AspGD Curated Papers

Author(s)	Citation
Niu J, Alazi E, Reid ID, Arentshorst M, Punt PJ, Visser J, Tsang A, Ram AF	*Niu J, et al.* (2017)** An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger. Genetics 205(1):169-183
Alazi E, Khosravi C, Homan TG, du Pre S, Arentshorst M, Di Falco M, Pham TTM, Peng M, Aguilar-Pontes MV, Visser J, Tsang A, de Vries RP, Ram AFJ	*Alazi E, et al.* (2017)** The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger. FEBS Lett 591(10):1408-1418
Wanka F, Arentshorst M, Cairns TC, Jorgensen T, Ram AF, Meyer V	*Wanka F, et al.* (2016)** Highly active promoters and native secretion signals for protein production during extremely low growth rates in Aspergillus niger. Microb Cell Fact 15(1):145
Rocha MC, Fabri JH, Godoy KF, Castro PA, Hori JI, Cunha AF, Arentshorst M, Ram AF, van den Hondel CA, Goldman GH, Malavazi I	*Rocha MC, et al.* (2016)** Aspergillus fumigatus MADS-Box Transcription Factor rlmA Is Required for Regulation of the Cell Wall Integrity and Virulence. G3 (Bethesda) 6(9):2983-3002
Paun L, Nitsche B, Homan T, Ram AF, Kempken F	*Paun L, et al.* (2016)** An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader. Appl Microbiol Biotechnol 100(14):6309-17
Patyshakuliyeva A, Arentshorst M, Allijn IE, Ram AF, de Vries RP, Gelber IB	*Patyshakuliyeva A, et al.* (2016)** Improving cellulase production by Aspergillus niger using adaptive evolution. Biotechnol Lett 38(6):969-74
Park J, Hulsman M, Arentshorst M, Breeman M, Alazi E, Lagendijk EL, Rocha MC, Malavazi I, Nitsche BM, van den Hondel CA, Meyer V, Ram AF	*Park J, et al.* (2016)** Transcriptomic and molecular genetic analysis of the cell wall salvage response of Aspergillus niger to the absence of galactofuranose synthesis. Cell Microbiol 18(9):1268-84
Niu J, Arentshorst M, Seelinger F, Ram AF, Ouedraogo JP	*Niu J, et al.* (2016)** A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger. Arch Microbiol 198(9):861-8
Burggraaf AM, Ram AF	Burggraaf AM and Ram AF (2016) Autophagy is dispensable to overcome ER stress in the filamentous fungus Aspergillus niger. Microbiologyopen 5(4):647-58
van Munster JM, Nitsche BM, Akeroyd M, Dijkhuizen L, van der Maarel MJ, Ram AF	*van Munster JM, et al.* (2015)** Systems approaches to predict the functions of glycoside hydrolases during the life cycle of Aspergillus niger using developmental mutants brlA and flbA. PLoS One 10(1):e0116269
Park J, Tefsen B, Heemskerk MJ, Lagendijk EL, van den Hondel CA, van Die I, Ram AF	*Park J, et al.* (2015)** Identification and functional analysis of two Golgi-localized UDP-galactofuranose transporters with overlapping functions in Aspergillus niger. BMC Microbiol 15:253
Niu J, Homan TG, Arentshorst M, de Vries RP, Visser J, Ram AF	*Niu J, et al.* (2015)** The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger. Fungal Genet Biol 82:32-42
Kwon MJ, Arentshorst M, Fiedler M, de Groen FL, Punt PJ, Meyer V, Ram AF	*Kwon MJ, et al.* (2014)** Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi. Microbiology 160(Pt 2):316-29
Franken AC, Lechner BE, Werner ER, Haas H, Lokman BC, Ram AF, van den Hondel CA, de Weert S, Punt PJ	*Franken AC, et al.* (2014)** Genome mining and functional genomics for siderophore production in Aspergillus niger. Brief Funct Genomics 13(6):482-92
van Veluw GJ, Teertstra WR, de Bekker C, Vinck A, van Beek N, Muller WH, Arentshorst M, van der Mei HC, Ram AF, Dijksterhuis J, Wosten HA	*van Veluw GJ, et al.* (2013)** Heterogeneity in liquid shaken cultures of Aspergillus niger inoculated with melanised conidia or conidia of pigmentation mutants. Stud Mycol 74(1):47-57
van Munster JM, Nitsche BM, Krijgsheld P, van Wijk A, Dijkhuizen L, Wosten HA, Ram AF, van der Maarel MJ	*van Munster JM, et al.* (2013)** Chitinases CtcB and CfcI modify the cell wall in sporulating aerial mycelium of Aspergillus niger. Microbiology 159(Pt 9):1853-67
