4.8 Article

Correlative metabologenomics of 110 fungi reveals metabolite-gene cluster pairs

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biochemistry & Molecular Biology

Fungal-fungal co-culture: a primer for generating chemical diversity

Sonja L. Knowles et al.

Summary: This review summarizes the development of fungal-fungal co-culture studies from 2002 to 2020. It has been found that growing fungi in co-culture in the laboratory, replicating the competitive environment, can lead to the discovery of new secondary metabolites. The review discusses principles for pairing fungal strains, methods for growing fungi in co-culture, approaches to screening for chemical diversity, determining the strain that produces secondary metabolites, and final thoughts on the fungal-fungal co-culture approach.

NATURAL PRODUCT REPORTS (2022)

Article Plant Sciences

Cytotoxic Naphthoquinone Analogues, Including Heterodimers, and Their Structure Elucidation Using LR-HSQMBC NMR Experiments

Laura Flores-Bocanegra et al.

Summary: A series of new naphthoquinones, including two heterodimers, were isolated from Pyrenochaetopsis sp. During the study, the structure of these compounds was elucidated using various experimental methods, and their cytotoxicity against human cancer cell lines was evaluated, with IC50 values ranging from 1 to 20 μM.

JOURNAL OF NATURAL PRODUCTS (2021)

Article Biochemistry & Molecular Biology

BiG-FAM: the biosynthetic gene cluster families database

Satria A. Kautsar et al.

Summary: BiG-FAM is a database containing 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and MAGs. The database offers rich functionalities, such as GCF searches, direct links to BGC databases, and rapid annotation of user-supplied BGCs.

NUCLEIC ACIDS RESEARCH (2021)

Article Biology

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

Satria A. Kautsar et al.

Summary: BiG-SLiCE is a tool designed to cluster massive numbers of BGCs by representing them in Euclidean space to group BGCs into GCFs in a non-pairwise, near-linear fashion. It was used to analyze over 1.2 million BGCs collected from microbial genomes and metagenome-assembled genomes within 10 days. The tool offers a query mode to efficiently place newly sequenced BGCs into previously computed GCFs, along with a powerful output visualization engine for user-friendly data exploration.

GIGASCIENCE (2021)

Article Biochemistry & Molecular Biology

A community resource for paired genomic and metabolomic data mining

Michelle A. Schorn et al.

Summary: Genomics and metabolomics are commonly used to explore the diversity of specialized metabolites. The Paired Omics Data Platform aims to systematically document the connections between metabolome and (meta)genome data to aid in the identification of natural product biosynthetic origins and metabolite structures.

NATURE CHEMICAL BIOLOGY (2021)

Article Plant Sciences

Opportunities and Limitations for Assigning Relative Configurations of Antibacterial Bislactones using GIAO NMR Shift Calculations

Sonja L. Knowles et al.

Summary: Four new bislactones were isolated from cultures of two fungal strains and identified as Clonostachys spp. based on molecular data. These compounds showed antimicrobial activities, with compounds 1 and 4 being the most potent against Staphylococcus aureus.

JOURNAL OF NATURAL PRODUCTS (2021)

Article Biochemistry & Molecular Biology

antiSMASH 6.0: improving cluster detection and comparison capabilities

Kai Blin et al.

Summary: antiSMASH, a tool for detecting biosynthetic gene clusters in microorganisms, has been updated to version 6, which increases the supported cluster types, displays the structure of multi-modular BGCs, adds a new comparison algorithm, allows integration of results from other prediction tools, and improves detection of tailoring enzymes in RiPP clusters.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes

Matthew T. Robey et al.

Summary: This study provides detailed annotation and analysis of fungal biosynthetic and chemical space, enabling genome mining and discovery of fungal natural products. The taxonomic landscape of fungal gene cluster families is largely species specific, revealing dramatic differences between fungal and bacterial biosynthetic logic and chemical space.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemical Research Methods

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions

Grimur Hjoerleifsson Eldjarn et al.

Summary: Specialised metabolites from microbial sources, particularly antibiotics, are widely used in biomedical applications. The challenge lies in establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites due to the lack of detailed biosynthetic knowledge for most BGCs. The software framework NPLinker is introduced to address this challenge by combining strain correlation analysis and feature-based analysis methods for improved performance in linking genomic and metabolomic data.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Chemistry, Analytical

CFM-ID 4.0: More Accurate ESI-MS/MS Spectral Prediction and Compound Identification

Fei Wang et al.

Summary: Mass spectrometry (MS) is commonly used in metabolomics for identifying and annotating metabolites. CFM-ID is a computer program that accurately predicts EST-MS/MS spectrum for a given compound structure, improving compound-to-mass-spectrum prediction and in silico mass-spectrum-to-compound identification. This new version of CFM-ID (version 4.0) demonstrates significantly increased accuracy in both ET-MS/MS spectral prediction and compound identification.

ANALYTICAL CHEMISTRY (2021)

Article Biotechnology & Applied Microbiology

Media and strain studies for the scaled production of cis-enone resorcylic acid lactones as feedstocks for semisynthesis

Zeinab Y. Al Subeh et al.

Summary: This study aimed to identify fungi that biosynthesize compounds 1 and 2, optimize fermentation conditions on a lab scale, and develop straightforward purification processes. Gram-scale quantities of RALs and other compounds were successfully obtained as a result.

JOURNAL OF ANTIBIOTICS (2021)

Article Chemistry, Medicinal

Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach

Ira Handayani et al.

