Dissection of floral induction pathways using global expression analysis

On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development

The ABC model of flower development explains how three classes of homeotic genes confer identity to the four types of floral organs. In Arabidopsis thaliana, APETALA2 (AP2) and AGAMOUS (AG) represent A- and C-class genes that act in an antagonistic fashion to specify perianth and reproductive organs, respectively. An apparent paradox was the finding that AP2 mRNA is supposedly uniformly distributed throughout young floral primordia. Although miR172 has a role in preventing AP2 protein accumulation, miR172 was reported to disappear from the periphery only several days after AG activation in the center of the flower. Here, we resolve the enigmatic behavior of AP2 and its negative regulator miR172 through careful expression analyses. We find that AP2 mRNA accumulates predominantly in the outer floral whorls, as expected for an A-class homeotic gene. Its pattern overlaps only transiently with that of miR172, which we find to be restricted to the center of young floral primordia from early stages on. MiR172 also accumulates in the shoot meristem upon floral induction, compatible with its known role in regulating AP2-related genes with a role in flowering. Furthermore, we show that AP2 can cause striking organ proliferation defects that are not limited to the center of the floral meristem, where its antagonist AG is required for terminating stem cell proliferation. Moreover, AP2 never expands uniformly into the center of ag mutant flowers, while miR172 is largely unaffected by loss of AG activity. We present a model in which the decision whether stamens or petals develop is based on the balance between AP2 and AG activities, rather than the two being mutually exclusive.

Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data

In a plant, the progression from vegetative growth to reproductive growth is called the floral transition. Over the past several decades, the floral transition has been shown to be determined not by a single gene but by a complicated gene network. This important biological process, however, has not been investigated at a genome-wide network level. We collected Arabidopsis (Arabidopsis thaliana) protein-protein interaction data from several public databases and compiled them into a genome-wide Arabidopsis interactome. Then, we integrated gene expression profiles during the Arabidopsis floral transition process into the established protein-protein interaction network to identify two types of anticorrelated modules associated with vegetative and reproductive growth. Generally, the vegetative modules are conserved in plants, while the reproductive modules are more specific to advanced plants. The existence of floral transition switches demonstrates that vegetative and reproductive processes might be coordinated by the interacting interface of these modules. Our work also provides many candidates for mediating the interactions between these modules, which may play important roles during the Arabidopsis vegetative/reproductive switch.

A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana

Many targets of plant microRNAs (miRNAs) are thought to play important roles in plant physiology and development. However, because plant miRNAs are typically encoded by medium-size gene families, it has often been difficult to assess their precise function. We report the generation of a large-scale collection of knockdowns for Arabidopsis thaliana miRNA families; this has been achieved using artificial miRNA target mimics, a recently developed technique fashioned on an endogenous mechanism of miRNA regulation. Morphological defects in the aerial part were observed for ∼20% of analyzed families, all of which are deeply conserved in land plants. In addition, we find that non-cleavable mimic sites can confer translational regulation in cis. Phenotypes of plants expressing target mimics directed against miRNAs involved in development were in several cases consistent with previous reports on plants expressing miRNA–resistant forms of individual target genes, indicating that a limited number of targets mediates most effects of these miRNAs. That less conserved miRNAs rarely had obvious effects on plant morphology suggests that most of them do not affect fundamental aspects of development. In addition to insight into modes of miRNA action, this study provides an important resource for the study of miRNA function in plants.

MiRNAs are small RNA molecules that play an important role in regulating gene function, both in animals and in plants. In plants, miRNA target mimicry is an endogenous mechanism used to negatively regulate the activity of a specific miRNA family, through the production of a false target transcript that cannot be cleaved. This mechanism can be engineered to target different miRNA families. Using this technique, we have generated artificial target mimics predicted to reduce the activity of most of the miRNA families in Arabidopsis thaliana and have observed their effects on plant development. We found that deeply conserved miRNAs tend to have a strong impact on plant growth, while more recently evolved ones had generally less obvious effects, suggesting either that they primarily affect processes other than development, or else that they have more subtle or conditional functions or are even dispensable. In several cases, the effects on plant development that we observed closely resembled those seen in plants expressing miRNA–resistant versions of the major predicted targets, indicating that a limited number of targets mediates most effects of these miRNAs. Analyses of mimic expressing plants also support that plant miRNAs affect both transcript stability and protein accumulation. The artificial target mimic collection will be a useful resource to further investigate the function of individual miRNA families.

ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals

In temperate cereals, such as wheat (Triticum aestivum) and barley (Hordeum vulgare), the transition to reproductive development can be accelerated by prolonged exposure to cold (vernalization). We examined the role of the grass-specific MADS box gene ODDSOC2 (OS2) in the vernalization response in cereals. The barley OS2 gene (HvOS2) is expressed in leaves and shoot apices but is repressed by vernalization. Vernalization represses OS2 independently of VERNALIZATION1 (VRN1) in a VRN1 deletion mutant of einkorn wheat (Triticum monococcum), but VRN1 is required to maintain down-regulation of OS2 in vernalized plants. Furthermore, barleys that carry active alleles of the VRN1 gene (HvVRN1) have reduced expression of HvOS2, suggesting that HvVRN1 down-regulates HvOS2 during development. Overexpression of HvOS2 delayed flowering and reduced spike, stem, and leaf length in transgenic barley plants. Plants overexpressing HvOS2 showed reduced expression of barley homologs of the Arabidopsis (Arabidopsis thaliana) gene FLOWERING PROMOTING FACTOR1 (FPF1) and increased expression of RNase-S-like genes. FPF1 promotes floral development and enhances cell elongation, so down-regulation of FPF1-like genes might explain the phenotypes of HvOS2 overexpression lines. We present an extended model of the genetic pathways controlling vernalization-induced flowering in cereals, which describes the regulatory relationships between VRN1, OS2, and FPF1-like genes. Overall, these findings highlight differences and similarities between the vernalization responses of temperate cereals and the model plant Arabidopsis.

Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2

The Arabidopsis thaliana transcription factor APETALA2 (AP2) has numerous functions, including roles in seed development, stem cell maintenance, and specification of floral organ identity. To understand the relationship between these different roles, we mapped direct targets of AP2 on a genome-wide scale in two tissue types. We find that AP2 binds to thousands of loci in the developing flower, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two microRNA genes that influence AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We compare the genome-wide direct target repertoire of AP2 with that of SCHLAFMUTZE, a closely related transcription factor that also represses the transition to flowering. We detect clear similarities and important differences in the direct target repertoires that are also tissue specific. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions as both a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE15 and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1.

