Ju Y, Zhou J, Guo J, Gu Q, Xu J, Zhou H. Structural and Biochemical Characterization of SbnC as a Representative Type B Siderophore Synthetase. ACS Chem Biol 2020; 15:2731-2740. [PMID: 32880431 DOI: 10.1021/acschembio.0c00523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Staphyloferrin B is a key siderophore secreted by Staphylococcus aureus to acquire ferric ions from a host during infection, and its biosynthetic pathway has been validated to develop efficient antibacterial agents. Herein, we report the crystal structure of AMP-bound SbnC from S. aureus (SaSbnC) as the first representative structure of type B synthetases in the biosynthesis of α-hydroxycarboxylate siderophores. While type B synthetases specifically use α-ketoglutarate (α-KG) as their carboxylic acid substrate, SaSbnC showed unique structural features in the substrate pocket compared with the type A and C synthetases. Screening of α-KG analogues suggested that the hydrogen-bonding interaction between the α-carbonyl group of α-KG and residue Lys552 is a key determinant for the substrate selectivity of type B synthetases. Interestingly, citrate, the product of the tricarboxylic acid cycle and the substrate of type A synthetases, was found to inhibit the activity of SaSbnC with an IC50 value of 83 μM by mimicking α-KG binding, suggesting a potential regulatory role of the tricarboxylic acid cycle, whose activity is under the control of the intracellular iron concentration, to SaSbnC and other type B synthetases. These results provide critical new information to understand the structure, function, and regulation of type B synthetases in the siderophore-based iron acquisition system employed by a large number of pathogenic microbes.
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Affiliation(s)
- Jieyu Tang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingwei Zhou
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Junsong Guo
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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21
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Hoffmann KM, Goncuian ES, Karimi KL, Amendola CR, Mojab Y, Wood KM, Prussia GA, Nix J, Yamamoto M, Lathan K, Orion IW. Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family. Biochemistry 2020; 59:3427-3437. [PMID: 32885650 DOI: 10.1021/acs.biochem.9b00899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from Streptomyces coelicolor, to structurally characterize using a combination of a wild-type and a Arg306Gln variant in apo, cofactor product AMP-bound, and cofactor reactant ATP-bound complexes. The kinetics in the family has been limited by solubility and reporter assays, so we have developed a label-free kinetics assay utilizing a single-injection isothermal-titration-calorimetry-based method. We report second-order rate constants that are 50 times higher than the previous estimations for DesD. Our Arg306Gln DesD variant was also tested under identical buffer and substrate conditions, and its undetectable activity was confirmed. These are the first reported structures for DesD, and they describe the critical cofactor coordination. This is also the first label-free assay to unambiguously determine the kinetics for an NIS synthetase.
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Affiliation(s)
- Katherine M Hoffmann
- Department of Chemistry, California Lutheran University, 60 West Olsen Road #3700, Thousand Oaks, California 91360, United States
| | - Eliana S Goncuian
- Department of Chemistry, California Lutheran University, 60 West Olsen Road #3700, Thousand Oaks, California 91360, United States
| | - Kimya L Karimi
- Department of Chemistry, California Lutheran University, 60 West Olsen Road #3700, Thousand Oaks, California 91360, United States
| | - Caroline R Amendola
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, United States
| | - Yasi Mojab
- Department of Chemistry, California Lutheran University, 60 West Olsen Road #3700, Thousand Oaks, California 91360, United States
| | - Kaitlin M Wood
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, United States
| | - Gregory A Prussia
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, United States
| | - Jay Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Margaret Yamamoto
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, United States
| | - Kiera Lathan
- Department of Chemistry, California Lutheran University, 60 West Olsen Road #3700, Thousand Oaks, California 91360, United States
| | - Iris W Orion
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, United States
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22
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Wellawa DH, Allan B, White AP, Köster W. Iron-Uptake Systems of Chicken-Associated Salmonella Serovars and Their Role in Colonizing the Avian Host. Microorganisms 2020; 8:E1203. [PMID: 32784620 PMCID: PMC7465098 DOI: 10.3390/microorganisms8081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/09/2023] Open
Abstract
Iron is an essential micronutrient for most bacteria. Salmonella enterica strains, representing human and animal pathogens, have adopted several mechanisms to sequester iron from the environment depending on availability and source. Chickens act as a major reservoir for Salmonella enterica strains which can lead to outbreaks of human salmonellosis. In this review article we summarize the current understanding of the contribution of iron-uptake systems to the virulence of non-typhoidal S. enterica strains in colonizing chickens. We aim to address the gap in knowledge in this field, to help understand and define the interactions between S. enterica and these important hosts, in comparison to mammalian models.
