The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis

Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana

In Arabidopsis thaliana the CLAVATA1 (CLV1) receptor and GENERAL CONTROL NON DEREPRESSIBLE 5 (GCN5) histone acetyltransferase both regulate inflorescence meristem size and affect the expression of the meristem-promoting transcription factor WUSCHEL (WUS). Single and multiple mutants of GCN5 and CLAVATA members, were analysed for their gynoecium development, using morphological, physiological, genetic and molecular approaches. The clv1-1gcn5-1 double mutants exhibited novel phenotypes including elongated gynoecia with reduced valves and enlarged stigma and style, indicating a synergistic action of CLAVATA signaling and GCN5 action in the development of the gynoecium. Reporter line and gene expression analysis showed that clv1-1gcn5-1 plants have altered auxin and cytokinin response, distribution and ectopic overexpression of WUS. WUS expression was found in the style of wild-type gynoecia stage 10-13, suggesting a possible novel role for WUS in the development of the style. CLV1 and GCN5 are regulators of apical-basal and mediolateral polarity of the Arabidopsis gynoecium. They affect gynoecium morphogenesis through the negative regulation of auxin biosynthesis and promotion of polar auxin transport. They also promote cytokinin signaling in the carpel margin meristem and negatively regulate it at the stigma. Finally, they synergistically suppress WUS at the centre of the gynoecium.

The COP1 Target SHI-RELATED SEQUENCE5 Directly Activates Photomorphogenesis-Promoting Genes

Plant seedlings undergo distinct developmental processes in the dark and in the light. Several genes, including ELONGATED HYPOCOTYL5 (HY5), B-BOX PROTEIN21 (BBX21), and BBX22, have been identified as photomorphogenesis-promoting factors in Arabidopsis thaliana; however, the overexpression of these genes does not induce photomorphogenesis in the dark. Using an activation-tagging approach, we identified SRS5ox, which overexpresses SHI-RELATED SEQUENCE5 (SRS5) following induction with estradiol. SRS5 overexpression in SRS5ox and Pro35S:SRS5-GFP seedlings results in a constitutive photomorphogenesis phenotype in the dark, whereas SRS5 loss of function in the srs5-2 mutant results in long hypocotyls in the light. This indicates that SRS5 is a positive regulator of photomorphogenesis. Furthermore, SRS5 promotes photomorphogenesis by directly binding to the promoters of photomorphogenesis-promoting genes, such as HY5, BBX21, and BBX22, and activating their expression, thus affecting the expression of downstream light-signaling genes. These data indicate that SRS5 acts in the upregulation of photomorphogenesis-promoting genes. In addition, CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), which plays a central repressive role in seedling photomorphogenesis, directly ubiquitinates SRS5, promoting its degradation in the dark. Taken together, our results demonstrate that SRS5 directly activates the expression of downstream genes HY5, BBX21, and BBX22 and is a target of COP1-mediated degradation in Arabidopsis.

A molecular network for functional versatility of HECATE transcription factors

During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix-loop-helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.

Essential Roles of Local Auxin Biosynthesis in Plant Development and in Adaptation to Environmental Changes

It has been a dominant dogma in plant biology that the self-organizing polar auxin transport system is necessary and sufficient to generate auxin maxima and minima that are essential for almost all aspects of plant growth and development. However, in the past few years, it has become clear that local auxin biosynthesis is required for a suite of developmental processes, including embryogenesis, endosperm development, root development, and floral initiation and patterning. Moreover, it was discovered that local auxin biosynthesis maintains optimal plant growth in response to environmental signals, including light, temperature, pathogens, and toxic metals. In this article, I discuss the recent progress in auxin biosynthesis research and the paradigm shift in recognizing the important roles of local auxin biosynthesis in plant biology.

Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense

Most plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat. RNA-sequencing with de novo assembly revealed that the transcripts of very long chain fatty acid (VLCFA) biosynthesis genes, auxin biosynthesis/signaling-related genes and lateral root developmental genes are highly abundant in the haustoria. Gene co-expression network analysis identified a network module linking VLCFAs and the auxin-responsive lateral root development pathway. GC-TOF-MS analysis consistently revealed a unique metabolome profile with many types of fatty acids in the T. chinense root system, including the accumulation of a 25-carbon long chain saturated fatty acid in the haustoria. Our field-omics data provide evidence supporting the hypothesis that the molecular developmental machinery used for lateral root formation in non-parasitic plants has been co-opted into the developmental reprogramming of haustorial formation in the linage of parasitic plants.

Key Hormonal Components Regulate Agronomically Important Traits in Barley

The development and growth of plant organs is regulated by phytohormones, which constitute an important area of plant science. The last decade has seen a rapid increase in the unravelling of the pathways by which phytohormones exert their influence. Phytohormones function as signalling molecules that interact through a complex network to control development traits. They integrate metabolic and developmental events and regulate plant responses to biotic and abiotic stress factors. As such, they influence the yield and quality of crops. Recent studies on barley have emphasised the importance of phytohormones in promoting agronomically important traits such as tillering, plant height, leaf blade area and spike/spikelet development. Understanding the mechanisms of how phytohormones interact may help to modify barley architecture and thereby improve its adaptation and yield. To achieve this goal, extensive functional validation analyses are necessary to better understand the complex dynamics of phytohormone interactions and phytohormone networks that underlie the biological processes. The present review summarises the current knowledge on the crosstalk between phytohormones and their roles in barley development. Furthermore, an overview of how phytohormone modulation may help to improve barley plant architecture is also provided.

