The evolution of genome mining in microbes - a review.
暂无分享,去创建一个
[1] M. Marahiel,et al. Lasso peptides from proteobacteria: Genome mining employing heterologous expression and mass spectrometry. , 2013, Biopolymers.
[2] Daniel W. Udwary,et al. Type III polyketide synthase beta-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. , 2006, Journal of the American Chemical Society.
[3] R. Müller,et al. Myxobacteria: proficient producers of novel natural products with various biological activities--past and future biotechnological aspects with the focus on the genus Sorangium. , 2003, Journal of biotechnology.
[4] Tilmann Weber,et al. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs) , 2005, Nucleic acids research.
[5] H. Matter,et al. Targeting DnaN for tuberculosis therapy using novel griselimycins , 2015, Science.
[6] Peter Man-Un Ung,et al. Automated genome mining for natural products , 2009, BMC Bioinformatics.
[7] T. Thomas,et al. Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges , 2013, The ISME Journal.
[8] M. Bibb,et al. Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes , 2010, Proceedings of the National Academy of Sciences.
[9] Paula Y. Calle,et al. Discovery and synthetic refactoring of tryptophan dimer gene clusters from the environment. , 2013, Journal of the American Chemical Society.
[10] J. Ravel,et al. Origin and variation of tunicate secondary metabolites. , 2012, Journal of natural products.
[11] D. Haft,et al. SMURF: Genomic mapping of fungal secondary metabolite clusters. , 2010, Fungal genetics and biology : FG & B.
[12] Pieter C. Dorrestein,et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics , 2011, Nature chemical biology.
[13] Sean F. Brady,et al. Chemical-biogeographic survey of secondary metabolism in soil , 2014, Proceedings of the National Academy of Sciences.
[14] C. Hertweck,et al. The molecular basis of conjugated polyyne biosynthesis in phytopathogenic bacteria. , 2014, Angewandte Chemie.
[15] Christophe Corre,et al. Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens , 2011, Proceedings of the National Academy of Sciences.
[16] Carla S. Jones,et al. Minimum Information about a Biosynthetic Gene cluster. , 2015, Nature chemical biology.
[17] A. L. Demain,et al. Antimicrobials, drug discovery, and genome mining , 2012, Applied Microbiology and Biotechnology.
[18] Andrew W. Han,et al. Genome streamlining and chemical defense in a coral reef symbiosis , 2012, Proceedings of the National Academy of Sciences.
[19] David J Newman,et al. Natural products as sources of new drugs over the 30 years from 1981 to 2010. , 2012, Journal of natural products.
[20] Gerard D. Wright,et al. Intrinsic antibiotic resistance: mechanisms, origins, challenges and solutions. , 2013, International journal of medical microbiology : IJMM.
[21] H. Ikeda,et al. Genetic studies of avermectin biosynthesis in Streptomyces avermitilis , 1987, Journal of bacteriology.
[22] Christopher T. Walsh,et al. The evolution of gene collectives: How natural selection drives chemical innovation , 2008, Proceedings of the National Academy of Sciences.
[23] A. Davidson,et al. A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans. , 2009, Journal of the American Chemical Society.
[24] Oscar P. Kuipers,et al. BAGEL2: mining for bacteriocins in genomic data , 2010, Nucleic Acids Res..
[25] Harald Gross,et al. Overproduction of Ristomycin A by Activation of a Silent Gene Cluster in Amycolatopsis japonicum MG417-CF17 , 2014, Antimicrobial Agents and Chemotherapy.
[26] V. Deshpande,et al. Bacteriophage Lambda as a Cloning Vector , 1992, Microbiological reviews.
[27] R. Gonzalez. From the New Editor-in-Chief , 2015, Journal of Industrial Microbiology & Biotechnology.
[28] D. Hopwood,et al. CDA is a new chromosomally-determined antibiotic from Streptomyces coelicolor A3(2). , 1983, Journal of general microbiology.
[29] B. Shen,et al. Enediynes: Exploration of microbial genomics to discover new anticancer drug leads , 2014, Bioorganic & medicinal chemistry letters.
