The Genomisotopic Approach: A Systematic Method to Isolate Products of Orphan Biosynthetic Gene Clusters

Gross, Harald; Stockwell, Virginia O.; Henkels, Marcella D.; Nowak-Thompson, Brian; Loper, Joyce E.; Gerwick, William H.

doi:10.1016/j.chembiol.2006.11.007

Cited by 272 publications

(278 citation statements)

References 47 publications

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“…S3 and S4). Unexpectedly, 13 C and 15 N gHMBC experiments to confirm the amino acid connectivity revealed a heterodimeric peptide with the sequence Dhb-Arg-Gly-Gly-Ser-HOOrn-Gly-Gly-Arg-Dhb (Table 1 (Fig. S6).…”

Section: Resultsmentioning

confidence: 99%

“…NMR solvents were purchased from Cambridge Isotope Laboratories. 1 H, 13 C, 15 N, and 1 H-13 C correlation spectra were acquired on a Varian INOVA 500 MHz ( 1 H) NMR spectrometer with VNMR 6.1C software. Spectra were processed by using MestReC version 4.9.9.8 software.…”

Section: Methodsmentioning

confidence: 99%

“…NRP synthetases are large, multidomain enzymes catalyzing the assembly of peptides by a thioester-templated mechanism (10). Identification of amino acid building blocks is possible from analysis of the sequence of the NRP synthetase adenylation domains (12)(13)(14)(15). By using this information in combination with the frequently observed colinearity of the biosynthetic genes with the product, prediction of the peptide structure is possible.…”

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confidence: 99%

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Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca

Dimise

Widboom

Bruner

2008

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria belonging to the order Actinomycetales have proven to be an important source of biologically active and often therapeutically useful natural products. The characterization of orphan biosynthetic gene clusters is an emerging and valuable approach to the discovery of novel small molecules. Analysis of the recently sequenced genome of the thermophilic actinomycete Thermobifida fusca revealed an orphan nonribosomal peptide biosynthetic gene cluster coding for an unknown siderophore natural product. T. fusca is a model organism for the study of thermostable cellulases and is a major degrader of plant cell walls. Here, we report the isolation and structure elucidation of the fuscachelins, siderophore natural products produced by T. fusca. In addition, we report the purification and biochemical characterization of the termination module of the nonribosomal peptide synthetase. Biochemical analysis of adenylation domain specificity supports the assignment of this gene cluster as the producer of the fuscachelin siderophores. The proposed nonribosomal peptide biosynthetic pathway exhibits several atypical features, including a macrocyclizing thioesterase that produces a 10-membered cyclic depsipeptide and a nonlinear assembly line, resulting in the unique heterodimeric architecture of the siderophore natural product.natural product isolation ͉ nonribosomal peptide biosynthesis ͉ genome mining

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca

Dimise

Widboom

Bruner

2008

Proc. Natl. Acad. Sci. U.S.A.

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“…29 In a similar approach, a novel cyclic lipopeptide, designated orfamide (Figure 1), was identified from the Pseudomonas fluorescens genome. 30 In this case, the bioinformatic prediction that the peptide contained four leucine residues suggested feeding with 15 N-Leu, which facilitated compound purification and characterization. Orfamide shows a moderate antifungal activity against amphotericin-resistant strains of Candida albicans and may prove beneficial in agriculture and crop protection.…”

Section: Approaches Leading To New Antibiotic Classesmentioning

confidence: 99%

Antibiotic discovery in the twenty-first century: current trends and future perspectives

Donadio¹,

Maffioli²,

Monciardini³

et al. 2010

J Antibiot

215

122

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New antibiotics are necessary to treat microbial pathogens that are becoming increasingly resistant to available treatment. Despite the medical need, the number of newly approved drugs continues to decline. We offer an overview of the pipeline for new antibiotics at different stages, from compounds in clinical development to newly discovered chemical classes. Consistent with historical data, the majority of antibiotics under clinical development are natural products or derivatives thereof. However, many of them also represent improved variants of marketed compounds, with the consequent risk of being only partially effective against the prevailing resistance mechanisms. In the discovery arena, instead, compounds with promising activities have been obtained from microbial sources and from chemical modification of antibiotic classes other than those in clinical use. Furthermore, new natural product scaffolds have also been discovered by ingenious screening programs. After providing selected examples, we offer our view on the future of antibiotic discovery.

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“…This connection can be done either in the genotype-tochemotype direction by in silico-guided approaches (19) or in the chemotype-to-genotype direction by experiment-guided approaches (20). Many effective in silico-guided strategies have been developed using genetics (21), substrate labeling (22), and screening for predicted physicochemical properties (23) to characterize new natural products from cryptic and even silent gene clusters in genomes. However, these approaches target only one biosynthetic pathway per experiment, thereby resulting in a slow discovery rate.…”

mentioning

confidence: 99%

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

Kersten

Ziemert

Gonzalez³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

101

107

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Glycosyl groups are an essential mediator of molecular interactions in cells and on cellular surfaces. There are very few methods that directly relate sugar-containing molecules to their biosynthetic machineries. Here, we introduce glycogenomics as an experimentguided genome-mining approach for fast characterization of glycosylated natural products (GNPs) and their biosynthetic pathways from genome-sequenced microbes by targeting glycosyl groups in microbial metabolomes. Microbial GNPs consist of aglycone and glycosyl structure groups in which the sugar unit(s) are often critical for the GNP's bioactivity, e.g., by promoting binding to a target biomolecule. GNPs are a structurally diverse class of molecules with important pharmaceutical and agrochemical applications. Herein, O-and N-glycosyl groups are characterized in their sugar monomers by tandem mass spectrometry (MS) and matched to corresponding glycosylation genes in secondary metabolic pathways by a MS-glycogenetic code. The associated aglycone biosynthetic genes of the GNP genotype then classify the natural product to further guide structure elucidation. We highlight the glycogenomic strategy by the characterization of several bioactive glycosylated molecules and their gene clusters, including the anticancer agent cinerubin B from Streptomyces sp. SPB74 and an antibiotic, arenimycin B, from Salinispora arenicola CNB-527.secondary metabolite | drug discovery | microbial genomics | deoxysugar | polyketide

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The Genomisotopic Approach: A Systematic Method to Isolate Products of Orphan Biosynthetic Gene Clusters

Cited by 272 publications

References 47 publications

Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca

Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca

Antibiotic discovery in the twenty-first century: current trends and future perspectives

Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules

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