A molecular framework controlling style morphology in Brassicaceae

Organ formation in multicellular organisms depends on the coordinated activities of regulatory components that integrate developmental and hormonal cues to control gene expression and mediate cell-type specification. For example, development of the Arabidopsis gynoecium is tightly controlled by distribution and synthesis of the plant hormone auxin. The functions of several transcription factors (TFs) have been linked with auxin dynamics during gynoecium development; yet how their activities are coordinated is not known. Here, we show that five such TFs function together to ensure polarity establishment at the gynoecium apex. The auxin response factor ETTIN (ARF3; herein, ETT) is a central component of this framework. Interaction of ETT with TF partners is sensitive to the presence of auxin and our results suggest that ETT forms part of a repressive gene-regulatory complex. We show that this function is conserved between members of the Brassicaceae family and that variation in an ETT subdomain affects interaction strengths and gynoecium morphology. These results suggest that variation in affinities between conserved TFs can lead to morphological differences and thus contribute to the evolution of diverse organ shapes.

Summary: Variation in interaction affinity between transcription factors of an ETTIN-containing complex underlies diversity of gynoecium style structure among members of the Brassicacea family.

Developmental cartography: coordination via hormonal and genetic interactions during gynoecium formation

Development in multicellular organisms requires the establishment of tissue identity through polarity cues. The Arabidopsis gynoecium presents an excellent model to study this coordination, as it comprises a complex tissue structure which is established through multiple polarity systems. The gynoecium is derived from the fusion of two carpels and forms in the centre of the flower. Many regulators of carpel development also have roles in leaf development, emphasizing the evolutionary origin of carpels as modified leaves. The gynoecium can therefore be considered as having evolved from a simple setup followed by adjustment in tissue polarity to facilitate efficient reproduction. Here, we discuss concepts to understand how hormonal and genetic systems interact to pattern the gynoecium.

Class VIIIb APETALA2 Ethylene Response Factors in Plant Development

The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.

SHI/STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis

In flowering plants, mature sperm cells are enclosed in pollen grains formed in structures called anthers. Several cell layers surrounding the central sporogenous cells of the anther are essential for directing the developmental processes that lead to meiosis, pollen formation, and the subsequent pollen release. The specification and function of these tissues are regulated by a large number of genetic factors. Additionally, the plant hormone auxin has previously been shown to play important roles in the later phases of anther development. Using the R2D2 auxin sensor system we here show that auxin is sensed also in the early phases of anther cell layer development, suggesting that spatiotemporal regulation of auxin levels is important for early anther morphogenesis. Members of the SHI/STY transcription factor family acting as direct regulators of YUC auxin biosynthesis genes have previously been demonstrated to affect early anther patterning. Using reporter constructs we show that SHI/STY genes are dynamically active throughout anther development and their expression overlaps with those of three additional downstream targets, PAO5, EOD3 and PGL1. Characterization of anthers carrying mutations in five SHI/STY genes clearly suggests that SHI/STY transcription factors affect anther organ identity. In addition, their activity is important to repress periclinal cell divisions as well as premature entrance into programmed cell death and cell wall lignification, which directly influences the timing of anther dehiscence and the pollen viability. The SHI/STY proteins also prevent premature pollen germination suggesting that they may play a role in the induction or maintenance of pollen dormancy.

Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage

In Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) revealed a candidate region of 0.52 Mb (A06: 1,824,886~2,347,097 bp) containing genes enriched for plant hormone signal transduction. RNA Sequencing (RNA-Seq) analysis supported the hormone pathway enrichment leading to the identification of two key candidate genes, BrGH3.12 and BrABF1. The regulated homologous genes and the relationship between genes in this pathway were also revealed. Expression of BrGH3.12 varied significantly in the apical portion of the leaf, consistent with the morphological differences between overlapping and outward curling leaves. Transcript levels of BrABF1 in the top, middle and basal segments of the leaf were significantly different between the two types. The two morphotypes contained different concentrations of IAA in the apical portion of their leaves while levels of ABA differed significantly between plant types in the top, middle, and basal leaf segments. Results from Seq-BSA, RNA-Seq and metabolite analyses all support a role for IAA and ABA in heading type formation. These findings increase our understanding of the molecular basis for pattern formation of the leafy head in Chinese cabbage and will contribute to future work developing more desirable leafy head patterns.

How hormones regulate floral architecture in barley

A defining characteristic of grasses, including major cereal crops, is the way in which flowers are arranged on an inflorescence. A new study finds that regulation of hormone levels during development is crucial for determining the arrangement of flowers on a barley inflorescence, opening new doors for increasing grain yield.

DORNRÖSCHEN, DORNRÖSCHEN-LIKE, and PUCHI redundantly control floral meristem identity and organ initiation in Arabidopsis

The biphasic floral transition in Arabidopsis thaliana involves many redundant intersecting regulatory networks. The related AP2 transcription factors DORNRÖSCHEN (DRN), DORNRÖSCHEN-LIKE (DRNL), and PUCHI individually execute well-characterized functions in diverse developmental contexts, including floral development. Here, we show that their combined loss of function leads to synergistic floral phenotypes, including reduced floral merosity in all whorls, which reflects redundant functions of all three genes in organ initiation rather than outgrowth. Additional loss of BLADE-ON-PETIOLE1 (BOP1) and BOP2 functions results in the complete conversion of floral meristems into secondary inflorescence shoots, demonstrating that all five genes define an essential regulatory network for establishing floral meristem identity, and we show that their functions converge to regulate LEAFY expression. Thus, despite their largely discrete spatiotemporal expression domains in the inflorescence meristem and early floral meristem, PUCHI, DRN, and DRNL interdependently contribute to cellular fate decisions. Auxin might represent one potential non-cell-autonomous mediator of their gene functions, because PUCHI, DRN, and DRNL all interact with auxin transport and biosynthesis pathways.

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

BACKGROUND

Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae).

RESULTS

The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species.

CONCLUSIONS

The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.

