Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research

Mass spectrometry searches using MASST

(2020) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Dual sgRNA‐directed gene deletion in basidiomycete Ganoderma lucidum using the CRISPR/Cas9 system

(2020) Ke Liu et al.   Microbial Biotechnology

Lefamulin: A Novel Semisynthetic Pleuromutilin Antibiotic for Community-acquired Bacterial Pneumonia

(2020) Richard R Watkins et al.   CLINICAL INFECTIOUS DISEASES

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

(2020) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Engineering isoprenoid quinone production in yeast

(2020) Divjot Kaur et al.   ACS Synthetic Biology

Ustilago maydis Serves as a Novel Production Host for the Synthesis of Plant and Fungal Sesquiterpenoids

(2020) Jungho Lee et al.   Frontiers in Microbiology

Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture

(2020) Sean K. McKenzie et al.   GENOMICS

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

(2019) Sarah Goldstein et al.   BMC GENOMICS

Optimizing genome editing strategy by primer-extension-mediated sequencing

(2019) Jianhang Yin et al.   Cell Discovery

Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides

(2019) Peter B. Otoupal et al.   mSphere

Highly efficient single base editing in Aspergillus niger with CRISPR/Cas9 cytidine deaminase fusion

(2019) Lianggang Huang et al.   MICROBIOLOGICAL RESEARCH

Ascomycota Aspergillus oryzae is an efficient expression host for production of Basidiomycota terpenes using genomic DNA sequences

(2019) Shota Nagamine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Modulating Fatty Acid Epoxidation vs Hydroxylation in a Fungal Peroxygenase

(2019) Juan Carro et al.   ACS Catalysis

High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins

(2019) Peter Jan Vonk et al.   Scientific Reports

Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production

(2019) Antoine Vassaux et al.   BIOTECHNOLOGY ADVANCES

CRISPR/Cas9-mediated gene replacement in the basidiomycetous yeast Pseudozyma antarctica

(2019) Emi Kunitake et al.   FUNGAL GENETICS AND BIOLOGY

Efficient Reconstitution of Basidiomycota Diterpene Erinacine Gene Cluster in Ascomycota Host Aspergillus oryzae Based on Genomic DNA Sequences

(2019) Chengwei Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

(2019) Jeffrey A. van Santen et al.   ACS Central Science

CRISPR-Cas9 assisted functional gene editing in the mushroom Ganoderma lucidum

(2019) Ping-An Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer

(2019) Korena K Mafune et al.   BIOTECHNIQUES

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

(2019) Hadjer Ouldali et al.   NATURE BIOTECHNOLOGY

Comparative analyses of secreted proteins in plant pathogenic smut fungi and related basidiomycetes

(2018) Mariana Schuster et al.   FUNGAL GENETICS AND BIOLOGY

Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum

(2018) Xiao-Yan Xu et al.   Frontiers in Microbiology

HEx: A heterologous expression platform for the discovery of fungal natural products

(2018) Colin J. B. Harvey et al.   Science Advances

Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger

(2018) Letian Song et al.   PLoS One

Strobilurin biosynthesis in Basidiomycete fungi

(2018) Risa Nofiani et al.   Nature Communications

Forced Recycling of an AMA1-Based Genome-Editing Plasmid Allows for Efficient Multiple Gene Deletion/Integration in the Industrial Filamentous Fungus Aspergillus oryzae

(2018) Takuya Katayama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of sesquiterpene synthases from the Basidiomycota Coniophora puteana for the efficient and highly selective β-copaene and cubebol production in E. coli

(2018) Wolfgang Mischko et al.   Microbial Cell Factories

CRISPR system in filamentous fungi: Current achievements and future directions

(2017) Huaxiang Deng et al.   GENE

Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast

(2017) Hui-Yeng Yeannie Yap et al.   Microbial Cell Factories

Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products

(2017) Niels S van der Velden et al.   Nature Chemical Biology

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas9 assisted gene disruption in the higher fungus Ganoderma species

(2017) Hao Qin et al.   PROCESS BIOCHEMISTRY

Heterologous expression reveals the biosynthesis of the antibiotic pleuromutilin and generates bioactive semi-synthetic derivatives

(2017) Fabrizio Alberti et al.   Nature Communications

Limb proportions show developmental plasticity in response to embryo movement

(2017) A. S. Pollard et al.   Scientific Reports

Natural products from filamentous fungi and production by heterologous expression

