Considerations for Domestication of Novel Strains of Filamentous Fungi

Pullen, Randi M.; Decker, Stephen R.; Subramanian, Venkataramanan; Adler, Meaghan J.; Tobias, Alexander V.; Perisin, Matthew; Sund, Christian J.; Servinsky, Matthew D.; Kozlowski, Mark T.

doi:10.1021/acssynbio.4c00672

Title: Considerations for Domestication of Novel Strains of Filamentous Fungi

Journal Article · Thu Jan 30 00:00:00 UTC 2025 · ACS Synthetic Biology

DOI: https://doi.org/10.1021/acssynbio.4c00672 · OSTI ID:2507354

Pullen, Randi M. ^[1]; Decker, Stephen R. ^[2]; Subramanian, Venkataramanan ^[2]; Adler, Meaghan J. ^[3]; Tobias, Alexander V. ^[4]; Perisin, Matthew ^[5]; Sund, Christian J. ^[1]; Servinsky, Matthew D. ^[1];

^[1]

DEVCOM Army Research Laboratory, Adelphi, MD (United States)
National Renewable Energy Laboratory (NREL), Golden, CO (United States)
DEVCOM Army Research Laboratory, Adelphi, MD (United States); University of Tennessee-Knoxville, TN (United States)
DEVCOM Army Research Laboratory, Adelphi, MD (United States); The MITRE Corporation, McLean, VA (United States)
DEVCOM Army Research Laboratory, Adelphi, MD (United States); Lallemand Inc, Lebanon, NH (United States)

Fungi, especially filamentous fungi, are a relatively understudied, biotechnologically useful resource with incredible potential for commercial applications. These multicellular eukaryotic organisms have long been exploited for their natural production of useful commodity chemicals and proteins such as enzymes used in starch processing, detergents, food and feed production, pulping and paper making and biofuels production. The ability of filamentous fungi to use a wide range of feedstocks is another key advantage. As chassis organisms, filamentous fungi can express cellular machinery, and metabolic and signal transduction pathways from both prokaryotic and eukaryotic origins. Their genomes abound with novel genetic elements and metabolic processes that can be harnessed for biotechnology applications. Synthetic biology tools are becoming inexpensive, modular, and expansive while systems biology is beginning to provide the level of understanding required to design increasingly complex synthetic systems. This review covers the challenges of working in filamentous fungi and offers a perspective on the approaches needed to exploit fungi as microbial cell factories.

View Journal Article

Cite

Export

Save

Research Organization:: DEVCOM Army Research Laboratory, Adelphi, MD (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE; USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 2507354

Report Number(s):: NREL/JA--2700-90063; NREL/JA--2700-93971

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 2 Vol. 14; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (272)

