A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
Mitja M. Zdouc
Mohammad M. Alanjary
Guadalupe S. Zarazúa
Sonia I. Maffioli
Max Crüsemann
Marnix H. Medema
Stefano Donadio
Margherita Sosio
Cell Chemical Biology, 2020
Max Crüsemann
Crüsemann Max
ORCID: 0000-0001-6660-2715
Feature-Based Molecular Networking for the Targeted Identification of Gq -Inhibiting FR900359 Derivatives
10.1021/acs.jnatprod.1c00194
Isolation of fungi using the diffusion chamber device FIND technology
10.3762/bjoc.15.216
Corrigendum: An environmental bacterial taxon with a large and distinct metabolic repertoire
10.1038/nature13126
Volatiles from the fungal microbiome of the marine sponge: Callyspongia cf. flammea
10.1039/c7ob01837a
Evolution-guided engineering of nonribosomal peptide synthetase adenylation domains
10.1039/c2sc21722h
An experimental strategy to probe Gq contribution to signal transduction in living cells
10.1016/j.jbc.2021.100472
Insights into the biosynthesis of hormaomycin, an exceptionally complex bacterial signaling metabolite
10.1016/j.chembiol.2010.12.018
Biosynthetic Studies on Acetosellin and Structure Elucidation of a New Acetosellin Derivative
10.1055/s-0042-124493
An environmental bacterial taxon with a large and distinct metabolic repertoire
10.1038/nature12959
Rational design of a heterotrimeric G protein subunit with artificial inhibitor sensitivity
10.1074/jbc.RA118.007250
Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from salinispora species
10.1016/j.chembiol.2015.03.010
Triterpene glycosides from the leaves of pittosporum angustifolium
10.1055/s-0033-1350806
Function-related replacement of bacterial siderophore pathways
10.1038/ismej.2017.137
Metabolome of the phyllidiella pustulosa species Complex (Nudibranchia, Heterobranchia, Gastropoda) reveals rare dichloroimidic sesquiterpene derivatives from a phylogenetically distinct and undescribed clade
10.1021/acs.jnatprod.0c00783
Biosynthetic origin of the antibiotic cyclocarbamate brabantamide A (SB-253514) in Plant-associated pseudomonas
10.1002/cbic.201300527
Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows
10.3390/md19030142
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols
10.1021/acs.jnatprod.6b00722
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
10.1016/j.chembiol.2020.11.009
Planomonospora: A metabolomics perspective on an underexplored actinobacteria genus
10.1101/2020.07.19.210815
Direct capture and heterologous expression of salinispora natural product genes for the biosynthesis of enterocin
10.1021/np500664q
Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq-Signaling Inhibitor FR900359
10.1002/anie.201707996
Biosynthesis of phenylnannolone A, a multidrug resistance reversal agent from the halotolerant myxobacterium Nannocystis pusilla B150
10.1002/cbic.201300676
Applying Molecular Networking for the Detection of Natural Sources and Analogues of the Selective Gq Protein Inhibitor FR900359
10.1021/acs.jnatprod.8b00222
Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria
10.1111/1462-2920.15382
Diversity and antimicrobial potential of predatory bacteria from the peruvian coastline
10.3390/md15100308
Identification and heterologous expression of the kocurin biosynthetic gene cluster
10.1099/mic.0.000538
Effective approaches to discover new microbial metabolites in a large strain library
10.1093/jimb/kuab017
Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites
10.1038/s41598-018-34954-y
Microbial and biochemical basis of a Fusarium wilt-suppressive soil
10.1038/ismej.2015.95
PCR-Independent Method of Transformation-Associated Recombination Reveals the Cosmomycin Biosynthetic Gene Cluster in an Ocean Streptomycete
10.1021/acs.jnatprod.6b01121
Antimicrobial Dialkylresorcins from Marine-Derived Microorganisms: Insights into Their Mode of Action and Putative Ecological Relevance
10.1055/a-0653-7451
Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites
10.3762/bjoc.12.96
Salinipyrone and Pacificanone Are Biosynthetic By-products of the Rosamicin Polyketide Synthase
10.1002/cbic.201500177
Biosynthetic Basis for Structural Diversity of Aminophenylpyrrole-Derived Alkaloids
10.1021/acschembio.8b00993
A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters
10.1101/2020.07.21.214643
Cyclopropane-containing fatty acids from the marine bacterium Labrenzia sp. 011 with antimicrobial and GPR84 activity
10.3390/md16100369
Deciphering Specificity Determinants for FR900359-Derived Gq α Inhibitors Based on Computational and Structure-Activity Studies.
