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Dell’Anno F, Vitale GA, Buonocore C, Vitale L, Palma Esposito F, Coppola D, Della Sala G, Tedesco P, de Pascale D. Novel Insights on Pyoverdine: From Biosynthesis to Biotechnological Application. Int J Mol Sci 2022; 23:ijms231911507. [PMID: 36232800 PMCID: PMC9569983 DOI: 10.3390/ijms231911507] [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: 09/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Pyoverdines (PVDs) are a class of siderophores produced mostly by members of the genus Pseudomonas. Their primary function is to accumulate, mobilize, and transport iron necessary for cell metabolism. Moreover, PVDs also play a crucial role in microbes’ survival by mediating biofilm formation and virulence. In this review, we reorganize the information produced in recent years regarding PVDs biosynthesis and pathogenic mechanisms, since PVDs are extremely valuable compounds. Additionally, we summarize the therapeutic applications deriving from the PVDs’ use and focus on their role as therapeutic target themselves. We assess the current biotechnological applications of different sectors and evaluate the state-of-the-art technology relating to the use of synthetic biology tools for pathway engineering. Finally, we review the most recent methods and techniques capable of identifying such molecules in complex matrices for drug-discovery purposes.
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Brown CJM, Codd R. Directing macrocyclic architecture using iron(III)-, gallium(III)-, or zirconium(IV)-assisted ring closure of linear dimeric endo-hydroxamic acid ligands. J Inorg Biochem 2020; 216:111337. [PMID: 33360106 DOI: 10.1016/j.jinorgbio.2020.111337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/11/2020] [Accepted: 12/04/2020] [Indexed: 11/17/2022]
Abstract
Dimeric hydroxamic acid macrocycles are a subclass of bacterial siderophores produced for iron acquisition. Limited yields from natural sources provides the impetus to develop synthetic routes to improve access to these compounds, which have potential utility in metal ion binding applications in the environment and medicine. This work has examined the role of metal ions in forming pre-complexes with linear endo-hydroxamic acid (endo-HXA) ligands bearing terminal amine and carboxylic acid groups optimally configured for in situ ring closure reactions. The 1:1 reaction between Fe(III) and the dimeric endo-HXA ligand 5-((5-(5-((5-aminopentyl)(hydroxy)amino)-5-oxopentanamido)pentyl)(hydroxy)amino)-5-oxopentanoic acid (PPH-PPH) (1) formed the pre-complex (PC) [Fe(PP-PP)-PC]+ with in situ amide coupling generating the macrocycle (MC) [Fe(PP)2-MC]+ and, following Fe(III) removal, the apo-macrocycle 1,13-dihydroxy-1,7,13,19-tetraazacyclotetracosane-2,6,14,18-tetraone (PPH)2-MC (2). The 1:2 reaction system between Fe(III) and the monomeric endo-HXA ligand 5-((5-aminopentyl)(hydroxy)amino)-5-oxopentanoic acid (PPH) gave significantly less [Fe(PP)2-MC]+ than the former system, due to the requirement to form two rather than one amide bond(s). The 1:1 Ga(III):1 system yielded [Ga(PP-PP)-PC]+ and [Ga(PP)2-MC]+. Neither [Zr(PP-PP)-PC]2+ nor [Zr(PP)2-MC]2+ was detected in the 1:1 Zr(IV):1 system. Instead, the Zr(IV) system showed the formation of a 1:2 Zr(IV):1 pre-complex [Zr(PP-PP)2-PC], which following in situ amide bond forming chemistry, generated two Zr(IV) macrocyclic complexes with distinct architectures: a dimer-of-dimers complex [Zr((PP)2)2-MC] and an end-to-end macrocycle [Zr(PP)4-MC]. The formation of [Fe(PP)2-MC]+, [Ga(PP)2-MC]+ or [Zr((PP)2)2-MC] was confirmed from reconstitution experiments with 2. The work has shown that the choice of metal ion in metal-assisted ring closure reactions directs the assembly of macrocyclic complexes with distinct architectures.
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Affiliation(s)
- Christopher J M Brown
- The University of Sydney, School of Medical Sciences (Pharmacology), New South Wales 2006, Australia
| | - Rachel Codd
- The University of Sydney, School of Medical Sciences (Pharmacology), New South Wales 2006, Australia.
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3
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Detection and Characterization of Antibacterial Siderophores Secreted by Endophytic Fungi from Cymbidium aloifolium. Biomolecules 2020; 10:biom10101412. [PMID: 33036284 PMCID: PMC7600725 DOI: 10.3390/biom10101412] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 11/28/2022] Open
Abstract
Endophytic fungi from orchid plants are reported to secrete secondary metabolites which include bioactive antimicrobial siderophores. In this study endophytic fungi capable of secreting siderophores were isolated from Cymbidium aloifolium, a medicinal orchid plant. The isolated extracellular siderophores from orchidaceous fungi act as chelating agents forming soluble complexes with Fe3+. The 60% endophytic fungi of Cymbidium aloifolium produced hydroxamate siderophore on CAS agar. The highest siderophore percentage was 57% in Penicillium chrysogenum (CAL1), 49% in Aspergillus sydowii (CAR12), 46% in Aspergillus terreus (CAR14) by CAS liquid assay. The optimum culture parameters for siderophore production were 30 °C, pH 6.5, maltose and ammonium nitrate and the highest resulting siderophore content was 73% in P. chrysogenum. The total protein content of solvent-purified siderophore increased four-fold compared with crude filtrate. The percent Fe3+ scavenged was detected by atomic absorption spectra analysis and the highest scavenging value was 83% by P. chrysogenum. Thin layer chromatography of purified P. chrysogenum siderophore showed a wine-colored spot with Rf value of 0.54. HPLC peaks with Rts of 10.5 and 12.5 min were obtained for iron-free and iron-bound P. chrysogenum siderophore, respectively. The iron-free P. chrysogenum siderophore revealed an exact mass-to-charge ratio (m/z) of 400.46 and iron-bound P. chrysogenum siderophore revealed a m/z of 453.35. The solvent-extracted siderophores inhibited the virulent plant pathogens Ralstonia solanacearum, that causes bacterial wilt in groundnut and Xanthomonas oryzae pv. oryzae which causes bacterial blight disease in rice. Thus, bioactive siderophore-producing endophytic P. chrysogenum can be exploited in the form of formulations for development of resistance against other phytopathogens in crop plants.
