LUX

LUX or Phytoclock1 (PCL1) is a gene that codes for LUX ARRHYTHMO, a protein necessary for circadian rhythms in "Arabidopsis thaliana". LUX protein associates with Early Flowering 3 (ELF3) and Early Flowering 4 (ELF4) to form the Evening Complex (EC), a core component of the "Arabidopsis" repressilator model of the plant circadian clock. The LUX protein functions as a transcription factor that negatively regulates "Pseudo-Response Regulator 9" ("PRR9"), a core gene of the Midday Complex, another component of the "Arabidopsis" repressilator model. LUX is also associated with circadian control of hypocotyl growth factor genes "PHYTOCHROME INTERACTING FACTOR 4" ("PIF4)" and "PHYTOCHROME INTERACTING FACTOR 5" ("PIF5)".
Discovery.
In 2000, the "LUX" gene was first sequenced in "Arabidopsis thaliana" by a team at the Plant Gene Expression Center at UC Berkeley as a part of the Arabidopsis Genome Initiative. In 2003, scientists from the Plant Gene Expression Center and the Genomic Analysis Laboratory at the Salk Institute for Biological Studies collaborated to identify expression of the "LUX" gene in Arabidopsis using cDNA arrays. In 2005, scientists at the Center for Gene Research at Nagoya University and the Steve Kay lab at the Scripps Research Institute studied null mutations of "LUX" and the other Evening Complex genes to show that "LUX" was necessary for circadian rhythms in "A. thaliana."
Structure.
The "LUX" gene is located on the third chromosome of "Arabidopsis thaliana" and contains three exons. Upstream of the "LUX" gene is a promoter containing a "cis-"regulatory element known as the "evening element" (EE) with the sequence AAAATATCT. It is overrepresented in evening-expressed genes in the Arabidopsis repressilator. The EE may be bound by Circadian Clock Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY) proteins to suppress expression of "LUX". The LUX ARRHYTHMO protein has a length of 323 amino acids and contains a Myb-like GARP family transcription factor DNA-binding domain.
Function.
Circadian oscillator.
The LUX ARRHYTHMO protein encoded by the "LUX" gene participates in the regulation of the "Arabidopsis thaliana" circadian clock. Along with ELF3 and ELF4, it is a member of the Evening Complex, a component of the Arabidopsis repressilator model of gene regulation. This three-protein complex is expressed and assembled during the evening to repress transcription of the "PRR9" gene, which codes for a component of the Midday Complex. LUX likely represses "PRR9" via direct binding to a DNA sequence that has not yet been elucidated. PRR9 protein subsequently represses "CCA1" and "LHY", genes which express components of the Morning Complex. Although "LUX" and "ELF4" are induced by low intensity, non-damaging UV-B radiation, the direct molecular mechanism of light input into the "Arabidopsis" circadian clock has yet to be elucidated.
Additionally, as a part of the "Arabidopsis thaliana" repressilator, the "LUX" gene also represses its own transcription.
"Arabidopsis thaliana" growth and flowering.
The EC binds to promoters of "Phytochrome Interacting Factor 4" ("PIF4") and "Phytochrome Interacting Factor 5" ("PIF5"), repressing their expression and subsequently inhibiting plant growth in the evening. PIF4 and PIF5 proteins are both basic helix-loop-helix (bHLH) domain transcription factors that are implicated in the induction of "Flowering Locus T" ("FT"), which expresses a florigen involved in promoting "A. thaliana" flowering. Mutants lacking functional "LUX" are unable to repress "PIF4" and "PIF5", leading to early accumulation of PIF4 and PIF5 transcription factors and thus premature growth; consequently, "LUX" mutants often express an elongated hypocotyl phenotype due to excess growth during the night.
Temperature input.
The EC also plays a role in the detection and response to temperature. Despite variations in temperature which would normally reduce the expression of "GI" ("GIGANTEA"), "LUX", "PIF4", "PRR7", and "PRR9," these genes showed constitutively high expression in "LUX" (as well as "ELF3" and "ELF4") mutants. This suggested that "LUX" mutants abolished the temperature-responsiveness of those clock genes. In addition, ELF3 association to LUX was found to be abolished at high temperatures, suggesting that temperature may play a role in recruiting EC components to their targeted promoters.
