Diurnal Lhc gene expression is present in many but not all species of the plant kingdom

Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes

Circadian regulation plays a vital role in optimizing plant responses to the environment. However, while circadian regulation has been extensively studied in angiosperms, very little is known for lycophytes and ferns, leaving a gap in our understanding of the evolution of circadian rhythms across the plant kingdom. Here, we investigated circadian regulation in gas exchange through stomatal conductance and photosynthetic efficiency in a phylogenetically broad panel of 21 species of lycophytes and ferns over a 46 h period under constant light and a selected few under more natural conditions with day-night cycles. No rhythm was detected under constant light for either lycophytes or ferns, except for two semi-aquatic species of the family Marsileaceae (Marsilea azorica and Regnellidium diphyllum), which showed rhythms in stomatal conductance. Furthermore, these results indicated the presence of a light-driven stomatal control for ferns and lycophytes, with a possible passive fine-tuning through leaf water status adjustments. These findings support previous evidence for the fundamentally different regulation of gas exchange in lycophytes and ferns compared to angiosperms, and they suggest the presence of alternative stomatal regulations in Marsileaceae, an aquatic family already well known for numerous other distinctive physiological traits. Overall, our study provides evidence for heterogeneous circadian regulation across plant lineages, highlighting the importance of broad taxonomic scope in comparative plant physiology studies.

No Evidence That Homologs of Key Circadian Clock Genes Direct Circadian Programs of Development or mRNA Abundance in Verticillium dahliae

Many organisms harbor circadian clocks that promote their adaptation to the rhythmic environment. While a broad knowledge of the molecular mechanism of circadian clocks has been gained through the fungal model Neurospora crassa, little is known about circadian clocks in other fungi. N. crassa belongs to the same class as many important plant pathogens including the vascular wilt fungus Verticillium dahliae. We identified homologs of N. crassa clock proteins in V. dahliae, which showed high conservation in key protein domains. However, no evidence for an endogenous, free-running and entrainable rhythm was observed in the daily formation of conidia and microsclerotia. In N. crassa the frequency (frq) gene encodes a central clock protein expressed rhythmically and in response to light. In contrast, expression of Vdfrq is not light-regulated. Temporal gene expression profiling over 48 h in constant darkness and temperature revealed no circadian expression of key clock genes. Furthermore, RNA-seq over a 24 h time-course revealed no robust oscillations of clock-associated transcripts in constant darkness. Comparison of gene expression between wild-type V. dahliae and a ΔVdfrq mutant showed that genes involved in metabolism, transport and redox processes are mis-regulated in the absence of Vdfrq. In addition, VdΔfrq mutants display growth defects and reduced pathogenicity in a strain dependent manner. Our data indicate that if a circadian clock exists in Verticillium, it is based on alternative mechanisms such as post-transcriptional interactions of VdFRQ and the WC proteins or the components of a FRQ-less oscillator. Alternatively, it could be that whilst the original functions of the clock proteins have been maintained, in this species the interactions that generate robust rhythmicity have been lost or are only triggered when specific environmental conditions are met. The presence of conserved clock genes in genomes should not be taken as definitive evidence of circadian function.

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.

No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)

The identification and cloning of full-length homologs of circadian clock genes from Picea abies represent a first step to study the function and evolution of the circadian clock in gymnosperms. Phylogenetic analyses suggest that the sequences of key circadian clock genes are conserved between angiosperms and gymnosperms. though fewer homologous copies were found for most gene families in P. abies. We detected diurnal cycling of circadian clock genes in P. abies using quantitative real-time PCR; however, cycling appeared to be rapidly dampened under free-running conditions. Given the unexpected absence of transcriptional cycling during constant conditions, we employed a complementary method to assay circadian rhythmic outputs and measured delayed fluorescence in seedlings of Norway spruce. Neither of the two approaches to study circadian rhythms in Norway spruce could detect robust ∼24 h cycling behavior under constant conditions. These data suggest gene conservation but fundamental differences in clock function between gymnosperms and other plant taxa.

Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens

The evolution of circadian clocks in land plants is not understood, because circadian rhythms have received little attention in plants other than angiosperms. We have characterized two genes, PpCCA1a and PpCCA1b, homologs of the Arabidopsis thaliana clock genes CCA1/LHY, from the moss Physcomitrella patens. PpCCA1a and PpCCA1b, together with angiosperm CCA1/LHY homologs, belong to the clock-associated single-myb gene family of green plants (including green algae and land plants). The accumulation of PpCCA1a and PpCCA1b mRNA showed rhythms with a period of approximately 1 day, phased as are those of angiosperm homologs, under 24 h light/dark cycles or in continuous dark. However, in marked contrast to angiosperm homologs, both genes showed arrhythmic profiles in continuous light. The timing of the PpCCA1b peak is determined by the time of the last light to dark transition, suggesting that the arrhythmicity in continuous light is due to dysfunction of the core clock. We generated single and double disruptants for PpCCA1a and PpCCA1b, and found that the double disruptants showed: (i) short periodicity and damped amplitude in the PpCCA1b rhythm, (ii) similar changes in the rhythmically expressed genes PpSIG5 and PpPRRa, and (iii) de-repression of PpCCA1b transcription levels, indicating negative feedback regulation. These observations indicate that the two genes are not merely structural homologs but also functional counterparts of CCA1/LHY. Together, our results illustrate similarities as well as divergence of the clock machineries between P. patens and A. thaliana, two distantly placed species in land plant phylogeny.

