Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa

Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses

Brachypodium distachyon (Brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. Comparison of the Brachypodium genome (accession Bd21) with those of the model dicot Arabidopsis thaliana and the tropical cereal rice (Oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. We analysed the homologies of genes controlling the induction of flowering using pathways curated in Arabidopsis Reactome as a starting point. Pathways include those detecting and responding to the environmental cues of day length (photoperiod) and extended periods of low temperature (vernalization). Variation in these responses has been selected during cereal domestication, providing an interesting comparison with the wild genome of Brachypodium. Brachypodium Bd21 has well conserved homologues of circadian clock, photoperiod pathway and autonomous pathway genes defined in Arabidopsis and homologues of vernalization pathway genes defined in cereals with the exception of VRN2 which was absent. Bd21 also lacked a member of the CO family (CO3). In both cases flanking genes were conserved showing that these genes are deleted in at least this accession. Segmental duplication explains the presence of two CO-like genes in temperate cereals, of which one (Hd1) is retained in rice, and explains many differences in gene family structure between grasses and Arabidopsis. The conserved fine structure of duplications shows that they largely evolved to their present structure before the divergence of the rice and Brachypodium. Of four flowering-time genes found in rice but absent in Arabidopsis, two were found in Bd21 (Id1, OsMADS51) and two were absent (Ghd7, Ehd1). Overall, results suggest that an ancient core photoperiod pathway promoting flowering via the induction of FT has been modified by the recruitment of additional lineage specific pathways that promote or repress FT expression.

Expression of flowering-time genes in soybean E1 near-isogenic lines under short and long day conditions

Control of soybean flowering time is important for geographic adaptation and maximizing yield. Plant breeders have identified a series of genes (E genes) that condition time to flowering; however, the molecular basis in the control of flowering by these E genes, in conjunction with canonical flowering-time genes, has not been studied. Time to flowering in near-isogenic lines (NILs) at the E1 locus was tested using a reciprocal transfer experiment under short day (SD) and long day (LD) conditions. Beginning 8 days after planting, three plant samples were harvested every 3 h for a 48-h period. RNA was isolated from these plants, and RNA samples were pooled for each line and each time period for cDNA synthesis. RT-PCR analysis was performed using primers synthesized for a number of putative flowering-time genes based on homology of soybean EST and genomic sequences to Arabidopsis genes. The results of the reciprocal transfer experiment suggest that the pre-inductive photoperiod-sensitive phase of the E1 NILs responsible for inducing flowering is perceived as early as 5-7-day post-planting. No gene expression differences were found between the E1 and e1 NILs, suggesting that the E1 gene does not directly affect the flowering-time genes during the time period tested; however, differences were observed in gene expression between SD and LD treatments for the putative soybean TOC1, CO, and FT genes. The gene expression results in this study were similar to those of flowering-time genes found in other SD species, suggesting that the selected genes correspond to the soybean flowering-time orthologs.

The role of casein kinase II in flowering time regulation has diversified during evolution

Casein kinase II (CK2) is a protein kinase with an evolutionarily conserved function as a circadian clock component in several organisms, including the long-day plant Arabidopsis (Arabidopsis thaliana). The circadian clock component CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is a CK2 target in Arabidopsis, where it influences photoperiodic flowering. In rice (Oryza sativa), a short-day plant, Heading date6 (Hd6) encodes a CK2alpha subunit that delays flowering time under long-day conditions. Here, we demonstrate that control of flowering time in rice by the Hd6 CK2alpha subunit requires a functional Hd1 gene (an Arabidopsis CONSTANS ortholog) and is independent of the circadian clock mechanism. Our findings from overexpressing the dominant-negative CK2 allele in rice support the independence of CK2 function from the circadian clock. This lack of control of the circadian clock by Hd6 CK2alpha might be due to the presence of glutamate in OsLHY (a CCA1 ortholog in rice) instead of the serine at the corresponding CK2 target site in CCA1. However, this glutamate is critical for the control of the OsPRR1 gene (a rice ortholog of the Arabidopsis TOC1/PRR1 gene) by OsLHY for regulation of the circadian clock. We also demonstrated that the other conserved CK2 target sites in OsLHY conferred robust rhythmic expression of OsLHY-LUC under diurnal conditions. These findings imply that the role of CK2 in flowering-time regulation in higher plants has diversified during evolution.

