At the pulse of time: protein interactions determine the pace of circadian clocks

Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton

The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.

On the move through time - a historical review of plant clock research

The circadian clock is an important regulator of growth and development that has evolved to help organisms to anticipate the predictably occurring events on the planet, such as light-dark transitions, and adapt growth and development to these. This review looks back in history on how knowledge about the endogenous biological clock has been acquired over the centuries, with a focus on discoveries in plants. Key findings at the physiological, genetic and molecular level are described and the role of the circadian clock in important molecular processes is reviewed.

Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation

The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.

HSP90 Contributes to Entrainment of the Arabidopsis Circadian Clock via the Morning Loop

The plant circadian clock allows the synchronization of internal physiological responses to match the predicted environment. HSP90.2 is a molecular chaperone that has been previously described as required for the proper functioning of the Arabidopsis oscillator under both ambient and warm temperatures. Here, we have characterized the circadian phenotype of the hsp90.2-3 mutant. As previously reported using pharmacological or RNA interference inhibitors of HSP90 function, we found that hsp90.2-3 lengthens the circadian period and that the observed period lengthening was more exaggerated in warm-cold-entrained seedlings. However, we observed no role for the previously identified interactors of HSP90.2, GIGANTEA and ZEITLUPPE, in HSP90-mediated period lengthening. We constructed phase-response curves (PRCs) in response to warmth pulses to identify the entry point of HSP90.2 to the oscillator. These PRCs revealed that hsp90.2-3 has a circadian defect within the morning. Analysis of the cca1, lhy, prr9, and prr7 mutants revealed a role for CCA1, LHY, and PRR7, but not PRR9, in HSP90.2 action to the circadian oscillator. Overall, we define a potential pathway for how HSP90.2 can entrain the Arabidopsis circadian oscillator.

Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves

Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants

Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism’s transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants.

Time to flower: interplay between photoperiod and the circadian clock

Plants precisely time the onset of flowering to ensure reproductive success. A major factor in seasonal control of flowering time is the photoperiod. The length of the daily light period is measured by the circadian clock in leaves, and a signal is conveyed to the shoot apex to initiate floral transition accordingly. In the last two decades, the molecular players in the photoperiodic pathway have been identified in Arabidopsis thaliana. Moreover, the intricate connections between the circadian clockwork and components of the photoperiodic pathway have been unravelled. In particular, the molecular basis of time-of-day-dependent sensitivity to floral stimuli, as predicted by Bünning and Pittendrigh, has been elucidated. This review covers recent insights into the molecular mechanisms underlying clock regulation of photoperiodic responses and the integration of the photoperiodic pathway into the flowering time network in Arabidopsis. Furthermore, examples of conservation and divergence in photoperiodic flower induction in other plant species are discussed.

RNA around the clock - regulation at the RNA level in biological timing

The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.

Mapping-by-sequencing identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 locus modulating the circadian clock and photoperiodic flowering in barley

Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering.

Immunoprecipitation-based analysis of protein-protein interactions

Several techniques allow the detection of protein-protein interactions. In vivo co-immunoprecipitation (Co-IP) studies are an important complement to other commonly used techniques such as yeast two-hybrid or fluorescence complementation, as they reveal interactions between functional proteins at physiological relevant concentrations. Here, we describe an in vivo Co-IP approach using either GFP affinity matrix or specific antibodies to purify proteins of interests and their interacting partners.

HvLUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways

Photoperiodic flowering is a major factor determining crop performance and is controlled by interactions between environmental signals and the circadian clock. We proposed Hvlux1, an ortholog of the Arabidopsis circadian gene LUX ARRHYTHMO, as a candidate underlying the early maturity 10 (eam10) locus in barley (Hordeum vulgare L.). The link between eam10 and Hvlux1 was discovered using high-throughput sequencing of enriched libraries and segregation analysis. We conducted functional, phylogenetic, and diversity studies of eam10 and HvLUX1 to understand the genetic control of photoperiod response in barley and to characterize the evolution of LUX-like genes within barley and across monocots and eudicots. We demonstrate that eam10 causes circadian defects and interacts with the photoperiod response gene Ppd-H1 to accelerate flowering under long and short days. The results of phylogenetic and diversity analyses indicate that HvLUX1 was under purifying selection, duplicated at the base of the grass clade, and diverged independently of LUX-like genes in other plant lineages. Taken together, these findings contribute to improved understanding of the barley circadian clock, its interaction with the photoperiod pathway, and evolution of circadian systems in barley and across monocots and eudicots.

BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock

BROTHER OF LUX ARRHYTHMO (BOA) is a GARP family transcription factor in Arabidopsis thaliana and is regulated by circadian rhythms. Transgenic lines that constitutively overexpress BOA exhibit physiological and developmental changes, including delayed flowering time and increased vegetative growth under standard growing conditions. Arabidopsis circadian clock protein CIRCADIAN CLOCK ASSOCIATED1 (CCA1) binds to the evening element of the BOA promoter and negatively regulates its expression. Furthermore, the period of BOA rhythm was shortened in cca1-11, lhy-21 (for LATE ELONGATED HYPOCOTYL), and cca1-11 lhy-21 genetic backgrounds. BOA binds to the promoter of CCA1 through newly identified promoter binding sites and activates the transcription of CCA1 in vivo and in vitro. In transgenic Arabidopsis lines that overexpress BOA, the period length of CCA1 rhythm was increased and the amplitude was enhanced. Rhythmic expression of other clock genes, including LHY, GIGANTEA (GI), and TIMING OF CAB EXPRESSION1 (TOC1), was altered in transgenic lines that overexpress BOA. Rhythmic expression of BOA was also affected in mutant lines of toc1-1, gi-3, and gi-4. Results from these studies indicate that BOA is a critical component of the regulatory circuit of the circadian clock.

Spotlight on post-transcriptional control in the circadian system

An endogenous timing mechanism, the circadian clock, causes rhythmic expression of a considerable fraction of the genome of most organisms to optimally align physiology and behavior with their environment. Circadian clocks are self-sustained oscillators primarily based on transcriptional feedback loops and post-translational modification of clock proteins. It is increasingly becoming clear that regulation at the RNA level strongly impacts the cellular circadian transcriptome and proteome as well as the oscillator mechanism itself. This review focuses on posttranscriptional events, discussing RNA-binding proteins that, by influencing the timing of pre-mRNA splicing, polyadenylation and RNA decay, shape rhythmic expression profiles. Furthermore, recent findings on the contribution of microRNAs to orchestrating circadian rhythms are summarized.

Modeling the Drosophila melanogaster circadian oscillator via phase optimization

The circadian clock, which coordinates daily physiological behaviors of most organisms, maintains endogenous (approximately 24 h) cycles and simultaneously synchronizes to the 24-h environment due to its inherent robustness to environmental perturbations coupled with a sensitivity to specific environmental stimuli. In this study, the authors develop a detailed mathematical model that characterizes the Drosophila melanogaster circadian network. This model incorporates the transcriptional regulation of period, timeless, vrille , PAR-domain protein 1, and clock gene and protein counterparts. The interlocked positive and negative feedback loops that arise from these clock components are described primarily through mass-action kinetics (with the exception of regulated gene expression) and without the use of explicit time delays. System parameters are estimated via a genetic algorithm-based optimization of a cost function that relies specifically on circadian phase behavior since amplitude measurements are often noisy and do not account for the unique entrainment features that define circadian oscillations. Resulting simulations of this 29-state ordinary differential equation model comply with fitted wild-type experimental data, demonstrating accurate free-running (23.24-h periodic) and entrained (24-h periodic) circadian dynamics. This model also predicts unfitted mutant phenotype behavior by illustrating short and long periodicity, robust oscillations, and arrhythmicity. This mechanistic model also predicts light-induced circadian phase resetting (as described by the phase-response curve) that are in line with experimental observations.

Salt tolerance (STO), a stress-related protein, has a major role in light signalling

The salt tolerance protein (STO) of Arabidopsis was identified as a protein conferring salt tolerance to yeast cells. In order to uncover its function, we isolated an STO T-DNA insertion line and generated RNAi and overexpressor Arabidopsis plants. Here we present data on the hypocotyl growth of these lines indicating that STO acts as a negative regulator in phytochrome and blue-light signalling. Transcription analysis of STO uncovered a light and circadian dependent regulation of gene expression, and analysis of light-regulated genes revealed that STO is involved in the regulation of CHS expression during de-etiolation. In addition, we could show that CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) represses the transcription of STO and contributes to the destabilization of the protein in etiolated seedlings. Microscopic analysis revealed that the STO:eGFP fusion protein is located in the nucleus, accumulates in a light-dependent manner, and, in transient transformation assays in onion epidermal cells, co-localizes with COP1 in nuclear and cytoplasmic aggregations. However, the analysis of gain- and loss-of-function STO mutants in the cop1-4 background points towards a COP1-independent role during photomorphogenesis.

Regulation of output from the plant circadian clock

Plants, like many other organisms, have endogenous biological clocks that enable them to organize their physiological, metabolic and developmental processes so that they occur at optimal times. The best studied of these biological clocks are the circadian systems that regulate daily (approximately 24 h) rhythms. At the core of the circadian system in every organism are oscillators responsible for generating circadian rhythms. These oscillators can be entrained (set) by cues from the environment, such as daily changes in light and temperature. Completing the circadian clock model are the output pathways that provide a link between the oscillator and the various biological processes whose rhythms it controls. Over the past few years there has been a tremendous increase in our understanding of the mechanisms of the oscillator and entrainment pathways in plants and many useful reviews on the subject. In this review we focus on the output pathways by which the oscillator regulates rhythmic plant processes. In the first part of the review we describe the role of the circadian system in regulation at all stages of a plant's development, from germination and growth to reproductive development as well as in multiple cellular processes. Indeed, the importance of a circadian clock for plants can be gauged by the fact that so many facets of plant development are under its control. In the second part of the review we describe what is known about the mechanisms by which the circadian system regulates these output processes.

