LAFL Factors in Seed Development and Phase Transitions

Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes (44, 71, 98-100), more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed (63, 43, 65, 81). Recent advances in cell biology and genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.

ABA guides stomatal proliferation and patterning through the EPF-SPCH signaling pathway in Arabidopsis thaliana

Adaptation to dehydration stress requires plants to coordinate environmental and endogenous signals to inhibit stomatal proliferation and modulate their patterning. The stress hormone abscisic acid (ABA) induces stomatal closure and restricts stomatal lineage to promote stress tolerance. Here, we report that mutants with reduced ABA levels, xer-1, xer-2 and aba2-2, developed stomatal clusters. Similarly, the ABA signaling mutant snrk2.2/2.3/2.6, which lacks core ABA signaling kinases, also displayed stomatal clusters. Exposure to ABA or inhibition of ABA catabolism rescued the increased stomatal density and spacing defects observed in xer and aba2-2, suggesting that basal ABA is required for correct stomatal density and spacing. xer-1 and aba2-2 displayed reduced expression of EPF1 and EPF2, and enhanced expression of SPCH and MUTE. Furthermore, ABA suppressed elevated SPCH and MUTE expression in epf2-1 and epf1-1, and partially rescued epf2-1 stomatal index and epf1-1 clustering defects. Genetic analysis demonstrated that XER acts upstream of the EPF2-SPCH pathway to suppress stomatal proliferation, and in parallel with EPF1 to ensure correct stomatal spacing. These results show that basal ABA and functional ABA signaling are required to fine-tune stomatal density and patterning.

Epigenetic silencing of callose synthase by VIL1 promotes bud-growth transition in lily bulbs

In plants, restoring intercellular communication is required for cell activity in buds during the growth transition from slow to fast growth after dormancy release. However, the epigenetic regulation of this phenomenon is far from understood. Here we demonstrate that lily VERNALIZATION INSENSITIVE 3-LIKE 1 (LoVIL1) confers growth transition by mediating plasmodesmata opening via epigenetic repression of CALLOSE SYNTHASE 3 (LoCALS3). Moreover, we found that a novel transcription factor, NUCLEAR FACTOR Y, SUBUNIT A7 (LoNFYA7), is capable of recruiting the LoVIL1-Polycomb Repressive Complex 2 (PRC2) and enhancing H3K27me3 at the LoCALS3 locus by recognizing the CCAAT cis-element (Cce) of its promoter. The LoNFYA7-LoVIL1 module serves as a key player in orchestrating the phase transition from slow to fast growth in lily bulbs. These studies also indicate that LoVIL1 is a suitable marker for the bud-growth-transition trait following dormancy release in lily cultivars.

BASIC PENTACYSTEINE2 fine-tunes corm dormancy release in Gladiolus

Bud dormancy is an important trait in geophytes that largely affects their flowering process and vegetative growth after dormancy release. Compared with seed dormancy, the regulation of bud dormancy is still largely unclear. Abscisic acid (ABA) acts as the predominant hormone that regulates the whole dormancy process. In Gladiolus (Gladiolus hybridus), cold storage promotes corm dormancy release (CDR) by repressing ABA biosynthesis and signaling. However, the mechanisms governing ABA-related processes during CDR via epigenetics are poorly understood. Here, we show that class I BASIC PENTACYSTEINE2, (GhBPC2) directly binds to 9-CIS-EPOXYCAROTENOID DIOXYGENASE (GhNCED) and ABA INSENSITIVE5 (GhABI5) loci and down-regulates their expression to accelerate CDR. During CDR, histone modifications change dramatically at the GhBPC2-binding loci of GhABI5 with an increase in H3K27me3 and a decrease in H3K4me3. GhBPC2 is involved in both H3K27me3 and H3K4me3 and fine-tunes GhABI5 expression by recruiting polycomb repressive complex 2 (PRC2) and the chromatin remodeling factor EARLY BOLTING IN SHORT DAYS (GhEBS). These results show GhBPC2 epigenetically regulates CDR in Gladiolus by mediating GhABI5 expression with PRC2 and GhEBS.

