Agarwal N, Ansari A (2016) Enhancement of transcription by a splicing-competent intron is dependent on promoter directionality. PLoS Genet 12: 20 doi: 10.1371/journal.pgen.1006047
Akao T, Gomi K, Goto K, Okazaki N, Akita O (2002) Subtractive cloning of cDNA from Aspergillus oryzae differentially regulated between solid-state culture and liquid (submerged) culture. Curr Genet 41: 275−281 doi: 10.1007/s00294-002-0314-y
Akao T, Sano M, Yamada O, Akeno T, Fujii K, Goto K, Ohasi-Kunihiro S, Takase K, Yasukawa-Watanabe M, Yamaguchi K, et al. (2007) Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions. DNA Research 14: 47−57 doi: 10.1093/dnares/dsm008
Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J (2008) A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A 105: 4387−4392 doi: 10.1073/pnas.0709964105
Armitt S, McCullough W, Roberts CF (1976) Analysis of acetate non-utilizing (acu) mutants in Aspergillus nidulans. J Gen Microbiol 92: 263−282 doi: 10.1099/00221287-92-2-263
Asai T, Tsukada K, Ise S, Shirata N, Hashimoto M, Fujii I, Gomi K, Nakagawara K, Kodama KN, Oshima Y (2015) Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides. Nat Chem 7:737−743 doi: 10.1038/nchem.2308
Ayoubi TAY, VanDeVen WJM (1996) Regulation of gene expression by alternative promoters. FASEB J 10: 453−460 doi: 10.1096/fasebj.10.4.8647344
Barbesgaard P, Heldt-Hansen HP, Diderichsen B (1992) On the safety of Aspergillus oryzae: a review. Appl Microbiol Biotechnol 36:569–572. doi:10.1007/bf00183230
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202−W208 doi: 10.1093/nar/gkp335
Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ (2012) Introns in UTRs: Why we should stop ignoring them. Bioessays 34: 1025-1034 doi: 10.1002/bies.201200073
Bradford MM (1976) Rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal Biochem 72: 248−254 doi: 10.1006/abio.1976.9999
Brown SH, Bashkirova L, Berka R, Chandler T, Doty T, McCall K, McCulloch M, McFarland S, Thompson S, Yaver D, Berry A (2013) Metabolic engineering of Aspergillus oryzae NRRL 3488 for increased production of L-malic acid. Appl Microbiol Biotechnol 97: 8903−8912 doi: 10.1007/s00253-013-5132-2
Cheng CK, Au CH, Wilke SK, Stajich JE, Zolan ME, Pukkila PJ, Kwan HS (2013) 5′- Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. BMC Genomics 14: 17 doi: 10.1186/1471-2164-14-195
Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang THM (2008) The functional consequences of alternative promoter use in mammalian genomes. Trends Genet 24: 167−177 doi: 10.1016/j.tig.2008.01.008
Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, et al. (2014) A promoter-level mammalian expression atlas. Nature 507: 462-+ doi: 10.1038/nature13182
Fujii R, Ugai T, Ichinose H, Hatakeyama M, Kosaki T, Gomi K, Fujii I, Minami A, Oikawa H (2016) Reconstitution of biosynthetic machinery of fungal polyketides: Unexpected oxidations of biosynthetic intermediates by expression host. Biosci Biotechnol Biochem 80:426−431 doi: 10.1080/09168451.2015.1104234
Fujioka T, Mizutani O, Furukawa K, Sato N, Yoshimi A, Yamagata Y, Nakajima T, Abe K (2007) MpkA-dependent and -independent cell wall integrity signaling in Aspergillus nidulans. Eukaryot Cell 6: 1497−1510 doi: 10.1128/ec.00281-06
Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A (2012) The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr Biol 22:1403–1409 doi: 10.1016/j.cub.2012.05.033.
Gibbons JG, Rokas A (2013) The function and evolution of the Aspergillus genome. Trends Microbiol 21: 14–22. doi:10.1016/j.tim.2012.09.005.