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Atencio LA, Boya P. CA, Martin H. C, Mejía LC, Dorrestein PC, Gutiérrez M. Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama. Mar Drugs 2020; 18:md18090456. [PMID: 32899199 PMCID: PMC7551054 DOI: 10.3390/md18090456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 01/20/2023] Open
Abstract
The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D' (11-12).
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Affiliation(s)
- Librada A. Atencio
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Cristopher A. Boya P.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Christian Martin H.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Smithsonian Tropical Research Institute, Balboa Ancón, Panama City 0843-03092, Panama
- Correspondence: (L.C.M.); (M.G.); Tel.: +507-517-0700 (L.C.M. & M.G.); Fax: +507-517-0701 (L.C.M. & M.G.)
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA;
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Correspondence: (L.C.M.); (M.G.); Tel.: +507-517-0700 (L.C.M. & M.G.); Fax: +507-517-0701 (L.C.M. & M.G.)
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Ganley JG, Pandey A, Sylvester K, Lu KY, Toro-Moreno M, Rütschlin S, Bradford JM, Champion CJ, Böttcher T, Xu J, Derbyshire ER. A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity. Cell Chem Biol 2020; 27:817-826.e5. [PMID: 32619453 DOI: 10.1016/j.chembiol.2020.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/18/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Advances in infectious disease control strategies through genetic manipulation of insect microbiomes have heightened interest in microbially produced small molecules within mosquitoes. Herein, 33 mosquito-associated bacterial genomes were mined and over 700 putative biosynthetic gene clusters (BGCs) were identified, 135 of which belong to known classes of BGCs. After an in-depth analysis of the 135 BGCs, iron-binding siderophores were chosen for further investigation due to their high abundance and well-characterized bioactivities. Through various metabolomic strategies, eight siderophore scaffolds were identified in six strains of mosquito-associated bacteria. Among these, serratiochelin A and pyochelin were found to reduce female Anopheles gambiae overall fecundity likely by lowering their blood-feeding rate. Serratiochelin A and pyochelin were further found to inhibit the Plasmodium parasite asexual blood and liver stages in vitro. Our work supplies a bioinformatic resource for future mosquito-microbiome studies and highlights an understudied source of bioactive small molecules.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Ashmita Pandey
- Department of Biology, Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Kayla Sylvester
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Sina Rütschlin
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | | | - Cody J Champion
- Department of Biology, Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Jiannong Xu
- Department of Biology, Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, Durham, NC, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
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6
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Oyewole OA, Mitchell J, Thresh S, Zinkevich V. The purification and functional study of new compounds produced by Escherichia coli that influence the growth of sulfate reducing bacteria. ACTA ACUST UNITED AC 2020. [DOI: 10.1080/2314808x.2020.1752033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Julian Mitchell
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Sarah Thresh
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Vitaly Zinkevich
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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7
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Chemistry and Biology of Siderophores from Marine Microbes. Mar Drugs 2019; 17:md17100562. [PMID: 31569555 PMCID: PMC6836290 DOI: 10.3390/md17100562] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/22/2019] [Accepted: 09/29/2019] [Indexed: 12/30/2022] Open
Abstract
Microbial siderophores are multidentate Fe(III) chelators used by microbes during siderophore-mediated assimilation. They possess high affinity and selectivity for Fe(III). Among them, marine siderophore-mediated microbial iron uptake allows marine microbes to proliferate and survive in the iron-deficient marine environments. Due to their unique iron(III)-chelating properties, delivery system, structural diversity, and therapeutic potential, marine microbial siderophores have great potential for further development of various drug conjugates for antibiotic-resistant bacteria therapy or as a target for inhibiting siderophore virulence factors to develop novel broad-spectrum antibiotics. This review covers siderophores derived from marine microbes.
