Comparison and analysis of the genomes of two aspergillus oryzae strains

Journal of Agricultural and Food Chemistry

Volumn 61, Issue 32, 2013, Pages 7805-7809

  Zhao, Guozhong ^a,b   Yao, Yunping ^a   Chen, Wei ^a   Cao, Xiaohong ^b  

^a JIANGNAN UNIVERSITY   (China)

^b TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

A. oryzae; comparative genomic; energy; flavor; mycelial growth

Indexed keywords

A. ORYZAE; COMPARATIVE GENOMIC; COMPARISON AND ANALYSIS; ENERGY; ENVIRONMENTAL STRESS; MYCELIAL GROWTH; PROTEIN-CODING GENES; REGIONAL DIFFERENCES;

ASPERGILLUS; FLAVORS; GENETIC ENGINEERING; METABOLISM; SIGNAL TRANSDUCTION;

GENES;

FUNGAL PROTEIN;

ARTICLE; ASPERGILLUS ORYZAE; COMPARATIVE STUDY; DNA SEQUENCE; FUNGAL GENOME; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ASPERGILLUS ORYZAE; BASE SEQUENCE; FUNGAL PROTEINS; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

EID: 84881627784     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf400080g     Document Type: Article

References (42)

1. Zhao, G.; Yao, Y.; Wang, X.; Hou, L.; Wang, C.; Cao, X. Functional properties of soy sauce and metabolism genes of strains for fermentation Int. J. Food Sci. Technol. 2012, 48, 903-909
2. Zhao, G.; Hou, L.; Yao, Y.; Wang, C.; Cao, X. Comparative proteome analysis of Aspergillus oryzae 3.042 and A. oryzae 100-8 strains: Towards the production of different soy sauce flavors J. Proteomics 2012, 75, 3914-3924
3. Machida, M.; Asai, K.; Sano, M.; Tanaka, T.; Kumagai, T.; Terai, G.; Kusumoto, K.-I.; Arima, T.; Akita, O.; Kashiwagi, Y. Genome sequencing and analysis of Aspergillus oryzae Nature 2005, 438, 1157-1161
4. Puente, X. S.; Sánchez, L. M.; Overall, C. M.; López-Otín, C. Human and mouse proteases: a comparative genomic approach Nat. Rev. Genet. 2003, 4, 544-558
5. Wang, B.; Guo, G.; Wang, C.; Lin, Y.; Wang, X.; Zhao, M.; Guo, Y.; He, M.; Zhang, Y.; Pan, L. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing Nucleic Acids Res. 2010, 38, 5075-5087
6. Zhao, G.; Hou, L.; Lu, M.; Wei, Y.; Zeng, B.; Wang, C.; Cao, X. Construction of the mutant strain in Aspergillus oryzae 3.042 for abundant proteinase production by the Nion implantation mutagenesis Int. J. Food Sci. Technol. 2012, 47, 504-510
7. Murakami, K.; Ishida, Y.; Masaki, A.; Tatsumi, H.; Murakami, S.; Nakano, E.; Motai, H.; Kawabe, H.; Arimura, H. Isolation and characterization of the alkaline protease gene of Aspergillus oryzae Agric. Biol. Chem. 1991, 55, 2807
8. Mardis, E. R. Next-generation DNA sequencing methods Annu. Rev. Genomics Hum. Genet. 2008, 9, 387-402
9. Chaisson, M. J.; Pevzner, P. A. Short read fragment assembly of bacterial genomes Genome Res. 2008, 18, 324
10. Li, R.; Li, Y.; Kristiansen, K.; Wang, J. SOAP: short oligonucleotide alignment program Bioinformatics 2008, 24, 713
11. Stanke, M.; Sch ffmann, O.; Morgenstern, B.; Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources BMC Bioinf. 2006, 7, 62
12. Haas, B. J.; Salzberg, S. L.; Zhu, W.; Pertea, M.; Allen, J. E.; Orvis, J.; White, O.; Buell, C. R.; Wortman, J. R. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Genome Biol. 2008, 9, R7
13. Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results J. Am. Soc. Mass Spectrom. 2002, 13, 378-386
14. Schattner, P.; Brooks, A. N.; Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs Nucleic Acids Res. 2005, 33, W686-W689
15. Zhao, G.; Yao, Y.; Qi, W.; Wang, C.; Hou, L.; Zeng, B.; Cao, X. Draft genome sequence of Aspergillus oryzae strain 3.042 Eukaryotic Cell 2012, 11, 1178-1178
16. Delcher, A. L.; Salzberg, S. L.; Phillippy, A. M. Using MUMmer to identify similar regions in large sequence sets Curr. Protoc. Bioinf. 2003, 10.3.1-10.3.18
17. Li, L.; Stoeckert, C. J.; Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes Genome Res. 2003, 13, 2178-2189
18. Motteram, J.; Küfner, I.; Deller, S.; Brunner, F.; Hammond-Kosack, K. E.; Nürnberger, T.; Rudd, J. J. Molecular characterization and functional analysis of MgNLP, the sole NPP1 domain-containing protein, from the fungal wheat leaf pathogen Mycosphaerella graminicola Mol. Plant-Microbe Interact. 2009, 22, 790-799
19. Mosavi, L. K.; Cammett, T. J.; Desrosiers, D. C.; Peng, Z. y. The ankyrin repeat as molecular architecture for protein recognition Protein Sci. 2004, 13, 1435-1448