(2016) Fabrizio Alberti et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Heterologous expression of fungal cytochromes P450 (CYP5136A1 and CYP5136A3) from the white-rot basidiomycete Phanerochaete chrysosporium : Functionalization with cytochrome b 5 in Escherichia coli

(2016) Mayumi Hatakeyama et al.   ENZYME AND MICROBIAL TECHNOLOGY

Laccase Gene Family in Cerrena sp. HYB07: Sequences, Heterologous Expression and Transcriptional Analysis

(2016) Jie Yang et al.   MOLECULES

Gene-edited CRISPR mushroom escapes US regulation

(2016) Emily Waltz   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

(2016) Andy M. Bailey et al.   Scientific Reports

A native promoter and inclusion of an intron is necessary for efficient expression of GFP or mRFP in Armillaria mellea

(2016) Kathryn L. Ford et al.   Scientific Reports

Discovery of novel xylosides in co-culture of basidiomycetes Trametes versicolor and Ganoderma applanatum by integrated metabolomics and bioinformatics

(2016) Lu Yao et al.   Scientific Reports

Involutin Is an Fe3+Reductant Secreted by the Ectomycorrhizal Fungus Paxillus involutus during Fenton-Based Decomposition of Organic Matter

(2015) Firoz Shah et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The diversity of fungal genome

(2015) Tapan Kumar Mohanta et al.   BIOLOGICAL PROCEDURES ONLINE

Tandem-yeast expression system for engineering and producing unspecific peroxygenase

(2015) Patricia Molina-Espeja et al.   ENZYME AND MICROBIAL TECHNOLOGY

A novel laccase from basidiomycete Cerrena sp.: Cloning, heterologous expression, and characterization

(2015) Jie Yang et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

(2015) Takeshi Maruyama et al.   NATURE BIOTECHNOLOGY

Minimum Information about a Biosynthetic Gene cluster

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

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

(2014) Zachary L. Wescoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biosynthesis of fungal indole alkaloids

(2014) Wei Xu et al.   NATURAL PRODUCT REPORTS

Antioxidant polyketide phenolic metabolites from the edible mushroom Cortinarius purpurascens

(2013) Ming-Sheng Bai et al.   FOOD CHEMISTRY

Draft Genome of Omphalotus olearius Provides a Predictive Framework for Sesquiterpenoid Natural Product Biosynthesis in Basidiomycota

(2012) Grayson T. Wawrzyn et al.   CHEMISTRY & BIOLOGY

Screening of Medicinal Higher Basidiomycetes Mushrooms from Turkey for Lovastatin Production

(2012) Burcu Atli et al.   INTERNATIONAL JOURNAL OF MEDICINAL MUSHROOMS

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

(2011) M. B. Arnaud et al.   NUCLEIC ACIDS RESEARCH

Acetylcholinesterase inhibitors from the toadstool Cortinarius infractus

(2010) Torsten Geissler et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Improvement of the Coprinopsis cinerea molecular toolkit using new construct design and additional marker genes

(2010) Catherine M. Collins et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Elucidation of the complete ferrichrome A biosynthetic pathway inUstilago maydis

(2010) Britta Winterberg et al.   MOLECULAR MICROBIOLOGY

Structure and absolute configuration of toxic polyketide pigments from the fruiting bodies of the fungus Cortinarius rufo-olivaceus

(2010) Jin-Ming Gao et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation

(2010) Anne Osbourn   TRENDS IN GENETICS

An efficient gene deletion procedure for the mushroom-forming basidiomycete Schizophyllum commune

(2010) Robin A. Ohm et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Sterelactones: New Isolactarane Type Sesquiterpenoids with Antifungal Activity from Stereum sp. IBWF 01060

(2009) Till Opatz et al.   JOURNAL OF ANTIBIOTICS

Diversity of sesquiterpene synthases in the basidiomyceteCoprinus cinereus

(2009) Sean Agger et al.   MOLECULAR MICROBIOLOGY

Determination ofβ‐carboline alkaloids in fruiting bodies ofHygrophorusspp. by liquid chromatography/electrospray ionisation tandem mass spectrometry

(2008) Axel Teichert et al.   PHYTOCHEMICAL ANALYSIS

The pleuromutilin drugs tiamulin and valnemulin bind to the RNA at the peptidyl transferase centre on the ribosome

(2003) Susan M. Poulsen et al.   MOLECULAR MICROBIOLOGY