An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium
Tài liệu tham khảo
Awakawa, 2012, A heptaketide naphthaldehyde produced by a polyketide synthase from Nectria haematococca, Bioorg. Med. Chem. Lett., 22, 4338, 10.1016/j.bmcl.2012.05.005
Baayen, 2000, Gene genealogies and AFLP analyses in the Fusarium oxysporum complex identify monophyletic and nonmonophyletic formae speciales causing wilt and rot disease, Phytopathology, 90, 891, 10.1094/PHYTO.2000.90.8.891
Bachmann, 2009, Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data
Birch, 1968, Metabolites of Aspergillus indicus: the structure and some aspects of the biosynthesis of dihydrocanadensolide, Aust. J. Chem., 21, 2775, 10.1071/CH9682775
Birkinshaw, 1942, Studies in the biochemistry of micro-organisms 71. Fumaryl-dl-alanine (Fumaromono-dl-alanide), a metabolic product of Penicillium resticulosum sp.nov, Biochem. J., 36, 829, 10.1042/bj0360829
Boc, 2012, T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks, Nucleic Acids Res., 40, W573, 10.1093/nar/gks485
Brown, 2012, Phylogenomic and functional domain analysis of polyketide synthases in Fusarium, Fungal Biol., 116, 318, 10.1016/j.funbio.2011.12.005
Brown, 2012, Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioides, Fungal Genet. Biol., 49, 521, 10.1016/j.fgb.2012.05.010
Brudno, 2003, Glocal alignment: finding rearrangements during alignment, Bioinformatics, 19, i54, 10.1093/bioinformatics/btg1005
Bushley, 2010, Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships, BMC Evol. Biol., 10
Carr, 1985, Structure determination of a new cyclodepsipeptide antibiotic from Fusaria fungi, J. Org. Chem., 50, 2854, 10.1021/jo00216a008
Chiang, 2009, A gene cluster containing two fungal polyketide synthases encodes the biosynthetic pathway for a polyketide, asperfuranone, in Aspergillus nidulans, J. Am. Chem. Soc., 131, 2965, 10.1021/ja8088185
Coleman, 2009, The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion, PLoS Genet., 5
Cuomo, 2007, The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization, Science, 317, 1400, 10.1126/science.1143708
Felsenstein, 1989, PHYLIP – Phylogeny Inference Package (Version 3.2), Cladistics, 5, 164
Frandsen, 2011, Two novel classes of enzymes are required for the biosynthesis of aurofusarin in Fusarium graminearum, J. Biol. Chem., 286, 10419, 10.1074/jbc.M110.179853
Fujii, 2001, Identification of Claisen cyclase domain in fungal polyketide synthase WA, a naphthopyrone synthase of Aspergillus nidulans, Chem. Biol., 8, 189, 10.1016/S1074-5521(00)90068-1
Gaffoor, 2005, Functional analysis of the polyketide synthase genes in the filamentous fungus Gibberella zeae (Anamorph Fusarium graminearum), Eukaryot. Cell, 4, 1926, 10.1128/EC.4.11.1926-1933.2005
Gardiner, 2012, Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts, PLoS Pathol., 8
Gardiner, 2014, Genome sequence of Fusarium graminearum isolate CS3005, Genome Announce, 2, 5, 10.1128/genomeA.00227-14
Graziani, 2004, Novel polyketide synthase from Nectria haematococca, Appl. Environ. Microbiol., 70, 2984, 10.1128/AEM.70.5.2984-2988.2004
Hansen, 2012, Overexpression of NRPS4 leads to increased surface hydrophobicity in Fusarium graminearum, Fungal Biol., 116, 855, 10.1016/j.funbio.2012.04.014
Hansen, 2012, Quick guide to polyketide synthase and nonribosomal synthetase genes in Fusarium, Int. J. Food Microbiol., 155, 128, 10.1016/j.ijfoodmicro.2012.01.018
Helaers, 2010, MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics, BMC Bioinformatics, 11, 379, 10.1186/1471-2105-11-379
Hestbjerg, 2002, Production of trichothecenes and other secondary metabolites by Fusarium culmorum and Fusarium equiseti on common laboratory media and a soil organic matter agar: An ecological interpretation, J. Agric. Food Chem., 50, 7593, 10.1021/jf020432o
