Bentley DL (2014) Coupling mRNA processing with
transcription in time and space. Nat Rev Genet
15:163–175
Bergquist PL, Te’o VSJ, Gibbs MD, Curach NC, Nevalainen KMH (2004) Recombinant enzymes from
thermophilic micro-organisms expressed in fungal
hosts. Biochem Soc Trans 32:293–297
Bitinaite J, Rubino M, Varma KH, Schildkraut I, Vaisvila R, Vaiskunaite R (2007) USER friendly DNA
engineering and cloning method by uracil excision. Nucleic Acids Res 35:1992–2002
Bleichrodt RJ, Read ND (2019) Flow cytometry and
FACS applied to filamentous fungi. Fungal Biol
Rev 33:1–15
Blumhoff M, Steiger MG, Marx H, Mattanovich D,
Sauer M (2013) Six novel constitutive promoters
for metabolic engineering of Aspergillus niger.
Appl Microbiol Biotechnol 97:259–267
Boeke J, Lacroute F, Fink G (1984) A positive selection
for mutants lacking orotidine-5
0 phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid
resistance. Mol Gen Genet 197:346–346
Boel E, Hansen MT, Hjort I, Høegh I, Fiil NP (1984)
Two different types of intervening sequences in
the glucoamylase gene from Aspergillus niger.
Eur Mol Biol Organ 3:1581–1585
Bok JW, Ye R, Clevenger KD, Mead D, Wagner M,
Krerowicz A, Albright JC, Goering AW, Thomas
PM, Kelleher NL, Keller NP, Wu CC (2015) Fungal
artificial chromosomes for mining of the fungal
secondary metabolome. BMC Genomics 16:1–10
Breakspear A, Momany M (2007) The first fifty microarray studies in filamentous fungi. Microbiology
153:7–15
Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil KR (2010) Improved vanillin production in baker’s yeast through in silico design.
Microb Cell Factories 9:1–15
Bulakhov AG, Volkov PV, Rozhkova AM, Gusakov AV,
Nemashkalov VA, Satrutdinov AD, Sinitsyn AP
(2017) Using an inducible promoter of a gene
encoding Penicillium verruculosum glucoamylase
for production of enzyme preparations with
enhanced cellulase performance. PLoS One
12:1–13
Buxton FP, Gwynne DI, Davies RW (1985) Transformation of Aspergillus niger using the argB gene of
Aspergillus nidulans. Gene 37:207–214
Cairns TC, Nai C, Meyer V (2018) How a fungus shapes
biotechnology: 100 years of Aspergillus niger
research. Fungal Biol Biotechnol 5:1–14
Cairns TC, Zheng X, Zheng P, Sun J, Meyer V (2019)
Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories.
Biotechnol Biofuels 12:1–18
Carrington JC, Dougherty WG (1988) A viral cleavage
site cassette: identification of amino acid
sequences required for tobacco etch virus polyprotein processing. Biochemistry 85:3391–3395
Carvalho NDSP, Arentshorst M, Kooistra R, Stam H,
Sagt CM, Van Den Hondel CAMJJ, Ram AFJ (2011)
Effects of a defective ERAD pathway on growth
and heterologous protein production in Aspergillus niger. Appl Microbiol Biotechnol 89:357–373
Chaga G, Bochkariov DE, Jokhadze GG, Hopp J, Nelson
P (1999) Natural poly-histidine affinity tag for
purification of recombinant proteins on cobalt
(II)-carboxymethylaspartate crosslinked agarose.
J Chromatogr A 864:247–256
Chanda A, Roze LV, Kang S, Artymovich KA, Hicks GR,
Raikhel NV, Calvo AM, Linz JE (2009) A key role
for vesicles in fungal secondary metabolism. Proc
Natl Acad Sci USA 106:19533–19538
Chang KY, Georgianna RD, Heber S, Payne GA, Muddiman DC (2010) Detection of alternative splice variants at the proteome level in Aspergillus flavus. J
Proteome Res 9:1209–1217
Chen X, Zaro J, Shen WC (2013) Fusion protein linkers:
property, design and functionality. Adv Drug Deliv
Rev 65:1357–1369
Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen
TW, Rangarajan S, Shivalila CS, Dadon DB,
Jaenisch R (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23:1163–1171
Cherry JR, Fidantsef AL (2003) Directed evolution of
industrial enzymes: an update. Curr Opin Biotechnol 14:438–443
Chiang YM, Szewczyk E, Davidson AD, Keller N, Oakley
BR, Wang CCC (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–
2970
Chiang Y-M, Oakley CE, Ahuja M, Entwistle R, Schultz
A, Chang S-L, Sung CT, Wang CCC, Oakley BR
(2013) An efficient system for heterologous
expression of secondary metabolite genes in
Aspergillus nidulans. J Am Chem Soc 135:7720–
7731
Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan
A, Zutz C, Wang CCC, Oakley BR (2016) Development of genetic dereplication strains in Aspergillus
nidulans results in the discovery of aspercryptin.