Circadian Expression of the PpLhcb2 Gene Encoding a Major Light-Harvesting Chlorophyll a/b-Binding Protein in the Moss Physcomitrella patens

Circadian clocks control the expression of Lhcb genes encoding the chlorophyll a/b-binding proteins broadly in seed plants. We show here that this regulation is also conserved in the primitive moss Physcomitrella patens. Northern blotting analyses revealed a robust daily oscillation of Lhcb mRNA levels in protonema cells in 12-h : 12-h light-dark cycles (12 : 12LD) that damped rapidly in continuous darkness (DD). In continuous light (LL), by contrast with typical profiles in higher plants, Lhcb mRNA levels only peaked during the first day and thereafter it showed constant levels. Reverse transcription (RT)-PCR analyses showed similar patterns of expression in LL for three distinct Lhcb genes (PpLhcb1, PpLhcb2 and Zlab1). Moreover, transgenic reporter strains expressing luciferase under the control of the PpLhcb2 promoter showed bioluminescence patterns consistent with the Northern and RT-PCR data. At a higher concentration (4.5%) of glucose in the medium, the reporter strain showed self-sustained rhythms in DD, which was entrained to a differently phased 12 : 12LD, revealing a circadian regulation on the transcription. Kinetics of bioluminescent peaks in 12 : 12LD from gametophore was different to those from protonema, indicating a developmental regulation on PpLhcb2. Together, the regulatory link between the clock and Lhcb genes in P. patens shows characteristics that appear to differ from those in higher plants.

Origins of phytochrome-modulated Lhcb mRNA expression in seed plants

The levels of Lhcb mRNA in higher plants are regulated by phytochrome, cryptochrome, and an endogenous circadian oscillator. To determine whether similar regulatory mechanisms operate in the ancient gymnosperm Ginkgo biloba, we measured Lhcb mRNA levels in seedlings in response to different light conditions. Removal of a diurnally oscillating light stimulus caused dampening of maximal Lhcb mRNA accumulation levels, with little change in periodicity. Although low fluence pulses of both red and blue light given to etiolated seedlings caused maximal accumulation of Lhcb mRNAs characteristic of the phasic/circadian response seen in flowering plants, the additional initial acute response seen in flowering plants was absent. The induction of Lhcb gene expression in both cases was at least partially reversible by far-red light, and appeared biphasic over a range of red fluences. Together, these data indicate that Lhcb genes in G. biloba appear to be regulated in a manner similar to that of flowering plants, whereas signaling and attenuation of mRNA levels through the photoreceptor systems and circadian clock show features distinct from those characterized to date. The implications for these findings are discussed in light of the evolution of circadian clock input signaling.

Circadian expression of the light-harvesting complex protein genes in plants

Photosynthesis is one of the important processes that enable life on earth. To optimize photosynthesis reactions during a solar day, most of them are timed to be active during the light phase. This includes the components of the thylakoid membranes in chloroplasts. Prominent representatives are the proteins of the light-harvesting complex (LHC). The synthesis of both the Lhc mRNA and the LHC protein occurs during the day and is regulated by the circadian clock, exhibiting the following pattern: increasing levels after sunrise, reaching a maximum around noon, and decreasing levels in the afternoon. To elucidate the involved control elements and regulatory circuits, the following strategies were applied: (1) analysis of promoters of Lhc genes, (2) analysis of DNA binding proteins, and (3) screening and investigation of mutants. The most promising elements found so far that may be involved in mediating the circadian rhythmicity of Lhc mRNA oscillations are a myb-like transcription factor CCA1 (Wang et al. 1997) and the corresponding DNA binding sequence (Piechulla et al. 1998).

The genetics of phototransduction and circadian rhythms in Arabidopsis

A wide range of biological processes, in all eukaryotes and in some prokaryotes, are controlled by rhythms with a period close to 24 hours. The circadian oscillator, which is responsible for generating these rhythms, is controlled by light signals that maintain its synchrony with the environmental day/night cycle. Higher plants exhibit many circadian rhythms, including rhythms in the transcription of specific genes. Molecular tools derived from such clock-controlled genes have led to the identification of several circadian rhythm mutants in the genetic model, Arabidopsis thaliana. The extensive understanding of photoperception in this species will make it a powerful system with which to investigate the light regulation of circadian rhythms. We compare Arabidopsis rhythms to the results from other systems, and discuss these data with respect to the current phototransduction models.

Circadian oscillations of Lhc mRNAs in a photoautotrophic cell culture of Lycopersicon peruvianum

Fourteen genes encoding proteins of the light harvesting complex (Lhc) are expressed in a photoautotrophic cell culture from the wild species of tomato (Lycopersicon peruvianum). For two genes, Lhca2 (cab7) and Lhcb2(*)1 (cab4), a rhythmic oscillation of the transcript accumulation is observed under light/dark and constant dark conditions indicating that gene expression is controlled by a circadian clock in the tomato cell culture. The circadian expression of the Lhc genes remains present after application of 2,2'-dipyridyl. However, the amplitude of Lhc mRNA oscillations and the photosynthetic capacity (Fmax/Fo) decrease significantly. The transcript accumulations of psbA, rbcS and rbcL are less or not at all affected by 2,2'-dipyridyl.