An Evolutionary Framework for Carpel Developmental Control Genes

Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana. Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4). However, the timing of the origin and their subsequent molecular evolution of these carpel developmental regulators are largely unknown. Here, we have sampled homologs of these carpel developmental regulators from the sequenced genomes of a wide taxonomic sampling of the land plants, such as Physcomitrella patens, Selaginella moellendorfii, Picea abies, and several angiosperms. Careful phylogenetic analyses were carried out that provide a phylogenetic background for the different gene families and provide minimal estimates for the ages of these developmental regulators. Our analyses and published work show that LUG-, SEU-, and SHI/STY-like genes were already present in the Most Recent Common Ancestor (MRCA) of all land plants, AG- and SEP-like genes were present in the MRCA of seed plants and their origin may coincide with the ξ Whole Genome Duplication. Our work shows that the carpel development regulatory network was, in part, recruited from preexisting network components that were present in the MRCA of angiosperms and modified to regulate gynoecium development.

Methodological Advances in Auxin and Cytokinin Biology

The history of auxin and cytokinin biology including the initial discoveries by father-son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.

The Role of SHI/STY/SRS Genes in Organ Growth and Carpel Development Is Conserved in the Distant Eudicot Species Arabidopsis thaliana and Nicotiana benthamiana

Carpels are a distinctive feature of angiosperms, the ovule-bearing female reproductive organs that endow them with multiple selective advantages likely linked to the evolutionary success of flowering plants. Gene regulatory networks directing the development of carpel specialized tissues and patterning have been proposed based on genetic and molecular studies carried out in Arabidopsis thaliana. However, studies on the conservation/diversification of the elements and the topology of this network are still scarce. In this work, we have studied the functional conservation of transcription factors belonging to the SHI/STY/SRS family in two distant species within the eudicots, Eschscholzia californica and Nicotiana benthamiana. We have found that the expression patterns of EcSRS-L and NbSRS-L genes during flower development are similar to each other and to those reported for Arabidopsis SHI/STY/SRS genes. We have also characterized the phenotypic effects of NbSRS-L gene inactivation and overexpression in Nicotiana. Our results support the widely conserved role of SHI/STY/SRS genes at the top of the regulatory network directing style and stigma development, specialized tissues specific to the angiosperm carpels, at least within core eudicots, providing new insights on the possible evolutionary origin of the carpels.

Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

VRS2 regulates hormone-mediated inflorescence patterning in barley

Plant architecture has clear agronomic and economic implications for crops such as wheat and barley, as it is a critical factor for determining grain yield. Despite this, only limited molecular information is available about how grain-bearing inflorescences, called spikes, are formed and maintain their regular, distichous pattern. Here we elucidate the molecular and hormonal role of Six-rowed spike 2 (Vrs2), which encodes a SHORT INTERNODES (SHI) transcriptional regulator during barley inflorescence and shoot development. We show that Vrs2 is specifically involved in floral organ patterning and phase duration by maintaining hormonal homeostasis and gradients during normal spike development and similarly influences plant stature traits. Furthermore, we establish a link between the SHI protein family and sucrose metabolism during organ growth and development that may have implications for deeper molecular insights into inflorescence and plant architecture in crops.

Genome-wide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice

Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.

Hormonal control of the development of the gynoecium

Flowering plants are called angiosperms and most of their flowers produce at their center a pistil or a gynoecium, which is the female reproductive structure. After a double fertilization event, the gynoecium develops into a fruit with great importance for the plant because it protects and helps the dispersion of a new generation, and, for humans is a key nutritional source. Over 20 years, Arabidopsis thaliana has been used to discover important genes for gynoecium development, and in the early years, auxin was already proposed to play a role. More recently, new discoveries are unveiling the importance of other hormones, particularly cytokinins, and providing insights about the action of these hormones in gynoecium development, which is the focus of this review. One of the next challenges is to further refine the knowledge about the mechanisms by which hormones shape the gynoecium, understand the communication among them and their interactions with transcription factors that altogether guide gynoecium development.

Boosting AthaMap Database Content with Data from Protein Binding Microarrays

The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. With the advent of protein binding microarrays (PBM), the number of known TFBS for A. thaliana transcription factors (TFs) has increased dramatically. Using 113 positional weight matrices (PWMs) generated from a single PBM study and representing a total number of 68 different TFs, the number of predicted TFBS in AthaMap was now increased by about 3.8 × 10(7) to 4.9 × 10(7). The number of TFs with PWM-predicted TFBS annotated in AthaMap has increased to 126, representing a total of 29 TF families and newly including ARF, AT-Hook, YABBY, LOB/AS2 and SRS. Furthermore, links from all Arabidopsis TFs and genes to the newly established Arabidopsis Information Portal (AIP) have been implemented. With this qualitative and quantitative update, the improved AthaMap increases its value as a resource for the analysis of A. thaliana gene expression regulation at www.athamap.de.

Profiling of the Early Nitrogen Stress Response in the Diatom Phaeodactylum tricornutum Reveals a Novel Family of RING-Domain Transcription Factors

Diatoms often inhabit highly variable habitats where they are confronted with a wide variety of stresses, frequently including starvation of nutrients such as nitrogen. In this study, the transcriptome of the model diatom Phaeodactylum tricornutum was profiled during the onset of nitrogen starvation by RNA sequencing, and overrepresented motifs were determined in promoters of genes that were early and strongly up-regulated during the nitrogen stress response. One of these motifs could be bound by a nitrogen starvation-inducible RING-domain protein termed RING-GAF-Gln-containing protein (RGQ1), which was shown to act as a transcription factor and belongs to a previously uncharacterized family that is conserved in heterokont algae.

