Analysis of nutrient-dependent transcript variations in Neurospora crassa

Fungal Genetics and Biology

Volumn 40, Issue 3, 2003, Pages 225-233

  Aign, Verena ^a   Hoheisel, Jörg D ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Acetate metabolism; Correspondence analysis; DNA microarray analysis; Neurospora crassa; Transcriptional profiling

Indexed keywords

ACETIC ACID; COMPLEMENTARY DNA; PROTEIN; RNA;

ARTICLE; CELL GROWTH; CONTROLLED STUDY; CULTURE MEDIUM; DEVICE; DNA MICROARRAY; FUNGAL GENE; FUNGAL METABOLISM; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HYBRIDIZATION; MOLECULAR CLONING; NEUROSPORA CRASSA; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT; PRIORITY JOURNAL; PROTEIN EXPRESSION; REGULATORY MECHANISM; RNA ANALYSIS; RNA ISOLATION; UNINDEXED SEQUENCE;

FUNGI; NEUROSPORA; NEUROSPORA CRASSA;

EID: 0242289251     PISSN: 10871845     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1087-1845(03)00106-3     Document Type: Article

References (41)

1. Aign V., Schulte U., Hoheisel J.D. Hybridization-based mapping of Neurospora crassa linkage groups II and V. Genetics. 157:2001;1015-1020.
2. Beadle G.W., Tatum E.L. Genetic control of biochemical reactions in Neurospora. Proc. Natl. Acad. Sci. USA. 27:1941;499-506.
3. Beissbarth T., Fellenberg K., Brors B., ArribasPrat R., Boer J.M., Hauser N.C., Scheideler M., Hoheisel J.D., Schütz G., Poustka A., Vingron M. Processing and quality control of DNA array hybridization data. Bioinformatics. 16:2000;1014-1022.
4. Bell-Pedersen D. Understanding circadian rhythmicity in Neurospora crassa: from behavior to genes and back again. Fungal Genet. Biol. 29:2000;1-18.
5. Choi G.H., Marek E.T., Schardl C.L., Richey M.G., Chang S.Y., Smith D.A. Sti35, a stress-responsive gene in Fusarium spp. J. Bacteriol. 172:1990;4522-4528.
6. Cotelle V., Meek S.E., Provan F., Milne F.C., Morrice N., MacKintosh C. 14-3-3s regulate global cleavage of their diverse binding partners in sugar-starved Arabidopsis cells. EMBO J. 19:2000;2869-2876.
7. Davis R.H. Neurospora: Contributions of a Model Organism. 2000;Oxford University Press, New York.
8. Diehl F., Grahlmann S., Beier M., Hoheisel J.D. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res. 29:2001;e38.
9. Diehl F., Beckmann B., Kellner N., Hauser N.C., Diehl S., Hoheisel J.D. Manufacturing DNA microarrays from unpurified PCR products. Nucleic Acids Res. 30:2002;e79.
10. Diehl S., Diehl F., El-Sayed N.M., Clayton C., Hoheisel J.D. Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray. Mol. Biochem. Parasit. 123:2002;115-123.
11. Eberle J., Russo V.E. Neurospora crassa blue-light-inducible gene bli-7 encodes a short hydrophobic protein. DNA Seq. 3:1992;131-141.
12. Eisen M.B., Brown P.O. DNA arrays for analysis of gene expression. Methods Enzymol. 303:1999;179-205.
13. Fellenberg K., Hauser N.C., Brors B., Neutzner A., Hoheisel J.D., Vingron M. Correspondence analysis applied to microarray data. Proc. Natl. Acad. Sci. USA. 98:2001;10781-10786.
14. Fellenberg K., Hauser N.C., Brors B., Hoheisel J.D., Vingron M. Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics. 18:2002;423-433.
15. Flavell R.B., Fincham J.R.S. Acetate non-utilizing mutants of Neurospora crassa. I. Mutant isolation, complementation studies and linkage relationships. J. Bacteriol. 95:1968;1056-1062.
16. Flavell R.B., Fincham J.R.S. Acetate non-utilizing mutants of Neurospora crassa. II. Biochemical deficiencies and the roles of certain enzymes. J. Bacteriol. 95:1968;1063-1068.
17. Flavell R.B., Woodward D.O. Metabolic role, regulation of synthesis, cellular location, and genetic control of the glyoxylate cycle enzymes in Neurospora crassa. J. Bacteriol. 105:1971;200-210.
18. Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D., Jaffe D., FitzHugh W., Ma L.-J., Smirnov S.et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 422:2003;859-868.
