Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches

Walsh, 2003, Where will new antibiotics come from?, Nat Rev Microbiol, 1, 65, 10.1038/nrmicro727 Sharma, 2014, Drugs and drug intermediates from fungi: striving for greener processes, Crit Rev Microbiol, 7828, 1, 10.3109/1040841X.2014.947240 Avalos, 2014, Biological roles of fungal carotenoids, Curr Genet, 61, 309, 10.1007/s00294-014-0454-x Brakhage, 2012, Regulation of fungal secondary metabolism, Nat Rev Microbiol, 11, 21, 10.1038/nrmicro2916 Tedersoo, 2014, Disentangling global soil fungal diversity, Science, 346, 1052, 10.1126/science.1256688 Mar Rodríguez, 2015, Obesity changes the human gut mycobiome, Sci Rep, 5, 14600, 10.1038/srep14600 Gruninger, 2014, Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential, FEMS Microbiol Ecol, 90, 1, 10.1111/1574-6941.12383 O'Brien, 2005, Fungal community analysis by large-scale sequencing of environmental samples, Appl Environ Microbiol, 71, 5544, 10.1128/AEM.71.9.5544-5550.2005 Blackwell, 2011, The fungi: 1, 2, 3... 5.1 million species?, Am J Bot, 98, 426, 10.3732/ajb.1000298 Grigoriev, 2014, MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Res, 42, D699, 10.1093/nar/gkt1183 Charlop-Powers, 2016, Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity, Proc Natl Acad Sci, 113, 14811, 10.1073/pnas.1615581113 Haitjema, 2017, A parts list for fungal cellulosomes revealed by comparative genomics, Nat Microbiol, 2, 17087, 10.1038/nmicrobiol.2017.87 Hoffmeister, 2007, Natural products of filamentous fungi: enzymes, genes, and their regulation, Nat Prod Rep, 24, 393, 10.1039/B603084J Gressler, 2015, A new high-performance heterologous fungal expression system based on regulatory elements from the Aspergillus terreus terrein gene cluster, Front Microbiol, 6, 184, 10.3389/fmicb.2015.00184 Chai, 2016, Sesterterpene ophiobolin biosynthesis involving multiple gene clusters in Aspergillus ustus, Sci Rep, 6, 27181, 10.1038/srep27181 Keller, 2005, Fungal secondary metabolism — from biochemistry to genomics, Nat Rev Microbiol, 3, 937, 10.1038/nrmicro1286 Subhan, 2016, Exploitation of Aspergillus terreus for the production of natural statins, J Fungi, 2, 13 Shen, 2003, Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms, Curr Opin Chem Biol, 7, 285, 10.1016/S1367-5931(03)00020-6 Hashimoto, 2014, Fungal type III polyketide synthases, Nat Prod Rep, 31, 1306, 10.1039/C4NP00096J Chang, 2013, Genome-wide analysis of the Zn(II)2Cys6 zinc cluster-encoding gene family in Aspergillus flavus, Appl Microbiol Biotechnol, 97, 4289, 10.1007/s00253-013-4865-2 Wiemann, 2014, Strategies for mining fungal natural products, J Ind Microbiol Biotechnol, 41, 301, 10.1007/s10295-013-1366-3 van den Berg, 2007, Functional characterization of the penicillin biosynthetic gene cluster of Penicillium chrysogenum Wisconsin54-1255, Fungal Genet Biol, 44, 830, 10.1016/j.fgb.2007.03.008 Weber, 2016, The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production, Synth Syst Biotechnol, 1, 69, 10.1016/j.synbio.2015.12.002 Khaldi, 2010, SMURF: genomic mapping of fungal secondary metabolite clusters, Fungal Genet Biol, 47, 736, 10.1016/j.fgb.2010.06.003 Weber, 2015, AntiSMASH 3.0-A comprehensive resource for the genome mining of biosynthetic gene clusters, Nucleic Acids Res, 43, W237, 10.1093/nar/gkv437 Inglis, 2013, Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae, BMC Microbiol, 13, 91, 10.1186/1471-2180-13-91 Nielsen, 2017, Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species, Nat Microbiol, 2, 17044, 10.1038/nmicrobiol.2017.44 Johnston, 2015, An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products, Nat