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Affiliation(s)
- Dinesh H. Wellawa
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Brenda Allan
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
| | - Aaron P. White
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Wolfgang Köster
- Vaccine & Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Rd., Saskatoon, SK S7N 5E3, Canada; (D.H.W.); (B.A.); (A.P.W.)
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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23
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Hofmann M, Martin del Campo JS, Sobrado P, Tischler D. Biosynthesis of desferrioxamine siderophores initiated by decarboxylases: A functional investigation of two lysine/ornithine-decarboxylases from Gordonia rubripertincta CWB2 and Pimelobacter simplex 3E. Arch Biochem Biophys 2020; 689:108429. [DOI: 10.1016/j.abb.2020.108429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
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24
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Mydy LS, Bailey DC, Patel KD, Rice MR, Gulick AM. The Siderophore Synthetase IucA of the Aerobactin Biosynthetic Pathway Uses an Ordered Mechanism. Biochemistry 2020; 59:2143-2153. [PMID: 32432457 DOI: 10.1021/acs.biochem.0c00250] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biosynthesis of the hydroxamate siderophore aerobactin requires the activity of four proteins encoded within the iuc operon. Recently, we biochemically reconstituted the biosynthetic pathway and structurally characterized IucA and IucC, two enzymes that sequentially couple N6-acetyl-N6-hydroxylysine to the primary carboxylates of citrate. IucA and IucC are members of a family of non-ribosomal peptide synthetase-independent siderophore (NIS) synthetases that are involved in the production of other siderophores, including desferrioxamine, achromobactin, and petrobactin. While structures of several members of this family were solved previously, there is limited mechanistic insight into the reaction catalyzed by NIS synthetases. Therefore, we performed a terreactant steady-state kinetic analysis and herein provide evidence for an ordered mechanism in which the chemistry is preceded by the formation of the quaternary complex. We further probed two regions of the active site with site-directed mutagenesis and identified several residues, including a conserved motif that is present on a dynamic loop, that are important for substrate binding and catalysis.
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Affiliation(s)
- Lisa S Mydy
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Daniel C Bailey
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Ketan D Patel
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Matthew R Rice
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, New York 14203, United States
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Linearized Siderophore Products Secreted via MacAB Efflux Pump Protect Salmonella enterica Serovar Typhimurium from Oxidative Stress. mBio 2020; 11:mBio.00528-20. [PMID: 32371597 PMCID: PMC7403778 DOI: 10.1128/mbio.00528-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nontyphoidal Salmonella bacteria induce a classic inflammatory diarrhea by eliciting a large influx of neutrophils, producing a robust oxidative burst. Despite substantial progress understanding the benefits to the host of the inflammatory response to Salmonella, little is known regarding how Salmonella can simultaneously resist the damaging effects of the oxidative burst. The multidrug efflux pump MacAB is important for survival of oxidative stress both in vitro and during infection. We describe a new pathway used by Salmonella Typhimurium to detoxify extracellular reactive oxygen species using a multidrug efflux pump (MacAB) to secrete a linear siderophore, a metabolite of enterobactin. The natural substrates of many multidrug efflux pumps are unknown, and functional roles of the linear metabolites of enterobactin are unknown. We bring two novel discoveries together to highlight an important mechanism used by Salmonella to survive under the oxidative stress conditions that this organism encounters during the classic inflammatory diarrhea that it also induces. Nontyphoidal salmonellae (NTS) are exposed to reactive oxygen species (ROS) during their residency in the gut. To survive oxidative stress encountered during infection, salmonellae employ several mechanisms. One of these mechanisms involves the multidrug efflux pump MacAB, although the natural substrate of this pump has not been identified. MacAB homologs in pseudomonads secrete products of nonribosomal peptide synthesis (NRPS). In Salmonella enterica serovar Typhimurium, the siderophore enterobactin is produced by NRPS in response to iron starvation and this molecule can be processed into salmochelin and several linear metabolites. We found that Salmonella mutants lacking the key NRPS enzyme EntF are sensitive to peroxide mediated killing and cannot detoxify extracellular H2O2. Moreover, EntF and MacAB function in a common pathway to promote survival of Salmonella during oxidative stress. We further demonstrated that S. Typhimurium secretes siderophores in iron-rich media when peroxide is present and that these MacAB-secreted metabolites participate in protection of bacteria against H2O2. We showed that secretion of anti-H2O2 molecules is independent of the presence of the known siderophore efflux pumps EntS and IroC, well-described efflux systems involved in secretion of enterobactin and salmochelin. Both salmochelin and enterobactin are dispensable for S. Typhimurium protection against ROS; however, linear metabolites of enterobactin produced by esterases IroE and Fes are needed for bacterial survival in peroxide-containing media. We determined that linearized enterobactin trimer protects S. Typhimurium against peroxide-mediated killing in a MacAB-dependent fashion. Thus, we suggest that linearized enterobactin trimer is a natural substrate of MacAB and that its purpose is to detoxify extracellular reactive oxygen species.