Orchestration of floral initiation by APETALA1

The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. Although AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, at more advanced stages it also activates regulatory genes required for floral organ formation, indicating a dynamic mode of action. Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning, and hormonal pathways.

Flower development

Flowers are the most complex structures of plants. Studies of Arabidopsis thaliana, which has typical eudicot flowers, have been fundamental in advancing the structural and molecular understanding of flower development. The main processes and stages of Arabidopsis flower development are summarized to provide a framework in which to interpret the detailed molecular genetic studies of genes assigned functions during flower development and is extended to recent genomics studies uncovering the key regulatory modules involved. Computational models have been used to study the concerted action and dynamics of the gene regulatory module that underlies patterning of the Arabidopsis inflorescence meristem and specification of the primordial cell types during early stages of flower development. This includes the gene combinations that specify sepal, petal, stamen and carpel identity, and genes that interact with them. As a dynamic gene regulatory network this module has been shown to converge to stable multigenic profiles that depend upon the overall network topology and are thus robust, which can explain the canalization of flower organ determination and the overall conservation of the basic flower plan among eudicots. Comparative and evolutionary approaches derived from Arabidopsis studies pave the way to studying the molecular basis of diverse floral morphologies.

Recent advances in regulation of flowering

The control of flowering time in plants is critical for plant fitness and for agriculture. The genetic pathways governing this developmental transition are reasonably well understood in Arabidopsis, although substantial new gains are still being made in this system. Much new work is focusing on how the genetic networks governing flowering function in other species.

Small RNAs in flower development

Development of multi-cellular organisms depends on the correct spatial and temporal expression of numerous genes acting in concert to form regulatory networks. The expression of individual genes can be controlled at different levels, e.g. at the transcriptional level by sequence-specific binding of transcription factors and/or by epigenetic modifications, or at the post-transcriptional level, e.g., by modulating translation or protein stability. Within the last decade the picture of gene regulatory mechanisms has been substantially enriched by the identification of small RNAs (sRNAs) of several distinct subspecies. Non-coding regulatory sRNAs contribute to transcriptional and post-transcriptional gene regulation by different modes of sequence-specific interaction with their targets. MicroRNAs (miRNAs), which guide post-transcriptional gene silencing, have been found to contribute to a variety of developmental programs in plants and animals. Here we provide an overview about generation and action of miRNAs and other small RNAs, and their contribution to an important developmental process in plants, flower formation.

Sculpting the flower; the role of microRNAs in flower development

microRNAs (miRNAs) are small approximately 21-nucleotide RNAs that function posttranscriptionally to regulate gene activity. miRNAs function by binding to complementary sites in target genes causing mRNA degradation and/or translational repression of the target. Since the discovery of miRNAs in plants in 2002 much has been learned about the function of these small regulatory RNAs. miRNAs function broadly to control many aspects of plant biology and plant development. This review focuses on the role of miRNAs in flower development. miRNAs function throughout flower development, from the earliest stages (floral induction) to very late stages (floral organ cell type specification). miRNAs such as miR156 and miR172 play a key role in vegetative phase change and in the vegetative to reproductive transition in both Arabidopsis and maize. miR172 in Arabidopsis and maize and miR169 in Petunia and Antirrhinum function to control floral organ identity fate during the early stages of flower development by regulating the spatial boundaries of expression of target genes. miR164, miR319, miR159, and miR167 function to specify particular cell types during later stages of flower development. Although much has been learned about the role of miRNAs in flower development in the last 8 years, many challenges remain to fully elucidate the function of these important regulatory molecules.

Comparative analysis of flowering in annual and perennial plants

In plants the switch from vegetative growth to flowering involves a major transition in the development of the shoot apex. This transition can occur once, in annual species, or repeatedly, in perennial plants. In annuals, flowering is associated with senescence and death of the whole plant, whereas perennials flower in consecutive years and maintain vegetative development after flowering. The perennial life strategy depends on differential behavior of meristems on a single plant so that some remain in the vegetative state while others undergo the floral transition. A. thaliana provides a powerful model system for understanding the mechanisms of flowering in annuals. Here we review the events that occur in the meristem of A. thaliana during the floral transition and compare these with our understanding of flowering in perennial systems.

Role of A-type ARABIDOPSIS RESPONSE REGULATORS in meristem maintenance and regeneration

In Arabidopsis, the network responsible for the maintenance of the shoot apical meristem (SAM) is built on a negative feedback loop involving the peptide ligand CLAVATA3 (CLV3) and the homeodomain transcription factor WUSCHEL (WUS). The local WUS/CLV3 regulatory module is linked to the organism-wide cytokinin signalling system by direct transcriptional control of A-type ARABIDOPSIS RESPONSE REGULATOR genes (ARRs) by WUS. Here we investigate two A-type ARR genes, ARR7 and ARR15, which are negative regulators of cytokinin signalling. We show that the expression of ARR7, WUS and CLV3 is dependent on cytokinin signalling. While ARR7 expression strongly responds to variations in cytokinin activity, WUS and CLV3 appeared to be much more buffered against this type of variation. As earlier studies had shown that pertubation of A-type ARR activity only causes mild effects on SAM function, we employed tissue regeneration assays as a sensitised background. Root explants pre-treated on auxin and cytokinin-rich callus-inducing medium showed severely suppressed shoot regeneration when ARR7 and ARR15 were overexpressed, whereas loss of function of these genes had a strongly promoting effect. This phenotype was even aggravated in the arr3,4,5,6,7,8,9 septuple mutant. Futhermore, loss-of A-type ARR function in arr7 and arr3,4,5,6,7,8,9 mutants strongly stimulated callus development, indicating that cell proliferation is repressed by A-type ARRs. To elucidate the mechanisms underlying the enhanced capacity of the arr3,4,5,6,7,8,9 septuple mutant to develop shoot tissue in culture, we used whole-genome expression profiling. Among the transcripts with increased abundance in arr3,4,5,6,7,8,9 inflorescence apices a strong enrichment for functions in pollen development was apparent, while the reduced transcripts showed a more heterogeneous distribution of functional categories, ranging from development to pathogen defence.

Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis

FLOWERING LOCUS T (FT) plays a key role as a mobile floral induction signal that initiates the floral transition. Therefore, precise control of FT expression is critical for the reproductive success of flowering plants. Coexistence of bivalent histone H3 lysine 27 trimethylation (H3K27me3) and H3K4me3 marks at the FT locus and the role of H3K27me3 as a strong FT repression mechanism in Arabidopsis have been reported. However, the role of an active mark, H3K4me3, in FT regulation has not been addressed, nor have the components affecting this mark been identified. Mutations in Arabidopsis thaliana Jumonji4 (AtJmj4) and EARLY FLOWERING6 (ELF6), two Arabidopsis genes encoding Jumonji (Jmj) family proteins, caused FT-dependent, additive early flowering correlated with increased expression of FT mRNA and increased H3K4me3 levels within FT chromatin. Purified recombinant AtJmj4 protein possesses specific demethylase activity for mono-, di-, and trimethylated H3K4. Tagged AtJmj4 and ELF6 proteins associate directly with the FT transcription initiation region, a region where the H3K4me3 levels were increased most significantly in the mutants. Thus, our study demonstrates the roles of AtJmj4 and ELF6 as H3K4 demethylases directly repressing FT chromatin and preventing precocious flowering in Arabidopsis.

From ABC genes to regulatory networks, epigenetic landscapes and flower morphogenesis: making biological sense of theoretical approaches

The ABC model postulates that expression combinations of three classes of genes (A, B and C) specify the four floral organs at early stages of flower development. This classic model provides a solid framework to study flower development and has been the foundation for multiple studies in different plant species, as well as for new evolutionary hypotheses. Nevertheless, it has been shown that in spite of being necessary, these three gene classes are not sufficient for flower organ specification. Rather, flower organ specification depends on complex interactions of several genes, and probably other non-genetic factors. Being useful to study systems of complex interactions, mathematical and computational models have enlightened the origin of the A, B and C stereotyped and robust expression patterns and the process of early flower morphogenesis. Here, we present a brief introduction to basic modeling concepts and techniques and review the results that these models have rendered for the particular case of the Arabidopsis thaliana flower organ specification. One of the main results is the uncovering of a robust functional module that is sufficient to recover the gene configurations characterizing flower organ primordia. Another key result is that the temporal sequence with which such gene configurations are attained may be recovered only by modeling the aforementioned functional module as a noisy or stochastic system. Finally, modeling approaches enable testable predictions regarding the role of non-genetic factors (noise, mechano-elastic forces, etc.) in development. These predictions, along with some perspectives for future work, are also reviewed and discussed.

Graft-transmissible induction of potato tuberization by the microRNA miR172

The photoreceptor phytochrome B (PHYB) and the homeodomain protein BEL5 are involved in the response of potato tuber induction to the photoperiod. However, whether they act in the same tuberization pathway is unknown. Here we show the effect of a microRNA, miR172, on this developmental event. miR172 levels are higher under tuber-inducing short days than under non-inductive long days and are upregulated in stolons at the onset of tuberization. Overexpression of this microRNA in potato promotes flowering, accelerates tuberization under moderately inductive photoperiods and triggers tuber formation under long days. In plants with a reduced abundance of PHYB, which tuberize under long days, both BEL5 mRNA and miR172 levels are reduced in leaves and increased in stolons. This, together with the presence of miR172 in vascular bundles and the graft transmissibility of its effect on tuberization, indicates that either miR172 might be mobile or it regulates long-distance signals to induce tuberization. Consistent with this, plants overexpressing miR172 show increased levels of BEL5 mRNA, which has been reported to be transmissible through grafts. Furthermore, we identify an APETALA2-like mRNA containing a miR172 binding site, which is downregulated in plants overexpressing miR172 and plants in which PHYB is silenced. Altogether, our results suggest that miR172 probably acts downstream of the tuberization repressor PHYB and upstream of the tuberization promoter BEL5 and allow us to propose a model for the control of tuberization by PHYB, miR172 and BEL5.

Small RNAs and developmental timing in plants

MicroRNAs (miRNAs) were originally discovered as regulators of developmental timing in C. elegans. Recent results have revealed that miRNAs also regulate developmental timing in plants, and have provided a long-awaited molecular connection between the juvenile-to-adult transition and flowering. Specifically, the transition from juvenile to adult development in flowering plants is regulated by two temporally expressed miRNAs, miR156 and miR172. These miRNAs target two families of plant-specific transcription factors (respectively, SBP-box and AP2-like factors) that cooperate to regulate phase-specific vegetative traits, as well as genes involved in flowering. Small RNAs have also been shown to play a role in the transition between different stages of gametophyte development in the moss Physcomitrella patens. The use of small RNAs for temporal regulation is therefore quite ancient in plants.

The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1

When to form flowers is a developmental decision that profoundly impacts the fitness of flowering plants. In Arabidopsis this decision is ultimately controlled by the induction and subsequent activity of the transcription factors LEAFY (LFY), FRUITFULL (FUL), and APETALA1 (AP1). Despite their central importance, our current understanding of the regulation of LFY, FUL, and AP1 expression is still incomplete. We show here that all three genes are directly activated by the microRNA-targeted transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3). Our findings suggest that SPL3 acts together with other microRNA-regulated SPL transcription factors to control the timing of flower formation. Moreover, the identified SPL activity defines a distinct pathway in control of this vital developmental decision.

Just say no: floral repressors help Arabidopsis bide the time

Floral repressors ensure correct reproductive timing by safeguarding against premature flowering. In the past decade, several mechanisms of floral repression have come to light. Discrimination between direct and indirect repressors has been facilitated by increasing the use of chromatin immunoprecipitation assays. Certain MADS-domain transcription factors such as SHORT VEGETATIVE PHASE and FLOWERING LOCUS C bind directly to target euchromatin to repress specific loci including FLOWERING LOCUS T (FT) and FD. The AP2-domain transcription factor TEMPRANILLO 1 has also been shown to directly repress FT by binding its 5' UTR. We highlight emerging systems level approaches, including genome-scale direct binding studies (ChIP-chip and ChIP-Seq), which stand out in their promise to elucidate the complex network underlying the transition to flowering at an unprecedented level.

miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana

The FT gene integrates several external and endogenous cues controlling flowering, including information on day length. A complex of the mobile FT protein and the bZIP transcription factor FD in turn has a central role in activating genes that execute the switch from vegetative to reproductive development. Here we reveal that microRNA156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes not only act downstream of FT/FD, but also define a separate endogenous flowering pathway. High levels of miR156 in young plants prevent precocious flowering. A subsequent day length-independent decline in miR156 abundance provides a permissive environment for flowering and is paralleled by a rise in SPL levels. At the shoot apex, FT/FD and SPLs converge on an overlapping set of targets, with SPLs directly activating flower-promoting MADS box genes, providing a molecular substrate for both the redundant activities and the feed-forward action of the miR156/SPL and FT/FD modules in flowering control.

