A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 11, 2008, Pages 4387-4392

  Andersen, Mikael R ^a   Vongsangnak, Wanwipa ^a   Panagiotou, Gianni ^a   Salazar, Margarita P ^a   Lehmann, Linda ^a   Nielsen, Jens ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Aspergillus nidulans; Aspergillus niger; Aspergillus oryzae; XlnR

Indexed keywords

ENZYME; GLUCOSE; HEMICELLULOSE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR XLNR; TRANSCRIPTOME; XYLOSE; FUNGAL PROTEIN; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG; XLNR PROTEIN, ASPERGILLUS;

ARTICLE; ASPERGILLUS NIDULANS; ASPERGILLUS NIGER; ASPERGILLUS ORYZAE; BINDING SITE; CULTURE MEDIUM; FUNGAL GENE; FUNGUS CULTURE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; LAB ON A CHIP; METHODOLOGY; MICROARRAY ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SPECIES DIFFERENCE; TRANSCRIPTOMICS; UPREGULATION; ASPERGILLUS; CLASSIFICATION; COMPARATIVE STUDY; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION PROFILING; GENETICS; METABOLISM;

ASPERGILLUS; ASPERGILLUS NIGER; ASPERGILLUS ORYZAE; ASPERGILLUS SP.; EMERICELLA NIDULANS; FUNGI;

ASPERGILLUS; DOWN-REGULATION; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANS-ACTIVATORS; UP-REGULATION;

EID: 41949120307     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0709964105     Document Type: Article

References (38)

1. Baker SE, Bennett JW (2008) in The Aspergilli: Genomics, Medical Aspects, Biotechnology, and Research Methods, eds Osmani SA, Goldman GH (CRC Press, Boca Raton, FL), pp 3-13.
2. Hjort CM (2003) in Genetically Engineered Food, ed Heller KJ (Wiley, VCH, Wennheim, Germany), pp 86-99.
3. Nevalainen KH, Te'o VSJ, Bergquist P (2005) Heterologous protein expression in filamentous fungi. Trends Biotechnol 23:468-474.
4. Pontecorvo G (1953) The genetics of Aspergillus nidulans. Adv Genet 5:141-238.
5. Galagan JE, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105-1115.
6. Baker S (2006) Aspergillus niger genomics: past, present and into the future. Med Mycol 44:S17-S21.
7. Pel HJ, et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25:221-231.
8. Machida M, et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438:1157-1161.
9. Jørgensen TR, et al. (2007) Glucose uptake and growth of glucose-limited chemostat cultures of Aspergillus niger and a disruptant lacking MstA, a high-affinity glucose transporter. Microbiology 153:1963-1973.
10. van Peij N, Visser J, de Graaff L (1998) Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Mol Microbiol 27:131-142.
11. Marui J, et al. (2002) A transcriptional activator, AoXlnR, controls the expression of genes encoding xylanolytic enzymes in Aspergillus oryzae. Fungal Genet Biol 35:157-169.
12. Hasper AA, Visser J, de Graaf LH (2000) The Aspergillus niger transcriptional activator XlnR, which is involved in the degradation of the polysaccharides xylan and cellulose, also regulates D-xylose reductase gene expression. Mol Microbiol 36:193-200.
13. van Peij NN, Gielkens MM, de Vries RP, Visser J, de Graaff LH (1998) The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger. Appl Environ Microbiol 64:3615-3619.
14. Tsukagoshi N, Kobayashi T, Kato M (2001) Regulation of the amylolytic and (hemi-)cellulolytic genes in aspergilli. J Gen Appl Microbiol 47:1-19.
15. vanKuyk PA, de Groot MJL, Ruijter GJG, de Vries RP, Visser J (2001) The Aspergillus niger D-xululose kinase gene is co-expressed with genes encoding arabinan degrading enzymes, and is essential for growth on D-xylose and L-arabinose. Eur J Biochem 268:5414-5423.
16. de Vries RP, van de Vondervoort P, Hendriks L, van de Belt M, Visser J (2002) Regulation of the α-glucuronidase-encoding gene (aguA) from Aspergillus niger. Mol Genet Genom 268:96-102.
17. de Vries RP, Visser J (1996) Regulation of the feruloyl esterase (faeA) gene from Aspergillus niger. Appl Environ Microbiol 65:5500-5503.
18. de Vries RP, et al. (1996) Differential expression of three α-galactosidase genes and a single β-galactosidase gene from Aspergillus niger. Appl Environ Microbiol 65:2453-2460.
19. Gielkens MM, Dekkers E, Visser J, de Graaff LH (1996) Two cellobiohydrolase-encoding genes from Aspergillus niger require D-xylose and the xylanolytic transcriptional activator XlnR for their expression. Appl Environ Microbiol 65:4340-4345.
20. Hasper AA, Dekkers E, van Mil M, van de Vondervoort PJI, de Graaf LH (2002) EglC, a new endoglucanase from Aspergillus niger with major activity towards xyloglucan. Appl Environ Microbiol 68:1556-1560.
21. Marui J, Kitamoto N, Kato M, Kobayashi T, Tsukagoshi N (2002) Transcriptional activator, AoXlnR, mediates cellulose-inductive expression of the xylanolytic and cellulolytic genes in Aspergillus oryzae. FEBS Lett 528:279-282.
22. Pérez-Gonzalez JA, de Graaff LH, Visser J, Ramón D (1996) Molecular cloning and expression in Saccharomyces cerevisiae of two Aspergillus nidulans xylanase genes. Appl Environ Microbiol 62:2179-2182.
23. MacCabe AP, Orejas M, Pérez-González JA, Ramón D (1998) Opposite patterns of expression of two Aspergillus nidulans xylanase genes with respect to ambient pH. J Bacteriol 180:1331-1333.
24. MacCabe AP, Fernández-Espinar MT, de Graaff LH, Visser J, Ramón D (1996) Identification, isolation and sequence of the Aspergillus nidulans xlnC gene encoding the 34-kDa xylanase Gene 175:29-33.
25. Pettersen RC (1984) in The Chemistry of Solid Wood, ed Rowell RM (Am Chem Soc, Washington, DC), pp 57-126.
26. Carpita NC, Gibeaut DM (1993) Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Plant J 3:1-30.
27. Nielsen H, Wernersson R, Knudsen S (2003) Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31:3491-3496.
28. Wernersson R, Nielsen H (2005) OligoWiz 2.0-integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res 33:W611-615.
29. Bentley S, et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
30. Affymetrix (2007) GeneChip Expression Analysis Technical Manual, P/N 702232. (Affymetrix, Santa Clara, CA), Rev. 2.
31. R Development Core Team (2007) R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna).
32. Irizarry R, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264.
33. Bolstad B, Irizarry R, Åstrand M, Speed T (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
34. Gautier L, Cope L, Bolstad B, Irizarry R (2004) Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307-315.
35. Smyth G (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article 3.
36. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing J R Stat Soc B 57:289-300.
37. McGinnis S, Madden T (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32:W20-W25.
38. Bembom O, Keles S, van der Laan M (2007) Supervised detection of conserved motifs in DNA sequences with cosmo Stat Appl Genet Mol Biol 6:Article 8.