Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

Fungal Polyketide Synthase Product Chain-Length Control by Partnering Thiohydrolase

(2014) Angelica O. Zabala et al.   ACS Chemical Biology

AnIn Planta-Expressed Polyketide Synthase Produces (R)-Mellein in the Wheat Pathogen Parastagonospora nodorum

(2014) Yit-Heng Chooi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys

(2014) Jeremy Semeiks et al.   BMC GENOMICS

New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics

(2014) Gerald Bills et al.   NATURAL PRODUCT REPORTS

Biosynthesis of fungal indole alkaloids

(2014) Wei Xu et al.   NATURAL PRODUCT REPORTS

Fungal type III polyketide synthases

(2014) Makoto Hashimoto et al.   NATURAL PRODUCT REPORTS

MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data

(2014) Myco Umemura et al.   PLoS One

A Non-Canonical NRPS Is Involved in the Synthesis of Fungisporin and Related Hydrophobic Cyclic Tetrapeptides in Penicillium chrysogenum

(2014) Hazrat Ali et al.   PLoS One

Apicidin F: Characterization and Genetic Manipulation of a New Secondary Metabolite Gene Cluster in the Rice Pathogen Fusarium fujikuroi

(2014) Eva-Maria Niehaus et al.   PLoS One

Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases

(2014) Y. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens

(2014) Yit-Heng Chooi et al.   Frontiers in Microbiology

Two Related Pyrrolidinedione Synthetase Loci in Fusarium heterosporum ATCC 74349 Produce Divergent Metabolites

(2013) Thomas B. Kakule et al.   ACS Chemical Biology

Complexity Generation in Fungal Polyketide Biosynthesis: A Spirocycle-Forming P450 in the Concise Pathway to the Antifungal Drug Griseofulvin

(2013) Ralph A. Cacho et al.   ACS Chemical Biology

Complexity Generation in Fungal Peptidyl Alkaloid Biosynthesis: A Two-Enzyme Pathway to the Hexacyclic MDR Export Pump Inhibitor Ardeemin

(2013) Stuart W. Haynes et al.   ACS Chemical Biology

Nonproteinogenic Amino Acid Building Blocks for Nonribosomal Peptide and Hybrid Polyketide Scaffolds

(2013) Christopher T. Walsh et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

LovG: The Thioesterase Required for Dihydromonacolin L Release and Lovastatin Nonaketide Synthase Turnover in Lovastatin Biosynthesis

(2013) Wei Xu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Characterization of the Biosynthetic Genes for 10,11-Dehydrocurvularin, a Heat Shock Response-Modulating Anticancer Fungal Polyketide from Aspergillus terreus

(2013) Yuquan Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Point Mutation inftmDBlocks the Fumitremorgin Biosynthetic Pathway inAspergillus fumigatusStrain Af293

(2013) Naoki KATO et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis

(2013) Li Chen et al.   BMC GENOMICS

Genetic Manipulation of the Fusarium fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway

(2013) Eva-Maria Niehaus et al.   CHEMISTRY & BIOLOGY

EcdGHK Are Three Tailoring Iron Oxygenases for Amino Acid Building Blocks of the Echinocandin Scaffold

(2013) Wei Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combinatorial Generation of Complexity by Redox Enzymes in the Chaetoglobosin A Biosynthesis

(2013) Kan’ichiro Ishiuchi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Cytochrome P450 Serves as an Unexpected Terpene Cyclase during Fungal Meroterpenoid Biosynthesis

(2013) Yit-Heng Chooi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discovery and development of first in class antifungal caspofungin (CANCIDAS®)—A case study

(2013) James M. Balkovec et al.   NATURAL PRODUCT REPORTS

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Genome Mining of a Prenylated and Immunosuppressive Polyketide from Pathogenic Fungi

(2013) Yit-Heng Chooi et al.   ORGANIC LETTERS

Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40

(2013) Myco Umemura et al.   PLoS One

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

(2013) Aarti Desai et al.   PLoS One

Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures

(2013) Dimitrios Kleftogiannis et al.   PLoS One

Prototype of an intertwined secondary-metabolite supercluster

(2013) P. Wiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

(2013) Philipp Wiemann et al.   PLoS Pathogens

Molecular Diversity Sculpted by Fungal PKS-NRPS Hybrids

(2012) Daniela Boettger et al.   CHEMBIOCHEM

Characterization of the Suillus grevillei Quinone Synthetase GreA Supports a Nonribosomal Code for Aromatic α-Keto Acids

(2012) Barbara Wackler et al.   CHEMBIOCHEM

Characterization of a Silent Azaphilone Gene Cluster from Aspergillus niger ATCC 1015 Reveals a Hydroxylation-Mediated Pyran-Ring Formation

(2012) Angelica O. Zabala et al.   CHEMISTRY & BIOLOGY

Dothistromin genes at multiple separate loci are regulated by AflR

(2012) Pranav Chettri et al.   FUNGAL GENETICS AND BIOLOGY

Navigating the Fungal Polyketide Chemical Space: From Genes to Molecules

(2012) Yit-Heng Chooi et al.   JOURNAL OF ORGANIC CHEMISTRY

Discovery and Characterization of a Group of Fungal Polycyclic Polyketide Prenyltransferases

(2012) Yit-Heng Chooi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification and Characterization of the Chaetoviridin and Chaetomugilin Gene Cluster in Chaetomium globosum Reveal Dual Functions of an Iterative Highly-Reducing Polyketide Synthase