Schachtschabel D, Arentshorst M, Nitsche BM, Morris S, Nielsen KF, van den Hondel CA, Klis FM, Ram AF	*Schachtschabel D, et al.* (2013)** The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability. PLoS One 8(10):e78102
Nitsche BM, Burggraaf-van Welzen AM, Lamers G, Meyer V, Ram AF	*Nitsche BM, et al.* (2013)** Autophagy promotes survival in aging submerged cultures of the filamentous fungus Aspergillus niger. Appl Microbiol Biotechnol 97(18):8205-18
Kwon MJ, Nitsche BM, Arentshorst M, Jorgensen TR, Ram AF, Meyer V	*Kwon MJ, et al.* (2013)** The transcriptomic signature of RacA activation and inactivation provides new insights into the morphogenetic network of Aspergillus niger. PLoS One 8(7):e68946
Krijgsheld P, Nitsche BM, Post H, Levin AM, Muller WH, Heck AJ, Ram AF, Altelaar M, Wosten HA	*Krijgsheld P, et al.* (2013)** Deletion of flbA results in increased secretome complexity and reduced secretion heterogeneity in colonies of Aspergillus niger. J Proteome Res 12(4):1808-19
Franken AC, Werner ER, Haas H, Lokman BC, Van Den Hondel CA, Ram AF, de Weert S, Punt PJ	*Franken AC, et al.* (2013)** The role of coproporphyrinogen III oxidase and ferrochelatase genes in heme biosynthesis and regulation in Aspergillus niger. Appl Microbiol Biotechnol 97(22):9773-85
Tefsen B, Ram AF, van Die I, Routier FH	*Tefsen B, et al.* (2012)** Galactofuranose in eukaryotes: aspects of biosynthesis and functional impact. Glycobiology 22(4):456-69
Tefsen B, Lagendijk EL, Park J, Akeroyd M, Schachtschabel D, Winkler R, van Die I, Ram AF	*Tefsen B, et al.* (2012)** Fungal alpha-arabinofuranosidases of glycosyl hydrolase families 51 and 54 show a dual arabinofuranosyl- and galactofuranosyl-hydrolyzing activity. Biol Chem 393(8):767-75
Schachtschabel D, Arentshorst M, Lagendijk EL, Ram AF	*Schachtschabel D, et al.* (2012)** Vacuolar H(+)-ATPase plays a key role in cell wall biosynthesis of Aspergillus niger. Fungal Genet Biol 49(4):284-93
Nitsche BM, Ram AF, Meyer V	*Nitsche BM, et al.* (2012)** The use of open source bioinformatics tools to dissect transcriptomic data. Methods Mol Biol 835:311-31
Nitsche BM, Jorgensen TR, Akeroyd M, Meyer V, Ram AF	*Nitsche BM, et al.* (2012)** The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome. BMC Genomics 13:380
Kwon MJ, Jorgensen TR, Nitsche BM, Arentshorst M, Park J, Ram AF, Meyer V	*Kwon MJ, et al.* (2012)** The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger. BMC Genomics 13:701
Franken AC, Lokman BC, Ram AF, Van Den Hondel CA, de Weert1 S, Punt PJ	*Franken AC, et al.* (2012)** Analysis of the role of the Aspergillus niger aminolevulinic acid synthase (hemA) gene illustrates the difference between regulation of yeast and fungal haem- and sirohaem-dependent pathways. FEMS Microbiol Lett 335(2):104-12
Carvalho ND, Jorgensen TR, Arentshorst M, Nitsche BM, van den Hondel CA, Archer DB, Ram AF	*Carvalho ND, et al.* (2012)** Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress. BMC Genomics 13:350
Nitsche BM, Crabtree J, Cerqueira GC, Meyer V, Ram AF, Wortman JR	*Nitsche BM, et al.* (2011)** New resources for functional analysis of omics data for the genus Aspergillus. BMC Genomics 12:486
Meyer V, Wanka F, van Gent J, Arentshorst M, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2011)** Fungal gene expression on demand: an inducible, tunable, and metabolism-independent expression system for Aspergillus niger. Appl Environ Microbiol 77(9):2975-83
Meyer V, Wu B, Ram AF	*Meyer V, et al.* (2011)** Aspergillus as a multi-purpose cell factory: current status and perspectives. Biotechnol Lett 33(3):469-76
Kwon MJ, Arentshorst M, Roos ED, van den Hondel CA, Meyer V, Ram AF	*Kwon MJ, et al.* (2011)** Functional characterization of Rho GTPases in Aspergillus niger uncovers conserved and diverged roles of Rho proteins within filamentous fungi. Mol Microbiol 79(5):1151-67
Jorgensen TR, Park J, Arentshorst M, van Welzen AM, Lamers G, Vankuyk PA, Damveld RA, van den Hondel CA, Nielsen KF, Frisvad JC, Ram AF	*Jorgensen TR, et al.* (2011)** The molecular and genetic basis of conidial pigmentation in Aspergillus niger. Fungal Genet Biol 48(5):544-53