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Nocardamin glucuronide, a new member of the ferrioxamine siderophores isolated from the ascamycin-producing strain Streptomyces sp. 80H647. J Antibiot (Tokyo) 2019; 72:991-995. [DOI: 10.1038/s41429-019-0217-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/04/2019] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
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9
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Brown CJM, Gotsbacher MP, Holland JP, Codd R. endo-Hydroxamic Acid Monomers for the Assembly of a Suite of Non-native Dimeric Macrocyclic Siderophores Using Metal-Templated Synthesis. Inorg Chem 2019; 58:13591-13603. [DOI: 10.1021/acs.inorgchem.9b00878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Christopher J. M. Brown
- School of Medical Sciences (Pharmacology), The University of Sydney, 2006 Sydney, New South Wales, Australia
| | - Michael P. Gotsbacher
- School of Medical Sciences (Pharmacology), The University of Sydney, 2006 Sydney, New South Wales, Australia
| | - Jason P. Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, 2006 Sydney, New South Wales, Australia
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10
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Zhao W, Peng F, Wang CX, Xie Y, Lin R, Fang ZK, Sun F, Lian YY, Jiang H. FW0622, a new siderophore isolated from marine Verrucosispora sp. by genomic mining. Nat Prod Res 2019; 34:3082-3088. [DOI: 10.1080/14786419.2019.1608541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Wei Zhao
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Fei Peng
- College of Pharmacy, Quanzhou Medical College, Quanzhou, P.R. China
| | - Chuan-xi Wang
- College of Pharmacy, Jinan University, Guangzhou, P.R. China
| | - Yang Xie
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Ru Lin
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Zhi-kai Fang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Fei Sun
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Yun-yang Lian
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
| | - Hong Jiang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, P.R. China
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11
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Cloning of the Bisucaberin B Biosynthetic Gene Cluster from the Marine Bacterium Tenacibaculum mesophilum, and Heterologous Production of Bisucaberin B. Mar Drugs 2018; 16:md16090342. [PMID: 30235820 PMCID: PMC6164419 DOI: 10.3390/md16090342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 11/17/2022] Open
Abstract
The biosynthetic gene cluster for bisucaberin B (1, bsb gene cluster), an N-hydroxy-N-succinyl diamine (HSD)-based siderophore, was cloned from the marine bacterium Tenacibaculum mesophilum, originated from a marine sponge. The bsb gene cluster consists of six open reading frames (ORFs), in contrast to the four ORFs typically seen in biosynthetic gene clusters of the related molecules. Heterologous expression of the key enzyme, BsbD2, which is responsible for the final biosynthetic step of 1 resulted in production of bisucaberin B (1), but not bisucaberin (2) a macrocyclic counterpart of 1. To date, numbers of related enzymes producing macrocyclic analogues have been reported, but this work represents the first example of the HSD-based siderophore biosynthetic enzyme which exclusively produces a linear molecule rather than macrocyclic counterparts.
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12
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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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13
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Dimeric and trimeric homo- and heteroleptic hydroxamic acid macrocycles formed using mixed-ligand Fe(III)-based metal-templated synthesis. J Inorg Biochem 2017; 177:344-351. [DOI: 10.1016/j.jinorgbio.2017.07.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/08/2017] [Accepted: 07/26/2017] [Indexed: 11/22/2022]
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14
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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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15
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Tieu W, Lifa T, Katsifis A, Codd R. Octadentate Zirconium(IV)-Loaded Macrocycles with Varied Stoichiometry Assembled From Hydroxamic Acid Monomers using Metal-Templated Synthesis. Inorg Chem 2017; 56:3719-3728. [DOI: 10.1021/acs.inorgchem.7b00362] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William Tieu
- School of Medical
Sciences (Pharmacology) and Bosch Institute, The University of Sydney, New
South Wales 2006, Australia
| | - Tulip Lifa
- School of Medical
Sciences (Pharmacology) and Bosch Institute, The University of Sydney, New
South Wales 2006, Australia
| | - Andrew Katsifis
- Department of Molecular Imaging, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
| | - Rachel Codd
- School of Medical
Sciences (Pharmacology) and Bosch Institute, The University of Sydney, New
South Wales 2006, Australia
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16
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Fazary AE, Ju YH, Al-Shihri AS, Alfaifi MY, Alshehri MA. Biodegradable siderophores: survey on their production, chelating and complexing properties. REV INORG CHEM 2016. [DOI: 10.1515/revic-2016-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.
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Abstract
This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Abstract
Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology.
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Heterologous Production of Desferrioxamines with a Fusion Biosynthetic Gene Cluster. Biosci Biotechnol Biochem 2014; 77:2467-72. [DOI: 10.1271/bbb.130597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Soe CZ, Codd R. Unsaturated macrocyclic dihydroxamic acid siderophores produced by Shewanella putrefaciens using precursor-directed biosynthesis. ACS Chem Biol 2014; 9:945-56. [PMID: 24483365 DOI: 10.1021/cb400901j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To acquire iron essential for growth, the bacterium Shewanella putrefaciens produces the macrocyclic dihydroxamic acid putrebactin (pbH2; [M + H(+)](+), m/zcalc 373.2) as its native siderophore. The assembly of pbH2 requires endogenous 1,4-diaminobutane (DB), which is produced from the ornithine decarboxylase (ODC)-catalyzed decarboxylation of l-ornithine. In this work, levels of endogenous DB were attenuated in S. putrefaciens cultures by augmenting the medium with the ODC inhibitor 1,4-diamino-2-butanone (DBO). The presence in the medium of DBO together with alternative exogenous non-native diamine substrates, (15)N2-1,4-diaminobutane ((15)N2-DB) or 1,4-diamino-2(E)-butene (E-DBE), resulted in the respective biosynthesis of (15)N-labeled pbH2 ((15)N4-pbH2; [M + H(+)](+), m/zcalc 377.2, m/zobs 377.2) or the unsaturated pbH2 variant, named here: E,E-putrebactene (E,E-pbeH2; [M + H(+)](+), m/zcalc 369.2, m/zobs 369.2). In the latter system, remaining endogenous DB resulted in the parallel biosynthesis of the monounsaturated DB-E-DBE hybrid, E-putrebactene (E-pbxH2; [M + H(+)](+), m/zcalc 371.2, m/zobs 371.2). These are the first identified unsaturated macrocyclic dihydroxamic acid siderophores. LC-MS measurements showed 1:1 complexes formed between Fe(III) and pbH2 ([Fe(pb)](+); [M](+), m/zcalc 426.1, m/zobs 426.2), (15)N4-pbH2 ([Fe((15)N4-pb)](+); [M](+), m/zcalc 430.1, m/zobs 430.1), E,E-pbeH2 ([Fe(E,E-pbe)](+); [M](+), m/zcalc 422.1, m/zobs 422.0), or E-pbxH2 ([Fe(E-pbx)](+); [M](+), m/zcalc 424.1, m/zobs 424.2). The order of the gain in siderophore-mediated Fe(III) solubility, as defined by the difference in retention time between the free ligand and the Fe(III)-loaded complex, was pbH2 (ΔtR = 8.77 min) > E-pbxH2 (ΔtR = 6.95 min) > E,E-pbeH2 (ΔtR = 6.16 min), which suggests one possible reason why nature has selected for saturated rather than unsaturated siderophores as Fe(III) solubilization agents. The potential to conduct multiple types of ex situ chemical conversions across the double bond(s) of the unsaturated macrocycles provides a new route to increased molecular diversity in this class of siderophore.