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Abstract
Siderophores have important functions for bacteria in iron acquisition and as virulence factors. In this chapter we will discuss the engineering of cyclic hydroxamate siderophores by various biochemical approaches based on the example of Shewanella algae. The marine gamma-proteobacterium S. algae produces three different cyclic hydroxamate siderophores as metabolites via a single biosynthetic gene cluster and one of them is an important key player in interspecies competition blocking swarming of Vibrio alginolyticus. AvbD is the key metabolic enzyme assembling the precursors into three different core structures and hence an interesting target for metabolic and biochemical engineering. Synthetic natural and unnatural precursors can be converted in vitro with purified AvbD to generate siderophores with various ring sizes ranging from analytical to milligram scale. These engineered siderophores can be applied, for example, as swarming inhibitors against V. alginolyticus. Here, we describe the synthesis of the natural and unnatural siderophore precursors HS[X]A and provide our detailed protocols for protein expression of AvbD, conversion of HS[X]A with the enzyme to produce ring-size engineered siderophores and secondly for a biosynthetic feeding strategy that allows to extract engineered siderophores in the milligram scale.
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Carmichael JR, Zhou H, Butler A. A suite of asymmetric citrate siderophores isolated from a marine Shewanella species. J Inorg Biochem 2019; 198:110736. [DOI: 10.1016/j.jinorgbio.2019.110736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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Ramakrishnan G, Pérez NM, Carroll C, Moore MM, Nakamoto RK, Fox TE. Citryl Ornithine Is an Intermediate in a Three-Step Biosynthetic Pathway for Rhizoferrin in Francisella. ACS Chem Biol 2019; 14:1760-1766. [PMID: 31260252 DOI: 10.1021/acschembio.9b00297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Gram-negative bacterium Francisella tularensis secretes the siderophore rhizoferrin to scavenge necessary iron from the environment. Rhizoferrin, also produced by a variety of fungi and bacteria, comprises two citrate molecules linked by amide bonds to a central putrescine (diaminobutane) moiety. Genetic analysis has determined that rhizoferrin production in F. tularensis requires two enzymes: FslA, a siderophore synthetase of the nonribosomal peptide synthetase-independent siderophore synthetase (NIS) family, and FslC, a pyridoxal-phosphate-dependent decarboxylase. To discern the steps in the biosynthetic pathway, we tested F. tularensis strain LVS and its ΔfslA and ΔfslC mutants for the ability to incorporate potential precursors into rhizoferrin. Unlike putrescine supplementation, supplementation with ornithine greatly enhanced siderophore production by LVS. Radioactivity from L-[U-14C] ornithine, but not from L-[1-14C] ornithine, was efficiently incorporated into rhizoferrin by LVS. Although neither the ΔfslA nor the ΔfslC mutant produced rhizoferrin, a putative siderophore intermediate labeled by both [U-14C] ornithine and [1-14C] ornithine was secreted by the ΔfslC mutant. Rhizoferrin was identified by liquid chromatography and mass spectrometry in LVS culture supernatants, while citryl-ornithine was detected as the siderophore intermediate in the culture supernatant of the ΔfslC mutant. Our findings support a three-step pathway for rhizoferrin production in Francisella; unlike the fungus Rhizopus delemar, where putrescine functions as a primary precursor for rhizoferrin, biosynthesis in Francisella preferentially starts with ornithine as the substrate for FslA-mediated condensation with citrate. Decarboxylation of this citryl ornithine intermediate by FslC is necessary for a second condensation reaction with citrate to produce rhizoferrin.
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Affiliation(s)
| | | | - Cassandra Carroll
- Department of Biological Sciences, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby V5A 1S6, Canada
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Årstøl E, Hohmann-Marriott MF. Cyanobacterial Siderophores-Physiology, Structure, Biosynthesis, and Applications. Mar Drugs 2019; 17:E281. [PMID: 31083354 PMCID: PMC6562677 DOI: 10.3390/md17050281] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022] Open
Abstract
Siderophores are low-molecular-weight metal chelators that function in microbial iron uptake. As iron limits primary productivity in many environments, siderophores are of great ecological importance. Additionally, their metal binding properties have attracted interest for uses in medicine and bioremediation. Here, we review the current state of knowledge concerning the siderophores produced by cyanobacteria. We give an overview of all cyanobacterial species with known siderophore production, finding siderophores produced in all but the most basal clades, and in a wide variety of environments. We explore what is known about the structure, biosynthesis, and cycling of the cyanobacterial siderophores that have been characterized: Synechobactin, schizokinen and anachelin. We also highlight alternative siderophore functionality and technological potential, finding allelopathic effects on competing phytoplankton and likely roles in limiting heavy-metal toxicity. Methodological improvements in siderophore characterization and detection are briefly described. Since most known cyanobacterial siderophores have not been structurally characterized, the application of mass spectrometry techniques will likely reveal a breadth of variation within these important molecules.
