RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
Alexander M. Kloosterman
Kyle E. Shelton
Gilles P. van Wezel
Marnix H. Medema
Douglas A. Mitchell
Gilles van Wezel
van Wezel Gilles
ORCID: 0000-0003-0341-1561
Off the wall
10.7554/elife.05427
Novel Aspects of Signaling in Streptomyces Development
10.1016/s0065-2164(04)56002-1
Morphogenesis of Streptomyces in Submerged Cultures
10.1016/b978-0-12-800259-9.00001-9
Structured morphological modeling as a framework for rational strain design of Streptomyces species
10.1007/s10482-012-9760-9
Constitutive expression of ftsZ overrides the whi developmental genes to initiate sporulation of Streptomyces coelicolor
10.1007/s10482-011-9678-7
The evolution of actinomycetes: papers from the 16th International Symposium on the Biology of Actinomycetes
10.1007/s10482-012-9805-0
The SsgA-like proteins in actinomycetes: small proteins up to a big task
10.1007/s10482-008-9225-3
The tmRNA-tagging mechanism and the control of gene expression: a review
10.1002/wrna.48
The regulation of the secondary metabolism of Streptomyces: new links and experimental advances
10.1039/c1np00003a
The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA
10.1046/j.1365-2958.2000.02046.x
Cell division and DNA segregation in Streptomyces: how to build a septum in the middle of nowhere?
10.1111/j.1365-2958.2012.08107.x
Triggers and cues that activate antibiotic production by actinomycetes
10.1007/s10295-013-1309-z
Altered desferrioxamine-mediated iron utilization is a common trait of bald mutants of Streptomyces coelicolor
10.1039/c4mt00068d
Single particle tracking of dynamically localizing TatA complexes in Streptomyces coelicolor
10.1016/j.bbrc.2013.07.016
A novel plasmid vector that uses the glucose kinase gene (glkA) for the positive selection of stable gene disruptants in Streptomyces
10.1016/s0378-1119(96)00563-x
Chemical, structural and biological studies of cis-[Pt(3-Acpy)2Cl2]
10.1016/j.jinorgbio.2009.06.009
Phenanthroline Derivatives with Improved Selectivity as DNA-Targeting Anticancer or Antimicrobial Drugs
10.1002/cmdc.200800097
Imaging of Streptomyces coelicolor A3(2) with Reduced Autofluorescence Reveals a Novel Stage of FtsZ Localization
10.1371/journal.pone.0004242
Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies
10.1038/nrmicro3178
Correlative Cryo-Fluorescence Light Microscopy and Cryo-Electron Tomography of Streptomyces
10.1016/b978-0-12-801075-4.00010-0
Relative quantification of proteasome activity by activity-based protein profiling and LC-MS/MS
10.1038/nprot.2013.065
Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees
10.1007/s10482-014-0139-y
A novel function of Streptomyces integration host factor (sIHF) in the control of antibiotic production and sporulation in Streptomyces coelicolor
10.1007/s10482-011-9657-z
Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces
10.1007/s10482-014-0209-1
Identification and isolation of lantibiotics from culture: a bioorthogonal chemistry approach
10.1039/c2ob26050f
Structure, cytotoxicity, and DNA-cleavage properties of the complex [CuII(pbt)Br2]
10.1021/ic702306f
Analysis of two distinct mycelial populations in liquid-grown Streptomyces cultures using a flow cytometry-based proteomics approach
10.1007/s00253-012-4490-5
The permease gene nagE2 is the key to N-acetylglucosamine sensing and utilization in Streptomyces coelicolor and is subject to multi-level control
10.1111/j.1365-2958.2009.07020.x
Platinum(II) compounds with chelating ligands based on pyridine and pyrimidine: DNA and protein binding studies
10.1016/j.jinorgbio.2009.07.003
DNA cleavage and antitumour activity of platinum(II) and copper(II) compounds derived from 4-methyl-2-N-(2-pyridylmethyl)aminophenol: spectroscopic, electrochemical and biological investigation
10.1039/b911542k
The square-planar cytotoxic [CuII(pyrimol)Cl] complex acts as an efficient DNA cleaver without reductant
10.1021/ja056970+
Transcription of the sporulation gene ssgA is activated by the IcIR-type regulator SsgR in a whi-independent manner in Streptomyces A3(2)
10.1111/j.1365-2958.2004.04186.x
