LUX
LUX, also known as Phytoclock1 or PCL1, is a gene in the small flowering plant Arabidopsis thaliana that holds something surprisingly complex inside it: the molecular machinery of a clock. Not a clock that ticks in seconds, but one that keeps biological time across a full day-night cycle, coordinating when the plant grows, when it flowers, and how it responds to the world around it.
In 2000, scientists first sequenced this gene at the Plant Gene Expression Center at UC Berkeley. What they found set off years of research across multiple continents. The protein LUX encodes, called LUX ARRHYTHMO, turns out to be essential. Without it, the plant's timekeeping falls apart entirely. It becomes arrhythmic, unable to coordinate the basic rhythms of life.
So what exactly is this gene doing? How does a single stretch of DNA help a plant know that night has fallen? And why does a molecule discovered in a humble laboratory weed have counterparts in barley, peas, and even single-celled algae? Those are the questions this documentary will trace.
At the heart of LUX's story is a three-protein assembly called the Evening Complex. LUX ARRHYTHMO joins with two other proteins, Early Flowering 3 (ELF3) and Early Flowering 4 (ELF4), to form this complex. Together they constitute a core component of what researchers call the Arabidopsis repressilator model of the plant circadian clock.
The Evening Complex is expressed and assembled during the evening hours. Its job, in the simplest terms, is to act as a brake. It represses transcription of the PRR9 gene, which codes for a component of another assembly called the Midday Complex. PRR9, in turn, represses CCA1 and LHY, genes whose proteins make up the Morning Complex.
This is a chain of mutual suppression. Evening tells midday to quiet down. Midday tells morning to do the same. Morning, through the CCA1 and LHY proteins, can bind to the evening element in the LUX promoter and suppress LUX expression in turn. The clock keeps itself running by having each phase of the day silence the next.
LUX also represses its own transcription as part of this repressilator system. The protein helps shut off the gene that made it, a form of self-regulation built directly into the architecture of the clock.
Arabidopsis chromosome three is where the LUX gene sits, and it contains three exons. Upstream of the coding sequence lies a promoter with a short regulatory element called the evening element, with the precise DNA sequence AAAATATCT. This nine-letter sequence is overrepresented among genes expressed in the evening in Arabidopsis, suggesting the plant uses it as a shared molecular label for evening activity.
The protein that LUX encodes is 323 amino acids long and contains a Myb-like GARP family transcription factor DNA-binding domain. This domain is what allows LUX to physically contact DNA and suppress target genes.
Five years passed between the gene's first sequencing in 2000 and the clearest evidence of its function. In 2003, scientists from the Plant Gene Expression Center and the Genomic Analysis Laboratory at the Salk Institute for Biological Studies worked together to detect LUX gene expression in Arabidopsis using cDNA arrays. Then in 2005, researchers 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. Those experiments demonstrated that LUX is necessary for circadian rhythms in Arabidopsis. Plants missing a working copy of LUX lose the regular oscillation entirely.
Phytochrome Interacting Factor 4 (PIF4) and Phytochrome Interacting Factor 5 (PIF5) are the genes through which LUX shapes how the plant grows. The Evening Complex binds to the promoters of PIF4 and PIF5, suppressing their expression in the evening hours. Both PIF4 and PIF5 proteins belong to a class called basic helix-loop-helix transcription factors, and both are connected to the induction of Flowering Locus T (FT), which expresses a florigen involved in promoting flowering in Arabidopsis.
When LUX is absent, this suppression breaks down. Mutant plants lacking functional LUX cannot hold PIF4 and PIF5 in check at night. The transcription factors accumulate too early and drive excess growth in the dark. The result is a characteristic phenotype: an elongated hypocotyl, meaning the seedling stem stretches abnormally long because the plant keeps growing through the night when it should be resting.
The same pathway connects to flowering time. Because PIF4 and PIF5 feed into the florigen cascade, disrupting LUX-mediated repression means the plant's flowering schedule can shift. The clock and the developmental calendar of the plant are not separate systems. They are woven together, with the Evening Complex sitting at a shared junction between timekeeping and growth.
LUX and ELF4 are both induced by low intensity, non-damaging UV-B radiation, linking the Evening Complex to light input. Despite this, the precise molecular mechanism by which light feeds into the Arabidopsis circadian clock has not yet been worked out.
Temperature adds another dimension. Ordinarily, variations in temperature reduce expression of several clock genes, including GIGANTEA, LUX itself, PIF4, PRR7, and PRR9. In mutants lacking LUX, ELF3, and ELF4, those same genes showed constitutively high expression regardless of temperature changes. The mutants had effectively lost the ability to modulate clock gene activity in response to warmth or cold.
Beyond that, ELF3's physical association with LUX was found to disappear at high temperatures. This suggests temperature may work partly by influencing how the Evening Complex assembles, with heat capable of pulling ELF3 away from LUX and thereby preventing the complex from reaching its target promoters. A clock that does not account for temperature would drift badly across seasons. The Evening Complex appears to be part of how the plant avoids that drift, though the exact mechanisms remain an active area of research.