10.1002/cmdc.201800304
Thioesterase-mediated side chain transesterification generates potent Gq signaling inhibitor FR900359
10.1038/s41467-020-20418-3
Biosynthesis and Mechanism of Action of the Cell Wall Targeting Antibiotic Hypeptin
10.1002/anie.202102224
From Persian Gulf to Indonesia: interrelated phylogeographic distance and chemistry within the genus Peronia (Onchidiidae, Gastropoda, Mollusca)
10.1038/s41598-020-69996-8
Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus
10.1021/acs.jnatprod.0c00807
Manipulation of regulatory genes reveals complexity and fidelity in hormaomycin biosynthesis
10.1016/j.chembiol.2013.04.018
Heterologe Expression, Biosynthese und ökologische Funktion des selektiven Gq‐Signaltransduktionsinhibitors FR900359
10.1002/ange.201707996
The chromodepsins – chemistry, biology and biosynthesis of a selective Gq inhibitor natural product family
10.1039/D1NP00005E
Marnix H. Medema
Medema Marnix H.
ORCID: 0000-0002-2191-2821
antiSMASH
10.1007/978-1-4899-7478-5_703
Bioinformatics Approaches and Software for Detection of Secondary Metabolic Gene Clusters
10.1007/978-1-62703-122-6_2
Synthetic Biology in Streptomyces Bacteria
10.1016/b978-0-12-385075-1.00021-4
Computational approaches to natural product discovery
10.1038/nchembio.1884
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
10.1038/nrmicro2478
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
10.1371/journal.pcbi.1004016
Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
10.1016/j.febslet.2011.06.014
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
10.1371/journal.pone.0051511
The future of industrial antibiotic production: From random mutagenesis to synthetic biology
10.4161/bbug.2.4.16114
Metabolomics methods for the synthetic biology of secondary metabolism
10.1016/j.febslet.2012.02.008
Computational tools for the synthetic design of biochemical pathways
10.1038/nrmicro2717
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis
10.1186/1471-2164-11-299
Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
10.1111/j.1751-7915.2010.00226.x
Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea
10.1111/j.1462-2920.2008.01724.x
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters
10.1016/j.cell.2014.06.034
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
10.1371/journal.pcbi.1003822
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
10.1093/nar/gkv437
Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice
10.1016/j.copbio.2013.03.006
Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block
10.1021/sb500368w
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers
10.1093/nar/gkt449
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
10.1093/nar/gkr466
The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways
10.1093/gbe/evq013
MS/MS networking guided analysis of molecule and gene cluster families
10.1073/pnas.1303471110
Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
10.1093/molbev/mst025
Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii
10.1128/jb.02132-12
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity
10.1093/nar/gkr323
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
10.1128/mmbr.00037-08
Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.
10.1186/s12864-015-2154-4
Leucanicidin and endophenasides result from methyl-rhamnosylation by the same tailoring enzymes in Kitasatospora sp. MBT66
10.1021/acschembio.5b00801
Computational strategies for genome-based natural product discovery and engineering in fungi
10.1016/j.fgb.2016.01.006
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
10.1093/nar/gkw960
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
10.1038/nmicrobiol.2016.197
Editorial: Synthetic biology and bioinformatics
10.1039/c6np90031c
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1093/nar/gkx305
Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus
10.1186/s12864-017-3966-1
Mining prokaryotes for antimicrobial compounds: from diversity to function
10.1093/femsre/fux014
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
10.1093/bib/bbx146
Standardization for natural product synthetic biology
10.1039/c6np00030d
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways
10.1039/c6np00035e
Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium , Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic Valinomycin
10.1128/genomea.00453-17
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
10.1093/bioinformatics/btx400
Collaborating with Undergraduates To Contribute to Biochemistry Community Resources
10.1021/acs.biochem.7b00872
Road MAPs to engineer host microbiomes.
10.1016/j.mib.2017.11.023
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.
10.1111/1462-2920.13927
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
10.1073/pnas.1705567114
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
10.1093/nar/gkx319
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products.