(2012) Jaclyn M. Winter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assembly of Asperlicin Peptidyl Alkaloids from Anthranilate and Tryptophan: A Two-Enzyme Pathway Generates Heptacyclic Scaffold Complexity in Asperlicin E

(2012) Stuart W. Haynes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification and Characterization of the Echinocandin B Biosynthetic Gene Cluster from Emericella rugulosa NRRL 11440

(2012) Ralph A. Cacho et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Illuminating the Diversity of Aromatic Polyketide Synthases in Aspergillus nidulans

(2012) Manmeet Ahuja et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain

(2012) Xue Gao et al.   Nature Chemical Biology

Comparative analysis of the biosynthetic systems for fungal bicyclo[2.2.2]diazaoctane indole alkaloids: the (+)/(−)-notoamide, paraherquamide and malbrancheamide pathways

(2012) Shengying Li et al.   MedChemComm

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Penicillin: the medicine with the greatest impact on therapeutic outcomes

(2011) Nelson Kardos et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

A putative ABC transporter gene, ZRA1, is required for zearalenone production in Gibberella zeae

(2011) Seunghoon Lee et al.   CURRENT GENETICS

Two Novel Classes of Enzymes Are Required for the Biosynthesis of Aurofusarin inFusarium graminearum

(2011) Rasmus J. N. Frandsen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Based Deletion Analysis Reveals the Prenyl Xanthone Biosynthesis Pathway inAspergillus nidulans

(2011) James F. Sanchez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fungal Indole Alkaloid Biosynthesis: Genetic and Biochemical Investigation of the Tryptoquialanine Pathway inPenicillium aethiopicum

(2011) Xue Gao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comparative Characterization of Fungal Anthracenone and Naphthacenedione Biosynthetic Pathways Reveals an α-Hydroxylation-Dependent Claisen-like Cyclization Catalyzed by a Dimanganese Thioesterase

(2011) Yanran Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1

(2011) Kangjian Qiao et al.   METABOLIC ENGINEERING

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

Metabolic Engineering for the Production of Natural Products

(2011) Lauren B. Pickens et al.   Annual Review of Chemical and Biomolecular Engineering

Anthranilate-Activating Modules from Fungal Nonribosomal Peptide Assembly Lines

(2010) Brian D. Ames et al.   BIOCHEMISTRY

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

(2010) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

Identification of the Viridicatumtoxin and Griseofulvin Gene Clusters from Penicillium aethiopicum

(2010) Yit-Heng Chooi et al.   CHEMISTRY & BIOLOGY

Nonribosomal peptide synthetases: structures and dynamics

(2010) Matthias Strieker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

(2010) Minou Nowrousian   EUKARYOTIC CELL

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Classification, Prediction, and Verification of the Regioselectivity of Fungal Polyketide Synthase Product Template Domains

(2010) Yanran Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enzymatic Synthesis of Resorcylic Acid Lactones by Cooperation of Fungal Iterative Polyketide Synthases Involved in Hypothemycin Biosynthesis

(2010) Hui Zhou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fungal cyclooligomerdepsipeptides: From classical biochemistry to combinatorial biosynthesis

(2010) Roderich Süssmuth et al.   NATURAL PRODUCT REPORTS

New insights into the formation of fungal aromatic polyketides

(2010) Jason M. Crawford et al.   NATURE REVIEWS MICROBIOLOGY

A historical perspective on the discovery of statins

(2010) Akira ENDO   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis

(2010) T. P. Korman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physically Discrete β-Lactamase-Type Thioesterase Catalyzes Product Release in Atrochrysone Synthesis by Iterative Type I Polyketide Synthase

(2009) Takayoshi Awakawa et al.   CHEMISTRY & BIOLOGY

Directed Evolution and Structural Characterization of a Simvastatin Synthase

(2009) Xue Gao et al.   CHEMISTRY & BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Acyltransferase Mediated Polyketide Release from a Fungal Megasynthase

(2009) Xinkai Xie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Gene Cluster Containing Two Fungal Polyketide Synthases Encodes the Biosynthetic Pathway for a Polyketide, Asperfuranone, inAspergillus nidulans

(2009) Yi-Ming Chiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization

(2009) Jason M. Crawford et al.   NATURE

Genes for the Biosynthesis of the Fungal Polyketides Hypothemycin from Hypomyces subiculosus and Radicicol from Pochonia chlamydosporia

(2008) C. D. Reeves et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biosynthesis of the Cyclooligomer Depsipeptide Beauvericin, a Virulence Factor of the Entomopathogenic Fungus Beauveria bassiana

(2008) Yuquan Xu et al.   CHEMISTRY & BIOLOGY

Functional Characterization of the Biosynthesis of Radicicol, an Hsp90 Inhibitor Resorcylic Acid Lactone from Chaetomium chiversii

(2008) Shuhao Wang et al.   CHEMISTRY & BIOLOGY

A survey of nonribosomal peptide synthetase (NRPS) genes in Aspergillus nidulans

(2008) Hans von Döhren   FUNGAL GENETICS AND BIOLOGY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Deconstruction of Iterative Multidomain Polyketide Synthase Function

(2008) J. M. Crawford et al.   SCIENCE

Iron and siderophores in fungal–host interactions

(2008) Linda Johnson  

Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation

(2007) Koichi Tamano et al.   FUNGAL GENETICS AND BIOLOGY