de la Pen ˜a AH, Goodall EA, Gates SN, Lander GC,
Martin A (2018) Substrate-engaged 26S proteasome structures reveal mechanisms for ATPhydrolysis-driven translocation. Science 362:
eaav0725
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G,
Amillis S, Uchima CA, Anderluh G, Asadollahi M,
Askin M, Barry K, Battaglia E, Bayram O ¨ , Benocci
T, Braus-Stromeyer SA, Caldana C, Cánovas D,
Cerqueira GC, Chen F, Chen W, Choi C, Clum A,
dos Santos RAC, de Damásio ARL, Diallinas G,
Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A,
Gournas C, Habgood R, Hainaut M, Harispe ML,
Henrissat B, Hilde ´n KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kras ˇevec N, Kuo A,
Kusch H, LaButti K, Lagendijk EL, Lapidus A,
Levasseur A, Lindquist E, Lipzen A, Logrieco AF,
MacCabe A, Ma ¨kela ¨ MR, Malavazi I, Melin P,
Meyer V, Mielnichuk N, Miskei M, Molnár A ´ P,
Mule ´ G, Ngan CY, Orejas M, Orosz E, Ouedraogo
JP, Overkamp KM, Park H-S, Perrone G, Piumi F,
Punt PJ, Ram AFJ, Ramo ´n A, Rauscher S, Record
E, Rian ˜o-Pacho ´n DM, Robert V, Ro ¨hrig J, Ruller R,
Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schu ¨tze T, Sepc ˇic ´ K, Shelest E, Sherlock
G, Sophianopoulou V, Squina FM, Sun H, Susca A,
Todd RB, Tsang A, Unkles SE, van de Wiele N, van
Rossen-Uffink D, de Oliveira JVC, Vesth TC, Visser J, Yu J-H, Zhou M, Andersen MR, Archer DB,
Baker SE, Benoit I, Brakhage AA, Braus GH,
Fischer R, Frisvad JC, Goldman GH, Houbraken
J, Oakley B, Po ´csi I, Scazzocchio C, Seiboth B,
vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV
(2017) Comparative genomics reveals high
biological diversity and specific adaptations in
the industrially and medically important fungal
genus Aspergillus. Genome Biol 18:28
Draht O, Busch S, Hofmann K, Braus-Stromeyer S,
Helmstaedt K, Goldman G, Braus G (2007)
Amino acid supply of Aspergillus. In: Osmani SA,
Goldman GH (eds) The Aspergilli: genomics, medical aspects, biotechnology, and research methods.
CRC Press/Taylor & Francis Group, Boca Raton,
FL, pp 143–175
Du L, Sánchez C, Shen B (2001) Hybrid peptide–polyketide natural products: biosynthesis and prospects toward engineering novel molecules.
Metab Eng 3:78–95
Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M,
Schulman BA (2008) Structural insights into
NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 134:995–
1006
Estrada AF, Avalos J (2008) The white collar protein
WcoA of Fusarium fujikuroi is not essential for
photocarotenogenesis, but is involved in the regulation of secondary metabolism and conidiation.
Fungal Genet Biol 45:705–718
Fang W, Price MS, Toffaletti DL, Tenor J, BetancourtQuiroz M, Price JL, Pan W, Liao W, Perfect JR
(2012) Pleiotropic effects of deubiquitinating
enzyme Ubp5 on growth and pathogenesis of
Cryptococcus neoformans. PLoS One 7:38326
Finley D (2009) Recognition and processing of
ubiquitin-protein conjugates by the proteasome.
