Detection and response of the Neurospora crassa circadian clock to light and temperature

Ashmore, 2003, A fly’s eye view of circadian entrainment, Journal of Biological Rhythms, 18, 206, 10.1177/0748730403018003003 Baker, 2009, Quantitative proteomics reveals a dynamic interactome and phase-specific phosphorylation in the Neurospora circadian clock, Molecular Cell, 34, 354, 10.1016/j.molcel.2009.04.023 Ballario, 1996, White collar-1, a central regulator of blue-light responses in Neurospora crassa, is a zinc-finger protein, EMBO Journal, 15, 1650, 10.1002/j.1460-2075.1996.tb00510.x Belden, 2007, Execution of the circadian negative feedback loop in Neurospora requires the ATP-dependent chromatin-remodeling enzyme CLOCKSWITCH, Molecular Cell, 25, 587, 10.1016/j.molcel.2007.01.010 Bieszke, 1999, The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins, Proceedings of the National Academy of Sciences of the United States of America, 96, 8034, 10.1073/pnas.96.14.8034 Bieszke, 2007, The fungal opsin gene nop-1 is negatively-regulated by a component of the blue light sensing pathway and influences conidiation-specific gene expression in Neurospora crassa, Current Genetics, 52, 149, 10.1007/s00294-007-0148-8 Bieszke, 1999, A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment, Biochemistry, 38, 14138, 10.1021/bi9916170 Borgs, 2009, Cell “circadian” cycle: new role for mammalian core clock genes, Cell Cycle, 8, 832, 10.4161/cc.8.6.7869 Chen, 2009, Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora, EMBO Journal, 28, 1029, 10.1038/emboj.2009.54 Chen, 2010, Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora, Proceedings of the National Academy of Sciences of the United States of America, 107, 16715, 10.1073/pnas.1011190107 Cheng, 2005, Regulation of the Neurospora circadian clock by an RNA helicase, Genes & Development, 19, 234, 10.1101/gad.1266805 Cheng, 2003, Functional conservation of light, oxygen, or voltage domains in light sensing, Proceedings of the National Academy of Sciences of the United States of America, 100, 5938, 10.1073/pnas.1031791100 Collett, 2001, Circadian clock-specific roles for the light response protein WHITE COLLAR-2, Molecular and Cellular Biology, 21, 2619, 10.1128/MCB.21.8.2619-2628.2001 Colot, 2005, Temperature-modulated alternative splicing and promoter use in the circadian clock gene frequency, Molecular Biology of the Cell, 16, 5563, 10.1091/mbc.E05-08-0756 Correa, 2003, Multiple oscillators regulate circadian gene expression in Neurospora, Proceedings of the National Academy of Sciences of the United States of America, 100, 13597, 10.1073/pnas.2233734100 Crosthwaite, 2004, Circadian clocks and natural antisense RNA, FEBS Letters, 567, 49, 10.1016/j.febslet.2004.04.073 Crosthwaite, 1997, Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity, Science, 276, 763, 10.1126/science.276.5313.763 Crosthwaite, 1995, Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript, Cell, 81, 1003, 10.1016/S0092-8674(05)80005-4 Dharmananda, 1980 Diernfellner, 2007, Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythms, FEBS Letters, 581, 5759, 10.1016/j.febslet.2007.11.043 Diernfellner, 2005, Molecular mechanism of temperature sensing by the circadian clock of Neurospora crassa, Genes & Development, 19, 1968, 10.1101/gad.345905 Dodd, 2005, Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage, Science, 309, 630, 10.1126/science.1115581 Dowson-Day, 1999, Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis, Plant Journal, 17, 63, 10.1046/j.1365-313X.1999.00353.x Dragovic, 2002, Light reception and circadian behavior in ‘blind’ and ‘clock-less’ mutants of Neurospora crassa, EMBO Journal, 21, 3643, 10.1093/emboj/cdf377 Dunlap, 2007, Enabling a community to dissect an organism: overview of the Neurospora functional genomics project, Advances in Genetics, 57, 49, 10.1016/S0065-2660(06)57002-6 Dunlap, 2004, The Neurospora circadian system, Journal of Biological Rhythms, 19, 414, 10.1177/0748730404269116 Dunlap, 2004 Elvin, 2005, The PAS/LOV protein VIVID supports a rapidly dampened daytime oscillator that facilitates entrainment of the Neurospora circadian clock, Genes & Development, 19, 2593, 10.1101/gad.349305 Fleissner, 1992, Feedback loops in the circadian system, 79 Francis, 1979, Effects