CAB gene

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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. [1] 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. [2] The genes code for proteins that associate with chlorophyll and xanthophylls. [3] This association aids the absorption of sunlight, which transfers energy to photosystem II to drive photosynthetic electron transport.

Contents

Discovery

Critical research on the clock components and mechanisms involving genetic studies proliferated in the late 1900s. Dr. Steve Kay is a chronobiologist who developed novel methods for real time examination of daily gene expression and studied the circadian gene expression in plants further. He discovered that CAB was regulated by a circadian clock, which switched the gene on in the morning and off in the late afternoon. [4] As a German botanist who focused on molecular plant physiology, Klaus Kloppstech discovered the potential regulation of circadian rhythm in peas by transcripts of chlorophyll a/b binding protein (LHCB/CAB). [5] [6] The transcripts’ abundance fluctuation correlates to the circadian rhythm in peas. CAB, the subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, is light-induced. The replicated study in wheat showed that circadian rhythm regulates the CAB1 gene's transcription rate. [7] Later, the mechanism of the CAB gene was studied in Arabidopsis thaliana and it was shown that both CAB1 and CAB2 genes transcription are circadian regulated. [8] Due to its fit for positional gene cloning, [9] Arabidopsis thaliana received wide recognition as a potent organism to study with forward genetics and gene cloning and was gradually developed into a model organism for studying biological clocks in plants.  The result showed that the CAB gene displayed circadian control for transcription rate and accumulation of Arabidopsis CAB and many other genes. [8] [10]

Function

The Cab gene, responsible for encoding the chlorophyll a/b-binding protein in Arabidopsis, plays a crucial role in the absorption of excitation energy necessary for photosynthetic mechanisms in plants. Its rapid induction upon exposure to light. In continuous light, the gene has been shown to trigger robust circadian rhythms in seedlings. [11]

Mechanism

The circadian clock interacts with a specific phototransduction pathway that involves the CAB2 promoter. One proposed mechanism implicates transcription factors that are under circadian control. The -111 to -38 region sequence of the CAB promote in Arabidopsis contains special motifs. It includes a CCAAT box and three GATA motifs. The orientations and spacing of these motifs are conserved in CAB promoters across many species. A protein called CAB GATA factor 1 (CGT-1) binds to the GATA repeats and promotes CAB2 production. A mutation that prevents CGT-1 and GATA binding results in reduced CAB2 production. [12]

A different proposed mechanism suggests calcium ion plays a role in CAB gene regulation. The reciprocal control model suggests gene expression is upregulated in a calcium/calmodulin-dependent manner. Transcription levels are dampened via a cGMP-dependent pathway, which is under circadian control, leading to a rhythmic flux of CAB expression that responds to light. [13]

Beyond regulation via photo cytochrome input, specific CAB genes can be independently regulated via blue light input. In Arabidopsis, CAB1 is regulated through a blue light system. CAB1 mRNA levels increase following exposure to the blue light. Other gene subtypes, such as CAB2 and CAB3, are not regulated by blue light. There are distinct, but related, pathways involving blue light and phytochromes that affect CAB regulation. [14]

Chronobiology

Because the expression of the CAB mRNA is rhythmic, it is often used as a marker for circadian rhythm in plants. [15] CAB is confined to the mesophyll and guard cells and the cycling of CAB expression in the Arabidopsis plant suggests that there is a circadian clock that controls the CAB gene. [16] [17] When the plants were moved from light/dark cycles to constant darkness, CAB2 and CAB3 genes showed an exaggerated circadian cycling. [17] Presence of various rhythms in plants suggests that there are many copies of the circadian clock in the plant circadian system, CAB genes are only a subset of these clocks. [17] In light-dark cycles with long photoperiods, CAB expression is delayed because of the entrainment of the circadian oscillator that controls the expression of CAB. [18] A study done comparing the rhythms of CAB with a photoreceptor gene Phytochrome B (PHYB), the most abundant photoreceptor in plants, showed that PHYB had a longer free-running period than CAB expression. [16] Though there is a difference in the period between CAB and Phytochrome B (PHYB), there are many similarities in the circadian clocks that control the expression of each gene, including photoreceptors and clock-related genes, which indicates some overlap in the biochemical mechanisms. [16]

Steady-state mRNA levels of the CAB2 and CAB3 genes showed a dramatic circadian cycling in plants shifted from light/dark cycles to constant darkness, whereas the cabl mRNA level exhibited little or no cycling under the same conditions. [8]

Application of Research

Contribution in space biology

The purpose of researching plant space biology is to investigate how plants are affected by the space environment. The data obtained from studying Arabidopsis plant's biological responses can be used to improve and innovate aerospace hardware, reducing the impact of engineering on  living organism. Additionally, molecular genetic tools are being utilized to study how spaceflight affects plants, and these studies could lead to a better understanding of aerospace biology. [19]

Research on Arabidopsis plants, using DNA microarrays, has shown that wide-scale genome expression changes can occur in the spaceflight environment. Further analysis using quantitative RT-PCR confirmed that the expression of CAB 4.9, a subset of CAB genes, was significantly suppressed in spaceflight samples compared to ground control samples. CAB genes are known to respond to temperature and light separately, so better environmental control of hardware management would help eliminate these gene expression differences by mitigating simple environmental challenges such as lighting and heat exchange. By monitoring these biological responses, scientists and engineers can gain insight into hardware development. Moreover, this further suggests that environmental factors can affect gene expression. [19]

Related Research Articles

A circadian clock, or circadian oscillator, is a biochemical oscillator that cycles with a stable phase and is synchronized with solar time.