Jorgensen TR, Nielsen KF, Arentshorst M, Park J, Van Den Hondel CA, Frisvad JC, Ram AF	*Jorgensen TR, et al.* (2011)** Submerged conidiation and product formation by Aspergillus niger at low specific growth rates are affected in aerial developmental mutants. Appl Environ Microbiol 77(15):5270-7
Guillemette T, Ram AF, Carvalho ND, Joubert A, Simoneau P, Archer DB	*Guillemette T, et al.* (2011)** Methods for investigating the UPR in filamentous fungi. Methods Enzymol 490:1-29
Franken AC, Lokman BC, Ram AF, Punt PJ, Van Den Hondel CA, de Weert S	*Franken AC, et al.* (2011)** Heme biosynthesis and its regulation: towards understanding and improvement of heme biosynthesis in filamentous fungi. Appl Microbiol Biotechnol 91(3):447-60
Carvalho ND, Arentshorst M, Weenink XO, Punt PJ, Van Den Hondel CA, Ram AF	*Carvalho ND, et al.* (2011)** Functional YFP-tagging of the essential GDP-mannose transporter reveals an important role for the secretion related small GTPase SrgC protein in maintenance of Golgi bodies in Aspergillus niger. Fungal Biol 115(3):253-64
Carvalho ND, Arentshorst M, Kooistra R, Stam H, Sagt CM, van den Hondel CA, Ram AF	*Carvalho ND, et al.* (2011)** Effects of a defective ERAD pathway on growth and heterologous protein production in Aspergillus niger. Appl Microbiol Biotechnol 89(2):357-73
Meyer V, Minkwitz S, Schutze T, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2010)** The Aspergillus niger RmsA protein: A node in a genetic network? Commun Integr Biol 3(2):195-7
Jorgensen TR, Nitsche BM, Lamers GE, Arentshorst M, Van Den Hondel CA, Ram AF	*Jorgensen TR, et al.* (2010)** Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero. Appl Environ Microbiol 76(16):5344-55
Carvalho ND, Arentshorst M, Jin Kwon M, Meyer V, Ram AF	*Carvalho ND, et al.* (2010)** Expanding the ku70 toolbox for filamentous fungi: establishment of complementation vectors and recipient strains for advanced gene analyses. Appl Microbiol Biotechnol 87(4):1463-73
de Groot PW, Brandt BW, Horiuchi H, Ram AF, de Koster CG, Klis FM	*de Groot PW, et al.* (2009)** Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans. Fungal Genet Biol 46 Suppl 1:S72-81
Meyer V, Arentshorst M, Flitter SJ, Nitsche BM, Kwon MJ, Reynaga-Pena CG, Bartnicki-Garcia S, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2009)** Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics. Eukaryot Cell 8(11):1677-91
Jorgensen TR, Goosen T, Hondel CA, Ram AF, Iversen JJ	*Jorgensen TR, et al.* (2009)** Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway. BMC Genomics 10:44
Jacobs DI, Olsthoorn MM, Maillet I, Akeroyd M, Breestraat S, Donkers S, van der Hoeven RA, van den Hondel CA, Kooistra R, Lapointe T, Menke H, Meulenberg R, Misset M, Muller WH, van Peij NN, Ram A, Rodriguez S, Roelofs MS, Roubos JA, van Tilborg MW, Verkleij AJ, Pel HJ, Stam H, Sagt CM	*Jacobs DI, et al.* (2009)** Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics. Fungal Genet Biol 46 Suppl 1:S141-52
Yuan XL, Roubos JA, van den Hondel CA, Ram AF	*Yuan XL, et al.* (2008)** Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger. Mol Genet Genomics 279(1):11-26
Yuan XL, van der Kaaij RM, Van Den Hondel CA, Punt PJ, van der Maarel MJ, Dijkhuizen L, Ram AF	*Yuan XL, et al.* (2008)** Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics 279(6):545-61
Meyer V, Arentshorst M, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2008)** The polarisome component SpaA localises to hyphal tips of Aspergillus niger and is important for polar growth. Fungal Genet Biol 45(2):152-64
Damveld RA, Franken A, Arentshorst M, Punt PJ, Klis FM, van den Hondel CA, Ram AF	*Damveld RA, et al.* (2008)** A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis. Genetics 178(2):873-81