[30] Mark Hildebrand,et al. Identification of the putative bryostatin polyketide synthase gene cluster from "Candidatus Endobugula sertula", the uncultivated microbial symbiont of the marine bryozoan Bugula neritina. , 2007, Journal of natural products.
[31] Nicholas Waglechner,et al. Identifying producers of antibacterial compounds by screening for antibiotic resistance , 2013, Nature Biotechnology.
[32] Emmanuel Zazopoulos,et al. Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. , 2005, Journal of natural products.
[33] M. Fischbach,et al. Small molecules from the human microbiota , 2015, Science.
[34] T. Hemscheidt,et al. Post‐translational Modification in Microviridin Biosynthesis , 2008, Chembiochem : a European journal of chemical biology.
[35] Roger G. Linington,et al. Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei. , 2015, ACS chemical biology.
[36] Liisa Holm,et al. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes , 2014, Proceedings of the National Academy of Sciences.
[37] Michael Gale,et al. Genetic Diversity in the Collaborative Cross Model Recapitulates Human West Nile Virus Disease Outcomes , 2015, mBio.
[38] M. Staver,et al. Cloning of genes involved in erythromycin biosynthesis from Saccharopolyspora erythraea using a novel actinomycete-Escherichia coli cosmid. , 1990, Gene.
[39] Chiaki Nakano,et al. Identification of the First Bacterial Monoterpene Cyclase, a 1,8‐Cineole Synthase, that Catalyzes the Direct Conversion of Geranyl Diphosphate , 2011, Chembiochem : a European journal of chemical biology.
[40] J. Zucko,et al. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures , 2008, Nucleic acids research.
[41] C. Kerfeld,et al. Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria , 2014, BMC Genomics.
[42] Mihai Pop,et al. ARDB—Antibiotic Resistance Genes Database , 2008, Nucleic Acids Res..
[43] J. Merritt,et al. Mutanobactin A from the human oral pathogen Streptococcus mutans is a cross-kingdom regulator of the yeast-mycelium transition. , 2010, Organic & biomolecular chemistry.
[44] S. Holmström,et al. Siderophores in environmental research: roles and applications , 2014, Microbial biotechnology.
[45] O. Kohlbacher,et al. The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494. , 2012, Environmental microbiology.
[46] B. Birren,et al. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. , 1992, Nucleic acids research.
[47] S. Lee,et al. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. , 2015, Trends in biotechnology.
[48] F. Barona-Gómez,et al. Recapitulation of the evolution of biosynthetic gene clusters reveals hidden chemical diversity on bacterial genomes , 2015 .
[49] Gitanjali Yadav,et al. SEARCHPKS: a program for detection and analysis of polyketide synthase domains , 2003, Nucleic Acids Res..
[50] Hong Xu,et al. Systematic unravelling of the biosynthesis of poly (L-diaminopropionic acid) in Streptomyces albulus PD-1 , 2015, Scientific Reports.
[51] Michael Gribskov,et al. Methods and Statistics for Combining Motif Match Scores , 1998, J. Comput. Biol..
[52] M. Nett. Genome mining: concept and strategies for natural product discovery. , 2014, Progress in the chemistry of organic natural products.
[53] J. Badger,et al. The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity , 2012, PloS one.
[54] Clay C C Wang,et al. Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans , 2014, Journal of Industrial Microbiology & Biotechnology.
[55] G. V. van Wezel,et al. Natural product proteomining, a quantitative proteomics platform, allows rapid discovery of biosynthetic gene clusters for different classes of natural products. , 2014, Chemistry & biology.
[56] R. Müller,et al. Discovery of the Rhizopodin Biosynthetic Gene Cluster in Stigmatella aurantiaca Sg a15 by Genome Mining , 2012, Chembiochem : a European journal of chemical biology.
[57] M. Marahiel,et al. Caulosegnins I-III: a highly diverse group of lasso peptides derived from a single biosynthetic gene cluster. , 2013, Journal of the American Chemical Society.
[58] Viral diversity and clonal evolution from unphased genomic data , 2014, BMC Genomics.
[59] Michael A Fischbach,et al. Computational approaches to natural product discovery. , 2015, Nature chemical biology.
[60] Jennifer A. Doudna,et al. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 , 2014, Nature.
