Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants

Abstract

Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.

Graphical abstract

Introduction

A Circadian clock is a timekeeper watch that rotates to coordinate the internal physiology of an organism with changing external cues [1] (“See Fig. 1A”). Plants receive these environmental cues to coordinate their circadian clock with current environmental conditions, a process known as “entrainment” [2]. The term circadian is composed of two Latin words, Circa and Diem, which means “around the day” and was made up by Franz Halberg in the 1950s [3]. The fundamental mechanism of the circadian was first defined in detail in the 1920s. The mechanism of this circadian rotator is divided into three main pathways, which consists of input component, oscillator component, and output component through which signals are transmitted from photoreceptors to an oscillator that oscillates for a period of 24 h [4] to maintain periodicity and an output pathway that induces clear rhythm with regard to the oscillator [5] (“See Fig. 2A”). The oscillator is set at an accurate period, by the observation of external cues or signals like temperature and light [1]. The oscillator modifies the insight of the input signal and sets its exposure to a certain time of day [6, 7]. These input signals maintain processes like gene transcriptions or translation processes and metabolic resetting, that can be called the output of the rotator [8]. Numerous activities in photosynthetic organisms that are under circadian control are carbon fixation, transpiration, additional eco-physiological character, cell cycle, flowering time which alter or change from species to species laterally along a latitudinal cline [9, 10], expression of genes, plant responses during stress [11, 12], flowering bud opening, synthesis of plant hormones and signaling [13–15], and pathogen–plant interaction [16]. Many of the genes that are under circadian control are also controlled by phytochrome [17]. In addition to phytochrome (phy), cryptochrome (cry), which is a blue-light photoreceptor, controls various other activities in plants like growth, development like seedling de-etiolation, flowering initiation, growth elongation, and entrainment of clock as well [18, 19]. Numerous genetic components and pathways that regulate the circadian system, in response to environmental cues have been explained in A. thaliana model [20–22]. About 30 per. of the genes of Arabidopsis thaliana’s are expressed and managed by this rotating wheel which acts as the principle manager of plant’s gene expression [14, 23].

Fig. 1.

The circadian clock contains various positive or negative feedback loops which receive external cues to regulate various activities. A This graphical presentation shows the no. of processes that are associated with circadian clock. B This generally describes the role of PRR (PSEUDO RESPONSE REGULATOR) genes in determining various properties in plants

Fig. 2.

The circadian rotator mediates the regulation of plant activities. A This figure generally describes the mechanism behind circadian regulation of plant activity, i.e., there are several external cues such as day, night, and climatic conditions which are responsible for entraining the circadian clock through various receptors located on the plant cell membrane to reset the clock according to these cues, which in turn give output signals that in turn induce gene expression of plants to regulate their activity according to these signals. B This graphical presentation shows different plants’ activities that are under the circadian clock

Mutations are heritable changes that occur in organisms, and the main agents that are responsible for these mutations are not only chemicals or physical agents, but biological agents as well, which play a role in changing the genetic framework of an organism [24]. These environmentally induced mutations provide a way to study all those molecular pathways and genes in plants, specifically Arabidopsis thaliana, that are associated with them [25]. In eukaryotes, circadian clock consists of a network of interconnected positive as well as negative [26, 27] transcription or translation feedback loops or gene components [28, 29] such as CCA1 (CIRCADIAN CLOCK ASSOCIATED 1), PRR (PSEUDO RESPONSE REGULATOR), TOC1 (TIMING OF CAB EXPRESSSION 1), GI (GIGANTEA), ELF (EARLY FLOWERING) genes, and LUX (LUX ARRHYTHMO) act as negative core circadian interlocked feedback loop [30], while RVE (REVEILLE) genes, LWD (LIGHT REGULATED WD) gene, and LNK (NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED) genes act as positive feedback loops [31–33]. The positive gene component or feedback loop of the circadian rotator is generally familiar for producing bistability in organism [34, 35], even though the negative feedback loop is helpful to maintain sustainability in circadian oscillation [36]. The three gene components such as LUX, ELF 3/4 (EARLY FLOWERING 3/4) assemble to make twilight complex [37]. ELF3 (EARLY FLOWERING 3) gene does not encode for oscillator, but modify light stimulus to the central oscillator that is why plant with elf3 mutant who is at constant [38] exposure to light inhibit rhythmicity [39, 40]. elf 3 mutant phenotype causes continuous expression of CO in all circadian period [41]. CCA1/LHY controls genetic expression of GI (GIGANTEA), so plant with double mutant (cca1/lhy) causes 4 h earlier expression of GI under long-day photoperiod [42]. Plant with double mutant (lhy/cca) and single mutant (toc1) causes the initial flowering in short days as compared with wild or non-mutated type [42, 43]. All genes of circadian clock whose mutation delay flowering under long days by reducing daylength or photoperiod are, GI, CO (CONSTANS), and FT (FLOWERING LOCUS T) [44]. Additional changes that occur in rhythmicity of plants due to gi mutation are quicker circadian rhythm cycle and undetermined red signals from phyB (phytochrome B) [45, 46]. Protein phosphorylation or protein targeted degradation is a kind of post-translational modifications that showed their importance in managing circadian clock, e.g., a light-sensitive protein called ZTL (ZEITLUPE) which is balanced by GI when plants is under the sway of blue light [1]. Arabidopsis’s PRR regulate various clock’s function like flowering initiation period [47, 48], climatic characteristic entrainment, and temperature compensation [49–51], conservation of mitochondrial homeostatis [52], thermal stress responses [53], stomatal conductance, oxidative stresses [54], and photosynthetic starch formation and degradation [55] (“See Fig. 1B”). Several auxin genes are under circadian clock that gate hormone susceptibility dependant on the day conditions [13, 56]. Different studies explore that how this circadian oscillator reacts to abiotic stress, but minimal information has been given regarding the interconnection between clock and biotic stress [57]. Circadian rhythms functionally play an important role in organizing plants’ photosynthetic activity with circadian changes in light durability [58]. The high productivity was matched with low levels of CCA 1 expression and during clock mediated enhanced photosynthetic carbon (C) assimilation [59]. Along with controlling many metabolic functions in plants, the plant's circadian regulator also controls pathogen defense [60–62]. The coordination between disease management and plant’s clock brings about efficient control on disease and reduced crop yield damage [63, 64]. In the event of a microbes penetration, major transitions happen in the cuticle or outermost layer that are recognized on plant and it instantly begins plant’s defense pathways [65]. Therefore, this study will help us to understand circadian gene component alteration effect due to mutation that may be induced either by environmental factors or by genetic alteration inside cells.