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Affiliation(s)
- Cho Z. Soe
- School of Medical Sciences
(Pharmacology) and Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences
(Pharmacology) and Bosch Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
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Böttcher T, Clardy J. A chimeric siderophore halts swarming Vibrio. Angew Chem Int Ed Engl 2014; 53:3510-3. [PMID: 24615751 DOI: 10.1002/anie.201310729] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Indexed: 11/08/2022]
Abstract
Some bacteria swarm under some circumstances; they move rapidly and collectively over a surface. In an effort to understand the molecular signals controlling swarming, we isolated two bacterial strains from the same red seaweed, Vibrio alginolyticus B522, a vigorous swarmer, and Shewanella algae B516, which inhibits V. alginolyticus swarming in its vicinity. Plate assays combined with NMR, MS, and X-ray diffraction analyses identified a small molecule, which was named avaroferrin, as a potent swarming inhibitor. Avaroferrin, a previously unreported cyclic dihydroxamate siderophore, is a chimera of two well-known siderophores: putrebactin and bisucaberin. The sequenced genome of S. algae revealed avaroferrin's biosynthetic gene cluster to be a mashup of putrebactin and bisucaberin biosynthetic genes. Avaroferrin blocks swarming through its ability to bind iron in a form that cannot be pirated by V. alginolyticus, thereby securing this essential resource for its producer.
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Affiliation(s)
- Thomas Böttcher
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115 (USA)
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Böttcher T, Clardy J. Ein chimärer Siderophor stoppt das Schwarmverhalten vonVibrio. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Bioactive heterocyclic natural products from actinomycetes having effects on cancer-related signaling pathways. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2014; 99:147-98. [PMID: 25296439 DOI: 10.1007/978-3-319-04900-7_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ishibashi M, Tamai Y, Toume K, A. Arai M. GRISEOVIRIDIN AND CYCLIC HYDROXAMATES FOUND IN A SCREENING PROGRAM FOR Wnt SIGNAL INHIBITOR. HETEROCYCLES 2012. [DOI: 10.3987/com-12-s(n)64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Fujita MJ, Kimura N, Yokose H, Otsuka M. Heterologous production of bisucaberin using a biosynthetic gene cluster cloned from a deep sea metagenome. MOLECULAR BIOSYSTEMS 2011; 8:482-5. [PMID: 22051782 DOI: 10.1039/c1mb05431g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A siderophore biosynthetic gene cluster was cloned from a metagenomic library generated from deep sea sediment. The gene cluster was successfully expressed in Escherichia coli to produce bisucaberin, a siderophore originally reported from the marine bacterium Alteromonas haloplanktis. The cloned bisucaberin biosynthetic gene cluster was moderately similar to that of the known bisucaberin producer Vibrio salmonicida. However, the cloned gene cluster consists of four genes rather than three genes found in the V. salmonicida cluster. The low overall homology of the amino acid and nucleotide sequences with those of other species suggests that the cloned genes were derived from one of the unsequenced bacteria including uncultured species.
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Affiliation(s)
- Masaki J Fujita
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan.
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Mansson M, Gram L, Larsen TO. Production of bioactive secondary metabolites by marine vibrionaceae. Mar Drugs 2011; 9:1440-1468. [PMID: 22131950 PMCID: PMC3225927 DOI: 10.3390/md9091440] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/11/2011] [Accepted: 08/15/2011] [Indexed: 11/25/2022] Open
Abstract
Bacteria belonging to the Vibrionaceae family are widespread in the marine environment. Today, 128 species of vibrios are known. Several of them are infamous for their pathogenicity or symbiotic relationships. Despite their ability to interact with eukaryotes, the vibrios are greatly underexplored for their ability to produce bioactive secondary metabolites and studies have been limited to only a few species. Most of the compounds isolated from vibrios so far are non-ribosomal peptides or hybrids thereof, with examples of N-containing compounds produced independent of nonribosomal peptide synthetases (NRPS). Though covering a limited chemical space, vibrios produce compounds with attractive biological activities, including antibacterial, anticancer, and antivirulence activities. This review highlights some of the most interesting structures from this group of bacteria. Many compounds found in vibrios have also been isolated from other distantly related bacteria. This cosmopolitan occurrence of metabolites indicates a high incidence of horizontal gene transfer, which raises interesting questions concerning the ecological function of some of these molecules. This account underlines the pending potential for exploring new bacterial sources of bioactive compounds and the challenges related to their investigation.
