Flowering in time: genes controlling photoperiodic flowering in Arabidopsis

Comparative transcriptomic and proteomic profiling reveals molecular models of light signal regulation of shade tolerance in bowl lotus (Nelumbo nucifera)

Bowl lotus is categorized as a heliophyte, and shaded environments can severely retard its development and blossoming. We conducted a comparative omics study of light response difference between two cultivars, 'HongYunDieYing' (shade tolerant) and 'YingYing' (shade intolerant), to understand the mechanisms behind the shade tolerance response. The results indicated that 'HongYunDieYing' had a faster light signal response than that in 'YingYing'. Furthermore, 214 proteins in 'HongYunDieYing' and 171 proteins in 'YingYing' were differentially expressed at both the transcriptional and protein levels. These correlated members were mainly involved in photosynthesis, metabolism, secondary metabolites, ribosome, and protein biosynthesis. However, glycolysis/gluconeogenesis, carbon metabolism, fatty acid metabolism, glutathione metabolism, and hormone signaling, were unique to 'HongYunDieYing'. The molecular model of light signal regulation of shade tolerance was constructed: the upstream light signal transduction related gene (cryptochrome 1, phytohormone B, phytochrome-interacting factor 3/5, ELONGATED HYPOCOTYL 5, and SUPPRESSOR OF PHYA-1) played a decisive role in regulating shade tolerance traits. Some transcription factors (MYBs, bHLHs and WRKYs) and hormone signaling (auxin, gibberellin and ethylene) were involved in mediating light signaling to regulate downstream biological events. These regulators and biological processes synergistically regulated the shade tolerance of lotus. SIGNIFICANCE: Lotus requires sufficient sunlight for growth and development, and shaded environments will severely retard lotus growth and blossoming. At present, there are few reports on the systematic identification and characterization of light signal response-related regulators in lotus. This study focuses on the comparative analysis two bowl lotus cultivars with the different shade tolerance traits at transcriptome and proteome levels to uncover the novel insight of the light signal-related biological network and potential candidates involved in the mechanism. The results provide a theoretical basis for the bowl lotus breeding and the expansion of its applications.

Circadian control of ORE1 by PRR9 positively regulates leaf senescence in Arabidopsis

The circadian clock is involved in aging in animals, where mutations in core clock genes accelerate aging. However, little is known about the relationship between aging and the circadian clock in plants. Using the well-studied process of leaf senescence in Arabidopsis, a higher plant, as a model for aging, we show that the circadian clock has a critical role in regulating the aging process in plants. Specifically, we show that PSEUDO-RESPONSE REGULATOR 9 (PRR9), a core clock component, positively regulates leaf senescence. ORESARA 1 (ORE1), an aging regulator, is controlled by PRR9 via direct transcriptional activation and indirectly by suppressing miR164, a posttranscriptional repressor of ORE1, thus forming a coherent feed-forward regulatory loop.

The circadian clock coordinates the daily cyclic rhythm of numerous biological processes by regulating a large portion of the transcriptome. In animals, the circadian clock is involved in aging and senescence, and circadian disruption by mutations in clock genes frequently accelerates aging. Conversely, aging alters circadian rhythmicity, which causes age-associated physiological alterations. However, interactions between the circadian clock and aging have been rarely studied in plants. Here, we investigated potential roles for the circadian clock in the regulation of leaf senescence in plants. Members of the evening complex in Arabidopsis circadian clock, EARLY FLOWERING 3 (ELF3), EARLY FLOWERING 4 (ELF4), and LUX ARRHYTHMO (LUX), as well as the morning component PSEUDO-RESPONSE REGULATOR 9 (PRR9), affect both age-dependent and dark-induced leaf senescence. The circadian clock regulates the expression of several senescence-related transcription factors. In particular, PRR9 binds directly to the promoter of the positive aging regulator ORESARA1 (ORE1) gene to promote its expression. PRR9 also represses miR164, a posttranscriptional repressor of ORE1. Consistently, genetic analysis revealed that delayed leaf senescence of a prr9 mutant was rescued by ORE1 overexpression. Thus, PRR9, a core circadian component, is a key regulator of leaf senescence via positive regulation of ORE1 through a feed-forward pathway involving posttranscriptional regulation by miR164 and direct transcriptional regulation. Our results indicate that, in plants, the circadian clock and leaf senescence are intimately interwoven as are the clock and aging in animals.

FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana

Flowering is a hot topic in Plant Biology and important progress has been made in Arabidopsis thaliana toward unraveling the genetic networks involved. The increasing complexity and the explosion of literature however require development of new tools for information management and update. We therefore created an evolutive and interactive database of flowering time genes, named FLOR-ID (Flowering-Interactive Database), which is freely accessible at http://www.flor-id.org. The hand-curated database contains information on 306 genes and links to 1595 publications gathering the work of >4500 authors. Gene/protein functions and interactions within the flowering pathways were inferred from the analysis of related publications, included in the database and translated into interactive manually drawn snapshots.

A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control

Molecular analysis of floral induction in Arabidopsis has identified several flowering time genes related to 4 response networks defined by the autonomous, gibberellin, photoperiod, and vernalization pathways. Although grass flowering processes include ancestral functions shared by both mono- and dicots, they have developed their own mechanisms to transmit floral induction signals. Despite its high production capacity and its important role in biofuel production, almost no information is available about the flowering process in sugarcane. We searched the Sugarcane Expressed Sequence Tags database to look for elements of the flowering signaling pathway under photoperiodic control. Sequences showing significant similarity to flowering time genes of other species were clustered, annotated, and analyzed for conserved domains. Multiple alignments comparing the sequences found in the sugarcane database and those from other species were performed and their phylogenetic relationship assessed using the MEGA 4.0 software. Electronic Northerns were run with Cluster and TreeView programs, allowing us to identify putative members of the photoperiod-controlled flowering pathway of sugarcane.

The genetic architecture of flowering time and photoperiod sensitivity in maize as revealed by QTL review and meta analysis

The control of flowering is not only important for reproduction, but also plays a key role in the processes of domestication and adaptation. To reveal the genetic architecture for flowering time and photoperiod sensitivity, a comprehensive evaluation of the relevant literature was performed and followed by meta analysis. A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development. Besides, a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits. Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.). Our results suggest that the combination of literature review, meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering. Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection, such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.

Systems biology for plant breeding: the example of flowering time in pea

As part of a breeding strategy applied to pea (Pisum sativum L.), we propose the use of modelling as a tool for studying flowering time. The pea, both a crop and a model species for developmental processes, represents a valuable tool for systems biology approaches. A preliminary computational model for flowering control was previously developed based on genetic and physiological approaches. This paper discusses possible improvements of the model based on recent molecular advances on the regulation of flowering in peas and the model species Arabidopsis thaliana. A combination of a genetic approach together with agroecophysiological models that are not based on genotype, built into a complete model for flowering time prediction is also proposed. This complete model should allow an accurate prediction of flower initiation and also provide an integrative tool that will be useful for various purposes, from genetic networks to crop models.

The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis

Regulated RNA metabolism appears to be a critical component of molecular mechanisms directing flowering initiation in plants. A group of RNA binding proteins exerts their roles through the autonomous flowering pathway. Posttranscriptional mechanisms regulated by microRNAs (miRNAs) also play a key role in flowering-time control. Here, we demonstrate that the GIGANTEA (GI)-regulated miR172 defines a unique genetic pathway that regulates photoperiodic flowering by inducing FLOWERING LOCUS T (FT) independent of CONSTANS (CO). A late-flowering mutant in which a miR172 target gene, TARGET OF EAT1, is constitutively activated by the nearby insertion of the cauliflower mosaic virus 35S enhancer normally responded to vernalization and gibberellic acid treatments. By contrast, its response to daylength changes was severely disrupted. In the mutant, FT was significantly repressed, but other flowering genes were unaffected. Notably, miR172 abundance is regulated by photoperiod via GI-mediated miRNA processing. Accordingly, miR172-overproducing plants exhibit early flowering under both long days and short days, even in the absence of functional CO, indicating that miR172 promotes photoperiodic flowering through a CO-independent genetic pathway. Therefore, it appears that GI-mediated photoperiodic flowering is governed by the coordinated interaction of two distinct genetic pathways: one mediated via CO and the other mediated via miR172 and its targets.