Summary: Studying the microbial diversity in Indonesia for novel antibiotics, 422 actinomycete strains were isolated from three unique areas and nine bioactive strains were identified. By combining gene cluster and molecular networking approaches, novel compounds were discovered from these strains, indicating the potential for accelerating natural product identification.

MARINE DRUGS (2021)

Article Multidisciplinary Sciences

Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi

Milton T. Drott et al.

Summary: Our study reveals that more than 25% of pangenomic BGCs in Aspergillus flavus show population-specific patterns of presence/absence or protein divergence. These population-specific BGCs make up most of the accessory-genome BGCs, indicating that different ecological forces may maintain accessory genomes through population-specific differences in secondary metabolism. Furthermore, we find that several population-specific BGCs from A. flavus are present in Aspergillus parasiticus and Aspergillus minisclerotigenes, suggesting that the microevolutionary patterns we uncover can inform macroevolutionary inferences and align fungal secondary metabolism with existing evolutionary theory.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Review Biochemistry & Molecular Biology

Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities

Lindsay K. Caesar et al.

Summary: Organisms in nature have evolved specialized enzymatic machinery to biosynthesize a variety of secondary metabolites, which has profound impacts on human health. Recent advancements in metabolomics and genomics have allowed for efficient exploration of new chemical spaces in natural product discovery. Integrated strategies now enable researchers to simultaneously identify expressed secondary metabolites and their biosynthetic machinery.

NATURAL PRODUCT REPORTS (2021)

Article Biochemistry & Molecular Biology

A computational framework to explore large-scale biosynthetic diversity

Jorge C. Navarro-Munoz et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Discovery of the Biosynthetic Machinery for Stravidins, Biotin Antimetabolites

Rana Montaser et al.

ACS CHEMICAL BIOLOGY (2020)

Article Multidisciplinary Sciences

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products

Nishanth J. Merwin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Microbiology

Comparative Genomics and Metabolomics in the Genus Nocardia

Daniel Maennle et al.

MSYSTEMS (2020)

Review Mycology

The amazing potential of fungi: 50 ways we can exploit fungi industrially

Kevin D. Hyde et al.

FUNGAL DIVERSITY (2019)

Article Chemistry, Multidisciplinary

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

Jeffrey A. van Santen et al.

ACS CENTRAL SCIENCE (2019)

Review Microbiology

Fungal secondary metabolism: regulation, function and drug discovery

Nancy P. Keller

NATURE REVIEWS MICROBIOLOGY (2019)

Review Chemistry, Applied

Natural products for human health: an historical overview of the drug discovery approaches

S. Bernardini et al.

NATURAL PRODUCT RESEARCH (2018)

Article Biochemistry & Molecular Biology

HMMER web server: 2018 update

Simon C. Potter et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Gene-guided discovery and engineering of branched cyclic peptides in plants

Roland D. Kersten et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemical Research Methods

Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites

Arvind K. Chavali et al.

BRIEFINGS IN BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Enhanced dereplication of fungal cultures via use of mass defect filtering

Noemi D. Paguigan et al.

JOURNAL OF ANTIBIOTICS (2017)

Article Biochemistry & Molecular Biology

GenBank

Karen Clark et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Medicinal

Aspernigrins with anti-HIV-1 activities from the marine-derived fungus Aspergillus niger SCSIO Jcsw6F30

Xuefeng Zhou et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2016)

Article Genetics & Heredity

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products

Yong Fuga Li et al.

FUNGAL GENETICS AND BIOLOGY (2016)

Article Plant Sciences

Penipyridones A-F, Pyridone Alkaloids from Penicillium funiculosum

Haibo Zhou et al.

JOURNAL OF NATURAL PRODUCTS (2016)

Article Biotechnology & Applied Microbiology

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

Mingxun Wang et al.

NATURE BIOTECHNOLOGY (2016)

Article Microbiology

Biologically Active Secondary Metabolites from the Fungi

Gerald F. Bills et al.

MICROBIOLOGY SPECTRUM (2016)

Article Biochemistry & Molecular Biology

Large-Scale Metabolomics Reveals a Complex Response of Aspergillus nidulans to Epigenetic Perturbation

Jessica C. Albright et al.

ACS CHEMICAL BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Fungal artificial chromosomes for mining of the fungal secondary metabolome

Jin Woo Bok et al.

BMC GENOMICS (2015)

Editorial Material Biochemistry & Molecular Biology

Minimum Information about a Biosynthetic Gene cluster

Marnix H. Medema et al.

NATURE CHEMICAL BIOLOGY (2015)

Article Multidisciplinary Sciences

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

Chad W. Johnston et al.

NATURE COMMUNICATIONS (2015)

Article Plant Sciences

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

Hosein Mohimani et al.

JOURNAL OF NATURAL PRODUCTS (2014)

Article Biochemistry & Molecular Biology

A roadmap for natural product discovery based on large-scale genomics and metabolomics

James R. Doroghazi et al.

NATURE CHEMICAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Henrik Nordberg et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Letter Biotechnology & Applied Microbiology

A cross-platform toolkit for mass spectrometry and proteomics

Matthew C. Chambers et al.

NATURE BIOTECHNOLOGY (2012)

Article Biochemistry & Molecular Biology

Molecular cloning and functional identification of a novel phenylacetyl-CoA ligase gene from Penicillium chrysogenum

Fu-Qiang Wang et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Plant Sciences

New natural products from the sponge-derived fungus Aspergillus niger

J Hiort et al.

JOURNAL OF NATURAL PRODUCTS (2004)