Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock

PLoS ONE

Volumn 2, Issue 8, 2007, Pages

  Michael, Todd P ^a,b   Park, Sohyun ^a   Kim, Tae Sung ^a   Booth, Jim ^c   Byer, Amanda ^b   Sun, Qi ^a   Chory, Joanne ^b,d   Lee, Kwangwon ^a  

^a Department of Obstetrics Gynecology   (United States)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^c Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; POLYGLUTAMINE; UNCLASSIFIED DRUG; WHITE COLLAR 1 PROTEIN; MICROSATELLITE DNA;

AMINO TERMINAL SEQUENCE; ARTICLE; ASEXUAL REPRODUCTION; CIRCADIAN RHYTHM; CONTROLLED STUDY; CORRELATION ANALYSIS; FUNGAL METABOLISM; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME SIZE; GENOTYPE ENVIRONMENT INTERACTION; NEUROSPORA CRASSA; NONHUMAN; PHENOTYPIC VARIATION; PROTEIN FUNCTION; SIMPLE SEQUENCE REPEAT; TEMPERATURE SENSE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHENOTYPE; PHYSIOLOGY;

FUNGI; NEUROSPORA CRASSA;

CIRCADIAN RHYTHM; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENETIC VARIATION; MICROSATELLITE REPEATS; NEUROSPORA CRASSA; PHENOTYPE;

EID: 39849099440     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000795     Document Type: Article

References (54)