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.

Integrating ELF4 into the circadian system through combined structural and functional studies

The circadian clock is a timekeeping mechanism that enables anticipation of daily environmental changes. In the plant Arabidopsis thaliana, the circadian system is a multiloop series of interlocked transcription-translation feedbacks. Several genes have been arranged in these oscillation loops, but the position of the core-clock gene ELF4 in this network was previously undetermined. ELF4 lacks sequence similarity to known domains, and functional homologs have not yet been identified. Here we show that ELF4 is functionally conserved within a subclade of related sequences, and forms an alpha-helical homodimer with a likely electrostatic interface that could be structurally modeled. We support this hypothesis by expression analysis of new elf4 hypomorphic alleles. These weak mutants were found to have expression level phenotypes of both morning and evening clock genes, implicating multiple entry points of ELF4 within the multiloop network. This could be mathematically modeled. Furthermore, morning-expression defects were particular to some elf4 alleles, suggesting predominant ELF4 action just preceding dawn. We provide a new hypothesis about ELF4 in the oscillator-it acts as a homodimer to integrate two arms of the circadian clock.

DIE NEUTRALIS and LATE BLOOMER 1 contribute to regulation of the pea circadian clock

The DIE NEUTRALIS (DNE) locus in garden pea (Pisum sativum) was previously shown to inhibit flowering under noninductive short-day conditions and to affect a graft-transmissible flowering signal. In this study, we establish that DNE has a role in diurnal and/or circadian regulation of several clock genes, including the pea GIGANTEA (GI) ortholog LATE BLOOMER 1 (LATE1) and orthologs of the Arabidopsis thaliana genes LATE ELONGATED HYPOCOTYL and TIMING OF CHLOROPHYLL A/B BINDING PROTEIN EXPRESSION 1. We also confirm that LATE1 participates in the clock and provide evidence that DNE is the ortholog of Arabidopsis EARLY FLOWERING4 (ELF4). Circadian rhythms of clock gene expression in wild-type plants under constant light were weaker in pea than in Arabidopsis, and a number of differences were also seen in the effects of both DNE/ELF4 and LATE1/GI on clock gene expression. Grafting studies suggest that DNE controls flowering at least in part through a LATE1-dependent mobile stimulus, and dne mutants show elevated expression of a FLOWERING LOCUS T homolog under short-day conditions. However, the early flowering of the dne mutant is not associated with altered expression of a previously described CONSTANS-like gene. Collectively, our results characterize the clock system and reveal its importance for photoperiod responsiveness in a model legume.

OsEF3, a homologous gene of Arabidopsis ELF3, has pleiotropic effects in rice

Heading date is an important agronomic trait in rice. A rice mutant with a late heading date and no photoperiodic sensitivity in long or short day conditions was obtained from rice T-DNA insertion mutants in Zhonghua11 (ZH11). Through isolation and analysis of the flanking sequence of the T-NDA insertion site, the target sequence of insertion was obtained and found to locate in AP003296, the sequence accession number of rice chromosome 1 of RGP (http://rgp.dna.affrc.go.jp). The putative amino acid sequences of this target gene are homologous to the Arabidopsis protein ELF3 encoded by an early flowering gene. The rice target gene orthologous to Arabidopsis ELF3 is named OsEF3; this encodes a putative nematode responsive protein-like protein. OsEF3 has pleiotropic effects in rice that differ from the effects of Arabidopsis ELF3, which only affects biological rhythms. OsEF3 regulates heading date by influencing the BVG stage and does not affect photoperiodic sensitivity, which suggests that the OsEF3 gene may be involved in an autonomous pathway in rice. OsEF3 may affect root development and kilo-grain weight by delaying cell division or cell elongation.