[61] R. Süssmuth,et al. A Genomic Screening Approach to the Structure‐Guided Identification of Drug Candidates from Natural Sources , 2007, Chembiochem : a European journal of chemical biology.
[62] M. Schorn,et al. Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. , 2014, ACS chemical biology.
[63] Neetika Nath,et al. CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes , 2015, Bioinform..
[64] J. Eisen,et al. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[65] J B McAlpine,et al. Modular organization of genes required for complex polyketide biosynthesis. , 1991, Science.
[66] T. V. van Beek,et al. Genome‐based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species , 2007, Molecular microbiology.
[67] I. Abe,et al. Pyranonigrin E: A PKS‐NRPS Hybrid Metabolite from Aspergillus niger Identified by Genome Mining , 2013, Chembiochem : a European journal of chemical biology.
[68] T. Weber,et al. Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365 , 2016, Journal of Industrial Microbiology & Biotechnology.
[69] Sylvie Lautru,et al. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining , 2005, Nature chemical biology.
[70] Paula Y. Calle,et al. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors , 2015, Proceedings of the National Academy of Sciences.
[71] D. Hopwood,et al. Actinorhodin is a chromosomally-determined antibiotic in Streptomyces coelicolar A3(2). , 1976, Journal of general microbiology.
[72] H. Jenke-Kodama,et al. Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection , 2008, Nature Biotechnology.
[73] Jörn Piel,et al. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[74] M. Bibb,et al. Streptomyces coelicolor as an expression host for heterologous gene clusters. , 2012, Methods in enzymology.
[75] M. Donia,et al. Linking chemistry and genetics in the growing cyanobactin natural products family. , 2011, Chemistry & biology.
[76] M. Ojika,et al. Isolation and Biosynthetic Analysis of Haliamide, a New PKS-NRPS Hybrid Metabolite from the Marine Myxobacterium Haliangium ochraceum , 2016, Molecules.
[77] Imke Schmitt,et al. Phylogenetic methods in natural product research. , 2009, Natural product reports.
[78] G. Challis,et al. 2-Alkyl-4-hydroxymethylfuran-3-carboxylic acids, antibiotic production inducers discovered by Streptomyces coelicolor genome mining , 2008, Proceedings of the National Academy of Sciences.
[79] G. B. Golding,et al. Antibiotic resistance is ancient , 2011, Nature.
[80] Krystle L. Chavarria,et al. Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora , 2014, Proceedings of the National Academy of Sciences.
[81] P. Mäntsälä,et al. Molecular Evolution of Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and 16S Ribosomal DNA Genes from Various Streptomyces Species , 2002, Applied and Environmental Microbiology.
[82] Dan Søndergaard,et al. Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases , 2016, Bioinform..
[83] Mikael R. Andersen,et al. Accurate prediction of secondary metabolite gene clusters in filamentous fungi , 2012, Proceedings of the National Academy of Sciences.
[84] D. G. Gibson,et al. Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.
[85] Tilmann Weber,et al. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production , 2016, Synthetic and systems biotechnology.
[86] Brian O. Bachmann,et al. Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? , 2014, Journal of Industrial Microbiology & Biotechnology.
[87] Victor M. Markowitz,et al. IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites , 2015, mBio.
[88] Oscar P. Kuipers,et al. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides , 2013, Nucleic Acids Res..
[89] Ronald W Davis,et al. Computational identification and analysis of orphan assembly-line polyketide synthases , 2013, The Journal of Antibiotics.
[90] Roger G. Linington,et al. Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters , 2014, Cell.
[91] B. Roe,et al. Genomic Island TnSmu2 of Streptococcus mutans Harbors a Nonribosomal Peptide Synthetase-Polyketide Synthase Gene Cluster Responsible for the Biosynthesis of Pigments Involved in Oxygen and H2O2 Tolerance , 2010, Applied and Environmental Microbiology.
[92] Oscar P. Kuipers,et al. BAGEL: a web-based bacteriocin genome mining tool , 2006, Nucleic Acids Res..
[93] E. Dittmann,et al. Cyanobacteria as a source of natural products. , 2012, Methods in enzymology.