TCP15 modulates cytokinin and auxin responses during gynoecium development in Arabidopsis

We studied the role of Arabidopsis thaliana TCP15, a member of the TEOSINTE BRANCHED1-CYCLOIDEA-PCF (TCP) transcription factor family, in gynoecium development. Plants that express TCP15 from the 35S CaMV promoter (35S:TCP15) develop flowers with defects in carpel fusion and a reduced number of stigmatic papillae. In contrast, the expression of TCP15 fused to a repressor domain from its own promoter causes the development of outgrowths topped with stigmatic papillae from the replum. 35S:TCP15 plants show lower levels of the auxin indoleacetic acid and reduced expression of the auxin reporter DR5 and the auxin biosynthesis genes YUCCA1 and YUCCA4, suggesting that TCP15 is a repressor of auxin biosynthesis. Treatment of plants with cytokinin enhances the developmental effects of expressing TCP15 or its repressor form. In addition, treatment of a knock-out double mutant in TCP15 and the related gene TCP14 with cytokinin causes replum enlargement, increased development of outgrowths, and the induction of the auxin biosynthesis genes YUCCA1 and YUCCA4. A comparison of the phenotypes observed after cytokinin treatment of plants with altered expression levels of TCP15 and auxin biosynthesis genes suggests that TCP15 modulates gynoecium development by influencing auxin homeostasis. We propose that the correct development of the different tissues of the gynoecium requires a balance between auxin levels and cytokinin responses, and that TCP15 participates in a feedback loop that helps to adjust this balance.

Current aspects of auxin biosynthesis in plants

Auxin is an important plant hormone essential for many aspects of plant growth and development. Indole-3-acetic acid (IAA) is the most studied auxin in plants, and its biosynthesis pathway has been investigated for over 70 years. Although the complete picture of auxin biosynthesis remains to be elucidated, remarkable progress has been made recently in understanding the mechanism of IAA biosynthesis. Genetic and biochemical studies demonstrate that IAA is mainly synthesized from l-tryptophan (Trp) via indole-3-pyruvate by two-step reactions in Arabidopsis. While IAA is also produced from Trp via indole-3-acetaldoxime in Arabidopsis, this pathway likely plays an auxiliary role in plants of the family Brassicaceae. Recent studies suggest that the Trp-independent pathway is not a major route for IAA biosynthesis, but they reveal an important role for a cytosolic indole synthase in this pathway. In this review, I summarize current views and future prospects of IAA biosynthesis research in plants.

Arabidopsis HECATE genes function in phytohormone control during gynoecium development

The fruit, which develops from the fertilised gynoecium formed in the innermost whorl of the flower, is the reproductive organ and one of the most complex structures of an angiosperm plant. Phytohormones play important roles during flower and fruit patterning, morphogenesis and growth, and there is emerging evidence for a cross-talk between different classes of plant hormones throughout these processes. Here, we show that the bHLH transcription factors HECATE 1 (HEC1), HEC2 and HEC3, which have previously been identified as essential components of transmitting tract formation, affect both auxin and cytokinin responses during reproductive tissue development. We find that HEC1 interacts with SPATULA (SPT) to control carpel fusion and that both transcription factors restrict sensitivity to cytokinin in the gynoecium. In addition, HEC1 is tightly integrated into the auxin-signalling network at the levels of biosynthesis, transport and transcriptional response. Based on this data, we propose that HEC1 acts as a local modulator of auxin and cytokinin responses to control gynoecium development in Arabidopsis.

Highlighted article: In the developing reproductive tissue of plants, HECATE 1 and SPATULA coordinate auxin and cytokinin signalling to orchestrate the development of the gynoecium.

Transcriptional feedback regulation of YUCCA genes in response to auxin levels in Arabidopsis

The IPyA pathway, the major auxin biosynthesis pathway, is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels. The phytohormone auxin plays an important role in plant growth and development, and levels of active free auxin are determined by biosynthesis, conjugation, and polar transport. Unlike conjugation and polar transport, little is known regarding the regulatory mechanism of auxin biosynthesis. We discovered that expression of genes encoding indole-3-pyruvic acid (IPyA) pathway enzymes is regulated by elevated or reduced active auxin levels. Expression levels of TAR2, YUC1, YUC2, YUC4, and YUC6 were downregulated in response to synthetic auxins [1-naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D)] exogenously applied to Arabidopsis thaliana L. seedlings. Concomitantly, reduced levels of endogenous indole-3-acetic acid (IAA) were observed. Alternatively, expression of these YUCCA genes was upregulated by the auxin biosynthetic inhibitor kynurenine in Arabidopsis seedlings, accompanied by reduced IAA levels. These results indicate that expression of YUCCA genes is regulated by active auxin levels. Similar results were also observed in auxin-overproduction and auxin-deficient mutants. Exogenous application of IPyA to Arabidopsis seedlings preincubated with kynurenine increased endogenous IAA levels, while preincubation with 2,4-D reduced endogenous IAA levels compared to seedlings exposed only to IPyA. These results suggest that in vivo conversion of IPyA to IAA was enhanced under reduced auxin levels, while IPyA to IAA conversion was depressed in the presence of excess auxin. Based on these results, we propose that the IPyA pathway is transcriptionally regulated through a negative feedback mechanism in response to active auxin levels.

The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis

Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.

Conserved regulatory mechanism controls the development of cells with rooting functions in land plants

Land plants develop filamentous cells-root hairs, rhizoids, and caulonemata-at the interface with the soil. Members of the group XI basic helix-loop-helix (bHLH) transcription factors encoded by LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) genes positively regulate the development of root hairs in the angiosperms Lotus japonicus, Arabidopsis thaliana, and rice (Oryza sativa). Here we show that auxin promotes rhizoid and caulonema development by positively regulating the expression of PpLRL1 and PpLRL2, the two LRL genes in the Physcomitrella patens genome. Although the group VIII bHLH proteins, AtROOT HAIR DEFECTIVE6 and AtROOT HAIR DEFECTIVE SIX-LIKE1, promote root-hair development by positively regulating the expression of AtLRL3 in A. thaliana, LRL genes promote rhizoid development independently of PpROOT HAIR DEFECTIVE SIX-LIKE1 and PpROOT HAIR DEFECITVE SIX-LIKE2 (PpRSL1 and PpRSL2) gene function in P. patens. Together, these data demonstrate that both LRL and RSL genes are components of an ancient auxin-regulated gene network that controls the development of tip-growing cells with rooting functions among most extant land plants. Although this network has diverged in the moss and the angiosperm lineages, our data demonstrate that the core network acted in the last common ancestor of the mosses and angiosperms that existed sometime before 420 million years ago.

LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signalling downstream of the Aux/IAA gene rootless with undetectable meristem 1

Only little is known about target genes of auxin signalling downstream of the Aux/IAA-ARF module. In the present study, it has been demonstrated that maize lateral root primordia 1 (lrp1) encodes a transcriptional activator that is directly regulated by the Aux/IAA protein ROOTLESS WITH UNDETECTABLE MERISTEM 1 (RUM1). Expression of lrp1 is confined to early root primordia and meristems and is auxin-inducible. Based on its primary protein structure, LRP1 is predicted to be a transcription factor. This notion is supported by exclusive LRP1 localization in the nucleus and its ability to activate downstream gene activity. Based on the observation that lrp1 transcription is completely repressed in the semi-dominant gain of function mutant rum1, it was demonstrated that the lrp1 promoter is a direct target of RUM1 proteins. Subsequently, promoter activation assays indicated that RUM1 represses the expression of a GFP reporter fused to the native promoter of lrp1. Constitutive repression of lrp1 in rum1 mutants is a consequence of the stability of mutated rum1 proteins which cannot be degraded by the proteasome and thus constitutively bind to the lrp1 promoter and repress transcription. Taken together, the repression of the transcriptional activator lrp1 by direct binding of RUM1 to its promoter, together with specific expression of lrp1 in root meristems, suggests a function in maize root development via the RUM1-dependent auxin signalling pathway.

Transcriptional repression caused by Dof5.8 is involved in proper vein network formation in Arabidopsis thaliana leaves

Vascular plants have a network of vasculature in their leaves, which supplies water and nutrients and exports photoassimilates to other tissues. The vascular network is patterned during the development of leaf primordia through the induction of provascular differentiation by auxin. Arabidopsis thaliana Dof5.8, encoding a Dof-type transcription factor, is expressed early in provascular cells under the control of the MONOPTEROS transcription factor, also known as auxin response factor 5 (ARF5). Here, we report the effect of overexpressing Dof5.8 in provascular cells on the formation of the vascular network. Overexpression of Dof5.8 inhibited the formation of higher-order veins in cotyledons and leaves, probably through transcriptional repression by Dof5.8. The expression of auxin-associated transcription factor genes, DORNRöSCHEN and SHI-RELATED SEQUENCE 5, was downregulated in the Dof5.8 overexpressors, and overexpression of these genes partially rescued the impaired formation of higher-order veins in Dof5.8-overexpressing lines, suggesting that the overexpression of Dof5.8 modulates the auxin response and leads to impaired vein formation in A. thaliana.

Ethylene is integrated into the nitric oxide regulation of Arabidopsis somatic embryogenesis

The study confirms the role of the two Arabidopsis hemoglobin genes (Glb1 and Glb2) during somatic embryogenesis and proposes the involvement of ethylene in the regulation of embryo development. Suppression of both Glb1 and Glb2 results in accumulation of nitric oxide (NO) and a different embryogenic response. Compared to WT tissue, down-regulation of Glb1 (Glb1 RNAi line) compromises the embryogenic process, while repression of Glb2 (Glb2-/- line) increases the number of embryos. These differences were ascribed to the differential accumulation of NO in the two lines, as Glb1 is a more effective NO scavenger compared to Glb2. A high elevation of NO level [achieved pharmacologically using the NO donor sodium nitroprusside (SNP), or genetically using the Glb1 suppressing line], activated the two ethylene biosynthetic genes 1-aminocyclopropane-1-carboxylate synthase (ACC synthase) and 1-aminocyclopropane-1-carboxylate oxidase (ACC oxidase). Ethylene accumulation repressed embryogenesis, as shown by the decreased embryo number observed in tissue treated with the ethylene releasing agent Ethephon (ETH), as well as by the increased embryo production obtained with the two ethylene insensitive mutant lines (ein2-1 and ein3-1). A repression in ethylene level increased the expression of many auxin biosynthetic genes and favored the accumulation of the auxin indole-acetic acid (IAA) at the sites of the explants where embryogenic tissue will form. Collectively these data reveal that high levels of NO, generated by the Glb1 suppressing line, but not by the Glb2 suppressing line, might increase the level of ethylene, which represses the production of auxin. Auxin is the inductive signal required for the formation of the embryogenic tissue.

Molecular basis for three-dimensional elaboration of the Aquilegia petal spur

By enforcing specific pollinator interactions, Aquilegia petal nectar spurs maintain reproductive isolation between species. Spur development is the result of three-dimensional elaboration from a comparatively two-dimensional primordium. Initiated by localized, oriented cell divisions surrounding the incipient nectary, this process creates a pouch that is extended by anisotropic cell elongation. We hypothesized that the development of this evolutionary novelty could be promoted by non-mutually exclusive factors, including (i) prolonged, KNOX-dependent cell fate indeterminacy, (ii) localized organ sculpting and/or (iii) redeployment of hormone-signalling modules. Using cell division markers to guide transcriptome analysis of microdissected spur tissue, we present candidate mechanisms underlying spur outgrowth. We see dynamic expression of factors controlling cell proliferation and hormone signalling, but no evidence of contribution from indeterminacy factors. Transcriptome dynamics point to a novel recruitment event in which auxin-related factors that normally function at the organ margin were co-opted to this central structure. Functional perturbation of the transition between cell division and expansion reveals an unexpected asymmetric component of spur development. These findings indicate that the production of this three-dimensional form is an example of organ sculpting via localized cell division with novel contributions from hormone signalling, rather than a product of prolonged indeterminacy.