Hunter, 2012, InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Res., 40, D306, 10.1093/nar/gkr948
Inokoshi, 2013, Epi-trichosetin, a new undecaprenyl pyrophosphate synthase inhibitor, produced by Fusarium oxysporum FKI-4553, J. Antibiot., 66, 549, 10.1038/ja.2013.44
Jin, 2010, Functional characterization and manipulation of the apicidin biosynthetic pathway in Fusarium semitectum, Mol. Microbiol., 76, 456, 10.1111/j.1365-2958.2010.07109.x
Jørgensen, 2014, Fusarium graminearum PKS14 is involved in orsellinic acid and orcinol synthesis, Fungal Genet. Biol., 70, 24, 10.1016/j.fgb.2014.06.008
Kakule, 2013, Two related pyrrolidinedione synthetase loci in Fusarium heterosporum ATCC 74349 produce divergent metabolites, ACS Chem. Biol., 8, 1549, 10.1021/cb400159f
Keller, 2011, A novel hybrid gene prediction method employing protein multiple sequence alignments, Bioinformatics, 27, 757, 10.1093/bioinformatics/btr010
Kobayashi, 1995, Isolation and structures of an antifungal antibiotic, fusarielin A, and related compounds produced by a Fusarium sp, J. Antibiot., 48, 42, 10.7164/antibiotics.48.42
Kokkonen, 2010, Mycotoxin production of selected Fusarium species at different culture conditions, Int. J. Food Microbiol., 143, 17, 10.1016/j.ijfoodmicro.2010.07.015
Kroken, 2003, Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes, Proc. Natl. Acad. Sci. USA, 100, 15670, 10.1073/pnas.2532165100
Lawrence, 2011, Interkingdom gene transfer of a hybrid NPS/PKS from bacteria to filamentous Ascomycota, PLoS One, 6, e28231, 10.1371/journal.pone.0028231
Li, 2010, Classification, prediction, and verification of the regioselectivity of fungal polyketide synthase product template domains, J. Biol. Chem., 285, 22762
Lysøe, 2014, The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism, PLoS One, 9, e112703, 10.1371/journal.pone.0112703
Ma, 2010, Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, 464, 367, 10.1038/nature08850
Marchler-Bauer, 2011, CDD: a Conserved Domain Database for the functional annotation of proteins, Nucleic Acids Res., 39, D225, 10.1093/nar/gkq1189
McDaniel, 1994, Engineered biosynthesis of novel polyketides: actVII and actIV genes encode aromatase and cyclase enzymes, respectively, J. Am. Chem. Soc., 116, 10855, 10.1021/ja00103a001
Meier, 2009, The chemical biology of modular biosynthetic enzymes, Chem. Soc. Rev., 38, 2012, 10.1039/b805115c
Moolhuijzen, 2013, Genome sequences of six wheat-infecting Fusarium species isolates, Genome Announce., 1
Munawar, 2013, Isolation and characterisation of a ferrirhodin synthetase gene from the sugarcane pathogen Fusarium sacchari, ChemBioChem, 14, 388, 10.1002/cbic.201200587
Nenkep, 2010, Induced production of bromomethylchlamydosporols A and B from the marine-derived fungus Fusarium tricinctum, J. Nat. Prod., 73, 2061, 10.1021/np1005289
Niehaus, 2013, Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway, Chem. Biol., 20, 1055, 10.1016/j.chembiol.2013.07.004
Niehaus, 2014, Apicidin F: characterization and genetic manipulation of a new secondary metabolite gene cluster in the rice pathogen Fusarium fujikuroi, PLoS One, 9, e103336, 10.1371/journal.pone.0103336
Niehaus, 2014, Characterization of the fusaric acid gene cluster in Fusarium fujikuroi, Appl. Microbiol. Biotechnol., 98, 1749, 10.1007/s00253-013-5453-1
Nihei, 1998, Antifungal cyclodepsipeptides, W493 A and B, from Fusarium sp.: Isolation and structural determination, Biosci. Biotechnol. Biochem., 62, 858, 10.1271/bbb.62.858
O’Donnell, 2013, Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria, Fungal Genet. Biol., 52, 20, 10.1016/j.fgb.2012.12.004
Oide, 2006, NPS6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes, Plant Cell., 18, 2836, 10.1105/tpc.106.045633
ApSimon, 1994, The biosynthetic diversity of secondary metabolites, 3