[94] Susana P. Gaudêncio,et al. Sequence-Based Analysis of Secondary-Metabolite Biosynthesis in Marine Actinobacteria , 2010, Applied and Environmental Microbiology.
[95] J. Asenjo,et al. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. , 2015, The Journal of organic chemistry.
[96] J. Recktenwald,et al. Identification and Analysis of the Balhimycin Biosynthetic Gene Cluster and Its Use for Manipulating Glycopeptide Biosynthesis in Amycolatopsis mediterranei DSM5908 , 1999, Antimicrobial Agents and Chemotherapy.
[97] G. Challis,et al. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[98] M. Smanski,et al. Mechanisms of self-resistance in the platensimycin- and platencin-producing Streptomyces platensis MA7327 and MA7339 strains. , 2014, Chemistry & biology.
[99] Gilles P van Wezel,et al. The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. , 2011, Natural product reports.
[100] Neil L Kelleher,et al. A Roadmap for Natural Product Discovery Based on Large-Scale Genomics and Metabolomics , 2014, Nature chemical biology.
[101] Kai Blin,et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..
[102] F. Ayala. “Nothing in biology makes sense except in the light of evolution” Theodosius Dobzhansky: 1900–1975 , 1977 .
[103] J. Martín,et al. Evolution of the clusters of genes for β-lactam antibiotics: a model for evolutive combinatorial assembly of new β-lactams , 1998 .
[104] Nuno Bandeira,et al. MS/MS networking guided analysis of molecule and gene cluster families , 2013, Proceedings of the National Academy of Sciences.
[105] R. Gibbs,et al. Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.
[106] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[107] Michael A. Skinnider,et al. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM) , 2015, Nucleic acids research.
[108] Gitanjali Yadav,et al. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases , 2004, Nucleic Acids Res..
[109] Wenjun Zhang,et al. Bacterial Genome Mining of Enzymatic Tools for Alkyne Biosynthesis. , 2015, ACS chemical biology.
[110] Shawn French,et al. Assembly and clustering of natural antibiotics guides target identification. , 2016, Nature chemical biology.
[111] P. Dorrestein,et al. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds , 2015, Front. Microbiol..
[112] C. Hertweck,et al. A genomic approach to the cryptic secondary metabolome of the anaerobic world. , 2013, Natural product reports.
[113] M. Moffitt,et al. Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria , 2015, BMC Genomics.
[114] Jurica Zucko,et al. Horizontal gene transfer and gene conversion drive evolution of modular polyketide synthases , 2012, Journal of Industrial Microbiology & Biotechnology.
[115] K. Lewis,et al. A new antibiotic kills pathogens without detectable resistance , 2015, Nature.
[116] Kai Blin,et al. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..
[117] M. Marahiel,et al. Lasso peptides: an intriguing class of bacterial natural products. , 2015, Accounts of chemical research.
[118] D. Hopwood,et al. Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host , 1984, Nature.
[119] C. Fraser,et al. Phylogenomics: Intersection of Evolution and Genomics , 2003, Science.
[120] R. Müller,et al. Myxobacteria--'microbial factories' for the production of bioactive secondary metabolites. , 2009, Molecular bioSystems.
[121] J. Sohng,et al. Genome-based cryptic gene discovery and functional identification of NRPS siderophore peptide in Streptomyces peucetius , 2012, Applied Microbiology and Biotechnology.
[122] William Fenical,et al. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica , 2007, Proceedings of the National Academy of Sciences.
[123] M. Thaker,et al. Antibiotic resistance–mediated isolation of scaffold-specific natural product producers , 2014, Nature Protocols.
[124] R. Ueoka,et al. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms. , 2015, Nature chemical biology.
[125] Jacques Ravel,et al. Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians , 2006, Nature chemical biology.
[126] I. Hoof,et al. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. , 2009, Journal of biotechnology.
[127] G. Berg,et al. The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization. , 2015, Molecular plant-microbe interactions : MPMI.
[128] Kai Blin,et al. NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity , 2011, Nucleic Acids Res..
[129] R. Breitling,et al. Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast , 2013, Molecular biology and evolution.
[130] P. Dorrestein,et al. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A , 2014, Proceedings of the National Academy of Sciences.