van der Kaaij RM, Yuan XL, Franken A, Ram AF, Punt PJ, van der Maarel MJ, Dijkhuizen L	*van der Kaaij RM, et al.* (2007)** Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger. Eukaryot Cell 6(7):1178-88
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H	*Pel HJ, et al.* (2007)** Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2):221-31
Meyer V, Damveld RA, Arentshorst M, Stahl U, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2007)** Survival in the presence of antifungals: genome-wide expression profiling of Aspergillus niger in response to sublethal concentrations of caspofungin and fenpropimorph. J Biol Chem 282(45):32935-48
Meyer V, Arentshorst M, El-Ghezal A, Drews AC, Kooistra R, Van Den Hondel CA, Ram AF	*Meyer V, et al.* (2007)** Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol 128(4):770-5
Goosen C, Yuan XL, van Munster JM, Ram AF, van der Maarel MJ, Dijkhuizen L	*Goosen C, et al.* (2007)** Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity. Eukaryot Cell 6(4):674-81
Yuan XL, Goosen C, Kools H, van der Maarel MJ, van den Hondel CA, Dijkhuizen L, Ram AF	*Yuan XL, et al.* (2006)** Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. Microbiology 152(Pt 10):3061-73
Weenink XO, Punt PJ, van den Hondel CA, Ram AF	*Weenink XO, et al.* (2006)** A new method for screening and isolation of hypersecretion mutants in Aspergillus niger. Appl Microbiol Biotechnol 69(6):711-7
Ram AF, Klis FM	Ram AF and Klis FM (2006) Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat Protoc 1(5):2253-6
te Biesebeke R, Levin A, Sagt C, Bartels J, Goosen T, Ram A, van den Hondel C, Punt P	*te Biesebeke R, et al.* (2005)** Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization. Mol Genet Genomics 273(1):33-42
Vinck A, Terlou M, Pestman WR, Martens EP, Ram AF, Van Den Hondel CA, Wosten HA	*Vinck A, et al.* (2005)** Hyphal differentiation in the exploring mycelium of Aspergillus niger. Mol Microbiol 58(3):693-9
Damveld RA, Arentshorst M, Franken A, vanKuyk PA, Klis FM, van den Hondel CA, Ram AF	*Damveld RA, et al.* (2005)** The Aspergillus niger MADS-box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress. Mol Microbiol 58(1):305-19
Damveld RA, vanKuyk PA, Arentshorst M, Klis FM, van den Hondel CA, Ram AF	*Damveld RA, et al.* (2005)** Expression of agsA, one of five 1,3-alpha-D-glucan synthase-encoding genes in Aspergillus niger, is induced in response to cell wall stress. Fungal Genet Biol 42(2):165-77
Damveld RA, Arentshorst M, vanKuyk PA, Klis FM, Van Den Hondel CA, Ram AF	*Damveld RA, et al.* (2005)** Characterisation of CwpA, a putative glycosylphosphatidylinositol-anchored cell wall mannoprotein in the filamentous fungus Aspergillus niger. Fungal Genet Biol 42(10):873-85
Ram AF, Arentshorst M, Damveld RA, vanKuyk PA, Klis FM, van den Hondel CA	*Ram AF, et al.* (2004)** The cell wall stress response in Aspergillus niger involves increased expression of the glutamine : fructose-6-phosphate amidotransferase-encoding gene (gfaA) and increased deposition of chitin in the cell wall. Microbiology 150(Pt 10):3315-26
Michielse CB, Ram AF, van den Hondel CA	*Michielse CB, et al.* (2004)** The Aspergillus nidulans amdS gene as a marker for the identification of multicopy T-DNA integration events in Agrobacterium-mediated transformation of Aspergillus awamori. Curr Genet 45(6):399-403
Punt PJ, Seiboth B, Weenink XO, van Zeijl C, Lenders M, Konetschny C, Ram AF, Montijn R, Kubicek CP, van den Hondel CA	*Punt PJ, et al.* (2001)** Identification and characterization of a family of secretion-related small GTPase-encoding genes from the filamentous fungus Aspergillus niger: a putative SEC4 homologue is not essential for growth. Mol Microbiol 41(2):513-25
Gordon CL, Khalaj V, Ram AF, Archer DB, Brookman JL, Trinci AP, Jeenes DJ, Doonan JH, Wells B, Punt PJ, Van Den Hondel CA, Robson GD	*Gordon CL, et al.* (2000)** Glucoamylase::green fluorescent protein fusions to monitor protein secretion in Aspergillus niger. Microbiology 146 ( Pt 2):415-26

