LUX

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LUX ARRHYTHMO
Identifiers
Organism Arabidopsis thaliana (thale cress)
SymbolLUX
Alt. symbolsPCL1
Entrez 823817
HomoloGene 90991
UniProt Q9SNB4
Search for
Structures Swiss-model
Domains InterPro

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. [1] 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). [2]

Contents

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. [3] 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. [4] 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. [1] [5]

Structure

The LUX gene is located on the third chromosome of Arabidopsis thaliana and contains three exons. [6] 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. [7] The LUX ARRHYTHMO protein has a length of 323 amino acids and contains a Myb-like GARP family transcription factor DNA-binding domain. [8] [9]

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. [1] [9] 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. [7]

Additionally, as a part of the Arabidopsis thaliana repressilator, the LUX gene also represses its own transcription. [7]

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. [9]

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. [9] 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. [7]

Homologs

Paralogs

Paralogs of LUX have been found to act in conjunction with LUX in Arabidopsis circadian clock regulation pathways. [7]

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. [7]

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. [1]

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. [1] [7]

Orthologs

Specific studies of LUX (and ELF3) orthologous mutant alleles have identified variants in flowering and photoperiod-dependent growth. [7]

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. [10]

Gene loci orthologous to ArabidopsisELF3, 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. [10]

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. [11]

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. [11]

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. [7]

See also

Related Research Articles

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<span class="mw-page-title-main">ABC model of flower development</span> Model for genetics of flower development

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The repressilator is a genetic regulatory network consisting of at least one feedback loop with at least three genes, each expressing a protein that represses the next gene in the loop. In biological research, repressilators have been used to build cellular models and understand cell function. There are both artificial and naturally-occurring repressilators. Recently, the naturally-occurring repressilator clock gene circuit in Arabidopsis thaliana and mammalian systems have been studied.

<span class="mw-page-title-main">Phototropism</span> Growth of a plant in response to a light stimulus

In biology, phototropism is the growth of an organism in response to a light stimulus. Phototropism is most often observed in plants, but can also occur in other organisms such as fungi. The cells on the plant that are farthest from the light contain a hormone called auxin that reacts when phototropism occurs. This causes the plant to have elongated cells on the furthest side from the light. Phototropism is one of the many plant tropisms, or movements, which respond to external stimuli. Growth towards a light source is called positive phototropism, while growth away from light is called negative phototropism. Negative phototropism is not to be confused with skototropism, which is defined as the growth towards darkness, whereas negative phototropism can refer to either the growth away from a light source or towards the darkness. Most plant shoots exhibit positive phototropism, and rearrange their chloroplasts in the leaves to maximize photosynthetic energy and promote growth. Some vine shoot tips exhibit negative phototropism, which allows them to grow towards dark, solid objects and climb them. The combination of phototropism and gravitropism allow plants to grow in the correct direction.

<i>Cycle</i> (gene)

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Timing of CAB expression 1 is a protein that in Arabidopsis thaliana is encoded by the TOC1 gene. TOC1 is also known as two-component response regulator-like APRR1.

Circadian Clock Associated 1 (CCA1) is a gene that is central to the circadian oscillator of angiosperms. It was first identified in Arabidopsis thaliana in 1993. CCA1 interacts with LHY and TOC1 to form the core of the oscillator system. CCA1 expression peaks at dawn. Loss of CCA1 function leads to a shortened period in the expression of many other genes.

Steve A. Kay is a British-born chronobiologist who mainly works in the United States. Dr. Kay has pioneered methods to monitor daily gene expression in real time and characterized circadian gene expression in plants, flies and mammals. In 2014, Steve Kay celebrated 25 years of successful chronobiology research at the Kaylab 25 Symposium, joined by over one hundred researchers with whom he had collaborated with or mentored. Dr. Kay, a member of the National Academy of Sciences, U.S.A., briefly served as president of The Scripps Research Institute. and is currently a professor at the University of Southern California. He also served on the Life Sciences jury for the Infosys Prize in 2011.

Andrew John McWalter Millar, FRS, FRSE is a Scottish chronobiologist, systems biologist, and molecular geneticist. Millar is a professor at The University of Edinburgh and also serves as its chair of systems biology. Millar is best known for his contributions to plant circadian biology; in the Steve Kay lab, he pioneered the use of luciferase imaging to identify circadian mutants in Arabidopsis. Additionally, Millar's group has implicated the ELF4 gene in circadian control of flowering time in Arabidopsis. Millar was elected to the Royal Society in 2012 and the Royal Society of Edinburgh in 2013.

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The Late Elongated Hypocotyl gene (LHY), is an oscillating gene found in plants that functions as part of their circadian clock. LHY encodes components of mutually regulatory negative feedback loops with Circadian Clock Associated 1 (CCA1) in which overexpression of either results in dampening of both of their expression. This negative feedback loop affects the rhythmicity of multiple outputs creating a daytime protein complex. LHY was one of the first genes identified in the plant clock, along with TOC1 and CCA1. LHY and CCA1 have similar patterns of expression, which is capable of being induced by light. Single loss-of-function mutants in both genes result in seemingly identical phenotypes, but LHY cannot fully rescue the rhythm when CCA1 is absent, indicating that they may only be partially functionally redundant. Under constant light conditions, CCA1 and LHY double loss-of-function mutants fail to maintain rhythms in clock-controlled RNAs.