The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis

The transition from the juvenile to the adult phase of shoot development in plants is accompanied by changes in vegetative morphology and an increase in reproductive potential. Here, we describe the regulatory mechanism of this transition. We show that miR156 is necessary and sufficient for the expression of the juvenile phase, and regulates the timing of the juvenile-to-adult transition by coordinating the expression of several pathways that control different aspects of this process. miR156 acts by repressing the expression of functionally distinct SPL transcription factors. miR172 acts downstream of miR156 to promote adult epidermal identity. miR156 regulates the expression of miR172 via SPL9 which, redundantly with SPL10, directly promotes the transcription of miR172b. Thus, like the larval-to-adult transition in Caenorhabditis elegans, the juvenile-to-adult transition in Arabidopsis is mediated by sequentially operating miRNAs. miR156 and miR172 are positively regulated by the transcription factors they target, suggesting that negative feedback loops contribute to the stability of the juvenile and adult phases.

Identification and characterization of 27 conserved microRNAs in citrus

MicroRNAs (miRNAs) are a class of non-protein-coding small RNAs. Considering the conservation of many miRNA genes in different plant genomes, the identification of miRNAs from non-model organisms is both practicable and instrumental in addressing miRNA-guided gene regulation. Citrus is an important staple fruit tree, and publicly available expressed sequence tag (EST) database for citrus are increasing. However, until now, little has been known about miRNA in citrus. In this study, 27 known miRNAs from Arabidopsis were searched against citrus EST databases for miRNA precursors, of which 13 searched precursor sequences could form fold-back structures similar with those of Arabidopsis. The ubiquitous expression of those 13 citrus microRNAs and other 13 potential citrus miRNAs could be detected in citrus leaf, young shoot, flower, fruit and root by northern blotting, and some of them showed differential expression in different tissues. Based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences, a total of 41 potential targets were identified for 15 citrus miRNAs. The majority of the targets are transcription factors that play important roles in citrus development, including leaf, shoot, and root development. Additionally, some other target genes appear to play roles in diverse physiological processes. Four target genes have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in Poncirus trifoliate. Overall, this study in the identification and characterization of miRNAs in citrus can initiate further study on citrus miRNA regulation mechanisms, and it can help us to know more about the important roles of miRNAs in citrus.

Gene activation cascade triggered by a single photoperiodic cycle inducing flowering in Sinapis alba

Molecular genetic analyses in Arabidopsis disclosed a genetic pathway whereby flowering is induced by the photoperiod. This cascade is examined here within the time course of floral transition in the long-day (LD) plant Sinapis alba induced by a single photoperiodic cycle. In addition to previously available sequences, the cloning of CONSTANS (SaCO) and FLOWERING LOCUS T (SaFT) homologues allowed expression analyses to be performed to follow the flowering process step by step. A diurnal rhythm in SaCO expression in the leaves was observed and transcripts of SaFT were detected when light was given in phase with SaCO kinetics only. This occurred when day length was extended or when a short day was shifted towards a 'photophile phase'. The steady-state level of SaFT transcripts in the various physiological situations examined was found to correlate like a rheostat with floral induction strength. Kinetics of SaFT activation were also consistent with previous estimations of translocation of florigen out of leaves, which could actually occur after the inductive cycle. In response to one 22-h LD, initiation of floral meristems by the shoot apical meristem (SAM) started about 2 days after activation of SaFT and was marked by expression of APETALA1 (SaAP1). Meanwhile, LEAFY (SaLFY) was first up-regulated in leaf primordia and in the SAM. FRUITFULL (SaFUL) was later activated in the whole SAM but excluded from floral meristems. These patterns are integrated with previous observations concerning upregulation of SUPPRESSOR OF OVEREXPRESSION OF CO1 (SaSOC1) to provide a temporal and spatial map of floral transition in Sinapis.

Repression of flowering by the miR172 target SMZ

A small mobile protein, encoded by the FLOWERING LOCUS T (FT) locus, plays a central role in the control of flowering. FT is regulated positively by CONSTANS (CO), the output of the photoperiod pathway, and negatively by FLC, which integrates the effects of prolonged cold exposure. Here, we reveal the mechanisms of regulation by the microRNA miR172 target SCHLAFMUTZE (SMZ), a potent repressor of flowering. Whole-genome mapping of SMZ binding sites demonstrates not only direct regulation of FT, but also of many other flowering time regulators acting both upstream and downstream of FT, indicating an important role of miR172 and its targets in fine tuning the flowering response. A role for the miR172/SMZ module as a rheostat in flowering time is further supported by SMZ binding to several other genes encoding miR172 targets. Finally, we show that the action of SMZ is completely dependent on another floral repressor, FLM, providing the first direct connection between two important classes of flowering time regulators, AP2- and MADS-domain proteins.

From decision to commitment: the molecular memory of flowering

During the floral transition the shoot apical meristem changes its identity from a vegetative to an inflorescence state. This change in identity can be promoted by external signals, such as inductive photoperiod conditions or vernalization, and is accompanied by changes in expression of key developmental genes. The change in meristem identity is usually not reversible, even if the inductive signal occurs only transiently. This implies that at least some of the key genes must possess an intrinsic memory of the newly acquired expression state that ensures irreversibility of the process. In this review, we discuss different molecular scenarios that may underlie a molecular memory of gene expression.

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch requires relevant proteins to be stored in the mature pollen, where they have to retain functionality in a desiccated environment. Using a shotgun proteomics approach, we unambiguously identified approximately 3500 proteins in Arabidopsis pollen, including 537 proteins that were not identified in genetic or transcriptomic studies. To generate this comprehensive reference data set, which extends the previously reported pollen proteome by a factor of 13, we developed a novel deterministic peptide classification scheme for protein inference. This generally applicable approach considers the gene model-protein sequence-protein accession relationships. It allowed us to classify and eliminate ambiguities inherently associated with any shotgun proteomics data set, to report a conservative list of protein identifications, and to seamlessly integrate data from previous transcriptomics studies. Manual validation of proteins unambiguously identified by a single, information-rich peptide enabled us to significantly reduce the false discovery rate, while keeping valuable identifications of shorter and lower abundant proteins. Bioinformatic analyses revealed a higher stability of pollen proteins compared to those of other tissues and implied a protein family of previously unknown function in vesicle trafficking. Interestingly, the pollen proteome is most similar to that of seeds, indicating physiological similarities between these developmentally distinct tissues.

AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana

The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promoter of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.

A role for Arabidopsis PUCHI in floral meristem identity and bract suppression

At the onset of flowering, the Arabidopsis thaliana primary inflorescence meristem starts to produce flower meristems on its flank. Determination of floral fate is associated with changes in the growth pattern and expression of meristem identity genes and suppression of a subtending leaf called a bract. Here, we show a role in floral fate determination and bract suppression for the PUCHI gene, an AP2/EREBP family gene that has previously been reported to play roles in lateral root morphogenesis. Mutations in PUCHI cause partial conversion of flowers to inflorescences, indicating that PUCHI is required for flower meristem identity. PUCHI is transiently expressed in the early flower meristem and accelerates meristem bulging while it prevents the growth of the bract primordium. The function of PUCHI in floral fate determination and bract suppression overlaps that of the BLADE-ON-PETIOLE1 (BOP1) and BOP2 genes, which encode a pair of redundant regulatory proteins involved in various developmental processes, including leaf morphogenesis and flower patterning. We also show that PUCHI acts together with BOP1 and BOP2 to promote expression of LEAFY and APETALA1, two central regulators of floral meristem identity. Expression patterns of the PUCHI and BOP genes point to a role in spatial control of flower-specific activation of these meristem identity genes.

The phylogeny and expression pattern of APETALA2-like genes in rice

The multigene families undergo birth-and-death evolution and thus contribute to biological innovations. The APETALA2-like genes belong to the euAP2 group of the AP2 gene family. These genes are characterized by several distinct motifs and exist in ferns, gymnosperms, and angiosperms. The phylogenetic analysis indicated that these genes have undergone the birth-and-death evolution. The five APETALA2-like genes in rice (Oryza sativa L.) display redundant but distinct expression patterns as demonstrated by RT-PCR and in situ hybridization. The potential functions of these genes were discussed on the basis of phylogenetic and expression pattern.

Molecular processes underlying the floral transition in the soybean shoot apical meristem

The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in the SAM of the crop legume, soybean (Glycine max). A total of 331 transcripts displayed significant changes in their expression profiles. The in silico and RT-PCR analysis on differentially regulated transcripts implies the intriguing involvement of sugar, auxin or abscisic acid (ABA) in events prior to the induction of floral homeotic transcripts. The novel involvement of ABA in the floral transition is further implicated by immunoassay, suggesting an increase in ABA levels in the SAM during this developmental transition. Furthermore, in situ localization, together with in silico data demonstrating a marked enhancement of abiotic stress-related transcripts, such as trehalose metabolism genes in SAMs, points to an overlap of abiotic stress and floral signalling pathways.

SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing.

Background

Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study.

Results

In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo.

Conclusions

Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization.

Comparative genomic analysis of light-regulated transcripts in the Solanaceae

Background

Plants use different light signals to adjust their growth and development to the prevailing environmental conditions. Studies in the model species Arabidopsis thaliana and rice indicate that these adjustments are mediated by large changes in the transcriptome. Here we compared transcriptional responses to light in different species of the Solanaceae to investigate common as well as species-specific changes in gene expression.

Results

cDNA microarrays were used to identify genes regulated by a transition from long days (LD) to short days (SD) in the leaves of potato and tobacco plants, and by phytochrome B (phyB), the photoreceptor that represses tuberization under LD in potato. We also compared transcriptional responses to photoperiod in Nicotiana tabacum Maryland Mammoth (MM), which flowers only under SD, with those of Nicotiana sylvestris, which flowers only under LD conditions. Finally, we identified genes regulated by red compared to far-red light treatments that promote germination in tomato.

Conclusion

Most of the genes up-regulated in LD were associated with photosynthesis, the synthesis of protective pigments and the maintenance of redox homeostasis, probably contributing to the acclimatization to seasonal changes in irradiance. Some of the photoperiodically regulated genes were the same in potato and tobacco. Others were different but belonged to similar functional categories, suggesting that conserved as well as convergent evolutionary processes are responsible for physiological adjustments to seasonal changes in the Solanaceae. A β-ZIP transcription factor whose expression correlated with the floral transition in Nicotiana species with contrasting photoperiodic responses was also regulated by photoperiod and phyB in potato, and is a candidate gene to act as a general regulator of photoperiodic responses. Finally, GIGANTEA, a gene that controls flowering time in Arabidopsis thaliana and rice, was regulated by photoperiod in the leaves of potato and tobacco and by red compared to far-light treatments that promote germination in tomato seeds, suggesting that a conserved light signaling cascade acts across developmental contexts and species.

DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana

Intercellular signaling plays an important role in controlling cellular behavior in apical meristems and developing organs in plants. One prominent example in Arabidopsis is the regulation of floral organ shape, ovule integument morphogenesis, the cell division plane, and root hair patterning by the leucine-rich repeat receptor-like kinase STRUBBELIG (SUB). Interestingly, kinase activity of SUB is not essential for its in vivo function, indicating that SUB may be an atypical or inactive receptor-like kinase. Since little is known about signaling by atypical receptor-like kinases, we used forward genetics to identify genes that potentially function in SUB-dependent processes and found recessive mutations in three genes that result in a sub-like phenotype. Plants with a defect in DETORQEO (DOQ), QUIRKY (QKY), and ZERZAUST (ZET) show corresponding defects in outer integument development, floral organ shape, and stem twisting. The mutants also show sub-like cellular defects in the floral meristem and in root hair patterning. Thus, SUB, DOQ, QKY, and ZET define the STRUBBELIG-LIKE MUTANT (SLM) class of genes. Molecular cloning of QKY identified a putative transmembrane protein carrying four C(2) domains, suggesting that QKY may function in membrane trafficking in a Ca(2+)-dependent fashion. Morphological analysis of single and all pair-wise double-mutant combinations indicated that SLM genes have overlapping, but also distinct, functions in plant organogenesis. This notion was supported by a systematic comparison of whole-genome transcript profiles during floral development, which molecularly defined common and distinct sets of affected processes in slm mutants. Further analysis indicated that many SLM-responsive genes have functions in cell wall biology, hormone signaling, and various stress responses. Taken together, our data suggest that DOQ, QKY, and ZET contribute to SUB-dependent organogenesis and shed light on the mechanisms, which are dependent on signaling through the atypical receptor-like kinase SUB.