Goebels C, Thonn A, Gonzalez-Hilarion S, Rolland O, Moyrand F, Beilharz TH, Janbon G (2013) Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway. PLoS Genet 9: 15 doi: 10.1371/journal.pgen.1003686
Gomi K (2019) Regulatory mechanisms for amylolytic gene expression in the koji mold Aspergillus oryzae. Biosci Biotechnol Biochem 83: 1385−1401. doi:10.1080/09168451.2019.1625265
Gomi K, Iimura Y, Hara S (1987) Integrative transformation of Aspergillus oryzae with a plasmid containing the Aspergillus nidulans argB gene. Agric Biol Chem 51: 2549−2555 doi: 10.1271/bbb1961.51.2549.
Guo N, Qian Y, Zhang QQ, Chen XX, Zeng GH, Zhang X, Mi WB, Xu C, Leger RJS, Fang WG (2017) Alternative transcription start site selection in Mr-OPY2 controls lifestyle transitions in the fungus Metarhizium robertsii. Nat Commun 8: 13 doi: 10.1038/s41467-017-01756-1
Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557−580 doi: 10.1016/s0022-2836(83)80284-8
Hashimoto S, Suzuki Y, Kasai Y, Morohoshi K, Yamada T, Sese J, Morishita S, Sugano S, Matsushima K (2004) 5′-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol 22: 1146−1149 doi: 10.1038/nbt998
Holland MJ, Holland JP (1978) Isolation and identification of yeast messenger ribonucleic acids coding for enolase, glyceraldehyde-3-phosphate dehydrogenase, and phosphoglycerate kinase. Biochemistry 17: 4900−4907 doi:10.1021/bi00616a007
Hunter AJ, Jin B, Kelly JM (2011) Independent duplications of α-amylase in different strains of Aspergillus oryzae. Fungal Genet Biol 48:438–444 doi: 10.1016/j.fgb.2011.01.006.
Hynes MJ, Szewczyk E, Murray SL, Suzuki Y, Davis MA, Lewis HMS (2007) Transcriptional control of gluconeogenesis in Aspergillus nidulans. Genetics 176: 139−150 doi: 10.1534/genetics.107.070904
Inoue H, Nojima H, Okayama H (1990) High-efficiency transformation of Escherichia coli with plasmids. Gene 96: 23−28 doi: 10.1016/0378-1119(90)90336-p
Jefferson RA (1989) The GUS reporter gene system. Nature 342: 837−838 doi: 10.1038/342837a0
Kaur JN, Panepinto JC (2016) Morphotype-specific effector functions of Cryptococcus neoformans PUM1. Sci Rep 6: 9 doi: 10.1038/srep23638
Li H, Hou JY, Bai L, Hu CS, Tong P, Kang YN, Zhao XD, Shao ZF (2015) Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE. RNA Biol 12: 525−537 doi: 10.1080/15476286.2015.1022704
Liu C, Tagami K, Minami A, Matsumoto T, Frisvad JC, Suzuki H, Ishikawa J, Gomi K, Oikawa H (2015) Reconstitution of biosynthetic machinery for the synthesis of the highly elaborated indole diterpene penitrem. Angew Chem Int Ed 54:5748−5752 doi: 10.1002/anie.201501072
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real- time quantitative PCR and the 2−ΔΔCT method. Methods 25: 402−408 doi: 10.1006/meth.2001.1262
Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto KI, Arima T, Akita O, Kashiwagi Y, et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 1157−1161 doi: 10.1038/nature04300
Machida M, Chang YC, Manabe M, Yasukawa M, Kunihiro S, Jigami Y (1996) Molecular cloning of a cDNA encoding enolase from the filamentous fungus, Aspergillus oryzae. Curr Genet 30: 423−431 doi: 10.1007/s002940050152