Rapid differentiation of experimental populations of wheat for heading time in response to local climatic conditions

BACKGROUND AND AIMS

Dynamic management (DM) of genetic resources aims at maintaining genetic variability between different populations evolving under natural selection in contrasting environments. In 1984, this strategy was applied in a pilot experiment on wheat (Triticum aestivum). Spatio-temporal evolution of earliness and its components (partial vernalization sensitivity, daylength sensitivity and earliness per se that determines flowering time independently of environmental stimuli) was investigated in this multisite and long-term experiment.

METHODS

Heading time of six populations from the tenth generation was evaluated under different vernalization and photoperiodic conditions.

KEY RESULTS

Although temporal evolution during ten generations was not significant, populations of generation 10 were genetically differentiated according to a north-south latitudinal trend for two components out of three: partial vernalization sensitivity and narrow-sense earliness.

CONCLUSIONS

It is concluded that local climatic conditions greatly influenced the evolution of population earliness, thus being a major factor of differentiation in the DM system. Accordingly, a substantial proportion (approximately 25 %) of genetic variance was distributed among populations, suggesting that diversity was on average conserved during evolution but was differently distributed by natural selection (and possibly drift). Earliness is a complex trait and each genetic factor is controlled by multiple homeoalleles; the next step will be to look for spatial divergence in allele frequencies.

A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana

APRR1 (ARABIDPSIS PSUEDO-RESPONSE REGULATOR 1) (or TOC1, TIMING OF CAB EXPRESSION 1) is believed to be a crucial component of biological clocks of Arabidopsis thaliana. Nevertheless, its molecular function remains to be fully elucidated. Based on the results of yeast two-hybrid and in vitro binding assays, we previously showed that APRR1/TOC1 interacts with certain bHLH factors (i.e. PIF3 and PIL1, which are PHYTOCHROME INTERACTING FACTOR 3 and its homolog (PIF3-LIKE 1), respectively). To critically examine the relevance of PIL1 with reference to the function of APRR1/TOC1, T-DNA insertion mutants were isolated for PIL1. No phenotype was observed for such homozygous pil1 mutants, in terms of circadian-associated events in plants. We then examined more extensively a certain set of bHLH factors, which are considerably similar to PIL1 in their structural designs. The results of extensive analyses of such bHLH factors (namely, HFR1, PIL2, PIF4, PIL5 and PIL6) in wild-type and APRR1-overexressing (APRR1-ox) transgenic lines provided us with several new insights into a link between APRR1/TOC1 and these bHLH factors. In yeast two-hybrid assays, APRR1/TOC1 showed the ability to interact with these proteins (except for HFR1), as well as PIL1 and PIF3. Among them, it was found that the expressions of PIF4 and PIL6 were regulated in a circadian-dependent manner, exhibiting free-running robust rhythms. The expressions of PIF4 and PIL6 were regulated also by light in a manner that their transcripts were rapidly accumulated upon exposure of etiolated seedlings to light. The light-induced expressions of PIF4 and PIL6 were severely impaired in APRR1-ox transgenic lines. Taken together, here we propose the novel view that these bHLH factors (PIF4 and PIL6) might play roles, in concert with APRR1/TOC1, in the integration of light-signals to control both circadian and photomorphogenic processes.

Cell autonomous circadian waves of the APRR1/TOC1 quintet in an established cell line of Arabidopsis thaliana

A small family of genes, named Arabidopsis Pseudo Response Regulator (APRR), are intriguing with special reference to circadian rhythms in plants, based on the fact that one of the members (APRR1) is identical to TOC1 (Timing of CAB Expression 1) that is believed to encode a clock component. In Arabidopsis plants, each transcript of the APRR1/TOC1 quintet genes starts accumulating after dawn rhythmically and one after another at intervals in the order of APRR9 --> APRR7 --> APRR5 --> APRR3 --> APRR1/TOC1. To characterize such intriguing circadian-associated events, we employed an established Arabidopsis cell line (named T87). When T87 cells were grown in an appropriate light and dark cycle, cell autonomous diurnal oscillations of the APRR1/TOC1 quintet genes were observed at the level of transcription, as seen in intact plants. After transfer to the conditions without any environmental time cues, particularly in constant dark, we further showed that free-running circadian rhythms persisted in the cultured cells, not only for the APRR1/TOC1 quintet genes, but also other typical circadian-controlled genes including CCA1 (Circadian Clock Associated 1), LHY (Late Elongated Hypocotyl) and CCR2 (Cold Circadian Rhythm RNA Binding 2). To our knowledge, this is the first indication of cell autonomous circadian rhythms in cultured cells in Arabidopsis thaliana, which will provide us with an alternative and advantageous means to characterize the plant biological clock.

Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis

In Arabidopsis thaliana, the transcripts of the APRR1/TOC1 family genes each start accumulating after dawn rhythmically and one after another at intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1 under continuous light. Except for the well-characterized APRR1/TOC1, however, no evidence has been provided that other APRR1/TOC1 family genes are indeed implicated in the mechanisms underlying circadian rhythms. We here attempted to provide such evidence by characterizing transgenic plants that constitutively express the APRR5 gene. The resulting APRR5-overexpressing (APRR5-ox) plants showed intriguing properties with regard to not only circadian rhythms, but also control of flowering time and light response. First, the aberrant expression of APRR5 in such transgenic plants resulted in a characteristic phenotype with regard to transcriptional events, in which free-running rhythms were considerably altered for certain circadian-regulated genes, including CCA1, LHY, APRR1/TOC1, other APRR1/TOC1 members, GI and CAB2, although each rhythm was clearly sustained even after plants were transferred to continuous light. With regard to biological events, APRR5-ox plants flowered much earlier than wild-type plants, more or less, in a manner independent of photoperiodicity (or under short-day conditions). Furthermore, APRR5-ox plants showed an SRL (short-hypocotyls under red light) phenotype that is indicative of hypersensitiveness to red light in early photomorphogenesis. Both APRR1-ox and APRR9-ox plants also showed the same phenotype. Therefore, APRR5 (together with APRR1/TOC1 and APRR9) must be taken into consideration for a better understanding of the molecular links between circadian rhythms, control of flowering time through the photoperiodic long-day pathway, and also light signaling-controlled plant development.

Aberrant expression of the light-inducible and circadian-regulated APRR9 gene belonging to the circadian-associated APRR1/TOC1 quintet results in the phenotype of early flowering in Arabidopsis thaliana

Several Arabidopsis genes have been proposed to encode potential clock-associated components, including the Myb-related CCA1 and LHY transcription factors and a member (APRR1/TOC1) of the family of pseudo-response regulators. We previously showed that transcripts of the APRR1/TOC1 family genes each start accumulating after dawn rhythmically and sequentially at intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1, under the conditions of continuous light. Nevertheless, no evidence has been provided that each member of the APRR1/TOC1 quintet, except for APRR1/TOC1, is indeed relevant to the mechanisms underlying circadian rhythms. Here we attempt to provide such evidence by characterizing transgenic plants that aberrantly (or constitutively) express the APRR9 gene in a manner independent of circadian rhythms. The resulting APRR9-ox plants showed intriguing phenotypes with regard to circadian rhythms, in two aspects. First, the aberrant expression of APRR9 resulted in a characteristic phenotype with regard to transcriptional events, in which short-period rhythms were commonly observed for certain circadian-regulated genes, including CCA1, LHY, APRR1/TOC1, other APRR1/TOC1 members, ELF3, and CAB2. With regard to biological consequences, such APRR9-ox plants flowered much earlier than wild-type plants, in a manner independent of photoperiodicity (or under short-day conditions). These results suggest that APRR9 (and perhaps other members of the APRR1/TOC1 quintet) must also be taken into consideration for a better understanding of the molecular mechanisms underlying circadian rhythms, and also underlying control of the flowering time through the photoperiodic long-day pathway.

Picking out parallels: plant circadian clocks in context

Molecular models have been described for the circadian clocks of representatives of several different taxa. Much of the work on the plant circadian system has been carried out using the thale cress, Arabidopsis thaliana, as a model. We discuss the roles of genes implicated in the plant circadian system, with special emphasis on Arabidopsis. Plants have an endogenous clock that regulates many aspects of circadian and photoperiodic behaviour. Despite the discovery of components that resemble those involved in the clocks of animals or fungi, no coherent model of the plant clock has yet been proposed. In this review, we aim to provide an overview of studies of the Arabidopsis circadian system. We shall compare these with results from different taxa and discuss them in the context of what is known about clocks in other organisms.