form to identify fungal secondary metabolites and
their gene clusters. Nat Chem Biol 13:895–901
Collis CM, Hall RM (1985) Identification of a Tn5
determinant conferring resistance to phleomycins,
bleomycins,
and
tallysomycins.
Plasmid
14:143–151
Cullen D, Leong SA, Wilson LJ, Henner DJ (1987)
Transformation of Aspergillus nidulans with the
hygromycin-resistance gene, hph. Gene 57:21–26
Curran KA, Karim AS, Gupta A, Alper HS (2013) Use of
high capacity terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve
gene expression control for metabolic engineering
applications. Metab Eng 19:88–97
Curran KA, Morse NJ, Markham KA, Wagman AM,
Gupta A, Alper HS (2015) Short synthetic terminators for improved heterologous gene expression
in yeast. ACS Synth Biol 4:824–832
Czymmek KJ, Bourett TM, Howard RJ (2005) Fluorescent protein probes in fungi. In: Savidge T, Pothulakis C (eds) Microbial imaging, vol 34. Academic,
San Diego, pp 27–62
Dave K, Prabha VL, Ahuja M, Dave K, Tejaswini S,
Punekar NS (2015) Expanding the repertoire of
selectable markers for Aspergillus transformation.
In: van den Berg MA, Maruthachalam K (eds)
Genetic transformation systems in fungi, vol 1.
Springer International Publishing, Cham, pp
141–153
de Graaff L, Visser J (1988) Structure of the Aspergillus
nidulans pyruvate kinase gene. Curr Genet 14:553–
560
de Vries RP, Grigoriev IV, Tsang A (2018) Introduction:
overview of fungal genomics. In: de Vries RP,
Tsang A, Grigoriev IV (eds) Fungal genomics.
Methods in molecular biology, vol 1775. Humana
Press, New York, NY
Deaner M, Alper HS (2017) Systematic testing of
enzyme perturbation sensitivities via graded
dCas9 modulation in Saccharomyces cerevisiae.
Metab Eng 40:14–22
Dı ´ez B, Mellado E, Rodrı ´guez M, Bernasconi E, Barredo
JL (1999) The NADP-dependent glutamate dehydrogenase gene from Penicillium chrysogenum
and the construction of expression vectors for
filamentous fungi. Appl Microbiol Biotechnol
52:196–207
dos Santos Castro S, de Paula RG, Antonie ˆto ACC,
Persinoti GF, Silva-Rocha R, Silva RN (2016)
Understanding the role of the master regulator
XYR1 in Trichoderma reesei by global transcriptional analysis. Front Microbiol 7:1–16
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales
M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ
(2017) Genetic interaction mapping in mammalian
cells using CRISPR interference. Nat Methods
14:577–583
Eberle J, Russo V (1994) Neurospora crassa blue lightinducible gene bli-3. Biochem Mol Biol Int
34:737–744
Engler C, Marillonnet S (2014) Golden gate cloning. In:
Valla S, Lale R (eds) DNA cloning and assembly
methods, vol 1116. Springer Science Business
Media, New York, pp 119–131
Fiedler MRM, Barthel L, Kubisch C, Nai C, Meyer V
(2018) Construction of an improved Aspergillus
niger platform for enhanced glucoamylase secretion. Microb Cell Factories 17:1–12
Fierro F, Kosalkova ´ K, Gutie ´rrez S, Martı ´n JF (1996)
Autonomously replicating plasmids carrying the
AMA1 region in Penicillium chrysogenum. Curr
Genet 29:482–489
Finnigan GC, Thorner J (2015) Complex in vivo ligation
using homologous recombination and highefficiency plasmid rescue from Saccharomyces cerevisiae. Bio-protocol 5:1–13
Fisch KM, Skellam E, Ivison D, Cox RJ, Bailey AM,
Lazarus CM, Simpson TJ (2010) Catalytic role of
the C-terminal domains of a fungal non-reducing
polyketide synthase. Chem Commun 46:5331–
5333
Fitz E, Wanka F, Seiboth B (2018) The promoter toolbox for recombinant gene expression in Trichoderma reesei. Front Bioeng Biotechnol 6:1–15
Fleissner A, Dersch P (2010) Expression and export:
recombinant protein production systems for
Aspergillus.