Loss of the controlled localization of growth stage-specific cell-wall synthesis pleiotropically affects developmental gene expression in an ssgA mutant of Streptomyces coelicolor
10.1111/j.1365-2958.2007.05732.x
MreB of Streptomyces coelicolor is not essential for vegetative growth but is required for the integrity of aerial hyphae and spores
10.1111/j.1365-2958.2006.05134.x
Substrate induction and glucose repression of maltose utilization by Streptomyces coelicolor A3(2) is controlled by malR, a member of the lacI-galR family of regulatory genes
10.1046/j.1365-2958.1997.d01-1878.x
Cloning and sequencing of the tuf genes of Streptomyces coelicolor A3(2)
10.1016/0167-4781(94)90085-x
Unsuspected control of siderophore production by N-acetylglucosamine in streptomycetes
10.1111/j.1758-2229.2012.00354.x
SsgA-like proteins determine the fate of peptidoglycan during sporulation of Streptomyces coelicolor
10.1111/j.1365-2958.2005.04883.x
Identification of glucose kinase-dependent and -independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics
10.1111/mmi.12072
Unique Ligand-Based Oxidative DNA Cleavage by Zinc(II) Complexes of Hpyramol and Hpyrimol
10.1002/chem.200601525
Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence
10.1038/srep01109
A new piece of an old jigsaw: Glucose kinase is activated posttranslationally in a glucose transport-dependent manner in Streptomyces coelicolor A3(2)
10.1159/000096461
Natural Product Proteomining, a Quantitative Proteomics Platform, Allows Rapid Discovery of Biosynthetic Gene Clusters for Different Classes of Natural Products
10.1016/j.chembiol.2014.03.011
Conserved cis-acting elements upstream of genes composing the chitinolytic system of streptomycetes are DasR-responsive elements
10.1159/000096460
Structure and DNA cleavage properties of two copper(ii) complexes of the pyridine-pyrazole-containing ligands mbpzbpy and Hmpzbpya
10.1039/b704390b
PREDetector: A new tool to identify regulatory elements in bacterial genomes
10.1016/j.bbrc.2007.03.180
From dormant to germinating spores of Streptomyces coelicolor A3(2): New perspectives from the crp null mutant
10.1021/pr050155b
Transfer–messenger RNA controls the translation of cell-cycle and stress proteins in Streptomyces
10.1038/embor.2009.255
Chapter 5 Applying the Genetics of Secondary Metabolism in Model Actinomycetes to the Discovery of New Antibiotics
10.1016/s0076-6879(09)04805-8
Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces
10.1038/embor.2008.83
Engineering of N-acetylglucosamine metabolism for improved antibiotic production in Streptomyces coelicolor A3(2) and an unsuspected role of NagA in glucosamine metabolism
10.4161/bioe.21371
Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes
10.1371/journal.pone.0041359
The Streptomyces coelicolor ssgB gene is required for early stages of sporulation
10.1016/s0378-1097(03)00481-6
Objective comparison of particle tracking methods
10.1038/nmeth.2808
A comparative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rrnA
10.1093/nar/19.16.4399
Dynamic Localization of Tat Protein Transport Machinery Components in Streptomyces coelicolor
10.1128/jb.01425-12
Positive control of cell division: FtsZ is recruited by SsgB during sporulation of Streptomyces
10.1101/gad.600211
ssgA Is Essential for Sporulation of Streptomyces coelicolor A3(2) and Affects Hyphal Development by Stimulating Septum Formation
10.1128/jb.182.20.5653-5662.2000
Unlocking Streptomyces spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering
10.1128/aem.01853-06
Elongation Factor Tu3 (EF-Tu3) from the Kirromycin Producer Streptomyces ramocissimus Is Resistant to Three Classes of EF-Tu-Specific Inhibitors
10.1128/jb.01810-06
The chitobiose-binding protein, DasA, acts as a link between chitin utilization and morphogenesis in Streptomyces coelicolor
10.1099/mic.0.2007/011940-0
The Secreted Signaling Protein Factor C Triggers the A-factor Response Regulon in Streptomyces griseus: Overlapping Signaling Routes
10.1074/mcp.m600367-mcp200
Functional Analysis of the N-Acetylglucosamine Metabolic Genes of Streptomyces coelicolor and Role in Control of Development and Antibiotic Production