Machida M, Yamada O, Gomi K (2008) Genomics of Aspergillus oryzae: Learning from the history of koji mold and exploration of its future. DNA Res 15: 173−183 doi: 10.1093/dnares/dsn020
Maeda H, Sano M, Maruyama Y, Tanno T, Akao T, Totsuka Y, Endo M, Sakurada R, Yamagata Y, Machida M, et al. (2004) Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags. Appl Microbiol Biotechnol 65: 74−83 doi: 10.1007/s00253-004-1608-4
Minetoki T, Nunokawa Y, Gomi K, Kitamoto K, Kumagai C, Tamura G (1996) Deletion analysis of promoter elements of the Aspergillus oryzae agdA encoding α- glucosidase. Curr Genet 30: 432-438 doi: 10.1007/s002940050153
Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T (2006) A large- scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A 103: 17846−17851 doi: 10.1073/pnas.0605645103
Mizutani O, Kudo Y, Saito A, Matsuura T, Inoue H, Abe K, Gomi K (2008) A defect of ligD (human lig4 homolog) for nonhomologous end joining significantly improves efficiency of gene-targeting in Aspergillus oryzae. Fungal Genet Biol 45: 878−889 doi: 10.1016/j.fgb.2007.12.010
Morris DR, Geballe AP (2000) Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol 20: 8635−8642 doi: 10.1128/mcb.20.23.8635- 8642.2000
Nakajima K, Kunihiro S, Sano M, Zhang Y, Eto S, Chang YC, Suzuki T, Jigami Y, Machida M (2000) Comprehensive cloning and expression analysis of glycolytic genes from the filamentous fungus, Aspergillus oryzae. Curr Genet 37: 322−327 doi: 10.1007/s002940050534
Oda K, Kakizono D, Yamada O, Iefuji H, Akita O, Iwashita K (2006) Proteomic analysis of extracellular proteins from Aspergillus oryzae grown under submerged and solid-state culture conditions. Appl Environ Microbiol 72: 3448−3457 doi: 10.1128/aem.72.5.3448-3457.2006
Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, Dean RA, Bhatnagar D, Cleveland TE, Machida M, Yu J (2006) Whole genome comparison of Aspergillus flavus and A. oryzae. Med Mycol 44:S9–S11 doi: 10.1080/13693780600835716.
Prade RA, Timberlake WE (1993) The Aspergillus nidulans brlA regulatory locus consists of overlapping transcription units that are individually required for conidiophore development. EMBO J 12: 2439−2447 doi: 10.1002/j.1460- 2075.1993.tb05898.x
Rojas-Duran MF, Gilbert WV (2012) Alternative transcription start site selection leads to large differences in translation activity in yeast. RNA 18: 2299−2305 doi: 10.1261/rna.035865.112
Rose AB, Emami S, Bradnam K, Korf I (2011) Evidence for a DNA-based mechanism of intron-mediated enhancement. Front Plant Sci 2: 9 doi: 10.3389/fpls.2011.00098
Roumelioti K, Vangelatos I, Sophianopoulou V (2010) A cryptic role of a glycolytic- gluconeogenic enzyme (aldolase) in amino acid transporter turnover in Aspergillus nidulans. Fungal Genet Biol 47: 254−267 doi: 10.1016/j.fgb.2009.12.004
Sakai K, Kinoshita H, Nihira T (2012) Heterologous expression system in Aspergillus oryzae for fungal biosynthetic gene clusters of secondary metabolites. Appl Microbiol Biotechnol 93: 2011−2022 doi: 10.1007/s00253-011-3657-9
Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y (2011) Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. DNA Res 18:165–176 doi: 10.1093/dnares/dsr009.