Wood‐Derived Functional Polymeric Materials Wang, Jifu; Zhang, Daihui; Chu, Fuxiang Advanced Materials, Vol. 33, Issue 28 https://doi.org/10.1002/adma.202001135	journal	June 2020
Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin Chiang, Yi-Ming; Ahuja, Manmeet; Oakley, C. Elizabeth Angewandte Chemie International Edition, Vol. 55, Issue 5 https://doi.org/10.1002/anie.201507097	journal	November 2015
CRISPR/Cas9‐based genome engineering: A new breakthrough in the genetic manipulation of filamentous fungi Ullah, Mati; Xia, Lin; Xie, Shangxian Biotechnology and Applied Biochemistry, Vol. 67, Issue 6 https://doi.org/10.1002/bab.2077	journal	November 2020
Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters Blazeck, John; Garg, Rishi; Reed, Ben Biotechnology and Bioengineering, Vol. 109, Issue 11 https://doi.org/10.1002/bit.24552	journal	May 2012
Tailor‐made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus Arazoe, Takayuki; Miyoshi, Kennosuke; Yamato, Tohru Biotechnology and Bioengineering, Vol. 112, Issue 12 https://doi.org/10.1002/bit.25662	journal	July 2015
High‐Throughput Gene Replacement in Aspergillus fumigatus Zhao, Can; Fraczek, Marcin G.; Dineen, Lauren Current Protocols in Microbiology, Vol. 54, Issue 1 https://doi.org/10.1002/cpmc.88	journal	August 2019
Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae. Bundock, P.; den Dulk-Ras, A.; Beijersbergen, A. The EMBO Journal, Vol. 14, Issue 13, p. 3206-3214 https://doi.org/10.1002/j.1460-2075.1995.tb07323.x	journal	July 1995
Yield and cold storage of Trichoderma conidia is influenced by substrate pH and storage temperature Steyaert, Johanna M.; Chomic, Anastasia; Nieto‐Jacobo, Maria Journal of Basic Microbiology, Vol. 57, Issue 5 https://doi.org/10.1002/jobm.201600616	journal	February 2017
Autonomous Plasmid Replication inAspergillus nidulans:AMA1 and MATE Elements Aleksenko, A.; Clutterbuck, A. J. Fungal Genetics and Biology, Vol. 21, Issue 3 https://doi.org/10.1006/fgbi.1997.0980	journal	June 1997
High-Throughput Construction of Gene Deletion Cassettes for Generation of Neurospora crassa Knockout Strains Collopy, Patrick D.; Colot, Hildur V.; Park, Gyungsoon Molecular and Cell Biology Methods for Fungi https://doi.org/10.1007/978-1-60761-611-5_3	book	January 2010
A dominant selectable marker that is meiotically stable in Neurospora crassa: the amdS gene of Aspergillus nidulans Yamashiro, Carl T.; Yarden, Oded; Yanofsky, Charles Molecular and General Genetics MGG, Vol. 236, Issue 1 https://doi.org/10.1007/BF00279650	journal	December 1992
Isolation of uridine auxotrophs from Trichoderma reesei and efficient transformation with the cloned ura3 and ura5 genes Bergès, Thierry; Barreau, Christian Current Genetics, Vol. 19, Issue 5, p. 359-365 https://doi.org/10.1007/BF00309596	journal	May 1991
The development of a heterologous transformation system for the cellulolytic fungus Trichoderma reesei based on a pyrG-negative mutant strain Gruber, F.; Visser, J.; Kubicek, C. P. Current Genetics, Vol. 18, Issue 1 https://doi.org/10.1007/BF00321118	journal	July 1990
Cloning of an Aspergillus niger invertase gene by expression in Trichoderma reesei Berg�s, Thierry; Barreau, Christian; Peberdy, John F. Current Genetics, Vol. 24, Issue 1-2 https://doi.org/10.1007/BF00324665	journal	July 1993
The development of a homologous transformation system for Aspergillus oryzae based on the nitrate assimilation pathway: A convenient and general selection system for filamentous fungal transformation Unkles, Shiela E.; Campbell, Edward I.; de Ruiter-Jacobs, Yolanda M. J. T. Molecular and General Genetics MGG, Vol. 218, Issue 1 https://doi.org/10.1007/BF00330571	journal	July 1989
Transformation of Trichoderma reesei based on hygromycin B resistance using homologous expression signals Mach, Robert L.; Schindler, Martin; Kubicek, Christian P. Current Genetics, Vol. 25, Issue 6 https://doi.org/10.1007/BF00351679	journal	June 1994
Cloning of the blasticidin S deaminase gene (BSD) from Aspergillus terreus and its use as a selectable marker for Schizosaccharomyces pombe and Pyricularia oryzae Kimura, Makoto; Kamakura, Takashi; Zhou Tao, Quan Molecular and General Genetics MGG, Vol. 242, Issue 2 https://doi.org/10.1007/BF00391004	journal	January 1994
A gene transfer system based on the homologous pyrG gene and efficient expression of bacterial genes in Aspergillus oryzae de Ruiter-Jacobs, Yolanda M. J. T.; Broekhuijsen, Martien; Unkles, Sheila E. Current Genetics, Vol. 16, Issue 3 https://doi.org/10.1007/BF00391472	journal	September 1989
Influence of manganese on morphology and cell wall composition of Aspergillus niger during citric acid fermentation Kisser, Monika; Kubicek, C. P.; R�hr, M. Archives of Microbiology, Vol. 128, Issue 1 https://doi.org/10.1007/BF00422301	journal	November 1980
Efficient gene targeting in the filamentous fungusAlternaria alternata Shiotani, Hiroshi; Tsuge, Takashi Molecular and General Genetics MGG, Vol. 248, Issue 2 https://doi.org/10.1007/BF02190795	journal	July 1995
A review of studies and measures to improve the mycotoxicological safety of traditional Japanese mold-fermented foods Tanaka, K.; Kushiro, M.; Manabe, M. Mycotoxin Research, Vol. 22, Issue 3 https://doi.org/10.1007/BF02959268	journal	September 2006
The cell functions of phospholipase C-1, Ca2+/H+ exchanger-1, and secretory phospholipase A2 in tolerance to stress conditions and cellulose degradation in Neurospora crassa Baruah, Darshana; Tamuli, Ranjan Archives of Microbiology, Vol. 205, Issue 10 https://doi.org/10.1007/s00203-023-03662-1	journal	September 2023
Preparation and comparative characterization of immobilized Aspergillus oryzae expressing Fusarium heterosporum lipase for enzymatic biodiesel production Hama, Shinji; Tamalampudi, Sriappareddy; Suzuki, Yuya Applied Microbiology and Biotechnology, Vol. 81, Issue 4 https://doi.org/10.1007/s00253-008-1689-6	journal	December 2008
New tools for the genetic manipulation of filamentous fungi Kück, Ulrich; Hoff, Birgit Applied Microbiology and Biotechnology, Vol. 86, Issue 1 https://doi.org/10.1007/s00253-009-2416-7	journal	January 2010
The roots—a short history of industrial microbiology and biotechnology Buchholz, Klaus; Collins, John Applied Microbiology and Biotechnology, Vol. 97, Issue 9 https://doi.org/10.1007/s00253-013-4768-2	journal	March 2013
Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology Aghcheh, Razieh Karimi; Kubicek, Christian P. Applied Microbiology and Biotechnology, Vol. 99, Issue 15 https://doi.org/10.1007/s00253-015-6763-2	journal	June 2015
The filamentous fungal pellet—relationship between morphology and productivity Veiter, Lukas; Rajamanickam, Vignesh; Herwig, Christoph Applied Microbiology and Biotechnology, Vol. 102, Issue 7 https://doi.org/10.1007/s00253-018-8818-7	journal	February 2018
Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi Kluge, Janina; Terfehr, Dominik; Kück, Ulrich Applied Microbiology and Biotechnology, Vol. 102, Issue 15 https://doi.org/10.1007/s00253-018-9115-1	journal	June 2018
CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective Song, Runjie; Zhai, Qing; Sun, Lu Applied Microbiology and Biotechnology, Vol. 103, Issue 17 https://doi.org/10.1007/s00253-019-10007-w	journal	July 2019
A comparative study on the transformation of Aspergillus nidulans by microprojectile bombardment of conidia and a more conventional procedure using protoplasts treated with polyethyleneglycol Herzog, R. W.; Daniell, H.; Singh, N. K. Applied Microbiology and Biotechnology, Vol. 45, Issue 3 https://doi.org/10.1007/s002530050692	journal	April 1996
Microbially influenced corrosion of glass Drewello, R.; Weissmann, R. Applied Microbiology and Biotechnology, Vol. 47, Issue 4 https://doi.org/10.1007/s002530050937	journal	April 1997
Sequential gene deletions in Hypocrea jecorina using a single blaster cassette Hartl, Lukas; Seiboth, Bernhard Current Genetics, Vol. 48, Issue 3 https://doi.org/10.1007/s00294-005-0011-8	journal	August 2005
Agrobacterium-mediated transformation as a tool for functional genomics in fungi Michielse, Caroline B.; Hooykaas, Paul J. J.; van den Hondel, Cees A. M. J. J. Current Genetics, Vol. 48, Issue 1 https://doi.org/10.1007/s00294-005-0578-0	journal	May 2005
Comparison between polyethylene glycol- and polyethylenimine-mediated transformation of Aspergillus nidulans Kuwano, Tetsuya; Shirataki, Chikako; Itoh, Yasuo Current Genetics, Vol. 54, Issue 2 https://doi.org/10.1007/s00294-008-0204-z	journal	July 2008
Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation Catalano, Valentina; Vergara, Mariarosaria; Hauzenberger, Jasmin R. Current Genetics, Vol. 57, Issue 1 https://doi.org/10.1007/s00294-010-0322-2	journal	September 2010
Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae Takahashi, Tadashi; Masuda, Tsutomu; Koyama, Yasuji Molecular Genetics and Genomics, Vol. 275, Issue 5 https://doi.org/10.1007/s00438-006-0104-1	journal	February 2006
Functional analysis of the cellobiohydrolase I promoter of the filamentous fungus Ilmén, M.; Onnela, M. -L.; Klemsdal, S. MGG Molecular & General Genetics, Vol. 253, Issue 3 https://doi.org/10.1007/s004380050326	journal	January 1996
A historical perspective on mycorrhizal mutualism emphasizing arbuscular mycorrhizas and their emerging challenges Sportes, Antoine; Hériché, Mathilde; Boussageon, Raphaël Mycorrhiza, Vol. 31, Issue 6 https://doi.org/10.1007/s00572-021-01053-2	journal	October 2021
Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans Yaegashi, Junko; Oakley, Berl R.; Wang, Clay C. C. Journal of Industrial Microbiology and Biotechnology, Vol. 41, Issue 2 https://doi.org/10.1007/s10295-013-1386-z	journal	February 2014
Synthetic biology advances and applications in the biotechnology industry: a perspective Katz, Leonard; Chen, Yvonne Y.; Gonzalez, Ramon Journal of Industrial Microbiology & Biotechnology, Vol. 45, Issue 7 https://doi.org/10.1007/s10295-018-2056-y	journal	June 2018
Ultra-high-throughput picoliter-droplet microfluidics screening of the industrial cellulase-producing filamentous fungus Trichoderma reesei He, Ronglin; Ding, Ruihua; Heyman, John A. Journal of Industrial Microbiology and Biotechnology, Vol. 46, Issue 11 https://doi.org/10.1007/s10295-019-02221-2	journal	November 2019
Multiple gene disruptions by marker recycling with highly efficient gene-targeting background (ΔligD) in Aspergillus oryzae Maruyama, Jun-Ichi; Kitamoto, Katsuhiko Biotechnology Letters, Vol. 30, Issue 10 https://doi.org/10.1007/s10529-008-9763-9	journal	June 2008
Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae Katayama, Takuya; Tanaka, Yuki; Okabe, Tomoya Biotechnology Letters, Vol. 38, Issue 4 https://doi.org/10.1007/s10529-015-2015-x	journal	December 2015
Optimization of cellulase production by Aspergillus nidulans: application in the biosoftening of cotton fibers Anuradha Jabasingh, S.; ValliNachiyar, C. World Journal of Microbiology and Biotechnology, Vol. 27, Issue 1 https://doi.org/10.1007/s11274-010-0431-6	journal	May 2010
A ku70 null mutant improves gene targeting frequency in the fungal pathogen Verticillium dahliae Qi, Xiliang; Su, Xiaofeng; Guo, Huiming World Journal of Microbiology and Biotechnology, Vol. 31, Issue 12 https://doi.org/10.1007/s11274-015-1907-1	journal	October 2015
The application of powerful promoters to enhance gene expression in industrial microorganisms Zhou, Shenghu; Du, Guocheng; Kang, Zhen World Journal of Microbiology and Biotechnology, Vol. 33, Issue 2 https://doi.org/10.1007/s11274-016-2184-3	journal	January 2017
Deletion of TpKu70 facilitates gene targeting in Talaromyces pinophilus and identification of TpAmyR involvement in amylase production Zhang, Ting; Zhao, Shuai; Liao, Lu-Sheng World Journal of Microbiology and Biotechnology, Vol. 33, Issue 9 https://doi.org/10.1007/s11274-017-2331-5	journal	August 2017
Construction of Stable T7 Expression System in Saccharomyces cerevisiae by Improving Nuclear Membrane Permeability with Viroporin HIV-1 Vpu Yan, Kun; Li, Jun; Wang, Wenya Applied Biochemistry and Biotechnology, Vol. 193, Issue 12 https://doi.org/10.1007/s12010-021-03665-y	journal	October 2021
The effects of deletion of cellobiohydrolase genes on carbon source-dependent growth and enzymatic lignocellulose hydrolysis in Trichoderma reesei Ren, Meibin; Wang, Yifan; Liu, Guoxin Journal of Microbiology, Vol. 58, Issue 8 https://doi.org/10.1007/s12275-020-9630-5	journal	June 2020
A versatile transformation system for the cellulolytic filamentous fungus Trichoderma reesei Penttilä, Merja; Nevalainen, Helena; Rättö, Marjaana Gene, Vol. 61, Issue 2, p. 155-164 https://doi.org/10.1016/0378-1119(87)90110-7	journal	January 1987
Optimized vectors and selection for transformation of Neurospora crassa and Aspergillus nidulans to bleomycin and phleomycin resistance Austin, Barbara; Hall, Ruth M.; Tyler, Brett M. Gene, Vol. 93, Issue 1 https://doi.org/10.1016/0378-1119(90)90152-H	journal	September 1990
Thiamine‐regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch‐like domain in the 5′‐UTR Kubodera, Takafumi; Watanabe, Mutsumi; Yoshiuchi, Kumi FEBS Letters, Vol. 555, Issue 3 https://doi.org/10.1016/S0014-5793(03)01335-8	journal	November 2003
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R. Fungal Genomics https://doi.org/10.1016/S0065-2660(06)57002-6	book	March 2007
A novel improved method for Aspergillus nidulans transformation Koukaki, Marina; Giannoutsou, Eleni; Karagouni, Amalia Journal of Microbiological Methods, Vol. 55, Issue 3 https://doi.org/10.1016/S0167-7012(03)00208-2	journal	December 2003
Interactions between yeasts and bacteria in the smear surface-ripened cheeses Corsetti, A.; Rossi, J.; Gobbetti, M. International Journal of Food Microbiology, Vol. 69, Issue 1-2 https://doi.org/10.1016/S0168-1605(01)00567-0	journal	September 2001
The interaction between yeasts and bacteria in dairy environments Viljoen, Bennie C. International Journal of Food Microbiology, Vol. 69, Issue 1-2 https://doi.org/10.1016/S0168-1605(01)00570-0	journal	September 2001
Mould starter cultures for dry sausages—selection, application and effects Sunesen, L. O.; Stahnke, L. H. Meat Science, Vol. 65, Issue 3 https://doi.org/10.1016/S0309-1740(02)00281-4	journal	November 2003
Weathering of rocks induced by lichen colonization — a review Chen, Jie; Blume, Hans-Peter; Beyer, Lothar CATENA, Vol. 39, Issue 2 https://doi.org/10.1016/S0341-8162(99)00085-5	journal	March 2000
Sugar Catabolism in Aspergillus and Other Fungi Related to the Utilization of Plant Biomass Khosravi, Claire; Benocci, Tiziano; Battaglia, Evy Advances in Applied Microbiology, Vol. 90, p. 1-28 https://doi.org/10.1016/bs.aambs.2014.09.005	book	November 2014
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks Gerlt, John A.; Bouvier, Jason T.; Davidson, Daniel B. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1854, Issue 8 https://doi.org/10.1016/j.bbapap.2015.04.015	journal	August 2015
A novel transformation system using a bleomycin resistance marker with chemosensitizers for Aspergillus oryzae Suzuki, Satoshi; Tada, Sawaki; Fukuoka, Mari Biochemical and Biophysical Research Communications, Vol. 383, Issue 1 https://doi.org/10.1016/j.bbrc.2009.03.108	journal	May 2009
An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger Sarkari, Parveen; Marx, Hans; Blumhoff, Marzena L. Bioresource Technology, Vol. 245 https://doi.org/10.1016/j.biortech.2017.05.004	journal	December 2017
Prevention of melanin formation during aryl alcohol oxidase production under growth-limited conditions using an Aspergillus nidulans cell factory Pardo-Planas, Oscar; Prade, Rolf A.; Müller, Michael Bioresource Technology, Vol. 243 https://doi.org/10.1016/j.biortech.2017.06.183	journal	November 2017
Heterologous protein expression in Hypocrea jecorina: A historical perspective and new developments Singh, Arjun; Taylor, Larry E.; Vander Wall, Todd A. Biotechnology Advances, Vol. 33, Issue 1 https://doi.org/10.1016/j.biotechadv.2014.11.009	journal	January 2015
Bacteriophage T7 transcription system: an enabling tool in synthetic biology Wang, Wenya; Li, Yuwenbin; Wang, Yaqiong Biotechnology Advances, Vol. 36, Issue 8 https://doi.org/10.1016/j.biotechadv.2018.10.001	journal	December 2018
Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy Guo, Minliang; Ye, Jingyang; Gao, Dawei Biotechnology Advances, Vol. 37, Issue 1 https://doi.org/10.1016/j.biotechadv.2018.12.008	journal	January 2019
Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity Meng, Xiangfeng; Fang, Yu; Ding, Mingyang Biotechnology Advances, Vol. 54 https://doi.org/10.1016/j.biotechadv.2021.107866	journal	January 2022
Design patterns for engineering genetic stability Son, Hye-In; Weiss, Andrea; You, Lingchong Current Opinion in Biomedical Engineering, Vol. 19 https://doi.org/10.1016/j.cobme.2021.100297	journal	September 2021
Metabolic engineering for the microbial production of 1,3-propanediol Nakamura, Charles E; Whited, Gregory M Current Opinion in Biotechnology, Vol. 14, Issue 5, p. 454-459 https://doi.org/10.1016/j.copbio.2003.08.005	journal	October 2003
Protein interactors of Spindle Pole Body (SPB) components and septal proteins in fungus Neurospora crassa: A mass spectrometry-based dataset Espino-Vázquez, Astrid N.; Cota, Rosa Ramírez; Callejas-Negrete, Olga Alicia Data in Brief, Vol. 52 https://doi.org/10.1016/j.dib.2023.109980	journal	February 2024
Technological advances for improving fungal cellulase production from fruit wastes for bioenergy application: A review Srivastava, Neha; Srivastava, Manish; Alhazmi, Alaa Environmental Pollution, Vol. 287 https://doi.org/10.1016/j.envpol.2021.117370	journal	October 2021
CRISPR/Cas9 technology enables the development of the filamentous ascomycete fungus Penicillium subrubescens as a new industrial enzyme producer Salazar-Cerezo, Sonia; Kun, Roland S.; de Vries, Ronald P. Enzyme and Microbial Technology, Vol. 133 https://doi.org/10.1016/j.enzmictec.2019.109463	journal	February 2020
Detoxification of trichothecene mycotoxins by a novel bacterium, Eggerthella sp. DII-9 Gao, Xiaojuan; Mu, Peiqiang; Wen, Jikai Food and Chemical Toxicology, Vol. 112 https://doi.org/10.1016/j.fct.2017.12.066	journal	February 2018
Development of a novel quadruple auxotrophic host transformation system byargBgene disruption usingadeAgene and exploiting adenine auxotrophy inAspergillus oryzae Jin, Feng Jie; Maruyama, Jun-ichi; Juvvadi, Praveen Rao FEMS Microbiology Letters, Vol. 239, Issue 1 https://doi.org/10.1016/j.femsle.2004.08.025	journal	October 2004