1. Dunlap JC (2006) Proteins in the Neurospora circadian clockworks. J Biol Chem 281: 28489-28493.
2. Wijnen H, Young MW (2006) Interplay of circadian clocks and metabolic rhythms. Annu Rev Genet 40: 409-448.
3. Hotta CT, Gardner MJ, Hubbard KE, Baek SJ, Dalchau N, et al. (2007) Modulation of environmental responses of plants by circadian clocks. Plant Cell Environ 30: 333-349.
4. Ruoff P, Vinsjevik M, Rensing L (2000) Temperature compensation in biological oscillators: a challenge for joint experimental and theoretical analysis. Comments Theor Biol 5: 361-382.
5. Gu YZ, Hogenesch JB, Bradfield CA (2000) The PAS superfamily: sensors of environmental and developmental signals. Annual Review of Pharmacology&-Toxicology 40: 519-561.
6. Froehlich AC, Liu Y, Loros JJ, Dunlap JC (2002) White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter. Science 297: 815-819.
7. Elvin M, Loros JJ, Dunlap JC, Heintzen C (2005) The PAS/LOV protein VIVID supports a rapidly dampened daytime oscillator that facilitates entrainment of the Neurospora circadian clock. Genes Dev 19: 2593-2605.
8. Cheng P, Yang Y, Wang L, He Q, Liu Y (2003) 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: 3801-3808.
9. Christie JM, Salomon M, Nozue K, Wada M, Briggs WR (1999) LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nphl): Binding sites for the chromophore flavin mononucleotide. Proc Natl Acad Sci USA 96: 8779-8783.
10. He Q, Cheng P, Yang Y, Wang L, Gardner KH, et al. (2002) White Collar-1, a DNA binding transcription factor and a light sensor, Science 297: 840-843.
11. Lee K, Dunlap CJ, Loros JJ (2003) Roles for WHITE COLLAR-1 in Circadian and General Photoperception in Neurospora crassa. Genetics 163: 103-114.
12. Toyota K, Onai K, Nakashima. H (2002) A new wc-1 mutant of Neurospora crassa shows unique light sensitivity in the circadian conidiation rhythm. Mol Gen Genomics 268: 56-61.
13. Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, et al. (1996) White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. EMBO J'15: 1650-1657.
14. Liu Y (2003) Molecular mechanisms of entrainment in the Neurospora circadian clock. J Biol Rhythms 18: 195-205.
15. Borstnik B, Pumpernik D (2002) Tandem Repeats in Protein.Coding Regions of Primate Genes. Genome Res 12: 909-915.
16. Levinson G, Gutman G (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221.
17. Sawyer LA, Hennessy JM, Peixoto AA, Rosato E, Parkinson H, et al. (1997) Natural Variation in a Drosophila Clock Gene and Temperature Compensation. Science 278: 2117-2120.
18. Nadkarni NA, Weale ME, von Schantz M, Thomas MG (2005) Evolution of a Length Polymorphism in the Human PER3 Gene, a Component of the Circadian System. J Biol Rhythms 20: 490-499.
19. Michael TP, Salome PA, Yu HJ, Spencer TR, Sharp EL, et al. (2003) Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock. Science 302: 1049-1053.
20. Edwards KD, Lynn JR, Gyula P, Nagy F, Millar AJ (2005) Natural allclic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock. Genetics 170: 387-400.
21. Pittendrigh CS, Takamura T (1989) Latitudinal clines in the properties of a circadian pacemaker. J Biol Rhythms 4: 217-235.
22. Brown SA, Fleury-Olcla F, Nagoshi E, Hauser C, Juge C, et al. (2005) The period length of fibroblast circadian gene expression varies widely among human individuals. PLoS Biol 3: e338.
23. Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
24. Jacobson DJ, Powell AJ, Dettman JR, Saenz GS, Barton MM, et al. (?004) Neurospora in temperate forests of western North America. Mycologia 96: 66-74.
25. Jacobson DJ, Dettman JR, Adams RI, Boesl C, Sultana S, et al. (2006) New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales. Mycologia 98: 550-559.
26. Turner BC, Perkins DD, Fairfield A (2001) Neurospora from Natural Populations: A Global Study. Fungal Genetics and Biology 32: 67-92.
27. Bhat A, Noubissi FK, Vyas M, Kasbekar DP (2003) Genetic Analysis of Wild-Isolated Neurospora crassa Strains Identified as Dominant Suppressors of Repeat-Induced Point Mutation. Genetics 164: 947-961.
28. Sargent ML, Kaltenborn SH (1972) Effects of medium composition and carbon dioxide on circadian conidiation in Neurospora. Plant Physiol 50: 171-175.
29. Park S, Lee K (2004) Inverted Race Tube Assay for Circadian Clock Studies of the Neurospora Accessions. Fungal Gen Newsl 51: 12-14.
30. Karaoglu H, Lee CM, Meyer W (2005) Survey of simple sequence repeats in completed fungal gcnomes. Mol Biol Evol 22: 639-649.
31. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
32. Springer ML, Yanofsky C (1989) A morphological and genetic analysis of conidiophore development in Neurospora crassa. Genes Dev 3: 559-571.
33. Springer ML (1993) Genetic control of fungal differentiation: the three sporulation pathways of Neurospora crassa. Bioessays 15: 365-374.
34. Davis RH (2000) Neurospora, contributions of a model organism. New York: Oxford University Press, Inc.
35. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818-822.
36. Schmale DGI, Shields EJ, Bergstrom GC (2006) Night-time spore deposition of the fusarium head blight pathogen, Gibberella zeac in rotational wheat fields. Can J Plant Pathol 28: 100-108.
37. Brown JK, Hovmoller MS (2002) Aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science 297: 537-541.
38. Aylor DE, Taylor GS (1982) Aerial dispersal and drying of Peronospora tabacina conidia in tobacco shade tents. Proc Natl Acad Sci U S A 79: 697-700.
39. Kim CK, Min HS, Yoshino R (1990) Epidemiological studies of rice blast disease caused by Pyricularia oryzae Cavara (III); Diurnal pattern of conidial release and dispersal under the natural conditions. Ann Phytopath Soc Japan 56: 315-321.
40. Merrow M, Boesl C, Ricken J, Messerschmitt M, Goedel M, et al. (2006) Entrainment of the Neurospora circadian clock. Chronobiol Int 23: 71-80.
41. Pregueiro AM, Liu Q, Baker CL, Dunlap JC, Loros JJ (2006) The Neurospora checkpoint kinase 2: a regulatory link between the circadian and cell cycles. Science 313: 644-649.
42. Oke TR (1987) Boundary layer climates. Cambridge, UK: Cambridge University Press.
43. Harmer SL, Hogenesch JB, Straume M, Chang H-S, Han B, et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113.
44. Yanovsky MJ, Kay SA (2002) Molecular basis of seasonal time measurement in Arabidopsis. Nature 419: 308-312.
45. Kurosawa G, Goldbeter A (2006) Amplitude of circadian oscillations entrained by 24-h light-dark cycles. J Theor Biol 242: 478-488.
46. Heintzen C, Loros JJ, Dunlap JC (2001) The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 104: 453-464.
47. Sanchez I, Mahlke C, Yuan J (2003) Pivotal role of aligomerization in expanded polyglutamine neurodegenerative disorders. Nature 421: 373-379.
48. Terashima K, Yuki K, Muraguchi H, Akiyama M, Kamada T (2005) The dstl gene involved in mushroom photomorphogenesis of Coprinus cinereus encodes a putative photoreceptor for blue light. Genetics 171: 101-108.
49. Dunlap JC, Loros JJ (2004) The Neurospora Circadian System. J Biol Rhythms 19: 414-424.
50. Loros JJ, Dunlap JC (2001) Genetic and molecular analysis of circadian rhythms in Neurospora. Annu Rev Physiol 63: 757-794.
51. Lakin-Thomas PL, Brody S (2004) CIRCADIAN RHYTHMS IN MICRO-ORGANISMS: New Complexities. Annual Review of Microbiology 58: 489-519.
52. Kaldi K, Gonzalez BH, Brunner M (2006) Transcriptional regulation of the Neurospora, circadian clock gene wc-I affects the phase of circadian output. EMBO Rep 7: 199-204.
53. Roenneberg T, Taylor W (2000) Automated recordings of bioluminescence with special reference to the analysis of circadian rhythms. Methods Enzymol 305: 104-119.
54. Rozen S, Skaletsky HJ (1998) Primer3. http://www-genomewimitedu/ genome_software/other/primer3html.