Copper mediates auxin signalling to control cell differentiation in the copper moss Scopelophila cataractae

The copper (Cu) moss Scopelophila cataractae (Mitt.) Broth. is often found in Cu-enriched environments, but it cannot flourish under normal conditions in nature. Excess Cu is toxic to almost all plants, and therefore how this moss species thrives in regions with high Cu concentration remains unknown. In this study, we investigated the effect of Cu on gemma germination and protonemal development in S. cataractae. A high concentration of Cu (up to 800 µM) did not affect gemma germination. In the protonemal stage, a low concentration of Cu promoted protonemal gemma formation, which is the main strategy adopted by S. cataractae to expand its habitat to new locations. Cu-rich conditions promoted auxin accumulation and induced differentiation of chloronema into caulonema cells, whereas it repressed protonemal gemma formation. Under low-Cu conditions, auxin treatment mimicked the effects of high-Cu conditions. Furthermore, Cu-induced caulonema differentiation was severely inhibited in the presence of the auxin antagonist α-(phenylethyl-2-one)-indole-3-acetic acid, or the auxin biosynthesis inhibitor l-kynurenine. These results suggest that S. cataractae flourishes in Cu-rich environments via auxin-regulated cell differentiation. The copper moss might have acquired this mechanism during the evolutionary process to benefit from its advantageous Cu-tolerance ability.

Identification of direct targets of plant transcription factors using the GR fusion technique

The glucocorticoid receptor-dependent activation of plant transcription factors has proven to be a powerful tool for the identification of their direct target genes. In the absence of the synthetic steroid hormone dexamethasone (dex), transcription factors fused to the hormone-binding domain of the glucocorticoid receptor (TF-GR) are held in an inactive state, due to their cytoplasmic localization. This requires physical interaction with the heat shock protein 90 (HSP90) complex. Hormone binding leads to disruption of the interaction between GR and HSP90 and allows TF-GR fusion proteins to enter the nucleus. Once inside the nucleus, they bind to specific DNA sequences and immediately activate or repress expression of their targets. This system is well suited for the identification of direct target genes of transcription factors in plants, as (A) there is little basal protein activity in the absence of dex, (B) steroid application leads to rapid transcription factor activation, (C) no side effects of dex treatment are observed on the physiology of the plant, and (D) secondary effects of transcription factor activity can be eliminated by simultaneous application of an inhibitor of protein biosynthesis, cycloheximide (cyc). In this chapter, we describe detailed protocols for the preparation of plant material, for dex and cyc treatment, for RNA extraction, and for the PCR-based or genome-wide identification of direct targets of transcription factors fused to GR.

SCI1 is a component of the auxin-dependent control of cell proliferation in Arabidopsis upper pistil

To characterize the recently described SCI1 (stigma/style cell cycle inhibitor 1) gene relationship with the auxin pathway, we have taken the advantage of the Arabidopsis model system and its available tools. At first, we have analyzed the At1g79200 T-DNA insertion mutants and constructed various transgenic plants. The loss- and gain-of-function plants displayed cell number alterations in upper pistils that were controlled by the amino-terminal domain of the protein. These data also confirmed that this locus holds the functional homolog (AtSCI1) of the Nicotiana tabacum SCI1 gene. Then, we have provided some evidences the auxin synthesis/signaling pathways are required for downstream proper AtSCI1 control of cell number: (a) its expression is downregulated in yuc2yuc6 and npy1 auxin-deficient mutants, (b) triple (yuc2yuc6sci1) and double (npy1sci1) mutants mimicked the auxin-deficient phenotypes, with no synergistic interactions, and (c) the increased upper pistil phenotype in these last mutants, which is a consequence of an increased cell number, was able to be complemented by AtSCI1 overexpression. Taken together, our data strongly suggests SCI1 as a component of the auxin signaling transduction pathway to control cell proliferation/differentiation in stigma/style, representing a molecular effector of this hormone on pistil development.

Plasma membrane-targeted PIN proteins drive shoot development in a moss

Background

Plant body plans arise by the activity of meristematic growing tips during development and radiated independently in the gametophyte (n) and sporophyte (2n) stages of the life cycle during evolution. Although auxin and its intercellular transport by PIN family efflux carriers are primary regulators of sporophytic shoot development in flowering plants, the extent of conservation in PIN function within the land plants and the mechanisms regulating bryophyte gametophytic shoot development are largely unknown.

Results

We have found that treating gametophytic shoots of the moss Physcomitrella patens with exogenous auxins and auxin transport inhibitors disrupts apical function and leaf development. Two plasma membrane-targeted PIN proteins are expressed in leafy shoots, and pin mutants resemble plants treated with auxins or auxin transport inhibitors. PIN-mediated auxin transport regulates apical cell function, leaf initiation, leaf shape, and shoot tropisms in moss gametophytes. pin mutant sporophytes are sometimes branched, reproducing a phenotype only previously seen in the fossil record and in rare natural moss variants.

Conclusions

Our results show that PIN-mediated auxin transport is an ancient, conserved regulator of shoot development.

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PIN proteins have polar plasma membrane localizations in the moss Physcomitrella

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PIN-mediated auxin transport drives gametophytic shoot development in Physcomitrella

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PIN-mediated auxin transport suppresses branching in Physcomitrella sporophytes

Emergence of a new step towards understanding the molecular mechanisms underlying nitrate-regulated gene expression

Nitrogen is one of the primary macronutrients of plants, and nitrate is the most abundant inorganic form of nitrogen in soils. Plants take up nitrate in soils and utilize it both for nitrogen assimilation and as a signalling molecule. Thus, an essential role for nitrate in plants is triggering changes in gene expression patterns, including immediate induction of the expression of genes involved in nitrate transport and assimilation, as well as several transcription factor genes and genes related to carbon metabolism and cytokinin biosynthesis and response. Significant progress has been made in recent years towards understanding the molecular mechanisms underlying nitrate-regulated gene expression in higher plants; a new stage in our understanding of this process is emerging. A key finding is the identification of NIN-like proteins (NLPs) as transcription factors governing nitrate-inducible gene expression. NLPs bind to nitrate-responsive DNA elements (NREs) located at nitrate-inducible gene loci and activate their NRE-dependent expression. Importantly, post-translational regulation of NLP activity by nitrate signalling was strongly suggested to be a vital process in NLP-mediated transcriptional activation and subsequent nitrate responses. We present an overview of the current knowledge of the molecular mechanisms underlying nitrate-regulated gene expression in higher plants.