Arabidopsis cold shock domain proteins: relationships to floral and silique development

Cold shock domain proteins (CSPs) are highly conserved from bacteria to higher plants and animals. Bacterial cold shock proteins function as RNA chaperones by destabilizing RNA secondary structures and promoting translation as an adaptative mechanism to low temperature stress. In animals, cold shock domain proteins exhibit broad functions related to growth and development. In order to understand better the function of CSPs in planta, detailed analyses were performed for Arabidopsis thaliana CSPs (AtCSPs) on the transcript and protein levels using an extensive series of tissue harvested throughout developmental stages within the entire life cycle of Arabidopsis. On both the transcript and protein levels, AtCSPs were enriched in shoot apical meristems and siliques. Although all AtCSPs exhibited similar expression patterns, AtCSP2 was the most abundantly expressed gene. In situ hybridization analyses were also used to confirm that AtCSP2 and AtCSP4 transcripts accumulate in developing embryos and shoot apices. AtCSPs transcripts were also induced during a controlled floral induction study. In vivo ChIP analysis confirmed that an embryo expressed MADS box transcription factor, AGL15, interacts within two AtCSP promoter regions and alters the respective patterns of AtCSP transcription. Comparative analysis of AtCSP gene expression between Landsberg and Columbia ecotypes confirmed a 1000-fold reduction of AtCSP4 gene expression in the Landsberg background. Analysis of the AtCSP4 genomic locus identified multiple polymorphisms in putative regulatory cis-elements between the two ecotypes. Collectively, these data support the hypothesis that AtCSPs are involved in the transition to flowering and silique development in Arabidopsis.

Plant responses to photoperiod

Photoperiod controls many developmental responses in animals, plants and even fungi. The response to photoperiod has evolved because daylength is a reliable indicator of the time of year, enabling developmental events to be scheduled to coincide with particular environmental conditions. Much progress has been made towards understanding the molecular mechanisms involved in the response to photoperiod in plants. These mechanisms include the detection of the light signal in the leaves, the entrainment of circadian rhythms, and the production of a mobile signal which is transmitted throughout the plant. Flowering, tuberization and bud set are just a few of the many different responses in plants that are under photoperiodic control. Comparison of what is known of the molecular mechanisms controlling these responses shows that, whilst common components exist, significant differences in the regulatory mechanisms have evolved between these responses.

Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model

MOTIVATION

MicroRNAs miRNAs play important roles in gene regulation and are regarded as key components in gene regulatory pathways. Systematically understanding functional roles of miRNAs is essential to define core transcriptional units regulating key biological processes. Here, we propose a method based on the probabilistic graphical model to identify the regulatory modules of miRNAs and the core regulatory motifs involved in their ability to regulate gene expression.

RESULTS

We applied our method to datasets of different sources from Arabidopsis consisting of miRNA-target pair information, upstream sequences of miRNAs, transcriptional regulatory motifs and gene expression profiles. The graphical model used in this study can efficiently capture the relationship between miRNAs and diverse conditions such as various developmental processes, thus allowing us to detect functionally correlated miRNA regulatory modules involved in specific biological processes. Furthermore, this approach can reveal core transcriptional elements associated with their miRNAs. The proposed method found clusters of miRNAs, as well as putative regulators controlling the expression of miRNAs, which were highly related to diverse developmental processes of Arabidopsis. Consequently, our method can provide hypothetical miRNA regulatory circuits for functional testing that represent transcriptional events of miRNAs and transcriptional factors involved in gene regulatory pathways.

Control of jasmonate biosynthesis and senescence by miR319 targets

Considerable progress has been made in identifying the targets of plant microRNAs, many of which regulate the stability or translation of mRNAs that encode transcription factors involved in development. In most cases, it is unknown, however, which immediate transcriptional targets mediate downstream effects of the microRNA-regulated transcription factors. We identified a new process controlled by the miR319-regulated clade of TCP (TEOSINTE BRANCHED/CYCLOIDEA/PCF) transcription factor genes. In contrast to other miRNA targets, several of which modulate hormone responses, TCPs control biosynthesis of the hormone jasmonic acid. Furthermore, we demonstrate a previously unrecognized effect of TCPs on leaf senescence, a process in which jasmonic acid has been proposed to be a critical regulator. We propose that miR319-controlled TCP transcription factors coordinate two sequential processes in leaf development: leaf growth, which they negatively regulate, and leaf senescence, which they positively regulate.

Short, single-stranded RNA molecules called microRNAs (miRNAs) regulate gene expression by negatively controlling both the stability and translation of target messenger RNAs that they recognize through sequence complementarity. In plants, miRNAs mostly regulate other regulators, the DNA-binding transcription factors. We investigated the downstream events regulated by five TCP (TEOSINTE BRANCHED/CYCLOIDEA/PCF) transcription factors that are controlled by the microRNA miR319 in Arabidopsis thaliana. The miR319-regulated TCPs were previously known to be important for limiting the growth of leaves. By applying a combination of genome-wide, biochemical, and genetic studies, we identified new TCP targets that include enzymes responsible for the synthesis of the hormone jasmonic acid. Our analysis of leaf extracts from plants with increased activity of miR319 confirms that altered expression of the biosynthetic genes leads to changed jasmonic acid levels. These plants show also an altered senescence behavior that becomes more normal again when the plants are treated with jasmonate. We propose that the miR319-regulated TCP factors thus coordinate different aspects of leaf development and physiology: growth, which they negatively regulate, and aging, which they positively regulate.

A plant microRNA and its targets turn out to regulate both early and late stages of leaf development: early on, they inhibit growth, while later on, they promote the onset of senescence.

Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape

In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5–10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development.