Environment-mediated regulation of plant growth and development

About 60 years ago, an external model was presented to show how photoperiodic organisms recognize daylength or photoperiod signals [66]. This model consists of a light-inducible phase that coincides with light and is set aside by the circadian wheel to manage flowering initiation in (long-day) LD plants, and delay flowering initiation in (short-day) SD plants [41]. In photosynthetic organisms, several endogenous or environmental signals control cell as well as organ growth that is influenced by the circadian oscillator [67]. These signals also control various other processes in plants, like flower initiation, the commencement of bud dormancy, and the formation of storage organs in plants like bulbs and tubers [41]. The English botanist Arthur Henfrey (1852) was the first man to identify the importance of photoperiod, or daylength, in controlling flowering [68]. The Circadian clock controls flower initiation for successful pollination after flowering in plant developmental stages [69]. Volatile compounds, nectar formation, and release at the appropriate time of day to attract pollinators are all controlled by the clock [70–72] (“See Fig. 2B”), and modification in the central core clock component during domestication helps plants improve crop yield and growth [69] and cause an improved flowering period [73]. The environmental cues called light entrained the circadian clock to change seasons [74]. A minimum of 4 out of 5 phytochromes (PHYA, B, D, E) and 2 cryptochromes (cry 1, cry 2) are involved in the entraining mechanism [41]. Light has the ability to reset the phase of the clock [75] and modify both the amplitude and period of circadian oscillation [20] (“See Fig. 2A”). High irradiance or low irradiance of light is also one of the environmental cues that affect chlorophyll formation and degradation [76]. For shady as well as sunny leaves, i.e., high irradiance for sun leaves and low irradiance for shady leaves, it is important for regulating their photosynthetic activity [77]. In wild-type barley, the plant shows rapid flower initiation in the long-day (LD) photoperiod and delay floral initiation in the short-day photoperiod, and the main locus that controls the long-day photoperiod flowering is Ppd-H1 [78], a PRR gene [79]. Barley does not need vernalization treatment and has a reduced daylength response due to the PPD-H1 mutation for growing in cold winter and wet/dry summer areas [10, 78]. Despite controlling flowering, photoperiod also controls the formation of tubers in Solanum tuberosum (potato), the commencement of bud dormancy in perennial plants, e.g., deciduous trees [80]. It has been supposed that a good synchronization between environmental factors and clock helps Arabidopsis grow fast, make and increase a larger amount of chlorophyll, and maintain fitness when compared with mutants with altered circadian clocks [81]. The early maturity 8 (eam-8) mutation, also known as mat-a, causes a day-neutral plant phenotype and a rapid flowering phenotype in either the LD or SD photoperiod [82, 83]. Early maturation 8 (eam-8) mutation impairs circadian clock gene expression and disrupts downstream signaling pathways [79]. During the night, (eam-8) mutant plants show enhanced accumulation of Ppd-H1 protein [67]. Faure et al. [79] found that the EAM 8 mutant affects circadian clock function by regulating both PRR and the Ppd-H1 (Photoperriod-H1) gene. In Arabidopsis thaliana, the lhy1 (long hypocotyl 1) mutant [84] showed a similar period of circadian oscillation when related with their wild-type (WD) under the long photoperiod of light, but has reduced circadian oscillation under continuous red light, and this knowledge helps us to establish that one or more phytochrome species are present in Arabidopsis thaliana to control or entrain the circadian clock [20]. A (lhy-4) mutant of Arabidopsis thaliana [85] lacked the capability to prevent elongation of hypocotyl in blue-light radiation, but showed normal phytochrome-controlled inhibition in far-red photoperiod. In actuality, PIF4, PIF5 (Phytochrome-interacting factor 4,5) are engaged in controlling the extension of hypocotyl in Arabidopsis [86, 87], but their gene expression is inhibited by LUX, ELF3, and ELF4 during the early twilight [37], which suggests that elongation of hypocotyl is restricted to dark period. Elongation of hypocotyl is generally non-rhythmic in a continuous night period [86] while rhythmic in the continuous day [88], which proved that light is an essential environmental cue to regulate circadian rhythmicity. The cca1/lhy double mutant plant does not abolish the circadian wheel function, but becomes the clock quicker as compared with its normal running period [89–91] (Table 1). Plants with triple mutants (lhy/cca1/gi) exhibit defects in seed germination and induced seed dormancy, which show the significance of the circadian rotator in seed development [3]. In spite of circadian wheel, vernalization is also required for all plant species to flower under different seasonal cues like temperature and daylength [92–94]. Dominant alleles of the FLC or FRI gene are responsible for controlling vernalization in summer annual Arabidopsis, and this can be accomplished by sequencing FLC or FRI in Arabidopsis thaliana grown in various regions of the world, containing mutations in the FRI coding region and FLC gene that result in loss of vernalization requirement in Arabidopsis. FLC generally prevents flowering initiation by suppressing FT and SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO 1) gene expression [95]. Various other processes that are under circadian control are seed germination [69], in which the gene expression of gibberellin and abscisic acid hormone is regulated by it, and gas exchange in the free-running period of dry onion seeds [96]. Dusk or night also acts as an environmental signal to entrain the plant’s circadian clock [1], such as lipid modification and starch degradation, whose gene expression peaks during the night or dusk [97, 98]. In contrast to environmental factors, plant age and stage of plant development also act as an internal signal to regulate flowering mechanisms [41].

Table 1.