A genome-wide compilation of the two-component systems in Lotus japonicus

The two-component systems (TCS), or histidine-to-aspartate phosphorelays, are evolutionarily conserved common signal transduction mechanisms that are implicated in a wide variety of cellular responses to environmental stimuli in both prokaryotes and eukaryotes including plants. Among higher plants, legumes including Lotus japonicus have a unique ability to engage in beneficial symbiosis with nitrogen-fixing bacteria. We previously presented a genome-wide compiled list of TCS-associated components of Mesorhizobium loti, which is a symbiont specific to L. japonicus (Hagiwara et al. 2004, DNA Res., 11, 57-65). To gain both general and specific insights into TCS of this currently attractive model legume, here we compiled TCS-associated components as many as possible from a genome-wide viewpoint by taking advantage that the efforts of whole genome sequencing of L. japonicus are almost at final stage. In the current database (http://www.kazusa.or.jp/lotus/index.html), it was found that L. japonicus has, at least, 14 genes each encoding a histidine kinase, 7 histidine-containing phosphotransmitter-related genes, 7 type-A response regulator (RR)-related genes, 11 type-B RR-related genes, and also 5 circadian clock-associated pseudo-RR genes. These results suggested that most of the L. japonicus TCS-associated genes have already been uncovered in this genome-wide analysis, if not all. Here, characteristics of these TCS-associated components of L. japonicus were inspected, one by one, in comparison with those of Arabidopsis thaliana. In addition, some critical experiments were also done to gain further insights into the functions of L. japonicus TCS-associated genes with special reference to cytokinin-mediated signal transduction and circadian clock.

Ecological implications of plants ability to tell the time

The circadian clock (the endogenous mechanism that anticipates diurnal cycles) acts as a central coordinator of plant activity. At the molecular and organism level, it regulates key traits for plant fitness, including seed germination, gas exchange, growth and flowering, among others. In this article, we explore current evidence on the effect of the clock for the scales of interest to ecologists. We begin by synthesizing available knowledge on the effect of the clock on biosphere-atmosphere interactions and observe that, at least in the systems where it has been tested, the clock regulates gas exchange from the leaf to the ecosystem level, and we discuss its implications for estimates of the carbon balance. Then, we analyse whether incorporating the action of the clock may help in elucidating the effects of climate change on plant distributions. Circadian rhythms are involved in regulating the range of temperatures a species can survive and affects plant interactions. Finally, we review the involvement of the clock in key phenological events, such as flowering time and seed germination. Because the clock may act as a common mechanism affecting many of the diverse branches of ecology, our ultimate goal is to stimulate further research into this pressing, yet unexplored, topic.

Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

BACKGROUND

Helitrons are a class of transposable elements which have been identified in a number of species of plants, animals and fungi. They are unique in their proposed rolling-circle mode of replication, have a highly variable copy-number and have been implicated in the restructuring of coding sequences both by their insertion into existing genes and by their incorporation of transcriptionally competent gene fragments. Helitron discovery depends on identifying associated DNA signature sequences and comprehensive evaluation of helitron contribution to a particular genome requires detailed computational analysis of whole genome sequence. Therefore, the role which helitrons have played in modelling non-model plant genomes is largely unknown.

RESULTS

Cloning of the flowering gene GIGANTEA (GI) from a BAC library of the Pooideae grass Lolium perenne (perennial ryegrass) identified the target gene and several GI pseudogene fragments spanning the first five exons. Analysis of genomic sequence 5' and 3' of one these GI fragments revealed motifs consistent with helitron-type transposon insertion, specifically a putative 5'-A (downward arrow) T-3' insertion site containing 5'-TC and CTAG-3' borders with a sub-terminal 16 bp hairpin. Screening of a BAC library of the closely related grass species Festuca pratensis (meadow fescue) indicated similar helitron-associated GI fragments present in this genome, as well as non-helitron associated GI fragments derived from the same region of GI. In order to investigate the possible extent of ancestral helitron-activity in L. perenne, a methylation-filtered GeneThresher genomic library developed from this species was screened for potential helitron 3' hairpin sequences associated with a 3'-CTRR motif. This identified 7 potential helitron hairpin-types present between at least 9 and 51 times within the L. perenne methylation-filtered library.

