201
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Sigrist R, da Costa BZ, Marsaioli AJ, de Oliveira LG. Nature-inspired enzymatic cascades to build valuable compounds. Biotechnol Adv 2015; 33:394-411. [PMID: 25795056 DOI: 10.1016/j.biotechadv.2015.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/09/2015] [Indexed: 11/30/2022]
Abstract
Biocatalysis currently is focusing on enzymatic and multi-enzymatic cascade processes instead of single steps imbedded into chemical pathways. Alongside this scientific revolution, this review provides an overview on multi-enzymatic cascades that are responsible for the biosynthesis of some terpenes, alkaloids and polyethers, which are important classes of natural products. Herein, we illustrate the development of studies inspired by multi- and chemo-enzymatic approaches to build the core moieties of polyethers, polypeptide alkaloids, piperidines and pyrrolidines promoted by the joint action of oxidoreductases, hydrolases, cyclases, transaminases and imine reductases.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Bruna Zucoloto da Costa
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Anita Jocelyne Marsaioli
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP, Brazil.
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202
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Isolation and structure determination of new siderophore albachelin from Amycolatopsis alba. Biometals 2015; 28:381-9. [PMID: 25749409 DOI: 10.1007/s10534-015-9842-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/23/2015] [Indexed: 10/23/2022]
Abstract
A new siderophore named albachelin was isolated from iron deficient culture of Amycolatopsis alba. The planar structure of albachelin was elucidated by the combination of ESI-MS/MS experiment and NMR spectroscopic analyses of the gallium (III) complex. The structure of albachelin was determined to be a linear peptide consisting of 6 mol of amino acids including 3 mol of serine, one mol each of N-α-acethyl-N-δ-hydroxy-N-δ-formylornithine, N-α-methyl-N-δ-hydroxyornithine, and cyclic N-hydroxyornithine. The stereochemistries of amino acids constituting albachelin were analyzed by applying modified Marfey method to the hydrolysate of albachelin. Based on bioinformatics, we deduced and discussed the possible biosynthetic gene cluster involved in albachelin biosynthesis from the genome sequence of A. alba. By prediction of substrates for adenylation domains, a non-ribosomal peptide biosynthetase gene (AMYAL_RS0130210) was proposed to be the main biosynthetic gene for albachelin biosynthesis. The related genes including transporter for siderophore were found near the NRPS gene as a gene cluster.
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203
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Acyl peptidic siderophores: structures, biosyntheses and post-assembly modifications. Biometals 2015; 28:445-59. [PMID: 25677460 DOI: 10.1007/s10534-015-9827-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/28/2015] [Indexed: 10/24/2022]
Abstract
Acyl peptidic siderophores are produced by a variety of bacteria and possess unique amphiphilic properties. Amphiphilic siderophores are generally produced in a suite where the iron(III)-binding headgroup remains constant while the fatty acid appendage varies by length and functionality. Acyl peptidic siderophores are commonly synthesized by non-ribosomal peptide synthetases; however, the method of peptide acylation during biosynthesis can vary between siderophores. Following biosynthesis, acyl siderophores can be further modified enzymatically to produce a more hydrophilic compound, which retains its ferric chelating abilities as demonstrated by pyoverdine from Pseudomonas aeruginosa and the marinobactins from certain Marinobacter species. Siderophore hydrophobicity can also be altered through photolysis of the ferric complex of certain β-hydroxyaspartic acid-containing acyl peptidic siderophores.
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204
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Badieyan S, Bach RD, Sobrado P. Mechanism of N-Hydroxylation Catalyzed by Flavin-Dependent Monooxygenases. J Org Chem 2015; 80:2139-47. [DOI: 10.1021/jo502651v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Somayesadat Badieyan
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Robert D. Bach
- Departments
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Pablo Sobrado
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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205
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Kem MP, Naka H, Iinishi A, Haygood MG, Butler A. Fatty Acid Hydrolysis of Acyl Marinobactin Siderophores by Marinobacter Acylases. Biochemistry 2015; 54:744-52. [DOI: 10.1021/bi5013673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Michelle P. Kem
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Hiroaki Naka
- Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Akira Iinishi
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Margo G. Haygood
- Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239-3098, United States
| | - Alison Butler
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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206
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Widhalm JR, Dudareva N. A familiar ring to it: biosynthesis of plant benzoic acids. MOLECULAR PLANT 2015; 8:83-97. [PMID: 25578274 DOI: 10.1016/j.molp.2014.12.001] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/19/2014] [Indexed: 05/20/2023]
Abstract
Plant benzoic acids (BAs) are building blocks or important structural elements for numerous primary and specialized metabolites, including plant hormones, cofactors, defense compounds, and attractants for pollinators and seed dispersers. Many natural products derived from plant BAs or containing benzoyl/benzyl moieties are also of medicinal or nutritional value to humans. Biosynthesis of BAs in plants is a network involving parallel and intersecting pathways spread across multiple subcellular compartments. In this review, a current overview on the metabolism of plant BAs is presented with a focus on the recent progress made on isolation and functional characterization of genes encoding biosynthetic enzymes and intracellular transporters. In addition, approaches for deciphering the complex interactions between pathways of the BAs network are discussed.
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Affiliation(s)
- Joshua R Widhalm
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA.
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207
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Abstract
ABSTRACT
Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.
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208
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Hamedi J, Mohammadipanah F. Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria. J Ind Microbiol Biotechnol 2014; 42:157-71. [PMID: 25410828 DOI: 10.1007/s10295-014-1537-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 11/25/2022]
Abstract
Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.
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Affiliation(s)
- Javad Hamedi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran,
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209
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Becerra G, Merchán F, Blasco R, Igeño MI. Characterization of a ferric uptake regulator (Fur)-mutant of the cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT5344. J Biotechnol 2014; 190:2-10. [DOI: 10.1016/j.jbiotec.2014.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/17/2014] [Accepted: 03/25/2014] [Indexed: 11/25/2022]
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210
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Identification of a surface glutamine residue (Q64) of Escherichia coli EntA required for interaction with EntE. Biochem Biophys Res Commun 2014; 453:625-30. [PMID: 25301558 DOI: 10.1016/j.bbrc.2014.09.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 09/30/2014] [Indexed: 11/23/2022]
Abstract
The enterobactin biosynthetic enzyme EntA forms a complex with EntE, the next enzyme in the pathway, to enhance activation of the enterobactin precursor 2,3-dihydroxybenzoate. Here we used phage display to identify an EntE-interacting region on the surface of EntA. Upon panning immobilized EntE with a random peptide phage library, we recovered 47 unique EntE-binding dodecamer peptide sequences that aligned to a region of the EntA primary sequence corresponding to helix α4. In order to further investigate this region, we mutagenized EntA Q64, a hydrogen-bonding residue found on the surface-exposed face α4. Far-UV circular dichroism, thermal denaturation experiments, and enzymatic assays showed that mutation of EntA residue Gln 64 to alanine (Q64A) had no deleterious effect on EntA structure or function. By following near-UV CD spectral changes, we found that the spectrum of wild-type EntA was altered in the presence of EntE, indicative of conformational changes in EntA aromatic chromophores upon formation of the EntA-EntE complex. However, EntE did not affect the CD spectrum of EntA variant Q64A, demonstrating that this variant did not interact with EntE in a manner similar to wild-type EntA. Analytical ultracentrifugation of wild-type and variant EntA proteins showed that EntA Q64A was predominantly dimeric at 20μM, unlike wild-type EntA which was predominantly tetrameric. Taken together, our findings establish that EntA α4 is required for efficient formation of the EntA-EntE as well as for EntA oligomerization.
