Analysis of circadian rhythms in Neurospora: Overview of assays and genetic and molecular biological manipulation

Methods in Enzymology

Volumn 393, Issue , 2005, Pages 3-22

  Dunlap, Jay C ^a   Loros, Jennifer J ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; PHOSPHOTRANSFERASE; PROTEIN; PROTEIN FRQ; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; WHITE COLLAR 1 PROTEIN; WHITE COLLAR 2 PROTEIN;

ASSAY; BIOLOGY; CHEMICAL COMPOSITION; CIRCADIAN RHYTHM; CULTURE MEDIUM; DARKNESS; DEVELOPMENT; DIMERIZATION; ENZYME METABOLISM; EUKARYOTE; FEEDBACK SYSTEM; FRQ GENE; FUNGAL GENETICS; FUNGUS; FUNGUS CULTURE; FUNGUS GROWTH; GENE; GENE ACTIVATION; GENE EXPRESSION; GENE INDUCTION; GENE MUTATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC PROCEDURES; GENETIC REGULATION; GENETIC TRANSFORMATION; GENOME ANALYSIS; GENOMICS; HETEROKARYON; HIGH TEMPERATURE; INOCULATION; KNOCKOUT GENE; LIGHT; MODEL; MOLECULAR BIOLOGY; MOLECULAR GENETICS; NEUROSPORA; NEUROSPORA CRASSA; NONHUMAN; OSCILLATION; PHOTORECEPTOR; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; REVIEW; SYNTHESIS; TEMPERATURE; UBIQUITINATION;

EUKARYOTA; FLOS; FUNGI; NEUROSPORA; NEUROSPORA CRASSA;

EID: 17044426840     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)93001-2     Document Type: Article

References (82)