CONCLUSION

This represents evidence for a possible ancestral role for helitrons in modelling the genomes of Lolium and related species.

At the end of the day: a common molecular mechanism for photoperiod responses in plants?

Photoperiod or daylength affects a diverse set of traits in plants, including flowering and tuberization in annuals, as well as growth cessation and bud set in perennials. During the last 10-15 years, great progress has been made in the understanding of molecular mechanisms controlling photoperiodic induction of flowering, in particular in the model species Arabidopsis thaliana. An obvious question is to what extent the molecular mechanisms revealed in A. thaliana are also shared by other species and other traits controlled by photoperiod. The purpose of this review is to summarize data on the molecular mechanisms of photoperiod control in plants with a focus of annual growth rhythm in perennial plants.

Circadian clock- and phytochrome-regulated Dof-like gene, Rdd1, is associated with grain size in rice

We report here on the characterization of a putative Dof transcription factor gene in rice (Oryza sativa)--rice Dof daily fluctuations 1 (Rdd1). Daily oscillations in Rdd1 expression were retained after transferring to continuous dark (DD) or light (LL) conditions, indicating circadian regulation. However, Rdd1 showed arrhythmic expression in etiolated coleoptiles. Experiments revealed that the Rdd1 transcript accumulated up to 1 h after transferring from DD to LL conditions and decreased thereafter. We examined Rdd1 expression using phytochrome (phy)-deficient mutants, and the results showed that phyA and most likely phyB contributed to the regulation of Rdd1 expression. To further examine the role of Rdd1, transgenic rice plants were produced that carried Rdd1 in either a sense (RDD1-S) or antisense (RDD1-AS) orientation, driven by a constitutive promoter. The expression of endogenous Rdd1 in response to far-red light was found to be modified in RDD1-AS plants compared with wild-type (WT) or RDD1-S plants. In addition, RDD1-AS plants were smaller and flowered later than WT or RDD1-S plants; decreases in grain length, width and 1000-grain weight were also recorded. This study demonstrates that Rdd1 is a circadian clock and phy-regulated gene, which is associated with grain size in rice.

Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2

LHY/CCA1 genes play a key role in the plant circadian clock system and are highly conserved among plant species. However, the evolutionary process of the LHY/CCA1 gene family remains unclear in angiosperms. To obtain details of the phylogeny of these genes, this study characterized LHY/CCA1 genes in a model woody plant,Populus tree.The evolutionary process of angiosperm LHY/CCA1 genes was elucidated using three approaches: comparison of exon–intron structures, reconstruction of phylogenetic trees and examination of syntenic relationships. In addition, the molecular evolutionary rates and the expression patterns of Populus LHYs were analyzed.Gene duplication events of Populus LHYs and Arabidopsis LHY/CCA1 had occurred independently by different chromosomal duplication events arising in each evolutionary lineage. Populus LHYs were under purifying selection by estimating substitution rates of these genes. Further, Populus LHYs conserved diurnal expressions in leaves and stems but the transcripts of LHY2 were more abundant than those of LHY1 in Populus plants.This study uncovered phylogenetic relationships of the LHY/CCA1 gene family in angiosperms. In addition, the transcript abundance and the evolutionary differences between Populus LHY1 and LHY2 imply that Populus LHY2, rather than LHY1, may have a major role in the Populus clock system.

Analysis of clock gene homologs using unifoliolates as target organs in soybean (Glycine max)

Soybean is a typical short-day crop, and its photoperiodic response of flowering is critical to its yield. This phenomenon was well studied during the last century, but the molecular mechanism governing it is unknown. The clock-gene homologs, GmLCL1 and GmLCL2 (Glycine max LHY/CCA1 Like 1 and 2) and GmTOC1 (Glycine max TOC1) were cloned from Glycine max L. KN18, and their expression patterns were analyzed using a system developed in this study. We employed 8h light/16h dark and 18h light/6h dark as short- and long-day conditions, respectively, because in these conditions soybean plants had significant indexes of flowering time. We also used unifoliolates, not the whole plant as Arabidopsis, as target organs for gene expression analysis. GmLCL1 and GmLCL2 had similar circadian expression patterns and both were morning genes, while GmTOC1 was an evening gene and peaked in the evening. The expressions of GmLCL1 and GmLCL2 were obviously antiphase to that of GmTOC1.Our study provided a system that simplified the experiments without compromising the quality of data obtained and was suitable for analyzing the molecular mechanism of flowering in soybean. GmLCL1, GmLCL2 and GmTOC1 may be the components of central clock in soybean.