Appl
Microbiol
Biotechnol
87:1255–1270
Ford KL, Baumgartner K, Henricot B, Bailey AM, Foster
GD (2016) A native promoter and inclusion of an
intron is necessary for efficient expression of GFP
or mRFP in Armillaria mellea. Sci Rep 6:1–10
Foster AJ, Martin-Urdiroz M, Yan X, Wright HS,
Soanes DM, Talbot NJ (2018) CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus. Sci Rep 8:1–12
Foureau E, Clastre M, Millerioux Y, Simkin AJ, Cornet
L, Dutilleul C, Besseau S, Marais E, Melin C, Guillard J, Cre `che J, Giglioli-Guivarc’h N, Courdavault
V, Papon N (2012) A TRP5/5-fluoroanthranilic
acid counter-selection system for gene disruption
in Candida guilliermondii. Curr Genet 58:245–254
Frandsen RJ, Khorsand-Jamal P, Kongstad KT, Nafisi
M, Kannangara RM, Staerk D, Okkels FT, Binderup K, Madsen B, Lindberg Møller B, Thrane
U, Mortensen UH (2018) Heterologous production
of the widely used natural food colorant carminic
acid in Aspergillus nidulans. Nat Sci Rep 8:1–10
Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific
oligonucleotide primer. Proc Natl Acad Sci USA
85:8998–9002
Fujii T, Yamaoka H, Gomi K, Kitamoto K, Kumaga C
(1995) Cloning and nucleotide sequence of the
ribonuclease T1 gene (rntA) from Aspergillus ory10 Filamentous Fungi as Hosts for Heterologous Production of Proteins and Secondary. . .
257
their gene clusters. Nat Chem Biol 13:895–901
Collis CM, Hall RM (1985) Identification of a Tn5
determinant conferring resistance to phleomycins,
bleomycins,
and
tallysomycins.
Plasmid
14:143–151
Cullen D, Leong SA, Wilson LJ, Henner DJ (1987)
Transformation of Aspergillus nidulans with the
hygromycin-resistance gene, hph. Gene 57:21–26
Curran KA, Karim AS, Gupta A, Alper HS (2013) Use of
high capacity terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve
gene expression control for metabolic engineering
applications. Metab Eng 19:88–97
Curran KA, Morse NJ, Markham KA, Wagman AM,
Gupta A, Alper HS (2015) Short synthetic terminators for improved heterologous gene expression
in yeast. ACS Synth Biol 4:824–832
Czymmek KJ, Bourett TM, Howard RJ (2005) Fluorescent protein probes in fungi. In: Savidge T, Pothulakis C (eds) Microbial imaging, vol 34. Academic,
San Diego, pp 27–62
Dave K, Prabha VL, Ahuja M, Dave K, Tejaswini S,
Punekar NS (2015) Expanding the repertoire of
selectable markers for Aspergillus transformation.
In: van den Berg MA, Maruthachalam K (eds)
Genetic transformation systems in fungi, vol 1.
Springer International Publishing, Cham, pp
141–153
de Graaff L, Visser J (1988) Structure of the Aspergillus
nidulans pyruvate kinase gene. Curr Genet 14:553–
560
de Vries RP, Grigoriev IV, Tsang A (2018) Introduction:
overview of fungal genomics. In: de Vries RP,
Tsang A, Grigoriev IV (eds) Fungal genomics.
Methods in molecular biology, vol 1775. Humana
Press, New York, NY
Deaner M, Alper HS (2017) Systematic testing of
enzyme perturbation sensitivities via graded
dCas9 modulation in Saccharomyces cerevisiae.
