Frédéric Cremer

Distinct Roles of GIGANTEA in Promoting Flowering and Regulating Circadian Rhythms in Arabidopsis

The circadian clock acts as the timekeeping mechanism in photoperiodism. In Arabidopsis thaliana, a circadian clock–controlled flowering pathway comprising the genes GIGANTEA (GI), CONSTANS (CO), and FLOWERING LOCUS T (FT) promotes flowering specifically under long days. Within this pathway, GI regulates circadian rhythms and flowering and acts earlier in the hierarchy than CO and FT, suggesting that GI might regulate flowering indirectly by affecting the control of circadian rhythms. We studied the relationship between the roles of GI in flowering and the circadian clock using late elongated hypocotyl circadian clock associated1 double mutants, which are impaired in circadian clock function, plants overexpressing GI (35S:GI), and gi mutants. These experiments demonstrated that GI acts between the circadian oscillator and CO to promote flowering by increasing CO and FT mRNA abundance. In addition, circadian rhythms in expression of genes that do not control flowering are altered in 35S:GI and gi mutant plants under continuous light and continuous darkness, and the phase of expression of these genes is changed under diurnal cycles. Therefore, GI plays a general role in controlling circadian rhythms, and this is different from its effect on the amplitude of expression of CO and FT. Functional GI:green fluorescent protein is localized to the nucleus in transgenic Arabidopsis plants, supporting the idea that GI regulates flowering in the nucleus. We propose that the effect of GI on flowering is not an indirect effect of its role in circadian clock regulation, but rather that GI also acts in the nucleus to more directly promote the expression of flowering-time genes.

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

Significance Daily rhythms of gene expression ensure that biological processes occur at the optimal time of day. In plants, temporally regulated processes include traits of ecological and agricultural importance, and understanding how changes in daily rhythms of expression modify such traits has broad implications. We find that natural genetic variation can accurately modify temporal gene expression waveforms during the day by influencing light signaling pathways, rather than circadian rhythms. We further show that changes in transcriptional patterns induced by natural alleles are sufficient to affect downstream molecular outputs and cause phenotypic diversity. Such natural alleles could provide an advantage by adjusting the activity of temporally regulated processes while avoiding the pleiotropic effects associated with severe disruptions of the circadian system. Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene GIGANTEA (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on PHYTOCHROME INTERACTING FACTOR 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system.

Distinct Patterns of Genetic Variation Alter Flowering Responses of Arabidopsis Accessions to Different Daylengths

Many plants flower in response to seasonal changes in daylength. This response often varies between accessions of a single species. We studied the variation in photoperiod response found in the model species Arabidopsis (Arabidopsis thaliana). Seventy-two accessions were grown under six daylengths varying in 2-h intervals from 6 to 16 h. The typical response was sigmoidal, so that plants flowered early under days longer than 14 h, late under days shorter than 10 h, and at intermediate times under 12-h days. However, many accessions diverged from this pattern and were clustered into groups showing related phenotypes. Thirty-one mutants and transgenic lines were also scored under the same conditions. Statistical comparisons demonstrated that some accessions show stronger responses to different daylengths than are found among the mutants. Genetic analysis of two such accessions demonstrated that different quantitative trait loci conferred an enhanced response to shortening the daylength from 16 to 14 h. Our data illustrate the spectrum of daylength response phenotypes present in accessions of Arabidopsis and demonstrate that similar phenotypic variation in photoperiodic response can be conferred by different combinations of loci.

Distinct photoperiodic responses are conferred by the same genetic pathway in Arabidopsis and in rice

Plants show diverse responses to daylength. For example, Arabidopsis and rice flower in response to long and short days, respectively. A recent comparison of the molecular control of flowering has shown that the proteins that confer these responses are conserved in both species. The function of a central transcriptional regulator, called CONSTANS in Arabidopsis, is reversed, so that it activates transcription of a downstream gene in Arabidopsis but represses the expression of the orthologous gene in rice. This provides the first indication of how diverse responses to daylength are generated.

Evening Expression of Arabidopsis GIGANTEA Is Controlled by Combinatorial Interactions among Evolutionarily Conserved Regulatory Motifs

Integration of environmental cues and circadian clock control confers daily rhythms in gene expression. GIGANTEA regulates flowering as well as stress responses, and its transcription peaks in the evening. In this work, evolutionary comparisons, whole-genome data, and dissection of promoters were used to define combinations of motifs that confer evening expression and light induction of GIGANTEA. Diurnal patterns of gene transcription are often conferred by complex interactions between circadian clock control and acute responses to environmental cues. Arabidopsis thaliana GIGANTEA (GI) contributes to photoperiodic flowering, circadian clock control, and photoreceptor signaling, and its transcription is regulated by the circadian clock and light. We used phylogenetic shadowing to identify three evolutionarily constrained regions (conserved regulatory modules [CRMs]) within the GI promoter and show that CRM2 is sufficient to confer a similar transcriptional pattern as the full-length promoter. Dissection of CRM2 showed that one subfragment (CRM2-A) contributes light inducibility, while another (CRM2-B) exhibits a diurnal response. Mutational analysis showed that three ABA RESPONSE ELEMENT LIKE (ABREL) motifs in CRM2-A and three EVENING ELEMENTs (EEs) in CRM2-B are essential in combination to confer a high amplitude diurnal pattern of expression. Genome-wide analysis identified characteristic spacing patterns of EEs and 71 A. thaliana promoters containing three EEs. Among these promoters, that of FLAVIN BINDING KELCH REPEAT F-BOX1 was analyzed in detail and shown to harbor a CRM functionally related to GI CRM2. Thus, combinatorial interactions among EEs and ABRELs confer diurnal patterns of transcription via an evolutionarily conserved module present in GI and other evening-expressed genes.

Pourquoi les plantes fleurissent

La floraison represente la maturation sexuelle des plantes superieures. Cet evenement, synchronise avec les variations climatiques saisonnieres, est controle par plusieurs dizaines de genes aux interactions encore mal connues.

Floral organs of the same type but at different positions within the flower of Sinapis alba (Brassicaceae) display identical protein patterns.

Summary Different interpretations of the flower of the Brassicaceae exist, suggesting the presence of either 4, 5 or 6 whorls of floral organs. In these models, the 2 short and 4 long stamens account for either 1or 2 whorls, as do the lateral and median sepals. We have searched for inside-whorl differences in gene expression in the Brassicaceae through 2D-PAGE analysis of the total protein pattern of short and long stamens, as well as lateral and median sepals, in Sinapis alba . No detected polypeptide is specific to one type of stamen, none is specific to one type of sepal. On the other hand, about 10% of the polypeptides are specific of one stage of development when long stamens from 4-mm flower buds are compared with long stamens sampled at anthesis. These results suggest that at the molecular level only 4 whorls are detectable and that subtle quantitative variations may account for inside-whorl differences in morphology.