171
Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster AL et al (2015) Genomes to
natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids
Res 43:9645–9662
Skinnider MA, Merwin NJ, Johnston CW, Magarvey NA (2017) PRISM 3: expanded prediction of
natural product chemical structures from microbial genomes. Nucleic Acids Res 45:W49–W54
Smits AH, Vermeulen M (2016) Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol 34:825–834
Sørensen JL, Knudsen M, Hansen FT, Olesen C, Fuertes PR, Lee TV et al (2014) Fungal NRPSdependent siderophores: from function to prediction. In: Martín JF, García-Estrada C, Zeilinger
S (eds) Biosynthesis and molecular genetics of fungal secondary metabolites. Springer,
New York, pp 317–339
Stachelhaus T, Mootz HD, Marahiel MA (1999) The specificity-conferring code of adenylation
domains in nonribosomal peptide synthetases. Chem Biol 6:493–505
Stadler M, Hoffmeister D (2015) Fungal natural products—the mushroom perspective. Front
Microbiol 6:127
Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G (2012) An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol 30:826
Thieken A, Winkelmann G (1992) Rhizoferrin: a complexone type siderophore of the mocorales
and entomophthorales (Zygomycetes). FEMS Microbiol Lett 94:37–41
Vansteelandt M, Kerzaon I, Blanchet E, Tankoua OF, Du Pont TR, Joubert Y et al (2012) Patulin
and secondary metabolite production by marine-derived Penicillium strains. Fungal Biol
116:954–961
Verne Lee T, Johnson RD, Arcus VL, Lott JS (2015) Prediction of the substrate for nonribosomal
peptide synthetase (NRPS) adenylation domains by virtual screening. Proteins: Struct Funct
Bioinf 83:2052–2066
Vesth TC, Brandl J, Andersen MR (2016) FunGeneClusterS: predicting fungal gene clusters from
genome and transcriptome data. Synth Syst Biotechnol 1:122–129
Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X et al (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(1):28
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, ..., Porto C (2016) Sharing and
community curation of mass spectrometry data with Global Natural Products Social Molecular
Networking. Nat Biotechnol 34:828
Weber T, Kim HU (2016) The secondary metabolite bioinformatics portal: computational tools to
facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 1:69–79
Wolf T, Shelest V, Nath N, Shelest E (2015) CASSIS and SMIPS: promoter-based prediction of
secondary metabolite gene clusters in eukaryotic genomes. Bioinformatics 32:1138–1143
Zanghellini J, Ruckerbauer DE, Hanscho M, Jungreuthmayer C (2013) Elementary flux modes in
a nutshell: properties, calculation and applications. Biotechnol J 8:1009–1016
Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM (2016)
Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating
and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep
33:54–72
Zhang W, Li F, Nie L (2010) Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156:287–301
10 Bioinformatics Applications in Fungal Siderophores: Omics Implications
Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster AL et al (2015) Genomes to
natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids
Res 43:9645–9662
Skinnider MA, Merwin NJ, Johnston CW, Magarvey NA (2017) PRISM 3: expanded prediction of
natural product chemical structures from microbial genomes. Nucleic Acids Res 45:W49–W54
Smits AH, Vermeulen M (2016) Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol 34:825–834
Sørensen JL, Knudsen M, Hansen FT, Olesen C, Fuertes PR, Lee TV et al (2014) Fungal NRPSdependent siderophores: from function to prediction. In: Martín JF, García-Estrada C, Zeilinger
S (eds) Biosynthesis and molecular genetics of fungal secondary metabolites. Springer,
New York, pp 317–339
Stachelhaus T, Mootz HD, Marahiel MA (1999) The specificity-conferring code of adenylation
domains in nonribosomal peptide synthetases. Chem Biol 6:493–505
Stadler M, Hoffmeister D (2015) Fungal natural products—the mushroom perspective. Front
Microbiol 6:127
Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G (2012) An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol 30:826
Thieken A, Winkelmann G (1992) Rhizoferrin: a complexone type siderophore of the mocorales
and entomophthorales (Zygomycetes). FEMS Microbiol Lett 94:37–41
Vansteelandt M, Kerzaon I, Blanchet E, Tankoua OF, Du Pont TR, Joubert Y et al (2012) Patulin
and secondary metabolite production by marine-derived Penicillium strains. Fungal Biol
116:954–961
Verne Lee T, Johnson RD, Arcus VL, Lott JS (2015) Prediction of the substrate for nonribosomal
peptide synthetase (NRPS) adenylation domains by virtual screening. Proteins: Struct Funct
Bioinf 83:2052–2066
Vesth TC, Brandl J, Andersen MR (2016) FunGeneClusterS: predicting fungal gene clusters from
genome and transcriptome data. Synth Syst Biotechnol 1:122–129
Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X et al (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(1):28
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, ..., Porto C (2016) Sharing and
community curation of mass spectrometry data with Global Natural Products Social Molecular
Networking. Nat Biotechnol 34:828
Weber T, Kim HU (2016) The secondary metabolite bioinformatics portal: computational tools to
facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 1:69–79
Wolf T, Shelest V, Nath N, Shelest E (2015) CASSIS and SMIPS: promoter-based prediction of
secondary metabolite gene clusters in eukaryotic genomes. Bioinformatics 32:1138–1143
Zanghellini J, Ruckerbauer DE, Hanscho M, Jungreuthmayer C (2013) Elementary flux modes in
a nutshell: properties, calculation and applications. Biotechnol J 8:1009–1016
Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM (2016)
Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating
and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep
33:54–72
Zhang W, Li F, Nie L (2010) Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156:287–301
10 Bioinformatics Applications in Fungal Siderophores: Omics Implications