CBF4/DREB1D represses XERICO to attenuate ABA, osmotic and drought stress responses in Arabidopsis

Water stress can severely impact plant growth, productivity and yield. Consequently, plants have evolved various strategies through which they can respond and adapt to their environment. XERICO (XER) is a stress-responsive RING E3 ubiquitin ligase that modulates abscisic acid (ABA) levels and promotes drought tolerance when overexpressed. To better understand the biological role of XER in stress responses, we characterized a xer-1 hypomorphic mutant and a CRISPR/Cas9-induced xer-2 null mutant in Arabidopsis. Both xer mutant alleles exhibited increased drought sensitivity, supporting the results from overexpression studies. Furthermore, we discovered that both xer mutants have greater stomatal indices and that XER is expressed in epidermal cells, indicating that XER functions in the epidermis to repress stomatal development. To explore XER spatiotemporal and stress-dependent regulation, we conducted a yeast one-hybrid screen and found that CBF4/DREB1D associates with the XER 5' untranslated region (5'-UTR). We generated three cbf4 null mutants with CRISPR/Cas9 and showed that CBF4 negatively regulates ABA responses, promotes stomatal development and reduces drought tolerance, in contrast to the roles shown for XER. CBF4 is induced by ABA and osmotic stress, and localizes to the nucleus where it downregulates XER expression via the DRE element in its 5'-UTR. Lastly, genetic interaction studies confirmed that xer is epistatic to cbf4 in stomatal development and in ABA, osmotic and drought stress responses. We propose that the repression of XER by CBF4 functions to attenuate ABA signaling and stress responses to maintain a balance between plant growth and survival under adverse environmental conditions.

Role of Basal ABA in Plant Growth and Development

Abscisic acid (ABA) regulates various aspects of plant physiology, including promoting seed dormancy and adaptive responses to abiotic and biotic stresses. In addition, ABA plays an im-portant role in growth and development under non-stressed conditions. This review summarizes phenotypes of ABA biosynthesis and signaling mutants to clarify the roles of basal ABA in growth and development. The promotive and inhibitive actions of ABA in growth are characterized by stunted and enhanced growth of ABA-deficient and insensitive mutants, respectively. Growth regulation by ABA is both promotive and inhibitive, depending on the context, such as concentrations, tissues, and environmental conditions. Basal ABA regulates local growth including hyponastic growth, skotomorphogenesis and lateral root growth. At the cellular level, basal ABA is essential for proper chloroplast biogenesis, central metabolism, and expression of cell-cycle genes. Basal ABA also regulates epidermis development in the shoot, by inhibiting stomatal development, and deposition of hydrophobic polymers like a cuticular wax layer covering the leaf surface. In the root, basal ABA is involved in xylem differentiation and suberization of the endodermis. Hormone crosstalk plays key roles in growth and developmental processes regulated by ABA. Phenotypes of ABA-deficient and insensitive mutants indicate prominent functions of basal ABA in plant growth and development.

Oxidative and salt stresses alter the 26S proteasome holoenzyme and associated protein profiles in Arabidopsis thaliana

BACKGROUND

The 26S proteasome, canonically composed of multi-subunit 19S regulatory (RP) and 20S core (CP) particles, is crucial for cellular proteostasis. Proteasomes are re-modeled, activated, or re-localized and this regulation is critical for plants in response to environmental stresses. The proteasome holoenzyme assembly and dissociation are therefore highly dynamic in vivo. However, the stoichiometric changes of the plant proteasomes and how proteasome associated chaperones vary under common abiotic stresses have not been systematically studied.

RESULTS

Here, we studied the impact of abiotic stresses on proteasome structure, activity, and interacting partners in Arabidopsis thaliana. We analyzed available RNA expression data and observed that expressions of proteasome coding genes varied substantially under stresses; however, the protein levels of a few key subunits did not change significantly within 24 h. Instead, a switch in the predominant proteasome complex, from 26S to 20S, occurs under oxidative or salt stress. Oxidative stress also reduced the cellular ATP content and the association of HSP70-family proteins to the 20S proteasome, but enhanced the activity of cellular free form CP. Salt stress, on the other hand, did not affect cellular ATP level, but caused subtle changes in proteasome subunit composition and impacted bindings of assembly chaperones. Analyses of an array of T-DNA insertional mutant lines highlighted important roles for several putative assembly chaperones in seedling establishment and stress sensitivity. We also observed that knockout of PBAC1, one of the α-ring assembly chaperones, resulted in reduced germination and tearing of the seed coat following sterilization.

CONCLUSIONS

Our study revealed an evolutionarily conserved mechanism of proteasome regulation during oxidative stress, involving dynamic regulation of the holoenzyme formation and associated regulatory proteins, and we also identified a novel role of the PBAC1 proteasome assembly chaperone in seed coat development.

ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective

Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.