Metab Eng 40:14–22
Dı ´ez B, Mellado E, Rodrı ´guez M, Bernasconi E, Barredo
JL (1999) The NADP-dependent glutamate dehydrogenase gene from Penicillium chrysogenum
and the construction of expression vectors for
filamentous fungi. Appl Microbiol Biotechnol
52:196–207
dos Santos Castro S, de Paula RG, Antonie ˆto ACC,
Persinoti GF, Silva-Rocha R, Silva RN (2016)
Understanding the role of the master regulator
XYR1 in Trichoderma reesei by global transcriptional analysis. Front Microbiol 7:1–16
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales
M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ
(2017) Genetic interaction mapping in mammalian
cells using CRISPR interference. Nat Methods
14:577–583
Eberle J, Russo V (1994) Neurospora crassa blue lightinducible gene bli-3. Biochem Mol Biol Int
34:737–744
Engler C, Marillonnet S (2014) Golden gate cloning. In:
Valla S, Lale R (eds) DNA cloning and assembly
methods, vol 1116. Springer Science Business
Media, New York, pp 119–131
Fiedler MRM, Barthel L, Kubisch C, Nai C, Meyer V
(2018) Construction of an improved Aspergillus
niger platform for enhanced glucoamylase secretion. Microb Cell Factories 17:1–12
Fierro F, Kosalkova ´ K, Gutie ´rrez S, Martı ´n JF (1996)
Autonomously replicating plasmids carrying the
AMA1 region in Penicillium chrysogenum. Curr
Genet 29:482–489
Finnigan GC, Thorner J (2015) Complex in vivo ligation
using homologous recombination and highefficiency plasmid rescue from Saccharomyces cerevisiae. Bio-protocol 5:1–13
Fisch KM, Skellam E, Ivison D, Cox RJ, Bailey AM,
Lazarus CM, Simpson TJ (2010) Catalytic role of
the C-terminal domains of a fungal non-reducing
polyketide synthase. Chem Commun 46:5331–
5333
Fitz E, Wanka F, Seiboth B (2018) The promoter toolbox for recombinant gene expression in Trichoderma reesei. Front Bioeng Biotechnol 6:1–15
Fleissner A, Dersch P (2010) Expression and export:
recombinant protein production systems for
Aspergillus.
Appl
Microbiol
Biotechnol
87:1255–1270
Ford KL, Baumgartner K, Henricot B, Bailey AM, Foster
GD (2016) A native promoter and inclusion of an
intron is necessary for efficient expression of GFP
or mRFP in Armillaria mellea. Sci Rep 6:1–10
Foster AJ, Martin-Urdiroz M, Yan X, Wright HS,
Soanes DM, Talbot NJ (2018) CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus. Sci Rep 8:1–12
Foureau E, Clastre M, Millerioux Y, Simkin AJ, Cornet
L, Dutilleul C, Besseau S, Marais E, Melin C, Guillard J, Cre `che J, Giglioli-Guivarc’h N, Courdavault
V, Papon N (2012) A TRP5/5-fluoroanthranilic
acid counter-selection system for gene disruption
in Candida guilliermondii. Curr Genet 58:245–254
Frandsen RJ, Khorsand-Jamal P, Kongstad KT, Nafisi
M, Kannangara RM, Staerk D, Okkels FT, Binderup K, Madsen B, Lindberg Møller B, Thrane
U, Mortensen UH (2018) Heterologous production
of the widely used natural food colorant carminic
acid in Aspergillus nidulans. Nat Sci Rep 8:1–10
Frohman MA, Dush MK, Martin GR (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific
oligonucleotide primer. Proc Natl Acad Sci USA
85:8998–9002
Fujii T, Yamaoka H, Gomi K, Kitamoto K, Kumaga C
(1995) Cloning and nucleotide sequence of the
ribonuclease T1 gene (rntA) from Aspergillus ory10 Filamentous Fungi as Hosts for Heterologous Production of Proteins and Secondary. . .
257