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211
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Hertlein G, Müller S, Garcia-Gonzalez E, Poppinga L, Süssmuth RD, Genersch E. Production of the catechol type siderophore bacillibactin by the honey bee pathogen Paenibacillus larvae. PLoS One 2014; 9:e108272. [PMID: 25237888 PMCID: PMC4169593 DOI: 10.1371/journal.pone.0108272] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/27/2014] [Indexed: 12/15/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood. This bacterial infection of honey bee brood is a notifiable epizootic posing a serious threat to global honey bee health because not only individual larvae but also entire colonies succumb to the disease. In the recent past considerable progress has been made in elucidating molecular aspects of host pathogen interactions during pathogenesis of P. larvae infections. Especially the sequencing and annotation of the complete genome of P. larvae was a major step forward and revealed the existence of several giant gene clusters coding for non-ribosomal peptide synthetases which might act as putative virulence factors. We here present the detailed analysis of one of these clusters which we demonstrated to be responsible for the biosynthesis of bacillibactin, a P. larvae siderophore. We first established culture conditions allowing the growth of P. larvae under iron-limited conditions and triggering siderophore production by P. larvae. Using a gene disruption strategy we linked siderophore production to the expression of an uninterrupted bacillibactin gene cluster. In silico analysis predicted the structure of a trimeric trithreonyl lactone (DHB-Gly-Thr)3 similar to the structure of bacillibactin produced by several Bacillus species. Mass spectrometric analysis unambiguously confirmed that the siderophore produced by P. larvae is identical to bacillibactin. Exposure bioassays demonstrated that P. larvae bacillibactin is not required for full virulence of P. larvae in laboratory exposure bioassays. This observation is consistent with results obtained for bacillibactin in other pathogenic bacteria.
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Affiliation(s)
- Gillian Hertlein
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Sebastian Müller
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Lena Poppinga
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | | | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
- Freie Universität Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
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212
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Maindad DV, Kasture VM, Chaudhari H, Dhavale DD, Chopade BA, Sachdev DP. Characterization and Fungal Inhibition Activity of Siderophore from Wheat Rhizosphere Associated Acinetobacter calcoaceticus Strain HIRFA32. Indian J Microbiol 2014; 54:315-22. [PMID: 24891739 PMCID: PMC4039728 DOI: 10.1007/s12088-014-0446-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/15/2014] [Indexed: 10/25/2022] Open
Abstract
Acinetobacter calcoaceticus HIRFA32 from wheat rhizosphere produced catecholate type of siderophore with optimum siderophore (ca. 92 % siderophore units) in succinic acid medium without FeSO4 at 28 °C and 24 h of incubation. HPLC purified siderophore appeared as pale yellow crystals with molecular weight [M(+1)] m/z 347.18 estimated by LCMS. The structure elucidated by (1)H NMR, (13)C NMR, HMQC, HMBC, NOESY and decoupling studies, revealed that siderophore composed of 2,3-dihydroxybenzoic acid with hydroxyhistamine and threonine as amino acid subunits. In vitro study demonstrated siderophore mediated mycelium growth inhibition (ca. 46.87 ± 0.5 %) of Fusarium oxysporum. This study accounts to first report on biosynthesis of acinetobactin-like siderophore by the rhizospheric strain of A. calcoaceticus and its significance in inhibition of F. oxysporum.
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Affiliation(s)
- D. V. Maindad
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
| | - V. M. Kasture
- />Department of Chemistry, University of Pune, Pune, 411007 India
| | - H. Chaudhari
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
| | - D. D. Dhavale
- />Department of Chemistry, University of Pune, Pune, 411007 India
| | - B. A. Chopade
- />Department of Microbiology, University of Pune, Pune, 411007 India
| | - D. P. Sachdev
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
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213
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Walsh CT. Blurring the lines between ribosomal and nonribosomal peptide scaffolds. ACS Chem Biol 2014; 9:1653-61. [PMID: 24883916 DOI: 10.1021/cb5003587] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Two of the canons of protein science have been (1) that there are 20-22 amino acids that are proteinogenic and (2), with the exception of achiral glycine, that the other residues are L-amino acids. By contrast, the presence of nonproteinogenic amino acid residues and D-enantiomers has been regarded as hallmarks of nonribosomal peptides. The recent discoveries that bottromycins and polytheonamides, containing β-methyl and D-amino acid residues, are of ribosomal origin blur the distinctions between peptide structures derivable by ribosomal and nonribosomal assembly lines and reveal new chemistry for posttranslational maturation of proteins.
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Affiliation(s)
- Christopher T. Walsh
- Department of Biological Chemistry & Molecular Pharmacology Harvard Medical School, Boston, Massachusetts 02115, United States
- Stanford
Institute of Chemical Biology, Stanford University, Stanford, California 94305, United States
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214
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Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia. ScientificWorldJournal 2014; 2014:698178. [PMID: 25162061 PMCID: PMC4138949 DOI: 10.1155/2014/698178] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/16/2014] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.
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215
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Datta B, Chakrabartty PK. Siderophore biosynthesis genes of Rhizobium sp. isolated from Cicer arietinum L. 3 Biotech 2014; 4:391-401. [PMID: 28324476 PMCID: PMC4145622 DOI: 10.1007/s13205-013-0164-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/12/2013] [Indexed: 11/03/2022] Open
Abstract
Rhizobium BICC 651, a fast-growing strain isolated from root nodule of chickpea (Cicer arietinum L.), produced a catechol siderophore to acquire iron under iron poor condition. A Tn5-induced mutant (B153) of the strain, BICC 651 impaired in siderophore biosynthesis was isolated and characterized. The mutant failed to grow on medium supplemented with iron chelator and grew less efficiently in deferrated broth indicating its higher iron requirement. The mutant produced less number of nodules than its parent strain. The Tn5 insertion in the mutant strain, B153, was located on a 2.8 kb SalI fragment of the chromosomal DNA. DNA sequence analysis revealed that the Tn5-adjoining genomic DNA region contained a coding sequence homologous to agbB gene of Agrobacterium tumefaciens MAFF301001. About 5 kb genomic DNA region of the strain BICC 651 was amplified using the primers designed from DNA sequence of agrobactin biosynthesis genes of A. tumefaciens MAFF 301001 found in the database. From the PCR product of the strain BICC 651, a 4,921 bp DNA fragment was identified which contained four open reading frames. These genes were designated as sid, after siderophore. The genes were identified to be located in the order of sidC, sidE, sidB, and sidA. Narrow intergenic spaces between the genes indicated that they constitute an operon. Phylogenetic analyses of deduced sid gene products suggested their sequence similarity with the sequences of the enzymes involved in biosynthesis of catechol siderophore in other bacteria.