SnRK1α1 Antagonizes Cell Death Induced by Transient Overexpression of Arabidopsis thaliana ABI5 Binding Protein 2 (AFP2)

Plants are continuously exposed to environmental stressors. They have thus evolved complex signaling pathways to govern responses to a variety of stimuli. The hormone abscisic acid (ABA) has been implicated in modulating both abiotic and biotic stress responses in plants. ABI5 Binding Proteins (AFPs) are a family of negative regulators of bZIP transcription factors of the AREB/ABF family, which promote ABA responses. AFP2 interacts with Snf1-Related protein Kinase 1 (SnRK1), which belongs to a highly conserved heterotrimeric kinase complex that is activated to re-establish energy homeostasis following stress. However, the role of this interaction is currently unknown. Here, we show that transient overexpression of Arabidopsis thaliana AFP2 in Nicotiana benthamiana leaves induces cell death (CD). Using truncated AFP2 constructs, we demonstrate that CD induction by AFP2 is dependent on the EAR domain. Co-expression of the catalytic subunit SnRK1α1, but not SnRK1α2, rescues AFP2-induced CD. Overexpression of SnRK1α1 has little effect on AFP2 protein level and does not affect AFP2 subcellular localization. Our results show that a high level of AFP2 is detrimental for cell function and that SnRK1α1 antagonizes AFP2-induced CD most likely through a mechanism that does not involve AFP2 protein degradation or a change in subcellular localization.

Spatiotemporal Restriction of FUSCA3 Expression by Class I BPCs Promotes Ovule Development and Coordinates Embryo and Endosperm Growth

Spatiotemporal regulation of gene expression is critical for proper developmental timing in plants and animals. The transcription factor FUSCA3 (FUS3) regulates developmental phase transitions by acting as a link between hormonal pathways in Arabidopsis (Arabidopsis thaliana). However, the mechanisms governing its spatiotemporal expression pattern are poorly understood. Here, we show that FUS3 is repressed in the ovule integuments and seed endosperm. FUS3 repression requires class I BASIC PENTACYSTEINE (BPC) proteins, which directly bind GA/CT cis-elements in FUS3 and restrict its expression pattern. During vegetative and reproductive development, FUS3 derepression in bpc1-1 bpc2 (bpc1/2) double mutant or misexpression in ProML1:FUS3 lines causes dwarf plants carrying defective flowers and aborted ovules. After fertilization, ectopic FUS3 expression in bpc1/2 endosperm or ProML1:FUS3 endosperm and endothelium increases endosperm nuclei proliferation and seed size, causing delayed or arrested embryo development. These phenotypes are rescued in bpc1/2 fus3-3 Finally, class I BPCs interact with FIS-PRC2 (FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex2), which represses FUS3 in the endosperm during early seed development. We propose that BPC1 and 2 promote the transition from reproductive to seed development by repressing FUS3 in ovule integuments. After fertilization, BPC1 and 2 and FIS-PRC2 repress FUS3 in the endosperm to coordinate early endosperm and embryo growth.

An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Yeast Snf1 (Sucrose non-fermenting1), mammalian AMPK (5′ AMP-activated protein kinase) and plant SnRK1 (Snf1-Related Kinase1) are conserved heterotrimeric kinase complexes that re-establish energy homeostasis following stress. The hormone abscisic acid (ABA) plays a crucial role in plant stress response. Activation of SnRK1 or ABA signaling results in overlapping transcriptional changes, suggesting these stress pathways share common targets. To investigate how SnRK1 and ABA interact during stress response in Arabidopsis thaliana, we screened the SnRK1 complex by yeast two-hybrid against a library of proteins encoded by 258 ABA-regulated genes. Here, we identify 125 SnRK1- interacting proteins (SnIPs). Network analysis indicates that a subset of SnIPs form signaling modules in response to abiotic stress. Functional studies show the involvement of SnRK1 and select SnIPs in abiotic stress responses. This targeted study uncovers the largest set of SnRK1 interactors, which can be used to further characterize SnRK1 role in plant survival under stress.

Carianopol et al. construct a detailed protein interaction network for the SnRK1 kinase complex to investigate the interaction of SnRK1 and ABA during stress response. They identify 125 proteins that interact with SnRK1, which can be used further to characterise the role of SnRK1 in plant survival under stress.