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Affiliation(s)
- Erland Årstøl
- Department of Biotechnology, PhotoSynLab, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Martin F Hohmann-Marriott
- Department of Biotechnology, PhotoSynLab, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
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Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota. Appl Environ Microbiol 2019; 85:AEM.02406-18. [PMID: 30578265 DOI: 10.1128/aem.02406-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022] Open
Abstract
Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed coculture inhibition assays between nasal Actinobacteria and Staphylococcus spp. We found that isolates of coagulase-negative staphylococci (CoNS) were sensitive to growth inhibition by Actinobacteria but that Staphylococcus aureus isolates were resistant to inhibition. Among Actinobacteria, we observed that Corynebacterium spp. were variable in their ability to inhibit CoNS. We sequenced the genomes of 10 Corynebacterium species isolates, including 3 Corynebacterium propinquum isolates that strongly inhibited CoNS and 7 other Corynebacterium species isolates that only weakly inhibited CoNS. Using a comparative genomics approach, we found that the C. propinquum genomes were enriched in genes for iron acquisition and harbored a biosynthetic gene cluster (BGC) for siderophore production, absent in the noninhibitory Corynebacterium species genomes. Using a chrome azurol S assay, we confirmed that C. propinquum produced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition by C. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced by C. propinquum as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed in vivo by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.IMPORTANCE Within the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal Staphylococcus species strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and posttranslationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by hindering access to or depleting essential nutrients. As the nasal cavity is a nutrient-limited environment, we hypothesized that exploitation competition occurs in this system. We determined that Corynebacterium propinquum produces an iron-chelating siderophore, and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Furthermore, we found that the genes required for siderophore production are expressed in vivo Thus, although siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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Ronan JL, Kadi N, McMahon SA, Naismith JH, Alkhalaf LM, Challis GL. Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0068. [PMID: 29685972 DOI: 10.1098/rstb.2017.0068] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 12/16/2022] Open
Abstract
Hydroxamate groups play key roles in the biological function of diverse natural products. Important examples include trichostatin A, which inhibits histone deacetylases via coordination of the active site zinc(II) ion with a hydroxamate group, and the desferrioxamines, which use three hydroxamate groups to chelate ferric iron. Desferrioxamine biosynthesis in Streptomyces species involves the DesD-catalysed condensation of various N-acylated derivatives of N-hydroxycadaverine with two molecules of N-succinyl-N-hydroxycadaverine to form a range of linear and macrocyclic tris-hydroxamates. However, the mechanism for assembly of the various N-acyl-N-hydroxycadaverine substrates of DesD from N-hydroxycadaverine has until now been unclear. Here we show that the desC gene of Streptomyces coelicolor encodes the acyl transferase responsible for this process. DesC catalyses the N-acylation of N-hydroxycadaverine with acetyl, succinyl and myristoyl-CoA, accounting for the diverse array of desferrioxamines produced by S. coelicolor The X-ray crystal structure of DesE, the ferrioxamine lipoprotein receptor, in complex with ferrioxamine B (which is derived from two units of N-succinyl-N-hydroxycadaverine and one of N-acetyl-N-hydroxycadaverine) was also determined. This showed that the acetyl group of ferrioxamine B is solvent exposed, suggesting that the corresponding acyl group in longer chain congeners can protrude from the binding pocket, providing insights into their likely function. This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Jade L Ronan
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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Maglangit F, Tong MH, Jaspars M, Kyeremeh K, Deng H. Legonoxamines A-B, two new hydroxamate siderophores from the soil bacterium, Streptomyces sp. MA37. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.11.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Boiteau RM, Fansler SJ, Farris Y, Shaw JB, Koppenaal DW, Pasa-Tolic L, Jansson JK. Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry. Metallomics 2019; 11:166-175. [DOI: 10.1039/c8mt00252e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calcareous soil microbes complete for scarce iron by synthesizing diverse suites of siderophores detectable by ultra-high resolution mass spectrometry.
