168
References
Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN toolbox and
its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS
Comput Biol 9:e1002980
Aleti G, Sessitsch A, Brader G (2015) Genome mining: prediction of lipopeptides and polyketides
from Bacillus and related Firmicutes. Comput Struct Biotechnol J 13:192–203
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: a knowledge-based resource
for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 32:W405–W413
Archibald F (1983) Lactobacillus plantarum, an organism not requiring iron. FEMS Microbiol
Lett 19:29–32
Baars O, Perlman DH (2016) Small molecule LC-MS/MS fragmentation data analysis and application to siderophore identification. In: Valdman J (ed) Applications from engineering with
MATLAB concepts. InTech University of South Bohemia in České Budějovice
Baars O, Zhang X, Morel FM, Seyedsayamdost MR (2016) The siderophore metabolome of
Azotobacter vinelandii. Appl Environ Microbiol 82:27–39
Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z (2014) New insights into the echinocandins and other
fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 31:1348–1375
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA et al (2017) antiSMASH 4.0—
improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids
Res 45:W36–W41
Bok JW, Ye R, Clevenger KD, Mead D, Wagner M, Krerowicz A et al (2015) Fungal artificial chromosomes for mining of the fungal secondary metabolome. BMC Genomics 16:343
Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3 (2)
metabolism. Genome Res 15:820–829
Bumpus SB, Evans BS, Thomas PM, Ntai I, Kelleher NL (2009) A proteomics approach to discovering natural products and their biosynthetic pathways. Nat Biotechnol 27:951
Büttel Z, Díaz R, Dirnberger B, Flak M, Grijseels S, Kwon MJ et al (2015) Unlocking the potential
of fungi: the QuantFung project. Fungal Biol Biotechnol 2:6
Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G (2007) NORINE: a database
of nonribosomal peptides. Nucleic Acids Res 36:D326–D331
Chen Y, Unger M, Ntai I, McClure RA, Albright JC, Thomson RJ, Kelleher NL (2013) Gobichelin
A and B: mixed-ligand siderophores discovered using proteomics. MedChemComm 4:233–238
Conway KR, Boddy CN (2012) ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res 41:D402–D407
Cornelis P, Andrews SC (2010) IIron uptake and homeostasis in microorganisms. Caister Academic
Press, Norfolk.
Daly P, van Munster JM, Kokolski M, Sang F, Blythe MJ, Malla S et al (2017) 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 102:4–21
Dejong CA, Chen GM, Li H, Johnston CW, Edwards MR, Rees PN et al (2016) Polyketide and
nonribosomal peptide retro-biosynthesis and global gene cluster matching. Nat Chem Biol
12:1007
Etchegaray A, Silva-Stenico ME, Moon DH, Tsai SM (2004) In silico analysis of nonribosomal
peptide synthetases of Xanthomonas axonopodis pv. citri: identification of putative siderophore
and lipopeptide biosynthetic genes. Microbiol Res 159:425–437
Fang J, Dorrestein PC (2014) Emerging mass spectrometry techniques for the direct analysis of
microbial colonies. Curr Opin Microbiol 19:120–129
Haas H (2014) Fungal siderophore metabolism with a focus on Aspergillus fumigatus. Nat Prod
Rep 31:1266–1276
Haas H, Eisendle M, Turgeon BG (2008) Siderophores in fungal physiology and virulence. Annu
Rev Phytopathol 46:149–187
D. Subramanian et al.
References
Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN toolbox and
its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS
Comput Biol 9:e1002980
Aleti G, Sessitsch A, Brader G (2015) Genome mining: prediction of lipopeptides and polyketides
from Bacillus and related Firmicutes. Comput Struct Biotechnol J 13:192–203
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: a knowledge-based resource
for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 32:W405–W413
Archibald F (1983) Lactobacillus plantarum, an organism not requiring iron. FEMS Microbiol
Lett 19:29–32
Baars O, Perlman DH (2016) Small molecule LC-MS/MS fragmentation data analysis and application to siderophore identification. In: Valdman J (ed) Applications from engineering with
MATLAB concepts. InTech University of South Bohemia in České Budějovice
Baars O, Zhang X, Morel FM, Seyedsayamdost MR (2016) The siderophore metabolome of
Azotobacter vinelandii. Appl Environ Microbiol 82:27–39
Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z (2014) New insights into the echinocandins and other
fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 31:1348–1375
Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA et al (2017) antiSMASH 4.0—
improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids
Res 45:W36–W41
Bok JW, Ye R, Clevenger KD, Mead D, Wagner M, Krerowicz A et al (2015) Fungal artificial chromosomes for mining of the fungal secondary metabolome. BMC Genomics 16:343
Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3 (2)
metabolism. Genome Res 15:820–829
Bumpus SB, Evans BS, Thomas PM, Ntai I, Kelleher NL (2009) A proteomics approach to discovering natural products and their biosynthetic pathways. Nat Biotechnol 27:951
Büttel Z, Díaz R, Dirnberger B, Flak M, Grijseels S, Kwon MJ et al (2015) Unlocking the potential
of fungi: the QuantFung project. Fungal Biol Biotechnol 2:6
Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G (2007) NORINE: a database
of nonribosomal peptides. Nucleic Acids Res 36:D326–D331
Chen Y, Unger M, Ntai I, McClure RA, Albright JC, Thomson RJ, Kelleher NL (2013) Gobichelin
A and B: mixed-ligand siderophores discovered using proteomics. MedChemComm 4:233–238
Conway KR, Boddy CN (2012) ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res 41:D402–D407
Cornelis P, Andrews SC (2010) IIron uptake and homeostasis in microorganisms. Caister Academic
Press, Norfolk.
Daly P, van Munster JM, Kokolski M, Sang F, Blythe MJ, Malla S et al (2017) 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 102:4–21
Dejong CA, Chen GM, Li H, Johnston CW, Edwards MR, Rees PN et al (2016) Polyketide and
nonribosomal peptide retro-biosynthesis and global gene cluster matching. Nat Chem Biol
12:1007
Etchegaray A, Silva-Stenico ME, Moon DH, Tsai SM (2004) In silico analysis of nonribosomal
peptide synthetases of Xanthomonas axonopodis pv. citri: identification of putative siderophore
and lipopeptide biosynthetic genes. Microbiol Res 159:425–437
Fang J, Dorrestein PC (2014) Emerging mass spectrometry techniques for the direct analysis of
microbial colonies. Curr Opin Microbiol 19:120–129
Haas H (2014) Fungal siderophore metabolism with a focus on Aspergillus fumigatus. Nat Prod
Rep 31:1266–1276
Haas H, Eisendle M, Turgeon BG (2008) Siderophores in fungal physiology and virulence. Annu
Rev Phytopathol 46:149–187
D. Subramanian et al.