Angew Chem Int Ed 55:1662–1665
Chou YC, Adney WS, Decker SR, Baker JO, Kunkel G,
Templeton DW, Himmel ME (2004) Cloning and
heterologous expression of the gene encoding a
family 7 glycosyl hydrolase from Penicillium funiculosum. In: Saha BC, Hayashi K (eds) Lignocellulose biodegradation, vol 889. American Chemical
Society, Washington, DC, pp 170–193
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH,
Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu
CC, Keller NP, Kelleher NL (2017) A scalable plat256
J. K. H. Rendsvig et al.
transcription in time and space. Nat Rev Genet
15:163–175
Bergquist PL, Te’o VSJ, Gibbs MD, Curach NC, Nevalainen KMH (2004) Recombinant enzymes from
thermophilic micro-organisms expressed in fungal
hosts. Biochem Soc Trans 32:293–297
Bitinaite J, Rubino M, Varma KH, Schildkraut I, Vaisvila R, Vaiskunaite R (2007) USER friendly DNA
engineering and cloning method by uracil excision. Nucleic Acids Res 35:1992–2002
Bleichrodt RJ, Read ND (2019) Flow cytometry and
FACS applied to filamentous fungi. Fungal Biol
Rev 33:1–15
Blumhoff M, Steiger MG, Marx H, Mattanovich D,
Sauer M (2013) Six novel constitutive promoters
for metabolic engineering of Aspergillus niger.
Appl Microbiol Biotechnol 97:259–267
Boeke J, Lacroute F, Fink G (1984) A positive selection
for mutants lacking orotidine-5
0 phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid
resistance. Mol Gen Genet 197:346–346
Boel E, Hansen MT, Hjort I, Høegh I, Fiil NP (1984)
Two different types of intervening sequences in
the glucoamylase gene from Aspergillus niger.
Eur Mol Biol Organ 3:1581–1585
Bok JW, Ye R, Clevenger KD, Mead D, Wagner M,
Krerowicz A, Albright JC, Goering AW, Thomas
PM, Kelleher NL, Keller NP, Wu CC (2015) Fungal
artificial chromosomes for mining of the fungal
secondary metabolome. BMC Genomics 16:1–10
Breakspear A, Momany M (2007) The first fifty microarray studies in filamentous fungi. Microbiology
153:7–15
Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil KR (2010) Improved vanillin production in baker’s yeast through in silico design.
Microb Cell Factories 9:1–15
Bulakhov AG, Volkov PV, Rozhkova AM, Gusakov AV,
Nemashkalov VA, Satrutdinov AD, Sinitsyn AP
(2017) Using an inducible promoter of a gene
encoding Penicillium verruculosum glucoamylase
for production of enzyme preparations with
enhanced cellulase performance. PLoS One
12:1–13
Buxton FP, Gwynne DI, Davies RW (1985) Transformation of Aspergillus niger using the argB gene of
Aspergillus nidulans. Gene 37:207–214
Cairns TC, Nai C, Meyer V (2018) How a fungus shapes
biotechnology: 100 years of Aspergillus niger
research. Fungal Biol Biotechnol 5:1–14
Cairns TC, Zheng X, Zheng P, Sun J, Meyer V (2019)
Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories.
Biotechnol Biofuels 12:1–18
Carrington JC, Dougherty WG (1988) A viral cleavage
site cassette: identification of amino acid
sequences required for tobacco etch virus polyprotein processing. Biochemistry 85:3391–3395
Carvalho NDSP, Arentshorst M, Kooistra R, Stam H,
Sagt CM, Van Den Hondel CAMJJ, Ram AFJ (2011)
Effects of a defective ERAD pathway on growth
and heterologous protein production in Aspergillus niger. Appl Microbiol Biotechnol 89:357–373
Chaga G, Bochkariov DE, Jokhadze GG, Hopp J, Nelson
P (1999) Natural poly-histidine affinity tag for
purification of recombinant proteins on cobalt
(II)-carboxymethylaspartate crosslinked agarose.
J Chromatogr A 864:247–256
Chanda A, Roze LV, Kang S, Artymovich KA, Hicks GR,
Raikhel NV, Calvo AM, Linz JE (2009) A key role
for vesicles in fungal secondary metabolism. Proc
Natl Acad Sci USA 106:19533–19538
Chang KY, Georgianna RD, Heber S, Payne GA, Muddiman DC (2010) Detection of alternative splice variants at the proteome level in Aspergillus flavus. J
Proteome Res 9:1209–1217
Chen X, Zaro J, Shen WC (2013) Fusion protein linkers:
property, design and functionality. Adv Drug Deliv
Rev 65:1357–1369
Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen
TW, Rangarajan S, Shivalila CS, Dadon DB,
Jaenisch R (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23:1163–1171
Cherry JR, Fidantsef AL (2003) Directed evolution of
industrial enzymes: an update. Curr Opin Biotechnol 14:438–443
Chiang YM, Szewczyk E, Davidson AD, Keller N, Oakley
BR, Wang CCC (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–
2970
Chiang Y-M, Oakley CE, Ahuja M, Entwistle R, Schultz
A, Chang S-L, Sung CT, Wang CCC, Oakley BR
(2013) An efficient system for heterologous
expression of secondary metabolite genes in
Aspergillus nidulans. J Am Chem Soc 135:7720–
7731
Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan
A, Zutz C, Wang CCC, Oakley BR (2016) Development of genetic dereplication strains in Aspergillus
nidulans results in the discovery of aspercryptin.
Angew Chem Int Ed 55:1662–1665
Chou YC, Adney WS, Decker SR, Baker JO, Kunkel G,
Templeton DW, Himmel ME (2004) Cloning and
heterologous expression of the gene encoding a
family 7 glycosyl hydrolase from Penicillium funiculosum. In: Saha BC, Hayashi K (eds) Lignocellulose biodegradation, vol 889. American Chemical
Society, Washington, DC, pp 170–193
Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH,
Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu
CC, Keller NP, Kelleher NL (2017) A scalable plat256
J. K. H. Rendsvig et al.