GhNAC83 inhibits corm dormancy release by regulating ABA signaling and cytokinin biosynthesis in Gladiolus hybridus

Corm dormancy is an important trait for breeding in many bulb flowers, including the most cultivated Gladiolus hybridus. Gladiolus corms are modified underground stems that function as storage organs and remain dormant to survive adverse environmental conditions. Unlike seed dormancy, not much is known about corm dormancy. Here, we characterize the mechanism of corm dormancy release (CDR) in Gladiolus. We identified an important ABA (abscisic acid) signaling regulator, GhPP2C1 (protein phosphatase 2C1), by transcriptome analysis of CDR. GhPP2C1 expression increased during CDR, and silencing of GhPP2C1 expression in dormant cormels delayed CDR. Furthermore, we show that GhPP2C1 expression is directly regulated by GhNAC83, which was identified by yeast one-hybrid library screening. In planta assays show that GhNAC83 is a negative regulator of GhPP2C1, and silencing of GhNAC83 promoted CDR. As expected, silencing of GhNAC83 decreased the ABA level, but also dramatically increased cytokinin (CK; zeatin) content in cormels. Binding assays demonstrate that GhNAC83 associates with the GhIPT (ISOPENTENYLTRANSFERASE) promoter and negatively regulates zeatin biosynthesis. Taken together, our results reveal that GhNAC83 promotes ABA signaling and synthesis, and inhibits CK biosynthesis pathways, thereby inhibiting CDR. These findings demonstrate that GhNAC83 regulates the ABA and CK pathways, and therefore controls corm dormancy.

GhTCP19 Transcription Factor Regulates Corm Dormancy Release by Repressing GhNCED Expression in Gladiolus

Dormancy is one of the least understood phenomena in plant biology; however, bud/corm dormancy is an important economic trait in agricultural/horticultural breeding. In this study, we isolated an ABA biosynthesis gene, GhNCED, from the transcriptome database of corm dormancy release (CDR), and characterized its negative role in regulating CDR. To understand transcriptional regulation of GhNCED, yeast one-hybrid screening was conducted and GhTCP19 was identified and shown to regulate GhNCED expression directly. An in planta assay showed that GhTCP19 negatively regulates GhNCED expression. GhTCP19 is dramatically induced by exogenous cytokinins (CKs) and is induced during CDR. Silencing of GhTCP19 in dormant cormels delayed CDR, resulting in higher expression of GhNCED and ABA levels. Meanwhile, endogenous CK biosynthesis and signaling were inhibited in GhTCP19-silenced cormels. Taken together, our results reveal that GhTCP19 is a positive regulator of the CDR process by repressing expression of an ABA biosynthesis gene (GhNCED), promoting CK biosynthesis (GhIPT) and signal transduction (GhARR) as well as inducing cyclin genes. This study expands our knowledge on CDR which is mediated by TCP family members.

SnRK1 phosphorylation of FUSCA3 positively regulates embryogenesis, seed yield, and plant growth at high temperature in Arabidopsis

The transcription factor FUSCA3 (FUS3) acts as a major regulator of seed maturation in Arabidopsis. FUS3 is phosphorylated by the SnRK1 catalytic subunit AKIN10/SnRK1α1, which belongs to a conserved eukaryotic kinase complex involved in energy homeostasis. Here we show that AKIN10 and FUS3 share overlapping expression patterns during embryogenesis, and that FUS3 is phosphorylated by AKIN10 in embryo cell extracts. To understand the role of FUS3 phosphorylation, we generated fus3-3 plants carrying FUS3 phosphorylation-null (FUS3S>A) and phosphorylation-mimic (FUS3S>D) variants. While FUS3S>A and FUS3S>D rescued all the fus3-3 seed maturation defects, FUS3S>A showed reduced transcriptional activity and enhanced fus3-3 previously uncharacterized phenotypes. FUS3S>A embryos displayed increased seed abortion due to maternal FUS3S>A and delayed embryo development, which correlated with a strong decrease in seed yield (~50%). Accordingly, the akin10 and akin11 mutants displayed a frequency of seed abortion similar to fus3-3. When plants were grown at elevated temperature, most phenotypes were exaggerated in FUS3S>A plants, and progeny seedlings overall grew poorly, suggesting that phosphorylation of FUS3 plays an important role during early embryogenesis and under heat stress. Collectively, these results suggest that FUS3 phosphorylation and SnRK1 are required for embryogenesis and integration of environmental cues to ensure the survival of the progeny.