Use of a nonhomologous end joining deficient strain (Δku70) of the ergot fungus Claviceps purpurea for identification of a nonribosomal peptide synthetase gene involved in ergotamine biosynthesis Haarmann, Thomas; Lorenz, Nicole; Tudzynski, Paul Fungal Genetics and Biology, Vol. 45, Issue 1 https://doi.org/10.1016/j.fgb.2007.04.008	journal	January 2008
Improved gene targeting in Magnaporthe grisea by inactivation of MgKU80 required for non-homologous end joining Villalba, François; Collemare, Jérôme; Landraud, Patricia Fungal Genetics and Biology, Vol. 45, Issue 1 https://doi.org/10.1016/j.fgb.2007.06.006	journal	January 2008
SMURF: Genomic mapping of fungal secondary metabolite clusters Khaldi, Nora; Seifuddin, Fayaz T.; Turner, Geoff Fungal Genetics and Biology, Vol. 47, Issue 9 https://doi.org/10.1016/j.fgb.2010.06.003	journal	September 2010
Establishing a versatile Golden Gate cloning system for genetic engineering in fungi Terfrüchte, Marius; Joehnk, Bastian; Fajardo-Somera, Rosa Fungal Genetics and Biology, Vol. 62 https://doi.org/10.1016/j.fgb.2013.10.012	journal	January 2014
Plant biomass degradation by fungi Mäkelä, Miia R.; Donofrio, Nicole; de Vries, Ronald P. Fungal Genetics and Biology, Vol. 72 https://doi.org/10.1016/j.fgb.2014.08.010	journal	November 2014
Genome editing in Ustilago maydis using the CRISPR–Cas system Schuster, Mariana; Schweizer, Gabriel; Reissmann, Stefanie Fungal Genetics and Biology, Vol. 89 https://doi.org/10.1016/j.fgb.2015.09.001	journal	April 2016
Establishment of CRISPR/Cas9 in Alternaria alternata Wenderoth, Maximilian; Pinecker, Christoph; Voß, Benjamin Fungal Genetics and Biology, Vol. 101 https://doi.org/10.1016/j.fgb.2017.03.001	journal	April 2017
New multi-marker strains and complementing genes for Aspergillus nidulans molecular biology Dohn, James W.; Grubbs, Alexander W.; Oakley, C. Elizabeth Fungal Genetics and Biology, Vol. 111 https://doi.org/10.1016/j.fgb.2018.01.003	journal	February 2018
Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli Nødvig, Christina S.; Hoof, Jakob B.; Kogle, Martin E. Fungal Genetics and Biology, Vol. 115 https://doi.org/10.1016/j.fgb.2018.01.004	journal	June 2018
FungalBraid: A GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology Hernanz-Koers, Miguel; Gandía, Mónica; Garrigues, Sandra Fungal Genetics and Biology, Vol. 116 https://doi.org/10.1016/j.fgb.2018.04.010	journal	July 2018
In the fungus where it happens: History and future propelling Aspergillus nidulans as the archetype of natural products research Caesar, Lindsay K.; Kelleher, Neil L.; Keller, Nancy P. Fungal Genetics and Biology, Vol. 144 https://doi.org/10.1016/j.fgb.2020.103477	journal	November 2020
Nanosized extracellular vesicles released by Neurospora crassa hyphae Medina-Castellanos, Elizabeth; Salgado-Bautista, Daniel A.; Martínez-Andrade, Juan M. Fungal Genetics and Biology, Vol. 165 https://doi.org/10.1016/j.fgb.2023.103778	journal	March 2023
Characterization of the need for galactofuranose during the Neurospora crassa life cycle Schaff, Hayden; Dey, Protyusha; Heiss, Christian Fungal Genetics and Biology, Vol. 168 https://doi.org/10.1016/j.fgb.2023.103826	journal	October 2023
RHO-3 plays a significant role in hyphal extension rate, conidiation, and the integrity of the Spitzenkörper in Neurospora crassa Ornelas-Llamas, Martha M.; Pérez-Mozqueda, Luis L.; Callejas-Negrete, Olga A. Fungal Genetics and Biology, Vol. 171 https://doi.org/10.1016/j.fgb.2024.103873	journal	March 2024
Disruption of ku70 involved in non-homologous end-joining facilitates homologous recombination but increases temperature sensitivity in the phytopathogenic fungus Penicillium digitatum Gandía, Mónica; Xu, Shaomei; Font, Cristina Fungal Biology, Vol. 120, Issue 3 https://doi.org/10.1016/j.funbio.2015.11.001	journal	March 2016
Highly efficient generation of signal transduction knockout mutants using a fungal strain deficient in the mammalian ku70 ortholog Pöggeler, Stefanie; Kück, Ulrich Gene, Vol. 378 https://doi.org/10.1016/j.gene.2006.03.020	journal	August 2006
CRISPR system in filamentous fungi: Current achievements and future directions Deng, Huaxiang; Gao, Ruijie; Liao, Xiangru Gene, Vol. 627 https://doi.org/10.1016/j.gene.2017.06.019	journal	September 2017
Overexpression of kojR and the entire koj gene cluster affect the kojic acid synthesis in Aspergillus oryzae 3.042 Zhang, Xuemei; Guo, Rui; Bi, Futi Gene, Vol. 892 https://doi.org/10.1016/j.gene.2023.147852	journal	January 2024
Improving the thermostability of a thermostable endoglucanase from Chaetomium thermophilum by engineering the conserved noncatalytic residue and N-glycosylation site Han, Chao; Liu, Yifan; Liu, Mengyu International Journal of Biological Macromolecules, Vol. 164 https://doi.org/10.1016/j.ijbiomac.2020.08.225	journal	December 2020
Modelling the effect of temperature, pH, water activity, and organic acids on the germination time of Penicillium camemberti and Penicillium roqueforti conidia Kalai, Safaa; Anzala, Lexane; Bensoussan, Maurice International Journal of Food Microbiology, Vol. 240 https://doi.org/10.1016/j.ijfoodmicro.2016.03.024	journal	January 2017
Self-excising Cre/mutant lox marker recycling system for multiple gene integrations and consecutive gene deletions in Aspergillus oryzae Zhang, Silai; Ban, Akihiko; Ebara, Naoki Journal of Bioscience and Bioengineering, Vol. 123, Issue 4 https://doi.org/10.1016/j.jbiosc.2016.11.001	journal	April 2017
Identification of a novel pyrithiamine resistance marker gene thiI for genome co-editing in Aspergillus oryzae Todokoro, Takehiko; Bando, Hiroki; Kotaka, Atsushi Journal of Bioscience and Bioengineering, Vol. 130, Issue 3 https://doi.org/10.1016/j.jbiosc.2020.04.013	journal	September 2020
Highly efficient gene targeting in the Aspergillus niger kusA mutant Meyer, Vera; Arentshorst, Mark; El-Ghezal, Aymen Journal of Biotechnology, Vol. 128, Issue 4 https://doi.org/10.1016/j.jbiotec.2006.12.021	journal	March 2007
Gene targeting in a nonhomologous end joining deficient Hypocrea jecorina Guangtao, Zhang; Hartl, Lukas; Schuster, Andre Journal of Biotechnology, Vol. 139, Issue 2 https://doi.org/10.1016/j.jbiotec.2008.10.007	journal	January 2009
CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea Králová, Michaela; Bergougnoux, Véronique; Frébort, Ivo Journal of Biotechnology, Vol. 325 https://doi.org/10.1016/j.jbiotec.2020.09.028	journal	January 2021
A review of approaches and techniques used in aquatic contaminated sediments: metal removal and stabilization by chemical and biotechnological processes Akcil, Ata; Erust, Ceren; Ozdemiroglu, Sevda Journal of Cleaner Production, Vol. 86 https://doi.org/10.1016/j.jclepro.2014.08.009	journal	January 2015
Yeast synthetic biology advances biofuel production Liu, Zihe; Wang, Junyang; Nielsen, Jens Current Opinion in Microbiology, Vol. 65 https://doi.org/10.1016/j.mib.2021.10.010	journal	February 2022
A guide to binary vectors and strategies for targeted genome modification in fungi using Agrobacterium tumefaciens-mediated transformation Frandsen, Rasmus John Normand Journal of Microbiological Methods, Vol. 87, Issue 3 https://doi.org/10.1016/j.mimet.2011.09.004	journal	December 2011
An efficient genetic transformation system for Chinese medicine fungus Tolypocladium ophioglossoides Chen, Xin-ai; He, Xian; Zhang, Min Journal of Microbiological Methods, Vol. 176 https://doi.org/10.1016/j.mimet.2020.106032	journal	September 2020
Deleting ku80 improves the efficiency of targeted gene editing in Neospora caninum Wu, Kaijian; Song, Xingju; Wu, Yayun Molecular and Biochemical Parasitology, Vol. 251 https://doi.org/10.1016/j.molbiopara.2022.111508	journal	September 2022
Fungi and fungal toxins as weapons Paterson, R. Russell M. Mycological Research, Vol. 110, Issue 9 https://doi.org/10.1016/j.mycres.2006.04.004	journal	September 2006
CRISPR-Cas9 assisted gene disruption in the higher fungus Ganoderma species Qin, Hao; Xiao, Han; Zou, Gen Process Biochemistry, Vol. 56 https://doi.org/10.1016/j.procbio.2017.02.012	journal	May 2017
Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges Singh, Anil Kumar; Bilal, Muhammad; Iqbal, Hafiz M. N. Science of The Total Environment, Vol. 777 https://doi.org/10.1016/j.scitotenv.2021.145988	journal	July 2021
Expression of fungal biosynthetic gene clusters in S. cerevisiae for natural product discovery Liu, Zihe; Lin, Zhenquan; Nielsen, Jens Synthetic and Systems Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1016/j.synbio.2021.01.003	journal	March 2021
Development of synthetic biology tools to engineer Pichia pastoris as a chassis for the production of natural products Gao, Jucan; Jiang, Lihong; Lian, Jiazhang Synthetic and Systems Biotechnology, Vol. 6, Issue 2 https://doi.org/10.1016/j.synbio.2021.04.005	journal	June 2021
Design and construction of microbial cell factories based on systems biology Yan, Wenlong; Cao, Zhibei; Ding, Mingzhu Synthetic and Systems Biotechnology, Vol. 8, Issue 1 https://doi.org/10.1016/j.synbio.2022.11.001	journal	March 2023
Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity Binder, Dennis; Drepper, Thomas; Jaeger, Karl-Erich Metabolic Engineering, Vol. 42 https://doi.org/10.1016/j.ymben.2017.06.009	journal	July 2017
Flavourzyme, an Enzyme Preparation with Industrial Relevance: Automated Nine-Step Purification and Partial Characterization of Eight Enzymes Merz, Michael; Eisele, Thomas; Berends, Pieter Journal of Agricultural and Food Chemistry, Vol. 63, Issue 23 https://doi.org/10.1021/acs.jafc.5b01665	journal	June 2015
Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans Chiang, Yi-Ming; Lin, Tzu-Shyang; Wang, Clay C. C. Journal of Natural Products, Vol. 85, Issue 10 https://doi.org/10.1021/acs.jnatprod.2c00487	journal	September 2022
Modular Synthetic Biology Toolkit for Filamentous Fungi Mózsik, László; Pohl, Carsten; Meyer, Vera ACS Synthetic Biology, Vol. 10, Issue 11 https://doi.org/10.1021/acssynbio.1c00260	journal	November 2021
CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum Pohl, C.; Kiel, J. A. K. W.; Driessen, A. J. M. ACS Synthetic Biology, Vol. 5, Issue 7 https://doi.org/10.1021/acssynbio.6b00082	journal	April 2016
Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species Portela, Rui M. C.; Vogl, Thomas; Kniely, Claudia ACS Synthetic Biology, Vol. 6, Issue 3 https://doi.org/10.1021/acssynbio.6b00178	journal	December 2016
Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering Cao, Mingfeng; Gao, Meirong; Lopez-Garcia, Carmen Lorena ACS Synthetic Biology, Vol. 6, Issue 8 https://doi.org/10.1021/acssynbio.7b00046	journal	April 2017
CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Glarea lozoyensis and Its Application in Manipulating gloF Wei, Teng-Yun; Wu, Yuan-Jie; Xie, Qiu-Ping ACS Synthetic Biology, Vol. 9, Issue 8 https://doi.org/10.1021/acssynbio.9b00491	journal	August 2020
An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans Chiang, Yi-Ming; Oakley, C. Elizabeth; Ahuja, Manmeet Journal of the American Chemical Society, Vol. 135, Issue 20 https://doi.org/10.1021/ja401945a	journal	May 2013
T-2 Toxin, a Trichothecene Mycotoxin: Review of Toxicity, Metabolism, and Analytical Methods Li, Yanshen; Wang, Zhanhui; Beier, Ross C. Journal of Agricultural and Food Chemistry, Vol. 59, Issue 8 https://doi.org/10.1021/jf200767q	journal	March 2011
Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system Liu, Rui; Chen, Ling; Jiang, Yanping Cell Discovery, Vol. 1, Article No. 15007 https://doi.org/10.1038/celldisc.2015.7	journal	May 2015
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae Galagan, James E.; Calvo, Sarah E.; Cuomo, Christina Nature, Vol. 438, Issue 7071 https://doi.org/10.1038/nature04341	journal	December 2005
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Agrobacterium tumefaciens-mediated transformation of filamentous fungi de Groot, Marcel J. A.; Bundock, Paul; Hooykaas, Paul J. J. Nature Biotechnology, Vol. 16, Issue 9, p. 839-842 https://doi.org/10.1038/nbt0998-839	journal	September 1998
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol Yim, Harry; Haselbeck, Robert; Niu, Wei Nature Chemical Biology, Vol. 7, Issue 7 https://doi.org/10.1038/nchembio.580	journal	May 2011
Neurospora: a model of model microbes Davis, Rowland H.; Perkins, David D. Nature Reviews Genetics, Vol. 3, Issue 5 https://doi.org/10.1038/nrg797	journal	May 2002
Bricks and blueprints: methods and standards for DNA assembly Casini, Arturo; Storch, Marko; Baldwin, Geoffrey S. Nature Reviews Molecular Cell Biology, Vol. 16, Issue 9 https://doi.org/10.1038/nrm4014	journal	June 2015
Engineering enhanced cellobiohydrolase activity Taylor, Larry E.; Knott, Brandon C.; Baker, John O. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03501-8	journal	March 2018
Establishment of Neurospora crassa as a model organism for fungal virology Honda, Shinji; Eusebio-Cope, Ana; Miyashita, Shuhei Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19355-y	journal	November 2020
A microbial supply chain for production of the anti-cancer drug vinblastine Zhang, Jie; Hansen, Lea G.; Gudich, Olga Nature, Vol. 609, Issue 7926 https://doi.org/10.1038/s41586-022-05157-3	journal	August 2022
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems Hossain, Ayaan; Lopez, Eriberto; Halper, Sean M. Nature Biotechnology, Vol. 38, Issue 12 https://doi.org/10.1038/s41587-020-0584-2	journal	July 2020
Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system Sugano, Shigeo S.; Suzuki, Hiroko; Shimokita, Eisuke Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-00883-5	journal	April 2017
Development of a versatile and conventional technique for gene disruption in filamentous fungi based on CRISPR-Cas9 technology Zheng, Yan-Mei; Lin, Fu-Long; Gao, Hao Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-10052-3	journal	August 2017
Novel genetic tools that enable highly pure protein production in Trichoderma reesei Rantasalo, Anssi; Vitikainen, Marika; Paasikallio, Toni Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41573-8	journal	March 2019
High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins Jan Vonk, Peter; Escobar, Natalia; Wösten, Han A. B. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-44133-2	journal	May 2019
CRISPR-based transcriptional activation tool for silent genes in filamentous fungi Mózsik, László; Hoekzema, Mirthe; de Kok, Niels A. W. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-020-80864-3	journal	January 2021
CRISPR/Cas9 mediated targeted knock-in of eglA gene to improve endoglucanase activity of Aspergillus fumigatus LMB-35Aa Benites-Pariente, J. S.; Samolski, I.; Ludeña, Y. Scientific Reports, Vol. 14, Issue 1 https://doi.org/10.1038/s41598-024-70397-4	journal	August 2024
Approaches to functional genomics in filamentous fungi Weld, Richard J.; Plummer, Kim M.; Carpenter, Margaret A. Cell Research, Vol. 16, Issue 1 https://doi.org/10.1038/sj.cr.7310006	journal	January 2006
The DmtA methyltransferase contributes to Aspergillus flavus conidiation, sclerotial production, aflatoxin biosynthesis and virulence Yang, Kunlong; Liang, Linlin; Ran, Fanlei Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep23259	journal	March 2016
High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics Beneyton, Thomas; Wijaya, I. Putu Mahendra; Postros, Prexilia Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27223	journal	June 2016
CRISPR/Cas9-mediated efficient genome editing via blastospore-based transformation in entomopathogenic fungus Beauveria bassiana Chen, Jingjing; Lai, Yiling; Wang, Lili Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep45763	journal	April 2017
Cell factory engineering for improved production of natural products Nielsen, Jens Natural Product Reports, Vol. 36, Issue 9 https://doi.org/10.1039/C9NP00005D	journal	January 2019
High-throughput optofluidic screening for improved microbial cell factories via real-time micron-scale productivity monitoring Rienzo, Matthew; Lin, Ke-Chih; Mobilia, Kellen C. Lab on a Chip, Vol. 21, Issue 15 https://doi.org/10.1039/D1LC00389E	journal	January 2021
The expanding CRISPR toolbox for natural product discovery and engineering in filamentous fungi Woodcraft, Clara; Chooi, Yit-Heng; Roux, Indra Natural Product Reports, Vol. 40, Issue 1 https://doi.org/10.1039/D2NP00055E	journal	January 2023
The plasmid replicator AMA1 in Aspergillus nidulans is an inverted duplication of a low-copy-number dispersed genomic repeat Aleksenko, Alexei; Clutterbuck, A. John Molecular Microbiology, Vol. 19, Issue 3, p. 565-574 https://doi.org/10.1046/j.1365-2958.1996.400937.x	journal	February 1996
Is microfluidics the “assembly line” for CRISPR-Cas9 gene-editing? Ahmadi, Fatemeh; Quach, Angela B. V.; Shih, Steve C. C. Biomicrofluidics, Vol. 14, Issue 6 https://doi.org/10.1063/5.0029846	journal	November 2020
From The Cover: Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining Ninomiya, Y.; Suzuki, K.; Ishii, C. Proceedings of the National Academy of Sciences, Vol. 101, Issue 33 https://doi.org/10.1073/pnas.0402780101	journal	August 2004
A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors Colot, H. V.; Park, G.; Turner, G. E. Proceedings of the National Academy of Sciences, Vol. 103, Issue 27 https://doi.org/10.1073/pnas.0601456103	journal	June 2006
Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (human Lig4 homolog) in Neurospora Ishibashi, K.; Suzuki, K.; Ando, Y. Proceedings of the National Academy of Sciences, Vol. 103, Issue 40 https://doi.org/10.1073/pnas.0604477103	journal	September 2006
Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system Xie, Kabin; Minkenberg, Bastian; Yang, Yinong Proceedings of the National Academy of Sciences, Vol. 112, Issue 11 https://doi.org/10.1073/pnas.1420294112	journal	March 2015
Genetic Control of Biochemical Reactions in Neurospora Beadle, G. W.; Tatum, E. L. Proceedings of the National Academy of Sciences, Vol. 27, Issue 11 https://doi.org/10.1073/pnas.27.11.499	journal	November 1941
Efficient transformation of Neurospora crassa by utilizing hybrid plasmid DNA Case, M. E.; Schweizer, M.; Kushner, S. R. Proceedings of the National Academy of Sciences, Vol. 76, Issue 10 https://doi.org/10.1073/pnas.76.10.5259	journal	October 1979
Construction of a shuttle vector for the filamentous fungus Neurospora crassa. Stohl, L. L.; Lambowitz, A. M. Proceedings of the National Academy of Sciences, Vol. 80, Issue 4 https://doi.org/10.1073/pnas.80.4.1058	journal	February 1983
NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design. Rebatchouk, D.; Daraselia, N.; Narita, J. O. Proceedings of the National Academy of Sciences, Vol. 93, Issue 20 https://doi.org/10.1073/pnas.93.20.10891	journal	October 1996
Strengthening microbial cell factories for efficient production of bioactive molecules Singh, Bharat; Kumar, Ankit; Saini, Adesh Kumar Biotechnology and Genetic Engineering Reviews, Vol. 39, Issue 2 https://doi.org/10.1080/02648725.2023.2177039	journal	February 2023