10.1128/jb.06370-11
The tuf3 gene of Streptomyces coelicolor A3(2) encodes an inessential elongation factor Tu that is apparently subject to positive stringent control
10.1099/13500872-141-10-2519
Lack of A-factor Production Induces the Expression of Nutrient Scavenging and Stress-related Proteins in Streptomyces griseus
10.1074/mcp.m900194-mcp200
Three tuf-like genes in the kirromycin producer Streptomyces ramocissimus
10.1099/00221287-140-4-983
The malEFG gene cluster of Streptomyces coelicolor A3(2): characterization, disruption and transcriptional analysis
10.1007/s004380050458
The ROK Family Regulator Rok7B7 Pleiotropically Affects Xylose Utilization, Carbon Catabolite Repression, and Antibiotic Production in Streptomyces coelicolor
10.1128/jb.02191-12
Unlocking Streptomyces spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering
10.1128/aem.00808-06
Developmental Regulation of the Streptomyces lividans ram Genes: Involvement of RamR in Regulation of the ramCSAB Operon
10.1128/jb.184.16.4420-4429.2002
The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island
10.1093/gbe/evt082
The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development
10.1111/j.1365-2958.2006.05319.x
Metabolomics in the natural products field - a gateway to novel antibiotics
10.1016/j.ddtec.2015.01.004
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing
10.1111/mmi.12810
Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils
10.1099/mic.0.078295-0
Multidimensional view of the bacterial cytoskeleton
10.1128/JB.02194-12
Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes
10.1074/jbc.M109.018564
Characterization of the sporulation control protein SsgA by use of an efficient method to create and screen random mutant libraries in streptoniycetes
10.1128/AEM.02755-06
GlcP constitutes the major glucose of uptake system of Streptomyces coelicolor A3(2)
10.1111/j.1365-2958.2004.04413.x
Glucose kinase of Streptomyces coelicolor A3(2): Large-scale purification and biochemical analysis
10.1023/A:1010234916745
Transcriptional and functional analysis of the gene for factor C, an extracellular signal protein involved in cytodifferentiation of Streptomyces griseus
10.1023/A:1010221407340
Effects of increased and deregulated expression of cell division genes on the morphology and on antibiotic production of Streptomycetes
10.1023/A:1010267708249
Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation.
10.1038/srep10868
Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets.
10.1371/journal.pone.0122479
A novel locus for mycelial aggregation forms a gateway to improved Streptomyces cell factories.
10.1186/s12934-015-0224-6
Identification of novel endophenaside antibiotics produced by Kitasatospora sp. MBT66
10.1038/ja.2015.14
A novel taxonomic marker that discriminates between morphologically complex actinomycetes.
10.1098/rsob.130073
Transcriptional analysis of the cell division-related ssg genes in Streptomyces coelicolor reveals direct control of ssgR by AtrA.
10.1007/s10482-015-0479-2
Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2)
10.1016/j.bbrc.2016.12.183
Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow
10.1021/acs.jnatprod.6b00478
Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens
10.1128/genomeA.01560-16
Aromatic Polyketide GTRI-02 is a Previously Unidentified Product of the act Gene Cluster in Streptomyces coelicolor A3(2)
10.1002/cbic.201700107
Morphology-driven downscaling of Streptomyces lividans to micro-cultivation
10.1101/159509
SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures
10.1101/159475
Intertwined Precursor Supply during Biosynthesis of the Catecholate–Hydroxamate Siderophores Qinichelins in Streptomyces sp. MBT76
10.1021/acschembio.7b00597
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity
10.1101/222844
Substrate Inhibition of VanA by d -Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner
10.1128/AAC.00276-16
Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity
10.1007/s10482-018-1014-z
Healthy scents: microbial volatiles as new frontier in antibiotic research?