The E3 ligase ABI3-INTERACTING PROTEIN2 negatively regulates FUSCA3 and plays a role in cotyledon development in Arabidopsis thaliana

FUSCA3 (FUS3) is a short-lived B3-domain transcription factor that regulates seed development and phase transitions in Arabidopsis thaliana. The mechanisms controlling FUS3 levels are currently poorly understood. Here we show that FUS3 interacts with the RING E3 ligase ABI3-INTERACTING PROTEIN2 (AIP2). AIP2-green fluorescent protein (GFP) is preferentially expressed in the protoderm during early embryogenesis, similarly to FUS3, suggesting that their interaction is biologically relevant. FUS3 degradation is delayed in the aip2-1 mutant and FUS3-GFP fluorescence is increased in aip2-1, but only during mid-embryogenesis, suggesting that FUS3 is negatively regulated by AIP2 at a specific time during embryogenesis. aip2-1 shows delayed flowering and therefore also functions post-embryonically to regulate developmental phase transitions. Plants overexpressing FUS3 post-embryonically in the L1 layer (ML1p:FUS3) show late flowering and other developmental phenotypes that can be rescued by ML1p:AIP2, further supporting a negative role for AIP2 in FUS3 accumulation. However, additional factors regulate FUS3 levels during embryogenesis, as ML1:AIP2 seeds do not resemble fus3-3. Lastly, targeted expression of a RING-inactive AIP2 variant to the protoderm/L1 layer causes FUS3 and ABI3 overexpression phenotypes and defects in cotyledon development. Taken together, these results indicate that AIP2 targets FUS3 for degradation and plays a role in cotyledon development and flowering time in Arabidopsis.

ABA-dependent inhibition of the ubiquitin proteasome system during germination at high temperature in Arabidopsis

During germination, endogenous and environmental factors trigger changes in the transcriptome, translatome and proteome to break dormancy. In Arabidopsis thaliana, the ubiquitin proteasome system (UPS) degrades proteins that promote dormancy to allow germination. While research on the UPS has focused on the identification of proteasomal substrates, little information is known about the regulation of its activity. Here we characterized the activity of the UPS during dormancy release and maintenance by monitoring protein ubiquitination and degradation of two proteasomal substrates: Suc-LLVY-AMC, a well characterized synthetic substrate, and FUSCA3 (FUS3), a dormancy-promoting transcription factor degraded by the 26S proteasome. Our data indicate that proteasome activity and protein ubiquitination increase during imbibition at optimal temperature (21°C), and are required for seed germination. However, abscisic acid (ABA) and supraoptimal temperature (32°C) inhibit germination by dampening both protein ubiquitination and proteasome activity. Inhibition of UPS function by high temperature is reduced by the ABA biosynthesis inhibitor, fluridone, and in ABA biosynthetic mutants, suggesting that it is ABA dependent. Accordingly, inhibition of FUS3 degradation at 32°C is also dependent on ABA. Native gels show that inhibition of proteasome activity is caused by interference with the 26S/30S ratio as well as free 19S and 20S levels, impacting the proteasome degradation cycle. Transfer experiments show that ABA-mediated inhibition of proteasome activity at 21°C is restricted to the first 2 days of germination, a time window corresponding to seed sensitivity to environmental and ABA-mediated growth inhibition. Our data show that ABA and high temperature inhibit germination under unfavourable growth conditions by repressing the UPS.

Inhibition of FUSCA3 degradation at high temperature is dependent on ABA signaling and is regulated by the ABA/GA ratio

During seed imbibition at supra-optimal temperature, an increase in the abscisic acid (ABA)/gibberellin (GA) ratio imposes secondary dormancy to prevent germination (thermoinhibition). FUSCA3 (FUS3), a positive regulator of seed dormancy, accumulates in seeds imbibed at high temperature and increases ABA levels to inhibit germination. Recently, we showed that ABA inhibits FUS3 degradation at high temperature, and that ABA and high temperature also inhibit the ubiquitin-proteasome system, by dampening both proteasome activity and protein polyubiquitination. Here, we investigated the role of ABA signaling components and the ABA antagonizing hormone, GA, in the regulation of FUS3 levels. We show that the ABA receptor mutant, pyl1-1, is less sensitive to ABA and thermoinhibition. In this mutant background, FUS3 degradation in vitro is faster. Similarly, GA alleviates thermoinhibition and also increases FUS3 degradation. These results indicate that inhibition of FUS3 degradation at high temperature is dependent on a high ABA/GA ratio and a functional ABA signaling pathway. Thus, FUS3 constitutes an important node in ABA-GA crosstalk during germination at supra-optimal temperature.