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Affiliation(s)
- Rene M. Boiteau
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
- College of Earth, Ocean, Atmospheric Sciences
| | - Sarah J. Fansler
- Biological Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Yuliya Farris
- College of Earth, Ocean, Atmospheric Sciences
- Oregon State University
- Corvallis
- USA
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - David W. Koppenaal
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Janet K. Jansson
- Biological Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
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Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
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Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
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36
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Bailey DC, Bohac TJ, Shapiro JA, Giblin DE, Wencewicz TA, Gulick AM. Crystal Structure of the Siderophore Binding Protein BauB Bound to an Unusual 2:1 Complex Between Acinetobactin and Ferric Iron. Biochemistry 2018; 57:6653-6661. [PMID: 30406986 DOI: 10.1021/acs.biochem.8b00986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The critical role that iron plays in many biochemical processes has led to an elaborate battle between bacterial pathogens and their hosts to acquire and withhold this critical nutrient. Exploitation of iron nutritional immunity is being increasingly appreciated as a potential antivirulence therapeutic strategy, especially against problematic multidrug resistant Gram-negative pathogens such as Acinetobacter baumannii. To facilitate iron uptake and promote growth, A. baumannii produces a nonribosomally synthesized peptide siderophore called acinetobactin. Acinetobactin is unusual in that it is first biosynthesized in an oxazoline form called preacinetobactin that spontaneously isomerizes to the final isoxazolidinone acinetobactin. Interestingly, both isomers can bind iron and both support growth of A. baumannii. To address how the two isomers chelate their ferric cargo and how the complexes are used by A. baumannii, structural studies were carried out with the ferric acinetobactin complex and its periplasmic siderophore binding protein BauB. Herein, we present the crystal structure of BauB bound to a bis-tridentate (Fe3+L2) siderophore complex. Additionally, we present binding studies that show multiple variants of acinetobactin bind BauB with no apparent change in affinity. These results are consistent with the structural model that depicts few direct polar interactions between BauB and the acinetobactin backbone. This structural and functional characterization of acinetobactin and its requisite binding protein BauB provides insight that could be exploited to target this critical iron acquisition system and provide a novel approach to treat infections caused by this important multidrug resistant pathogen.
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Affiliation(s)
- Daniel C Bailey
- Department of Structural Biology , Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo , 955 Main Street , Buffalo , New York 14203 , United States
| | - Tabbetha J Bohac
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Justin A Shapiro
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Daryl E Giblin
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Timothy A Wencewicz
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Andrew M Gulick
- Department of Structural Biology , Jacobs School of Medicine & Biomedical Sciences at the University at Buffalo , 955 Main Street , Buffalo , New York 14203 , United States
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Rütschlin S, Böttcher T. Dissecting the Mechanism of Oligomerization and Macrocyclization Reactions of NRPS-Independent Siderophore Synthetases. Chemistry 2018; 24:16044-16051. [DOI: 10.1002/chem.201803494] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/03/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sina Rütschlin
- Konstanz Research School Chemical Biology, Zukunftskolleg; Chemistry Department; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Thomas Böttcher
- Konstanz Research School Chemical Biology, Zukunftskolleg; Chemistry Department; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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Telfer TJ, Codd R. Fluorinated Analogues of Desferrioxamine B from Precursor-Directed Biosynthesis Provide New Insight into the Capacity of DesBCD. ACS Chem Biol 2018; 13:2456-2471. [PMID: 30081629 DOI: 10.1021/acschembio.8b00340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The siderophore desferrioxamine B (DFOB, 1) native to Streptomyces pilosus is biosynthesized by the DesABCD enzyme cluster. DesA-mediated decarboxylation of l-lysine gives 1,5-diaminopentane (DP) for processing by DesBCD. S. pilosus culture medium was supplemented with rac-1,4-diamino-2-fluorobutane ( rac-FDB) to compete against DP to generate fluorinated analogues of DFOB, as agents of potential clinical interest. LC-MS/MS analysis identified fluorinated analogues of DFOB with one, two, or three DP units (binary notation: 0) exchanged for one (DFOA-F1[001] (2), DFOA-F1[010] (3), DFOA-F1[100] (4)), two (DFOA-F2[011] (5), DFOA-F2[110] (6), DFOA-F2[101] (7)), or three (DFOA-F3[111] (8)) rac-FDB units (binary notation: 1). The two sets of constitutional isomers 2-4 and 5-7 arose from the position of the substrates in the N-acetyl, internal, or amine-containing regions of the DFOB trimer. N-Acetylated fluorinated DFOB analogues were formed where the rac-FDB substrate was positioned in the amine region ( e.g., N-Ac-DFOA-F1[001] (2a)). Other analogues contained two hydroxamic acid groups and three amide bonds. Experiments using rac-FDB, R-FDB, or S-FDB showed a similar species profile between rac-FDB and R-FDB. These data are consistent with the following. (i) DesB can act on rac-FDB. (ii) DesC can act directly on rac-FDB. (iii) The products of DesBC or DesC catalysis of rac-FDB can undergo a second round of DesC catalysis at the free amine. (iv) DesD catalysis of these products gives N, N'-diacetylated compounds. (v) A minimum of two hydroxamic acid groups is required to form a viable DesD-substrate(s) precomplex. (vi) One or more DesBCD-catalyzed steps in DFOB biosynthesis is enantioselective. This work has provided a potential path to access fluorinated analogues of DFOB and new insight into its biosynthesis.