Involvement of the MADS-box gene ZMM4 in floral induction and inflorescence development in maize

The switch from vegetative to reproductive growth is marked by the termination of vegetative development and the adoption of floral identity by the shoot apical meristem (SAM). This process is called the floral transition. To elucidate the molecular determinants involved in this process, we performed genome-wide RNA expression profiling on maize (Zea mays) shoot apices at vegetative and early reproductive stages using massively parallel signature sequencing technology. Profiling revealed significant up-regulation of two maize MADS-box (ZMM) genes, ZMM4 and ZMM15, after the floral transition. ZMM4 and ZMM15 map to duplicated regions on chromosomes 1 and 5 and are linked to neighboring MADS-box genes ZMM24 and ZMM31, respectively. This gene order is syntenic with the vernalization1 locus responsible for floral induction in winter wheat (Triticum monococcum) and similar loci in other cereals. Analyses of temporal and spatial expression patterns indicated that the duplicated pairs ZMM4-ZMM24 and ZMM15-ZMM31 are coordinately activated after the floral transition in early developing inflorescences. More detailed analyses revealed ZMM4 expression initiates in leaf primordia of vegetative shoot apices and later increases within elongating meristems acquiring inflorescence identity. Expression analysis in late flowering mutants positioned all four genes downstream of the floral activators indeterminate1 (id1) and delayed flowering1 (dlf1). Overexpression of ZMM4 leads to early flowering in transgenic maize and suppresses the late flowering phenotype of both the id1 and dlf1 mutations. Our results suggest ZMM4 may play roles in both floral induction and inflorescence development.

The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis

Throughout development the Arabidopsis shoot apical meristem successively undergoes several major phase transitions such as the juvenile-to-adult and floral transitions until, finally, it will produce flowers instead of leaves and shoots. Members of the Arabidopsis SBP-box gene family of transcription factors have been implicated in promoting the floral transition in dependence of miR156 and, accordingly, transgenics constitutively over-expressing this microRNA are delayed in flowering. To elaborate their roles in Arabidopsis shoot development, we analysed two of the 11 miR156 regulated Arabidopsis SBP-box genes, i.e. the likely paralogous genes SPL9 and SPL15. Single and double mutant phenotype analysis showed these genes to act redundantly in controlling the juvenile-to-adult phase transition. In addition, their loss-of-function results in a shortened plastochron during vegetative growth, altered inflorescence architecture and enhanced branching. In these aspects, the double mutant partly phenocopies constitutive MIR156b over-expressing transgenic plants and thus a major contribution to the phenotype of these transgenics as a result of the repression of SPL9 and SPL15 is strongly suggested.

Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana

Leaves of flowering plants are produced from the shoot apical meristem at regular intervals, with the time that elapses between the formation of two successive leaf primordia defining the plastochron. We have identified two genetic axes affecting plastochron length in Arabidopsis thaliana. One involves microRNA156 (miR156), which targets a series of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. In situ hybridization studies and misexpression experiments demonstrate that miR156 is a quantitative, rather than spatial, modulator of SPL expression in leaf primordia and that SPL activity nonautonomously inhibits initiation of new leaves at the shoot apical meristem. The second axis is exemplified by a redundantly acting pair of cytochrome P450 genes, CYP78A5/KLUH and CYP78A7, which are likely orthologs of PLASTOCHRON1 of rice (Oryza sativa). Inactivation of CYP78A5, which is expressed at the periphery of the shoot apical meristem, accelerates the leaf initiation rate, whereas cyp78a5 cyp78a7 double mutants often die as embryos with supernumerary cotyledon primordia. The effects of both miR156-targeted SPL genes and CYP78A5 on organ size are correlated with changes in plastochron length, suggesting a potential compensatory mechanism that links the rate at which leaves are produced to final leaf size.

Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis

During the transition from vegetative to reproductive growth, the shoot meristem of flowering plants acquires the inflorescence identity to generate flowers rather than vegetative tissues. An important regulator that promotes the inflorescence identity in Arabidopsis is AGAMOUS-LIKE 24 (AGL24), a MADS-box transcription factor. Using a functional estradiol-inducible system in combination with microarray analysis, we identified AGL24-induced genes, including SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), a floral pathway integrator. Chromatin immunoprecipitation (ChIP) analysis of a functional AGL24-6HA-tagged line revealed in vivo binding of AGL24-6HA to the regulatory region of SOC1. Mutagenesis of the AGL24 binding site in the SOC1 promoter decreased Pro(SOC1):GUS expression and compromised SOC1 function in promoting flowering. Our results show that SOC1 is one of the direct targets of AGL24, and that SOC1 expression is upregulated by AGL24 at the shoot apex at the floral transitional stage. ChIP assay using a functional SOC1-9myc-tagged line and promoter mutagenesis analysis also revealed in vivo binding of SOC1-9myc to the regulatory regions of AGL24 and upregulation of AGL24 at the shoot apex by SOC1. Furthermore, we found that as in other flowering genetic pathways, the effect of gibberellins on flowering under short-day conditions was mediated by the interaction between AGL24 and SOC1. These observations suggest that during floral transition, a positive-feedback loop conferred by direct transcriptional regulation between AGL24 and SOC1 at the shoot apex integrates flowering signals.

Requirement of B2-type cyclin-dependent kinases for meristem integrity in Arabidopsis thaliana

To maintain proper meristem function, cell division and differentiation must be coordinately regulated in distinct subdomains of the meristem. Although a number of regulators necessary for the correct organization of the shoot apical meristem (SAM) have been identified, it is still largely unknown how their function is integrated with the cell cycle machinery to translate domain identity into correct cellular behavior. We show here that the cyclin-dependent kinases CDKB2;1 and CDKB2;2 are required both for normal cell cycle progression and for meristem organization. Consistently, the CDKB2 genes are highly expressed in the SAM in a cell cycle-dependent fashion, and disruption of CDKB2 function leads to severe meristematic defects. In addition, strong alterations in hormone signaling both at the level of active hormones and with respect to transcriptional and physiological outputs were observed in plants with disturbed CDKB2 activity.

Regulation of flowering time by RNA processing

Plants control the time at which they flower by integrating environmental cues such as day length and temperature with an endogenous program of development. Flowering time is a quantitative trait and a model for how precision in gene regulation is delivered. In this review, we reveal that flowering time control is particularly rich in RNA processing-based gene regulatory phenomena. We review those factors which function in conserved RNA processing events like alternative 3' end formation, splicing, RNA export and miRNA biogenesis and how they affect flowering time. Likewise, we review the novel plant-specific RNA-binding proteins identified as regulators of flowering time control. In addition, we add to the network of flowering time control pathways, information on alternative processing of flowering time gene pre-mRNAs. Finally, we describe new approaches to dissect the mechanisms which underpin this control.