In developmental biology, photomorphogenesis is light-mediated development, where plant growth patterns respond to the light spectrum. This is a completely separate process from photosynthesis where light is used as a source of energy. Phytochromes, cryptochromes, and phototropins are photochromic sensory receptors that restrict the photomorphogenic effect of light to the UV-A, UV-B, blue, and red portions of the electromagnetic spectrum.

<span class="mw-page-title-main">Cryptochrome</span> Class of photoreceptors in plants and animals

Cryptochromes are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields in a number of species. The name cryptochrome was proposed as a portmanteau combining the chromatic nature of the photoreceptor, and the cryptogamic organisms on which many blue-light studies were carried out.

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.

Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. They mediate light responses as varied as visual perception, phototropism and phototaxis, as well as responses to light-dark cycles such as circadian rhythm and other photoperiodisms including control of flowering times in plants and mating seasons in animals.

In molecular biology, an oscillating gene is a gene that is expressed in a rhythmic pattern or in periodic cycles. Oscillating genes are usually circadian and can be identified by periodic changes in the state of an organism. Circadian rhythms, controlled by oscillating genes, have a period of approximately 24 hours. For example, plant leaves opening and closing at different times of the day or the sleep-wake schedule of animals can all include circadian rhythms. Other periods are also possible, such as 29.5 days resulting from circalunar rhythms or 12.4 hours resulting from circatidal rhythms. Oscillating genes include both core clock component genes and output genes. A core clock component gene is a gene necessary for to the pacemaker. However, an output oscillating gene, such as the AVP gene, is rhythmic but not necessary to the pacemaker.

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.

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).

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.

Pseudo-response regulator (PRR) refers to a group of genes that regulate the circadian oscillator in plants. There are four primary PRR proteins that perform the majority of interactions with other proteins within the circadian oscillator, and another (PRR3) that has limited function. These genes are all paralogs of each other, and all repress the transcription of Circadian Clock Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY) at various times throughout the day. The expression of PRR9, PRR7, PRR5 and TOC1/PRR1 peak around morning, mid-day, afternoon and evening, respectively. As a group, these genes are one part of the three-part repressilator system that governs the biological clock in plants.

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.

Transcription-translation feedback loop (TTFL) is a cellular model for explaining circadian rhythms in behavior and physiology. Widely conserved across species, the TTFL is auto-regulatory, in which transcription of clock genes is regulated by their own protein products.

Carla Beth Green is an American neurobiologist and chronobiologist. She is a professor in the Department of Neuroscience and a Distinguished Scholar in Neuroscience at the University of Texas Southwestern Medical Center. She is the former president of the Society for Research on Biological Rhythms (SRBR), as well as a satellite member of the International Institute for Integrative Sleep Medicine at the University of Tsukuba in Japan.

Dmitri Nusinow is an American chronobiologist who studies plant circadian rhythms. He was born on November 7, 1976 in Inglewood, California. He currently resides in St. Louis, and his research focus includes a combination of molecular, biochemical, genetic, genomic, and proteomic tools to discover the molecular connections between signaling networks, circadian oscillators, and specific outputs. By combining these methods, he hopes to apply the knowledge elucidated from the Arabidopsis model to other plant species.

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).