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216
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Tambadou F, Lanneluc I, Sablé S, Klein GL, Doghri I, Sopéna V, Didelot S, Barthélémy C, Thiéry V, Chevrot R. Novel nonribosomal peptide synthetase (NRPS) genes sequenced from intertidal mudflat bacteria. FEMS Microbiol Lett 2014; 357:123-30. [PMID: 25039651 DOI: 10.1111/1574-6968.12532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/25/2014] [Accepted: 07/07/2014] [Indexed: 01/22/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPS) are actively sought out, due to pharmacologically important activities of their metabolites. In marine environment, the most prevalent nonribosomal peptide antibiotic producers are sponges inhabiting microorganisms. Conversely, strains from marine sediments and more especially from intertidal mudflats have not been extensively screened for the presence of new NRPS. In this study, for the first time, a collection of one hundred intertidal mudflat bacterial isolates (Marennes-Oléron Bay, France) was assessed for (1) the presence of NRPS genes by degenerated PCR targeting conserved adenylation domains and (2) for their production of antimicrobial molecules. (1) Bacteria with adenylation domains (14 strains) were identified by 16S rRNA gene sequence analysis and grouped into Firmicutes (one strain) and Proteobacteria (13 strains). In silico analysis of the NRPS amino acid sequences (n = 7) showed 41-58% ID with sequences found in the NCBI database. Three new putative adenylation domain signatures were found. (2) The culture supernatant of one of these strains, identified as a Bacillus, was shown to strongly inhibit the growth of Staphylococcus aureus, S. epidermidis, and Enterococcus faecalis. This study portends that the intertidal mudflat niche could be of interest for the discovery of new NRPS genes and antimicrobial producing strains.
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Affiliation(s)
- Fatoumata Tambadou
- Laboratoire Littoral Environnement et Sociétés, Université de La Rochelle, LIENSs - UMR 7266 - CNRS, La Rochelle Cedex 1, France
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217
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The two-component regulators GacS and GacA positively regulate a nonfluorescent siderophore through the Gac/Rsm signaling cascade in high-siderophore-yielding Pseudomonas sp. strain HYS. J Bacteriol 2014; 196:3259-70. [PMID: 24982309 DOI: 10.1128/jb.01756-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Siderophores, which are produced to overcome iron deficiency, are believed to be closely related to the adaptability of bacteria. The high-siderophore-yielding Pseudomonas sp. strain HYS simultaneously secretes the fluorescent siderophore pyoverdine and another nonfluorescent siderophore that is a major contributor to the high siderophore yield. Transposon mutagenesis revealed siderophore-related genes, including the two-component regulators GacS/GacA and a special cluster containing four open reading frames (the nfs cluster). Deletion mutations of these genes abolished nonfluorescent-siderophore production, and expression of the nfs cluster depended on gacA, indicating that gacS-gacA may control the nonfluorescent siderophore through regulation of the nfs cluster. Furthermore, regulation of the nonfluorescent siderophore by GacS/GacA involved the Gac/Rsm pathway. In contrast, inactivation of GacS/GacA led to upregulation of the fluorescent pyoverdine. The two siderophores were secreted under different iron conditions, probably because of differential effects of GacS/GacA. The global GacS/GacA regulatory system may control iron uptake by modulating siderophore production and may enable bacteria to adapt to changing iron environments.
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218
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Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci U S A 2014; 111:9259-64. [PMID: 24927540 DOI: 10.1073/pnas.1401734111] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nonribosomal peptides and polyketides are a diverse group of natural products with complex chemical structures and enormous pharmaceutical potential. They are synthesized on modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzyme complexes by a conserved thiotemplate mechanism. Here, we report the widespread occurrence of NRPS and PKS genetic machinery across the three domains of life with the discovery of 3,339 gene clusters from 991 organisms, by examining a total of 2,699 genomes. These gene clusters display extraordinarily diverse organizations, and a total of 1,147 hybrid NRPS/PKS clusters were found. Surprisingly, 10% of bacterial gene clusters lacked modular organization, and instead catalytic domains were mostly encoded as separate proteins. The finding of common occurrence of nonmodular NRPS differs substantially from the current classification. Sequence analysis indicates that the evolution of NRPS machineries was driven by a combination of common descent and horizontal gene transfer. We identified related siderophore NRPS gene clusters that encoded modular and nonmodular NRPS enzymes organized in a gradient. A higher frequency of the NRPS and PKS gene clusters was detected from bacteria compared with archaea or eukarya. They commonly occurred in the phyla of Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria in bacteria and the phylum of Ascomycota in fungi. The majority of these NRPS and PKS gene clusters have unknown end products highlighting the power of genome mining in identifying novel genetic machinery for the biosynthesis of secondary metabolites.
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219
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Pontel LB, Scampoli NL, Porwollik S, Checa SK, McClelland M, Soncini FC. Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess. MICROBIOLOGY-SGM 2014; 160:1659-1669. [PMID: 24858080 DOI: 10.1099/mic.0.080473-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Copper and zinc are essential metal ions, but toxic in excess. Bacteria have evolved different strategies to control their intracellular concentrations, ensuring proper supply while avoiding toxicity, including the induction of metal-specific as well as non-specific mechanisms. We compared the transcriptional profiles of Salmonella Typhimurium after exposure to either copper or zinc ions in both rich and minimal media. Besides metal-specific regulatory networks many global stress-response pathways react to an excess of either of these metal ions. Copper excess affects both zinc and iron homeostasis by inducing transcription of these metal-specific regulons. In addition to the control of zinc-specific regulons, zinc excess affects the Cpx regulon and the σ(E) envelope-stress responses. Finally, novel metal-specific upregulated genes were detected including a new copper-detoxification pathway that involves the siderophore enterobactin and the outer-membrane protein TolC. This work sheds light onto the transcriptional landscape of Salmonella after copper or zinc overload, and discloses a new mechanism of copper detoxification.
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Affiliation(s)
- Lucas B Pontel
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Ocampo y Esmeralda, 2000-Rosario, Argentina
| | - Nadia L Scampoli
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Ocampo y Esmeralda, 2000-Rosario, Argentina
| | - Steffen Porwollik
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Ocampo y Esmeralda, 2000-Rosario, Argentina
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Ocampo y Esmeralda, 2000-Rosario, Argentina
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220
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Gerc AJ, Stanley-Wall NR, Coulthurst SJ. Role of the phosphopantetheinyltransferase enzyme, PswP, in the biosynthesis of antimicrobial secondary metabolites by Serratia marcescens Db10. MICROBIOLOGY-SGM 2014; 160:1609-1617. [PMID: 24847000 PMCID: PMC4117218 DOI: 10.1099/mic.0.078576-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Phosphopantetheinyltransferase (PPTase) enzymes fulfil essential roles in primary and secondary metabolism in prokaryotes, archaea and eukaryotes. PPTase enzymes catalyse the essential modification of the carrier protein domain of fatty acid synthases, polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs). In bacteria and fungi, NRPS and PKS enzymes are often responsible for the biosynthesis of secondary metabolites with clinically relevant properties; these secondary metabolites include a variety of antimicrobial peptides. We have previously shown that in the Gram-negative bacterium Serratia marcescens Db10, the PPTase enzyme PswP is essential for the biosynthesis of an NRPS-PKS dependent antibiotic called althiomycin. In this work we utilize bioinformatic analyses to classify PswP as belonging to the F/KES subfamily of Sfp type PPTases and to putatively identify additional NRPS substrates of PswP, in addition to the althiomycin NRPS-PKS, in Ser. marcescens Db10. We show that PswP is required for the production of three diffusible metabolites by this organism, each possessing antimicrobial activity against Staphylococcus aureus. Genetic analyses identify the three metabolites as althiomycin, serrawettin W2 and an as-yet-uncharacterized siderophore, which may be related to enterobactin. Our results highlight the use of an individual PPTase enzyme in multiple biosynthetic pathways, each contributing to the ability of Ser. marcescens to inhibit competitor bacteria by the production of antimicrobial secondary metabolites.