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Affiliation(s)
- Maria Mansson
- Center from Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Lone Gram
- National Food Institute, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark; E-Mail:
| | - Thomas O. Larsen
- Center from Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark; E-Mail:
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Kalinovskaya NI, Romanenko LA, Irisawa T, Ermakova SP, Kalinovsky AI. Marine isolate Citricoccus sp. KMM 3890 as a source of a cyclic siderophore nocardamine with antitumor activity. Microbiol Res 2011; 166:654-61. [PMID: 21376551 DOI: 10.1016/j.micres.2011.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/19/2011] [Accepted: 01/29/2011] [Indexed: 11/30/2022]
Abstract
A novel actinobacterium, designated KMM 3890 was isolated from a bottom sediment sample collected from the Sakhalin shallow environment. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated strain KMM 3890 affiliation to the genus Citricoccus. In addition to its hemolytic activity, this strain exhibited inhibitory activity against Gram-positive bacteria. It was found that the marine isolate Citricoccus sp. KMM 3890 produced and excreted into the culture medium a large amount of the compound, which was isolated and structurally characterized as known cyclic siderophore nocardamine on the basis of combined spectral analyses. Nocardamine showed inhibitory effects to colony formation of T-47D, SK-Mel-5, SK-Mel-28 and PRMI-7951 tumor cell lines and a weak antimicrobial against Gram-positive bacteria and no revealed cytotoxic activity. This study can be considered as the first report on marine isolate of the genus Citricoccus producing nocardamine with antitumor activity.
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Affiliation(s)
- Nataliya I Kalinovskaya
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok, Russian Federation.
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de Carvalho CCCR, Fernandes P. Production of metabolites as bacterial responses to the marine environment. Mar Drugs 2010; 8:705-27. [PMID: 20411122 PMCID: PMC2857360 DOI: 10.3390/md8030705] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 02/26/2010] [Accepted: 03/16/2010] [Indexed: 12/16/2022] Open
Abstract
Bacteria in marine environments are often under extreme conditions of e.g., pressure, temperature, salinity, and depletion of micronutrients, with survival and proliferation often depending on the ability to produce biologically active compounds. Some marine bacteria produce biosurfactants, which help to transport hydrophobic low water soluble substrates by increasing their bioavailability. However, other functions related to heavy metal binding, quorum sensing and biofilm formation have been described. In the case of metal ions, bacteria developed a strategy involving the release of binding agents to increase their bioavailability. In the particular case of the Fe3+ ion, which is almost insoluble in water, bacteria secrete siderophores that form soluble complexes with the ion, allowing the cells to uptake the iron required for cell functioning. Adaptive changes in the lipid composition of marine bacteria have been observed in response to environmental variations in pressure, temperature and salinity. Some fatty acids, including docosahexaenoic and eicosapentaenoic acids, have only been reported in prokaryotes in deep-sea bacteria. Cell membrane permeability can also be adapted to extreme environmental conditions by the production of hopanoids, which are pentacyclic triterpenoids that have a function similar to cholesterol in eukaryotes. Bacteria can also produce molecules that prevent the attachment, growth and/or survival of challenging organisms in competitive environments. The production of these compounds is particularly important in surface attached strains and in those in biofilms. The wide array of compounds produced by marine bacteria as an adaptive response to demanding conditions makes them suitable candidates for screening of compounds with commercially interesting biological functions. Biosurfactants produced by marine bacteria may be helpful to increase mass transfer in different industrial processes and in the bioremediation of hydrocarbon-contaminated sites. Siderophores are necessary e.g., in the treatment of diseases with metal ion imbalance, while antifouling compounds could be used to treat man-made surfaces that are used in marine environments. New classes of antibiotics could efficiently combat bacteria resistant to the existing antibiotics. The present work aims to provide a comprehensive review of the metabolites produced by marine bacteria in order to cope with intrusive environments, and to illustrate how such metabolites can be advantageously used in several relevant areas, from bioremediation to health and pharmaceutical sectors.
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Affiliation(s)
- Carla C C R de Carvalho
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
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Oves-Costales D, Kadi N, Challis GL. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem Commun (Camb) 2009:6530-41. [PMID: 19865642 DOI: 10.1039/b913092f] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Siderophores are high-affinity ferric iron chelators biosynthesised and excreted by most microorganisms that play an important role in iron acquisition. Siderophore-mediated scavenging of ferric iron from hosts contributes significantly to the virulence of pathogenic microbes. As a consequence siderophore biosynthesis is an attractive target for chemotherapeutic intervention. Two main pathways for siderophore biosynthesis exist in microbes. One pathway involves nonribosomal peptide synthetase (NRPS) multienzymes while the other is NRPS-independent. The enzymology of NRPS-mediated siderophore biosynthesis has been extensively studied for more than a decade. In contrast, the enzymology of NRPS-independent siderophore (NIS) biosynthesis was overlooked for almost thirty years since the first genetic characterisation of the NIS biosynthetic pathway to aerobactin. However, the past three years have witnessed an explosion of interest in the enzymology of NIS synthetases, the key enzymes in the assembly of siderophores via the NIS pathway. The biochemical characterisation of ten purified recombinant synthetases has been reported since 2007, along with the first structural characterisation of a synthetase by X-ray crystallography in 2009. In this feature article we summarise the recent progress that has been made in understanding the long-overlooked enzymology of NRPS-independent siderophore biosynthesis, highlight important remaining questions, and suggest likely directions for future research.