10.1016/j.mib.2018.02.011
Classification of the gifted natural product producer Streptomyces roseofaciens sp. nov. by polyphasic taxonomy
10.1101/310888
Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline
10.1002/pmic.201700332
Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606
10.1128/genomeA.00385-18
Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era
10.1039/C8NP00012C
Sporulation-specific cell division defects in ylmE mutants of Streptomyces coelicolor are rescued by additional deletion of ylmD
10.1038/s41598-018-25782-1
High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor
10.1128/JB.00290-18
Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces
10.1101/450833
Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces
10.1038/ncomms11836
Stress-induced formation of cell wall-deficient cells in filamentous actinomycetes
10.1038/s41467-018-07560-9
Discovery of Novel Glycerolated Quinazolinones from Streptomyces sp. MBT27
10.1101/484535
Lugdunomycin, an Angucycline‐Derived Molecule with Unprecedented Chemical Architecture
10.1002/anie.201814581
Lugdunomycin, an Angucycline‐Derived Molecule with Unprecedented Chemical Architecture
10.1002/ange.201814581
Discovery of novel glycerolated quinazolinones from Streptomyces sp. MBT27
10.1007/s10295-019-02140-2
Bagremycin Antibiotics and Ferroverdin iron-chelators are synthetized by the Same Gene Cluster
10.1101/631242
Phylogenomic analyses and distribution of terpene synthases among Streptomyces
10.3762/bjoc.15.115
Antibiotic production in Streptomyces is organized by a division of labour through terminal genomic differentiation
10.1101/560136
Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium
10.1101/714758
A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators
10.1128/mBio.01230-19
Spatial structure increases the benefits of antibiotic production in Streptomyces *
10.1111/evo.13817
A microbial expression system for high-level production of scFv HIV-neutralizing antibody fragments in Escherichia coli
10.1007/s00253-019-10145-1
Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species
10.1038/s41396-019-0537-2
Longitudinal cell division is associated with single mutations in the FtsZ-recruiting SsgB in Streptomyces
10.1101/860916
Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation
10.1126/sciadv.aay5781
Competition sensing alters antibiotic production in Streptomyces
10.1101/2020.01.24.918557
Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production
10.1101/796722
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
10.1101/2020.03.14.992123
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
Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium
10.1038/s42003-020-1038-6
Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases
10.1039/D0CB00045K
Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus
10.1021/acs.joc.0c01210
Iso ‐maleimycin, a Constitutional Isomer of Maleimycin, from Streptomyces sp. QL37
10.1002/ejoc.202000767
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
10.1128/mSystems.00267-20
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production
10.1016/j.isci.2020.101525
A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG
10.1101/2020.10.12.336396
Prodiginines Postpone the Onset of Sporulation in Streptomyces coelicolor
10.3390/antibiotics9120847
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
10.1371/journal.pbio.3001026
Branching of sporogenic aerial hyphae in sflA and sflB mutants of Streptomyces coelicolor correlates to ectopic localization of DivIVA and FtsZ in time and space
10.1101/2020.12.26.424426
Omics-based strategies to discover novel classes of RiPP natural products
10.1016/j.copbio.2020.12.008
The nucleoid-associated protein Gbn binds to GATC sequences and affects sporulation and antibiotic production in Streptomyces
10.1101/2021.02.06.430045
Competition Sensing Changes Antibiotic Production in Streptomyces
10.1128/mBio.02729-20
Ectopic positioning of the cell division plane is associated with single amino acid substitutions in the FtsZ-recruiting SsgB in Streptomyces
10.1098/rsob.200409
An Alternative and Conserved Cell Wall Enzyme That Can Substitute for the Lipid II Synthase MurG
10.1128/mBio.03381-20
A novel function of Streptomyces integration host factor (sIHF) in the control of antibiotic production and sporulation in Streptomyces coelicolor
http://dx.doi.org/10.1007/s10482-011-9657-z
A novel plasmid vector that uses the glucose kinase gene (glkA) for the positive selection of stable gene disruptants in Streptomyces
http://dx.doi.org/10.1016/s0378-1119(96)00563-x
ChemInform Abstract: The Regulation of the Secondary Metabolism of Streptomyces: New Links and Experimental Advances
http://dx.doi.org/10.1002/chin.201142269
Chemical, structural and biological studies of cis-[Pt(3-Acpy)2Cl2]
http://dx.doi.org/10.1016/j.jinorgbio.2009.06.009
