Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline

Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow

(2017) Changsheng Wu et al.   JOURNAL OF NATURAL PRODUCTS

Discovery of a Cryptic Antifungal Compound from Streptomyces albus J1074 Using High-Throughput Elicitor Screens

(2017) Fei Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Contribution of the β-glucosidase BglC to the onset of the pathogenic lifestyle of Streptomyces scabies

(2017) Samuel Jourdan et al.   MOLECULAR PLANT PATHOLOGY

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

(2017) Brett C. Covington et al.   NATURAL PRODUCT REPORTS

RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links

(2017) Priyesh Agrawal et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans

(2016) Matthew T. Henke et al.   ACS Chemical Biology

BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals

(2016) Minsuk Kim et al.   BIOINFORMATICS

Type III Polyketide Synthases: Functional Classification and Phylogenomics

(2016) Yugo Shimizu et al.   CHEMBIOCHEM

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Intertwining nutrient-sensory networks and the control of antibiotic production inStreptomyces

(2016) Mia Urem et al.   MOLECULAR MICROBIOLOGY

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks

(2016) Hosein Mohimani et al.   NATURAL PRODUCT REPORTS

Chemical proteomics approaches for identifying the cellular targets of natural products

(2016) M. H. Wright et al.   NATURAL PRODUCT REPORTS

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching

(2016) Chris A Dejong et al.   Nature Chemical Biology

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

(2016) Michael A. Skinnider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging new strategies for successful metabolite identification in metabolomics

(2016) Kerem Bingol et al.   Bioanalysis

Goodbye to brute force in antibiotic discovery?

(2016) Roberto Kolter et al.   Nature Microbiology

Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66

(2015) Changsheng Wu et al.   ACS Chemical Biology

Epigenetic Genome Mining of an Endophytic Fungus Leads to the Pleiotropic Biosynthesis of Natural Products

(2015) Xu-Ming Mao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains ofStreptomyces coelicolor

(2015) Minsuk Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

Active site-directed proteomic probes for adenylation domains in nonribosomal peptide synthetases

(2015) Sho Konno et al.   CHEMICAL COMMUNICATIONS

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

Metabolic profiling as a tool for prioritizing antimicrobial compounds

(2015) Changsheng Wu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by Streptomyces Species MBT28

(2015) Changsheng Wu et al.   JOURNAL OF NATURAL PRODUCTS

Taxonomy, Physiology, and Natural Products of Actinobacteria

(2015) Essaid Ait Barka et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Dereplication: racing to speed up the natural products discovery process

(2015) Susana P. Gaudêncio et al.   NATURAL PRODUCT REPORTS

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

(2015) Peter J. Rutledge et al.   NATURE REVIEWS MICROBIOLOGY

Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing

(2015) Areski Flissi et al.   NUCLEIC ACIDS RESEARCH

Socially mediated induction and suppression of antibiosis during bacterial coexistence

(2015) Monica I. Abrudan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cellobiose Sensor CebR Is the Gatekeeper of Streptomyces scabies Pathogenicity

(2015) Isolde M. Francis et al.   mBio

Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets

(2015) Magdalena A. Świątek-Połatyńska et al.   PLoS One

Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza

(2014) Wei Gao et al.   BMC GENOMICS

Natural Product Proteomining, a Quantitative Proteomics Platform, Allows Rapid Discovery of Biosynthetic Gene Clusters for Different Classes of Natural Products

(2014) Jacob Gubbens et al.   CHEMISTRY & BIOLOGY

A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

(2014) Rebecca A. Owens et al.   PLoS One

Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring

(2013) Kai Pong Law et al.   Expert Review of Proteomics

The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island

(2013) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways

(2013) Jessica C. Albright et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Triggers and cues that activate antibiotic production by actinomycetes

(2013) Hua Zhu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Molecular Networking as a Dereplication Strategy

(2013) Jane Y. Yang et al.   JOURNAL OF NATURAL PRODUCTS

Proteomics Guided Discovery of Flavopeptins: Anti-proliferative Aldehydes Synthesized by a Reductase Domain-Containing Non-ribosomal Peptide Synthetase

(2013) Yunqiu Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

(2013) G. Liu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

Chitin-Induced Gene Expression in Secondary Metabolic Pathways of Streptomyces coelicolor A3(2) Grown in Soil