10.1016/j.fgb.2016.01.012
Exploration and exploitation of the environment for novel specialized metabolites.
10.1016/j.copbio.2018.01.017
Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
10.1128/mSystems.00182-17
Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics.
10.1016/j.chembiol.2018.02.008
HEx: A heterologous expression platform for the discovery of fungal natural products.
10.1126/sciadv.aar5459
luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria.
10.1128/msystems.00208-17
A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.
10.1021/jacs.7b13292
Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.
10.3389/fmicb.2018.01158
Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.
10.1038/s41396-018-0186-x
Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH.
10.1007/978-1-4939-7874-8_15
A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences
10.1186/s40793-018-0318-y
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters
10.1093/nar/gky1060
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1101/463620
Mining bacterial genomes to reveal secret synergy
10.1074/jbc.H118.006669
Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
10.1038/s42003-019-0333-6
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
10.1111/tpj.14292
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
10.1186/s13104-019-4222-3
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
10.1093/nar/gkz310
MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools
10.1101/654459
BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs
10.1101/gr.243477.118
Genome Mining Approaches to Bacterial Natural Product Discovery
10.1016/b978-0-12-409547-2.14627-x
Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines
10.1039/C9NP00021F
PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters
10.1101/083535
MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools
10.3390/metabo9070144
Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.
10.3389/fpls.2019.00846
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
10.1126/science.aaw9285
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
10.1093/nar/gkz882
A metabolic pathway for bile acid dehydroxylation by the gut microbiome
10.1101/758557
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines
10.1101/669291
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
10.1021/acscentsci.9b00806
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology
10.1038/s41564-019-0588-1
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1101/856955
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae
10.1111/nph.16338
Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat
10.1098/rspb.2019.2527
Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota
10.1101/2020.03.06.976126
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
10.1101/2020.03.14.992123
Linking genomics and metabolomics to chart specialized metabolic diversity
10.1039/D0CS00162G
Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota
10.1099/mgen.0.000373
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
10.1093/nar/gkaa374
Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products
10.1101/2020.05.19.104752
Ecology and genomics of Actinobacteria: new concepts for natural product discovery
10.1038/s41579-020-0379-y
The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-0993-2
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
10.1101/2020.08.17.240838
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia
10.1074/jbc.RA120.013528
Microbial natural product databases: moving forward in the multi-omics era
10.1039/D0NP00053A
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01228-1
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
10.1128/mSystems.00267-20
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
10.1038/s42003-020-01271-y
BiG-FAM: the biosynthetic gene cluster families database
10.1093/nar/gkaa812
Coevolution-based prediction of protein–protein interactions in polyketide biosynthetic assembly lines
10.1093/bioinformatics/btaa595
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes
10.1093/nar/gkaa978
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
10.1038/s41598-020-77723-6
BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes
10.1101/2020.12.14.422671
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
10.1371/journal.pbio.3001026
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
10.1093/gigascience/giaa154
The year 2020 in natural product bioinformatics: an overview of the latest tools and databases
10.1039/D0NP00090F
Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis
10.1101/2021.02.11.430889
A systematic analysis of metabolic pathways in the human gut microbiota
10.1101/2021.02.25.432841
Omics-based strategies to discover novel classes of RiPP natural products
10.1016/j.copbio.2020.12.008
Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria
10.1038/s41467-021-21163-x
The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range
10.3389/fbioe.2021.623701
Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques
10.1101/2021.01.20.427441
Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes
10.3389/fmicb.2020.574053
A mammalian commensal of the oropharyngeal cavity produces antibiotic and antiviral valinomycin in vivo
10.21203/rs.3.rs-126949/v1
A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters
10.1016/j.chembiol.2020.11.009
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters
10.1101/2020.11.08.370601
antiSMASH 6.0: improving cluster detection and comparison capabilities
10.1093/nar/gkab335
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
10.1093/nar/gkab353
Mining genomes to illuminate the specialized chemistry of life
10.1038/s41576-021-00363-7
Dominant drivers of the human plasma metabolome
10.21203/rs.3.rs-688716/v1
A global survey of specialized metabolic diversity encoded in bacterial genomes
10.1101/2021.08.11.455920
cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters
10.1093/bioadv/vbab016