[131] M. Marahiel,et al. Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264. , 2008, Journal of the American Chemical Society.
[132] K. Sivonen,et al. Widespread Occurrence and Lateral Transfer of the Cyanobactin Biosynthesis Gene Cluster in Cyanobacteria , 2008, Applied and Environmental Microbiology.
[133] Yoshiyuki Sakaki,et al. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis , 2003, Nature Biotechnology.
[134] S. Brady,et al. Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study , 2014, Journal of the American Chemical Society.
[135] David J Newman,et al. Natural products: a continuing source of novel drug leads. , 2013, Biochimica et biophysica acta.
[136] J. Piel,et al. Recent advances in genome-based polyketide discovery. , 2014, Current opinion in biotechnology.
[137] M. Bibb,et al. Discovery of Unique Lanthionine Synthetases Reveals New Mechanistic and Evolutionary Insights , 2010, PLoS biology.
[138] M. Marahiel,et al. Xanthomonins I-III: a new class of lasso peptides with a seven-residue macrolactam ring. , 2014, Angewandte Chemie.
[139] C. Hertweck,et al. Multifactorial induction of an orphan PKS-NRPS gene cluster in Aspergillus terreus. , 2011, Chemistry & biology.
[140] J. Solbiati,et al. Genetic analysis of plasmid determinants for microcin J25 production and immunity , 1996, Journal of bacteriology.
[141] J. Nielsen,et al. Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster. , 2010, Metabolic engineering.
[142] Chad W. Johnston,et al. Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery , 2012, Proceedings of the National Academy of Sciences.
[143] Peter Cimermancic,et al. A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics , 2014, Cell.
[144] S. Brady,et al. eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes. , 2014, Chemistry & biology.
[145] S. Duquesne,et al. Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli. , 2007, Chemistry & biology.
[146] H. Koike,et al. Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi , 2015, Front. Microbiol..
[147] I. Abe,et al. Three Acyltetronic Acid Derivatives: Noncanonical Cryptic Polyketides from Aspergillus niger Identified by Genome Mining , 2014, Chembiochem : a European journal of chemical biology.
[148] Jurica Zucko,et al. Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing , 2013, Journal of Industrial Microbiology & Biotechnology.
[149] Paula Y. Calle,et al. Targeted metagenomics: finding rare tryptophan dimer natural products in the environment. , 2015, Journal of the American Chemical Society.
[150] J. Solbiati,et al. Sequence Analysis of the Four Plasmid Genes Required To Produce the Circular Peptide Antibiotic Microcin J25 , 1999, Journal of bacteriology.
[151] M. Bibb,et al. Regulation of secondary metabolism in streptomycetes. , 2005, Current opinion in microbiology.
[152] Carlos Prieto,et al. NRPSsp: non-ribosomal peptide synthase substrate predictor , 2012, Bioinform..
[153] Harald Gross,et al. The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. , 2007, Chemistry & biology.
[154] Pieter C Dorrestein,et al. Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. , 2015, Journal of natural products.
[155] C. Hertweck,et al. Anaerobic bacteria as producers of antibiotics , 2012, Applied Microbiology and Biotechnology.
[156] B. Moore,et al. Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. , 2015, ACS chemical biology.
[157] J. Eisen,et al. Phylogenetic analysis and gene functional predictions: phylogenomics in action. , 2002, Theoretical population biology.
[158] B. Bohannan,et al. The Biogeography of Putative Microbial Antibiotic Production , 2015, PloS one.
[159] B. Shen,et al. Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery , 2016, Journal of Industrial Microbiology & Biotechnology.
[160] Julian Brandl,et al. FunGeneClusterS: Predicting fungal gene clusters from genome and transcriptome data , 2016, Synthetic and systems biotechnology.
[161] J. Pernodet,et al. Organization of the biosynthetic gene cluster for the macrolide antibiotic spiramycin in Streptomyces ambofaciens. , 2007, Microbiology.
[162] P. Permi,et al. Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides. , 2013, Chemistry & biology.
[163] Gregory L. Challis,et al. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[164] Christopher N. Boddy,et al. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides , 2014, Journal of Industrial Microbiology & Biotechnology.
