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Frequency (gene)

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This is an old revision of this page, as edited by Gcheng94 (talk | contribs) at 14:32, 3 April 2015 (Rearranged sections (function/interaction), fixed faulty link to CLOCK gene (should link to circadian clock bc CLOCK is a mammalian gene)). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Frequency clock protein
Identifiers
SymbolFRQ
PfamPF09421
InterProIPR018554
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

Frequency (frq) is a gene discovered in the fungus Neurospora crassa in 1978 that encodes the protein frequency. The gene is 2,980bp long in Sordaria macrospora k-hell.[1] The FRQ protein plays a key role in the autoregulatory transcription translation negative feedback loop (TTFL), which is responsible for circadian rhythms in N. crassa and other fungi such as N. sitophita, N. tetrasperma, N. galapagosensis, C. spinulosa, and L. australiensis.[2]

Discovery

Malcolm L. Sargent, Winslow R. Briggs and Dow O. Woodward at Stanford University discovered the presence of a circadian clock in Neurospora crassa in 1966.[3] Jerry F. Feldman and Marian N. Hoyle discovered the frq mutant genes (frq-1, frq-2, and frq-3) in 1973.[4] In 1986, frq was first cloned, which allowed further research and understanding of the circadian clock.[5]

Function

Frq’s important circadian function is supported by experiments showing that deletion of the frq gene results in arrhythmicity. Frq forms two transcripts that encode two different FRQ proteins, a long form of 989 amino acids (lFRQ) and a shorter form of 890 amino acids (sFRQ).[6] Temperature determines the ratio at which both FRQ proteins are present, but both are required for strong rhythmicity. However, the CLOCK is able to persist at certain temperatures, albeit with a weaker rhythmicity, with just one of the proteins present.[7] FRQ protein has also been shown to interact with FRH (FRQ-interacting RNA helicase; an essential DEAD box-containing RNA helicase in Neurospora) to form a FRQ/FRH complex (FFC).[8]

Simplified Representation of Neurospora Circadian Clock[9]

Regulation

White collar-1 (WC-1) and white collar-2 (WC-2) are GATA transcription factors in Neurospora and they form a heterodimeric "white collar complex" (WCC) via their PAS domains.[10] When WCC is hypophosphorylated during subjective night, it binds to the frequency (frq) gene promotor and activates frq transcription. The frequency (FRQ) protein accumulates and is progressively phosphorylated by casein kinase 2 (CKII), reaching its peak around mid-subjective day. When FRQ is hyperphosphorylated, it is ubiquitinated and degraded by the proteasome. FRQ recruits kinases such as casein kinase 1a (CK-1a) that phosphorylates WCC. Hyperphosphorylated WCC is inactive and binds poorly to frq promotor. This results in inhibited frq gene transcription and a lower FRQ protein level, and eventually repression is relieved to allow frq transcription to build up again. This process occurs with a periodicity of around 22 hours in constant conditions.[9][11]

Mutation

Genetic analysis of the locus has identified alleles that alter the period length of asexual spore formation (conidiation). Mutations have been identified that cause both long and short periods relative to the wild-type value of 21.5 hours. Mutants attain a shorter or longer period due to the rate at which they are phosphorylated. Mutants that can reduce phosphorylation, due to a mutation in a binding site, will not degrade as rapidly and have a longer period. The reverse is true for mutants with a short period.[12] The period of the frq mutants at 25oC are as follows: frq-1 : 16.5 hrs, frq-2: 19.3 hrs; frq-3: 24.0 hrs, frq -4: 19.3 hrs, frq-6: 19.2 hrs, frq 7: 29.0 hrs, frq-8: 29 hrs. The first three mutations are very closely linked since no genetic recombination among them is detected. Each mutant segregates as a single nuclear gene.[13] In addition, one recessive allele, frq-9 results in conditional arrhythmicity and a complete loss of temperature compensation.[2]

FRQ-less Oscillator (FLO)

In frq null mutants Neurospora crassa, a rhythm of conidiospore development was still observed in constant darkness (DD).[14] The period for frq null mutants varied from 12 to 35 hours, and it could be stabilized by adding farnesol or geraniol (two intermediates of the sterol synthesis pathway) to the growth medium. In addition, although FRQ-less rhythm lost certain CLOCK characteristics such as temperature compensation, it could be reset by temperature pulses.[15] Therefore, there was evidence for a FRQ-less oscillator in Neurospora crassa. The mechanism and significance for FRQ-less oscillator (FLO) are still under research.

