Filamentous fungi are used in a variety of industrial processes including the production of primary metabolites (e.g., organic acid, vitamins, and extracellular enzymes) and secondary metabolites (e.g., antibiotics, alkaloids, and gibberellins). Moreover, filamentous fungi have become preferred cell factories for production of foreign (heterologous) proteins in biotechnology in recent years. Compared to bacterial and yeast hosts, filamentous fungi showed predominant features such as the ability of growing on rather simple and inexpensive substrates, producing and secreting exceptionally large amounts of proteins, post-translational modifications, and GRAS (generally regarded as safe) approval. Therefore, the exploration of filamentous fungi has been attractive recently. This review summarizes the recent development in genomics, comparative genomics, transcriptomics, proteomics and metabolomics of filamentous fungi, and describes their applications and functions in reconstruction of metabolic network, discovery of novel proteins and genes, investigation of cell physiological and biochemical reactions, and strain breeding. This review also analyzes the bottlenecks of heterologous protein expression in filamentous fungi. Furthermore, special emphasis is given on the strategies for improving the protein production, including fusion expression of heterologous proteins, RNAi technology, manipulations of secretion pathways, codon optimization of foreign genes, and screening of protease mutants. Lastly, this review proposes the future direction of meta-bolic engineering of filamentous fungi.
[1] Adrio JL, Demain AL. Fungal biotechnology. Int Microbiol, 2003, 6(3): 191-199.
[2] Fleiβner A, Dersch P. Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol, 2010, 87(4): 1255-1270.
[3] Cherry JR, Fidantsef AL. Directed evolution of industrial enzymes: an update. Curr Opin Biotechnol, 2003, 14(4): 438-443.
[4] Ward OP, Qin WM, Hanjoon J, Ye J, Singh A. Physiology and biotechnology of Aspergillus. Adv Appl Microbiol, 2006, 58(1): 1-75.
[5] Karnaukhova E, Ophir Y, Trinh L, Dalal N, Punt PJ, Golding B, Shiloach J. Expression of human α1-proteinase inhibitor in Aspergillus niger. Microb Cell Fact, 2007, 6: 34.
[6] 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, Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol, 2007, 25(2): 221-231.
[7] Clutterbuck AJ. The validity of the Aspergillus nidulans linkage map. Fungal Genet Biol, 1997, 21(3): 267-277.
[8] Monsanto. 2001, Microbial Sequence Database, http://microbial.cereon.com.
[9] Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Ba?türkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Birren BW. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 2005, 438(7071): 1105-1115.
[10] Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto KI, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kikuchi H. Genome sequencing and analysis of Aspergillus oryzae. Nature, 2005, 438(7071): 1157-1161.
[11] Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Barrell B, Denning DW. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature, 2005, 438(7071): 1151-1156.
[12] Jones MG. The first filamentous fungal genome sequences: Aspergillus leads the way for essential everyday resources or dusty museum specimens? Microbiology, 2007, 153(1): 1-6.
[13] Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Brettin TS. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol, 2008, 26(5): 553-560.
[14] Brakhage AA, Schroeckh V. Fungal secondary metabolites-strategies to activate silent gene clusters. Fungal Genet Biol, 2010, 48(1): 15-22.
[15] Lopez M, Edens L. Effective prevention of chillhaze in beer using an acid proline-specific endoprotease from Aspergillus niger. J Agric Food Chem, 2005, 53(20): 7944-7949.
[16] Edens L, Dekker P, van der Hoeven R, Deen F, de Roos A, Floris R. Extracellular prolyl endoprotease from Aspergillus niger and its use in the debittering of protein hydrolysates. J Agric Food Chem, 2005, 53(20): 7950-7957.
[17] Kobayashi T, Abe K, Asai K, Gomi K, Juvvadi PR, Kato M, Kitamoto K, Takeuchi M, Machida M. Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem, 2007, 71(3): 646-670.
[18] David H, Özçelik IS, Hofmann G, Nielsen J. Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics, 2008, 9: 163.
[19] Pinchuk GE, Rodionov DA, Yang C, Li XQ, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci USA, 2009, 106(8): 2874-2879.
[20] Yang C, Rodi