List of mutations reported in circadian genes

Sr. No.	Normal and mutated circadian gene	Function	Mutation	Author citation
1	CCA1	Defense response	Vulnerability in the evening period	Butt et al. [2]
2	CCA1 (ox)	Low temperature stresses	Elongated hypocotyl through mutation in elf3	Wang and Tobin [99], Zagotta et al. [100]
3	CCAI/LHY	Control on GI, starch synthesis	4 h earlier expression of GI in long-day, quicker clock function, early flowering in short-day, altered expression of gene involved in lipid metabolism	Alabadí et al. [89], Hsiao et al. [101], Locke et al. [90], Mizoguchi et al. [42], Mizoguchi et al. [91], Nakamura et al. [102]
4	TOC1	Drought resistance	Alter CO phase in short-day, alter plant response to drought, stomatal opening or closing, enhance survival rate in water scare condition	Bendix et al. [103], Sanchez et al. [1], Yanovsky and Kay [104]
5	cca1/lhy, toc1		Early flowering in SD	Mizoguchi et al. [42]
6	lhy-4		Lack the capability to inhibit elongation of hypocotyl in light radiation	Ahmad and Cashmore [85]
7	GI	Flowering, oxidative stress, starch metabolism, rosette arrangement	Quicker circadian cycle, undetermined red signaling, short period of leaf movement, plant metabolism, performance	Fukushima et al. [52], Huq et al. [46], Park and Somer David [45]
8	gi-1	Flowering, high salt resistance	Delay flowering, enhance periodicity of circadian clock	McWatters and Devlin [105]
9	lhy/cca1/gi		Seed germination, dormancy	Srivastava et al. [3]
10	PRR	Flowering initiation, temperature entrainment, compensation, mitochondrial homeostatis, thermal, oxidative stress response, stomatal conductance, starch metabolism	Reduce CO expression, late flowering in long-day, drought resistant, high freezing tolerance	Hayama et al. [106], Nakamichi et al. [107]
11	prr5,7,9		Diminished circadian rotator, enhance accumulation of ABA to resist water or freezing stress, defected chlorophyll, tocopherol, carotenoid biosynthetic pathway	Bhattacharya et al. [108]
12	toc1, prr5/7/9		Elongated hypocotyl	Hayama et al. [106]
13	Ppd-H1	Flowering in long-day	Loss of vernalization requirement	Turner et al. [78]
14	eam-8		Day-neutral, rapid flowering phenotype in long/short-day, impair circadian activity, disrupt signaling pathways, enhanced accumulation of Ppd-H1	Börner et al. [82], Faure et al. [79], Franckowiak et al. [83]
15	elf3		Continuous expression of CO, inhibit rhythmicity	Hicks et al. [40], Liu et al. [109], McWatters et al. [39]
16	FKF1	Flowering	Delayed flowering in (LD)	Nelson et al. [110]

Genetic mechanism of circadian in controlling flowering

The three main floral integrators that are responsible for the initiation of flowering are: LFY (LEAFY), FT, and SOC1 [111, 112]. Gibberellin hormone is responsible for controlling gene expression of SOC1 [82, 113, 114], or a flower meristematic gene called LFY [115]. FT is synthesized in the phloem’s companion cells of the leaves and then transfer through the meristem by sieve elements of phloems [22]. Initiation of photoperiodic flowering pathways leads to the initiation of gene expression of FT, which happens only under long-day photoperiod to promote flowering, but for this if Blázquez initiation FT requires CO [116]. Internal circadian clock signals and light stimulus are responsible for regulating CO gene expression, which causes up-regulation of the flower regulator gene, i.e., FT [66, 104, 117]. The genetic data established that the blue light, far-red-light photoreceptors, i.e., cryptochrome 1 (cry 1), cryptochrome 2 (cry 2), and phytochrome A (phy A) are responsible for the initiation of flowering and stabilization of CO protein, while red-light photoreceptors, i.e., phytochrome B (phy B) cause delayed flowering and promote deprivation of CO [104, 118–123]. COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) and SPA1 (SUPPRESSOR OF PHYTOCHROME A) are the two ubiquitin ligases, that activate deprivation of CO in the night and are repressed by the day (such as in light Cryptochrome 2 (cry2) directly binds with COP1 [124–126] and SPA1, or inhibits their property of CO degradation to promote CO gene expression at the ending of the long- day photoperiod [123, 127]. The gene mutation in phytochrome B (phy B) results in early flowering [128, 129]. The peak of the CO mRNA is generally observed, 12–16 h after sunrise under long-day photoperiod to stimulate flowering [130–132], which is regulated by GI (i.e., no domain-containing plant-specific protein) [22]. Arabidopsis thaliana’s GI is important for regulating rhythmicity, flowering initiation by controlling FT and CO [45, 117, 132, 133] gene expression, and signaling pathways operate in blue light. In Arabidopsis thaliana, the gene transcription and translation of GI or CO are under the influence of the circadian rotator [78]. The peak range of CO mRNA is also controlled by a circadian rotator component called FKF1 (FLAVIN BINDING KELTCH REPEAT BOX 1) [68] during the evening time [110]. These two plant-specific proteins, GI and FKF1, interact with each other in the presence of light, and in turn induce gene expression of CONSTANS (CO). Arabidopsis thaliana plants show earlier flowering in the long-day (LD) photoperiod; in addition, the fkf1 mutant is responsible for delayed flowering in Arabidopsis under the long-day photoperiod [110]. Long-light photoperiod-dependent interaction of FKF1 and GI induced proteasomal degradation of CDF (CYCLING OF DOF FACTORS), a CO mRNA repressor [132]. Out of the three main parts of the circadian rotator (input part, central oscillator, and output part) [4, 28], GIGANTEA mainly belongs to central oscillator, that is why (gi-2) mutation in Arabidopsis thaliana does not diminish circadian functionality, but generally changes length of period and reduce amplitude of the rotator, i.e., shortening the period length of leaf movement [45]. The mutation in GI is aimed at delaying flowering and enhancing the periodicity of the circadian clock [105]. Plants with loss-of-function mutations in CO, GI, and LD (LUMINIDEPENDENS) flower late under long-day photoperiod conditions [68]. (gi-1) are considered as a weak allele that keeps some light-dependant flowering response in their phenotype, while gi-2 (mutant) is a more efficient allele that shows complete in-sensitivity to their photoperiod [134, 135]. PRR (PSEUDO RESPONSE REGULATOR) protein accumulates during the day photoperiod, and is degraded during the dark [136–139] which proves that PRR accumulation promotes CO stabilization in the light. Allelic variation at PRR protein-encoding genes, i.e., Ppd-H1, Ppd-1, BvBTC1 (BOLTING TIME CONTROL 1), PRR37, and SbPRR37 (Sorghum bicolor PSEUDO RESPONSE REGULATOR 37) results in natural diversity in the timing of flowering of wheat, rice, barley, beet, and sorghum [78, 140–144], but in Arabidopsis thaliana, PRR protein is encoded by TOC1, PRR3,5,7 and 9 [145–147]. The blue-light photoreceptor called ZTL, increase free-running period of genes that are under circadian control, cell growth, and also changes light-mediated shifting of floral initiation from the vegetative condition. Current data suggest that TOC1 is one of the targets of ZEITLUPE by doing its 26 s proteasomal degradation during the dark period [136, 148]. TOC1 mutation affects the level of CO phase, i.e., in short-day-growing wild plants, and the minimum level of CO mRNA is observed during day, while the maximum level of CO mRNA is night limited to dark [104]. (prr) Mutation reduces CONSTANS (CO) gene expression [106] at post-transcriptional level, and ultimately leads to phenotype with delayed flowering in LD (Long-day) plants [137]. First evidence regarding the connection between catabolism, anabolism, and the circadian rotator is given by a detailed study of the triple mutants called prr5, prr7, and prr9 [1]. The triple mutant (prr5, prr7, and prr9) exhibits drought resistance as well as high freezing tolerance responses and directly increases the accumulation of cold-responsive gene expression [107]. TOC1 mutation generally alters plant responses to drought conditions, i.e., control stomatal opening and closing, and gas exchange [1]. COP1 and SPA1 are the two ubiquitin ligases, that activate deprivation of CO in the night and are repressed by the day (such as in light Cryptochrome 2 (cry2) directly binds with COP1 [124–126] and SPA1 [124]), also inhibits their property of CO degradation to promote CO gene expression at the completion of the LD (long-day) photoperiod [123, 127]. Some of the negative regulators that inhibit CO accumulation are HOS1, TOE 1 (TARGET OF EAT 1), family protein of AP2 (APETALA2), and GI [149, 150] (“See Fig. 3A and B”).