Annu Rev Biochem 78:477–513
Fisch KM, Gillaspy AF, Gipson M, Henrikson JC,
Hoover AR, Jackson L, Najar FZ, Wa ¨gele H, Cichewicz RH (2009) Biosynthetic pathway transcription in Aspergillus niger. J Ind Microbiol
Biotechnol 36:1199–1213
Fischer R, Aguirre J, Herrera-Estrella A, Corrochano
LM (2016) The complexity of fungal vision. Microbiol Spectr 4:1–22
Flick K, Kaiser P (2013) Set them free: F-box protein
exchange by Cand1. Cell Res 23:870–871
Gacek-Matthews A, Noble LM, Gruber C, Berger H,
Sulyok M, Marcos AT, Strauss J, Andrianopoulos
A (2015) KdmA, a histone H3 demethylase with
bipartite function, differentially regulates primary
and secondary metabolism in Aspergillus nidulans. Mol Microbiol 96:839–860
Gacek-Matthews A, Berger H, Sasaki T, Wittstein K,
Gruber C, Lewis ZA, Strauss J (2016) KdmB, a
jumonji histone H3 demethylase, regulates
genome-wide H3K4 trimethylation and is required
for normal induction of secondary metabolism in
Aspergillus nidulans. PLoS Genet 12:e1006222
Garcı ´a-Esquivel M, Esquivel-Naranjo EU, HernándezOn ˜ate MA, Ibarra-Laclette E, Herrera-Estrella A
(2016) The Trichoderma atroviride cryptochrome/photolyase genes regulate the expression
of blr1-independent genes both in red and blue
light. Fungal Biol 120:500–512
Garcı ´a-Martı ´nez J, Brunk M, Avalos J, Terpitz U (2015)
The CarO rhodopsin of the fungus Fusarium fujikuroi is a light-driven proton pump that retards
spore germination. Sci Rep 5:7798
Gerke J, Braus GH (2014) Manipulation of fungal development as source of novel secondary metabolites
for biotechnology. Appl Microbiol Biotechnol
98:8443–8455
Gerke J, Bayram O ¨ , Feussner K, Landesfeind M, Shelest
E, Feussner I, Braus GH (2012) Breaking the
silence: protein stabilization uncovers silenced
biosynthetic gene clusters in the fungus Aspergillus nidulans. Appl Environ Microbiol 78:8234–
8244
Gessler NN, Aver AA, Belozerskaya TA (2007) Reactive
oxygen species in regulation of fungal development. Biochemist 72:1091–1109
González A, Hall MN (2017) Nutrient sensing and TOR
signaling in yeast and mammals. EMBO J 36:397–
408
Greer EL, Shi Y (2012) Histone methylation: a dynamic
mark in health, disease and inheritance. Nat Rev
Genet 13:343–357
Gressler M, Hortschansky P, Geib E, Brock M (2015) A
new high-performance heterologous fungal
expression system based on regulatory elements
from the Aspergillus terreus terrein gene cluster.
Front Microbiol 6:184
198
J. Gerke et al.
Martin A (2018) Substrate-engaged 26S proteasome structures reveal mechanisms for ATPhydrolysis-driven translocation. Science 362:
eaav0725
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G,
Amillis S, Uchima CA, Anderluh G, Asadollahi M,
Askin M, Barry K, Battaglia E, Bayram O ¨ , Benocci
T, Braus-Stromeyer SA, Caldana C, Cánovas D,
Cerqueira GC, Chen F, Chen W, Choi C, Clum A,
dos Santos RAC, de Damásio ARL, Diallinas G,
Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A,
Gournas C, Habgood R, Hainaut M, Harispe ML,
Henrissat B, Hilde ´n KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kras ˇevec N, Kuo A,
Kusch H, LaButti K, Lagendijk EL, Lapidus A,
Levasseur A, Lindquist E, Lipzen A, Logrieco AF,
MacCabe A, Ma ¨kela ¨ MR, Malavazi I, Melin P,
Meyer V, Mielnichuk N, Miskei M, Molnár A ´ P,
Mule ´ G, Ngan CY, Orejas M, Orosz E, Ouedraogo
JP, Overkamp KM, Park H-S, Perrone G, Piumi F,
Punt PJ, Ram AFJ, Ramo ´n A, Rauscher S, Record
E, Rian ˜o-Pacho ´n DM, Robert V, Ro ¨hrig J, Ruller R,
Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schu ¨tze T, Sepc ˇic ´ K, Shelest E, Sherlock
G, Sophianopoulou V, Squina FM, Sun H, Susca A,
Todd RB, Tsang A, Unkles SE, van de Wiele N, van
Rossen-Uffink D, de Oliveira JVC, Vesth TC, Visser J, Yu J-H, Zhou M, Andersen MR, Archer DB,
Baker SE, Benoit I, Brakhage AA, Braus GH,
Fischer R, Frisvad JC, Goldman GH, Houbraken
J, Oakley B, Po ´csi I, Scazzocchio C, Seiboth B,
vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV
(2017) Comparative genomics reveals high
biological diversity and specific adaptations in
the industrially and medically important fungal
genus Aspergillus. Genome Biol 18:28
Draht O, Busch S, Hofmann K, Braus-Stromeyer S,
Helmstaedt K, Goldman G, Braus G (2007)
Amino acid supply of Aspergillus. In: Osmani SA,
Goldman GH (eds) The Aspergilli: genomics, medical aspects, biotechnology, and research methods.