Author(s)

Citation

Niu J, Alazi E, Reid ID, Arentshorst M, Punt PJ, Visser J, Tsang A, Ram AF

Niu J, et al. (2017) An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger. Genetics 205(1):169-183

Alazi E, Khosravi C, Homan TG, du Pre S, Arentshorst M, Di Falco M, Pham TTM, Peng M, Aguilar-Pontes MV, Visser J, Tsang A, de Vries RP, Ram AFJ

Alazi E, et al. (2017) The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger. FEBS Lett 591(10):1408-1418

Wanka F, Arentshorst M, Cairns TC, Jorgensen T, Ram AF, Meyer V

Wanka F, et al. (2016) Highly active promoters and native secretion signals for protein production during extremely low growth rates in Aspergillus niger. Microb Cell Fact 15(1):145

Rocha MC, Fabri JH, Godoy KF, Castro PA, Hori JI, Cunha AF, Arentshorst M, Ram AF, van den Hondel CA, Goldman GH, Malavazi I

Rocha MC, et al. (2016) Aspergillus fumigatus MADS-Box Transcription Factor rlmA Is Required for Regulation of the Cell Wall Integrity and Virulence. G3 (Bethesda) 6(9):2983-3002

Paun L, Nitsche B, Homan T, Ram AF, Kempken F

Paun L, et al. (2016) An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader. Appl Microbiol Biotechnol 100(14):6309-17

Patyshakuliyeva A, Arentshorst M, Allijn IE, Ram AF, de Vries RP, Gelber IB

Patyshakuliyeva A, et al. (2016) Improving cellulase production by Aspergillus niger using adaptive evolution. Biotechnol Lett 38(6):969-74

Park J, Hulsman M, Arentshorst M, Breeman M, Alazi E, Lagendijk EL, Rocha MC, Malavazi I, Nitsche BM, van den Hondel CA, Meyer V, Ram AF

Park J, et al. (2016) Transcriptomic and molecular genetic analysis of the cell wall salvage response of Aspergillus niger to the absence of galactofuranose synthesis. Cell Microbiol 18(9):1268-84

Niu J, Arentshorst M, Seelinger F, Ram AF, Ouedraogo JP

Niu J, et al. (2016) A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger. Arch Microbiol 198(9):861-8

Burggraaf AM, Ram AF

Burggraaf AM and Ram AF (2016) Autophagy is dispensable to overcome ER stress in the filamentous fungus Aspergillus niger. Microbiologyopen 5(4):647-58

van Munster JM, Nitsche BM, Akeroyd M, Dijkhuizen L, van der Maarel MJ, Ram AF

van Munster JM, et al. (2015) Systems approaches to predict the functions of glycoside hydrolases during the life cycle of Aspergillus niger using developmental mutants brlA and flbA. PLoS One 10(1):e0116269

Park J, Tefsen B, Heemskerk MJ, Lagendijk EL, van den Hondel CA, van Die I, Ram AF

Park J, et al. (2015) Identification and functional analysis of two Golgi-localized UDP-galactofuranose transporters with overlapping functions in Aspergillus niger. BMC Microbiol 15:253

Niu J, Homan TG, Arentshorst M, de Vries RP, Visser J, Ram AF

Niu J, et al. (2015) The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger. Fungal Genet Biol 82:32-42

Kwon MJ, Arentshorst M, Fiedler M, de Groen FL, Punt PJ, Meyer V, Ram AF

Kwon MJ, et al. (2014) Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi. Microbiology 160(Pt 2):316-29

Franken AC, Lechner BE, Werner ER, Haas H, Lokman BC, Ram AF, van den Hondel CA, de Weert S, Punt PJ

Franken AC, et al. (2014) Genome mining and functional genomics for siderophore production in Aspergillus niger. Brief Funct Genomics 13(6):482-92

van Veluw GJ, Teertstra WR, de Bekker C, Vinck A, van Beek N, Muller WH, Arentshorst M, van der Mei HC, Ram AF, Dijksterhuis J, Wosten HA

van Veluw GJ, et al. (2013) Heterogeneity in liquid shaken cultures of Aspergillus niger inoculated with melanised conidia or conidia of pigmentation mutants. Stud Mycol 74(1):47-57

van Munster JM, Nitsche BM, Krijgsheld P, van Wijk A, Dijkhuizen L, Wosten HA, Ram AF, van der Maarel MJ

van Munster JM, et al. (2013) Chitinases CtcB and CfcI modify the cell wall in sporulating aerial mycelium of Aspergillus niger. Microbiology 159(Pt 9):1853-67

