Lessons learned from the transformation of natural product discovery to a genome-driven endeavor.

PubWeight™: 0.83‹?›

🔗 View Article (PMC 3946952)

Published in J Ind Microbiol Biotechnol on October 19, 2013

Authors

Caitlin D Deane1, Douglas A Mitchell

Author Affiliations

1: Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Articles cited by this

(truncated to the top 100)

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature (2002) 19.35

Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod (2012) 13.27

Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A (2006) 10.24

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature (2003) 8.53

Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol (2001) 7.97

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol (2007) 6.21

The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol (2003) 6.11

Genome sequencing and analysis of Aspergillus oryzae. Nature (2005) 5.47

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep (2013) 5.38

Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol (2007) 4.66

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol (2005) 4.65

Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol (2008) 4.59

Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci U S A (2001) 4.56

Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res (2000) 4.11

Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. J Bacteriol (2007) 4.07

Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host. Nature (1984) 3.61

Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat Biotechnol (2007) 3.45

Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci U S A (2006) 3.35

Genomic mining for Aspergillus natural products. Chem Biol (2006) 3.22

Discovery of a widely distributed toxin biosynthetic gene cluster. Proc Natl Acad Sci U S A (2008) 3.20

Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat Chem Biol (2005) 3.17

Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol (2007) 3.14

Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A (2009) 2.86

Physical and genetic characterisation of the gene cluster for the antibiotic actinorhodin in Streptomyces coelicolor A3(2). Mol Gen Genet (1986) 2.61

Chromatin-level regulation of biosynthetic gene clusters. Nat Chem Biol (2009) 2.50

A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. J Am Chem Soc (2009) 2.45

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol (2004) 2.41

Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat Biotechnol (2008) 2.35

Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies. BMC Genomics (2005) 2.34

ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res (2008) 2.34

The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol (2007) 2.32

Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. DNA Res (2008) 2.31

Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J Bacteriol (2006) 2.29

Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. Proc Natl Acad Sci U S A (2009) 2.22

Genome mining for novel natural product discovery. J Med Chem (2008) 2.22

The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis. Proc Natl Acad Sci U S A (2007) 2.22

Thiostrepton biosynthesis: prototype for a new family of bacteriocins. J Am Chem Soc (2009) 2.19

Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic. Proc Natl Acad Sci U S A (2006) 2.19

Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Proc Natl Acad Sci U S A (2010) 2.18

Biosynthesis and structure of aeruginoside 126A and 126B, cyanobacterial peptide glycosides bearing a 2-carboxy-6-hydroxyoctahydroindole moiety. Chem Biol (2007) 2.11

Structure of trichamide, a cyclic peptide from the bloom-forming cyanobacterium Trichodesmium erythraeum, predicted from the genome sequence. Appl Environ Microbiol (2006) 2.07

Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A (2007) 2.06

Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens. Proc Natl Acad Sci U S A (2011) 2.05

A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat Chem Biol (2011) 2.05

The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. Proc Natl Acad Sci U S A (2004) 2.04

A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science (2012) 2.00

Marcel Faber Roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration? J Ind Microbiol Biotechnol (2006) 1.94

Thiopeptide biosynthesis featuring ribosomally synthesized precursor peptides and conserved posttranslational modifications. Chem Biol (2009) 1.93

Ribosomally synthesized thiopeptide antibiotics targeting elongation factor Tu. J Am Chem Soc (2009) 1.92

Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. J Nat Prod (2005) 1.88

Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. Proc Natl Acad Sci U S A (2008) 1.88

Microcyclamide biosynthesis in two strains of Microcystis aeruginosa: from structure to genes and vice versa. Appl Environ Microbiol (2008) 1.79

Advances in Aspergillus secondary metabolite research in the post-genomic era. Nat Prod Rep (2012) 1.75

Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights. PLoS Biol (2010) 1.74

Genetic and biochemical characterization of the red gene cluster of Streptomyces coelicolor A3(2). J Gen Microbiol (1985) 1.68

Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol (2009) 1.68

Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. Curr Opin Chem Biol (2011) 1.67

Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis. Proc Natl Acad Sci U S A (2003) 1.67

Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the emericellamide biosynthetic pathway. Chem Biol (2008) 1.66

A chemical epigenetics approach for engineering the in situ biosynthesis of a cryptic natural product from Aspergillus niger. Org Biomol Chem (2008) 1.65

BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Res (2006) 1.64

Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol (2010) 1.58

Gamma-butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation. Curr Opin Microbiol (2006) 1.55

Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio (2012) 1.55

Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. J Biol Chem (2004) 1.54

Lantibiotics from Geobacillus thermodenitrificans. Proc Natl Acad Sci U S A (2012) 1.53

Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc Natl Acad Sci U S A (2010) 1.52

Hopanoids are formed during transition from substrate to aerial hyphae in Streptomyces coelicolor A3(2). FEMS Microbiol Lett (2000) 1.52

YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations. Nat Chem Biol (2012) 1.50

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. BMC Biol (2010) 1.49

Type III polyketide synthase beta-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. J Am Chem Soc (2006) 1.48

Physically discrete beta-lactamase-type thioesterase catalyzes product release in atrochrysone synthesis by iterative type I polyketide synthase. Chem Biol (2009) 1.48

Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2). J Biol Chem (2008) 1.48

Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264. J Am Chem Soc (2008) 1.47

Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42. J Bacteriol (2010) 1.47

Identification of a cluster of genes that directs desferrioxamine biosynthesis in Streptomyces coelicolor M145. J Am Chem Soc (2004) 1.43

Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease. J Biotechnol (2008) 1.42

Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. BMC Genomics (2011) 1.38

Molecular genetic analysis of the orsellinic acid/F9775 gene cluster of Aspergillus nidulans. Mol Biosyst (2009) 1.37

Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc (2012) 1.34

Staphylococcus aureus nonribosomal peptide secondary metabolites regulate virulence. Science (2010) 1.33

Discovery of aspoquinolones A-D, prenylated quinoline-2-one alkaloids from Aspergillus nidulans, motivated by genome mining. Org Biomol Chem (2006) 1.33

Thailandepsins: bacterial products with potent histone deacetylase inhibitory activities and broad-spectrum antiproliferative activities. J Nat Prod (2011) 1.30

A cryptic type I polyketide synthase (cpk) gene cluster in Streptomyces coelicolor A3(2). Arch Microbiol (2006) 1.28

Genomic analyses lead to novel secondary metabolites. Part 3. ECO-0501, a novel antibacterial of a new class. J Antibiot (Tokyo) (2006) 1.28

Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics. ACS Chem Biol (2011) 1.27

Bacillaene, a novel inhibitor of procaryotic protein synthesis produced by Bacillus subtilis: production, taxonomy, isolation, physico-chemical characterization and biological activity. J Antibiot (Tokyo) (1995) 1.25

Plantazolicin A and B: structure elucidation of ribosomally synthesized thiazole/oxazole peptides from Bacillus amyloliquefaciens FZB42. Org Lett (2011) 1.23

A genome-wide polyketide synthase deletion library uncovers novel genetic links to polyketides and meroterpenoids in Aspergillus nidulans. FEMS Microbiol Lett (2011) 1.22

Identification of a novel two-peptide lantibiotic, haloduracin, produced by the alkaliphile Bacillus halodurans C-125. FEMS Microbiol Lett (2007) 1.21

Highly diverse cyanobactins in strains of the genus Anabaena. Appl Environ Microbiol (2009) 1.18

Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria. Biochemistry (2012) 1.18

Comparative genomic analysis of fruiting body formation in Myxococcales. Mol Biol Evol (2010) 1.17

Structure and biosynthesis of the antibiotic bottromycin D. Org Lett (2012) 1.16

The unique DKxanthene secondary metabolite family from the myxobacterium Myxococcus xanthus is required for developmental sporulation. Proc Natl Acad Sci U S A (2006) 1.15

Precursor-centric genome-mining approach for lasso peptide discovery. Proc Natl Acad Sci U S A (2012) 1.14

Articles by these authors

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep (2013) 5.38

Discovery of a widely distributed toxin biosynthetic gene cluster. Proc Natl Acad Sci U S A (2008) 3.20

Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69

Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. Curr Opin Chem Biol (2011) 1.67

Bottom-up determination of air-sea momentum exchange under a major tropical cyclone. Science (2007) 1.66

YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations. Nat Chem Biol (2012) 1.50

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. BMC Biol (2010) 1.49

Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42. J Bacteriol (2010) 1.47

Streptolysin S-like virulence factors: the continuing sagA. Nat Rev Microbiol (2011) 1.42

Selectivity, directionality, and promiscuity in peptide processing from a Bacillus sp. Al Hakam cyclodehydratase. J Am Chem Soc (2012) 1.31

Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics. ACS Chem Biol (2011) 1.27

Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum. J Biol Chem (2010) 1.25

Multitarget drug discovery for tuberculosis and other infectious diseases. J Med Chem (2014) 1.24

Identification of a potent and selective pharmacophore for Cdc25 dual specificity phosphatase inhibitors. Mol Pharmacol (2002) 1.20

Subcellular targeting and differential S-nitrosylation of endothelial nitric-oxide synthase. J Biol Chem (2005) 1.16

Insights into the mechanism of peptide cyclodehydrations achieved through the chemoenzymatic generation of amide derivatives. J Am Chem Soc (2013) 1.11

Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis. Proc Natl Acad Sci U S A (2013) 1.03

Extreme waves under Hurricane Ivan. Science (2005) 0.98

Orchestration of enzymatic processing by thiazole/oxazole-modified microcin dehydrogenases. Biochemistry (2014) 0.98

Engineering unnatural variants of plantazolicin through codon reprogramming. ACS Chem Biol (2013) 0.98

Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. J Mol Biol (2011) 0.97

Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol (2013) 0.94

Catalase-peroxidase activity of iron(III)-TAML activators of hydrogen peroxide. J Am Chem Soc (2008) 0.90

HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis. ACS Med Chem Lett (2012) 0.85

Nucleophilic 1,4-additions for natural product discovery. ACS Chem Biol (2014) 0.80

YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev (2017) 0.79

Synthesis of plantazolicin analogues enables dissection of ligand binding interactions of a highly selective methyltransferase. Org Lett (2013) 0.78

Crystallization and preliminary X-ray diffraction analysis of YisP protein from Bacillus subtilis subsp. subtilis strain 168. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 0.78

Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem (2014) 0.78

Profiling of microbial colonies for high-throughput engineering of multi-step enzymatic reactions via optically guided MALDI MS. J Am Chem Soc (2017) 0.75

Mechanism of a Class C Radical SAM Thiazole Methyl Transferase. J Am Chem Soc (2017) 0.75

Correction to Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis. Biochemistry (2017) 0.75