Homologs.
Paralogs.
Paralogs of LUX have been found to act in conjunction with LUX in Arabidopsis circadian clock regulation pathways.
"NOX"/"BOA".
In the absence of LUX, ELF3 and ELF4 have also been found to form a complex with LUX paralog NOX (meaning “night” in Latin), also called BROTHER OF LUX ARRHYTHMO (BOA). NOX is a homologous Myb-like GARP transcription factor that binds to DNA sequences similar to LUX's binding, interacts directly with ELF4, and peaks in the late evening.
Experiments involving artificial microRNA (amiRNA) methods have shown that both NOX and LUX are required to recruit the EC to the "PIF4" and "PIF5" promoters. There is evidence for NOX having an important role in the regulation of the plant circadian oscillator; overexpression of NOX has been found to have circadian phenotypes of long periods, as well as altered expressions of "CCA1", "LHY", "GI", and "TOC1". In particular, overexpression of NOX showed increased amplitudes of "CCA1" expression. NOX likely regulates "CCA1" through direct binding to the "CCA1" promoter, and, conversely, CCA1 protein has been found to bind to the "NOX" promoter and inhibit "NOX" expression.
In contrast to "LUX", amiRNA knockouts of "NOX" have shown that NOX is not required for circadian rhythms, suggesting that the functionality of LUX and NOX are not completely redundant. RNAi experiments reducing "NOX" expression showed a continuation of circadian rhythms, whereas "LUX" null mutants are arrhythmic. Currently, more research must be done to determine how LUX and NOX differ in their contributions to the EC.
Orthologs.
Specific studies of "LUX" (and "ELF3") orthologous mutant alleles have identified variants in flowering and photoperiod-dependent growth.
"STERILE NODES".
An ortholog for "LUX" named "STERILE NODES (SN)" was discovered in "Pisum sativum". The name STERILE NODES came from the observation that photoperiod-responsive "P. sativum" lines formed more vegetative nodes before flowering compared to less photoperiod-responsive lines. The relationship of "LUX" and "SN" as orthologs was concluded based on the discovery of functionally and phenotypically similar mutations in "SN" and "LUX", as well as apparent causal linkages between specific polymorphisms and "SN" mutant phenotypes. Like "LUX", "SN" was found to be a major gene locus that controls regulation of circadian clock function and photoperiod-sensitive flowering. Also similar to LUX, SN protein is expressed rhythmically when exposed to light-dark cycles.
Gene loci orthologous to "Arabidopsis" "ELF3", "ELF4", and "GI" have also been found in "P. sativum", named "HIGH RESPONSE TO PHOTOPERIOD" ("HR"), "DIE NEUTRALIS" ("DNE"), and "LATE BLOOMER1" ("LATE1") respectively. However, they have not yet been discovered to form a functional complex equivalent to the EC in "Arabidopsis".
"HvLUX1".
"HvLUX1" in "Hordeum vulgare" has been identified as an ortholog of "LUX". The experiment leading to the discovery of "HvLUX1" involved a mutation in the "early maturity 10 "("eam10") locus in the "H. vulgare" genome. The mutation, called Bowman("eam10"), abolished the circadian rhythm observed in "H. vulgare" flowering. Via high throughput sequencing, "HvLUX1" has been identified as a candidate gene for this locus, though its specific mechanism of action in the circadian clock has yet to be demonstrated.
Gene loci homologous to "A. thaliana PRR" genes ("PRR7" and "PRR9"), "ELF3" and "FT" have also been found in "H. vulgare", named "PHOTOPERIOD 1" ("Ppd-H1"), "HvELF3", and "HvFT1", respectively.
"ROC15" and "ROC75".
Orthologs have been found for all three members of the "Arabidopsis thaliana" Evening Complex, but it is currently unknown if the EC is formed in species other than "A. thaliana". Two orthologs of "LUX", "ROC15" and "ROC75", have been discovered in "Chlamydomonas reinhardtii," but orthologs of "ELF3" and "ELF4" in "C. reinhardtii" have not yet been found.