NOX, whose name comes from the Latin word for night, is also called BROTHER OF LUX ARRHYTHMO, or BOA. It is a paralog of LUX: a related gene that arose through duplication within the Arabidopsis genome. Like LUX, NOX is a Myb-like GARP transcription factor. It binds DNA sequences similar to those LUX targets, interacts directly with ELF4, and peaks in the late evening.
When LUX is absent, ELF3 and ELF4 can form a complex with NOX instead. Artificial microRNA experiments showed that both NOX and LUX are required to recruit the Evening Complex to the PIF4 and PIF5 promoters. Overexpression of NOX produced plants with long-period circadian phenotypes and altered expression of CCA1, LHY, GIGANTEA, and TOC1. Notably, overexpressing NOX raised the amplitude of CCA1 expression. NOX likely acts through direct binding to the CCA1 promoter, and CCA1 protein in turn binds the NOX promoter and suppresses NOX expression, creating a reciprocal relationship.
Despite the similarities, NOX and LUX are not interchangeable. Knocking out NOX via RNA interference still left circadian rhythms intact. Knocking out LUX with null mutations produced arrhythmic plants. NOX appears important but not essential for the clock to keep ticking, while LUX is required. How exactly the two proteins divide their roles within the Evening Complex remains unresolved.
STERILE NODES, or SN, was discovered in Pisum sativum, the common pea. Its name came from an observation about flowering: photoperiod-responsive pea lines formed more vegetative nodes before they flowered compared to lines that were less sensitive to day length. Researchers concluded SN was an ortholog of LUX based on phenotypically and functionally similar mutations shared between the two genes, along with causal links between specific polymorphisms and SN mutant phenotypes. Like LUX, SN protein is expressed rhythmically under light-dark cycles and controls circadian clock function and photoperiod-sensitive flowering.
In barley, Hordeum vulgare, an ortholog called HvLUX1 was identified through a mutation at the early maturity 10 (eam10) locus. The specific mutation, named Bowman(eam10), abolished the circadian rhythm in H. vulgare flowering. High-throughput sequencing pointed to HvLUX1 as the candidate gene, though its precise mechanism in the barley clock has not yet been demonstrated.
In the green alga Chlamydomonas reinhardtii, two separate orthologs of LUX have been found: ROC15 and ROC75. No orthologs of ELF3 and ELF4 have been identified in that species, leaving open the question of whether C. reinhardtii assembles anything equivalent to the Evening Complex. Researchers have found orthologs for all three Evening Complex members in other species, but whether those proteins form a functional complex outside of Arabidopsis remains unknown, making the Evening Complex itself as much a puzzle across the tree of life as it is within the plant that first revealed it.
Common questions
What does the LUX gene do in Arabidopsis thaliana?
LUX encodes a protein called LUX ARRHYTHMO that is necessary for circadian rhythms in Arabidopsis thaliana. The LUX protein joins with ELF3 and ELF4 to form the Evening Complex, which represses transcription of clock genes including PRR9 to keep the plant's daily biological clock running. Plants with null mutations in LUX become arrhythmic and lose the ability to sustain regular circadian oscillations.
When and where was the LUX gene first discovered?
LUX was first sequenced in 2000 by a team at the Plant Gene Expression Center at UC Berkeley as part of the Arabidopsis Genome Initiative. Evidence that LUX is necessary for circadian rhythms came later, in 2005, from researchers at the Center for Gene Research at Nagoya University and the Steve Kay lab at the Scripps Research Institute.
What is the Evening Complex in Arabidopsis?
The Evening Complex is a three-protein assembly consisting of LUX ARRHYTHMO, Early Flowering 3 (ELF3), and Early Flowering 4 (ELF4). It is expressed during the evening and acts as a transcriptional repressor, silencing the PRR9 gene that codes for a component of the Midday Complex. The Evening Complex is a core component of the Arabidopsis repressilator model of the circadian clock.
Why do LUX mutants have elongated hypocotyls?
LUX mutants cannot repress Phytochrome Interacting Factor 4 (PIF4) and Phytochrome Interacting Factor 5 (PIF5) during the evening. Those transcription factors accumulate prematurely and drive excess growth during the night, resulting in an abnormally elongated hypocotyl phenotype.
What is the difference between LUX and its paralog NOX in Arabidopsis?
NOX, also called BROTHER OF LUX ARRHYTHMO (BOA), is a related Myb-like GARP transcription factor that peaks in the late evening and can interact with ELF4. Unlike LUX, NOX is not essential for circadian rhythms; RNA interference knockouts of NOX still produced oscillating plants, while LUX null mutants are arrhythmic.
Does the LUX gene have orthologs in other plant species?
Yes. STERILE NODES (SN) in peas (Pisum sativum) and HvLUX1 in barley (Hordeum vulgare) are both orthologs of LUX. Two orthologs, ROC15 and ROC75, have also been found in the alga Chlamydomonas reinhardtii, though it is unknown whether those species assemble a functional complex equivalent to the Arabidopsis Evening Complex.