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Abstract
In order to survive extremes of pH, temperature, salinity and pressure, organisms have been found to develop unique defences against their environment, leading to the biosynthesis of novel molecules ranging from simple osmolytes and lipids to complex secondary metabolites. This review highlights novel molecules isolated from microorganisms that either tolerate or favour extreme growth conditions.
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Affiliation(s)
- Zoe E Wilson
- Department of Chemistry, University of Auckland, 23 Symonds St, Auckland, 1010, New Zealand
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31
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Recent advances in siderophore biosynthesis. Curr Opin Chem Biol 2009; 13:205-15. [DOI: 10.1016/j.cbpa.2009.03.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 03/02/2009] [Accepted: 03/08/2009] [Indexed: 11/22/2022]
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Kadi N, Song L, Challis GL. Bisucaberin biosynthesis: an adenylating domain of the BibC multi-enzyme catalyzes cyclodimerization of N-hydroxy-N-succinylcadaverine. Chem Commun (Camb) 2008:5119-21. [PMID: 18956041 DOI: 10.1039/b813029a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bisucaberin biosynthetic gene cluster has been identified in Vibrio salmonicida and a domain from within the BibC multienzyme encoded by the cluster has been shown to catalyse ATP-dependent dimerisation and macrocyclisation of N-hydroxy-N-succinylcadaverine to form bisucaberin.
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Affiliation(s)
- Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, UKCV4 7AL
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Abstract
This review covers the 390 novel marine natural products described to date from deep-water (>50 m) marine fauna, with details on the source organism, its depth and country of origin, along with any reported biological activity of the metabolites. Relevant synthetic studies on the deep-sea natural products have also been included.
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Affiliation(s)
- Danielle Skropeta
- School of Chemistry, University of Wollongong, Wollongong, Australia.
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Kadi N, Oves-Costales D, Barona-Gomez F, Challis GL. A new family of ATP-dependent oligomerization-macrocyclization biocatalysts. Nat Chem Biol 2007; 3:652-6. [PMID: 17704771 DOI: 10.1038/nchembio.2007.23] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 07/06/2007] [Indexed: 11/09/2022]
Abstract
Oligomerization and macrocyclization reactions are key steps in the biosynthesis of many bioactive natural products. Important macrocycles include the antibiotic daptomycin (1; ref. 1), the immunosuppressant FK-506 (2; ref. 2), the anthelmintic avermectin B1a (3; ref. 3) and the insecticide spinosyn A (4; ref. 4); important oligomeric macrocycles include the siderophores enterobactin (5; ref. 5) and desferrioxamine E (6; ref. 6). Biosynthetic oligomerization and macrocyclization reactions typically involve covalently tethered intermediates and are catalyzed by thioesterase domains of polyketide synthase and nonribosomal peptide synthetase multienzymes. Here we report that the purified recombinant desferrioxamine siderophore synthetase DesD from Streptomyces coelicolor M145 catalyzes ATP-dependent trimerization-macrocyclization of a chemically synthesized 10-aminocarboxylic acid substrate via noncovalently bound intermediates. DesD is dissimilar to other known synthetase families but is similar to other enzymes known or proposed to be required for the biosynthesis of omega-aminocarboxylic acid-derived cyclodimeric siderophores. This suggests that DesD is the first biochemically characterized member of a new family of oligomerizing and macrocyclizing synthetases.
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Affiliation(s)
- Nadia Kadi
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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Brickman TJ, Anderson MT, Armstrong SK. Bordetella iron transport and virulence. Biometals 2007; 20:303-22. [PMID: 17295050 DOI: 10.1007/s10534-006-9031-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2006] [Accepted: 07/20/2006] [Indexed: 11/26/2022]
Abstract
Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica are pathogens with a complex iron starvation stress response important for adaptation to nutrient limitation and flux in the mammalian host environment. The iron starvation stress response is globally regulated by the Fur repressor using ferrous iron as the co-repressor. Expression of iron transport system genes of Bordetella is coordinated by priority regulation mechanisms that involve iron source sensing. Iron source sensing is mediated by distinct transcriptional activators that are responsive to the cognate iron source acting as the inducer.
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Affiliation(s)
- Timothy J Brickman
- Department of Microbiology, University of Minnesota Medical School, MMC 196, 420 Delaware Street S.E., Minneapolis, MN 55455-0312, USA
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Yasumoto-Hirose M, Nishijima M, Ngirchechol MK, Kanoh K, Shizuri Y, Miki W. Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:227-37. [PMID: 16763938 DOI: 10.1007/s10126-005-5015-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 09/18/2005] [Indexed: 05/10/2023]
Abstract
Polyurethane foam (PUF) supplemented with various agar media was used in situ to trap marine bacteria and it consequently provided a substrate on which they could be cultivated while exposed to natural seawater in the coral reef area. The bacterial population on the PUF blocks was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments. Changing the composition of the cultivation medium in the PUF blocks and selecting different sampling sites resulted in different bacteria being detected on the PUF blocks. For example, iron-utilizing (IU) bacteria, siderophore-producing (SP) bacteria, and petroleum-degrading (PD) bacteria were isolated from PUF blocks and it was discovered that IU and SP contained iron and PD contained hydrocarbon. This method opens up the possibility for isolating novel and useful marine bacteria.