Arabidopsis UEV1D promotes Lysine-63-linked polyubiquitination and is involved in DNA damage response

DNA damage tolerance (DDT) in budding yeast requires Lys-63-linked polyubiquitination of the proliferating cell nuclear antigen. The ubiquitin-conjugating enzyme Ubc13 and the Ubc enzyme variant (Uev) methyl methanesulfonate2 (Mms2) are required for this process. Mms2 homologs have been found in all eukaryotic genomes examined; however, their roles in multicellular eukaryotes have not been elucidated. We report the isolation and characterization of four UEV1 genes from Arabidopsis thaliana. All four Uev1 proteins can form a stable complex with At Ubc13 or with Ubc13 from yeast or human and can promote Ubc13-mediated Lys-63 polyubiquitination. All four Uev1 proteins can replace yeast MMS2 DDT functions in vivo. Although these genes are ubiquitously expressed in most tissues, UEV1D appears to express at a much higher level in germinating seeds and in pollen. We obtained and characterized two uev1d null mutant T-DNA insertion lines. Compared with wild-type plants, seeds from uev1d null plants germinated poorly when treated with a DNA-damaging agent. Those that germinated grew slower, and the majority ceased growth within 2 weeks. Pollen from uev1d plants also displayed a moderate but significant decrease in germination in the presence of DNA damage. This report links Ubc13-Uev with functions in DNA damage response in Arabidopsis.

OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a

Although flowering regulatory mechanisms have been extensively studied in Arabidopsis (Arabidopsis thaliana), those in other species have not been well elucidated. Here, we investigated the role of OsMADS51, a type I MADS-box gene in the short-day (SD) promotion pathway in rice (Oryza sativa). In SDs OsMADS51 null mutants flowered 2 weeks later than normal, whereas in long days loss of OsMADS51 had little effect on flowering. Transcript levels of three flowering regulators-Ehd1, OsMADS14, and Hd3a-were decreased in these mutants, whereas those of OsGI and Hd1 were unchanged. Ectopic expression of OsMADS51 caused flowering to occur about 7 d earlier only in SDs. In ectopic expression lines, transcript levels of Ehd1, OsMADS14, and Hd3a were increased, but those of OsGI and Hd1 remained the same. These results indicate that OsMADS51 is a flowering promoter, particularly in SDs, and that this gene functions upstream of Ehd1, OsMADS14, and Hd3a. To further investigate the relationship with other flowering promoters, we generated transgenic plants in which expression of Ehd1 or OsGI was suppressed. In Ehd1 RNA interference plants, OsMADS51 expression was not affected, supporting our conclusion that the MADS-box gene functions upstream of Ehd1. However, in OsGI antisense plants, the OsMADS51 transcript level was reduced. In addition, the circadian expression pattern for this MADS-box gene was similar to that for OsGI. These results demonstrate that OsMADS51 functions downstream of OsGI. In summary, OsMADS51 is a novel flowering promoter that transmits a SD promotion signal from OsGI to Ehd1.

Move on up, it's time for change--mobile signals controlling photoperiod-dependent flowering

Plants do not bloom randomly--but how do they know when and where to make flowers? Here, we review molecular mechanisms that integrate spatial and temporal information in day-length-dependent flowering. Primarily through genetic analyses in two species, Arabidopsis thaliana and rice, we today understand the essentials of two central issues in plant biology: how the appropriate photoperiod generates an inductive stimulus based on an external coincidence mechanism, and the nature of the mobile flowering signal, florigen, which relays photoperiod-dependent information from the leaf to the growing tip of the plant, the shoot apex.

A circadian rhythm set by dusk determines the expression of FT homologs and the short-day photoperiodic flowering response in Pharbitis

Seasonal control of flowering through responsiveness to daylength shows extreme variation. Different species flower in response to long days or short days (SDs), and this difference evolved several times. The molecular mechanisms conferring these responses have been compared in detail only in Arabidopsis thaliana and rice (Oryza sativa) and suggest that a conserved pathway confers daylength responses through regulation of FLOWERING LOCUS T (FT) transcription by CONSTANS (CO). We studied Pharbitis (Ipomoea nil; formerly, Pharbitis nil), a widely used SD model species and a member of the Convolvulaceae, and showed using transgenic plants together with detailed expression analysis that two putative orthologs of FT (Pn FT1 and Pn FT2) promote flowering specifically under SDs. These genes are expressed only under SDs, and light flashes given during the night reduce their expression and prevent flowering. We demonstrate that in Pharbitis a circadian rhythm set by the light-to-dark transition at dusk regulates Pn FT expression, which rises only when the night is longer than 11 h. Furthermore, Pharbitis accessions that differ in their critical night-length responses express Pn FT at different times after dusk, demonstrating that natural genetic variation influencing the clock regulating Pn FT expression alters the flowering response. In these assays, Pn FT mRNA abundance was not related to Pn CO expression, suggesting that Pn FT may be regulated by a different transcription factor in Pharbitis. We conclude that SD response in Pharbitis is controlled by a dedicated light sensitive clock, set by dusk, that activates Pn FT transcription in darkness, a different mechanism for measuring daylength than described for Arabidopsis and rice.

Flowering of strict photoperiodic Nicotiana varieties in non-inductive conditions by transgenic approaches

The genus Nicotiana contains species and varieties that respond differently to photoperiod for flowering time control as day-neutral, short-day and long-day plants. In classical photoperiodism studies, these varieties have been widely used to analyse the physiological nature for floral induction by day length. Since key regulators for flowering time control by day length have been identified in Arabidopsis thaliana by molecular genetic studies, it was intriguing to analyse how closely related plants in the Nicotiana genus with opposite photoperiodic requirements respond to certain flowering time regulators. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FRUITFULL (FUL) are two MADS box genes that are involved in the regulation of flowering time in Arabidopsis. SOC1 is a central flowering time pathway integrator, whereas the exact role of FUL for floral induction has not been established yet. The putative Nicotiana orthologs of SOC1 and FUL, NtSOC1 and NtFUL, were studied in day-neutral tobacco Nicotiana tabacum cv Hicks, in short-day tobacco N. tabacum cv Hicks Maryland Mammoth (MM) and long-day N. sylvestris plants. Both genes were similarly expressed under short- and long-day conditions in day-neutral and short-day tobaccos, but showed a different expression pattern in N. sylvestris. Overexpression of NtSOC1 and NtFUL caused flowering either in strict short-day (NtSOC1) or long-day (NtFUL) Nicotiana varieties under non-inductive photoperiods, indicating that these genes might be limiting for floral induction under non-inductive conditions in different Nicotiana varieties.