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Affiliation(s)
- Thomas J. Telfer
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
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Bailey DC, Buckley BP, Chernov MV, Gulick AM. Development of a High-Throughput Biochemical Assay to Screen for Inhibitors of Aerobactin Synthetase IucA. SLAS DISCOVERY 2018; 23:1070-1082. [PMID: 29991301 DOI: 10.1177/2472555218787140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Acquiring sufficient quantities of iron to support survival is often a critical limitation for pathogenic bacteria. To meet this demand, bacteria have evolved unique strategies to scavenge iron and circumvent the nutritional immunity exerted by their hosts. One common strategy, which is often a key virulence factor for bacterial pathogens, involves the synthesis, secretion, and reuptake of iron chelators known as siderophores. In vitro and in vivo studies have demonstrated that the siderophore aerobactin is critical for virulence in the hypervirulent pathotype of Klebsiella pneumoniae (hvKP). Given the high rate of multidrug resistance in K. pneumoniae, and in light of the ever-increasing demand for novel Gram-negative therapeutic targets, we identified aerobactin production as a promising antivirulence target in hvKP. Herein, we describe the development of a high-throughput biochemical assay for identifying inhibitors of the aerobactin synthetase IucA. The assay was employed to screen ~110,000 compounds across several commercially available small-molecule libraries. IucA inhibitors with activity at micromolar concentrations were identified in our screening campaigns and confirmed using secondary orthogonal assays. However, the most potent compounds also exhibited some properties commonly observed with promiscuous/nonspecific inhibitors, including incubation time and target enzyme concentration dependence, as well as the potential to antagonize unrelated enzymes.
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Affiliation(s)
- Daniel C Bailey
- 1 Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,2 The Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - Brian P Buckley
- 3 Small Molecule Screening Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mikhail V Chernov
- 3 Small Molecule Screening Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andrew M Gulick
- 1 Department of Structural Biology, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,2 The Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
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Codd R, Soe CZ, Pakchung AAH, Sresutharsan A, Brown CJM, Tieu W. The chemical biology and coordination chemistry of putrebactin, avaroferrin, bisucaberin, and alcaligin. J Biol Inorg Chem 2018; 23:969-982. [PMID: 29946977 DOI: 10.1007/s00775-018-1585-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Dihydroxamic acid macrocyclic siderophores comprise four members: putrebactin (putH2), avaroferrin (avaH2), bisucaberin (bisH2), and alcaligin (alcH2). This mini-review collates studies of the chemical biology and coordination chemistry of these macrocycles, with an emphasis on putH2. These Fe(III)-binding macrocycles are produced by selected bacteria to acquire insoluble Fe(III) from the local environment. The macrocycles are optimally pre-configured for Fe(III) binding, as established from the X-ray crystal structure of dinuclear [Fe2(alc)3] at neutral pH. The dimeric macrocycles are biosynthetic products of two endo-hydroxamic acid ligands flanked by one amine group and one carboxylic acid group, which are assembled from 1,4-diaminobutane and/or 1,5-diaminopentane as initial substrates. The biosynthesis of alcH2 includes an additional diamine C-hydroxylation step. Knowledge of putH2 biosynthesis supported the use of precursor-directed biosynthesis to generate unsaturated putH2 analogues by culturing Shewanella putrefaciens in medium supplemented with unsaturated diamine substrates. The X-ray crystal structures of putH2, avaH2 and alcH2 show differences in the relative orientations of the amide and hydroxamic acid functional groups that could prescribe differences in solvation and other biological properties. Functional differences have been borne out in biological studies. Although evolved for Fe(III) acquisition, solution coordination complexes have been characterised between putH2 and oxido-V(IV/V), Mo(VI), or Cr(V). Retrosynthetic analysis of 1:1 complexes of [Fe(put)]+, [Fe(ava)]+, and [Fe(bis)]+ that dominate at pH < 5 led to a forward metal-templated synthesis approach to generate the Fe(III)-loaded macrocycles, with apo-macrocycles furnished upon incubation with EDTA. This mini-review aims to capture the rich chemistry and chemical biology of these seemingly simple compounds.