Trehalose-6-phosphate and SnRK1 kinases in plant development and signaling: the emerging picture

Carbohydrates, or sugars, regulate various aspects of plant growth through modulation of cell division and expansion. Besides playing essential roles as sources of energy for growth and as structural components of cells, carbohydrates also regulate the timing of expression of developmental programs. The disaccharide trehalose is used as an energy source, as a storage and transport molecule for glucose, and as a stress-responsive compound important for cellular protection during stress in all kingdoms. Trehalose, however, is found in very low amounts in most plants, pointing to a signaling over metabolic role for this non-reducing disaccharide. In the last decade, trehalose-6-phosphate (T6P), an intermediate in trehalose metabolism, has been shown to regulate embryonic and vegetative development, flowering time, meristem determinacy, and cell fate specification in plants. T6P acts as a global regulator of metabolism and transcription promoting plant growth and triggering developmental phase transitions in response to sugar availability. Among the T6P targets are members of the Sucrose-non-fermenting1-related kinase1 (SnRK1) family, which are sensors of energy availability and inhibit plant growth and development during metabolic stress to maintain energy homeostasis. In this review, we will discuss the opposite roles of the sugar metabolite T6P and the SnRK1 kinases in the regulation of developmental phase transitions in response to carbohydrate levels. We will focus on how these two global regulators of metabolic processes integrate environmental cues and interact with hormonal signaling pathways to modulate plant development.

Overlapping and distinct roles of AKIN10 and FUSCA3 in ABA and sugar signaling during seed germination

The Arabidopsis B3-domain transcription factor FUSCA3 (FUS3) is a master regulator of seed maturation and also a central modulator of hormonal responses during late embryogenesis and germination. Recently, we have identified AKIN10, the Arabidopsis ortholog of Snf1 (Sucrose Non-Fermenting-1)-Related Kinase1 (SnRK1), as a FUS3-interacting protein. We demonstrated that AKIN10 physically interacts with and phosphorylates FUS3 at its N-terminal region, and genetically interacts with FUS3 to regulate developmental phase transition and lateral organ growth. Snf1/AMPK/SnRK1 kinases are important sensors of the cellular energy level, and they are activated in response to starvation and cellular stress. Here we present findings that indicate FUS3 and AKIN10 functionally overlap in ABA signaling, but play different roles in sugar responses during germination. Seeds overexpressing FUS3 and AKIN10 both display ABA-hypersensitivity and delayed germination. The latter is partly dependent on de novo ABA synthesis in both genotypes, as delayed germination can be partially rescued by the ABA biosynthesis inhibitor, fluridone. However, seeds and seedlings overexpressing FUS3 and AKIN10 show different sugar responses. AKIN10-overexpressing seeds and seedlings are hypersensitive to glucose, while those overexpressing FUS3 display overall defects in osmotic stress, primarily during seedling growth, as they show increased sensitivity toward sorbitol and glucose. Hypersensitivity to sugar and/or osmotic stress during germination are partly dependent on de novo ABA synthesis for both genotypes, although are likely to act through distinct pathways. This data suggests that AKIN10 and FUS3 both act as positive regulators of seed responses to ABA, and that AKIN10 regulates sugar signaling while FUS3 mediates osmotic stress responses.

AKIN10 and FUSCA3 interact to control lateral organ development and phase transitions in Arabidopsis

The Snf1 (sucrose non-fermenting-1)/AMPK (AMP-activated protein kinase)/SnRK1 (Snf1-related protein kinase 1) kinases act as sensors of energy status in eukaryotes. Despite the important role of these kinases in regulation of cellular responses to metabolic stress, only a few SnRK1 substrates have been identified. Using yeast two-hybrid screens, we isolated AKIN10 as an interactor of the B3-domain transcription factor FUSCA3 (FUS3), an essential regulator of seed maturation in Arabidopsis. Pull-down and bi-molecular fluorescence complementation (BiFC) assays confirm the interaction in vitro and in planta, respectively. In-gel kinase assays show that AKIN10 phosphorylates FUS3 and that the N-terminal domain of FUS3 is required for AKIN10 phosphorylation. Mutations of three serines (fus3(S55A/S56A/S57A) ) within a partial SnRK1 consensus sequence in the N-terminal region of FUS3 reduce greatly FUS3 phosphorylation by AKIN10, which indicates that these serines are the predominant AKIN10 target sites. In a cell-free system, AKIN10 positively regulates FUS3 stability, as overexpression of AKIN10 delayed the degradation of the recombinant FUS3. Plants over-expressing AKIN10 show delayed seed germination, vegetative growth and flowering time, indicating that AKIN10 antagonizes the embryonic-to-vegetative and vegetative-to-reproductive phase transitions. Furthermore, overexpression of AKIN10 alters cotyledon, silique and floral organ development, suggesting that AKIN10 regulates lateral organ development. Genetic interaction studies show that the fus3-3 mutation partially rescues the phase transition and organ development defects caused by AKIN10 overexpression. Taken together, these findings indicate that FUS3 and AKIN10 interact physically and share overlapping pathways to regulate developmental phase transitions and organogenesis in Arabidopsis.