[165] Pieter C. Dorrestein,et al. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria , 2016, mSystems.
[166] T. Ravasi,et al. Actinomycetes from Red Sea Sponges: Sources for Chemical and Phylogenetic Diversity , 2014, Marine drugs.
[167] R. Saha,et al. Microbial siderophores: a mini review , 2013, Journal of basic microbiology.
[168] Nuno Bandeira,et al. Automated Genome Mining of Ribosomal Peptide Natural Products , 2014, ACS chemical biology.
[169] G. V. van Wezel,et al. Unsuspected control of siderophore production by N-acetylglucosamine in streptomycetes. , 2012, Environmental microbiology reports.
[170] J. Imhoff,et al. Streptocollin, a Type IV Lanthipeptide Produced by Streptomyces collinus Tü 365 , 2015, Chembiochem : a European journal of chemical biology.
[171] Tilmann Weber,et al. In silico tools for the analysis of antibiotic biosynthetic pathways. , 2014, International journal of medical microbiology : IJMM.
[172] T. Weber,et al. Exploiting the genetic potential of polyketide producing streptomycetes. , 2003, Journal of biotechnology.
[173] Douglas A Mitchell,et al. Using Genomics for Natural Product Structure Elucidation. , 2016, Current topics in medicinal chemistry.
[174] Raphaël Marée,et al. PREDetector: a new tool to identify regulatory elements in bacterial genomes. , 2007, Biochemical and biophysical research communications.
[175] M. Fillat. The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators. , 2014, Archives of biochemistry and biophysics.
[176] L. Heide,et al. Identification of the Novobiocin Biosynthetic Gene Cluster of Streptomyces spheroides NCIB 11891 , 2000, Antimicrobial Agents and Chemotherapy.
[177] A. Singh,et al. Activation of the SoxR Regulon in Streptomyces coelicolor by the Extracellular Form of the Pigmented Antibiotic Actinorhodin , 2010, Journal of bacteriology.
[178] Christian Rinke,et al. An environmental bacterial taxon with a large and distinct metabolic repertoire , 2014, Nature.
[179] Thomas E. Ferrin,et al. Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies , 2009, PloS one.
[180] J. Sohng,et al. Identification ofStreptomyces violaceoruber Tü22 genes involved in the biosynthesis of granaticin , 1995, Molecular and General Genetics MGG.
[181] E. Dittmann,et al. Exploiting the Natural Diversity of Microviridin Gene Clusters for Discovery of Novel Tricyclic Depsipeptides , 2010, Applied and Environmental Microbiology.
[182] H. Jenke-Kodama,et al. Evolution of metabolic diversity: insights from microbial polyketide synthases. , 2009, Phytochemistry.
[183] E. Dittmann,et al. Ribosomal synthesis of tricyclic depsipeptides in bloom-forming cyanobacteria. , 2008, Angewandte Chemie.
[184] W. Wohlleben,et al. Elucidation of the zinc-dependent regulation in Amycolatopsis japonicum enabled the identification of the ethylenediamine-disuccinate ([S,S]-EDDS) genes. , 2016, Environmental microbiology.
[185] I. Pelczer,et al. Precursor-centric genome-mining approach for lasso peptide discovery , 2012, Proceedings of the National Academy of Sciences.
[186] Chiaki Nakano,et al. Identification of a New Diterpene Biosynthetic Gene Cluster that Produces O‐Methylkolavelool in Herpetosiphon aurantiacus , 2015, Chembiochem : a European journal of chemical biology.
[187] M. Forsman,et al. Scaffolding of a bacterial genome using MinION nanopore sequencing , 2015, Scientific Reports.
[188] Bradley S Moore,et al. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules , 2013, Proceedings of the National Academy of Sciences.
[189] Rainer Breitling,et al. Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products , 2014, PLoS Comput. Biol..
[190] Jörn Piel,et al. Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides , 2012, Science.
[191] Thomas Börner,et al. Natural Biocombinatorics in the Polyketide Synthase Genes of the Actinobacterium Streptomyces avermitilis , 2006, PLoS Comput. Biol..