From in vivo to in silico biology and back

The massive acquisition of data in molecular and cellular biology has led to the renaissance of an old topic: simulations of biological systems. Simulations, increasingly paired with experiments, are being successfully and routinely used by computational biologists to understand and predict the quantitative behaviour of complex systems, and to drive new experiments. Nevertheless, many experimentalists still consider simulations an esoteric discipline only for initiates. Suspicion towards simulations should dissipate as the limitations and advantages of their application are better appreciated, opening the door to their permanent adoption in everyday research.

Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops

Circadian rhythms of gene activity, metabolism, physiology and behaviour are observed in all the eukaryotes and some prokaryotes. In this study, we present a model to represent the transcriptional regulatory network essential for the circadian rhythmicity in Drosophila. The model incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not assumed to describe the regulation of genes, instead of the explicit reactions of binding and unbinding processes of transcription factors to promoters are modelled. The model simulates sustained circadian oscillations in mRNA and protein concentrations in constant darkness in agreement with experimental observations. It also simulates entrainment by light-dark cycles, disappearance of the rhythmicity in constant light and the shape of phase response curves resembling that of the experimental results. The model is robust over a wide range of parameter variations. In addition, the simulated E-box mutation, per(S) and per(L) mutants are similar to that observed in the experiments. The deficiency between the simulated mRNA levels and experimental observations in per(01), tim(01) and clk(Jrk) mutants suggests some difference on the part of the model from reality.

Reevaluation of Drosophila melanogaster's neuronal circadian pacemakers reveals new neuronal classes

In the brain of the fly Drosophila melanogaster, approximately 150 clock-neurons are organized to synchronize and maintain behavioral rhythms, but the physiological and neurochemical bases of their interactions are largely unknown. Here we reevaluate the cellular properties of these pacemakers by application of a novel genetic reporter and several phenotypic markers. First, we describe an enhancer trap marker called R32 that specifically reveals several previously undescribed aspects of the fly's central neuronal pacemakers. We find evidence for a previously unappreciated class of neuronal pacemakers, the lateral posterior neurons (LPNs), and establish anatomical, molecular, and developmental criteria to establish a subclass within the dorsal neuron 1 (DN1) group of pacemakers. Furthermore, we show that the neuropeptide IPNamide is specifically expressed by this DN1 subclass. These observations implicate IPNamide as a second candidate circadian transmitter in the Drosophila brain. Finally, we present molecular and anatomical evidence for unrecognized phenotypic diversity within each of four established classes of clock neurons.

The proteasome-dependent degradation of CKB4 is regulated by the Arabidopsis biological clock

Most organisms have evolved an internal timing mechanism, the circadian clock, that is able to generate and maintain 24 h rhythmic oscillation in molecular, biochemical and metabolic activities. In Arabidopsis, the clock-dependent synchronization of physiology with the environment is essential for successful growth and development. The mechanisms of the Arabidopsis clockwork have been described as transcriptional feedback loops at the core of the oscillator. However, an increasing body of evidence points towards a key role of post-translational regulation of clock components as an essential mechanism of circadian function. Here, we identify CKB4, a CK2 regulatory subunit, as a component of the Arabidopsis circadian system. We demonstrate that the nuclear-localized CKB4 protein exists in vivo as different isoforms, resulting from phosphorylation on serine residues. Our findings show that the phosphorylated isoforms are the preferred substrate for ubiquitination and degradation by the proteasome pathway. We provide evidence of the involvement of the biological clock in the circadian regulation of CKB4 protein abundance, which itself is important for an accurate control of circadian period by the clock. Overexpression of CKB4 results in elevated CK2 overall activity and period-shortening of clock-controlled genes peaking at different phase angles. Restriction of CKB4 protein phosphorylation and/or degradation to specific phases within the circadian cycle might provide the cell with a fine-tuning mechanism to selectively regulate the CK2 phosphorylation activity on specific substrates.

Kinase and Phosphatase: The Cog and Spring of the Circadian Clock

Reversible phosphorylation is an important regulatory mechanism for many biological processes in eukaryotic organisms. The phosphorylation state of a protein is controlled dynamically by both protein kinases and phosphatases. Phosphorylation of circadian clock proteins is an essential posttranscriptional mechanism in the regulation of circadian clocks, and several protein kinases and phosphatases have been shown to regulate key clock components in eukaryotic systems, including Arabidopsis, Neurospora, Drosophila, and mice. In this review, recent progress in the characterization of protein kinases and phosphatases involved in circadian rhythms is summarized. The protein kinase CK2 has been proposed as an evolutionary link between the divergent circadian systems of plants, animals, and fungi. The roles of CK2 in this process are discussed here in detail.