Trimmomatic: a flexible trimmer for Illumina sequence data

MOTIVATION

Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data.

RESULTS

The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.

AVAILABILITY AND IMPLEMENTATION

Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic

CONTACT

usadel@bio1.rwth-aachen.de

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

EARLY BUD-BREAK 1 (EBB1) is a regulator of release from seasonal dormancy in poplar trees

Trees from temperate latitudes transition between growth and dormancy to survive dehydration and freezing stress during winter months. We used activation tagging to isolate a dominant mutation affecting release from dormancy and identified the corresponding gene EARLY BUD-BREAK 1 (EBB1). We demonstrate through positioning of the tag, expression analysis, and retransformation experiments that EBB1 encodes a putative APETALA2/Ethylene responsive factor transcription factor. Transgenic up-regulation of the gene caused early bud-flush, whereas down-regulation delayed bud-break. Native EBB1 expression was highest in actively growing apices, undetectable during the dormancy period, but rapidly increased before bud-break. The EBB1 transcript was localized in the L1/L2 layers of the shoot meristem and leaf primordia. EBB1-overexpressing transgenic plants displayed enlarged shoot meristems, open and poorly differentiated buds, and a higher rate of cell division in the apex. Transcriptome analyses of the EBB1 transgenics identified 971 differentially expressed genes whose expression correlated with the EBB1 expression changes in the transgenic plants. Promoter analysis among the differentially expressed genes for the presence of a canonical EBB1-binding site identified 65 putative target genes, indicative of a broad regulatory context of EBB1 function. Our results suggest that EBB1 has a major and integrative role in reactivation of meristem activity after winter dormancy.

A model for an early role of auxin in Arabidopsis gynoecium morphogenesis

The female reproductive organ of angiosperms, the gynoecium, often consists of the fusion of multiple ovule-bearing carpels. It serves the important function of producing and protecting ovules as well as mediating pollination. The gynoecium has likely contributed to the tremendous success of angiosperms over their 160 million year history. In addition, being a highly complex plant organ, the gynoecium is well suited to serving as a model system for use in the investigation of plant morphogenesis and development. The longstanding model of gynoecium morphogenesis in Arabidopsis holds that apically localized auxin biosynthesis in the gynoecium results in an apical to basal gradient of auxin that serves to specify along its length the development of style, ovary, and gynophore in a concentration-dependent manner. This model is based primarily on the observed effects of the auxin transport blocker N-1-naphthylphthalamic acid (NPA) as well as analyses of mutants of Auxin Response Factor (ARF) 3/ETTIN (ETT). Both NPA treatment and ett mutation disrupt gynoecium morphological patterns along the apical-basal axis. More than a decade after the model's initial proposal, however, the auxin gradient on which the model critically depends remains elusive. Furthermore, multiple observations are inconsistent with such an auxin-gradient model. Chiefly, the timing of gynoecium emergence and patterning occurs at a very early stage when the organ has little-to-no apical-basal dimension. Based on these observations and current models of early leaf patterning, we propose an alternate model for gynoecial patterning. Under this model, the action of auxin is necessary for the early establishment of adaxial-abaxial patterning of the carpel primordium. In this case, the observed gynoecial phenotypes caused by NPA and ett are due to the disruption of this early adaxial-abaxial patterning of the carpel primordia. Here we present the case for this model based on recent literature and current models of leaf development.

Auxin Input Pathway Disruptions Are Mitigated by Changes in Auxin Biosynthetic Gene Expression in Arabidopsis

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the primary auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. IAA is sequestered in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or through a two-carbon elongation forming indole-3-butyric acid. These sequestered forms of IAA alter hormone activity. To gain a better understanding of how auxin homeostasis is maintained, we have generated Arabidopsis (Arabidopsis thaliana) mutants that combine disruptions in the pathways, converting IAA conjugates and indole-3-butyric acid to free IAA. These mutants show phenotypes indicative of low auxin levels, including delayed germination, abnormal vein patterning, and decreased apical dominance. Root phenotypes include changes in root length, root branching, and root hair growth. IAA levels are reduced in the cotyledon tissue but not meristems or hypocotyls. In the combination mutants, auxin biosynthetic gene expression is increased, particularly in the YUCCA/Tryptophan Aminotransferase of Arabidopsis1 pathway, providing a feedback mechanism that allows the plant to compensate for changes in IAA input pathways and maintain cellular homeostasis.

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

The dynamic nature of gene regulatory networks allows cells to rapidly respond to environmental change. However, the underlying temporal connections are missed, even in kinetic studies, as transcription factor (TF) binding within at least one time point is required to identify primary targets. The TF-regulated but unbound genes are dismissed as secondary targets. Instead, we report that these genes comprise transient TF-target interactions most relevant to rapid signal transduction. We temporally perturbed a master TF (Basic Leucine Zipper 1, bZIP1) and the nitrogen (N) signal it transduces and integrated TF regulation and binding data from the same cell samples. Our enabling approach could identify primary TF targets based solely on gene regulation, in the absence of TF binding. We uncovered three classes of primary TF targets: (i) poised (TF-bound but not TF-regulated), (ii) stable (TF-bound and TF-regulated), and (iii) transient (TF-regulated but not TF-bound), the largest class. Unexpectedly, the transient bZIP1 targets are uniquely relevant to rapid N signaling in planta, enriched in dynamic N-responsive genes, and regulated by TF and N signal interactions. These transient targets include early N responders nitrate transporter 2.1 and NIN-like protein 3, bound by bZIP1 at 1-5 min, but not at later time points following TF perturbation. Moreover, promoters of these transient targets are uniquely enriched with cis-regulatory motifs coinherited with bZIP1 binding sites, suggesting a recruitment role for bZIP1. This transient mode of TF action supports a classic, but forgotten, "hit-and-run" transcription model, which enables a "catalyst TF" to activate a large set of targets within minutes of signal perturbation.