The embryonic leaf identity gene FUSCA3 regulates vegetative phase transitions by negatively modulating ethylene-regulated gene expression in Arabidopsis

Background

The embryonic temporal regulator FUSCA3 (FUS3) plays major roles in the establishment of embryonic leaf identity and the regulation of developmental timing. Loss-of-function mutations of this B3 domain transcription factor result in replacement of cotyledons with leaves and precocious germination, whereas constitutive misexpression causes the conversion of leaves into cotyledon-like organs and delays vegetative and reproductive phase transitions.

Results

Herein we show that activation of FUS3 after germination dampens the expression of genes involved in the biosynthesis and response to the plant hormone ethylene, whereas a loss-of-function fus3 mutant shows many phenotypes consistent with increased ethylene signaling. This FUS3-dependent regulation of ethylene signaling also impinges on timing functions outside embryogenesis. Loss of FUS3 function results in accelerated vegetative phase change, and this is again partially dependent on functional ethylene signaling. This alteration in vegetative phase transition is dependent on both embryonic and vegetative FUS3 function, suggesting that this important transcriptional regulator controls both embryonic and vegetative developmental timing.

Conclusion

The results of this study indicate that the embryonic regulator FUS3 not only controls the embryonic-to-vegetative phase transition through hormonal (ABA/GA) regulation but also functions postembryonically to delay vegetative phase transitions by negatively modulating ethylene-regulated gene expression.

The role of the Arabidopsis FUSCA3 transcription factor during inhibition of seed germination at high temperature

BACKGROUND

Imbibed seeds integrate environmental and endogenous signals to break dormancy and initiate growth under optimal conditions. Seed maturation plays an important role in determining the survival of germinating seeds, for example one of the roles of dormancy is to stagger germination to prevent mass growth under suboptimal conditions. The B3-domain transcription factor FUSCA3 (FUS3) is a master regulator of seed development and an important node in hormonal interaction networks in Arabidopsis thaliana. Its function has been mainly characterized during embryonic development, where FUS3 is highly expressed to promote seed maturation and dormancy by regulating ABA/GA levels.

RESULTS

In this study, we present evidence for a role of FUS3 in delaying seed germination at supraoptimal temperatures that would be lethal for the developing seedlings. During seed imbibition at supraoptimal temperature, the FUS3 promoter is reactivated and induces de novo synthesis of FUS3 mRNA, followed by FUS3 protein accumulation. Genetic analysis shows that FUS3 contributes to the delay of seed germination at high temperature. Unlike WT, seeds overexpressing FUS3 (ML1:FUS3-GFP) during imbibition are hypersensitive to high temperature and do not germinate, however, they can fully germinate after recovery at control temperature reaching 90% seedling survival. ML1:FUS3-GFP hypersensitivity to high temperature can be partly recovered in the presence of fluridone, an inhibitor of ABA biosynthesis, suggesting this hypersensitivity is due in part to higher ABA level in this mutant. Transcriptomic analysis shows that WT seeds imbibed at supraoptimal temperature activate seed-specific genes and ABA biosynthetic and signaling genes, while inhibiting genes that promote germination and growth, such as GA biosynthetic and signaling genes.

CONCLUSION

In this study, we have uncovered a novel function for the master regulator of seed maturation, FUS3, in delaying germination at supraoptimal temperature. Physiologically, this is important since delaying germination has a protective role at high temperature. Transcriptomic analysis of seeds imbibed at supraoptimal temperature reveal that a complex program is in place, which involves not only the regulation of heat and dehydration response genes to adjust cellular functions, but also the activation of seed-specific programs and the inhibition of germination-promoting programs to delay germination.

