System biology of the Clock in Neurospora crassa

PLoS ONE

Volumn 3, Issue 8, 2008, Pages

  Dong, Wubei ^a   Tang, Xiaojia ^b   Yu, Yihai ^b   Nilsen, Roger ^b   Kim, Rosemary ^b   Griffith, James ^b,c   Arnold, Jonathan ^a   Schüttler, H Bernd ^b  

^a University of Georgia   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAROTENOID; FREQUENCY PROTEIN; ISOPRENOID; PHOSPHATASE; PHOSPHOTRANSFERASE; RIBOSOME RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG; WHITE COLLAR 1 PROTEIN; WHITE COLLAR 2 PROTEIN;

ARTICLE; AUTOREGULATION; BIOGENESIS; BIOLOGICAL RHYTHM; BIOSYNTHESIS; CARBON METABOLISM; CELL CYCLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; DNA METABOLISM; FUNGAL GENE; GENETIC REGULATION; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; NEUROSPORA CRASSA; NONHUMAN; PHOTOREACTIVITY; PROTEIN METABOLISM; RNA METABOLISM; RNA PROCESSING; RNA TRANSPORT; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; PHYSIOLOGY;

NEUROSPORA CRASSA;

BIOLOGICAL CLOCKS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GENES, FUNGAL; MODELS, GENETIC; NEUROSPORA CRASSA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SYSTEMS BIOLOGY;

EID: 51849120153     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003105     Document Type: Article

References (96)

1. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.
2. Dunlap JC (1999) Molecular bases for circadian clocks. Cell 96: 271-290.
3. Crosthwaite SK, Dunlap JC, Loros JJ (1997) Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity. Science 276: 763-769.
4. 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.
5. Aronson BD, Johnson KA, Loros JJ, JC Dunlap JC (1994) Negative feedback defining a circadian clock: autoregulation of the clock gene frequency. Science 263: 1578-1584.
6. Schafmeier T, Haase A, Kaldi K, Scholz J, Fuchs M, et al. (2005) Transcriptional feedback of Neurospora Circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell 122: 235-246.
7. Yu Y, Dong W, Altimus C, Tang X, Griffith J, et al. (2007) A genetic network for the clock of Neurospora crassa. Proc Natl Acad Sci U S A 104: 2809-2814.
8. Correa A, Lewis ZA, Greene AV, Much IJ, Gomer RH, Bell-Pedersen D (2003) Multiple oscillators regulate circadian gene expression in Neurospora. Proc Natl Acad Sci U S A 100: 13597-13602.
9. Locke JWC, Southern MM, Kozma-Bognar L, Hibbard V, Brown PE, et al. (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Molecular Systems Biology 1: 10.1038.
10. Arnold J, Schüttler H-B, Logan DA, Battogtokh D, Griffith J, et al. (2004) Metabolomics Chapter 22. In: An Z, ed. Handbook of Industrial Mycology. NY, NY: Marcel-Dekker. pp 597-634.
11. Battogtokh D, Asch DK, Case ME , Arnold J, Schüttler H-B (2002) An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa, Proc Natl Acad Sci U S A 99: 16904-16909.
12. Brown KS, Sethna JP (2003) Statistical mechanical approaches to models with many poorly known parameters. Phys. Rev E 68: 021904-1-021904-9.
13. Yeung MK, Tegner J, Collins JJ (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A 99: 6163-6168.
14. Tegner J, Yeung MKS, Hasty J, Collins JJ (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A 100: 5944-5949.
15. Gardner TS, diBernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-104.
16. Xiong M, Li J, Fang X (2004) Identification of genetic networks. Genetics 166: 1037-1052.
17. Strogatz SH (2001) Exploring complex networks. Nature 410: 268-276.
18. Hughes TP, Marton MJ, Jones AR, Robers CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
19. Clarke DC, Betterton MD, Liu X (2006) TGF-β concentration dependence of Smad phosphorylation kinetics: a systems perspective. IEEE Systems Biology 153: 412-424.
20. 2- Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real Time cAMP Dynamics. J Biol Chem 283(5): 2949-2961.
21. Alves R, Savageau MA (2000) Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics 16: 534-547.
22. Muirhead RJ (1982) Aspects of Multivariate Statistical Theory. New York: Wiley.
23. Garceau NY, Liu Y, Loros JJ, Dunlap JC (1997) Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY. Cell 89: 469-476.
24. Lee K, Loros JJ, Dunlap JC (2000) Interconnected feedback loops in the Neurospora circadian system. Science 289: 107-110.
25. Görl M, Merrow M, Huttner B, Johnson J, Roenneberg T, Brunner M (2001) A PEST-like element in FREQUENCY determines the length of the circadian period in Neurospora crassa. EMBO J 20: 7074-7084.
26. See http://www.Intl-Light.com/handbook/; and especially http://www.IntlLight.com/handbook/ch05.html for spectral distributions and http://www.IntlLight.com/handbook/ch07.html for unit conversions.
27. Logan DA, Koch AL, Dong W, Griffith J, Schüttler H-B, et al. (2007) Genome-wide expression analysis of genetic networks in Neurospora crassa. Bioinformation 1(10): 390-395.
28. Nakashima H (1981) A liquid culture system for the biochemical analysis of the circadian clock of Neurospora. Plant Cell Physiol 22: 231-238.
29. Davis RH, De Serres FG (1970) Genetic and microbiological research techniques for Neurospora crassa. Microbiological Reviews 27: 79-143.
30. Dharmananda S (1980) Studies of the circadian clock of Neurospora crassa: light-induced phase shifting. Santa Cruz: Ph.D. dissertation. University of California- Santa Cruz.
31. Arnold J, Dong W, Griffith J, Choi D, Baldwin J, et al. (2006) Systems Biology of the Biological Clock. IEEE Proceedings of the First International Conference on Computational Systems Biology (ICCSB-2006), pp 119-125.
32. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
33. Dong W, Tang X, Yu Y, Griffith J, Nilsen R, et al. (2007) Systems biology of the Neurospora biological clock. IET Systems Biology 1(5): 257-265.
34. Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, et al. (2007) Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics 57: 49-96.
35. Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, et al. (2005) Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucl Acids Res 33: 6469-6485.
36. McDonald MJ, Rosbash M (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107: 567-578.
37. Mannhaupt G, Montrone C, Haase D, Mewes HW, Aign V, et al. (2003) What's in the genome of a filamentous fungus: analysis of the Neurospora crassa genome. Nucl Acids Res 31: 1944-1954.
38. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14063-14868.
39. De Hoon MJ, Imoto S, Nolan J, Miyano, S (2004) Open source clustering software. Bioinformatics 20: 1453-1454.
40. Saklanha AJ (2004) Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
41. Giles NH, Geever RF, Asch DK, Avalos J, Case ME (1991) Organization and regulation of the Qa (Quinic Acid) genes in Neurospora crassa and other fungi. J Heredity 82: 1-7.
42. Nowrousian M, Duffield GE, Loros JJ, Dunlap JC (2003) The gene frequency is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa. Genetics 164: 923-933.
43. Yu Y (2005) Monte Carlo studies of genetic networks with special reference to the biological clock of Neurospora crassa. Athens, GA. Ph.D. Dissertation. University of Georgia.
44. Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, et al. (2002) Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol Chem 277: 14048-14052.
45. Lin Y, Han M, Shimada B, Wang L, Gibler TM, et al. (2002) Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc Natl Acad Sci U S A 99: 9562-9567.
46. Gutierrez RA, Ewing RM, Cherry JM, Green PJ (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci U S A 99: 11513-11518.
47. 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.
48. Covington MF, Harmer SL (2004) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biology 5: 1773-1784.
49. Michael TP, McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiology 132: 629-639.
50. Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc B 64: 479-498.
51. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B 57: 289-300.
52. Dai J, Li L, Kim S, Kimball B, Jazwinski SM, et al. (2007) Exact sample size needed to detect dependence in 2×2×2 tables. Biometrics 63: 1245-1252.