Fig. 3.

Flowering induction in LD plants. A This graphical presentation simply defines that there are three genes named LFY, SOC1, and FT which are responsible for controlling flowering in plants. Out of these three, two (LFY and SOC1) are under the control of Gibberellin, while FT is controlled by the circadian rotator. The circadian rotator mediated FT activation is influenced under blue or far-red photoperiod, i.e., during evening time, the three photoreceptors such as phy A, cry 1, and cry 2 are activated and promote the formation of GI and the FKF1 complex, which in turn activates the gene expression of CO, so that it is available to binds the FT gene locus and promote flowering in (LD) long-day plants. The light photoperiod, the cry 2 photoreceptor causes the degradation of dark complex COP 1 and SPA 1 to enhance the accumulation of CO. HOS 1 inhibits the accumulation of CO and inhibits flowering initiation in the early morning period. Red cross designates inhibition, while green tick means gene transcription. B Circadian clock’s gene mediated activation or inhibition of CO gene including those involved in monitoring flowering. FL T and SPA1 the night complex, HOS1, ZTL, TOE1, and GI, make a complex in the early morning period and prevent the accumulation of CO gene, while cry1, phyA, COP1 the day complex enhances the accumulation of the CO

Overexpression is one of the phenomenon that is present in circadian gene components and positively or negatively regulate circadian gene function such as CO (CONSTANS) abundance is controlled by various genes including cryptochrome 2. fha-1 is one of the alleles of cry2 and designate as late-flowering mutant which is not capable to prevent flowering in LD plants when CO (CONSTANS) is present in overexpressed form [117] and shows overexpression dominance over mutation, while overexpressions of CCA and LHY cause arrhythmic behavior of certain circadian output and negatively regulate circadian functions [99].