of temperature perturbations on circadian conidiation in Neurospora crassa, Plant Physiology, 64, 1000, 10.1104/pp.64.6.1000 Froehlich, 2010, Genetic and molecular characterization of a cryptochrome from the filamentous fungus Neurospora crassa, Eukaryotic Cell, 9, 738, 10.1128/EC.00380-09 Froehlich, 2002, White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter, Science, 297, 815, 10.1126/science.1073681 Froehlich, 2003, Rhythmic binding of a WHITE COLLAR-containing complex to the frequency promoter is inhibited by FREQUENCY, Proceedings of the National Academy of Sciences of the United States of America, 100, 5914, 10.1073/pnas.1030057100 Froehlich, 2005, Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassa, Eukaryotic Cell, 4, 2140, 10.1128/EC.4.12.2140-2152.2005 Fu, 2002, The circadian gene Period2 plays an important role in tumor suppression and DNA damage response in vivo, Cell, 111, 41, 10.1016/S0092-8674(02)00961-3 Galagan, 2003, The genome sequence of the filamentous fungus Neurospora crassa, Nature, 422, 859, 10.1038/nature01554 Garceau, 1997, Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY, Cell, 89, 469, 10.1016/S0092-8674(00)80227-5 Gardner, 1980, The frq locus in Neurospora crassa: a key element in circadian clock organization, Genetics, 96, 877, 10.1093/genetics/96.4.877 Gillette, 2002, Signaling in the suprachiasmatic nucleus: selectively responsive and integrative, Cell & Tissue Research, 309, 99, 10.1007/s00441-002-0576-1 Gooch, 2008, Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock, Eukaryotic Cell, 7, 28, 10.1128/EC.00257-07 Gooch, 1994, Temperature effects on the resetting of the phase of the Neurospora circadian rhythm, Journal of Biological Rhythms, 9, 83, 10.1177/074873049400900108 Guo, 2009, The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop, Cell, 138, 1236, 10.1016/j.cell.2009.06.043 Hastings, 1958, A persistent diurnal rhythm of luminescence in Gonyaulax polyedra, The Biological Bulletin, 115, 440, 10.2307/1539108 He, 2006, CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop, Genes & Development, 20, 2552, 10.1101/gad.1463506 He, 2002, White collar-1, a DNA binding transcription factor and a light sensor, Science, 297, 840, 10.1126/science.1072795 He, 2005, Degradation of the Neurospora circadian clock protein FREQUENCY through the ubiquitin-proteasome pathway, Biochemistry Society Transactions, 33, 953, 10.1042/BST20050953 Heintzen, 2007, The Neurospora crassa circadian clock, Advances in Genetics, 58, 25, 10.1016/S0065-2660(06)58002-2 Heintzen, 2001, The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting, Cell, 104, 453, 10.1016/S0092-8674(01)00232-X Heschel, 2007, A new role for phytochromes in temperature-dependent germination, The New Phytologist, 174, 735, 10.1111/j.1469-8137.2007.02044.x Hicks, 1996, Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant, Science, 274, 790, 10.1126/science.274.5288.790 Honda, 2009, Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification, Genetics, 182, 11, 10.1534/genetics.108.098707 Hunt, 2007, The PAS/LOV protein VIVID controls temperature compensation of circadian clock phase and development in Neurospora crassa, Genes & Development, 21, 1964, 10.1101/gad.437107 Hunt, 2010, VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora, Proceedings of the National Academy of Sciences of the United States of America, 107, 16709, 10.1073/pnas.1009474107 Johnson, 1999, Forty years of PRCs—what have we learned?, Chronobiology International, 16, 711, 10.3109/07420529909016940 Johnson, 2004, Fundamental properties of circadian rhythms Johnson, 2003, Entrainment of circadian programs, Chronobiology International, 20, 741, 10.1081/CBI-120024211 Jones, 1999, Familial advanced sleep-phase syndrome: a short-period circadian rhythm variant in humans, Nature Medicine, 5, 1062, 10.1038/12502 Kramer, 2003, Role for antisense RNA in regulating circadian clock function in Neurospora crassa, Nature, 421, 948, 10.1038/nature01427 Lakin-Thomas, 1990, Circadian rhythms in Neurospora crassa: biochemistry and genetics, Critical Reviews in Microbiology, 17, 365, 10.3109/10408419009114762 Lamb, 2008, Time-resolved dimerization of a PAS-LOV protein measured with photocoupled small angle X-ray scattering, Journal of the American