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Gnann AD, Xia Y, Soule J, Barthélemy C, Mawani JS, Musoke SN, Castellano BM, Brignole EJ, Frueh DP, Dowling DP. High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding. J Biol Chem 2022; 298:102454. [PMID: 36063993 PMCID: PMC9547227 DOI: 10.1016/j.jbc.2022.102454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/01/2023] Open
Abstract
Nonribosomal peptide synthetase heterocyclization (Cy) domains generate biologically important oxazoline/thiazoline groups found in natural products, including pharmaceuticals and virulence factors such as some siderophores. Cy domains catalyze consecutive condensation and cyclodehydration reactions, although the mechanism is unknown. To better understand Cy domain catalysis, here we report the crystal structure of the second Cy domain (Cy2) of yersiniabactin synthetase from the causative agent of the plague, Yersinia pestis. Our high-resolution structure of Cy2 adopts a conformation that enables exploration of interactions with the extended thiazoline-containing cyclodehydration intermediate and the acceptor carrier protein (CP) to which it is tethered. We also report complementary electrostatic interfaces between Cy2 and its donor CP that mediate donor binding. Finally, we explored domain flexibility through normal mode analysis and identified small-molecule fragment-binding sites that may inform future antibiotic design targeting Cy function. Our results suggest how CP binding may influence global Cy conformations, with consequences for active-site remodeling to facilitate the separate condensation and cyclodehydration steps as well as potential inhibitor development.
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Affiliation(s)
- Andrew D. Gnann
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Yuan Xia
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Jess Soule
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Clara Barthélemy
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Jayata S. Mawani
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Sarah Nzikoba Musoke
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Brian M. Castellano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Edward J. Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dominique P. Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel P. Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA,For correspondence: Daniel P. Dowling
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2
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Hai Y, Wei MY, Wang CY, Gu YC, Shao CL. The intriguing chemistry and biology of sulfur-containing natural products from marine microorganisms (1987-2020). MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:488-518. [PMID: 37073258 PMCID: PMC10077240 DOI: 10.1007/s42995-021-00101-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/18/2021] [Indexed: 05/03/2023]
Abstract
Natural products derived from marine microorganisms have received great attention as a potential resource of new compound entities for drug discovery. The unique marine environment brings us a large group of sulfur-containing natural products with abundant biological functionality including antitumor, antibiotic, anti-inflammatory and antiviral activities. We reviewed all the 484 sulfur-containing natural products (non-sulfated) isolated from marine microorganisms, of which 59.9% are thioethers, 29.8% are thiazole/thiazoline-containing compounds and 10.3% are sulfoxides, sulfones, thioesters and many others. A selection of 133 compounds was further discussed on their structure-activity relationships, mechanisms of action, biosynthesis, and druggability. This is the first systematic review on sulfur-containing natural products from marine microorganisms conducted from January 1987, when the first one was reported, to December 2020. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00101-2.
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Affiliation(s)
- Yang Hai
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Mei-Yan Wei
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Yu-Cheng Gu
- Syngenta Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY UK
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
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Diettrich J, Kage H, Nett M. Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1. Beilstein J Org Chem 2019; 15:1298-1303. [PMID: 31293678 PMCID: PMC6604713 DOI: 10.3762/bjoc.15.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
A putative siderophore locus was detected in the genome of the violacein-producing bacterium Massilia sp. NR 4-1 and predicted to direct the biosynthesis of a molecule that is structurally related to the thiazoline-containing siderophore micacocidin. In order to track this compound, we analyzed the metabolic profiles of Massilia cultures grown under different iron concentrations. A compound which was found to be predominantly produced under iron deficiency was subsequently isolated. Its structural characterization by spectroscopic and bioinformatic analyses revealed a previously not known diastereomer of the cytotoxic alkaloid agrochelin. The structure of this natural product, which was named massiliachelin, corresponds to the assembly line encoded by the identified siderophore locus.
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Affiliation(s)
- Jan Diettrich
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Hirokazu Kage
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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(Propargylsulfanyl)-2-aza-1,3,5-trienes as a direct source for novel family of highly functionalized 4,5-dihydro-1,3-thiazoles. Tetrahedron 2017. [DOI: 10.1016/j.tet.2016.12.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Um S, Pyee Y, Kim EH, Lee SK, Shin J, Oh DC. Thalassospiramide G, a new γ-amino-acid-bearing peptide from the marine bacterium Thalassospira sp. Mar Drugs 2013; 11:611-22. [PMID: 23442790 PMCID: PMC3705361 DOI: 10.3390/md11030611] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/29/2013] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
In the chemical investigation of marine unicellular bacteria, a new peptide, thalassospiramide G (1), along with thalassospiramides A and D (2–3), was discovered from a large culture of Thalassospira sp. The structure of thalassospiramide G, bearing γ-amino acids, such as 4-amino-5-hydroxy-penta-2-enoic acid (AHPEA), 4-amino-3,5-dihydroxy-pentanoic acid (ADPA), and unique 2-amino-1-(1H-indol-3-yl)ethanone (AIEN), was determined via extensive spectroscopic analysis. The absolute configuration of thalassospiramide D (3), including 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA), was rigorously determined by 1H–1H coupling constant analysis and chemical derivatization. Thalassospiramides A and D (2–3) inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated mouse macrophage RAW 264.7 cells, with IC50 values of 16.4 and 4.8 μM, respectively.