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Affiliation(s)
- Amy J Gerc
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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221
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Endogenous siderophore 2,5-dihydroxybenzoic acid deficiency promotes anemia and splenic iron overload in mice. Mol Cell Biol 2014; 34:2533-46. [PMID: 24777603 DOI: 10.1128/mcb.00231-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eukaryotes produce a siderophore-like molecule via a remarkably conserved biosynthetic pathway. 3-OH butyrate dehydrogenase (BDH2), a member of the short-chain dehydrogenase (SDR) family of reductases, catalyzes a rate-limiting step in the biogenesis of the mammalian siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA). Depletion of the mammalian siderophore by inhibiting expression of bdh2 results in abnormal accumulation of intracellular iron and mitochondrial iron deficiency in cultured mammalian cells, as well as in yeast cells and zebrafish embryos We disrupted murine bdh2 by homologous recombination to analyze the effect of bdh2 deletion on erythropoiesis and iron metabolism. bdh2 null mice developed microcytic anemia and tissue iron overload, especially in the spleen. Exogenous supplementation with 2,5-DHBA alleviates splenic iron overload in bdh2 null mice. Additionally, bdh2 null mice exhibit reduced serum iron. Although BDH2 has been proposed to oxidize ketone bodies, we found that BDH2 deficiency did not alter ketone body metabolism in vivo. In sum, our findings demonstrate a key role for BDH2 in erythropoiesis.
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222
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Zane HK, Naka H, Rosconi F, Sandy M, Haygood MG, Butler A. Biosynthesis of amphi-enterobactin siderophores by Vibrio harveyi BAA-1116: identification of a bifunctional nonribosomal peptide synthetase condensation domain. J Am Chem Soc 2014; 136:5615-8. [PMID: 24701966 DOI: 10.1021/ja5019942] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The genome of Vibrio harveyi BAA-1116 contains a nonribosomal peptide synthetase (NRPS) gene cluster (aebA-F) resembling that for enterobactin, yet enterobactin is not produced. A gene predicted to encode a long-chain fatty acid CoA ligase (FACL), similar to enzymes involved in the biosynthesis of acyl peptides, resides 15 kb away from the putative enterobactin-like biosynthetic gene cluster (aebG). The proximity of this FACL gene to the enterobactin-like synthetase suggested that V. harveyi may produce amphiphilic enterobactin-like siderophores. Extraction of the bacterial cell pellet of V. harveyi led to the isolation and structure determination of a suite of eight amphi-enterobactin siderophores composed of the cyclic lactone of tris-2,3-dihydroxybenzoyl-L-serine and acyl-L-serine. The FACL knockout mutant, ΔaebG V. harveyi, and the NRPS knockout mutant, ΔaebF V. harveyi, do not produce amphi-enterobactins. The amphi-enterobactin biosynthetic machinery was heterologously expressed in Escherichia coli and reconstituted in vitro, demonstrating the condensation domain of AebF has unique activity, catalyzing two distinct condensation reactions.
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Affiliation(s)
- Hannah K Zane
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
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223
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Wang M, Zhao H. Characterization and Engineering of the Adenylation Domain of a NRPS-Like Protein: A Potential Biocatalyst for Aldehyde Generation. ACS Catal 2014; 4:1219-1225. [PMID: 24804152 PMCID: PMC3985451 DOI: 10.1021/cs500039v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/17/2014] [Indexed: 01/24/2023]
Abstract
The adenylation (A) domain acts as the first "gate-keeper" to ensure the activation and thioesterification of the correct monomer to nonribosomal peptide synthetases (NRPSs). Our understanding of the specificity-conferring code and our ability to engineer A domains are critical for increasing the chemical diversity of nonribosomal peptides (NRPs). We recently discovered a novel NRPS-like protein (ATEG_03630) that can activate 5-methyl orsellinic acid (5-MOA) and reduce it to 2,4-dihydroxy-5,6-dimethyl benzaldehyde. A NRPS-like protein is much smaller than multidomain NRPSs, but it still represents the thioesterification half-reaction, which is otherwise missed from a stand-alone A domain. Therefore, a NRPS-like protein may serve as a better model system for A domain engineering. Here, we characterize the substrate specificity of ATEG_03630 and conclude that the hydrogen-bond donor at the 4-position is crucial for substrate recognition. Next, we show that the substrate specificity of ATEG_03630 can be engineered toward our target substrate anthranilate via bioinformatics analysis and mutagenesis. The resultant mutant H358A increased its activity toward anthranilate by 10.9-fold, which led to a 26-fold improvement in specificity. Finally, we demonstrate one-pot chemoenzymatic synthesis of 4-hydroxybenzaldoxime from 4-hydroxybenzoic acid with high yield.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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224
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Wang M, Beissner M, Zhao H. Aryl-aldehyde formation in fungal polyketides: discovery and characterization of a distinct biosynthetic mechanism. CHEMISTRY & BIOLOGY 2014; 21:257-63. [PMID: 24412543 PMCID: PMC3943900 DOI: 10.1016/j.chembiol.2013.12.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 12/02/2013] [Accepted: 12/07/2013] [Indexed: 11/22/2022]
Abstract
Aryl-aldehydes are a common feature in fungal polyketides, which are considered to be exclusively generated by the R domain of nonreducing polyketide synthases (NR-PKSs). However, by cloning and heterologous expression of both cryptic NR-PKS and nonribosomal peptide synthase (NRPS)-like genes from Aspergillus terreus in Saccharomyces cerevisiae, we identified a distinct mechanism for aryl-aldehyde formation in which a NRPS-like protein activates and reduces an aryl-acid produced by the accompanying NR-PKS to an aryl-aldehyde. Bioinformatics study indicates that such a mechanism may be widely used throughout the fungi kingdom.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mirko Beissner
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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225
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Vizcaino MI, Guo X, Crawford JM. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J Ind Microbiol Biotechnol 2014; 41:285-99. [PMID: 24127069 PMCID: PMC3946945 DOI: 10.1007/s10295-013-1356-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/23/2013] [Indexed: 12/24/2022]
Abstract
The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions.