Safety evaluation of a fungal pectinesterase enzyme preparation and its use in food Lissau, Bodil G.; Pedersen, Peder Bjarne; Petersen, Bent Riber Food Additives and Contaminants, Vol. 15, Issue 6 https://doi.org/10.1080/02652039809374691	journal	August 1998
Bioproduction of porphyrins, phycobilins, and their proteins using microbial cell factories: engineering, metabolic regulations, challenges, and perspectives Ko, Young Jin; Lee, Myeong-Eun; Cho, Byeong-Hyeon Critical Reviews in Biotechnology https://doi.org/10.1080/07388551.2023.2168512	journal	February 2023
Increased enzyme production under liquid culture conditions in the industrial fungus Aspergillus oryzae by disruption of the genes encoding cell wall α-1,3-glucan synthase Miyazawa, Ken; Yoshimi, Akira; Zhang, Silai Bioscience, Biotechnology, and Biochemistry, Vol. 80, Issue 9 https://doi.org/10.1080/09168451.2016.1209968	journal	September 2016
Production of the plant polyketide curcumin in Aspergillus oryzae: strengthening malonyl-CoA supply for yield improvement Kan, Eiichiro; Katsuyama, Yohei; Maruyama, Jun-ichi Bioscience, Biotechnology, and Biochemistry, Vol. 83, Issue 7 https://doi.org/10.1080/09168451.2019.1606699	journal	July 2019
Genetic Manipulation and Transformation Methods for Aspergillus spp. Son, Ye-Eun; Park, Hee-Soo Mycobiology, Vol. 49, Issue 2 https://doi.org/10.1080/12298093.2020.1838115	journal	November 2020
Regulation of the mRNA levels of nimA, a gene required for the G2-M transition in Aspergillus nidulans. Osmani, S. A.; May, G. S.; Morris, N. R. The Journal of cell biology, Vol. 104, Issue 6 https://doi.org/10.1083/jcb.104.6.1495	journal	June 1987
Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239 Sato, A.; Oshima, K.; Noguchi, H. DNA Research, Vol. 18, Issue 3 https://doi.org/10.1093/dnares/dsr009	journal	June 2011
T7-RNA polymerase dependent RNAi system inAspergillus fumigatus: a proof of concept study Enayati, Somayeh; Azizi, Mohammad; Aminollahi, Elahe FEMS Microbiology Letters, Vol. 363, Issue 5 https://doi.org/10.1093/femsle/fnw029	journal	February 2016
Optimization of physicochemical parameters of tannase post-purification and its versatile bioactivity Hidayathulla, Syed; Shahat, Abdelaaty A.; Alsaid, Mansour S. FEMS Microbiology Letters, Vol. 365, Issue 12 https://doi.org/10.1093/femsle/fny051	journal	February 2018
CRISPR-Cas9, the new kid on the block of fungal molecular biology Krappmann, Sven Medical Mycology, Vol. 55, Issue 1 https://doi.org/10.1093/mmy/myw097	journal	November 2016
Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance Boulton, S. Nucleic Acids Research, Vol. 24, Issue 23 https://doi.org/10.1093/nar/24.23.4639	journal	December 1996
A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans Chaveroche, M. -K. Nucleic Acids Research, Vol. 28, Issue 22 https://doi.org/10.1093/nar/28.22.e97	journal	November 2000
CADRE: the Central Aspergillus Data REpository 2012 Mabey Gilsenan, J.; Cooley, J.; Bowyer, P. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr971	journal	November 2011
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
Fungal Ku prevents permanent cell cycle arrest by suppressing DNA damage signaling at telomeres de Sena-Tomás, Carmen; Yu, Eun Young; Calzada, Arturo Nucleic Acids Research, Vol. 43, Issue 4 https://doi.org/10.1093/nar/gkv082	journal	February 2015
A universal gene expression system for fungi Rantasalo, Anssi; Landowski, Christopher P.; Kuivanen, Joosu Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky558	journal	June 2018
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline Blin, Kai; Shaw, Simon; Steinke, Katharina Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz310	journal	April 2019
Ensembl Genomes 2020—enabling non-vertebrate genomic research Howe, Kevin L.; Contreras-Moreira, Bruno; De Silva, Nishadi Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz890	journal	October 2019
Improved catalytic activity and stability of cellobiohydrolase (Cel6A) from the Aspergillus fumigatus by rational design Dodda, Subba Reddy; Sarkar, Nibedita; Jain, Piyush Protein Engineering, Design and Selection, Vol. 33 https://doi.org/10.1093/protein/gzaa020	journal	September 2020
Effect of Media Composition on the Numbers of Bacterial and Fungal Colonies Developing in Petri Plates Tyner, L. E. Soil Science, Vol. 57, Issue 4 https://doi.org/10.1097/00010694-194404000-00003	journal	April 1944
Evolution of ‘pollinator’- attracting signals in fungi Schiestl, Florian P.; Steinebrunner, Fabrizio; Schulz, Claudia Biology Letters, Vol. 2, Issue 3 https://doi.org/10.1098/rsbl.2006.0479	journal	April 2006
Neurospora crassa, a Model System for Epigenetics Research Aramayo, R.; Selker, E. U. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 10 https://doi.org/10.1101/cshperspect.a017921	journal	October 2013
The art of vector engineering: towards the construction of next-generation genetic tools Nora, Luísa Czamanski; Westmann, Cauã Antunes; Martins-Santana, Leonardo Microbial Biotechnology, Vol. 12, Issue 1 https://doi.org/10.1111/1751-7915.13318	journal	September 2018
Dual sgRNA‐directed gene deletion in basidiomycete Ganoderma lucidum using the CRISPR/Cas9 system Liu, Ke; Sun, Bin; You, Hao Microbial Biotechnology, Vol. 13, Issue 2 https://doi.org/10.1111/1751-7915.13534	journal	August 2019
A novel carbon source-dependent genetic transformation system for the versatile cell factoryHypocrea jecorinaâ(anamorphTrichoderma reesei) Guangtao, Zhang; Seiboth, Bernhard; Wen, Cao FEMS Microbiology Letters, Vol. 303, Issue 1 https://doi.org/10.1111/j.1574-6968.2009.01851.x	journal	February 2010
Arbuscular mycorrhizal fungi increase grain yields: a meta‐analysis Zhang, Shujuan; Lehmann, Anika; Zheng, Weishuang New Phytologist, Vol. 222, Issue 1 https://doi.org/10.1111/nph.15570	journal	November 2018
Modified Cre- loxP Recombination in Aspergillus oryzae by Direct Introduction of Cre Recombinase for Marker Gene Rescue Mizutani, Osamu; Masaki, Kazuo; Gomi, Katsuya Applied and Environmental Microbiology, Vol. 78, Issue 12 https://doi.org/10.1128/AEM.00080-12	journal	June 2012
Transient Silencing of DNA Repair Genes Improves Targeted Gene Integration in the Filamentous Fungus Trichoderma reesei Chum, Pak Yang; Schmidt, Georg; Saloheimo, Markku Applied and Environmental Microbiology, Vol. 83, Issue 15 https://doi.org/10.1128/AEM.00535-17	journal	August 2017
Generation of Large Chromosomal Deletions in Koji Molds Aspergillus oryzae and Aspergillus sojae via a Loop-Out Recombination Takahashi, Tadashi; Jin, Feng Jie; Sunagawa, Misao Applied and Environmental Microbiology, Vol. 74, Issue 24 https://doi.org/10.1128/AEM.00692-08	journal	December 2008
Transformation System for Hypocrea jecorina ( Trichoderma reesei ) That Favors Homologous Integration and Employs Reusable Bidirectionally Selectable Markers Steiger, Matthias G.; Vitikainen, Marika; Uskonen, Pekka Applied and Environmental Microbiology, Vol. 77, Issue 1 https://doi.org/10.1128/AEM.02100-10	journal	November 2010
Extracellular Production of Neoculin, a Sweet-Tasting Heterodimeric Protein with Taste-Modifying Activity, by Aspergillus oryzae Nakajima, Ken-ichiro; Asakura, Tomiko; Maruyama, Jun-ichi Applied and Environmental Microbiology, Vol. 72, Issue 5 https://doi.org/10.1128/AEM.72.5.3716-3723.2006	journal	May 2006
Deletion and Allelic Exchange of the Aspergillus fumigatus veA Locus via a Novel Recyclable Marker Module Krappmann, Sven; Bayram, Özgür; Braus, Gerhard H. Eukaryotic Cell, Vol. 4, Issue 7 https://doi.org/10.1128/EC.4.7.1298-1307.2005	journal	July 2005
Gene Targeting in Aspergillus fumigatus by Homologous Recombination Is Facilitated in a Nonhomologous End- Joining-Deficient Genetic Background Krappmann, Sven; Sasse, Christoph; Braus, Gerhard H. Eukaryotic Cell, Vol. 5, Issue 1 https://doi.org/10.1128/EC.5.1.212-215.2006	journal	January 2006
Signal-mediated import of bacteriophage T7 RNA polymerase into the Saccharomyces cerevisiae nucleus and specific transcription of target genes. Benton, B. M.; Eng, W. K.; Dunn, J. J. Molecular and Cellular Biology, Vol. 10, Issue 1 https://doi.org/10.1128/MCB.10.1.353	journal	January 1990
Evaluation of Chemicals for Restricting Colony Spreading by a Xerophilic Mold, Eurotium amstelodami , on Dichloran-18% Glycerol Agar Beuchat, Larry R.; De Daza, Maria Soledad Tapia Applied and Environmental Microbiology, Vol. 58, Issue 6 https://doi.org/10.1128/aem.58.6.2093-2095.1992	journal	June 1992
Dramatic Improvement of CRISPR/Cas9 Editing in Candida albicans by Increased Single Guide RNA Expression Ng, Henry; Dean, Neta mSphere, Vol. 2, Issue 2 https://doi.org/10.1128/mSphere.00385-16	journal	April 2017
Phylogenetic Distribution of Plastic-Degrading Microorganisms Gambarini, Victor; Pantos, Olga; Kingsbury, Joanne M. mSystems, Vol. 6, Issue 1 https://doi.org/10.1128/mSystems.01112-20	journal	February 2021
Fungal Ligninolytic Enzymes and Their Applications Mäkelä, Miia R.; Bredeweg, Erin L.; Magnuson, Jon K. Microbiology Spectrum, Vol. 4, Issue 6 https://doi.org/10.1128/microbiolspec.FUNK-0017-2016	journal	December 2016