Schachtschabel D, Arentshorst M, Nitsche BM, Morris S, Nielsen KF, van den Hondel CA, Klis FM, Ram AF

Schachtschabel D, et al. (2013) The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability. PLoS One 8(10):e78102

Nitsche BM, Burggraaf-van Welzen AM, Lamers G, Meyer V, Ram AF

Nitsche BM, et al. (2013) Autophagy promotes survival in aging submerged cultures of the filamentous fungus Aspergillus niger. Appl Microbiol Biotechnol 97(18):8205-18

Kwon MJ, Nitsche BM, Arentshorst M, Jorgensen TR, Ram AF, Meyer V

Kwon MJ, et al. (2013) The transcriptomic signature of RacA activation and inactivation provides new insights into the morphogenetic network of Aspergillus niger. PLoS One 8(7):e68946

Krijgsheld P, Nitsche BM, Post H, Levin AM, Muller WH, Heck AJ, Ram AF, Altelaar M, Wosten HA

Krijgsheld P, et al. (2013) Deletion of flbA results in increased secretome complexity and reduced secretion heterogeneity in colonies of Aspergillus niger. J Proteome Res 12(4):1808-19

Franken AC, Werner ER, Haas H, Lokman BC, Van Den Hondel CA, Ram AF, de Weert S, Punt PJ

Franken AC, et al. (2013) The role of coproporphyrinogen III oxidase and ferrochelatase genes in heme biosynthesis and regulation in Aspergillus niger. Appl Microbiol Biotechnol 97(22):9773-85

Tefsen B, Ram AF, van Die I, Routier FH

Tefsen B, et al. (2012) Galactofuranose in eukaryotes: aspects of biosynthesis and functional impact. Glycobiology 22(4):456-69

Tefsen B, Lagendijk EL, Park J, Akeroyd M, Schachtschabel D, Winkler R, van Die I, Ram AF

Tefsen B, et al. (2012) Fungal alpha-arabinofuranosidases of glycosyl hydrolase families 51 and 54 show a dual arabinofuranosyl- and galactofuranosyl-hydrolyzing activity. Biol Chem 393(8):767-75

Schachtschabel D, Arentshorst M, Lagendijk EL, Ram AF

Schachtschabel D, et al. (2012) Vacuolar H(+)-ATPase plays a key role in cell wall biosynthesis of Aspergillus niger. Fungal Genet Biol 49(4):284-93

Nitsche BM, Ram AF, Meyer V

Nitsche BM, et al. (2012) The use of open source bioinformatics tools to dissect transcriptomic data. Methods Mol Biol 835:311-31

Nitsche BM, Jorgensen TR, Akeroyd M, Meyer V, Ram AF

Nitsche BM, et al. (2012) The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome. BMC Genomics 13:380

Kwon MJ, Jorgensen TR, Nitsche BM, Arentshorst M, Park J, Ram AF, Meyer V

Kwon MJ, et al. (2012) The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger. BMC Genomics 13:701

Franken AC, Lokman BC, Ram AF, Van Den Hondel CA, de Weert1 S, Punt PJ

Franken AC, et al. (2012) Analysis of the role of the Aspergillus niger aminolevulinic acid synthase (hemA) gene illustrates the difference between regulation of yeast and fungal haem- and sirohaem-dependent pathways. FEMS Microbiol Lett 335(2):104-12

Carvalho ND, Jorgensen TR, Arentshorst M, Nitsche BM, van den Hondel CA, Archer DB, Ram AF

Carvalho ND, et al. (2012) Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress. BMC Genomics 13:350

Nitsche BM, Crabtree J, Cerqueira GC, Meyer V, Ram AF, Wortman JR

Nitsche BM, et al. (2011) New resources for functional analysis of omics data for the genus Aspergillus. BMC Genomics 12:486

Meyer V, Wanka F, van Gent J, Arentshorst M, Van Den Hondel CA, Ram AF

Meyer V, et al. (2011) Fungal gene expression on demand: an inducible, tunable, and metabolism-independent expression system for Aspergillus niger. Appl Environ Microbiol 77(9):2975-83

Meyer V, Wu B, Ram AF

Meyer V, et al. (2011) Aspergillus as a multi-purpose cell factory: current status and perspectives. Biotechnol Lett 33(3):469-76

Kwon MJ, Arentshorst M, Roos ED, van den Hondel CA, Meyer V, Ram AF

Kwon MJ, et al. (2011) Functional characterization of Rho GTPases in Aspergillus niger uncovers conserved and diverged roles of Rho proteins within filamentous fungi. Mol Microbiol 79(5):1151-67