1. Aronson B., Johnson K., Loros J.J., Dunlap J.C. Negative feedback defining a circadian clock: Autoregulation in the clock gene frequency. Science. 263:1994a;1578-1584
2. Aronson B.D., Johnson K.A., Dunlap J.C. The circadian clock locus frequency: A single ORF defines period length and temperature compensation. Proc. Natl. Acad. Sci. USA. 91:1994b;7683-7687
3. Aronson B.D., Lindgren K.M., Dunlap J.C., Loros J.J. An efficient method for gene disruption in Neurospora crassa. Mol. Gen. Genet. 242:1994c;490-494
4. Bell-Pedersen D., Shinohara M., Loros J., Dunlap J.C. Circadian clock-controlled genes isolated from Neurospora crassa are late night to early morning specific. Proc. Natl. Acad. Sci. USA. 93:1996;13096-13101
5. Bertrand H., Collins R.A., Stohl L.L., Goewert R.R., Lambowitz A.M. Deletion mutants of Neurospora crassa mitochondrial DNA and their relationship to the "stop-start" growth phenotype. Proc. Natl. Acad. Sci. USA. 77:1980;6032-6036
6. Bünning E. "The Physiological Clock," revised 3rd Ed. :1973;Springer-Verlag, New York
7. Catlett N.L., Lee B., Yoder O.C., Turgeon B.G. Split-marker recombination for efficient targeted deletion of fungal genes. Fungal Genet News. 50:2003;9-11
8. Chang B., Nakashima H. Isolation of temperature sensitive rhythm mutant in Neurospora crassa. Genes Genet. Syst. 73:1998;71-73
9. Cheng P., Yang Y., Gardner K.H., Liu Y. PAS domain-mediated WC-1/WC-2 interaction is essential for maintaining the steady-state level of WC-1 and the function of both proteins in clock and light responses of Neurospora. Mol. Cell. Biol. 22:2002;517-524
10. Cheng P., Yang Y., Heintzen C., Liu Y. Coiled coil mediated FRQ-FRQ interaction is essential for circadian clock function in Neurospora. Embo J. 20:2001a;101-108
11. Cheng P., Yang Y., Liu Y. Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc. Natl. Acad. Sci. USA. 98:2001b;7408-7413
12. Cheng P., Yang Y., Wang L., He Q., Liu Y. WHITE COLLAR-1, a multifunctional Neurospora protein involved in the circadian feedback loops, light sensing, and transcription repression of wc-2. J. Biol. Chem. 278:2003;3801-3808
13. Cogoni C., Macino G. Suppression of gene expression by homologous transgenes. Antonie Van Leeuwenhoek. 65:1994;205-209
14. Cogoni C., Macino G. Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa. Proc. Natl. Acad. Sci. USA. 94:1997;10233-10238
15. Collett M.A., Garceau N., Dunlap J.C., Loros J.J. Light and clock expression of the Neurospora clock gene frequency is differentially driven by but dependent on WHITE COLLAR-2. Genetics. 160:2002;149-158
16. Collins M.E., Briggs G., Sawyer C., Sheffield P., Connerton I.F. An inducible gene expression system for Neurospora crassa. Enzyme Microb. Technol. 13:1991;400-403
17. Crosthwaite S.C., Dunlap J.C., Loros J.J. Neurospora wc-1 and wc-2: Transcription, photoresponses, and the origins of circadian rhythmicity. Science. 276:1997;763-769
18. Crosthwaite S.C., Loros J.J., Dunlap J.C. Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript. Cell. 81:1995;1003-1012
19. Davis R.L., deSerres D. Genetic and microbial research techniques for Neurospora crassa. Methods Enzymol. 27A:1970;79-143
20. Denault D.L., Loros J.J., Dunlap J.C. WC-2 mediates WC-1-FRQ interaction within the PAS protein-linked circadian feedback loop of Neurospora crassa. Embo J. 20:2001;109-117
21. Dunlap J.C., Feldman J.F. On the role of protein synthesis in the circadian clock of Neurospora crassa. Proc. Natl. Acad. Sci. USA. 85:1988;1096-1100
22. Dunlap J.C., Loros J.J., Decoursey P. "Chronobiology: Biological Timekeeping" 2003;Sinauer, Sunderland, MA
23. Dunlap J.C., Loros J.J., Denault D., Lee K., Froehlich A.F., Colot H., Shi M., Pregueiro A. Genetics and molecular biology of circadian rhythms. Brambl R., Marzluf G.A. "The Mycota III" 2004;209-229 Springer-Verlag, Berlin
24. Ebbole D., Sachs M. Targeting chromosomal insertion to the his-3 locus. Fung. Genet. News. 37:1990;15-16
25. Feldman J., Hoyle M.N. A direct comparison between circadian and noncircadian rhythms in Neurospora crassa. Plant Physiol. 53:1974;928-930
26. Feldman J.F. Lengthening the period of a biological clock in Euglena by cycloheximide, an inhibitor of protein synthesis. Proc. Natl. Acad. Sci. USA. 57:1967;1080-1087