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Affiliation(s)
- Maria I. Vizcaino
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Xun Guo
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06510, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
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226
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Diaz-Ochoa VE, Jellbauer S, Klaus S, Raffatellu M. Transition metal ions at the crossroads of mucosal immunity and microbial pathogenesis. Front Cell Infect Microbiol 2014; 4:2. [PMID: 24478990 PMCID: PMC3900919 DOI: 10.3389/fcimb.2014.00002] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/04/2014] [Indexed: 12/21/2022] Open
Abstract
Transition metal ions are essential micronutrients for all living organisms. In mammals, these ions are often protein-bound and sequestered within cells, limiting their availability to microbes. Moreover, in response to infection, mammalian hosts further reduce the availability of metal nutrients by activating epithelial cells and recruiting neutrophils, both of which release metal-binding proteins with antimicrobial function. Microorganisms, in turn, have evolved sophisticated systems to overcome these limitations and acquire the metal ions essential for their growth. Here we review some of the mechanisms employed by the host and by pathogenic microorganisms to compete for transition metal ions, with a discussion of how evading “nutritional immunity” benefits pathogens. Furthermore, we provide new insights on the mechanisms of host-microbe competition for metal ions in the mucosa, particularly in the inflamed gut.
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Affiliation(s)
- Vladimir E Diaz-Ochoa
- Department of Microbiology and Molecular Genetics, University of California, Irvine Irvine, CA, USA ; Institute for Immunology, University of California, Irvine Irvine, CA, USA
| | - Stefan Jellbauer
- Department of Microbiology and Molecular Genetics, University of California, Irvine Irvine, CA, USA ; Institute for Immunology, University of California, Irvine Irvine, CA, USA
| | - Suzi Klaus
- Department of Microbiology and Molecular Genetics, University of California, Irvine Irvine, CA, USA ; Institute for Immunology, University of California, Irvine Irvine, CA, USA
| | - Manuela Raffatellu
- Department of Microbiology and Molecular Genetics, University of California, Irvine Irvine, CA, USA ; Institute for Immunology, University of California, Irvine Irvine, CA, USA
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227
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Carpenter C, Payne SM. Regulation of iron transport systems in Enterobacteriaceae in response to oxygen and iron availability. J Inorg Biochem 2014; 133:110-7. [PMID: 24485010 DOI: 10.1016/j.jinorgbio.2014.01.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Iron is an essential nutrient for most bacteria. Depending on the oxygen available in the surrounding environment, iron is found in two distinct forms: ferrous (Fe(II)) or ferric (Fe(III)). Bacteria utilize different transport systems for the uptake of the two different forms of iron. In oxic growth conditions, iron is found in its insoluble, ferric form, and in anoxic growth conditions iron is found in its soluble, ferrous form. Enterobacteriaceae have adapted to transporting the two forms of iron by utilizing the global, oxygen-sensing regulators, ArcA and Fnr to regulate iron transport genes in response to oxygen.
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Affiliation(s)
- Chandra Carpenter
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Shelley M Payne
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States.
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228
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Self-poisoning of Mycobacterium tuberculosis by interrupting siderophore recycling. Proc Natl Acad Sci U S A 2014; 111:1945-50. [PMID: 24497493 DOI: 10.1073/pnas.1311402111] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Siderophores are small iron-binding molecules secreted by bacteria to scavenge iron. Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis, produces the siderophores mycobactin and carboxymycobactin. Complexes of the mycobacterial membrane proteins MmpS4 and MmpS5 with the transporters MmpL4 and MmpL5 are required for siderophore export and virulence in Mtb. Here we show that, surprisingly, mycobactin or carboxymycobactin did not rescue the low-iron growth defect of the export mutant but severely impaired growth. Exogenous siderophores were taken up by the export mutant, and siderophore-delivered iron was used, but the deferrated siderophores accumulated intracellularly, indicating a blockade of siderophore recycling. This hypothesis was confirmed by the observation that radiolabeled carboxymycobactin was taken up and secreted again by Mtb. Addition of iron salts to an Mtb siderophore biosynthesis mutant stimulated more growth in the presence of a limiting amount of siderophores than iron-loaded siderophores alone. Thus, recycling enables Mtb to acquire iron at lower metabolic cost because Mtb cannot use iron salts without siderophores. Exogenous siderophores were bactericidal for the export mutant in submicromolar quantities. High-resolution mass spectrometry revealed that endogenous carboxymycobactin also accumulated in the export mutant. Toxic siderophore accumulation is prevented by a drug that inhibits siderophore biosynthesis. Intracellular accumulation of siderophores was toxic despite the use of an alternative iron source such as hemin, suggesting an additional inhibitory mechanism independent of iron availability. This study indicates that targeting siderophore export/recycling would deliver a one-two punch to Mtb: restricting access to iron and causing toxic intracellular siderophore accumulation.
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229
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Niranjana SR, Hariprasad P. Understanding the Mechanism Involved in PGPR-Mediated Growth Promotion and Suppression of Biotic and Abiotic Stress in Plants. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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230
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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231
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Caza M, Kronstad JW. Shared and distinct mechanisms of iron acquisition by bacterial and fungal pathogens of humans. Front Cell Infect Microbiol 2013; 3:80. [PMID: 24312900 PMCID: PMC3832793 DOI: 10.3389/fcimb.2013.00080] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 10/30/2013] [Indexed: 12/12/2022] Open
Abstract
Iron is the most abundant transition metal in the human body and its bioavailability is stringently controlled. In particular, iron is tightly bound to host proteins such as transferrin to maintain homeostasis, to limit potential damage caused by iron toxicity under physiological conditions and to restrict access by pathogens. Therefore, iron acquisition during infection of a human host is a challenge that must be surmounted by every successful pathogenic microorganism. Iron is essential for bacterial and fungal physiological processes such as DNA replication, transcription, metabolism, and energy generation via respiration. Hence, pathogenic bacteria and fungi have developed sophisticated strategies to gain access to iron from host sources. Indeed, siderophore production and transport, iron acquisition from heme and host iron-containing proteins such as hemoglobin and transferrin, and reduction of ferric to ferrous iron with subsequent transport are all strategies found in bacterial and fungal pathogens of humans. This review focuses on a comparison of these strategies between bacterial and fungal pathogens in the context of virulence and the iron limitation that occurs in the human body as a mechanism of innate nutritional defense.
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Affiliation(s)
| | - James W. Kronstad
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British ColumbiaVancouver, BC, Canada
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232
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Geetha SJ, Joshi SJ. Engineering rhizobial bioinoculants: a strategy to improve iron nutrition. ScientificWorldJournal 2013; 2013:315890. [PMID: 24319357 PMCID: PMC3836376 DOI: 10.1155/2013/315890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. In order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. Competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. Iron sufficiency is an important factor determining the survival and nodulation by rhizobia in soil. Siderophores, a class of ferric specific ligands that are involved in receptor specific iron transport into bacteria, constitute an important part of iron acquisition systems in rhizobia and have been shown to play a role in symbiosis as well as in saprophytic survival. Soils predominantly have iron bound to hydroxamate siderophores, a pool that is largely unavailable to catecholate-utilizing rhizobia. Outer membrane receptors for uptake of ferric hydroxamates include FhuA and FegA which are specific for ferrichrome siderophore. Increase in nodule occupancy and enhanced plant growth of the fegA and fhuA expressing engineered bioinoculants rhizobial strain have been reported. Engineering rhizobia for developing effective bioinoculants with improved ability to utilize heterologous siderophores could provide them with better iron acquisition ability and consequently, rhizospheric stability.