Jorgensen TR, Park J, Arentshorst M, van Welzen AM, Lamers G, Vankuyk PA, Damveld RA, van den Hondel CA, Nielsen KF, Frisvad JC, Ram AF

Jorgensen TR, et al. (2011) The molecular and genetic basis of conidial pigmentation in Aspergillus niger. Fungal Genet Biol 48(5):544-53

Jorgensen TR, Nielsen KF, Arentshorst M, Park J, Van Den Hondel CA, Frisvad JC, Ram AF

Jorgensen TR, et al. (2011) Submerged conidiation and product formation by Aspergillus niger at low specific growth rates are affected in aerial developmental mutants. Appl Environ Microbiol 77(15):5270-7

Guillemette T, Ram AF, Carvalho ND, Joubert A, Simoneau P, Archer DB

Guillemette T, et al. (2011) Methods for investigating the UPR in filamentous fungi. Methods Enzymol 490:1-29

Franken AC, Lokman BC, Ram AF, Punt PJ, Van Den Hondel CA, de Weert S

Franken AC, et al. (2011) Heme biosynthesis and its regulation: towards understanding and improvement of heme biosynthesis in filamentous fungi. Appl Microbiol Biotechnol 91(3):447-60

Carvalho ND, Arentshorst M, Weenink XO, Punt PJ, Van Den Hondel CA, Ram AF

Carvalho ND, et al. (2011) Functional YFP-tagging of the essential GDP-mannose transporter reveals an important role for the secretion related small GTPase SrgC protein in maintenance of Golgi bodies in Aspergillus niger. Fungal Biol 115(3):253-64

Carvalho ND, Arentshorst M, Kooistra R, Stam H, Sagt CM, van den Hondel CA, Ram AF

Carvalho ND, et al. (2011) Effects of a defective ERAD pathway on growth and heterologous protein production in Aspergillus niger. Appl Microbiol Biotechnol 89(2):357-73

Meyer V, Minkwitz S, Schutze T, Van Den Hondel CA, Ram AF

Meyer V, et al. (2010) The Aspergillus niger RmsA protein: A node in a genetic network? Commun Integr Biol 3(2):195-7

Jorgensen TR, Nitsche BM, Lamers GE, Arentshorst M, Van Den Hondel CA, Ram AF

Jorgensen TR, et al. (2010) Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero. Appl Environ Microbiol 76(16):5344-55

Carvalho ND, Arentshorst M, Jin Kwon M, Meyer V, Ram AF

Carvalho ND, et al. (2010) Expanding the ku70 toolbox for filamentous fungi: establishment of complementation vectors and recipient strains for advanced gene analyses. Appl Microbiol Biotechnol 87(4):1463-73

de Groot PW, Brandt BW, Horiuchi H, Ram AF, de Koster CG, Klis FM

de Groot PW, et al. (2009) Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans. Fungal Genet Biol 46 Suppl 1:S72-81

Meyer V, Arentshorst M, Flitter SJ, Nitsche BM, Kwon MJ, Reynaga-Pena CG, Bartnicki-Garcia S, Van Den Hondel CA, Ram AF

Meyer V, et al. (2009) Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics. Eukaryot Cell 8(11):1677-91

Jorgensen TR, Goosen T, Hondel CA, Ram AF, Iversen JJ

Jorgensen TR, et al. (2009) Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway. BMC Genomics 10:44

Jacobs DI, Olsthoorn MM, Maillet I, Akeroyd M, Breestraat S, Donkers S, van der Hoeven RA, van den Hondel CA, Kooistra R, Lapointe T, Menke H, Meulenberg R, Misset M, Muller WH, van Peij NN, Ram A, Rodriguez S, Roelofs MS, Roubos JA, van Tilborg MW, Verkleij AJ, Pel HJ, Stam H, Sagt CM

Jacobs DI, et al. (2009) Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics. Fungal Genet Biol 46 Suppl 1:S141-52

Yuan XL, Roubos JA, van den Hondel CA, Ram AF

Yuan XL, et al. (2008) Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger. Mol Genet Genomics 279(1):11-26

Yuan XL, van der Kaaij RM, Van Den Hondel CA, Punt PJ, van der Maarel MJ, Dijkhuizen L, Ram AF

Yuan XL, et al. (2008) Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics 279(6):545-61

Meyer V, Arentshorst M, Van Den Hondel CA, Ram AF

Meyer V, et al. (2008) The polarisome component SpaA localises to hyphal tips of Aspergillus niger and is important for polar growth. Fungal Genet Biol 45(2):152-64

Damveld RA, Franken A, Arentshorst M, Punt PJ, Klis FM, van den Hondel CA, Ram AF