Proctor, 2007, Functional characterization, sequence comparisons and distribution of a polyketide synthase gene required for perithecial pigmentation in some Fusarium species, Food Addit. Contam., 24, 1076, 10.1080/02652030701546495
Salamov, 2000, Ab initio gene finding in Drosophila genomic DNA, Genome Res., 10, 516, 10.1101/gr.10.4.516
Song, 2004, Fusarin C biosynthesis in Fusarium moniliforme and Fusarium venenatum, ChemBioChem, 5, 1196, 10.1002/cbic.200400138
Sørensen, 2013, Influence of carbohydrates on secondary metabolism in Fusarium avenaceum, Toxins, 5, 1655, 10.3390/toxins5091655
Sørensen, 2009, Analysis of Fusarium avenaceum metabolites produced during wet apple core rot, J. Agric. Food Chem., 57, 1632, 10.1021/jf802926u
Sørensen, 2012, Production of novel fusarielins by ectopic activation of the polyketide synthase 9 cluster in Fusarium graminearum, Environ. Microbiol., 14, 1159, 10.1111/j.1462-2920.2011.02696.x
Sørensen, 2012, Redirection of pigment biosynthesis to isocoumarins in Fusarium, Fungal Genet. Biol., 49, 413, 10.1016/j.fgb.2012.06.004
Sørensen, 2013, Production of fusarielins by Fusarium, Int. J. Food Microbiol., 160, 206, 10.1016/j.ijfoodmicro.2012.10.016
Sørensen, 2014, Fungal NRPS-dependent siderophores: from function to prediction
Sørensen, 2014, Genetic transformation of Fusarium avenaceum by Agrobacterium tumefaciens mediated transformation and the development of a USER-Brick vector construction system, BMC Mol. Biol., 15, 15, 10.1186/1471-2199-15-15
Sørensen, 2014, Identification of the biosynthetic gene clusters for the lipopeptides fusaristatin A and W493 B in Fusarium graminearum and F. pseudograminearum, J. Nat. Prod., 77, 2615, 10.1021/np500436r
Stanke, 2008, Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, 24, 637, 10.1093/bioinformatics/btn013
Steinchen, 2013, Bimodular peptide synthetase SidE produces fumarylalanine in the human pathogen Aspergillus fumigatus, Appl. Environ. Microbiol., 79, 6670, 10.1128/AEM.02642-13
Strieker, 2010, Nonribosomal peptide synthetases: structures and dynamics, Curr. Opin. Struct. Biol., 20, 234, 10.1016/j.sbi.2010.01.009
Studt, 2012, Biosynthesis of fusarubins accounts for pigmentation of Fusarium fujikuroi perithecia, Appl. Environ. Microbiol., 78, 4468, 10.1128/AEM.00823-12
Summerell, 2010, Biogeography and phylogeography of Fusarium: a review, Fungal Diversity, 44, 3, 10.1007/s13225-010-0060-2
Tae, 2007, ASMPKS: an analysis system for modular polyketide synthases, BMC Bioinform., 8, 1, 10.1186/1471-2105-8-327
Tobiasen, 2007, Nonribosomal peptide synthetase (NPS) genes in Fusarium graminearum, F. culmorum and F. pseudograminearium and identification of NPS2 as the producer of ferricrocin, Curr. Genet., 51, 43, 10.1007/s00294-006-0103-0
Uhlig, 2005, 2-Amino-14,16-dimethyloctadecan-3-ol, a new sphingosine analogue toxin in the fungal genus Fusarium, Toxicon, 46, 513, 10.1016/j.toxicon.2005.06.016
Von Bargen, 2013, Structure elucidation and antimalarial activity of apicidin F: an apicidin-like compound produced by Fusarium fujikuroi, J. Nat. Prod., 76, 2136, 10.1021/np4006053
Wiemann, 2009, Biosynthesis of the red pigment bikaverin in Fusarium fujikuroi: genes, their function and regulation, Mol. Microbiol., 72, 931, 10.1111/j.1365-2958.2009.06695.x
Wiemann, 2012, The Sfp-type 4′-phosphopantetheinyl transferase Ppt1 of Fusarium fujikuroi controls development, secondary metabolism and pathogenicity, PLoS One, 7, e37519, 10.1371/journal.pone.0037519
Wiemann, 2013, Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites, PLoS Pathol., 9, 4, 10.1371/journal.ppat.1003475
Xu, 2008, Biosynthesis of the cyclooligomer depsipeptide beauvericin, a virulence Factor of the Entomopathogenic Fungus Beauveria bassiana, Chem. Biol., 15, 898, 10.1016/j.chembiol.2008.07.011
Zhang, 2012, EvolView, an online tool for visualizing, annotating and managing phylogenetic trees, Nucleic Acids Res., 40, W569, 10.1093/nar/gks576