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Affiliation(s)
- Mina Yasumoto-Hirose
- Marine Biotechnology Institute (MBI), 3-75-1 Heita, Kamaishi-shi, Iwate, 026-0001, Japan
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Martinez JS, Carter-Franklin JN, Mann EL, Martin JD, Haygood MG, Butler A. Structure and membrane affinity of a suite of amphiphilic siderophores produced by a marine bacterium. Proc Natl Acad Sci U S A 2003; 100:3754-9. [PMID: 12651947 PMCID: PMC152994 DOI: 10.1073/pnas.0637444100] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2002] [Indexed: 11/18/2022] Open
Abstract
Iron concentrations in the ocean are low enough to limit the growth of marine microorganisms, which raises questions about the molecular mechanisms these organisms use to acquire iron. Marine bacteria have been shown to produce siderophores to facilitate iron(III) uptake. We describe the structures of a suite of amphiphilic siderophores, named the amphibactins, which are produced by a nearshore isolate, gamma Proteobacterium, Vibrio sp. R-10. Each amphibactin has the same Tris-hydroxamate-containing peptidic headgroup composed of three ornithine residues and one serine residue but differs in the acyl appendage, which ranges from C-14 to C-18 and varies in the degree of saturation and hydroxylation. Although amphiphilic siderophores are relatively rare, cell-associated amphiphilic siderophores are even less common. We find that the amphibactins are cell-associated siderophores. As a result of the variation in the nature of the fatty acid appendage and the cellular location of the amphibactins, the membrane partitioning of these siderophores was investigated. The physiological mixture of amphibactins had a range of membrane affinities (3.8 x 10(3) to 8.3 x 10(2) M(-1)) that are larger overall than other amphiphilic siderophores, likely accounting for their cell association. This cell association is likely an important defense against siderophore diffusion in the oceanic environment. The phylogenetic affiliation of Vibrio sp. R-10 is discussed, as well as the observed predominance of amphiphilic siderophores produced by marine bacteria in contrast to those produced by terrestrial bacteria.
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Affiliation(s)
- Jennifer S Martinez
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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Terrestrial vs marine natural product diversity. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1460-1567(02)80018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Guan LL, Kanoh K, Kamino K. Effect of exogenous siderophores on iron uptake activity of marine bacteria under iron-limited conditions. Appl Environ Microbiol 2001; 67:1710-7. [PMID: 11282625 PMCID: PMC92789 DOI: 10.1128/aem.67.4.1710-1717.2001] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than 60% of species examined from a total of 421 strains of heterotrophic marine bacteria which were isolated from marine sponges and seawater were observed to have no detectable siderophore production even when Fe(III) was present in the culture medium at a concentration of 1.0 pM. The growth of one such non-siderophore-producing strain, alpha proteobacterium V0210, was stimulated under iron-limited conditions with the addition of an isolated exogenous siderophore, N,N'-bis (2,3-dihydroxybenzoyl)-O-serylserine from a Vibrio sp. Growth was also stimulated by the addition of three exogenous siderophore extracts from siderophore-producing bacteria. Radioisotope studies using (59)Fe showed that the iron uptake ability of V0210 increased only with the addition of exogenous siderophores. Biosynthesis of a hydroxamate siderophore by V0210 was shown by paper electrophoresis and chemical assays for the detection of hydroxamates and catechols. An 85-kDa iron-regulated outer membrane protein was induced only under iron-limited conditions in the presence of exogenous siderophores. This is the first report of bacterial iron uptake through an induced siderophore in response to exogenous siderophores. Our results suggest that siderophores are necessary signaling compounds for growth and for iron uptake by some non-siderophore-producing marine bacteria under iron-limited conditions.
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Affiliation(s)
- L L Guan
- Shimizu Laboratories, Marine Biotechnology Institute, 1900 Sodeshi-cho, Shimizu City, Shizuoka 424-0037, Japan.
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Trischman JA, Jensen PR, Fenical W. Guaymasol and Epiguaymasol: Aromatic Triols from a Deep-SeaBacillusIsolate. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/10575639808044960] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bernan VS, Greenstein M, Maiese WM. Marine microorganisms as a source of new natural products. ADVANCES IN APPLIED MICROBIOLOGY 1997; 43:57-90. [PMID: 9097412 DOI: 10.1016/s0065-2164(08)70223-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Over the past decade, marine microorganisms have become recognized as an important and untapped resource for novel bioactive compounds. The oceans cover greater than 70% of the earth's surface and, taking this into account by volume, represent better than 95% of the biosphere. Given this fact, the oceans present themselves as an unexplored area of opportunity for the discovery of pharmacologically active compounds. In this review, data have been presented to illustrate the diversity of microorganisms living in the sea and the plethora of chemical compounds that have been discovered from them. However, it is important to pursue basic research on the marine environment in order to permit the continued isolation of unique microorganisms. There is still limited knowledge of the physiological requirements of most marine microorganisms, and a greater understanding of their conditions for growth will offer new insights into the complex world of marine microbiology. Clearly, a greater investment in the development of marine biotechnology will produce novel compounds that may contribute significantly toward drug development over the next decade.