Circadian rotator in controlling photosynthesis

This circadian clock regulates the stomatal activity and the process of photosynthesis, which involves electron flow [151] in light availability, carbohydrate synthesis, and their distribution to the rest of the plant body [58]. Carbon (C) homeostasis by enhancement in photosynthetic activity and starch degradation over an accurate time-period is an important mechanism to prevent starch deficiency in plants [152]. In general, plant growth is influenced by starch degradation that occurs during the night photoperiod, which is under the control of the circadian cycle [22]. Plants grown under a long-day photoperiod longer or shorter than the circadian period from their germination to death show abnormal starch deprivation during the dark period. The main evidence that the rotator regulates starch degradation comes from the study of mutants lacking circadian function [59]. Apart from temperature, the age of plant leaves regulates maximum leaf development or growth in Arabidopsis thaliana [153], and the growth of plants is also controlled by (C) occurrence which is also dependent on rotator function [67]. The circadian clock regulates other processes like cell expansion, e.g., stomatal opening and closing [154–156], and changes in cell capacity of pulvini motor cells of touch-me-not [157, 158]. Reversible changes in the volume of cell cause circadian or 24 h changes in water availability, which sequentially influence the movement of the leaf of Phaseolus vulgaris [159]. In the case of Arabidopsis thaliana, the degree of cell division in different organs does not correlate with the circadian period, i.e., the rate of cell division that occurs inside the leaf organ is 1.0–1.6 cell divisions per day [160, 161]. Cell division of multi-cellular or uni-cellular algae performs during the dark period [162–166], and is influenced by the circadian clock to guard their DNA (deoxy-ribose nucleic acid) replication against UV (ultraviolet) radiation [167]. In rice and Arabidopsis thaliana, the rhythms of root growth are influenced by the diurnal cycle (light/dark), which is generally continuous during both light and dark periods [168–171]. The stomatal conductance and transpiration activities of plants are influenced by the circadian rotator [81, 172, 173]. There is not a single model which describes the co-relation between photoperiod and clock to regulate elongation of hypocotyl and shade escaping mechanism in A. thaliana [86, 174–177]. The oscillation in hypocotyl growth elongation of Arabidopsis thaliana is maximum in the night period of the diurnal cycle (day, night) and during light photoperiod under continuous light when an external sucrose is applied in their environment [86, 88], while elongation occurs only for 1 day, i.e., before the beginning of light and dark in its absence [87]. Because the starch synthesis, degradation, and transportation are linked to the timing of the circadian clock that can only occur when the extent of the long-day match with the period of the circadian rotator [59]. Dodd and his colleagues studied that if the circadian period matches with the period of long day, then plants are more productive in nature as compared with mutants with altered circadian clocks [81] (“See Fig. 4”). Under un-matching conditions, plants show a reduction in plant growth, chlorophyll content, and photosynthetic activity. Ni and his colleagues describe how the productivity of the crops can be maximized or minimized by the circadian clock, and this statement is made on the basis of a study of allopolyploids made from Arabidopsis accession [178]. Ni and his colleagues also supposed that higher starch content at the middle of the day is a positive regulator of growth, so growth measurement generally describes growth in plant organs, rather than carbon (C) accumulation in the plant’s body.

Fig. 4.

Circadian regulation of plant activity and photosynthetic activity in plants. This picture simply shows how coordination between photoperiod and the circadian clock is important to make successful processes in plants, such as photosynthetic activity, which in turn causes more starch production, making plants more productive in nature

Circadian clock’s role in regulating translational activity

The circadian clock’s gene LHY and CCA1 regulate vital circadian oscillation that occurs at the transcriptional, post-transcriptional, translation, and post-translation levels of genes. Firstly, it was assumed that about 6–15% genes of the A. thaliana are influenced by the circadian rotator, but experimental evidence dictates that about 30% of the transcriptome of Arabidopsis thaliana is under the control of the circadian rotator [14, 56, 179]. In spite of their role in controlling gene expression both at the transcription as well as translation level, plant responses during cold [180] and phytochrome production are also controlled by them [181]. The 24 h microarray datasets and diurnal data showed that about 89% of the transcribed genome of the plant body is rhythmic in natural or diurnal periods [23, 182]. The connection between clock and catabolic or anabolic pathways is best defined by plants with (gi) mutation [1], and shows how this mutation alters both plant metabolism and plant performance at the same time [52, 183]. GI controls various activities in plants, like flowering [183], oxidative stress [184], starch formation or degradation [185], rosette arrangement [186], and correct functioning of 24 h rotator [45, 183], and is responsible for altering circadian clock gene expression, which not only alters plant metabolism, but also produces a phenotype with less sensitivity toward abiotic stresses. It was actually unclear how mutations in circadian gene expression change or reset transcriptomic or metabolic activities of plants [1], i.e., circadian rhythm influences about 90% of the transcriptome in Arabidopsis thaliana or other model crops in both natural and stressful conditions [108] (“See Fig. 5”).

Fig. 5.

Circadian control of plant activity. This figure simply describes that the clock that has the ability to control various activities of plants both at transcription and post-transcription levels is in turn controlled by GIGANTEA. If GIGANTEA activates the gene expression of the circadian clock in the correct (green tick) way, then it is able to receive photoperiod on the exact time-period of the light and correctly regulate plant activities. If it alters (red cross) the gene expression of this circadian clock, it will in turn alter plant activities with different phenotypes

Circadian rhythm in monitoring signalling mechanisms

There are various photoreceptors in plant, who has an ability to receive light signals to set the circadian rotator. Phytochrome and cryptochrome are dominant receptors that receive blue, far-red region, and red regions of the electromagnetic range [187]. The gene transcription of these photoreceptors is controlled by the circadian wheel [188]. These external cues are required to influence various physiological activities, which in turn control plant growth via these receptors, and mutations in these receptors affect various metabolic and physiological activities such as plant fitness, plant development, and seedling growth during the dark period (de-etiolated seedling) [187]. It assumed that these photo-receptors’ roles within the rotator were intensity or wavelength dependent for performing photomorphogenesis: red-light receivers are phytochrome B (phy B), blue-light photoreceivers are cryptochrome 1 (cry1), and ZTL, while low fluence photoreceptors are phytochrome B (phy B) [43]. The coordination between phytochrome (phy) and cryptochrome (cry) is an important carrier for directing external signals to the circadian clock. General irradiance signaling has a greater effect on stomatal physiology like stomatal density, index, and pore length [189]. After receiving external signals from the environment, cryptochrome 1 or 2 (cry1/2) interacts with other protein components like COP1, SPA1, and CIB 1 (CRYPTOCHROME INTERACTING BASIC HELIX LOOP HELIX) to initiate the flowering mechanism [18, 19]. COP1 (CRY PHOTORECEPTOR PROMOTER 1), a cry (cryptochrome) photoreceptor-binding protein, inhibits CO gene expression during the day, but this inhibition can be overcome by light-activated complexes such as phytochrome A (phy A), cryptochrome 1 or 2 (cry1/2), allowing their gene expression to continue during the light [124, 190]. PRR promotes the accumulation of CO mRNA in the morning and evening, whereas enhances the skill of CO to attach to the floral regulator FT [106]. Plant phenotypes with triple mutants (prr5/7/9) show diminished circadian rotator function [107], while quadrate mutant (toc1/prr5/7/9) phenotypes show elongated hypocotyl growth, which suggests the role of PRR in inhibiting COP1 function in light-mediated signaling pathways [144]. Ca2 + ions can control signals generated from the input or output pathway of the circadian clock to regulate gene transcription or translation of various proteins like protein kinases [191], while other circadian processes like stomatal aperture movement [192] and leaf movement [193] are also influenced by Ca2 + -gated potassium ion channels (See Fig. 6).