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Affiliation(s)
- S. J. Geetha
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
| | - Sanket J. Joshi
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
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233
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Noble SM. Candida albicans specializations for iron homeostasis: from commensalism to virulence. Curr Opin Microbiol 2013; 16:708-15. [PMID: 24121029 DOI: 10.1016/j.mib.2013.09.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/06/2013] [Accepted: 09/13/2013] [Indexed: 01/23/2023]
Abstract
Candida albicans is a fungal commensal-pathogen that persistently associates with its mammalian hosts. Between the commensal and pathogenic lifestyles, this microorganism inhabits host niches that differ markedly in the levels of bioavailable iron. A number of recent studies have exposed C. albicans specializations for acquiring iron from specific host molecules in regions where iron is scarce, while also defending against iron-related toxicity in regions where iron occurs in surfeit. Together, these results point to a central role for iron homeostasis in the evolution of this important human pathogen.
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Affiliation(s)
- Suzanne M Noble
- Department of Microbiology & Immunology, 513 Parnassus Avenue, Box 0414, San Francisco, CA 94143-0414, United States; Division of Infectious Diseases, Department of Medicine, 513 Parnassus Avenue, Box 0414, San Francisco, CA 94143-0414, United States.
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234
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Kelson AB, Carnevali M, Truong-Le V. Gallium-based anti-infectives: targeting microbial iron-uptake mechanisms. Curr Opin Pharmacol 2013; 13:707-16. [DOI: 10.1016/j.coph.2013.07.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/22/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
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235
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Yan Q, Power KA, Cooney S, Fox E, Gopinath GR, Grim CJ, Tall BD, McCusker MP, Fanning S. Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility. Front Microbiol 2013; 4:256. [PMID: 24032028 PMCID: PMC3759002 DOI: 10.3389/fmicb.2013.00256] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 08/13/2013] [Indexed: 11/13/2022] Open
Abstract
Outbreaks of human infection linked to the powdered infant formula (PIF) food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC) and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC)], pSP291-2, [52.1-kb (49.2% GC)], and pSP291-3, [4.4-kb (54.0% GC)]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM), we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.
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Affiliation(s)
- Qiongqiong Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference and Training on Cronobacter, School of Public Health, Physiotherapy and Population Science, University College Dublin Dublin, Ireland
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236
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A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies. Biometals 2013; 26:561-75. [PMID: 23877277 DOI: 10.1007/s10534-013-9653-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
The structure of a pyoverdine produced by Pseudomonas putida, W15Oct28, was elucidated by combining mass spectrometric methods and bioinformatics by the analysis of non-ribosomal peptide synthetase genes present in the newly sequenced genome. The only form of pyoverdine produced by P. putida W15Oct28 is characterized to contain α-ketoglutaric acid as acyl side chain, a dihydropyoverdine chromophore, and a 12 amino acid peptide chain. The peptide chain is unique among all pyoverdines produced by Pseudomonas subspecies strains. It was characterized as -L-Asp-L-Ala-D-AOHOrn-L-Thr-Gly-c[L-Thr(O-)-L-Hse-D-Hya-L-Ser-L-Orn-L-Hse-L-Ser-O-]. The chemical formula and the detected and calculated molecular weight of this pyoverdine are: C65H93N17O32, detected mass 1624.6404 Da, calculated mass 1624.6245. Additionally, pyoverdine structures from both literature reports and bioinformatics prediction of the genome sequenced P. putida strains are summarized allowing us to propose a scheme based on pyoverdines structures as tool for the phylogeny of P. putida. This study shows the strength of the combination of in silico analysis together with analytical data and literature mining in determining the structure of secondary metabolites such as peptidic siderophores.
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237
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Engelhart CA, Aldrich CC. Synthesis of chromone, quinolone, and benzoxazinone sulfonamide nucleosides as conformationally constrained inhibitors of adenylating enzymes required for siderophore biosynthesis. J Org Chem 2013; 78:7470-81. [PMID: 23805993 DOI: 10.1021/jo400976f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MbtA catalyzes the first committed step of mycobactin biosynthesis in Mycobacterium tuberculosis (Mtb) and is responsible for the incorporation of salicylic acid into the mycobactin siderophores. 5'-O-[N-(Salicyl)sulfamoyl]adenosine (Sal-AMS) is an extremely potent nucleoside inhibitor of MbtA that possesses excellent activity against whole-cell Mtb but suffers from poor bioavailability. In an effort to improve the bioavailability, we have designed four conformationally constrained analogues of Sal-AMS that remove two rotatable bonds and the ionized sulfamate group on the basis of computational and structural studies. Herein we describe the synthesis, biochemical, and microbiological evaluation of chromone-, quinolone-, and benzoxazinone-3-sulfonamide derivatives of Sal-AMS. We developed new chemistry to assemble these three heterocycles from common β-ketosulfonamide intermediates. The synthesis of the chromone- and quinolone-3-sulfonamide intermediates features formylation of a β-ketosulfonamide employing dimethylformamide dimethyl acetal to afford an enaminone that can react intramolecularly with a phenol or intermolecularly with a primary amine via addition-elimination reaction(s). The benzoxazinone-3-sulfonamide was prepared by nitrosation of a β-ketosulfonamide followed by intramolecular nucleophilic aromatic substitution. Mitsunobu coupling of these bicyclic sulfonamides with a protected adenosine derivative followed by global deprotection provides a concise synthesis of the respective inhibitors.
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Affiliation(s)
- Curtis A Engelhart
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, USA
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238
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Kamada N, Chen GY, Inohara N, Núñez G. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol 2013; 14:685-90. [PMID: 23778796 PMCID: PMC4083503 DOI: 10.1038/ni.2608] [Citation(s) in RCA: 979] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/09/2013] [Indexed: 02/07/2023]
Abstract
A dense resident microbial community in the gut, referred as the commensal microbiota, coevolved with the host and is essential for many host physiological processes that include enhancement of the intestinal epithelial barrier, development of the immune system and acquisition of nutrients. A major function of the microbiota is protection against colonization by pathogens and overgrowth of indigenous pathobionts that can result from the disruption of the healthy microbial community. The mechanisms that regulate the ability of the microbiota to restrain pathogen growth are complex and include competitive metabolic interactions, localization to intestinal niches and induction of host immune responses. Pathogens, in turn, have evolved strategies to escape from commensal-mediated resistance to colonization. Thus, the interplay between commensals and pathogens or indigenous pathobionts is critical for controlling infection and disease. Understanding pathogen-commensal interactions may lead to new therapeutic approaches to treating infectious diseases.
