Comparative genomic analysis of Aspergillus oryzae strains 3.042 and RIB40 for soy sauce fermentation

International Journal of Food Microbiology

Volumn 164, Issue 2-3, 2013, Pages 148-154

  Zhao, Guozhong ^a   Yao, Yunping ^b   Wang, Chunling ^a   Hou, Lihua ^a   Cao, Xiaohong ^a  

^a TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b JIANGNAN UNIVERSITY   (China)

Author keywords

Aspergillus oryzae; Cell growth; Flavor; Genome comparison; Salt tolerance

Indexed keywords

AMINO ACID;

AMINO ACID METABOLISM; ARTICLE; ASPERGILLUS; CELL GROWTH; CHROMOSOME; COMPARATIVE GENOMIC HYBRIDIZATION; FERMENTATION; FLAVOR; FUNGAL STRAIN; GENE SEQUENCE; GENOME; MYCELIUM; NUCLEOTIDE SEQUENCE; SALT TOLERANCE;

EID: 84877914576     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2013.03.027     Document Type: Article

References (54)

1. Aharoni A., Keizer L.C.P., Bouwmeester H.J., Sun Z., Alvarez-Huerta M., Verhoeven H.A., Blaas J., van Houwelingen A.M.M.L., De Vos R.C.H., van der Voet H. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. The Plant Cell Online 2000, 12:647.
2. Altschul S.F., Madden T.L., Sch ffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389.
3. Auclair S.M., Bhanu M.K., Kendall D.A. Signal peptidase I: Cleaving the way to mature proteins. Protein Science 2011, 21:13-25.
4. Bard M., Bruner D., Pierson C., Lees N., Biermann B., Frye L., Koegel C., Barbuch R. Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase. Proceedings of the National Academy of Sciences 1996, 93:186.
5. Bockstaele L., Bisteau X., Paternot S., Roger P.P. Differential regulation of cyclin-dependent kinase 4 (CDK4) and CDK6, evidence that CDK4 might not be activated by CDK7, and design of a CDK6 activating mutation. Molecular and Cellular Biology 2009, 29:4188.
6. Chen Y.L., Montedonico A.E., Kauffman S., Dunlap J.R., Menn F.M., Reynolds T.B. Phosphatidylserine synthase and phosphatidylserine decarboxylase are essential for cell wall integrity and virulence in Candida albicans. Molecular Microbiology 2010, 75:1112-1132.
7. Chien C.W., Ho I., Lee T.C. Induction of neoplastic transformation by ectopic expression of human aldo-keto reductase 1C isoforms in NIH3T3 cells. Carcinogenesis 2009, 30:1813.
8. De Vries R.P., Flitter S.J., Van De Vondervoort P.J.I., Chaveroche M.K., Fontaine T., Fillinger S., Ruijter G.J.G., D¡-Enfert, C., Visser J. Glycerol dehydrogenase, encoded by gldB is essential for osmotolerance in Aspergillus nidulans. Molecular Microbiology 2003, 49:131-141.
9. de Waard M.A., Andrade A.C., Hayashi K., Schoonbeek H., Stergiopoulos I., Zwiers L.H. Impact of fungal drug transporters on fungicide sensitivity, multidrug resistance and virulence. Pest Management Science 2006, 62:195-207.
10. Fabian F., Bermoser K., Reiter R.J., Hanner M., Glossmann H. Yeast sterol C8-C7 isomerase: identification and characterization of a high-affinity binding site for enzyme inhibitors. Biochemistry 1996, 35:16871-16878.
11. Fan W., Idnurm A., Breger J., Mylonakis E., Heitman J. Eca1, a sarcoplasmic/endoplasmic reticulum Ca2+-ATPase, is involved in stress tolerance and virulence in Cryptococcus neoformans. Infection and Immunity 2007, 75:3394.
12. Goebl M., Yanagida M. The TPR snap helix: a novel protein repeat motif from mitosis to transcription. Trends in Biochemical Sciences 1991, 16:173.
13. Grana X., De Luca A., Sang N., Fu Y., Claudio P., Rosenblatt J., Morgan D., Giordano A. PITALRE, a nuclear CDC2-related protein kinase that phosphorylates the retinoblastoma protein in vitro. Proceedings of the National Academy of Sciences 1994, 91:3834.
14. 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 Biology 2008, 9:R7.
15. Hardie D.G. AMP-activated protein kinase-an energy sensor that regulates all aspects of cell function. Genes & Development 2011, 25:1895-1908.
16. Hesseltine C. Microbiology of oriental fermented foods. Annual Reviews in Microbiology 1983, 37:575-601.
17. Koide A., Bailey C.W., Huang X., Koide S. The fibronectin type III domain as a scaffold for novel binding proteins1. Journal of Molecular Biology 1998, 284:1141-1151.
18. Laber B., Gerbling K.P., Harde C., Neff K.H., Nordhoff E., Pohlenz H.D. Mechanisms of interaction of Escherichia coli threonine synthase with substrates and inhibitors. Biochemistry 1994, 33:3413-3423.
19. Latgé J.P. The cell wall: a carbohydrate armour for the fungal cell. Molecular Microbiology 2007, 66:279-290.
20. Li R., Li Y., Kristiansen K., Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713.
21. Li R., Zhu H., Ruan J., Qian W., Fang X., Shi Z., Li Y., Li S., Shan G., Kristiansen K. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 2010, 20:265-272.
22. Liaw S.H., Chen S.J., Ko T.P., Hsu C.S., Chen C.J., Wang A.H.J., Tsai Y.C. Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. Journal of Biological Chemistry 2003, 278:4957.
23. Lim H., Choi H.T. Enhanced expression of chitinase during the autolysis of mushroom in Coprinellus congregatus. The Journal of Microbiology 2009, 47:225-228.
24. Liu K., Li L., Luan S. An essential function of phosphatidylinositol phosphates in activation of plant shaker-type K+channels. The Plant Journal 2005, 42:433-443.
25. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 1997, 25:0955.
26. 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.
27. Mihara H., Kurihara T., Yoshimura T., Soda K., Esaki N. Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities. Journal of Biological Chemistry 1997, 272:22417.
28. Miller J.R., Delcher A.L., Koren S., Venter E., Walenz B.P., Brownley A., Johnson J., Li K., Mobarry C., Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24:2818-2824.
29. Mumby M.C., Walter G. Protein serine/threonine phosphatases: structure, regulation, and functions in cell growth. Physiological Reviews 1993, 73:673-699.
30. 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. Agricultural and Biological Chemistry 1991, 55:2807.
31. Paape R., Vorwerg L., Suckau D., Resemann A. Fast QC of intact monoclonal antibodies using MALDI-top-down sequencing. Journal of Biomolecular Techniques: JBT 2011, 22:S52.
32. Peddie H. Ester formation in brewery fermentations. Journal of the Institute of Brewing 1990, 96:327-331.
33. Perez-Victoria F.J., Bonifacino J.S. Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-Golgi network. Molecular and Cellular Biology 2009, 29:5251.
34. Pöggeler S., Kück U. A WD40 repeat protein regulates fungal cell differentiation and can be replaced functionally by the mammalian homologue striatin. Eukaryotic Cell 2004, 3:232-240.
35. Rothberg J.M., Leamon J.H. The development and impact of 454 sequencing. Nature Biotechnology 2008, 26:1117-1124.
36. Schatz M.C., Delcher A.L., Salzberg S.L. Assembly of large genomes using second-generation sequencing. Genome Research 2010, 20:1165-1173.
37. Sigal Y.J., McDERMOTT M.I., Morris A.J. Integral membrane lipid phosphatases/phosphotransferases: common structure and diverse functions. Biochemical Journal 2005, 387:281.
38. Speers A.E., Wu C.C. Proteomics of integral membrane proteins theory and application. Chemical Reviews 2007, 107:3687-3714.
39. 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 Bioinformatics 2006, 7:62.
40. Tan K., Li H., Zhang R., Gu M., Clancy S.T., Joachimiak A. Structures of open (R) and close (T) states of prephenate dehydratase (PDT)-Implication of allosteric regulation by l-phenylalanine. Journal of Structural Biology 2008, 162:94-107.
41. Tarailo-Graovac M., Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 2009, 4(10):11-14. (10. 14).
42. Verstrepen K.J., Van Laere S.D.M., Vanderhaegen B.M.P., Derdelinckx G., Dufour J.P., Pretorius I.S., Winderickx J., Thevelein J.M., Delvaux F.R. Expression levels of the yeast alcohol acetyltransferase genes ATF1, Lg-ATF1, and ATF2 control the formation of a broad range of volatile esters. Applied and Environmental Microbiology 2003, 69:5228.
43. Wang T., Leyh T.S. Three-stage assembly of the cysteine synthase complex from Escherichia coli. Journal of Biological Chemistry 2012, 287:4360-4367.
44. Watad A.E.A., Reuveni M., Bressan R.A., Hasegawa P.M. Enhanced net K+ uptake capacity of NaCl-adapted cells. Plant Physiology 1991, 95:1265.
45. Wiemann P., Brown D.W., Kleigrewe K., Bok J.W., Keller N.P., Humpf H.U., Tudzynski B. FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence. Molecular Microbiology 2010, 77:972-994.
46. Witteveen C.F.B., Visser J. Polyol pools in Aspergillus niger. FEMS Microbiology Letters 1995, 134:57-62.
47. Xu J., James R. Temperature stress affects the expression of immune response genes in the alfalfa leafcutting bee, Megachile rotundata. Insect Molecular Biology 2012, 21:269-280.
48. Yanfang Z., Wenyi T. Flavor and taste compounds analysis in Chinese solid fermented soy sauce. African Journal of Biotechnology 2010, 8.
49. Yong F., Wood B. Biochemical changes in experimental soy sauce koji. International Journal of Food Science and Technology 1977, 12:163-175.
50. Zeitouni B., Boeva V., Janoueix-Lerosey I., Loeillet S., Legoix-Né P., Nicolas A., Delattre O., Barillot E. SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 2010, 26:1895-1896.
51. Zhang L., Feng D., Fang W., Ouyang H., Luo Y., Du T., Jin C. Comparative proteomic analysis of an Aspergillus fumigatus mutant deficient in glucosidase I (AfCwh41). Microbiology 2009, 155:2157.
52. + ion implantation mutagenesis. International Journal of Food Science and Technology 2012, 47:504-510.
53. 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. Journal of Proteomics 2012, 75:3914-3924.
54. Zhu J.K. Genetic analysis of plant salt tolerance using Arabidopsis. Plant Physiology 2000, 124:941.