Constitutive expression of ftsZ overrides the whi developmental genes to initiate sporulation of Streptomyces coelicolor
http://dx.doi.org/10.1007/s10482-011-9678-7
Control of cell division in Streptomyces
http://dx.doi.org/10.1111/j.1365-2958.2012.08107.x
Imaging of Streptomyces coelicolor A3(2) with Reduced Autofluorescence Reveals a Novel Stage of FtsZ Localization
http://dx.doi.org/10.1371/journal.pone.0004242
Phenanthroline Derivatives with Improved Selectivity as DNA-Targeting Anticancer or Antimicrobial Drugs
http://dx.doi.org/10.1002/cmdc.200800097
Relative quantification of proteasome activity by activity-based protein profiling and LC-MS/MS
http://dx.doi.org/10.1038/nprot.2013.065
Structured morphological modeling as a framework for rational strain design of Streptomyces species
http://dx.doi.org/10.1007/s10482-012-9760-9
The SsgA-like proteins in actinomycetes: small proteins up to a big task
http://dx.doi.org/10.1007/s10482-008-9225-3
The regulation of the secondary metabolism of Streptomyces: new links and experimental advances
http://dx.doi.org/10.1039/c1np00003a
The tmRNA-tagging mechanism and the control of gene expression: a review
http://dx.doi.org/10.1002/wrna.48
The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA
http://dx.doi.org/10.1046/j.1365-2958.2000.02046.x
antiSMASH 6.0: improving cluster detection and comparison capabilities
10.1093/nar/gkab335
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics
10.1128/mSystems.01116-20
Adrenaline-mediated activation of antibiotic production in Streptomyces highlights catechol as elicitor of specialized metabolism
10.21203/rs.3.rs-715051/v1
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
Douglas Mitchell
Mitchell Douglas
ORCID: 0000-0002-9564-0953
Email: douglasm@illinois.edu
Erratum: Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature (Natural Product Reports (2013) 30 (108-160) DOI:10.1039/C2NP20085F)
10.1039/c3np90040a
In Vitro Biosynthesis of the Core Scaffold of the Thiopeptide Thiomuracin
10.1021/jacs.5b10194
FeIII-TAML-catalyzed green oxidative degradation of the azo dye Orange II by H2O2 and organic peroxides: Products, toxicity, kinetics, and mechanisms
10.1039/b604990g
Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature
10.1039/c2np20085f
Thioredoxin catalyzes the S-nitrosation of the caspase-3 active site cysteine.
10.1038/nchembio720
Antibacterial drug leads targeting isoprenoid biosynthesis
10.1073/pnas.1219899110
Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis
10.1073/pnas.1306101110
Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso peptide from an understudied halophilic actinomycete
10.1016/j.chembiol.2014.11.017
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis
10.1038/nchembio.1608
Expansion of ribosomally produced natural products: A nitrile hydratase- and Nif11-related precursor family
10.1186/1741-7007-8-70
Erratum: Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis (ACS Chemical Biology (2013) 8 (473-487) DOI: 10.1021/cb3005325)
10.1021/cb4002359
Crystal structure and absolute configuration of (3S,4aS,8aS)-N-tert-butyl-2-[(S)-3-(2-chloro-4-nitrobenzamido)-2-hydroxypropyl]decahydroisoquinoline-3-carboxamide and (3S,4aS,8aS)-N-tert-butyl-2-{(S)-2-[(S)-1-(2-chloro-4-nitrobenzoyl)pyrrolidin-2-yl]-2-hydroxyethyl}decahydroisoquinoline-3-carboxamide
10.1107/S2056989015020046
S-nitrosation and regulation of inducible nitric oxide synthase
10.1021/bi0474463
Synthesis of plantazolicin analogues enables dissection of ligand binding interactions of a highly selective methyltransferase
10.1021/ol402444a
YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations
10.1038/nchembio.944
Subcellular targeting and differential S-nitrosylation of endothelial nitric-oxide synthase
10.1074/jbc.M510421200
Multitarget drug discovery for tuberculosis and other infectious diseases
10.1021/jm500131s
Crystallization and preliminary X-ray diffraction analysis of YisP protein from Bacillus subtilis subsp. subtilis strain 168
10.1107/S1744309112049330
Streptolysin S-like virulence factors: The continuing sagA
10.1038/nrmicro2624
HIV-1 integrase inhibitor-inspired antibacterials targeting isoprenoid biosynthesis
10.1021/ml300038t
Undecaprenyl diphosphate synthase inhibitors: Antibacterial drug leads
10.1021/jm5004649
Lessons learned from the transformation of natural product discovery to a genome-driven endeavor
10.1007/s10295-013-1361-8
Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family
10.1186/s12866-015-0464-y
Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin
10.1021/cb501042a
Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis
10.1021/cb3005325
Catalase-peroxidase activity of iron(III)-TAML activators of hydrogen peroxide
10.1021/ja8043689
Design and characterization of an active site selective caspase-3 transnitrosating agent.