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Affiliation(s)
- V S Bernan
- Wyeth-Ayerst Research, Natural Products Research, Pearl River, New York 10965, USA
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Brickman TJ, Armstrong SK. The ornithine decarboxylase gene odc is required for alcaligin siderophore biosynthesis in Bordetella spp.: putrescine is a precursor of alcaligin. J Bacteriol 1996; 178:54-60. [PMID: 8550442 PMCID: PMC177620 DOI: 10.1128/jb.178.1.54-60.1996] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Chromosomal insertions defining Bordetella bronchiseptica siderophore phenotypic complementation group III mutants BRM3 and BRM5 were found to reside approximately 200 to 300 bp apart by restriction mapping of cloned genomic regions associated with the insertion markers. DNA hybridization analysis using B. bronchiseptica genomic DNA sequences flanking the cloned BRM3 insertion marker identified homologous Bordetella pertussis UT25 cosmids that complemented the siderophore biosynthesis defect of the group III B. bronchiseptica mutants. Subcloning and complementation analysis localized the complementing activity to a 2.8-kb B. pertussis genomic DNA region. Nucleotide sequencing identified an open reading frame predicted to encode a polypeptide exhibiting strong similarity at the primary amino acid level with several pyridoxal phosphate-dependent amino acid decarboxylases. Alcaligin production was fully restored to group III mutants by supplementation of iron-depleted culture media with putrescine (1,4-diaminobutane), consistent with defects in an ornithine decarboxylase activity required for alcaligin siderophore biosynthesis. Concordantly, the alcaligin biosynthesis defect of BRM3 was functionally complemented by the heterologous Escherichia coli speC gene encoding an ornithine decarboxylase activity. Enzyme assays confirmed that group III B. bronchiseptica siderophore-deficient mutants lack an ornithine decarboxylase activity required for the biosynthesis of alcaligin. Siderophore production by an analogous mutant of B. pertussis constructed by allelic exchange was undetectable. We propose the designation odc for the gene defined by these mutations that abrogate alcaligin siderophore production. Putrescine is an essential precursor of alcaligin in Bordetella spp.
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Affiliation(s)
- T J Brickman
- Department of Microbiology and Immunology, East Carolina University School of Medicine, Greenville, North Carolina 27858-4354, USA
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Imbert M, B�chet M, Blondeau R. Comparison of the main siderophores produced by some species of Streptomyces. Curr Microbiol 1995. [DOI: 10.1007/bf00294289] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Trischman JA, Jensen PR, Fenical W. Halobacillin: A cytotoxic cyclic acylpeptide of the iturin class produced by a marine Bacillus. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)77249-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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The Discovery of Marine Natural Products with Therapeutic Potential. DISCOVERY OF NOVEL NATURAL PRODUCTS WITH THERAPEUTIC POTENTIAL 1994. [PMCID: PMC7150297 DOI: 10.1016/b978-0-7506-9003-4.50011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
This chapter highlights the discovery of marine natural products with therapeutic potential. Deep water collections have been made by dredging and trawling. These are both cost-effective collection methods if the substratum does not cause damage to or snag the gear. There are several disadvantages to these approaches. It is difficult to photograph the organisms in their habitat, and encrusting organisms or organisms that grow in crevices, under ledges, or on steep rock faces cannot be easily collected unless the hard substrate that supports the organism is collected as well; dredging and trawling put all collected samples in close contact with each other and therefore, some organisms may chemically contaminate others because of exudations or secretions of various compounds and the environmental impact of dredging or trawling can be detrimental because the sampling is nonselective and habitats can be damaged or destroyed. A controversial facet of marine-derived microorganisms is their putative role with respect to the origin of bioactive natural products from marine macroorganism–microorganisms associations. Symbiotic microorganisms have been repeatedly suggested as being the direct or indirect sources of bioactive metabolites in marine sponges and other invertebrates, tunicates, and bryozoans.
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Reid RT, Live DH, Faulkner DJ, Butler A. A siderophore from a marine bacterium with an exceptional ferric ion affinity constant. Nature 1993; 366:455-8. [PMID: 8247152 DOI: 10.1038/366455a0] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Virtually all microorganisms require iron for growth. The paucity of iron in surface ocean water (approximately 0.02-1.0 nM (refs 1, 2)) has spurred a lively debate concerning iron limitation of primary productivity, yet little is known about the molecular mechanisms used by marine microorganisms to sequester iron. Terrestrial bacteria use a siderophore-mediated ferric uptake system. A siderophore is a low-molecular-mass compound with a high affinity for ferric ion which is secreted by microorganisms is response to low-iron environments; siderophore biosynthesis is regulated by iron levels, with repression by high iron. Although open-ocean marine microorganisms (such as phytoplankton and bacteria) produce siderophores, the nature of these siderophores has not been investigated. We report here the first structure determination, to our knowledge, of the siderophores from an open-ocean bacterium, alterobactin A and B from Alteromonas luteoviolacea. A. luteoviolacea is found in oligotrophic and coastal waters. Alterobactin A has an exceptionally high affinity constant for ferric ion. We suggest that at least some marine microorganisms may have developed higher-affinity iron chelators as part of an efficient iron-uptake mechanism which is more effective than that of their terrestrial counterparts.
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Affiliation(s)
- R T Reid
- Department of Chemistry, University of California, Santa Barbara 93106-6090
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Feistner GJ, Stahl DC, Gabrik AH. Proferrioxamine siderophores ofErwinia amylovora. A capillary liquid chromatographic/electrospray tandem mass spectrometric study. ACTA ACUST UNITED AC 1993. [DOI: 10.1002/oms.1210280307] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Michael JP, Pattenden G. Marine Metaboliten und die Komplexierung von Metall-Ionen: Tatsachen und Hypothesen. Angew Chem Int Ed Engl 1993. [DOI: 10.1002/ange.19931050104] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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