20. Kanemaki, M.; Makino, Y.; Yoshida, T.; Kishimoto, T.; Koga, A.; Yamamoto, K.; Yamamoto, M.; Moncollin, V.; Egly, J.-M.; Muramatsu, M. Molecular cloning of a rat 49-kDa TBP-interacting protein (TIP49) that is highly homologous to the bacterial RuvB Biochem. Biophys. Res. Commun. 1997, 235, 64-68
21. von der Haar, T.; Tuite, M. F. Regulated translational bypass of stop codons in yeast Trends Microbiol. 2007, 15, 78-86
22. Simon, M. A.; Bowtell, D. D.; Dodson, G. S.; Laverty, T. R.; Rubin, G. M. Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase Cell 1991, 67, 701-716
23. Wang, S.-W.; Toda, T.; MacCallum, R.; Harris, A. L.; Norbury, C. Cid1, a fission yeast protein required for SM checkpoint control when DNA polymerase δ or ε is inactivated Mol. Cell. Biol. 2000, 20, 3234-3244
24. Van Damme, M.; Huibers, R. P.; Elberse, J.; Van den Ackerveken, G. Arabidopsis DMR6 encodes a putative 2OG-Fe (II) oxygenase that is defense-associated but required for susceptibility to downy mildew Plant J. 2008, 54, 785-793
25. Ishikawa, J.; Yamashita, A.; Mikami, Y.; Hoshino, Y.; Kurita, H.; Hotta, K.; Shiba, T.; Hattori, M. The complete genomic sequence of Nocardia farcinica IFM 10152 Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14925
26. Prins, T. W.; Wagemakers, L.; Schouten, A.; Van Kan, J. A. L. Cloning and characterization of a glutathione S-transferase homologue from the plant pathogenic fungus Botrytis cinerea Mol. Plant Pathol. 2000, 1, 169-178
27. Yamano, S.; Shibata, M.; Kita, H.; Matsusue, K.; Narimatsu, S.; Taguchi, K.; Kumagai, Y. Two-electron quinone reductase (aldo-keto reductase 1C isozyme) augments the oxidative DNA damage induced by quinones in diesel exhaust particles by accelerating redox cycling J. Health Sci. 2011, 57, 107-114
28. Yin, W. B.; Amaike, S.; Wohlbach, D. J.; Gasch, A. P.; Chiang, Y. M.; Wang, C. C. C.; Bok, J. W.; Rohlfs, M.; Keller, N. P. An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR Mol. Microbiol. 2012, 83, 1024-1034
29. Arite, T.; Umehara, M.; Ishikawa, S.; Hanada, A.; Maekawa, M.; Yamaguchi, S.; Kyozuka, J. d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers Plant Cell Physiol. 2009, 50, 1416
30. Keller, N. P.; Turner, G.; Bennett, J. W. Fungal secondary metabolism-from biochemistry to genomics Nat. Rev. Microbiol. 2005, 3, 937-947
31. Jakoby, M.; Weisshaar, B.; Dröge-Laser, W.; Vicente-Carbajosa, J.; Tiedemann, J.; Kroj, T.; Parcy, F. bZIP transcription factors in Arabidopsis Trends Plant Sci. 2002, 7, 106-111
32. Xu, J.; James, R. Temperature stress affects the expression of immune response genes in the alfalfa leafcutting bee Megachile rotundata Insect Mol. Biol. 2012, 21, 269-280
33. Hatefi, Y. The mitochondrial electron transport and oxidative phosphorylation system Annu. Rev. Biochem. 1985, 54, 1015-1069
34. Zhu, X.; Yuasa, M.; Okada, K.; Suzuki, K.; Nakagawa, T.; Kawamukai, M.; Matsuda, H. Production of ubiquinone in Escherichia coli by expression of various genes responsible for ubiquinone biosynthesis J. Ferment. Bioeng. 1995, 79, 493-495
35. Manzano, C.; Candau, P.; Gomez-Moreno, C.; Relimpio, A.; Losada, M. Ferredoxin-dependent photosynthetic reduction of nitrate and nitrite by particles of Anacystis nidulans Mol. Cell. Biochem. 1976, 10, 161-169
36. Deckers-Hebestreit, G.; Altendorf, K. The F0F1-type ATP synthases of bacteria: structure and function of the F0 complex Annu. Rev. Microbiol. 1996, 50, 791-824
37. Zhu, J. K. Genetic analysis of plant salt tolerance using Arabidopsis Plant Physiol. 2000, 124, 941
38. Castellen, P.; Wassem, R.; Monteiro, R. A.; Cruz, L. M.; Steffens, M. B. R.; Chubatsu, L. S.; Maltempi de Souza, E.; Pedrosa, F. d. O. Structural organization of the glnBA region of the Azospirillum brasilense genome Eur. J. Soil Biol. 2009, 45, 100-105
39. Maltseva, O. V.; Solyanikova, I. P.; Golovleva, L. A.; Schlömann, M.; Knackmuss, H.-J. Dienelactone hydrolase from Rhodococcus erythropolis 1 CP: purification and properties Arch. Microbiol. 1994, 162, 368-374
40. Amorim, H. V.; Basso, L. C.; Crocomo, O. J.; Teixeira, A. A. Polyamines in green and roasted coffee J. Agric. Food Chem. 1977, 25, 957-958
41. Walters, D. R. Inhibition of polyamine biosynthesis in fungi Mycol. Res. 1995, 99, 129-139
42. Croteau, R.; Purkett, P. T. Geranyl pyrophosphate synthase: Characterization of the enzyme and evidence that this chain-length specific prenyltransferase is associated with monoterpene biosynthesis in sage (Salvia officinalis) Arch. Biochem. Biophys. 1989, 271, 524-535