27. Feldman J.F., Atkinson C.A. Genetic and physiological characterization of a slow growing circadian clock mutant of Neurospora crassa. Genetics. 88:1978;255-265
28. Feldman J.F., Gardner G.F., Dennison R.A. Genetic analysis of the circadian clock of Neurospora. Suda M. "Biological Rhythms and their Central Mechanism" 1979;57-66 Elsevier, Amsterdam
29. Feldman J.F., Hoyle M. Isolation of circadian clock mutants of Neurospora crassa. Genetics. 75:1973;605-613
30. Feldman J.F., Waser N. New mutations affecting circadian rhythmicity in Neurospora. Menaker M. "Biochronometry" 1971;652-656 National Academy of Sciences, Washington
31. Froehlich A.C. "Light and Circadian Regulation in Neurospora crassa," 2002;. Ph.D. thesis. Dartmouth.
32. Froehlich A.C., Loros J.J., Dunlap J.C. Rhythmic binding of a WHITE COLLAR containing complex to the frequency promoter is inhibited by FREQUENCY. Proc. Nat. Acad. Sci. USA. 100:2003;5914-5919
33. Gall A., Lysek G. Induction of circadian conidiation by rubidium chloride. Neurospora Newsl. 28:1981;13
34. Galagan J., Calvo S., Borkovich K., et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature. 422:2003;859-868
35. Garceau N., Liu Y., Loros J.J., Dunlap J.C. Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY. Cell. 89:1997;469-476
36. Gardner G.F., Feldman J.F. The frq locus in Neurospora crassa: A key element in circadian clock organization. Genetics. 96:1980;877-886
37. Geever R.F., Huiet L., Baum J., Tyler B., Patel V., Rutledge B., Case M., H., G.N. DNA sequence, organization and regulation of the qa gene cluster of Neurospora crassa. J. Mol. Biol. 207:1989;15-34
38. Giles N.H., Case M.E., Baum J., Geever R., Huiet L., Patel V., Tyler B. Gene organization and regulation in the qa (quinic acid) gene cluster of Neurospora crassa. Microbio. Rev. 49:1985;338-358
39. Gooch V., Freeman L., Lakin-Thomas P. J. Biol. Rhythms. 19:2004;493-503
40. Gorl M., Merrow M., Huttner B., Johnson J., Roenneberg T., Brunner M. A PEST-like element in FREQUENCY determines the length of the circadian period in Neurospora crassa. Embo J. 20:2001;7074-7084
41. He Q., Cheng P., Yang Y., He Q., Yu Q., Liu Y. FWD-1 mediated degradation of FREQUENCY in Neurospora establishes a conserved mechanism for circadian clock regulation. Embo J. 22:2003;4421-4430
42. Ingold C.T. "Fungal Spores." 1971;Clarendon Press, Oxford
43. Konopka R.J., Benzer S. Clock mutants of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA. 68:1971;2112-2116
44. Lakin-Thomas P. Effects of choline depletion on the circadian rhythm in Neurospora crassa. Biol. Rhythm Res. 27:1996;12-30
45. Lee K., Loros J.J., Dunlap J.C. Interconnected feedback loops in the Neurospora circadian system. Science. 289:2000;107-110
46. Liu Y. Analysis of posttranslational regulations in the Neurospora circadian clock. Methods Enzymol. 393:(17):2005;. 2005 (this volume)
47. Liu Y., Garceau N., Loros J.J., Dunlap J.C. Thermally regulated translational control mediates an aspect of temperature compensation in the Neurospora circadian clock. Cell. 89:1997;477-486
48. Liu Y., Loros J., Dunlap J.C. Phosphorylation of the Neurospora clock protein FREQUENCY determines its degradation rate and strongly influences the period length of the circadian clock. Proc. Nat. Acad. Sci. USA. 97:2000;234-239
49. Loros J.J. "Studies on frq-9, a Recessive Circadian Clock Mutant of Neurospora crassa," 1986
50. Loros J.J., Denome S.A., Dunlap J.C. Molecular cloning of genes under the control of the circadian clock in Neurospora. Science. 243:1989;385-388
51. Loros J.J., Dunlap J.C. Genetic and molecular analysis of circadian rhythms in Neurospora. Annu. Rev. Physiol. 63:2001;757-794
52. Loros J.J., Feldman J.F. Loss of temperature compensation of circadian period length in the frq-9 mutant of Neurospora crassa. J. Biol. Rhythms. 1:1986;187-198
53. Loros J.J., Richman A., Feldman J.F. A recessive circadian clock mutant at the frq locus in Neurospora crassa. Genetics. 114:1986;1095-1110
54. Luo C., Loros J.J., Dunlap J.C. Nuclear localization is required for function of the essential clock protein FREQUENCY. Embo J. 17:1998;1228-1235
55. Mattern D., Brody S. Circadian rhythms in Neurospora crassa: Effects of unsaturated fatty acids. J. Bacteriol. 139:1979;977-988
56. McClung C.R., Fox B.A., Dunlap J.C. The Neurospora clock gene frequency shares a sequence element with the Drosophila clock gene period. Nature. 339:1989;558-562