Fig. 6.

Flowering initiation in a light photoperiod. This picture generally describes how flower initiation occurs during the light photoperiod in five steps. Also, (one) after being activated by a light signal, the three photoreceptors, phy A, cry 1, and cry 2, interact with three proteins named COP1, CIB1, and SPA1 to inhibit COP1 gene expression in the second step, promote CO accumulation (third step), and interact with FT in the fourth step, to promote flowering (fifth) in Long-day (LD) plants. In addition to this, PRR gene promotes CO mRNA accumulation by inhibiting COP1 and influences its binding with FT

Circadian clock in plant defense mechanism

In spite of regulating various activities by the circadian clock, plant defense is also influenced by it [60–62]. The ability of the plant to endure or to inhibit a pathogen entry is defined as “inborn immunity” [194]. The circadian clock controls plant survivability during pathogen attacks by activating various defense responses in plants [103]. Plants consist of PRRs (Pattern Recognition Receptors) in their plasma membrane or in their cytoplasm to accept signals (Pathogen-Associated Molecular Patterns) released during bacterial invasion [2]. The first step after interaction between Pattern Recognition Receptors (PRR) and Pathogen-Associated Molecular Patterns (PAMP) is the closing of stomata to inhibit pathogen invasion [65, 195, 196]. In barley and other crops, there are some genes for plant pathogen responses (GRP (RNA-binding protein rich in glycine) which are under circadian control [62]. The Circadian clock provides protection against pathogens through stomatal closing [2], and this opening or closing is under the influence of two circadian clock gene components, i.e., CCA or LHY [62] (“See Fig. 7A”). The CCA1 or LHY genes are actually responsible for providing resistance against oomycete and bacterial pathogens, e.g., Pseudomonas syringae. Plants lacking CCA1 seem to have more vulnerability in the evening period [2] such as downy mildew in (cca1) mutated seedlings, while its overexpression provides resistance [16, 197] against it and hence shows CCA1 importance in the plant’s defense mechanism. The arrhythmic plants with overexpressed (ox) CCA1, mutated elf3-1, do not seem to have progressive variation in pathogenic vulnerability CCA1 [198]. It is actually unclear how CCA1 (ox) causes elongated hypocotyl through mutation in (elf3) [99, 100] ROS (reactive oxygen species) formation during metabolic activities or by the electron transport chain of the chloroplast [199] also provides a first line of defense in the morning time, but this defensive structure is not under circadian control [200]. This ROS acts as an intermediate between the circadian clock system and the redox state to create an equilibrium between the plant’s immunity and growth as well [201, 202]. To combat necrotrophic pathogens, plants can synthesize jasmonic acid (JA), which acts through an ethylene (a hormone) pathway [194, 203]. The positive regulation of the circadian rotator in regulating herbivore resistance or vulnerability is directly linked to the accumulation of jasmonic acid. The plant phytohormone named jasmonic acid and glucosinolates provides a defensive barrier against insect herbivory in various fruits and vegetables [103]. The plant phytohormones named jasmonic acid and glucosinolates provide a defensive barrier against insect herbivory in various fruits and vegetables [15, 103, 204]. Salicyclic acid formation during plant response causes cell wall firming, the formation and storage of phenolics, initiation of ion influxes, and initiation gene expression of R (resistance) or other associated genes, which leads to the activation of hypersensitive responses and ultimately causes the death of the cell [194, 205, 206]. The Circadian clock and light-mediated activation of defense responses in plants help them to control their activities during infection and enhance their resistance abilities, as well [207]. De-etiolated seedlings seem to have altered defense responses to fungal, bacterial, and viral pathogens [62, 208] (“See Fig. 7B”). In the case of antibacterial activity, nanoparticles can play an important role in defending plants from damage by entering into their cell membranes and modulating their cellular activity to make plants protective through their attack time [209], such as silver nanoparticles have a broad range of antibacterial and antifungal activity against Gram-negative and Gram-positive bacteria, fungi, and viruses [210].

Fig. 7.

Plant defense mechanism in plant. A Light-mediated closing of stomata occurs to prevent pathogen attack. This occurs by the interaction between Pathogen-Associated Molecular Patterns (PAMP), a signal released by any pathogen, that binds with a pathogen recognition receptor (PRR) located in the plasma membrane or the cytoplasm of the cell and mediates stomatal closing by light-activated two circadian clock components, named CCA1 and Late LHY. B Formalized this graphical presentation shows how the circadian clock, ROS, salicyclic acid, salicyclate, jasmonic acid, and gluco-sinolate provide defense against various pathogens such as Jasmonic acid is one of the secondary metabolites synthesized by plants to prevent necrotrophic and biotrophic pathogen attacks and insect herbivory. For insect herbivory, glucosinolates are also available to inhibit it, while salicyclate is there to prevent biotrophic pathogen attack, as well. These three components, named jasmonic acid, glucosinolates, and salicylate, are under circadian control. Salicyclic acid induces cell death by activating various defense responses