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Affiliation(s)
- Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Yuna Pyee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Korea; E-Mail:
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, Korea; E-Mails: (S.U.); (Y.P.); (S.K.L.); (J.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-2-880-2491; Fax: +82-2-762-8322
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Brandel J, Humbert N, Elhabiri M, Schalk IJ, Mislin GLA, Albrecht-Gary AM. Pyochelin, a siderophore of Pseudomonas aeruginosa: physicochemical characterization of the iron(III), copper(II) and zinc(II) complexes. Dalton Trans 2012; 41:2820-34. [PMID: 22261733 DOI: 10.1039/c1dt11804h] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen, synthesizing two major siderophores, pyoverdine (Pvd) and pyochelin (Pch), to cover its needs in iron(III). If the high affinity and specificity of Pvd toward iron(III) (pFe = 27.0) was well described in the literature, the physicochemical and coordination properties of Pch toward biologically relevant metals (Fe(III), Cu(II) or Zn(II)) have been only scarcely investigated. We report a thorough physico-chemical investigation of Pch (potentiometry, spectrophotometries, ESI/MS) that highlighted its moderate but significantly higher affinity for Fe(3+) (pFe = 16.0 at p[H] 7.4) than reported previously. We also demonstrated that Pch strongly chelates divalent metals such as Zn(II) (pZn = 11.8 at p[H] 7.4) and Cu(II) (pCu = 14.9 at p[H] 7.4) and forms predominantly 1 : 2 (M(2+)/Pch) complexes. Kinetic studies revealed that the formation of the ferric Pch complexes proceeds through a Eigen-Wilkins dissociative ligand interchange mechanism involving two protonated species of Pch and the Fe(OH)(2+) species of Fe(III). Our physico-chemical parameters supports the previous biochemical studies which proposed that siderophores are not only devoted to iron(III) shuttling but most likely display other specific biological role in the subtle metals homeostasis in microorganisms. This work also represents a step toward deciphering the role of siderophores throughout evolution.
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Affiliation(s)
- Jérémy Brandel
- Laboratoire de Physico-Chimie Bioinorganique, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, ECPM, Strasbourg, France
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Lozano-Vila AM, Cumbrera FL, Luna-Giles F, Ortiz AL, Bernalte-García A. Synthesis, Spectroscopic Study and Crystal Structure Determination by X-ray Powder Diffractometry of [CdCl2(TzTn)] [TzTn=2-(3,4-dichlorophenyl)imino-N-(2-thiazolin-2-yl)tetrahydro-1,3-thiazine]. Z Anorg Allg Chem 2007. [DOI: 10.1002/zaac.200700159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Structural characterization of a thiazoline-pyrazole ligand and its complexes with cobalt(II) and copper(II). Polyhedron 2006. [DOI: 10.1016/j.poly.2005.09.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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The coordination behaviour of two structural isomeric ligands towards cadmium (II): Synthesis, spectroscopic characterization and crystal structures. Polyhedron 2006. [DOI: 10.1016/j.poly.2005.06.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Ligation properties of 2-acetyl-2-thiazoline semicarbazone (ATsc): Isolation, spectroscopic and X-ray study of ATsc and its Cu(II) and Ni(II) complexes. Polyhedron 2005. [DOI: 10.1016/j.poly.2005.06.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Barros-García F, Bernalte-García A, Luna-Giles F, Maldonado-Rogado M, Viñuelas-Zahínos E. Preparation, characterization and X-ray structure determinations of the 2-acetyl-2-thiazoline schiff base of hydrazine (ATH) and its cadmium(II) complex [Cd(NO3)2(ATH)2]. Polyhedron 2005. [DOI: 10.1016/j.poly.2005.03.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Rondon MR, Ballering KS, Thomas MG. Identification and analysis of a siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58. MICROBIOLOGY-SGM 2005; 150:3857-3866. [PMID: 15528670 DOI: 10.1099/mic.0.27319-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using the complete genome sequence from Agrobacterium tumefaciens C58, the authors identified a secondary metabolite gene cluster that encodes the biosynthesis of a metabolite with siderophore activity. Support for this conclusion came from genetic and regulatory analysis of the gene cluster, along with the purification of a metabolite from A. tumefaciens C58 with iron-chelating activity. Genetic analysis of mutant strains disrupted in this gene cluster showed that these strains grew more slowly than the wild-type strain in medium lacking iron. Additionally, the mutant strains failed to produce a chrome-azurol-S-reactive material in liquid or solid medium, and failed to produce the metabolite with iron-chelating characteristics that was identified in the wild-type strain. Addition of this purified metabolite to the growth medium of a mutant strain restored its ability to grow in iron-deficient medium. Furthermore, expression of this gene cluster was induced by growth under iron-limiting conditions, suggesting that expression of this gene cluster occurs when iron is scarce. These data are all consistent with the proposal that the proteins encoded by this gene cluster are involved in the production of a siderophore. Interestingly, these proteins show the highest level of amino acid similarity to proteins from a gene cluster found in the filamentous cyanobacterium Nostoc sp. PCC7120, rather than to known siderophore biosynthetic enzymes. Given these properties, it is proposed that the siderophore produced by A. tumefaciens C58 will have a unique chemical structure. Production of the siderophore was not required for virulence of A. tumefaciens when tested with a standard stem inoculation assay.
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Affiliation(s)
- Michelle R Rondon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katie S Ballering
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael G Thomas
- Room 256 Biochemistry, 420 Henry Mall and Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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