Commun, 6, 8421, 10.1038/ncomms9421 Dejong, 2016, Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching, Nat Chem Biol, 12, 1007, 10.1038/nchembio.2188 Hughes, 2017, Synthetic DNA synthesis and assembly : putting the synthetic in synthetic biology, Cold Spring Harb Perspect Biol, 9, a023812, 10.1101/cshperspect.a023812 Chiang, 2013, An efficient system for heterologous expression of secondary metabolite genes in Aspergillus nidulans, J Am Chem Soc, 135, 7720, 10.1021/ja401945a Heneghan, 2010, First heterologous reconstruction of a complete functional fungal biosynthetic multigene cluster, ChemBioChem, 11, 1508, 10.1002/cbic.201000259 Montiel, 2015, Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters, Proc Natl Acad Sci, 112, 8953, 10.1073/pnas.1507606112 Bok, 2015, Fungal artificial chromosomes for mining of the fungal secondary metabolome, BMC Genomics, 16, 343, 10.1186/s12864-015-1561-x Nielsen, 2013, Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach, PLoS One, 8, e72871, 10.1371/journal.pone.0072871 Lambertz, 2014, Challenges and advances in the heterologous expression of cellulolytic enzymes: a review, Biotechnol Biofuels, 7, 135, 10.1186/s13068-014-0135-5 Liu, 2015, Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system, Cell Discov, 1, 15007, 10.1038/celldisc.2015.7 Pohl, 2016, CRISPR/Cas9 based genome editing of Penicillium chrysogenum, ACS Synth Biol, 5, 754, 10.1021/acssynbio.6b00082 Matsu-ura, 2015, Efficient gene editing in Neurospora crassa with CRISPR technology, Fungal Biol Biotechnol, 2, 4, 10.1186/s40694-015-0015-1 Richter, 2014, Engineering of Aspergillus niger for the production of secondary metabolites, Fungal Biol Biotechnol, 1, 4, 10.1186/s40694-014-0004-9 Shwab, 2007, Histone deacetylase activity regulates chemical diversity in Aspergillus, Eukaryot Cell, 6, 1656, 10.1128/EC.00186-07 Meijer, 2010, Peroxisomes are required for efficient penicillin biosynthesis in Penicillium chrysogenum, Appl Environ Microbiol, 76, 5702, 10.1128/AEM.02327-09 Akone, 2016, Inducing secondary metabolite production by the endophytic fungus Chaetomium sp. through fungal-bacterial co-culture and epigenetic modification, Tetrahedron, 72, 6340, 10.1016/j.tet.2016.08.022 Wu, 2015, Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation, Sci Rep, 5, 10868, 10.1038/srep10868 Schroeckh, 2009, Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans, Proc Natl Acad Sci, 106, 14558, 10.1073/pnas.0901870106 Yin, 2011, Transcriptional regulatory elements in fungal secondary metabolism, J Microbiol, 49, 329 Nützmann, 2011, Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation, Proc Natl Acad Sci, 108, 14282, 10.1073/pnas.1103523108 Netzker, 2015, Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters, Front Microbiol, 6, 1, 10.3389/fmicb.2015.00299 Krug, 2014, Secondary metabolomics: the impact of mass spectrometry-based approaches on the discovery and characterization of microbial natural products, Nat Prod Rep, 31, 768, 10.1039/c3np70127a Vansteelandt, 2012, Patulin and secondary metabolite production by marine-derived Penicillium strains, Fungal Biol, 116, 954, 10.1016/j.funbio.2012.06.005 Tautenhahn, 2012, An accelerated workflow for untargeted metabolomics using the METLIN database, Nat Biotechnol, 30, 826, 10.1038/nbt.2348 Wang, 2016, Sharing and community curation of mass spectrometry data with global natural products social molecular networking, Nat Biotechnol, 34, 828, 10.1038/nbt.3597 Fang, 2014, Emerging mass spectrometry techniques for the direct analysis of microbial colonies, Curr Opin Microbiol, 19, 120, 10.1016/j.mib.2014.06.014 Wang, 