Circadian rotator in influencing hormonal control

For the growth, development, and survival of organisms, a synchronization between external cues like light, temperature, dark period, and hormone regulation is very important [81, 211, 212]. There is a specific set of genes that are involved in regulating hormonal catabolism as well as anabolism in plants, and the utterance of these genes is also influenced by this circadian rotator [14]. It has been suggested that a variety of hormone signaling pathways in A. thaliana are controlled by the circadian rotator through collaboration with PIF) [213], such as PIF4, which shows its role in controlling the expression of all those genes involved in the synthesis of auxin, gibberellin, brassino-steriod, cytokinin, and ethylene [214]. The relationship between the up-regulation of phytohormones such as auxin, ethylene, gibberellin, brassino-steriods, and circadian clock genes is well described by various research conducted to understand this relationship in plants [211]. In addition to other phytohormones, cytokinin, salicyclic acid, auxin, and methyl jasmonate are also influenced by the circadian rotator gene [1]. Circadian clock alters hormone regulation, light signaling, and sugar level to maintain periodic growth of plant organs in the presence of external signals [22], such as auxin-dependent hypocotyl elongation via RVE 1 transcription factor that bind with auxin biosynthetic gene, i.e., YUCCA8 (YUC8) to activate their gene transcription during day time [215], and gene regulation of gibberellin phytohormone [216]. ELF3 as seen in monocots and dicots [217] is influenced by rotating wheel [215]. In the case of non-inductive photoperiod, GA (gibberellic acid) is the major requirement for flowering initiation, and a mutant which is incapable of the biosynthesis of gibberellic acid is not able to flower under short-day photoperiod [113], because gibberellic acid is important for flowering initiation in A. thaliana [218], while mutant with excessive gibberellic acid can flower earlier than the normal time-period [113]. It has been observed that not only those genes which are involved in mediating gene expression of ABA (Abscisic acid), but also the enzymes, i.e., NCED (9-cis-epoxy-carotenoid dioxygenase) [219] which are responsible for its formation during the day are controlled by the clock’s LHY. Circadian rotator is generally involve in regulating changes in ethylene (a gaseous phytohormone who has an ability to diffuse across the membrane and allow communication between plant to plant) emission during mid of the day through regulating ethylene precursor gene, i.e., ACC SYNTHASE (ACS) [214] (“See Fig. 8”).

Fig. 8.

Circadian clock role in regulating hormone synthesis in plants. Circadian clock control RVE 1 transcription factor that binds with auxin synthesizing gene named as YUCCA8 to promote auxin synthesis, so that its cable to control hypocotyl elongation during night period, while it also controls the synthesis of various hormone through their gene component such as LHY is involved in controlling ABA synthesis, while ELF3 is involved in Gibberellin synthesis. It influences the expression behavior of gene that acts as an ethylene precursor, i.e., ACC SYNTHASE (ACS) for the production of ethylene. While the synthesis of other hormone like methyl jasmonate, and salicylic acid is influenced by it. The synthesis of auxin, gibberellin, ethylene, cytokinin, and Brassino-steriod is also regulated by PIF4 in conjunction with the circadian rotator

Circadian rhythm-mediated stress tolerance

There are numerous biotic or abiotic stresses present in environment that affect leaf senescence rhythmicity like shade, draught, nutrient availability, and pollution [220]. Genes that are involved in providing resistance against environmental stresses, i.e., physical stresses, low-temperature conditions [221], nitrogen starvation, ultraviolet-B (UV-B) radiation [222], salt stresses [223], iron deficiency [224], and salt stresses [223], have a rhythmicity in their gene expression that occurs during the daytime [225–227] (“See Fig. 9A”). These stresses bring about de-synchronization and modification in clock components and affect both the physiological as well as biochemical activity of plants [228]. The transcriptomic examination displayed genes that are responsible for avoiding a-biotic stresses in A. thaliana, soyabean [229], are actually influenced by circadian rotator genes [14, 27, 56], while resistance against cold, salt, and drought is through cold-responsive genes via the two transcription factors such as CBF 1 (C repeat-binding factor 1) and DREB 1 (dehydration responsive element binding 1), whose gene expression is influenced by the circadian rotator [230, 231]. The gene enrichment analysis described that various stress-related pathways of heat shock, oxidative stress, and cold are interconnected and connected to all clock components [184]. There are several genes of circadian clock which act as activator and repressor, that bind with stress-responsive gene to activate or inhibit their gene expression such as CCA1, and LHY bind and activate their gene expression through their accumulation during morning, while TOC 1, and EC 1 (evening complex 1), bind and inhibit their expression in cold, or drought stress [108], while TOC 1 over-expression decreases plant react to drought stress [232, 233]. CCA1 also performs an significant role in resisting cold temperature stresses [234]. GI is responsible for providing tolerance in high salt conditions [183] (“See also Fig. 9B”). Gene such as ERD 10, 7 (EARLY RESPONSE TO DEHYDRATION 10,7), COR 15 A/B (COLD REGULATED 15 A, B), and RD29A (RESPONSE TO DISSECATION 29A) activates their gene transcription during the light period [235], and shows their involvement in water, drought, and osmotic stress condition [1]. It is known that the plant phytohormone ethylene is a major player to avoid both a-biotic and biotic stresses [108]. In addition to other plant phytohormones, abscisic acid is also involved in influencing plant’s reactions to stressful environmental conditions [236]. The plant phytohormone ABA is a significant regulator of growth that shows its increased concentration in plants under water stress condition [237]. PRR 5, 7, 9 is actually involve in providing tolerance in cold stresses and activate stress responses through periodic expression of stress response gene, such as DREB 1 (dehydration-responsive element binding 1), and CBF (C-repeat-binding factor 1). Plants with triple mutant such as (prr 5, 7, and 9) show enhanced accumulation of ABA to provide resistant in water or freezing stress, defected chlorophyll, tocopherol, and carotenoid biosynthetic pathways [108]. ABA, is a major player to resist drought, water, and frost stresses [1]. The gene expression of TOC 1 is increased by ABA, and show its importance in providing tolerance against drought by influencing oscillations in stomatal aperture through circadian clock, while its over-expression causes hyper-sensitivity to draught [238]. Mutation in toc 1 enhances survival rate in water scares condition by reduces water loss by decreases stomatal opening in plants [103]. While during draught stress in which plant increases photo-respiration and decreases gaseous exchanges between the environment lead to the establishment of ROS stress in plants [239], which can be diminish by over-expression of CCA1 [240] (“See also Fig. 9C”).

Fig. 9.