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Affiliation(s)
- Nobuhiko Kamada
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109, USA
| | - Grace Y. Chen
- Department of Internal Medicine and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109, USA
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239
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Brown MF, Mitton-Fry MJ, Arcari JT, Barham R, Casavant J, Gerstenberger BS, Han S, Hardink JR, Harris TM, Hoang T, Huband MD, Lall MS, Lemmon MM, Li C, Lin J, McCurdy SP, McElroy E, McPherson C, Marr ES, Mueller JP, Mullins L, Nikitenko AA, Noe MC, Penzien J, Plummer MS, Schuff BP, Shanmugasundaram V, Starr JT, Sun J, Tomaras A, Young JA, Zaniewski RP. Pyridone-conjugated monobactam antibiotics with gram-negative activity. J Med Chem 2013; 56:5541-52. [PMID: 23755848 DOI: 10.1021/jm400560z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Herein we describe the structure-aided design and synthesis of a series of pyridone-conjugated monobactam analogues with in vitro antibacterial activity against clinically relevant Gram-negative species including Pseudomonas aeruginosa , Klebsiella pneumoniae , and Escherichia coli . Rat pharmacokinetic studies with compound 17 demonstrate low clearance and low plasma protein binding. In addition, evidence is provided for a number of analogues suggesting that the siderophore receptors PiuA and PirA play a role in drug uptake in P. aeruginosa strain PAO1.
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Affiliation(s)
- Matthew F Brown
- Worldwide Medicinal Chemistry, ‡Computational Chemistry, §Antibacterials Research Unit, ∥Pharmacokinetics, Dynamics & Metabolism, ⊥Structural Biology, Pfizer Global Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States
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240
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Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads. J Bacteriol 2013; 195:3876-87. [PMID: 23794620 DOI: 10.1128/jb.00528-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.
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241
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Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. J Antibiot (Tokyo) 2013; 67:7-22. [DOI: 10.1038/ja.2013.49] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/22/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022]
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242
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Chen M, Ma X, Chen X, Jiang M, Song H, Guo Z. Identification of a hotdog fold thioesterase involved in the biosynthesis of menaquinone in Escherichia coli. J Bacteriol 2013; 195:2768-75. [PMID: 23564174 PMCID: PMC3697248 DOI: 10.1128/jb.00141-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/02/2013] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is used as a model organism for elucidation of menaquinone biosynthesis, for which a hydrolytic step from 1,4-dihydroxy-2-naphthoyl-coenzyme A (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate is still unaccounted for. Recently, a hotdog fold thioesterase has been shown to catalyze this conversion in phylloquinone biosynthesis, suggesting that its closest homolog, YbgC in Escherichia coli, may be the DHNA-CoA thioesterase in menaquinone biosynthesis. However, this possibility is excluded by the involvement of YbgC in the Tol-Pal system and its complete lack of hydrolytic activity toward DHNA-CoA. To identify the hydrolytic enzyme, we have performed an activity-based screen of all nine Escherichia coli hotdog fold thioesterases and found that YdiI possesses a high level of hydrolytic activity toward DHNA-CoA, with high substrate specificity, and that another thioesterase, EntH, from siderophore biosynthesis exhibits a moderate, much lower DHNA-CoA thioesterase activity. Deletion of the ydiI gene from the bacterial genome results in a significant decrease in menaquinone production, which is little affected in ΔybgC and ΔentH mutants. These results support the notion that YdiI is the DHNA-CoA thioesterase involved in the biosynthesis of menaquinone in the model bacterium.
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Affiliation(s)
- Minjiao Chen
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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243
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Wencewicz TA, Miller MJ. Biscatecholate-monohydroxamate mixed ligand siderophore-carbacephalosporin conjugates are selective sideromycin antibiotics that target Acinetobacter baumannii. J Med Chem 2013; 56:4044-52. [PMID: 23614627 PMCID: PMC3690592 DOI: 10.1021/jm400265k] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemical syntheses and biological evaluation of biscatecholate-monohydroxamate mixed ligand sideromycins utilizing the carbacephalosporin β-lactam antibiotic loracarbef and the fluoroquinolone antibiotic ciprofloxacin are described. The mixed ligand β-lactam sideromycin (1b) had remarkably selective and extremely potent antibacterial activity against the Gram-negative pathogen Acinetobacter baumannii ATCC 17961 (MIC = 0.0078 μM). The antibacterial activity of the β-lactam sideromycin was inversely related to the iron(III) concentration in the testing media and was antagonized by the presence of the competing parent siderophore. These data suggested that active transport of the mixed ligand β-lactam sideromycin across the outer cell membrane of A. baumannii via siderophore-uptake pathways was responsible for the selective and potent antibacterial activity.
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Affiliation(s)
- Timothy A. Wencewicz
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
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244
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Plasmid- and chromosome-encoded siderophore anguibactin systems found in marine vibrios: biosynthesis, transport and evolution. Biometals 2013; 26:537-47. [PMID: 23660776 DOI: 10.1007/s10534-013-9629-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/28/2013] [Indexed: 01/04/2023]
Abstract
Vibrio anguillarum is a marine pathogen that causes vibriosis, a hemorrhagic septicemia in aquatic invertebrate as well as vertebrate animals. The siderophore anguibactin system is one of the most important virulence factors of this bacterium. Most of the anguibactin biosynthesis and transport genes are located in the 65-kb pJM1 virulence plasmid although some of them are found in the chromosome of this fish pathogen. Over 30 years of research unveiled the role numerous chromosomal and pJM1 genes play in the synthesis of anguibactin and the transport of cognate ferric complexes into the bacterial cell. Furthermore, these studies showed that pJM1-carrying strains might be originated from pJM1-less strains producing the chromosome-mediated siderophore vanchrobactin. Additionally, we recently identified a chromosome-mediated anguibactin system in V. harveyi suggesting the possible evolutional origin of the V. anguillarum anguibactin system. In this review, we present our current understanding of the mechanisms and evolution hypothesis of the anguibactin system that might have occurred in these pathogenic vibrios.
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245
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Fujita MJ, Nakano K, Sakai R. Bisucaberin B, a linear hydroxamate class siderophore from the marine bacterium Tenacibaculum mesophilum. Molecules 2013; 18:3917-26. [PMID: 23549298 PMCID: PMC6270104 DOI: 10.3390/molecules18043917] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/11/2013] [Accepted: 03/22/2013] [Indexed: 12/03/2022] Open
Abstract
A siderophore, named bisucaberin B, was isolated from Tenacibaculum mesophilum bacteria separated from a marine sponge collected in the Republic of Palau. Using spectroscopic and chemical methods, the structure of bisucaberin B (1) was clearly determined to be a linear dimeric hydroxamate class siderophore. Although compound 1 is an open form of the known macrocyclic dimer bisucaberin (2), and was previously described as a bacterial degradation product of desferrioxamine B (4), the present report is the first description of the de novo biosynthesis of 1. To the best of our knowledge, compound 1 is the first chemically characterized siderophore isolated from a bacterium belonging to the phylum Bacteroidetes.
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Affiliation(s)
- Masaki J Fujita
- Creative Research Institution, Hokkaido University, Hakodate 041-8611, Japan.