19. Hansen K., Birse C.E., Proudfoot N.J. Nascent transcription from the nmt1 and nmt2 genes of Schizosaccharomyces pombe overlaps neighbouring genes. EMBO J. 17:1998;3066-3077.
20. de Jong-Gubbels P., Vanrolleghem P., Heijnen J.P., van Dijken J.P., Pronk J.T. Regulation of carbon metabolism in chemostat cultures of Saccharomyces cerevisiae grown on mixtures of glucose and ethanol. Yeast. 11:1999;407-418.
21. Joseph J.D., Heitmann J., Means A.R. Molecular cloning and characterization of Aspergillus nidulans cyclophilin B. Fungal Genet. Biol. 27:1999;55-66.
22. Kelkar H.S., Griffith J., Case M.E., Covert S.F., Hall R.D., Keith C.H., Oliver J.S., Orbach M.J., Sachs M.S., Wagner J.R., Weise M.J., Wunderlich J.K., Arnold J. The Neurospora crassa genome: cosmid libraries sorted by chromosome. Genetics. 157:2001;979-990.
23. Kuwana H., Okumura R. Genetics and some characteristics of acetate-requiring strains of Neurospora crassa. Jpn. J. Genet. 54:1979;235-244.
24. Lauter F.R. Molecular genetics of fungal photobiology. J. Genet. 75:1996;375-386.
25. Lauter F.R., Russo V.E., Yanofsky C. Developmental and light regulation of eas, the structural gene for the rodlet protein of Neurospora. Genes Dev. 6:1992;2373-2381.
26. Legerton T.L., Yanofsky C. Cloning and characterization of the multifunctional his-3 gene of Neurospora crassa. Gene. 39:1985;129-140.
27. Mannhaupt G., Montrone C., Haase D., Mewes H.W., Aign V., Hoheisel J.D., Fartmann B, Nyakatura G., Kempken F., Maier J., Schulte U. What's in the genome of a filamentous fungus. Analysis of the Neurospora genome sequence. Nucleic Acids Res. 31:2003;1944-1954.
28. Maundrell K. Nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J. Biol. Chem. 265:1990;10857-10864.
29. Nelson M.A., Kang S.C., Braun E.L., Crawford M.E., Dolan P.L., Leonard P.M., Mitchell J., Armijo A.M., Bean L., Blueyes E., Cushing T., Errett A., Fleharty M., Gorman M., Judson K., Miller R., Ortega J., Pavlova I., Perea J., Todisco S.et al. Expressed sequences from conidial, mycelial, and sexual stages of Neurospora crassa. Fungal Genet. Biol. 21:1997;348-363.
30. Oh M.K., Rohlin L., Kao K.C., Liao J.C. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277:2002;13175-13183.
31. Radford A., Parish J.H. The genome and genes of Neurospora crassa. Fungal Genet. Biol. 21:1997;258-266.
32. Santosa S., Kuwana H. Isolation and characterization of a new acetate-requiring strain, ace-9, of Neurospora crassa. Jpn. J. Genet. 67:1992;85-95.
33. Schulte U., Becker I., Mewes H.W., Mannhaupt G. Large scale analysis of sequences from Neurospora crassa. J. Biotechnol. 94:2002;3-13.
34. Sokolovsky V., Kaldenhoff R., Ricci M., Russo V.E.A. Fast and reliable mini-prep RNA extraction from Neurospora crassa. Fungal Genet. Newslett. 37:1990;41-43.
35. Stjepandic D., Weinel C., Hilbert H., Koo H.L., Diehl F., Nelson K.E., Tümmler B., Hoheisel J.D. The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis. Environ. Microbiol. 4:2002;819-823.
36. Strauss B.S. Oxalacetate carboxylase deficiency of the succinate-requiring mutants of Neurospora crassa. J. Biol. Chem. 225:1957;535-544.
37. ter Linde J.J.M., Liang H., Davis R.W., Steensma H.Y., van Dijken J.P. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol. 181:1999;7409-7413.
38. Townsend J.P., Hartl D.L. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple treatments or samples. Genome Biol. 3:2002;. research0071.0001-0071.0016.
39. Turian G., Bianchi D.E. Conidiation in Neurospora. Bot. Rev. 38:1972;119-154.
40. Vogel H.J. Distribution of lysine pathways among fungi: evolutionary implications. Am. Naturalist. 98:1964;435-446.
41. Wodicka L., Dong H., Mittmann M., Ho M.-H., Lockhart D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15:1997;1359-1367.