Different stresses in the environment and how different genes of the circadian clock and hormones diminish them. A This figure generally describes how signals are transmitted from these stresses to the circadian clock, which alters (red) or desynchronizes after receiving them and ultimately changes the plant’s physiological and other activities. B In this figure, three steps show how different circadian genes enhance or inhibit transcription or translation of all those genes responsible for combating stress and provide tolerance to plants, such as CCA1, LHY, and PRR 5, 7, and 9 bind with these genes to initiate their transcription which in turn provides tolerance against cold stress. In the second step, TOC1 and EC1 bind and inhibit gene expression, so that the plant body is not resistant to cold and drought stresses. In the third step, GI bind and activate gene expression of these genes to provide tolerance against high salt stress. C In this figure, the two hormones named ethylene and ABA are responsible for providing resistance against biotics, a-biotics, droughts, and water stresses. ABA is also responsible for activating gene transcription of TOC1, which in turn provides resistance to drought stress. While in drought conditions, there is a generation (green tick) of ROS in the plant body, which can be seen by the overexpressed CCA1 (ox) clock gene

Circadian clock in controlling enzymatic activity

In spite of controlling various activities in plants by the circadian clock, enzyme activities as well as various metabolic activities such as carbohydrate metabolism and lipid metabolism are actually regulated by it [241]. Cell membrane glycerophospholipids serve as a good source for the synthesis of various lipid messengers capable of activating various signaling pathways in plants to confer plant survival in adverse conditions [242]. The various genes that are related to glycerophospholipid metabolisms are controlled by the circadian rotator in A. thaliana, while plants with double mutant (cca1/lhy) or overexpressed CCA1 show altered gene expression [101, 102]. Also, the metabolic activities that are controlled by the circadian rotator also act as an input component to change the clock’s function according to them [243, 244]. This interconnection between the 24 h rotator and metabolism helps organisms survive in different environmental conditions [242]. In plants, the starch synthesis and its degradation are under the influence of circadian rotator [245] i.e., it is involved in regulating the transcript abundance of starch synthesizing enzymes, i.e., CCA1, and LHY is involved in controlling gene transcription of GBSS1 (Granule Bound Starch-Synthase 1), a major protein bound to starch and shows its importance in amylose formation in plant [246, 247], in the leaves of Arabidopsis thaliana leaves [248], while clock also controls the abundance of enzymes of starch degradation such as amylo-maltase, GWD (glucan water di-kinase), and plastidial β amylase [249], the LHY, CCA1 complex is also involved in degradation of starch complex through CaK (Ca2⁺ dependant kinase). TDP (Thiamine diphosphate) [250], one of the important coenzyme and a derivative of vitamin B1, is required for controlling functionality of all those enzymes involved in several metabolic pathways such as citric acid cycle, calvin cycle mediated carbon (C) fixation oxidative PPP (pentose phosphate pathways) [250], glycolysis, and the non-mevalonate pathways from which several hundreds of metabolite are synthesis like phytochrome (phy), and chlorophyll in plants [251] The synthesis and transport of this thiamine diphosphate are under the regulation of circadian rotator during their transcription [101]. In A. thaliana, the transcription of gene, or the accumulation of LHCB [5] (Light Harvesting Chlorophyll a,b Binding Protein), is influenced by circadian rotator [252]. This LHCB which is also known as CAB is generally encoded small unit of Rubisco (ribulose-1,5-bi-phosphate carboxylase or oxygenase [253], so in general term, circadian clock controls gene expression of Rubisco in long-light photoperiod [254, 255]. This Circadian rotator also normalizes gas exchanges in Crassulacean acid metabolism which provide metabolic adaptation to all terrestrial plant who have low level of co2 in their leaves during drought condition [256]. In CAM, co2 is fixed during night time by PEPC (phosphoenolpyruvate carboxylase) an enzyme active during night time, and promotes malate formation in the cytosol. There is an enzyme called PEPC kinase which is responsible for phosphorylating this PEPC to prevent its inhibition by malate during night time through de-phosphorylation sensitive pathway [257] (See Fig. 10).

Fig. 10.

Circadian clock regulation of various enzymes and metabolic activities. This figure simply describes circadian control on various enzymes and metabolic activities that run in plants, such as the gene responsible for controlling glycerophospholipid synthesis and degradation under its control, while various enzymes that show their involvement in starch metabolism are under its control, e.g., GBSS1 (granule-bound starch synthase 1), an enzyme involved in starch synthesis, is regulated by two clock components such as CCA1 and LHY, but this component carboxylase (PEPC), an enzyme involved in CAM photosynthesis, is protected by PEPC kinase from malate during the night by transferring the (P) group to it. The transcriptional level of PEPC kinase is under the control of the circadian rotator. The metabolism of TDP, a coenzyme, shows its involvement in controlling various metabolic pathways under the influence of the circadian rotator

Conclusion

Circadian clock is definitely an integral part of the plant system, and shows its critical importance in maintaining rhythmicity of the plants, while mutation in their gene component either affects rhythmicity of the plant activities such as prevention of hypocotyl elongation in lhy-4 mutant, flowering initiation in fkf1 or ppr mutant, and seed germination ability in triple mutant (lhy/cca1/gi) or sometimes shows its importance in maintaining survivability with changing environmental conditions like loss of vernalization treatment by doing mutation in PpD-H1 gene, resistance during drought stresses by toc1mutaion, and higher resistance against the bacterial pathogen (Pseudomonas syringae), insect herbivory through overexpression of CCA1 circadian gene, and hormonal regulation of jasmonic acid and glucosinolates. Knowledge gain from such searches helps us to simplified that why circadian arrangement is significant, and what will happen if its gene component is mutated or overexpressed, but the relation between mutation and overexpression is not well understood in this context that why overexpression behavior suppresses mutation effect to maintain normal behavior of clock, but generate arrhythmicity in its absence. Therefore, this provides an future insight to think more about the relationship where overexpression dominates over mutation.

Author contributions

Conception or designing of work has been done by MS. Data collection, analysis, and interpretation has been done by Nidhi and ST. Critical revision of the article and final approval of the version have done by PK.

Funding

The authors have not disclosed any funding.

Availability of data and materials

Data generated during the study are subject to data sharing mandate and available in a public repository that does not issue datasets with DOI.

Declarations

Conflict of interest

The authors declare that they have no competing interest.

Consent for publication

Not applicable.

Ethics approval and consent to participate

Not applicable.