CRC Press/Taylor & Francis Group, Boca Raton,
FL, pp 143–175
Du L, Sánchez C, Shen B (2001) Hybrid peptide–polyketide natural products: biosynthesis and prospects toward engineering novel molecules.
Metab Eng 3:78–95
Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M,
Schulman BA (2008) Structural insights into
NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 134:995–
1006
Estrada AF, Avalos J (2008) The white collar protein
WcoA of Fusarium fujikuroi is not essential for
photocarotenogenesis, but is involved in the regulation of secondary metabolism and conidiation.
Fungal Genet Biol 45:705–718
Fang W, Price MS, Toffaletti DL, Tenor J, BetancourtQuiroz M, Price JL, Pan W, Liao W, Perfect JR
(2012) Pleiotropic effects of deubiquitinating
enzyme Ubp5 on growth and pathogenesis of
Cryptococcus neoformans. PLoS One 7:38326
Finley D (2009) Recognition and processing of
ubiquitin-protein conjugates by the proteasome.
Annu Rev Biochem 78:477–513
Fisch KM, Gillaspy AF, Gipson M, Henrikson JC,
Hoover AR, Jackson L, Najar FZ, Wa ¨gele H, Cichewicz RH (2009) Biosynthetic pathway transcription in Aspergillus niger. J Ind Microbiol
Biotechnol 36:1199–1213
Fischer R, Aguirre J, Herrera-Estrella A, Corrochano
LM (2016) The complexity of fungal vision. Microbiol Spectr 4:1–22
Flick K, Kaiser P (2013) Set them free: F-box protein
exchange by Cand1. Cell Res 23:870–871
Gacek-Matthews A, Noble LM, Gruber C, Berger H,
Sulyok M, Marcos AT, Strauss J, Andrianopoulos
A (2015) KdmA, a histone H3 demethylase with
bipartite function, differentially regulates primary
and secondary metabolism in Aspergillus nidulans. Mol Microbiol 96:839–860
Gacek-Matthews A, Berger H, Sasaki T, Wittstein K,
Gruber C, Lewis ZA, Strauss J (2016) KdmB, a
jumonji histone H3 demethylase, regulates
genome-wide H3K4 trimethylation and is required
for normal induction of secondary metabolism in
Aspergillus nidulans. PLoS Genet 12:e1006222
Garcı ´a-Esquivel M, Esquivel-Naranjo EU, HernándezOn ˜ate MA, Ibarra-Laclette E, Herrera-Estrella A
(2016) The Trichoderma atroviride cryptochrome/photolyase genes regulate the expression
of blr1-independent genes both in red and blue
light. Fungal Biol 120:500–512
Garcı ´a-Martı ´nez J, Brunk M, Avalos J, Terpitz U (2015)
The CarO rhodopsin of the fungus Fusarium fujikuroi is a light-driven proton pump that retards
spore germination. Sci Rep 5:7798
Gerke J, Braus GH (2014) Manipulation of fungal development as source of novel secondary metabolites
for biotechnology. Appl Microbiol Biotechnol
98:8443–8455
Gerke J, Bayram O ¨ , Feussner K, Landesfeind M, Shelest
E, Feussner I, Braus GH (2012) Breaking the
silence: protein stabilization uncovers silenced
biosynthetic gene clusters in the fungus Aspergillus nidulans. Appl Environ Microbiol 78:8234–
8244
Gessler NN, Aver AA, Belozerskaya TA (2007) Reactive
oxygen species in regulation of fungal development. Biochemist 72:1091–1109
González A, Hall MN (2017) Nutrient sensing and TOR
signaling in yeast and mammals. EMBO J 36:397–
408
Greer EL, Shi Y (2012) Histone methylation: a dynamic
mark in health, disease and inheritance. Nat Rev
Genet 13:343–357
Gressler M, Hortschansky P, Geib E, Brock M (2015) A
new high-performance heterologous fungal
expression system based on regulatory elements
from the Aspergillus terreus terrein gene cluster.
Front Microbiol 6:184
198
J. Gerke et al.