2015, Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products, BMC Genomics, 16, 28, 10.1186/s12864-014-1190-9 Daly, 2016, Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression, Fungal Genet Biol, 102, 4, 10.1016/j.fgb.2016.04.005 Smits, 2016, Characterizing protein-protein interactions using mass spectrometry: challenges and opportunities, Trends Biotechnol, 34, 825, 10.1016/j.tibtech.2016.02.014 Ribeiro, 2017, Insights regarding fungal phosphoproteomic analysis, Fungal Genet Biol, 104, 38, 10.1016/j.fgb.2017.03.003 Bumpus, 2009, A proteomics approach to discovering natural products and their biosynthetic pathways, Nat Biotechnol, 27, 951, 10.1038/nbt.1565 Gutierrez, 2017, Transcriptomics, targeted metabolomics and gene expression of blackberry leaves and fruits indicate flavonoid metabolic flux from leaf to red fruit, Front Plant Sci, 8, 1, 10.3389/fpls.2017.00472 Karničar, 2016, Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea, Microb Cell Fact, 15, 93, 10.1186/s12934-016-0496-5 Lim, 2012, Toward awakening cryptic secondary merabolite gene clusters in filamentous fungi, Methods Enzymol, 517, 303, 10.1016/B978-0-12-404634-4.00015-2 Büttel, 2015, Unlocking the potential of fungi: the QuantFung project, Fungal Biol Biotechnol, 2, 6, 10.1186/s40694-015-0016-0 Solomon, 2016, Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes, Science, 351, 1192, 10.1126/science.aad1431 Imhoff, 2016, Natural products from marine fungi - still an underrepresented resource, Mar Drugs, 14, 19, 10.3390/md14010019 Orpin, 1975, Studies on the rumen flagellate neocallimastix frontalis, J Gen Microbiol, 91, 249, 10.1099/00221287-91-2-249 Haitjema, 2014, Anaerobic gut fungi: advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production, Biotechnol Bioeng, 111, 1471, 10.1002/bit.25264 Theodorou, 1996, Anaerobic fungi in the digestive tract of mammalian herbivores and their potential for exploitation, Proc Nutr Soc, 55, 913, 10.1079/PNS19960088 Grigoriev, 2011, Fueling the future with fungal genomics, Mycology, 2, 192 Nordberg, 2014, The genome portal of the Department of Energy Joint Genome Institute: 2014 updates, Nucleic Acids Res, 42, 26, 10.1093/nar/gkt1069 Musiol-Kroll, 2017, Polyketide bioderivatization using the promiscuous acyltransferase KirCII, ACS Synth Biol, 6, 421, 10.1021/acssynbio.6b00341 Yuzawa, 2016, Insights into polyketide biosynthesis gained from repurposing antibiotic-producing polyketide synthases to produce fuels and chemicals, J Antibiot (Tokyo), 69, 494, 10.1038/ja.2016.64 Yuzawa, 2017, Comprehensive in vitro analysis of acyltransferase domain exchanges in modular polyketide synthases and its application for short-chain Ketone production, ACS Synth Biol, 6, 139, 10.1021/acssynbio.6b00176 Endo, 2010, A historical perspective on the discovery of statins, Proc Jpn Acad Ser B, 86, 484, 10.2183/pjab.86.484 Demain, 1999, MINI-REVIEW Pharmaceutically active secondary metabolites of microorganisms, Appl Microbiol Biotechnol, 52, 455, 10.1007/s002530051546 Ventola, 2015, The antibiotic resistance crisis: part 1: causes and threats. [Internet], P T A peer-reviewed J Formul Manag, 40, 277 Bhosale, 2004, Environmental and cultural stimulants in the production of carotenoids from microorganisms, Appl Microbiol Biotechnol, 63, 351, 10.1007/s00253-003-1441-1 Beekman, 2014, Fungal metabolites as pharmaceuticals, Aust J Chem, 67, 827, 10.1071/CH13639 Singh, 2004, Nodulisporic acids D-F: structure, biological activities, and biogenetic relationships, J Nat Prod, 67, 1496, 10.1021/np0498455 Mata-Gómez, 2014, Biotechnological production of carotenoids by yeasts: an overview, Microb Cell Fact, 13, 12, 10.1186/1475-2859-13-12