57. Mehra A., Morgan L., Bell-Pedersen D., Loros J., Dunlap J.C. Watching the Neurospora Clock Tick. "Society for Research on Biological Rhythms." 2002;. Amelia Island, FL.
58. Merrow M., Bruner M., Roenneberg T. Assignment of circadian function for the Neurospora clock gene frequency. Nature. 399:1999;584-586
59. Merrow M., Franchi L., Dragovic Z., Gorl M., Johnson J., Brunner M., Macino G., Roenneberg T. Circadian regulation of the light input pathway in Neurospora crassa. Embo J. 20:2001;307-315
60. Morgan L.W., Greene A.V., Bell-Pedersen D. Circadian and light-induced expression of luciferase in Neurospora crassa. Fung. Genet. Biol. 38:2003;327-332
61. Nakashima H. A liquid culture system for the biochemical analysis of the circadian clock of Neurospora. Plant Cell Physiol. 22:1981;231-238
62. Orbach M.J. A cosmid with a HyR marker for fungal library construction and screening. Genes Dev. 150:1994;159-162
63. Perlman J., Nakashima H., Feldman J. Assay and characteristics of circadian rhythmicity in liquid cultures of Neurospora crassa. Plant Physiol. 67:1981;404-407
64. Pittendrigh C.S., Bruce V.G., Rosenzweig N.S., Rubin M.L. A biological clock in Neurospora. Nature. 184:1959;169-170
65. Roenneberg T., Taylor W. Automated recordings of bioluminescence with special reference to the analysis of circadian rhythms. Methods Enzymol. 305:2000;104-119
66. Ryan F.J., Beadle G.W., Tatum E.L. The tube method for measuring the growth rate of Neurospora. Am. J. Bot. 30:1943;784-799
67. Sargent M.L., Briggs W.R. The effect of light on a circadian rhythm of conidiation in Neurospora. Plant Physiol. 42:1967;1504-1510
68. Sargent M.L., Briggs W.R., Woodward D.O. The circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa. Plant Physiol. 41:1966;1343-1349
69. Sargent M.L., Kaltenborn S.H. Effects of medium composition and carbon dioxide on circadian conidiation in Neurospora. Plant Physiol. 50:1972;171-175
70. Sarkar S., Iyer G., Wu J., Glass N.L. Nonself recognition is mediated by HET-C heterocomplex formation during vegetative incompatibility. Embo J. 21:2002;4841-4850
71. Schilling B., Linden R.M., Kupper U., Lerch K. Expression of Neurospora crassa laccase under the control of the copper-inducible metallothionein- promoter. Curr. Genet. 22:1992;197-203
72. Selker E.U. Epigenetic phenomena in filamentous fungi. Trends. Genet. 13:1997;296-301
73. Stechmann A., Cavalier-Smith T. The root of the eukaryote tree pinpointed. Curr. Biol. 13:2003;R665-R666
74. Sussman A.S., Durkee T., Lowrey R.J. A model for rhythmic and temperature-independent growth in the "clock" mutants of Neurospora. Mycopathol. Mycol. Appl. 25:1965;381-396
75. Sweeney B.M. Circadian rhythms, definition and general characterization. Hastings J.W., Schweiger H.-G. "The Molecular Basis of Circadian Rhythms" 1976;77-83 Dahlem Konferenzen, Berlin
76. Temporini E.D., Alvarez M.E., Mautino M.R., Folco H.D., Rosa A.L. The Neurospora crassa cfp promoter drives a carbon source-dependent expression of transgenes in filamentous fungi. J. Appl. Microbiol. 96:2004;1256-1264
77. Wang Z., Deak M., Free S.J. A cis-acting region required for the regulated expression of grg-1, a Neurospora glucose-repressible gene. Two regulatory sites (CRE and NRS) are required to repress grg-1 expression. J. Mol. Biol. 237:1994;65-74
78. West D.J. Effects of pH and biotin on a circadian rhythm of conidiation in Neurospora crassa. J. Bacteriol. 123:1975;387-389
79. Yang Y., Cheng P., Liu Y. Regulation of the Neurospora circadian clock by casein kinase II. Genes Dev. 16:2002;994-1006
80. Yang Y., Cheng P., Qiyang Q., He Q., Wang L., Liu Y. Phosphorylation of FREQUENCY protein by casein kinase II is necessary for the function of the Neurospora circadian clock. Mol. Cell. Biol. 23:2003;6221-6228
81. Yang Y., Cheng P., Zhi G., Liu Y. Identification of a calcium/calmodulin-dependent protein kinase that phosphorylates the Neurospora circadian clock protein FREQUENCY. J. Biol. Chem. 276:2001;41064-41072
82. Zhu H., Nowrousian M., Kupfer D., Colot H., Berrocal-Tito G., Lai H., Bell-Pedersen D., Roe B., Loros J.J., Dunlap J.C. Analysis of expressed sequence tags from two starvation, time-of-day-specific libraries of Neurospora crassa reveals novel clock-controlled genes. Genetics. 157:2001;1057-1065