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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. ↑ Hall, Anthony; Kozma-Bognár, László; Bastow, Ruth M.; Nagy, Ferenc; Millar, Andrew J. (November 2002). "Distinct regulation of CAB and PHYB gene expression by similar circadian clocks". The Plant Journal: For Cell and Molecular Biology. 32 (4): 529–537. doi:10.1046/j.1365-313x.2002.01441.x. ISSN   0960-7412. PMID   12445124.
  2. ↑ Trivedi, Bijal (2009-10-27). "Profile of Steve Kay". Proceedings of the National Academy of Sciences. 106 (43): 18051–18053. doi: 10.1073/pnas.0910583106 . ISSN   0027-8424. PMC   2775350 . PMID   19846773.
  3. ↑ Liu, Rui; Xu, Yan-Hong; Jiang, Shang-Chuan; Lu, Kai; Lu, Yan-Fen; Feng, Xiu-Jing; Wu, Zhen; Liang, Shan; Yu, Yong-Tao; Wang, Xiao-Fang; Zhang, Da-Peng (December 2013). "Light-harvesting chlorophyll a/b-binding proteins, positively involved in abscisic acid signaling, require a transcription repressor, WRKY40, to balance their function". Journal of Experimental Botany. 64 (18): 5443–5456. doi:10.1093/jxb/ert307. ISSN   1460-2431. PMC   3871805 . PMID   24078667.
  4. ↑ Trivedi, Bijal (2009-10-27). "Profile of Steve Kay". Proceedings of the National Academy of Sciences. 106 (43): 18051–18053. doi:10.1073/pnas.0910583106. ISSN   0027-8424. PMC   2775350 . PMID   19846773.
  5. ↑ Montané, Marie-Hélène; Kloppstech, Klaus (2000-11-27). "The family of light-harvesting-related proteins (LHCs, ELIPs, HLIPs): was the harvesting of light their primary function?". Gene. 258 (1): 1–8. doi:10.1016/S0378-1119(00)00413-3. ISSN   0378-1119.
  6. ↑ Viro, M.; Kloppstech, K. (1980-11-01). "Differential expression of the genes for ribulose-1,5-bisphosphate carboxylase and light-harvesting chlorophyll a/b protein in the developing barley leaf". Planta. 150 (1): 41–45. doi:10.1007/BF00385613. ISSN   1432-2048.
  7. ↑ Nagy, F.; Kay, S. A.; Chua, N. H. (April 1988). "A circadian clock regulates transcription of the wheat CAB 1 gene". Genes & Development. 2 (4): 376–382. doi: 10.1101/gad.2.4.376 . ISSN   0890-9369. S2CID   84412430.
  8. 1 2 3 Millar, A. J.; Kay, S. A. (May 1991). "Circadian Control of CAB Gene Transcription and mRNA Accumulation in Arabidopsis". The Plant Cell. 3 (5): 541–550. doi:10.1105/tpc.3.5.541. ISSN   1532-298X. PMC   160021 . PMID   12324603.
  9. ↑ Somerville, Chris; Koornneef, Maarten (November 2002). "A fortunate choice: the history of Arabidopsis as a model plant". Nature Reviews. Genetics. 3 (11): 883–889. doi:10.1038/nrg927. ISSN   1471-0056. PMID   12415318. S2CID   37515057.
  10. ↑ McClung, C Robertson; Salomé, Patrice; Michael, Todd (27 March 2002). "The Arabidopsis circadian system". The Arabidopsis Book. 1: e0044. doi:10.1199/tab.0044. PMC   3243369 . PMID   22303209.
  11. ↑ Millar, Andrew J.; Kay, Steve A. (1996-12-24). "Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis". Proceedings of the National Academy of Sciences. 93 (26): 15491–15496. doi:10.1073/pnas.93.26.15491. ISSN   0027-8424. PMC   26432 . PMID   8986839.
  12. ↑ Carre, I. A.; Kay, S. A. (December 1995). "Multiple DNA-Protein Complexes at a Circadian-Regulated Promoter Element". The Plant Cell. 7 (12): 2039–2051. doi:10.1105/tpc.7.12.2039. PMC   161060 . PMID   12242368.
  13. ↑ Bowler, C.; Yamagata, H.; Neuhaus, G.; Chua, N. H. (1994-09-15). "Phytochrome signal transduction pathways are regulated by reciprocal control mechanisms". Genes & Development. 8 (18): 2188–2202. doi: 10.1101/gad.8.18.2188 . ISSN   0890-9369. PMID   7958888.
  14. ↑ Gao, J.; Kaufman, L. S. (April 1994). "Blue-Light Regulation of the Arabidopsis thaliana Cab1 Gene". Plant Physiology. 104 (4): 1251–1257. doi:10.1104/pp.104.4.1251. ISSN   1532-2548. PMC   159288 . PMID   12232164.
  15. ↑ Thomas, Brian; Vince-Prue, Daphne (1996-10-17). Photoperiodism in Plants. Elsevier. ISBN   978-0-08-053887-7.
  16. 1 2 3 Hall, Anthony; Kozma-Bognár, László; Bastow, Ruth M.; Nagy, Ferenc; Millar, Andrew J. (November 2002). "Distinct regulation of CAB and PHYB gene expression by similar circadian clocks". The Plant Journal. 32 (4): 529–537. doi:10.1046/j.1365-313X.2002.01441.x. PMID   12445124.
  17. 1 2 3 Thain, Simon C.; Murtas, Giovanni; Lynn, James R.; McGrath, Robert B.; Millar, Andrew J. (September 2002). "The Circadian Clock That Controls Gene Expression in Arabidopsis Is Tissue Specific". Plant Physiology. 130 (1): 102–110. doi:10.1104/pp.005405. PMC   166543 . PMID   12226490.
  18. ↑ Millar, Andrew J.; Kay, Steve A. (1996-12-24). "Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis". Proceedings of the National Academy of Sciences. 93 (26): 15491–15496. doi: 10.1073/pnas.93.26.15491 . ISSN   0027-8424. PMC   26432 . PMID   8986839.
  19. 1 2 Paul, Anna-Lisa; Popp, Michael P.; Gurley, William B.; Guy, Charles; Norwood, Kelly L.; Ferl, Robert J. (2005-01-01). "Arabidopsis gene expression patterns are altered during spaceflight". Advances in Space Research. Space Life Sciences: Gravity-Related Effects on Plants and Spacefight and Man-Made Environments on Biological Systems. 36 (7): 1175–1181. doi:10.1016/j.asr.2005.03.066. ISSN   0273-1177.
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