The essential role of NGATHA genes in style and stigma specification is widely conserved across eudicots

Carpel development and evolution are central issues for plant biology. The conservation of genetic functions conferring carpel identity has been widely studied in higher plants. However, although genetic networks directing the development of characteristic features of angiosperm carpels such as stigma and style are increasingly known in Arabidopsis thaliana, little information is available on the conservation and diversification of these networks in other species. Here, we have studied the functional conservation of NGATHA transcription factors in widely divergent species within the eudicots. We determined by in situ hybridization the expression patterns of NGATHA orthologs in Eschscholzia californica and Nicotiana benthamiana. Virus-induced gene silencing (VIGS)-mediated inactivation of NGATHA genes in both species was performed and different microscopy techniques were used for phenotypic characterization. We found the expression patterns of EcNGA and NbNGA genes during flower development to be highly similar to each other, as well as to those reported for Arabidopsis NGATHA genes. Inactivation of EcNGA and NbNGA also caused severe defects in style and stigma development in both species. These results demonstrate the widely conserved essential role of NGATHA genes in style and stigma specification and suggest that the angiosperm-specific NGATHA genes were likely recruited to direct a carpel-specific developmental program.

DNA-binding specificities of plant transcription factors and their potential to define target genes

Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes. In contrast to the genetic code, the transcriptional regulatory code is far from being deciphered and is determined by sequence specificity of TFs, combinatorial cooperation between TFs and chromatin competence. Here we addressed one of these determinants by characterizing the target sequence specificity of 63 plant TFs representing 25 families, using protein-binding microarrays. Remarkably, almost half of these TFs recognized secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptomic data from TFs mutants showed the functional significance of over 80% of all identified sequences and of at least one target sequence per TF. Moreover, combining the target sequence information with coexpression analysis we could predict the function of a TF as activator or repressor through a particular DNA sequence. Our data support the correlation between cis-regulatory elements and the sequence determined in vitro using the protein-binding microarray and provides a framework to explore regulatory networks in plants.

The NAC-like gene ANTHER INDEHISCENCE FACTOR acts as a repressor that controls anther dehiscence by regulating genes in the jasmonate biosynthesis pathway in Arabidopsis

ANTHER INDEHISCENCE FACTOR (AIF), a NAC-like gene, was identified in Arabidopsis. In AIF:GUS flowers, β-glucuronidase (GUS) activity was detected in the anther, the upper parts of the filaments, and in the pollen of stage 7-9 young flower buds; GUS activity was reduced in mature flowers. Yellow fluorescent protein (YFP)+AIF-C fusion proteins, which lacked a transmembrane domain, accumulated in the nuclei of the Arabidopsis cells, whereas the YFP+AIF fusion proteins accumulated in the membrane and were absent in the nuclei. Further detection of a cleaved AIF protein in flowers revealed that AIF needs to be processed and released from the endoplasmic reticulum in order to function. The ectopic expression of AIF-C caused a male-sterile phenotype with indehiscent anthers throughout flower development in Arabidopsis. The presence of a repressor domain in AIF and the similar phenotype of indehiscent anthers in AIF-C+SRDX plants suggest that AIF acts as a repressor. The defect in anther dehiscence was due to the down-regulation of genes that participate in jasmonic acid (JA) biosynthesis, such as DAD1/AOS/AOC3/OPR3/OPCL1. The external application of JA rescued the anther indehiscence in AIF-C and AIF-C+SRDX flowers. In AIF-C+VP16 plants, which are transgenic dominant-negative mutants in which AIF is converted to a potent activator via fusion to a VP16-AD motif, the anther dehiscence was promoted, and the expression of DAD1/AOS/AOC3/OPR3/OPCL1 was up-regulated. Furthermore, the suppression of AIF through an antisense strategy resulted in a mutant phenotype similar to that observed in the AIF-C+VP16 flowers. The present data suggest a role for AIF in controlling anther dehiscence by suppressing the expression of JA biosynthesis genes in Arabidopsis.

Expression of Terpenoids 1, a glandular trichome-specific transcription factor from tomato that activates the terpene synthase 5 promoter

Terpene biosynthesis in tomato glandular trichomes has been well studied, with most if not all terpene synthases (TPSs) being identified. However, transcription factors (TFs) that regulate TPSs have not yet been discovered from tomato. In order to unravel the transcriptional regulation of the Solanum lycopersicum linalool synthase (SlMTS1, recently renamed SlTPS5) gene in glandular trichomes, we functionally dissected its promoter. A 207 bp fragment containing the minimal promoter and the 5'UTR appeared to be sufficient for trichome-specific expression in transgenic plants. Yeast-one-hybrid screens with this fragment identified a glandular trichome-specific transcription factor, designated Expression of Terpenoids 1 (SlEOT1). SlEOT1 is a member of a conserved family of TFs that includes the Arabidopsis Stylish 1 (AtSTY1) and Short Internode (AtSHI) genes. The EOT1 protein localized to the nucleus and specifically transactivated the SlTPS5 promoter in Nicotiana benthamiana leaves.

DNA-binding specificities of plant transcription factors and their potential to define target genes

Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes. In contrast to the genetic code, the transcriptional regulatory code is far from being deciphered and is determined by sequence specificity of TFs, combinatorial cooperation between TFs and chromatin competence. Here we addressed one of these determinants by characterizing the target sequence specificity of 63 plant TFs representing 25 families, using protein-binding microarrays. Remarkably, almost half of these TFs recognized secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptomic data from TFs mutants showed the functional significance of over 80% of all identified sequences and of at least one target sequence per TF. Moreover, combining the target sequence information with coexpression analysis we could predict the function of a TF as activator or repressor through a particular DNA sequence. Our data support the correlation between cis-regulatory elements and the sequence determined in vitro using the protein-binding microarray and provides a framework to explore regulatory networks in plants.