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Affiliation(s)
- Rachel Codd
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Cho Zin Soe
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Amalie A H Pakchung
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Athavan Sresutharsan
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Christopher J M Brown
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology) and Bosch Institute, The University of Sydney, Sydney, NSW, 2006, Australia
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Carroll CS, Moore MM. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Crit Rev Biochem Mol Biol 2018; 53:356-381. [DOI: 10.1080/10409238.2018.1476449] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
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Rütschlin S, Gunesch S, Böttcher T. One Enzyme To Build Them All: Ring-Size Engineered Siderophores Inhibit the Swarming Motility of Vibrio. ACS Chem Biol 2018; 13:1153-1158. [PMID: 29653054 DOI: 10.1021/acschembio.8b00084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria compete for ferric iron by producing siderophores, and some microbes engage in piracy by scavenging siderophores of their competitors. The macrocyclic hydroxamate siderophore avaroferrin of Shewanella algae inhibits swarming of Vibrio alginolyticus by evading this piracy. Avaroferrin, as well as related putrebactin and bisucaberin, are produced by the IucC-like synthetases AvbD, PubC, and BibCC. Here, we have established that they are capable of synthesizing not only their native product but also other siderophores. Exploiting this relaxed substrate specificity by synthetic precursors generated 15 different ring-size engineered macrocycles ranging from 18- to 28-membered rings, indicating unprecedented biosynthetic flexibility of the enzymes. Two of the novel siderophores could be obtained in larger quantities by precursor-directed biosynthesis in S. algae. Both inhibited swarming motility of Vibrio and, similar to avaroferrin, the most active one exhibited a heterodimeric architecture. Our results demonstrate the impact of minor structural changes on biological activity, which may trigger the evolution of siderophore diversity.
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Affiliation(s)
- Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Sandra Gunesch
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
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Bailey DC, Alexander E, Rice MR, Drake EJ, Mydy LS, Aldrich CC, Gulick AM. Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae. J Biol Chem 2018; 293:7841-7852. [PMID: 29618511 DOI: 10.1074/jbc.ra118.002798] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/30/2018] [Indexed: 12/17/2022] Open
Abstract
Aerobactin, a citryl-hydroxamate siderophore, is produced by a number of pathogenic Gram-negative bacteria to aid in iron assimilation. Interest in this well-known siderophore was reignited by recent investigations suggesting that it plays a key role in mediating the enhanced virulence of a hypervirulent pathotype of Klebsiella pneumoniae (hvKP). In contrast to classical opportunistic strains of K. pneumoniae, hvKP causes serious life-threatening infections in previously healthy individuals in the community. Multiple contemporary reports have confirmed fears that the convergence of multidrug-resistant and hvKP pathotypes has led to the evolution of a highly transmissible, drug-resistant, and virulent "super bug." Despite hvKP harboring four distinct siderophore operons, knocking out production of only aerobactin led to a significant attenuation of virulence. Herein, we continue our structural and functional studies on the biosynthesis of this crucial virulence factor. In vivo heterologous production and in vitro reconstitution of aerobactin biosynthesis from hvKP was carried out, demonstrating the specificity, stereoselectivity, and kinetic throughput of the complete pathway. Additionally, we present a steady-state kinetic analysis and the X-ray crystal structure of the second aerobactin synthetase IucC, as well as describe a surface entropy reduction strategy that was employed for structure determination. Finally, we show solution X-ray scattering data that support a unique dimeric quaternary structure for IucC. These new insights into aerobactin assembly will help inform potential antivirulence strategies and advance our understanding of siderophore biosynthesis.
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Affiliation(s)
- Daniel C Bailey
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Evan Alexander
- the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Matthew R Rice
- the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Eric J Drake
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Lisa S Mydy
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203.,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
| | - Courtney C Aldrich
- the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Andrew M Gulick
- From the Department of Structural Biology, The Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, New York 14203, .,the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, and
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Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study. Curr Opin Struct Biol 2018; 53:1-11. [PMID: 29455106 DOI: 10.1016/j.sbi.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 01/03/2023]
Abstract
Microbes synthesize small, iron-chelating molecules known as siderophores to acquire iron from the environment. One way siderophores are generated is by nonribosomal peptide synthetases (NRPSs). The bioactive peptides generated by NRPS enzymes have unique chemical features, which are incorporated by accessory and tailoring domains or proteins. The first part of this review summarizes recent progress in NRPS structural biology. The second part uses the biosynthesis of pyochelin, a siderophore from Pseudomonas aeruginosa, as a case study to examine enzymatic methods for generating the observed diversity in NRPS-derived natural products.