[192] B. Rudd,et al. Genetics of actinorhodin biosynthesis by Streptomyces coelicolor A3(2). , 1979, Journal of general microbiology.
[193] Sailu Yellaboina,et al. IdeR in Mycobacteria: From Target Recognition to Physiological Function , 2006, Critical reviews in microbiology.
[194] M. Nishiyama,et al. Identification and Characterization of Bacterial Diterpene Cyclases that Synthesize the Cembrane Skeleton , 2013, Chembiochem : a European journal of chemical biology.
[195] Corinna Lange,et al. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. , 2007, Nature chemical biology.
[196] Paul D. Cotter,et al. Identification of a Novel Two-Peptide Lantibiotic, Lichenicidin, following Rational Genome Mining for LanM Proteins , 2009, Applied and Environmental Microbiology.
[197] W. Metcalf,et al. Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes , 2013, BMC Genomics.
[198] Kiyoshi Asai,et al. MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data , 2013, PloS one.
[199] Cody R. Goodwin,et al. Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps. , 2015, Chemistry & biology.
[200] Gang Liu,et al. Molecular Regulation of Antibiotic Biosynthesis in Streptomyces , 2013, Microbiology and Molecular Reviews.
[201] I. Abe,et al. Molecular Basis for Stellatic Acid Biosynthesis: A Genome Mining Approach for Discovery of Sesterterpene Synthases. , 2015, Organic letters.
[202] Chao Xie,et al. Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.
[203] Yuuki Yamada,et al. Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host , 2015, The Journal of Antibiotics.
[204] B. Barrell,et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) , 2002, Nature.
[205] D. Christianson. Unearthing the roots of the terpenome. , 2008, Current opinion in chemical biology.
[206] Pavel A. Pevzner,et al. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery , 2014, Journal of natural products.
[207] Kai Blin,et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..
[208] E. Dittmann,et al. Leader peptide and a membrane protein scaffold guide the biosynthesis of the tricyclic peptide microviridin. , 2011, Chemistry & biology.
[209] Jörn Piel,et al. Biosynthesis of polyketides by trans-AT polyketide synthases. , 2016, Natural product reports.
[210] Andrew C. Pawlowski,et al. The Comprehensive Antibiotic Resistance Database , 2013, Antimicrobial Agents and Chemotherapy.
[211] Anna Lechner,et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. , 2015, Chemistry and Biology.
[212] Brian O. Bachmann,et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways , 2003, Nature Biotechnology.
[213] D. Buckley,et al. Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin , 2014, BMC Genomics.
[214] S. Lautru,et al. An iterative nonribosomal peptide synthetase assembles the pyrrole-amide antibiotic congocidine in Streptomyces ambofaciens. , 2009, Chemistry & biology.
[215] S. Sudek,et al. Genetic evidence supports secondary metabolic diversity in Prochloron spp., the cyanobacterial symbiont of a tropical ascidian. , 2004, Journal of natural products.
[216] Morgan A. Wyatt,et al. Staphylococcus aureus Nonribosomal Peptide Secondary Metabolites Regulate Virulence , 2010, Science.
[217] M. Bibb,et al. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides , 2010, Proceedings of the National Academy of Sciences.
[218] M. Komatsu,et al. Terpene synthases are widely distributed in bacteria , 2014, Proceedings of the National Academy of Sciences.
[219] Vladimir Larionov,et al. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae , 2008, Nature Protocols.
[220] Jacques Ravel,et al. Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. , 2009, Methods in enzymology.
[221] The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles , 2015, BMC Genomics.
[222] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[223] Andrej Sali,et al. A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis , 2014, PLoS Comput. Biol..
[224] W. A. van der Donk,et al. Mechanistic Studies of Ser/Thr Dehydration Catalyzed by a Member of the LanL Lanthionine Synthetase Family , 2011, Biochemistry.
[225] Chad W. Johnston,et al. Automated Identification of Depsipeptide Natural Products by an Informatic Search Algorithm , 2015, Chembiochem : a European journal of chemical biology.
[226] B. Neilan,et al. Evolutionary Affiliations Within the Superfamily of Ketosynthases Reflect Complex Pathway Associations , 2003, Journal of Molecular Evolution.