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Umemura M, Koike H, Nagano N, Ishii T, Kawano J, Yamane N, Kozone I, Horimoto K, Shin-ya K, Asai K, Yu J, Bennett JW, Machida M. MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data. PLoS One 2013; 8:e84028. [PMID: 24391870 PMCID: PMC3877130 DOI: 10.1371/journal.pone.0084028] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022] Open
Abstract
Many bioactive natural products are produced as “secondary metabolites” by plants, bacteria, and fungi. During the middle of the 20th century, several secondary metabolites from fungi revolutionized the pharmaceutical industry, for example, penicillin, lovastatin, and cyclosporine. They are generally biosynthesized by enzymes encoded by clusters of coordinately regulated genes, and several motif-based methods have been developed to detect secondary metabolite biosynthetic (SMB) gene clusters using the sequence information of typical SMB core genes such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). However, no detection method exists for SMB gene clusters that are functional and do not include core SMB genes at present. To advance the exploration of SMB gene clusters, especially those without known core genes, we developed MIDDAS-M, a motif-independent de novodetection algorithm for SMB gene clusters. We integrated virtual gene cluster generation in an annotated genome sequence with highly sensitive scoring of the cooperative transcriptional regulation of cluster member genes. MIDDAS-M accurately predicted 38 SMB gene clusters that have been experimentally confirmed and/or predicted by other motif-based methods in 3 fungal strains. MIDDAS-M further identified a new SMB gene cluster for ustiloxin B, which was experimentally validated. Sequence analysis of the cluster genes indicated a novel mechanism for peptide biosynthesis independent of NRPS. Because it is fully computational and independent of empirical knowledge about SMB core genes, MIDDAS-M allows a large-scale, comprehensive analysis of SMB gene clusters, including those with novel biosynthetic mechanisms that do not contain any functionally characterized genes.
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Affiliation(s)
- Myco Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Hideaki Koike
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Nozomi Nagano
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Tomoko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Jin Kawano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Noriko Yamane
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan
| | - Katsuhisa Horimoto
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Kazuo Shin-ya
- Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Kiyoshi Asai
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan
| | - Jiujiang Yu
- Beltsville Agricultural Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Joan W. Bennett
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Masayuki Machida
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
- * E-mail:
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Yan YZ, Qian YL, Ji FD, Chen JY, Han BZ. Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods. Food Microbiol 2013; 34:189-95. [PMID: 23498197 DOI: 10.1016/j.fm.2012.12.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/10/2012] [Accepted: 12/27/2012] [Indexed: 01/06/2023]
Abstract
Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product.
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Affiliation(s)
- Yin-zhuo Yan
- College of Food Science and Nutritional Engineering, China Agricultural University, P.O. Box 398, No. 17, Qinghua East Road, Haidian District, Beijing 100083, China
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Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, Kikuzato I, Teruya M, Tsukahara M, Imada Y, Wachi Y, Miwa Y, Yano S, Tamano K, Kawarabayasi Y, Fujimori KE, Machida M, Hirano T. Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species. DNA Res 2012; 19:375-82. [PMID: 22912434 PMCID: PMC3473370 DOI: 10.1093/dnares/dss019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and compared the data with those of A. oryzae RIB40, a wild-type strain sequenced in 2005. The aim of this study was to evaluate the mutation pressure on the non-syntenic blocks (NSBs) of the genome, which were previously identified through comparative genomic analysis of A. oryzae, Aspergillus fumigatus, and Aspergillus nidulans. We found that genes within the NSBs of RIB326 accumulate mutations more frequently than those within the SBs, regardless of their distance from the telomeres or of their expression level. Our findings suggest that the high mutation frequency of NSBs might contribute to maintaining the diversity of the A. oryzae genome.
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Affiliation(s)
- Myco Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Nijo 17-2-1, Tsukisamu, Sapporo, Hokkaido 062-8517, Japan
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Rank C, Klejnstrup ML, Petersen LM, Kildgaard S, Frisvad JC, Held Gotfredsen C, Ostenfeld Larsen T. Comparative Chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357). Metabolites 2012; 2:39-56. [PMID: 24957367 PMCID: PMC3901201 DOI: 10.3390/metabo2010039] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/14/2011] [Accepted: 12/22/2011] [Indexed: 12/29/2022] Open
Abstract
Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence in the secondary metabolite production. In this study we report on the first comparison of secondary metabolite production between the full genome sequenced strains of A. oryzae (RIB40) and A. flavus (NRRL 3357). Surprisingly, the overall chemical profiles of the two strains were mostly very different across 15 growth conditions. Contrary to previous studies we found the aflatrem precursor 13-desoxypaxilline to be a major metabolite from A. oryzae under certain growth conditions. For the first time, we additionally report A. oryzae to produce parasiticolide A and two new analogues hereof, along with four new alkaloids related to the A. flavus metabolites ditryptophenalines and miyakamides. Generally the secondary metabolite capability of A. oryzae presents several novel end products likely to result from the domestication process from A. flavus.