The circadian system in higher plants

The circadian clock regulates diverse aspects of plant growth and development and promotes plant fitness. Molecular identification of clock components, primarily in Arabidopsis, has led to recent rapid progress in our understanding of the clock mechanism in higher plants. Using mathematical modeling and experimental approaches, workers in the field have developed a model of the clock that incorporates both transcriptional and posttranscriptional regulation of clock genes. This cell-autonomous clock, or oscillator, generates rhythmic outputs that can be monitored at the cellular and whole-organism level. The clock not only confers daily rhythms in growth and metabolism, but also interacts with signaling pathways involved in plant responses to the environment. Future work will lead to a better understanding of how the clock and other signaling networks are integrated to provide plants with an adaptive advantage.

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.

Functional conservation of clock-related genes in flowering plants: overexpression and RNA interference analyses of the circadian rhythm in the monocotyledon Lemna gibba

Circadian rhythms are found in organisms from cyanobacteria to plants and animals. In flowering plants, the circadian clock is involved in the regulation of various physiological phenomena, including growth, leaf movement, stomata opening, and floral transitions. Molecular mechanisms underlying the circadian clock have been identified using Arabidopsis (Arabidopsis thaliana); the functions and genetic networks of a number of clock-related genes, including CIRCADIAN CLOCK ASSOCIATED1, LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1, GIGANTEA (GI), and EARLY FLOWERING3 (ELF3), have been analyzed. The degree to which clock systems are conserved among flowering plants, however, is still unclear. We previously isolated homologs for Arabidopsis clock-related genes from monocotyledon Lemna plants. Here, we report the physiological roles of these Lemna gibba genes (LgLHYH1, LgLHYH2, LgGIH1, and LgELF3H1) in the circadian system. We studied the effects of overexpression and RNA interference (RNAi) of these genes on the rhythmic expression of morning- and evening-specific reporters. Overexpression of each gene disrupted the rhythmicity of either or both reporters, suggesting that these four homologs can be involved in the circadian system. RNAi of each of the genes except LgLHYH2 affected the bioluminescence rhythms of both reporters. These results indicated that these homologs are involved in the circadian system of Lemna plants and that the structure of the circadian clock is likely to be conserved between monocotyledons and dicotyledons. Interestingly, RNAi of LgGIH1 almost completely abolished the circadian rhythm; because this effect appeared to be much stronger than the phenotype observed in an Arabidopsis gi loss-of-function mutant, the precise role of each clock gene may have diverged in the clock systems of Lemna and Arabidopsis.

A systematic forward genetic analysis identified components of the Chlamydomonas circadian system

The molecular bases of circadian clocks have been studied in animals, fungi, bacteria, and plants, but not in eukaryotic algae. To establish a new model for molecular analysis of the circadian clock, here we identified a large number of components of the circadian system in the eukaryotic unicellular alga Chlamydomonas reinhardtii by a systematic forward genetic approach. We isolated 105 insertional mutants that exhibited defects in period, phase angle, and/or amplitude of circadian rhythms in bioluminescence derived from a luciferase reporter gene in their chloroplast genome. Simultaneous measurement of circadian rhythms in bioluminescence and growth rate revealed that some of these mutants had defects in the circadian clock itself, whereas one mutant had a defect in a specific process for the chloroplast bioluminescence rhythm. We identified 30 genes (or gene loci) that would be responsible for rhythm defects in 37 mutants. Classification of these genes revealed that various biological processes are involved in regulation of the chloroplast rhythmicity. Amino acid sequences of six genes that would have crucial roles in the circadian clock revealed features of the Chlamydomonas clock that have both partially plant-like and original components.