Chemical Society, 130, 12226, 10.1021/ja804236f Lee, 2000, Interconnected feedback loops in the Neurospora circadian system, Science, 289, 107, 10.1126/science.289.5476.107 Liu, 1997, Thermally regulated translational control of FRQ mediates aspects of temperature responses in the Neurospora circadian clock, Cell, 89, 477, 10.1016/S0092-8674(00)80228-7 McWatters, 2000, The ELF3 zeitnehmer regulates light signalling to the circadian clock, Nature, 408, 716, 10.1038/35047079 Mehra, 2009, A role for casein kinase 2 in the mechanism underlying circadian temperature compensation, Cell, 137, 749, 10.1016/j.cell.2009.03.019 Malzahn, 2010, Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains, Cell, 142, 762, 10.1016/j.cell.2010.08.010 Millar, 1996, Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis, Proceedings of the National Academy of Sciences of the United States of America, 93, 15491, 10.1073/pnas.93.26.15491 Nowrousian, 2003, The frequency gene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa, Genetics, 164, 923, 10.1093/genetics/164.3.923 Olmedo, 2010, A complex photoreceptor system mediates the regulation by light of the conidiation genes con-10 and con-6 in Neurospora crassa, Fungal Genetics and Biology, 47, 352, 10.1016/j.fgb.2009.11.004 Ouyang, 1998, Resonating circadian clocks enhance fitness in cyanobacteria, Proceedings of the National Academy of Sciences of the United States of America, 95, 8660, 10.1073/pnas.95.15.8660 Pittendrigh, 1981, Circadian systems: entrainment Pittendrigh, 1959, Growth patterns in Neurospora, Nature, 184, 169, 10.1038/184169a0 Price-Lloyd, 2005, Synchronizing the Neurospora crassa circadian clock with the rhythmic environment, Biochemistry Society Transactions, 33, 949, 10.1042/BST20050949 Querfurth, 2007, Posttranslational regulation of Neurospora circadian clock by CK1a-dependent phosphorylation, Cold Spring Harbor Symposia on Quantitative Biology, 72, 177, 10.1101/sqb.2007.72.025 Sargent, 1967, The effects of light on a circadian rhythm of conidiation in Neurospora, Plant Physiology, 42, 1504, 10.1104/pp.42.11.1504 Sargent, 1966, Circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa, Plant Physiology, 41, 1343, 10.1104/pp.41.8.1343 Schafmeier, 2008, Circadian activity and abundance rhythms of the Neurospora clock transcription factor WCC associated with rapid nucleo-cytoplasmic shuttling, Genes & Development, 22, 3397, 10.1101/gad.507408 Schafmeier, 2006, Phosphorylation-dependent maturation of Neurospora circadian clock protein from a nuclear repressor toward a cytoplasmic activator, Genes & Development, 20, 297, 10.1101/gad.360906 Schwerdtfeger, 2003, VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation, EMBO Journal, 22, 4846, 10.1093/emboj/cdg451 Shigeyoshi, 1997, Light-induced resetting of a mammalian circadian clock is associated with rapid induction of the mPer1 transcript, Cell, 91, 1043, 10.1016/S0092-8674(00)80494-8 Shrode, 2001, vvd is required for light adaptation of conidiation-specific genes of Neurospora crassa, but not circadian conidiation, Fungal Genetics and Biology, 32, 169, 10.1006/fgbi.2001.1264 Talavera, 2008, Neuronal TRP channels: thermometers, pathfinders and life-savers, Trends in Neurosciences, 31, 287, 10.1016/j.tins.2008.03.002 Tan, 2004, Entrainment dissociates transcription and translation of a circadian clock gene in Neurospora, Current Biology, 14, 433, 10.1016/j.cub.2004.02.035 Tang, 2009, Setting the pace of the Neurospora circadian clock by multiple independent FRQ phosphorylation events, Proceedings of the National Academy of Sciences of the United States of America, 106, 1, 10.1073/pnas.0904898106 Toh, 2001, An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome, Science, 291, 1040, 10.1126/science.1057499 Vitalini, 2006, The rhythms of life: circadian output pathways in Neurospora, Journal of Biological Rhythms, 21, 432, 10.1177/0748730406294396 Young, 2001, Timezones: a comparative genetics of circadian clocks, Nature Reviews Genetics, 2, 702, 10.1038/35088576 Zoltowski, 2008, Light activation of the LOV protein Vivid generates a rapidly exchanging dimer, Biochemistry, 47, 7012, 10.1021/bi8007017 Zoltowski, 2007, Conformational switching in the fungal light sensor Vivid, Science, 316, 1054, 10.1126/science.1137128