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Affiliation(s)
- Christian Rank
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Marie Louise Klejnstrup
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Lene Maj Petersen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Sara Kildgaard
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Jens Christian Frisvad
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Charlotte Held Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet B201, DK-2800 Kgs. Lyngby, Denmark.
| | - Thomas Ostenfeld Larsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
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Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y. Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. DNA Res 2011; 18:165-76. [PMID: 21659486 PMCID: PMC3111232 DOI: 10.1093/dnares/dsr009] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.
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Affiliation(s)
- Atsushi Sato
- Research and Development Division, Kikkoman Corporation, 399 Noda, Noda City, Chiba 278-0037, Japan
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Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin SB, Oliver RP. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 2011; 12:R45. [PMID: 21605470 PMCID: PMC3219968 DOI: 10.1186/gb-2011-12-5-r45] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 04/27/2011] [Accepted: 05/24/2011] [Indexed: 12/20/2022] Open
Abstract
Background Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa. Results These analyses identified a novel form of evolution in which genes are conserved within homologous chromosomes, but with randomized orders and orientations. This mode of evolution is designated mesosynteny, to differentiate it from micro- and macrosynteny seen in other organisms. Mesosynteny is an alternative evolutionary pathway very different from macrosyntenic conservation. Surprisingly, mesosynteny was not found in all fungal groups. Instead, mesosynteny appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes. Conclusions The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis.
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Affiliation(s)
- James K Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia
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Bhetariya PJ, Madan T, Basir SF, Varma A, Usha SP. Allergens/Antigens, toxins and polyketides of important Aspergillus species. Indian J Clin Biochem 2011; 26:104-19. [PMID: 22468035 PMCID: PMC3107401 DOI: 10.1007/s12291-011-0131-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 04/15/2011] [Indexed: 12/11/2022]
Abstract
The medical, agricultural and biotechnological importance of the primitive eukaryotic microorganisms, the Fungi was recognized way back in 1920. Among various groups of fungi, the Aspergillus species are studied in great detail using advances in genomics and proteomics to unravel biological and molecular mechanisms in these fungi. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Aspergillus nidulans and Aspergillus terreus are some of the important species relevant to human, agricultural and biotechnological applications. The potential of Aspergillus species to produce highly diversified complex biomolecules such as multifunctional proteins (allergens, antigens, enzymes) and polyketides is fascinating and demands greater insight into the understanding of these fungal species for application to human health. Recently a regulator gene for secondary metabolites, LaeA has been identified. Gene mining based on LaeA has facilitated new metabolites with antimicrobial activity such as emericellamides and antitumor activity such as terrequinone A from A. nidulans. Immunoproteomic approach was reported for identification of few novel allergens for A. fumigatus. In this context, the review is focused on recent developments in allergens, antigens, structural and functional diversity of the polyketide synthases that produce polyketides of pharmaceutical and biological importance. Possible antifungal drug targets for development of effective antifungal drugs and new strategies for development of molecular diagnostics are considered.
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Affiliation(s)
- Preetida J. Bhetariya
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012 India
| | - Taruna Madan
- National Institute for Research in Reproductive Health (NIRRH), Parel, Mumbai, 400012 India
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Anupam Varma
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012 India
| | - Sarma P. Usha
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012 India
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Affiliation(s)
- P Usha Sarma
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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Cleveland TE, Yu J, Fedorova N, Bhatnagar D, Payne GA, Nierman WC, Bennett JW. Potential of Aspergillus flavus genomics for applications in biotechnology. Trends Biotechnol 2009; 27:151-7. [PMID: 19195728 DOI: 10.1016/j.tibtech.2008.11.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 11/18/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
Abstract
Aspergillus flavus is a common saprophyte and opportunistic pathogen that produces numerous secondary metabolites. The primary objectives of the A. flavus genomics program are to reduce and eliminate aflatoxin contamination in food and feed and to discover genetic factors that contribute to plant and animal pathogenicity. A. flavus expressed sequence tags (ESTs) and whole-genome sequencing have been completed. Annotation of the A. flavus genome has revealed numerous genes and gene clusters that are potentially involved in the formation of aflatoxin and other secondary metabolites, as well as in the degradation of complex carbohydrate polymers. Analysis of putative secondary metabolism pathways might facilitate the discovery of new compounds with pharmaceutical properties, as well as new enzymes for biomass degradation.
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Affiliation(s)
- Thomas E Cleveland
- United States Department of Agriculture, Agricultural Research Service (USDA/ARS), Southern Regional Research Center, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA.
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