53. Pregueiro AM, Liu Q, Baker CL, Dunlap JC, Loros JJ (2006) The Neurospora Checkpoint Kinase 2: a regulatory link between circadian and cell cycles. Science 313: 644-649.
54. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
55. Heisenberg W (1949) The Physical Principles of the Quantum Theory. New York: Dover Publications.
56. Kaldi K, Gonzalez BH, Brunner M (2006) Transcriptional regulation of the Neurospora circadian dock gene wc-1 affects the phase of circadian output. EMBO Reports 7: 199-204.
57. Jones CA, Greer-Phillips SE, Borkovich KA (2007) The response regulator RRG-1 functions upstream of a MAPK pathway impacting asexual development, female fertility, osmotic stress and fungicide resistance in Neurospara crassa. Molecular Biology of the Cell 18: 2123-2136.
58. Vitalini MW, de Paula RM, Goldsmith CS, Jones CA, Borkovich KA, et al. (2007) Circadian rhythmicity mediated by temporal regulation of the activity of p38 MAPK. Proc Natl Acad Sci U S A 104: 18223-18228.
59. De Paula RM, Lewis ZA, Greene AV, Seo KS, Morgan LW, et al. (2006) Two circadin timing circuits in Neurospora crassa cells share components and regulate distinct rhythmic processes. J Biol Rhythms 21: 159-168.
60. Lewis ZA, Correa A, Schwerdtfeger C, Link KL, Xie X, et aL (2002) Overexpression of White Collar-1 (WC-1) activates circadian clock-associated genes, but is not sufficient to induce most light-regulated gene expression in Neurospora crassa. Molecular Microbiology 45: 917-931.
61. Ma L, Li J, Qu L, Hager J, Chen Z, et al. (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2607.
62. Crosthwaite SK, Loros JJ, Dunlap JC (1995) Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript. Cell 81: 1003-1012.
63. Fambrough D, McClure K, Kazlauskas A, Lander ES (1999) Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes. Cell 97: 727-741.
64. Pierani A, Brenner-Morton S, Chiang C, Jessell TM (1999) A sonic-hedgehog-independent, retinoid-activated pathway of neurogenesis in the ventral spinal cord. Cell 97: 903-915.
65. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103: 10352-10357.
66. Cheng P, He Q, Wang L, Liu Y (2005) Regulation of the Neurospora circadian clock by an RNA helicase. Genes and Develop 19: 234-241.
67. Inada M, Guthrie C (2004) Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc Natl Acad Sci U S A 101: 434-439.
68. Collis SJ, Barber LJ, Clark AJ, Martin JS, Ward JD, et al. (2007) HCLK2 is essential for the mammalian S-phase checkpoint and impacts on Chk1 stability. Nature Cell Biology 9: 391-401.
69. Miller BH, McDearmon EL, Panda S, Hayes KR, Zhang J, et al. (2007) Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation. Proc Natl Acad Sci U S A 104: 3342-3347.
70. Yang Y, He Q, Cheng P, Wrage P, Yarden O, et al. (2004) Distinct roles for PP1 and PP2A in the Neurospora circadian clock. Genes and Develop 18: 255-260.
71. He Q, Cha J, He Q, Lee H-C, Yang Y, et al. (2007) CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop. Genes and Develop 20: 2552-2565.
72. Masloff S, Jacobsen S, Poggeler S, Kuck U (2002) Functional analysis of the C6 zinc finger gene pro1 involved in fungal sexual development. Fungal Genet Biol 36: 17-116.
73. Gutierrez RA, Stokes TL, Thum K, Xu Y, Obertello M, et al. (2008) System approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A 105: 4939-4944.
74. Correa A, Bell-Pedersen D (2002) Distinct signaling pathways from the circadian clock participate in regulation of rhythmic conidiophore development in Neurospora crassa. Eukaryotic Cell 1: 273-280.
75. Youssar L, Avalos J (2006) Light-dependent regulation of the cut-1 of Neurospora, involved in the osmotic stress response. Fung Genet And Biol 43: 752-763.
76. Davidian M, Giltinan DM (1995) Nonlinear Models for Repeated Measurement Data. New York. Chapman and Hall.
77. Townsend JP (2004) Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC bioinformatics 5: 54. doi:10.1186/1471-2105-5-54..
78. Gerber AP, Herschlag D, Brown PO (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLOS Biology 2: 342-354.
79. Belden WJ, Loros JJ, Dunlap JC (2006) Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH. Molecular Cell 25: 587-600.
80. Froehlich AC, Loros JJ, Dunlap, JC (2003) Rhythmic binding of a WHITE COLLAR-containing complex to the frequency promoter is inhibited by FREQUENCY. Proc Natl Acad Sci U S A 100: 5914-5919.
81. Liu Y, Garceau NY, Loros JJ, Dunlap JC (1997) Thermally regulated translational control of FRQ mediates aspects of temperature responses in the Neurospora circadian clock. Cell 89: 477-486.
82. Ruoff P, Loros JJ, Dunlap JC (2005) The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock. Proc Natl Acad Sci U S A 102: 17681-17686.
83. 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.
84. Michael TP, Salome PA, Yu M, Spender TR, Sharp EL, et al. (2003) Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 302: 1049-1053.
85. Michael TP, Park S, Kim T-S, Booth J, Byer A, et al. (2007) Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock PLOS One 2(8): e795.
86. Wagner A (2005) Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc Natl Acad Sci U S A 102: 11775-11780.
87. Belden WJ, Larrondo LF, Frochlich AC, Shi M, Chen C-H, et al. (2007) The band mutation in Neurospara crassa is a dominant allele of ras-1 implicating RAS signaling in circadian output. Genes and Dev 21: 1494-1505.
88. Jazwinski SM (2002) Growing old: metabolic control and yeast ageing. Annu Rev Microbiol 56: 769-792.
89. D'mello NP, Childress AM, Franklin DS, Kale SP, Pinswasdi C, et al. (1994) Cloning and characterization of LAG1, a longevity-assurance gene in yeast. Journal of Biological Chemistry 269: 15451-15459.
90. Lakowski B, Hekimi S (1996) Determination of life-span in Caenorhabditis elegans by four dock genes. Science 272: 1010-1013.
91. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, et al. (2002) A genomic regulatory network for development. Science 295: 1669-1678.
92. Smith J, Theodoris C, Davidson EH (2007) A gene regulatory network subcircuit drives a dynamic pattern of gene expression. Science 318: 794-797.
93. Loros JJ, Dunlap JC (2001) Genetic and molecular analysis of Circadian rhythms in Neurospora. Annu Rev Physiol 63: 757-794.
94. Bloomfield P (1976) Fourier analysis of time series: an introduction. New York: Wiley.
95. Emery B, de la Cruz J, Rocak S, Deloche O, Linder P (2004) Haslp, a member of the DEAD-box family, is required for 40S ribosomal subunit biogenesis in Saccharomyces cervisiae. Mol. Microb. 52: 141-158.
96. Cheng P, Yang Y, Liu Y (2001) Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc Natl Acad Sci U S A 98: 7408-7413.