10.1021/cb600393x
Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum
10.1074/jbc.M110.118554
Oxidation of pinacyanol chloride by H2O2 catalyzed by FeIII complexed to tetraamidomacrocyclic ligand: Unusual kinetics and product identification
10.1080/00958972.2010.492426
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles
10.1186/s12864-015-2008-0
Nucleophilic 1,4-additions for natural product discovery
10.1021/cb500324n
HIV protease inhibitors block Streptolysin S production
10.1021/cb500843r
Insights into the mechanism of peptide cyclodehydrations achieved through the chemoenzymatic generation of amide derivatives
10.1021/ja4029507
A prevalent peptide-binding domain guides ribosomal natural product biosynthesis
10.1038/nchembio.1856
Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products
10.1021/jacs.5b04682
Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42
10.1128/JB.00784-10
Targeted treatment for bacterial infections: Prospects for pathogen-specific antibiotics coupled with rapid diagnostics
10.1016/j.tet.2015.09.069
Thiazole/oxazole-modified microcins: Complex natural products from ribosomal templates
10.1016/j.cbpa.2011.02.027
Discovery of a widely distributed toxin biosynthetic gene cluster
10.1073/pnas.0801338105
Orchestration of enzymatic processing by thiazole/oxazole-modified microcin dehydrogenases.
10.1021/bi401529y
Engineering unnatural variants of plantazolicin through codon reprogramming.
10.1021/cb4003392
Selectivity, directionality, and promiscuity in peptide processing from a Bacillus sp. Al Hakam cyclodehydratase.
10.1021/ja211675n
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1.
10.1016/j.jmb.2011.04.066
Structural and functional dissection of the heterocyclic peptide cytotoxin streptolysin S.
10.1074/jbc.M900802200
Thioredoxin is required for S-nitrosation of procaspase-3 and the inhibition of apoptosis in Jurkat cells.
10.1073/pnas.0704898104
Identification of a potent and selective pharmacophore for Cdc25 dual specificity phosphatase inhibitors.
10.1124/mol.61.4.720
Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products
10.1016/j.bmc.2016.05.021
Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS
10.1073/pnas.1406418111
In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products
10.1021/acschembio.6b00369
Effects of S-nitrosation of nitric oxide synthase
10.1016/S1872-2423(07)01007-1
Plantazolicin Is an Ultranarrow-Spectrum Antibiotic That Targets the Bacillus anthracis Membrane
10.1021/acsinfecdis.5b00115
A new genome-mining tool redefines the lasso peptide biosynthetic landscape
10.1038/nchembio.2319
YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function
10.1021/acs.chemrev.6b00623
Reconstitution and Substrate Specificity of the Radical S-Adenosyl-methionine Thiazole C-Methyltransferase in Thiomuracin Biosynthesis
10.1021/jacs.7b00693
Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea
10.1101/121111
Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products
10.1021/acscentsci.7b00141
Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
10.1021/jacs.7b04641
Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea
10.7554/eLife.29218
Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis
10.1021/acs.biochem.7b00771
Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis
10.1073/pnas.1716035114
Correction to Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis
10.1021/acs.biochem.7b01056
In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily
10.1021/jacs.7b09899
Mechanism of a Class C Radical S-Adenosyl-l-methionine Thiazole Methyl Transferase
10.1021/jacs.7b10203
Enzymatic reconstitution of ribosomal peptide backbone thioamidation
10.1073/pnas.1722324115
RiPP antibiotics: biosynthesis and engineering potential
10.1016/j.mib.2018.02.010
Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics
10.1021/jacs.8b03896
Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin
10.1039/C8CC04411B
Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin
10.1021/jacs.8b09928
Biosynthesis and Chemical Applications of Thioamides
10.1021/acschembio.8b01022
Mechanistic Basis for Ribosomal Peptide Backbone Modifications
10.1021/acscentsci.9b00124
Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides
10.1021/jacs.9b01519
Reconstitution and Substrate Specificity of the Thioether-Forming Radical S-Adenosylmethionine Enzyme in Freyrasin Biosynthesis
10.1021/acschembio.9b00457
Functional interactions between post-translationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans
10.1101/771238
Correction to “Orchestration of Enzymatic Processing by Thiazole/Oxazole-Modified Microcin Dehydrogenases”
10.1021/acs.biochem.9b01042
Microviridin 1777: A Toxic Chymotrypsin Inhibitor Discovered by a Metabologenomic Approach
10.1021/acs.jnatprod.9b00986
Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans
10.1371/journal.pbio.3000507
Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family
10.1101/2020.03.13.990614
RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery
10.1101/2020.03.14.992123
Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family
10.1186/s12864-020-06785-7