(2012) Behnam Nazari et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chemical Perturbation of Secondary Metabolism Demonstrates Important Links to Primary Metabolism

(2012) Arryn Craney et al.   CHEMISTRY & BIOLOGY

Thoughts and facts about antibiotics: Where we are now and where we are heading

(2012) János Bérdy   JOURNAL OF ANTIBIOTICS

Mass spectral molecular networking of living microbial colonies

(2012) J. Watrous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

(2012) A. Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unsuspected control of siderophore production byN-acetylglucosamine in streptomycetes

(2012) Matthias Craig et al.   Environmental Microbiology Reports

Significant Natural Product Biosynthetic Potential of Actinorhizal Symbionts of the Genus Frankia, as Revealed by Comparative Genomic and Proteomic Analyses

(2011) Daniel W. Udwary et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional Analysis of the N-Acetylglucosamine Metabolic Genes of Streptomyces coelicolor and Role in Control of Development and Antibiotic Production

(2011) M. A. Swiatek et al.   JOURNAL OF BACTERIOLOGY

A Proteomic Survey of Nonribosomal Peptide and Polyketide Biosynthesis in Actinobacteria

(2011) Yunqiu Chen et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics-Based Discovery of Koranimine, a Cyclic Imine Natural Product

(2011) Bradley S. Evans et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The regulation of the secondary metabolism of Streptomyces: new links and experimental advances

(2011) Gilles P. van Wezel et al.   NATURAL PRODUCT REPORTS

Fix the antibiotics pipeline

(2011) Matthew A. Cooper et al.   NATURE

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

Secondary metabolism in fungi: does chromosomal location matter?

(2010) Jonathan M Palmer et al.   CURRENT OPINION IN MICROBIOLOGY

Promomycin, a polyether promoting antibiotic production in Streptomyces spp.

(2010) Sho-ichi Amano et al.   JOURNAL OF ANTIBIOTICS

Carbon source regulation of antibiotic production

(2010) Sergio Sánchez et al.   JOURNAL OF ANTIBIOTICS

Current approaches to exploit actinomycetes as a source of novel natural products

(2010) Olga Genilloud et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

The permease genenagE2is the key toN-acetylglucosamine sensing and utilization inStreptomyces coelicolorand is subject to multi-level control

(2010) Harald Nothaft et al.   MOLECULAR MICROBIOLOGY

The pros and cons of peptide-centric proteomics

(2010) Mark W Duncan et al.   NATURE BIOTECHNOLOGY

An Orthogonal Active Site Identification System (OASIS) for Proteomic Profiling of Natural Product Biosynthesis

(2009) Jordan L. Meier et al.   ACS Chemical Biology

The Biosynthetic Logic of Polyketide Diversity

(2009) Christian Hertweck   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CebR as a Master Regulator for Cellulose/Cellooligosaccharide Catabolism Affects Morphological Development in Streptomyces griseus

(2009) K. Marushima et al.   JOURNAL OF BACTERIOLOGY

A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches

(2009) Vibhuti J. Patel et al.   JOURNAL OF PROTEOME RESEARCH

Epigenome manipulation as a pathway to new natural product scaffolds and their congeners

(2009) Robert H. Cichewicz   NATURAL PRODUCT REPORTS

A proteomics approach to discovering natural products and their biosynthetic pathways

(2009) Stefanie B Bumpus et al.   NATURE BIOTECHNOLOGY

Target profiling of small molecules by chemical proteomics

(2009) Uwe Rix et al.   Nature Chemical Biology

Dereplication and de novo sequencing of nonribosomal peptides

(2009) Julio Ng et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Renaissance in antibacterial discovery from actinomycetes

(2008) R BALTZ   CURRENT OPINION IN PHARMACOLOGY

Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces

(2008) Sébastien Rigali et al.   EMBO REPORTS

Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350

(2008) Y. Ohnishi et al.   JOURNAL OF BACTERIOLOGY

Fluorescent Profiling of Modular Biosynthetic Enzymes by Complementary Metabolic and Activity Based Probes

(2008) Jordan L. Meier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Top-down mass spectrometry on low-resolution instruments: Characterization of phosphopantetheinylated carrier domains in polyketide and non-ribosomal biosynthetic pathways

(2007) Dario Meluzzi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS