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Genomics of Industrial Aspergilli and Comparison with Toxigenic Relatives

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Genomics of Industrial Aspergilli and Comparison with Toxigenic Relatives This article was downloaded by: [USDA National Agricultural Library] On: 19 November 2008 Access details: Access Details: [subscription number 789040948] Publisher Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Food Additives & Contaminants: Part A Publication details, including instructions for authors and subscription information: http://www.informaworld.com/smpp/title~content=t713599661 Genomics of industrial Aspergilli and comparison with toxigenic relatives Masayuki Machida ab; Yoshinobu Terabayashi a; Motoaki Sano b; Noriko Yamane a; Koichi Tamano a; Gary A. Payne c; Jiujiang Yu d; Thomas E. Cleveland d; William C. Nierman ef a Research Institute of Cell Engineering, National Institute of Advanced Industrial Science and Technologies (AIST), Tsukuba, Ibaraki 305-8566, Japan b Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Hakusan, Ishikawa 924-0838, Japan c Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA d USDA/ARS, Southern Regional Research Center, New Orleans, LA 70124, USA e The Institute for Genomic Research, Rockville, MD 20850, USA f Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, DC 20037, USA Online Publication Date: 01 September 2008 To cite this Article Machida, Masayuki, Terabayashi, Yoshinobu, Sano, Motoaki, Yamane, Noriko, Tamano, Koichi, Payne, Gary A., Yu, Jiujiang, Cleveland, Thomas E. and Nierman, William C.(2008)'Genomics of industrial Aspergilli and comparison with toxigenic relatives',Food Additives & Contaminants: Part A,25:9,1147 — 1151 To link to this Article: DOI: 10.1080/02652030802273114 URL: http://dx.doi.org/10.1080/02652030802273114 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.informaworld.com/terms-and-conditions-of-access.pdf This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. Food Additives and Contaminants Vol. 25, No. 9, September 2008, 1147–1151 Genomics of industrial Aspergilli and comparison with toxigenic relatives Masayuki Machidaab*, Yoshinobu Terabayashia, Motoaki Sanob, Noriko Yamanea, Koichi Tamanoa, Gary A. Paynec, Jiujiang Yud, Thomas E. Clevelandd and William C. Niermanef aResearch Institute of Cell Engineering, National Institute of Advanced Industrial Science and Technologies (AIST), Central 6, 1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; bGenome Biotechnology Laboratory, Kanazawa Institute of Technology, Yatsukaho 3-1, Hakusan, Ishikawa 924-0838, Japan; cDepartment of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; dUSDA/ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA; eThe Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA; fDepartment of Biochemistry and Molecular Biology, The George Washington University School of Medicine, 2300 Eye Street NW, Washington, DC 20037, USA (Received 21 June 2007; final version received 12 June 2008) Aspergillus oryzae has been used in Japanese fermentation industries for more than a thousand years. The species produces large amounts of various hydrolytic enzymes and has been successfully applied to modern biotechnology. The size of the A. oryzae genome (37.5 Mb) is very close to that of A. flavus and A. niger, and 20–30% larger than that of either A. nidulans or A. fumigatus. A. oryzae and A. flavus have exactly the same number of aspartic proteinase genes, of which each orthologous pair shares highly conserved amino acid sequences. Synteny analysis with A. fumigatus and A. nidulans showed that the A. oryzae genome has a mosaic structure consisting of syntenic and non-syntenic blocks. In the microorganisms to be compared, the density of the genes having homologs was obviously higher on the syntenic than on the non-syntenic blocks. Expression analysis by the DNA microarray supported the significantly lower expression of genes on the non-syntenic than on the syntenic blocks. Keywords: fermentation industry; secondary metabolism; non-syntenic blocks Introduction Characteristics of the A. oryzae genome and genes Aspergillus oryzae has been used in Japanese fermenta- The eight chromosomes of the A. oryzae genome (sizes: tion industries, such as sake (Japanese alcohol 6.3, 6.2, 5.0, 4.8, 4.4, 4.1 and 3.4 Mb, including 0.7-Mb beverage), miso (soy bean paste), shoyu (soy sauce) rDNA repeats, and 3.3 Mb for chromosomes I–VIII, and su (vinegar) production, for more than a thousand respectively) have been sequenced (Machida et al. years. A. oryzae produces large amounts of various 2005). Centromeric sequences have not yet been hydrolytic enzymes including amylases and proteinases. obtained owing to unsuccessful cloning of the centro- A. oryzae has also found application in modern meric fragments, probably due to the extremely high biotechnology owing to its high secretory production AT-content and/or DNA curvature (Bechert et al. of proteins and enzymes. The extensive use of A. oryzae 1999). The A. oryzae genome has a remarkably large Downloaded By: [USDA National Agricultural Library] At: 13:11 19 November 2008 in the food fermentation industries over many years has number of AT-rich sequences; 1750 AT-stretches of prompted its industrial applications to be listed as 490% ATs longer than 50 b and 433 A/T-stretches of generally recognized as safe (GRAS) by the US Food 20 b, which are 5–9-fold and 2–4-fold larger than and Drug Administration (USFDA) (Tailor and those of A. fumigatus and A. nidulans, respectively. The Richardson 1979). The World Health Organization A. oryzae genome size (37.5 Mb) is very close in size to (WHO) also considers this organism safe (FAO/WHO that of A. flavus and A. niger (Archer and Dyer 2004), 1987). The genome sequencing of A. oryzae RIB40 and 20–30% larger than that of either A. nidulans (National Research Institute Culture Stock; (Galagan et al. 2005) or A. fumigatus (Nierman et al. ATCC42149) was completed in 2005. A. oryzae RIB40 2005). The total number of A. oryzae genes longer than is a wild-type strain, closely related to the strain used for 100 amino acids predicted by GeneDecoder (Asai et al. sake-brewing, but with a high capacity for the produc- 1998) and GlimmerM (Majoros et al. 2003), taking the tion of proteinases, which is an important characteristic large number of ESTs into consideration, has reached for soy sauce fermentation. 12 074. Thus, the average gene density is 3.1 kb/gene, *Corresponding author. Email: [email protected] ISSN 0265–203X print/ISSN 1464–5122 online ß 2008 Taylor & Francis DOI: 10.1080/02652030802273114 http://www.informaworld.com 1148 M. Machida et al. which is approximately 1.6-times less dense than that amino acid catabolism, in addition to the protease genes of S. cerevisiae (2 kb/gene) (Goffeau et al. 1996; described below, might be expanded to ensure effective Goffeau et al. 1997). utilization of external nitrogen sources in the raw A. oryzae possesses the largest number of genes materials. of the three Aspergilli, A. oryzae, A. fumigatus and A. nidulans. A comparison of the number of genes in each cluster of orthologous group’s (COG) functional Synteny and genomic expansion category between the two species indicated that most of Synteny analysis showed that the genomes of the three the genes expanded in the A. oryzae genome belong to Aspergilli, A. oryzae, A. fumigatus and A. nidulans, metabolism (C, G, E, F, H, I, P and Q), of which Q shared overall conserved synteny (Galagan et al. 2005; (secondary metabolism) genes are the most significant Machida et al. 2005). Furthermore, in addition to the (Machida et al., 2005). Some expansion was also evident segments common to all three Aspergilli, the A. oryzae in Y (nuclear structure) and V (defense mechanisms) genome has non-syntenic DNA segments specific to genes. Considering the distribution of the expanded A. oryzae, resulting in a mosaic structure consisting of genes and the absolute number of genes in terms of the two blocks of different character in terms of synteny. COG category, the expansion of metabolic genes There are two possible scenarios generating close contributes most to the expansion of the total gene relatives of different genome sizes through evolution number in A. oryzae. These observations are consistent (Figure 1). In the first, the ancestor common to the three with the previous suggestion, based on the comparison Aspergilli might have had a small genome size, similar between eubacterial and archaeal genomes, that meta- to A. fumigatus and A. nidulans, and A. oryzae might bolic flexibility may depend on genome size (Deckert have acquired genetic material during evolution. In the et al. 1998). The most highly expanded genes in metabolic pathways are
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