Identification of a common secondary mutation in the Neurospora crassa knockout collection conferring a cell fusion-defective phenotype Montenegro-Montero, Alejandro; Goity, Alejandra; Canessa, Paulo F. Microbiology Spectrum, Vol. 11, Issue 5 https://doi.org/10.1128/spectrum.02087-23	journal	October 2023
CRISPR/Cas Genome Editing in Filamentous Fungi Rozhkova, Aleksandra M.; Kislitsin, Valeriy Yu. Biochemistry (Moscow), Vol. 86, Issue S1 https://doi.org/10.1134/S0006297921140091	journal	January 2021
Aspergillus nidulans: A Potential Resource of the Production of the Native and Heterologous Enzymes for Industrial Applications Kumar, Amit International Journal of Microbiology, Vol. 2020 https://doi.org/10.1155/2020/8894215	journal	August 2020
Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae Inglis, Diane O.; Binkley, Jonathan; Skrzypek, Marek S. BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-91	journal	January 2013
Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides Koh, Chong Mei; Liu, Yanbin BMC Microbiology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2180-14-50	journal	January 2014
Achieving efficient protein expression in Trichoderma reesei by using strong constitutive promoters Li, Junxin; Wang, Juan; Wang, Shaowen Microbial Cell Factories, Vol. 11, Issue 1 https://doi.org/10.1186/1475-2859-11-84	journal	January 2012
A novel platform for heterologous gene expression in Trichoderma reesei (Teleomorph Hypocrea jecorina) Jørgensen, Mikael Skaanning; Skovlund, Dominique Aubert; Johannesen, Pia Francke Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/1475-2859-13-33	journal	March 2014
Aspergillus oryzae-based cell factory for direct kojic acid production from cellulose Yamada, Ryosuke; Yoshie, Toshihide; Wakai, Satoshi Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/1475-2859-13-71	journal	May 2014
Genetically shaping morphology of the filamentous fungus Aspergillus glaucus for production of antitumor polyketide aspergiolide A Cai, Menghao; Zhang, Ying; Hu, Wei Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/1475-2859-13-73	journal	May 2014
Generation of Trichoderma atroviride mutants with constitutively activated G protein signaling by using geneticin resistance as selection marker Gruber, Sabine; Omann, Markus; Rodrìguez, Carolina Escobar BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-641	journal	November 2012
Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants Álvarez-Escribano, Isidro; Sasse, Christoph; Bok, Jin Woo BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0702-0	journal	November 2019
Establishment of Neurospora crassa as a host for heterologous protein production using a human antibody fragment as a model product Havlik, David; Brandt, Ulrike; Bohle, Kathrin Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0734-5	journal	July 2017
Methods for genetic transformation of filamentous fungi Li, Dandan; Tang, Yu; Lin, Jun Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0785-7	journal	October 2017
Engineering yeast artificial core promoter with designated base motifs Liu, Rui; Liu, Lanqing; Li, Xia Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01305-4	journal	February 2020
High-efficient production of mushroom polyketide compounds in a platform host Aspergillus oryzae Han, Haiyan; Yu, Chunyan; Qi, Jianzhao Microbial Cell Factories, Vol. 22, Issue 1 https://doi.org/10.1186/s12934-023-02071-9	journal	March 2023
A GFP-fusion coupling FACS platform for advancing the metabolic engineering of filamentous fungi Wang, Guokun; Jia, Wendi; Chen, Na Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1223-8	journal	August 2018
Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories Cairns, Timothy C.; Zheng, Xiaomei; Zheng, Ping Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1400-4	journal	April 2019
Engineering growth phenotypes of Aspergillus oryzae for L-malate production Zuo, Huiyun; Ji, Lihao; Pan, Jingyu Bioresources and Bioprocessing, Vol. 10, Issue 1 https://doi.org/10.1186/s40643-023-00642-7	journal	April 2023
Efficient gene editing in Neurospora crassa with CRISPR technology Matsu-ura, Toru; Baek, Mokryun; Kwon, Jungin Fungal Biology and Biotechnology, Vol. 2, Issue 1 https://doi.org/10.1186/s40694-015-0015-1	journal	July 2015
Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper Meyer, Vera; Andersen, Mikael R.; Brakhage, Axel A. Fungal Biology and Biotechnology, Vol. 3, Issue 1 https://doi.org/10.1186/s40694-016-0024-8	journal	August 2016
A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi Idnurm, Alexander; Bailey, Andy M.; Cairns, Timothy C. Fungal Biology and Biotechnology, Vol. 4, Issue 1 https://doi.org/10.1186/s40694-017-0035-0	journal	September 2017
How a fungus shapes biotechnology: 100 years of Aspergillus niger research Cairns, Timothy C.; Nai, Corrado; Meyer, Vera Fungal Biology and Biotechnology, Vol. 5, Issue 1 https://doi.org/10.1186/s40694-018-0054-5	journal	May 2018
Development of microtiter plate scale CRISPR/Cas9 transformation method for Aspergillus niger based on in vitro assembled ribonucleoprotein complexes Kuivanen, Joosu; Korja, Veera; Holmström, Sami Fungal Biology and Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1186/s40694-019-0066-9	journal	March 2019
Increasing access to microfluidics for studying fungi and other branched biological structures Millet, Larry J.; Aufrecht, Jayde; Labbé, Jessy Fungal Biology and Biotechnology, Vol. 6, Issue 1 https://doi.org/10.1186/s40694-019-0071-z	journal	June 2019
Growing a circular economy with fungal biotechnology: a white paper Meyer, Vera; Basenko, Evelina Y.; Benz, J. Philipp Fungal Biology and Biotechnology, Vol. 7, Issue 1 https://doi.org/10.1186/s40694-020-00095-z	journal	April 2020
Functional production of human antibody by the filamentous fungus Aspergillus oryzae Huynh, Hung Hiep; Morita, Naoki; Sakamoto, Toshihiro Fungal Biology and Biotechnology, Vol. 7, Issue 1 https://doi.org/10.1186/s40694-020-00098-w	journal	May 2020
Filamentous fungal applications in biotechnology: a combined bibliometric and patentometric assessment Füting, Pamina; Barthel, Lars; Cairns, Timothy C. Fungal Biology and Biotechnology, Vol. 8, Issue 1 https://doi.org/10.1186/s40694-021-00131-6	journal	December 2021
Transformation System for Aspergillus oryzae with Double Auxotrophic Mutations, niaD and sC Yamada, Osamu; Lee, Byung Rho; Gomi, Katsuya Bioscience, Biotechnology, and Biochemistry, Vol. 61, Issue 8 https://doi.org/10.1271/bbb.61.1367	journal	January 1997
Adenine Auxotrophic Mutants ofAspergillus oryzae: Development of a Novel Transformation System with Triple Auxotrophic Hosts Jin, Feng Jie; Maruyama, Jun-ichi; Juvvadi, Praveen Rao Bioscience, Biotechnology, and Biochemistry, Vol. 68, Issue 3 https://doi.org/10.1271/bbb.68.656	journal	January 2004
Molecular and Genetic Studies ofFusariumTrichothecene Biosynthesis: Pathways, Genes, and Evolution Kimura, Makoto; Tokai, Takeshi; Takahashi-Ando, Naoko Bioscience, Biotechnology, and Biochemistry, Vol. 71, Issue 9 https://doi.org/10.1271/bbb.70183	journal	September 2007
A Modular Cloning System for Standardized Assembly of Multigene Constructs Weber, Ernst; Engler, Carola; Gruetzner, Ramona PLoS ONE, Vol. 6, Issue 2 https://doi.org/10.1371/journal.pone.0016765	journal	February 2011
GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I. PLoS ONE, Vol. 6, Issue 7, Article No. e21622 https://doi.org/10.1371/journal.pone.0021622	journal	July 2011
Deletion of the Pichia pastoris KU70 Homologue Facilitates Platform Strain Generation for Gene Expression and Synthetic Biology Näätsaari, Laura; Mistlberger, Beate; Ruth, Claudia PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0039720	journal	June 2012
Functional Analysis of the α-1,3-Glucan Synthase Genes agsA and agsB in Aspergillus nidulans: AgsB Is the Major α-1,3-Glucan Synthase in This Fungus Yoshimi, Akira; Sano, Motoaki; Inaba, Azusa PLoS ONE, Vol. 8, Issue 1 https://doi.org/10.1371/journal.pone.0054893	journal	January 2013
Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40 Umemura, Myco; Koyama, Yoshinori; Takeda, Itaru PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0063673	journal	May 2013
A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi Nødvig, Christina S.; Nielsen, Jakob B.; Kogle, Martin E. PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0133085	journal	July 2015
Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger Song, Letian; Ouedraogo, Jean-Paul; Kolbusz, Magdalena PLOS ONE, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pone.0202868	journal	August 2018
A Versatile and Efficient Gene-Targeting System for Aspergillus nidulans Nayak, Tania; Szewczyk, Edyta; Oakley, C. Elizabeth Genetics, Vol. 172, Issue 3 https://doi.org/10.1534/genetics.105.052563	journal	December 2005
A Centennial: George W. Beadle, 1903–1989 Horowitz, Norman H.; Berg, Paul; Singer, Maxine Genetics, Vol. 166, Issue 1 https://doi.org/10.1534/genetics.166.1.1	journal	January 2004
Understanding interactions between cementitious materials and microorganisms: a key to sustainable and safe concrete structures in various contexts Bertron, Alexandra Materials and Structures, Vol. 47, Issue 11 https://doi.org/10.1617/s11527-014-0433-1	journal	October 2014
A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning Taylor, D. Lee; Hollingsworth, Teresa N.; McFarland, Jack W. Ecological Monographs, Vol. 84, Issue 1 https://doi.org/10.1890/12-1693.1	journal	February 2014