Damveld RA, et al. (2008) A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis. Genetics 178(2):873-81

van der Kaaij RM, Yuan XL, Franken A, Ram AF, Punt PJ, van der Maarel MJ, Dijkhuizen L

van der Kaaij RM, et al. (2007) Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger. Eukaryot Cell 6(7):1178-88

Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H

Pel HJ, et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2):221-31

Meyer V, Damveld RA, Arentshorst M, Stahl U, Van Den Hondel CA, Ram AF

Meyer V, et al. (2007) Survival in the presence of antifungals: genome-wide expression profiling of Aspergillus niger in response to sublethal concentrations of caspofungin and fenpropimorph. J Biol Chem 282(45):32935-48

Meyer V, Arentshorst M, El-Ghezal A, Drews AC, Kooistra R, Van Den Hondel CA, Ram AF

Meyer V, et al. (2007) Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol 128(4):770-5

Goosen C, Yuan XL, van Munster JM, Ram AF, van der Maarel MJ, Dijkhuizen L

Goosen C, et al. (2007) Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity. Eukaryot Cell 6(4):674-81

Yuan XL, Goosen C, Kools H, van der Maarel MJ, van den Hondel CA, Dijkhuizen L, Ram AF

Yuan XL, et al. (2006) Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. Microbiology 152(Pt 10):3061-73

Weenink XO, Punt PJ, van den Hondel CA, Ram AF

Weenink XO, et al. (2006) A new method for screening and isolation of hypersecretion mutants in Aspergillus niger. Appl Microbiol Biotechnol 69(6):711-7

Ram AF, Klis FM

Ram AF and Klis FM (2006) Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat Protoc 1(5):2253-6

te Biesebeke R, Levin A, Sagt C, Bartels J, Goosen T, Ram A, van den Hondel C, Punt P

te Biesebeke R, et al. (2005) Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization. Mol Genet Genomics 273(1):33-42

Vinck A, Terlou M, Pestman WR, Martens EP, Ram AF, Van Den Hondel CA, Wosten HA

Vinck A, et al. (2005) Hyphal differentiation in the exploring mycelium of Aspergillus niger. Mol Microbiol 58(3):693-9

Damveld RA, Arentshorst M, Franken A, vanKuyk PA, Klis FM, van den Hondel CA, Ram AF

Damveld RA, et al. (2005) The Aspergillus niger MADS-box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress. Mol Microbiol 58(1):305-19

Damveld RA, vanKuyk PA, Arentshorst M, Klis FM, van den Hondel CA, Ram AF

Damveld RA, et al. (2005) Expression of agsA, one of five 1,3-alpha-D-glucan synthase-encoding genes in Aspergillus niger, is induced in response to cell wall stress. Fungal Genet Biol 42(2):165-77

Damveld RA, Arentshorst M, vanKuyk PA, Klis FM, Van Den Hondel CA, Ram AF

Damveld RA, et al. (2005) Characterisation of CwpA, a putative glycosylphosphatidylinositol-anchored cell wall mannoprotein in the filamentous fungus Aspergillus niger. Fungal Genet Biol 42(10):873-85

Ram AF, Arentshorst M, Damveld RA, vanKuyk PA, Klis FM, van den Hondel CA

Ram AF, et al. (2004) The cell wall stress response in Aspergillus niger involves increased expression of the glutamine : fructose-6-phosphate amidotransferase-encoding gene (gfaA) and increased deposition of chitin in the cell wall. Microbiology 150(Pt 10):3315-26

Michielse CB, Ram AF, van den Hondel CA

Michielse CB, et al. (2004) The Aspergillus nidulans amdS gene as a marker for the identification of multicopy T-DNA integration events in Agrobacterium-mediated transformation of Aspergillus awamori. Curr Genet 45(6):399-403

Punt PJ, Seiboth B, Weenink XO, van Zeijl C, Lenders M, Konetschny C, Ram AF, Montijn R, Kubicek CP, van den Hondel CA

Punt PJ, et al. (2001) Identification and characterization of a family of secretion-related small GTPase-encoding genes from the filamentous fungus Aspergillus niger: a putative SEC4 homologue is not essential for growth. Mol Microbiol 41(2):513-25

Gordon CL, Khalaj V, Ram AF, Archer DB, Brookman JL, Trinci AP, Jeenes DJ, Doonan JH, Wells B, Punt PJ, Van Den Hondel CA, Robson GD

Gordon CL, et al. (2000) Glucoamylase::green fluorescent protein fusions to monitor protein secretion in Aspergillus niger. Microbiology 146 ( Pt 2):415-26

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To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2014). The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42 (1); D705-10; see How to cite AspGD.