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Codd R, Richardson-Sanchez T, Telfer TJ, Gotsbacher MP. Advances in the Chemical Biology of Desferrioxamine B. ACS Chem Biol 2018; 13:11-25. [PMID: 29182270 DOI: 10.1021/acschembio.7b00851] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Desferrioxamine B (DFOB) was discovered in the late 1950s as a hydroxamic acid metabolite of the soil bacterium Streptomyces pilosus. The exquisite affinity of DFOB for Fe(III) identified its potential for removing excess iron from patients with transfusion-dependent hemoglobin disorders. Many studies have used semisynthetic chemistry to produce DFOB adducts with new properties and broad-ranging functions. More recent approaches in chemical biology have revealed some nuances of DFOB biosynthesis and discovered new DFOB-derived drugs and radiometal imaging agents. The current and potential applications of DFOB continue to inspire a rich body of chemical biology research focused on this bacterial metabolite.
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Affiliation(s)
- Rachel Codd
- School of Medical Sciences
(Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tomas Richardson-Sanchez
- School of Medical Sciences
(Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas J. Telfer
- School of Medical Sciences
(Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Michael P. Gotsbacher
- School of Medical Sciences
(Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
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46
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Szamosvári D, Rütschlin S, Böttcher T. From pirates and killers: does metabolite diversity drive bacterial competition? Org Biomol Chem 2018. [DOI: 10.1039/c8ob00150b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article discusses interspecies competition by sets of closely related metabolites with significantly different biological activities.
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Affiliation(s)
- Dávid Szamosvári
- Department of Chemistry
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
| | - Sina Rütschlin
- Department of Chemistry
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
| | - Thomas Böttcher
- Department of Chemistry
- Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
- Germany
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Carroll CS, Grieve CL, Murugathasan I, Bennet AJ, Czekster CM, Liu H, Naismith J, Moore MM. The rhizoferrin biosynthetic gene in the fungal pathogen Rhizopus delemar is a novel member of the NIS gene family. Int J Biochem Cell Biol 2017; 89:136-146. [DOI: 10.1016/j.biocel.2017.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/30/2017] [Accepted: 06/03/2017] [Indexed: 11/29/2022]
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48
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Hirschmann M, Grundmann F, Bode HB. Identification and occurrence of the hydroxamate siderophores aerobactin, putrebactin, avaroferrin and ochrobactin C as virulence factors from entomopathogenic bacteria. Environ Microbiol 2017; 19:4080-4090. [DOI: 10.1111/1462-2920.13845] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/10/2017] [Accepted: 06/21/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Merle Hirschmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Florian Grundmann
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie; Goethe-Universität Frankfurt; Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS); Goethe-Universität Frankfurt; Frankfurt am Main Germany
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Kudo K, Ozaki T, Shin-ya K, Nishiyama M, Kuzuyama T. Biosynthetic Origin of the Hydroxamic Acid Moiety of Trichostatin A: Identification of Unprecedented Enzymatic Machinery Involved in Hydroxylamine Transfer. J Am Chem Soc 2017; 139:6799-6802. [DOI: 10.1021/jacs.7b02071] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kei Kudo
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taro Ozaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Rütschlin S, Gunesch S, Böttcher T. One Enzyme, Three Metabolites: Shewanella algae Controls Siderophore Production via the Cellular Substrate Pool. Cell Chem Biol 2017; 24:598-604.e10. [PMID: 28434877 DOI: 10.1016/j.chembiol.2017.03.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 01/25/2017] [Accepted: 03/24/2017] [Indexed: 11/16/2022]
Abstract
Shewanella algae B516 produces avaroferrin, an asymmetric hydroxamate siderophore, which has been shown to inhibit swarming motility of Vibrio alginolyticus. We aimed to elucidate the biosynthesis of this siderophore and to investigate how S. algae coordinates the production of avaroferrin and its two symmetric counterparts. We reconstituted the reaction in vitro with the main enzyme AvbD and the putative biosynthetic precursors, and demonstrate that multispecificity of this enzyme results in the production of all three cyclic hydroxamate siderophores that were previously isolated as natural products from S. algae. Surprisingly, purified AvbD exhibited a clear preference for the larger cadaverine-derived substrate. In live cells, however, siderophore ratios are maximized toward avaroferrin production, and we demonstrate that these siderophore ratios are the result of a regulation on substrate pool level, which may allow rapid evolutionary adaptation to environmental changes. Our results thereby give insights into a unique evolutionary strategy toward metabolite diversity.
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Affiliation(s)
- Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sandra Gunesch
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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