Evolution

Since codon optimization of the frq gene results in impaired circadian feedback loop function, frq displays non-optimal codon usage bias across its open reading frame in contrast to most other genes.[16]

References

  1. ^ "frq frequency, clock protein FRQ [Sordaria macrospora k-hell]". Gene. NCBI.
  2. ^ a b Lewis MT, Feldman JF (November 1996). "Evolution of the Frequency (frq) clock locus in Ascomycete fungi" (PDF). Mol. Biol. Evol. 13 (9): 1233–41. doi:10.1093/oxfordjournals.molbev.a025689. PMID 8896376.
  3. ^ Sargent ML, Briggs WR, Woodward DO (October 1966). "Circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa". Plant Physiol. 41 (8): 1343–9. doi:10.1104/pp.41.8.1343. PMC 550529. PMID 5978549.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Feldman JF, Hoyle MN (December 1973). "Isolation of circadian clock mutants of Neurospora crassa". Genetics. 75 (4): 605–13. PMC 1213033. PMID 4273217.
  5. ^ McClung CR, Fox BA, Dunlap JC (June 1989). "The Neurospora clock gene Frequency shares a sequence element with the Drosophila clock gene period". Nature. 339 (6225): 558–62. doi:10.1038/339558a0. PMID 2525233.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Nakashima H, Onai K (December 1996). "The circadian conidiation rhythm in Neurospora crassa". Seminars in Cell & Developmental Biology. 7 (6): 765–774. doi:10.1006/scdb.1996.0094.
  7. ^ Liu Y, Garceau NY, Loros JJ, Dunlap JC (May 1997). "Thermally regulated translational control of FRQ mediates aspects of temperature responses in the neurospora circadian clock". Cell. 89 (3): 477–86. doi:10.1016/S0092-8674(00)80228-7. PMID 9150147.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ^ Cheng P, He Q, He Q, Wang L, Liu Y (January 2005). "Regulation of the Neurospora circadian clock by an RNA helicase". Genes Dev. 19 (2): 234–41. doi:10.1101/gad.1266805. PMC 545885. PMID 15625191.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ a b Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM (2012). "Comprehensive modelling of the Neurospora circadian clock and its temperature compensation". PLoS Comput. Biol. 8 (3): e1002437. doi:10.1371/journal.pcbi.1002437. PMC 3320131. PMID 22496627.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  10. ^ Cheng P, Yang Y, Liu Y (June 2001). "Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock". Proc. Natl. Acad. Sci. U.S.A. 98 (13): 7408–13. doi:10.1073/pnas.121170298. PMC 34682. PMID 11416214.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ Yang Y, Cheng P, He Q, Wang L, Liu Y (September 2003). "Phosphorylation of FREQUENCY protein by casein kinase II is necessary for the function of the Neurospora circadian clock". Mol. Cell. Biol. 23 (17): 6221–8. doi:10.1128/MCB.23.17.6221-6228.2003. PMC 180927. PMID 12917343.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ Liu Y, Loros J, Dunlap JC (January 2000). "Phosphorylation of the Neurospora clock protein FREQUENCY determines its degradation rate and strongly influences the period length of the circadian clock". Proc. Natl. Acad. Sci. U.S.A. 97 (1): 234–9. doi:10.1073/pnas.97.1.234. PMC 26646. PMID 10618401.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  13. ^ Dunlap JC (1996). "Genetics and molecular analysis of circadian rhythms". Annu. Rev. Genet. 30: 579–601. doi:10.1146/annurev.genet.30.1.579. PMID 8982466.
  14. ^ http://symposium.cshlp.org/content/72/279.long
  15. ^ Granshaw T, Tsukamoto M, Brody S (August 2003). "Circadian rhythms in Neurospora crassa: farnesol or geraniol allow expression of rhythmicity in the otherwise arrhythmic strains frq10, wc-1, and wc-2". J. Biol. Rhythms. 18 (4): 287–96. doi:10.1177/0748730403255934. PMID 12932081.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  16. ^ Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y (March 2013). "Non-optimal codon usage affects expression, structure and function of clock protein FRQ". Nature. 495 (7439): 111–5. doi:10.1038/nature11833. PMID 23417067.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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