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246
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Neres J, Engelhart CA, Drake EJ, Wilson DJ, Fu P, Boshoff HI, Barry CE, Gulick AM, Aldrich CC. Non-nucleoside inhibitors of BasE, an adenylating enzyme in the siderophore biosynthetic pathway of the opportunistic pathogen Acinetobacter baumannii. J Med Chem 2013; 56:2385-405. [PMID: 23437866 DOI: 10.1021/jm301709s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Siderophores are small-molecule iron chelators produced by bacteria and other microorganisms for survival under iron limiting conditions such as found in a mammalian host. Siderophore biosynthesis is essential for the virulence of many important Gram-negative pathogens including Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. We performed high-throughput screening against BasE, which is involved in siderophore biosynthesis in A. baumannii, and identified 6-phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid 15. Herein we report the synthesis, biochemical, and microbiological evaluation of a systematic series of analogues of the HTS hit 15. Analogue 67 is the most potent analogue with a KD of 2 nM against BasE. Structural characterization of the inhibitors with BasE reveals that they bind in a unique orientation in the active site, occupying all three substrate binding sites, and thus can be considered as multisubstrate inhibitors. These results provide a foundation for future studies aimed at increasing both enzyme potency and antibacterial activity.
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Affiliation(s)
- João Neres
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, USA
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247
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Kenney GE, Rosenzweig AC. Genome mining for methanobactins. BMC Biol 2013; 11:17. [PMID: 23442874 PMCID: PMC3621798 DOI: 10.1186/1741-7007-11-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/26/2013] [Indexed: 01/27/2023] Open
Abstract
Background Methanobactins (Mbns) are a family of copper-binding natural products involved in copper uptake by methanotrophic bacteria. The few Mbns that have been structurally characterized feature copper coordination by two nitrogen-containing heterocycles next to thioamide groups embedded in a peptidic backbone of varying composition. Mbns are proposed to derive from post-translational modification of ribosomally synthesized peptides, but only a few genes encoding potential precursor peptides have been identified. Moreover, the relevance of neighboring genes in these genomes has been unclear. Results The potential for Mbn production in a wider range of bacterial species was assessed by mining microbial genomes. Operons encoding Mbn-like precursor peptides, MbnAs, were identified in 16 new species, including both methanotrophs and, surprisingly, non-methanotrophs. Along with MbnA, the core of the operon is formed by two putative biosynthetic genes denoted MbnB and MbnC. The species can be divided into five groups on the basis of their MbnA and MbnB sequences and their operon compositions. Additional biosynthetic proteins, including aminotransferases, sulfotransferases and flavin adenine dinucleotide (FAD)-dependent oxidoreductases were also identified in some families. Beyond biosynthetic machinery, a conserved set of transporters was identified, including MATE multidrug exporters and TonB-dependent transporters. Additional proteins of interest include a di-heme cytochrome c peroxidase and a partner protein, the roles of which remain a mystery. Conclusions This study indicates that Mbn-like compounds may be more widespread than previously thought, but are not present in all methanotrophs. This distribution of species suggests a broader role in metal homeostasis. These data provide a link between precursor peptide sequence and Mbn structure, facilitating predictions of new Mbn structures and supporting a post-translational modification biosynthetic pathway. In addition, testable models for Mbn transport and for methanotrophic copper regulation have emerged. Given the unusual modifications observed in Mbns characterized thus far, understanding the roles of the putative biosynthetic proteins is likely to reveal novel pathways and chemistry.
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Affiliation(s)
- Grace E Kenney
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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248
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Naka H, Liu M, Crosa JH. Two ABC transporter systems participate in siderophore transport in the marine pathogen Vibrio anguillarum 775 (pJM1). FEMS Microbiol Lett 2013; 341:79-86. [PMID: 23350649 DOI: 10.1111/1574-6968.12092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 12/25/2012] [Accepted: 01/22/2013] [Indexed: 11/30/2022] Open
Abstract
ORF40 (named fatE) in the Vibrio anguillarum pJM1 plasmid-encoding anguibactin iron transport systems is a homolog of ATPase genes involved in ferric-siderophore transport. Mutation of fatE did not affect ferric-anguibactin transport, indicating that there must be other ATPase gene(s) in addition to fatE. By searching the genomic sequence of V. anguillarum 775(pJM1), we identified a homolog of fatE named fvtE on chromosome 2. It is of interest that in this locus, we also identified homologs of fatB, fatC, and fatD that we named fvtB, fvtC and fvtD, respectively. The fvtE mutant still showed ferric-anguibactin transport, while the double fatE and fvtE mutation completely abolished the ferric-anguibactin transport indicating that fatE and fvtE are functional ATPase homologs for ferric-anguibactin transport. Furthermore, we demonstrate that fvtB, fvtC, fvtD, and fvtE are essential for ferric-vanchrobactin and ferric-enterobactin transport.
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Affiliation(s)
- Hiroaki Naka
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA.
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Naka H, Actis LA, Crosa JH. The anguibactin biosynthesis and transport genes are encoded in the chromosome of Vibrio harveyi: a possible evolutionary origin for the pJM1 plasmid-encoded system of Vibrio anguillarum? Microbiologyopen 2013; 2:182-94. [PMID: 23335587 PMCID: PMC3584223 DOI: 10.1002/mbo3.65] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/22/2012] [Accepted: 12/03/2012] [Indexed: 12/31/2022] Open
Abstract
Many Vibrio anguillarum serotype O1 strains carry 65-kb pJM1-type plasmids harboring genes involved in siderophore anguibactin biosynthesis and transport. The anguibactin system is an essential factor for V. anguillarum to survive under iron-limiting conditions, and as a consequence, it is a very important virulence factor of this bacterium. Our comparative analysis of genomic data identified a cluster harboring homologs of anguibactin biosynthesis and transport genes in the chromosome of Vibrio harveyi. We have purified the putative anguibactin siderophore and demonstrated that it is indeed anguibactin by mass spectrometry and specific bioassays. Furthermore, we characterized two genes, angR and fatA, in this chromosome cluster that, respectively, participate in anguibactin biosynthesis and transport as determined by mutagenesis analysis. Furthermore, we found that the V. harveyi FatA protein is located in the outer membrane fractions as previously demonstrated in V. anguillarum. Based on our data, we propose that the anguibactin biosynthesis and transport cluster in the V. anguillarum pJM1 plasmid have likely evolved from the chromosome cluster of V. harveyi or vice versa.
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Affiliation(s)
- Hiroaki Naka
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.
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250
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Andrews S, Norton I, Salunkhe AS, Goodluck H, Aly WSM, Mourad-Agha H, Cornelis P. Control of iron metabolism in bacteria. Met Ions Life Sci 2013; 12:203-39. [PMID: 23595674 DOI: 10.1007/978-94-007-5561-1_7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria depend upon iron as a vital cofactor that enables a wide range of key metabolic activities. Bacteria must therefore ensure a balanced supply of this essential metal. To do so, they invest considerable resourse into its acquisition and employ elaborate control mechanisms to eleviate both iron-induced toxitiy as well as iron deficiency. This chapter describes the processes that bacteria engage in maintaining iron homeostasis. The focus is Escherichia coli, as this bacterium provides a well studied example. A summary of the current status of understanding of iron management at the 'omics' level is also presented.
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Affiliation(s)
- Simon Andrews
- The School of Biological Sciences, The University of Reading, Whiteknights, Reading, RG6 6AJ, UK,
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