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EARLY FLOWERING 3 (ELF3) is a plant-specific gene that encodes the hydroxyproline-rich glycoprotein and is required for the function of the circadian clock. ELF3 is one of the three components that make up the Evening Complex (EC) within the plant circadian clock, in which all three components reach peak gene expression and protein levels at dusk. ELF3 serves as a scaffold to bind EARLY FLOWERING 4 (ELF4) and LUX ARRHYTHMO (LUX), two other components of the EC, and functions to control photoperiod sensitivity in plants. ELF3 also plays an important role in temperature and light input within plants for circadian clock entrainment. Additionally, it plays roles in light and temperature signaling that are independent from its role in the EC.

Elaine Munsey Tobin is a professor of molecular, cell, and developmental biology at the University of California, Los Angeles (UCLA). Tobin is recognized as a Pioneer Member of the American Society of Plant Biologists (ASPB).

The chlorophyll a/b-binding protein gene, otherwise known as the CAB gene, is one of the most thoroughly characterized clock-regulated genes in plants. There are a variety of CAB proteins that are derived from this gene family. Studies on Arabidopsis plants have shed light on the mechanisms of biological clocks under the regulation of CAB genes. Dr. Steve Kay discovered that CAB was regulated by a circadian clock, which switched the gene on in the morning and off in the late afternoon. The genes code for proteins that associate with chlorophyll and xanthophylls. This association aids the absorption of sunlight, which transfers energy to photosystem II to drive photosynthetic electron transport.

Stacey Harmer is a chronobiologist whose work centers on the study of circadian rhythms in plants. Her research focuses on the molecular workings of the plant circadian clock and its influences on plant behaviors and physiology. She is a professor in the Department of Plant Biology at the University of California, Davis.

References

  1. 1 2 3 4 5 Troncoso-Ponce MA, Mas P (May 2012). "Newly described components and regulatory mechanisms of circadian clock function in Arabidopsis thaliana". Molecular Plant. 5 (3): 545–53. doi: 10.1093/mp/ssr117 . hdl: 10261/249493 . PMID   22230762.
  2. ↑ Yamashino T (2013-01-01). "From a repressilator-based circadian clock mechanism to an external coincidence model responsible for photoperiod and temperature control of plant architecture in Arabodopsis thaliana". Bioscience, Biotechnology, and Biochemistry. 77 (1): 10–6. doi:10.1271/bbb.120765. PMID   23291766. S2CID   33795797.
  3. ↑ Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, et al. (December 2000). "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana". Nature. 408 (6814): 820–2. Bibcode:2000Natur.408..820E. doi:10.1038/35048706. PMID   11130713.
  4. ↑ Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, et al. (October 2003). "Empirical analysis of transcriptional activity in the Arabidopsis genome". Science. 302 (5646): 842–6. Bibcode:2003Sci...302..842Y. doi:10.1126/science.1088305. PMID   14593172. S2CID   7076927.
  5. ↑ Onai K, Ishiura M (October 2005). "PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock". Genes to Cells. 10 (10): 963–72. doi:10.1111/j.1365-2443.2005.00892.x. PMID   16164597. S2CID   40094451.
  6. ↑ "PCL1 Homeodomain-like superfamily protein [Arabidopsis thaliana (thale cress)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-14.
  7. 1 2 3 4 5 6 7 8 9 Huang H, Nusinow DA (October 2016). "Into the Evening: Complex Interactions in the Arabidopsis Circadian Clock" (PDF). Trends in Genetics. 32 (10): 674–686. doi:10.1016/j.tig.2016.08.002. PMID   27594171.
  8. ↑ "LUX - Transcription factor LUX - Arabidopsis thaliana (Mouse-ear cress) - LUX gene & protein". www.uniprot.org. Retrieved 2017-04-14.
  9. 1 2 3 4 Nusinow DA, Helfer A, Hamilton EE, King JJ, Imaizumi T, Schultz TF, Farré EM, Kay SA (July 2011). "The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth". Nature. 475 (7356): 398–402. doi:10.1038/nature10182. PMC   3155984 . PMID   21753751.
  10. 1 2 Liew LC, Hecht V, Sussmilch FC, Weller JL (June 2014). "The Pea Photoperiod Response Gene STERILE NODES Is an Ortholog of LUX ARRHYTHMO". Plant Physiology. 165 (2): 648–657. doi:10.1104/pp.114.237008. PMC   4044833 . PMID   24706549.
  11. 1 2 Campoli C, Pankin A, Drosse B, Casao CM, Davis SJ, von Korff M (September 2013). "HvLUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways". The New Phytologist. 199 (4): 1045–59. doi:10.1111/nph.12346. PMC   3902989 . PMID   23731278.
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