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, et al. (2003) Cap analysis gene expression for high- throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776−15781 doi: 10.1073/pnas.2136655100
Sibthorp C, Wu HH, Cowley G, Wong PWH, Palaima P, Morozov IY, Weedall GD, Caddick MX (2013) Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. BMC Genomics 14: 18 doi: 10.1186/1471-2164-14-847
Suzuki Y, Murray SL, Wong KH, Davis MA, Hynes MJ (2012) Reprogramming of carbon metabolism by the transcriptional activators AcuK and AcuM in Aspergillus nidulans. Mol Microbiol 84: 942−964 doi: 10.1111/j.1365-2958.2012.08067.x
Tada S, Gomi K, Kitamoto K, Takahashi K, Tamura G, Hara S (1991) Construction of a fusion gene comprising the Taka-amylase A promoter and the Escherichia coli β- glucuronidase gene and analysis of its expression in Aspergillus oryzae. Mol Gen Genet 229: 301−306 doi: 10.1007/bf00272170
Tagami K, Liu C, Minami A, Noike M, Isaka T, Fueki S, Shichijo Y, Toshima H, Gomi K, Dairi T, Oikawa H (2013) Reconstitution of biosynthetic machinery for indole- diterpene paxilline in Aspergillus oryzae. J Am Chem Soc 135:1260−1263 doi: 10.1021/ja3116636.
Taggart J, MacDiarmid CW, Haws S, Eide DJ (2017) Zap1-dependent transcription from an alternative upstream promoter controls translation of RTC4 mRNA in zinc- deficient Saccharomyces cerevisiae. Mol Microbiol 106: 678−689 doi: 10.1111/mmi.13851
Tanaka M, Gomi K (2013) Strategies for increasing the production level of heterologous proteins in Aspergillus oryzae. In Anazawa H, Shimizu S (ed) Microbial production: From genome design to cell engineering, Springer Japan, Tokyo, pp.149−164 doi: 10.1007/978-4-431-54607-8_14
Tanaka M, Tokuoka M, Shintani T, Gomi K (2012) Transcripts of a heterologous gene encoding mite allergen Der f 7 are stabilized by codon optimization in Aspergillus oryzae. Appl Microbiol Biotechnol 96: 1275−1282 doi: 10.1007/s00253-012- 4169-y
Toda T, Sano M, Honda M, Rimoldi O, Yang Y, Yamamoto M, Takase K, Hirozumi K, Kitamoto K, Minetoki T, et al. (2001) Deletion analysis of the enolase gene (enoA) promoter from the filamentous fungus Aspergillus oryzae. Curr Genet 40: 260−267 doi: 10.1007/s00294-001-0258-7
Tresenrider A, Ünal E (2018) One-two punch mechanism of gene repression: a fresh perspective on gene regulation. Curr Genet 64: 581−588 doi: 10.1007/s00294- 017-0793-5.
Tsuboi H, Koda A, Toda T, Minetoki T, Hirotsune M, Machida M (2005) Improvement of the Aspergillus oryzae enolase promoter (P-enoA) by the introduction of cis- element repeats. Biosci Biotechnol Biochem 69: 206−208 doi: 10.1271/bbb.69.206
Wakai S, Yoshie T, Asai-Nakashima N, Yamada R, Ogino C, Tsutsumi H, Hata Y, Kondo A (2014) L-lactic acid production from starch by simultaneous saccharification and fermentation in a genetically engineered Aspergillus oryzae pure culture. Bioresour Technol 173: 376–383. doi: 10.1016/j.biortech.2014.09.094
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, et al. (2015) Enhancer evolution across 20 mammalian species. Cell 160: 554−566 doi: 10.1016/j.cell.2015.01.006
Yamada O, Lee BR, Gomi K (1997) Transformation system for Aspergillus oryzae with double auxotrophic mutations, niaD and sC. Biosci Biotechnol Biochem 61: 1367−1369 doi: 10.1271/bbb.61.1367
Yang L, Lubeck M, Lubeck PS (2017) Aspergillus as a versatile cell factory for organic acid production. Fungal Biol Rev 31: 33−49 doi: 10.1016/j.fbr.2016.11.001
Yoshimi A, Yamaguchi S, Fujioka T, Kawai K, Gomi K, Machida M, Abe K (2018) Heterologous production of a novel cyclic peptide compound, KK-1, in Aspergillus oryzae. Front Microbiol 9: 12 doi: 10.3389/fmicb.2018.00690