Idempotent Vector Design for Standard Assembly of Biobricks Knight, Tom https://doi.org/10.21236/ADA457791	report	January 2003
Mode of Action, Properties, Production, and Application of Laccase: A Review Patel, Naveen; Shahane, Shraddha Recent Patents on Biotechnology, Vol. 13, Issue 1 https://doi.org/10.2174/1872208312666180821161015	journal	February 2019
Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production Martins-Santana, Leonardo; Nora, Luisa C.; Sanches-Medeiros, Ananda Frontiers in Bioengineering and Biotechnology, Vol. 6 https://doi.org/10.3389/fbioe.2018.00117	journal	October 2018
Build Your Bioprocess on a Solid Strain—β-Carotene Production in Recombinant Saccharomyces cerevisiae López, Javiera; Cataldo, Vicente F.; Peña, Manuel Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00171	journal	July 2019
Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology Zhang, Shangjie; Guo, Feng; Yan, Wei Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00459	journal	January 2020
Genetic Engineering of Filamentous Fungi for Efficient Protein Expression and Secretion Wang, Qin; Zhong, Chao; Xiao, Han Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00293	journal	April 2020
Advances and Opportunities of CRISPR/Cas Technology in Bioengineering Non-conventional Yeasts Shan, Lu; Dai, Zongjie; Wang, Qinhong Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.765396	journal	October 2021
A facile and efficient synthesis approach of salidroside esters by whole-cell biocatalysts in organic solvents Yang, Rongling; Wang, Yu; Zhao, Xiangjie Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.1051117	journal	November 2022
Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi Mózsik, László; Iacovelli, Riccardo; Bovenberg, Roel A. L. Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.901037	journal	July 2022
Making recombinant proteins in filamentous fungi- are we expecting too much? Nevalainen, Helena; Peterson, Robyn Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00075	journal	February 2014
Efficient CRISPR-Cas9 Gene Disruption System in Edible-Medicinal Mushroom Cordyceps militaris Chen, Bai-Xiong; Wei, Tao; Ye, Zhi-Wei Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01157	journal	June 2018
Both Galactosaminogalactan and α-1,3-Glucan Contribute to Aggregation of Aspergillus oryzae Hyphae in Liquid Culture Miyazawa, Ken; Yoshimi, Akira; Sano, Motoaki Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02090	journal	September 2019
TrichoGate: An Improved Vector System for a Large Scale of Functional Analysis of Trichoderma Genes Nogueira-López, Guillermo; Padilla-Arizmendi, Fabiola; Inwood, Sarah Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02794	journal	December 2019
Inhibitory Effects of Eurotium cristatum on Growth and Aflatoxin B1 Biosynthesis in Aspergillus flavus Zhao, Qiannan; Qiu, Yue; Wang, Xin Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00921	journal	May 2020
Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi Jiang, Chunmiao; Lv, Gongbo; Tu, Yayi Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.638096	journal	February 2021
Advances in Genetic Engineering Technology and Its Application in the Industrial Fungus Aspergillus oryzae Jin, Feng-Jie; Hu, Shuang; Wang, Bao-Teng Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.644404	journal	February 2021
Unmasking host and microbial strategies in the Agrobacterium-plant defense tango Hwang, Elizabeth E.; Wang, Melinda B.; Bravo, Janis E. Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00200	journal	March 2015
The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast Ullah, Numan; Shahzad, Khuram; Wang, Mengzhi Biology, Vol. 10, Issue 7 https://doi.org/10.3390/biology10070632	journal	July 2021
Systematic Structure-Based Search for Ochratoxin-Degrading Enzymes in Proteomes from Filamentous Fungi Leitão, Ana Lúcia; Enguita, Francisco J. Biomolecules, Vol. 11, Issue 7 https://doi.org/10.3390/biom11071040	journal	July 2021
Upstream Regulation of Development and Secondary Metabolism in Aspergillus Species Moon, Heungyun; Han, Kap-Hoon; Yu, Jae-Hyuk Cells, Vol. 12, Issue 1 https://doi.org/10.3390/cells12010002	journal	December 2022
Aspergillus nidulans—Natural Metabolites Powerhouse: Structures, Biosynthesis, Bioactivities, and Biotechnological Potential Ghazawi, Kholoud F.; Fatani, Sarah A.; Mohamed, Shaimaa G. A. Fermentation, Vol. 9, Issue 4 https://doi.org/10.3390/fermentation9040325	journal	March 2023
The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species Zhang, Haoran; Zhou, Zengxuan; Guo, Jinhu International Journal of Molecular Sciences, Vol. 25, Issue 5 https://doi.org/10.3390/ijms25052574	journal	February 2024
Aspergillus oryzae as a Cell Factory: Research and Applications in Industrial Production Sun, Zeao; Wu, Yijian; Long, Shihua Journal of Fungi, Vol. 10, Issue 4 https://doi.org/10.3390/jof10040248	journal	March 2024
Function and Biosynthesis of Cell Wall α-1,3-Glucan in Fungi Yoshimi, Akira; Miyazawa, Ken; Abe, Keietsu Journal of Fungi, Vol. 3, Issue 4 https://doi.org/10.3390/jof3040063	journal	November 2017
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes Basenko, Evelina; Pulman, Jane; Shanmugasundram, Achchuthan Journal of Fungi, Vol. 4, Issue 1 https://doi.org/10.3390/jof4010039	journal	March 2018
Agrobacterium tumefaciens-Mediated Transformation of NHEJ Mutant Aspergillus nidulans Conidia: An Efficient Tool for Targeted Gene Recombination Using Selectable Nutritional Markers Casado-del Castillo, Virginia; MacCabe, Andrew P.; Orejas, Margarita Journal of Fungi, Vol. 7, Issue 11 https://doi.org/10.3390/jof7110961	journal	November 2021
CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species Jin, Feng-Jie; Wang, Bao-Teng; Wang, Zhen-Dong Journal of Fungi, Vol. 8, Issue 5 https://doi.org/10.3390/jof8050467	journal	April 2022
A Mad7 System for Genetic Engineering of Filamentous Fungi Vanegas, Katherina Garcia; Rendsvig, Jakob Kræmmer Haar; Jarczynska, Zofia Dorota Journal of Fungi, Vol. 9, Issue 1 https://doi.org/10.3390/jof9010016	journal	December 2022
Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review Wang, Duoduo; Jin, Shunda; Lu, Qianhui Journal of Fungi, Vol. 9, Issue 3 https://doi.org/10.3390/jof9030362	journal	March 2023
Platforms for High-Throughput Screening and Force Measurements on Fungi and Oomycetes Sun, Yiling; Tayagui, Ayelen; Sale, Sarah Micromachines, Vol. 12, Issue 6 https://doi.org/10.3390/mi12060639	journal	May 2021
Filamentous Fungal Human Pathogens from Food Emphasising Aspergillus, Fusarium and Mucor Paterson, R.; Lima, Nelson Microorganisms, Vol. 5, Issue 3 https://doi.org/10.3390/microorganisms5030044	journal	August 2017
The Fungi: 1, 2, 3 … 5.1 million species? Blackwell, Meredith American Journal of Botany, Vol. 98, Issue 3 https://doi.org/10.3732/ajb.1000298	journal	March 2011
Neurospora crassa: Looking back and looking forward at a model microbe Roche, C. M.; Loros, J. J.; McCluskey, K. American Journal of Botany, Vol. 101, Issue 12 https://doi.org/10.3732/ajb.1400377	journal	November 2014
Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus Boysen, Jana M.; Saeed, Nauman; Hillmann, Falk Beilstein Journal of Organic Chemistry, Vol. 17 https://doi.org/10.3762/bjoc.17.124	journal	July 2021
Optimized primers and other critical conditions for efficient fusion PCR to generate knockout vectors in filamentous fungi. Harrison, Nicholas; Cavinder, Brad; Townsend, Jeffrey P. Fungal Genetics Reports, Vol. 60, Issue 1 https://doi.org/10.4148/1941-4765.1006	journal	December 2013
The use of Ignite (Basta;glufosinate;phosphinothricin) to select transformants of bar-containing plasmids in Neurospora crassa Pall, Martin L. Fungal Genetics Reports, Vol. 40, Issue 1 https://doi.org/10.4148/1941-4765.1412	journal	January 1993
Versatile fungal transformation vectors carrying the selectable bar gene of Streptomyces hygroscopicus Straubinger, B.; Straubinger, E.; Wirsel, S. Fungal Genetics Reports, Vol. 39, Issue 1 https://doi.org/10.4148/1941-4765.1441	journal	January 1992
Fungal Bioconversion of Lignocellulosic Residues; Opportunities & Perspectives Dashtban, Mehdi; Schraft, Heidi; Qin, Wensheng International Journal of Biological Sciences, Vol. 5, Issue 6, p. 578-595 https://doi.org/10.7150/ijbs.5.578	journal	January 2009

Similar Records

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Journal Article · Sat Jan 21 00:00:00 UTC 2023 · Materials Today Bio · OSTI ID:1958544

Jo, Charles; Zhang, Jing; Tam, Jenny M.; +4 more

From the bench to the reactor: engineered filamentous fungi for biochemical and biomaterial production

Journal Article · Tue Nov 18 00:00:00 UTC 2025 · Biotechnology for Biofuels and Bioproducts · OSTI ID:3014851

Subramanian, Venkataramanan; Adler, Meaghan J.; Benyamin, Marcus; +4 more

Genomic Prospecting for Microbial Biodiesel Production

Book · Thu Mar 20 04:00:00 UTC 2008 · OSTI ID:929410

Lykidis, Athanasios; Lykidis, Athanasios; Ivanova, Natalia

Related Subjects

09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
biological databases
filamentous fungi
fungi
genetics
genomics
microbial cell factory
molecular biology
peptides and proteins
synthetic biology

Title: Considerations for Domestication of Novel Strains of Filamentous Fungi

Citation Formats

References (272)

Similar Records

Related Subjects