The C-terminal domain of FUSCA3 negatively regulates mRNA and protein levels, and mediates sensitivity to the hormones abscisic acid and gibberellic acid in Arabidopsis

The transcription factor FUSCA3 (FUS3) controls the transition from the embryonic to the vegetative phase of development by regulating abscisic acid (ABA) and gibberellic acid (GA) levels in Arabidopsis thaliana. In a feedback loop, FUS3 accumulation is negatively and positively regulated by GA and ABA, respectively, by an uncharacterized mechanism. Here, we use a FUS3-GFP construct to show that the level of the FUS3 protein decreases dramatically during mid to late embryogenesis, whereas its mRNA is present at a high level. Deletion studies identify a C-terminal domain (CTD) that negatively regulates mRNA and protein levels, and mediates sensitivity to ABA and GA. Indeed, a CTD-truncated FUS3 variant accumulates at high level, and is insensitive to the destabilizing and stabilizing effects of GA and ABA, respectively. In contrast, fusion of various fragments of the CTD with GFP is sufficient to greatly reduce GFP fluorescence. The GFP-CTD fluorescence can be increased by ABA and paclobutrazol, an inhibitor of GA biosynthesis. Cell-free degradation assays show that FUS3 is a short-lived protein. FUS3 degradation follows the 26S proteasome in vitro and in vivo, and the CTD affects its degradation rate. In contrast to the native form, the CTD-truncated FUS3 is unable to fully rescue the fus3-3 mutant, and is thus required for FUS3 function. In conclusion, this study identifies a CTD that maintains low levels of FUS3 during embryogenesis and early germination, and is required for normal FUS3 function and sensitivity to ABA and GA.

The C-terminal domain of FUSCA3 negatively regulates mRNA and protein levels, and mediates sensitivity to the hormones abscisic acid and gibberellic acid in Arabidopsis

The transcription factor FUSCA3 (FUS3) controls the transition from the embryonic to the vegetative phase of development by regulating abscisic acid (ABA) and gibberellic acid (GA) levels in Arabidopsis thaliana. In a feedback loop, FUS3 accumulation is negatively and positively regulated by GA and ABA, respectively, by an uncharacterized mechanism. Here, we use a FUS3-GFP construct to show that the level of the FUS3 protein decreases dramatically during mid to late embryogenesis, whereas its mRNA is present at a high level. Deletion studies identify a C-terminal domain (CTD) that negatively regulates mRNA and protein levels, and mediates sensitivity to ABA and GA. Indeed, a CTD-truncated FUS3 variant accumulates at high level, and is insensitive to the destabilizing and stabilizing effects of GA and ABA, respectively. In contrast, fusion of various fragments of the CTD with GFP is sufficient to greatly reduce GFP fluorescence. The GFP-CTD fluorescence can be increased by ABA and paclobutrazol, an inhibitor of GA biosynthesis. Cell-free degradation assays show that FUS3 is a short-lived protein. FUS3 degradation follows the 26S proteasome in vitro and in vivo, and the CTD affects its degradation rate. In contrast to the native form, the CTD-truncated FUS3 is unable to fully rescue the fus3-3 mutant, and is thus required for FUS3 function. In conclusion, this study identifies a CTD that maintains low levels of FUS3 during embryogenesis and early germination, and is required for normal FUS3 function and sensitivity to ABA and GA.

14-3-3 proteins regulate the potassium channel KAT1 by dual modes

KAT1 is a cloned plant potassium channel belonging to the superfamily of Shaker-like Kv channels. Previous studies have shown that 14-3-3 proteins significantly increase KAT1 current by modifying the channel open probability. Employing a 14-3-3 scavenger construct to lower the long-term availability of endogenous 14-3-3 proteins, we found that 14-3-3 proteins not only control the voltage dependency of the channel but also the number of channels in the plasma membrane.

Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis roots

In Arabidopsis four root-expressed AMT genes encode functional ammonium transporters, which raises the question of their role in primary ammonium uptake. After pre-culturing under nitrogen-deficiency conditions, we quantified the influx of (15)N-labeled ammonium in T-DNA insertion lines and observed that the loss of either AMT1;1 or AMT1;3 led to a decrease in the high-affinity ammonium influx of approximately 30%. Under nitrogen-sufficient conditions the ammonium influx was lower in Columbia glabra compared with Wassilewskija (WS), and AMT1;1 did not contribute significantly to the ammonium influx in Col-gl. Ectopic expression of AMT1;3 under the control of a 35S promoter in either of the insertion lines amt1;3-1 or amt1;1-1 increased the ammonium influx above the level of their corresponding wild types. In transgenic lines carrying AMT-promoter-GFP constructs, the promoter activities of AMT1;1 and AMT1;3 were both upregulated under nitrogen-deficiency conditions and were localized to the rhizodermis, including root hairs. AMT gene-GFP fusions that were stably expressed under the control of their own promoters were localized to the plasma membrane. The double insertion line amt1;1-1amt1;3-1 showed a decreased sensitivity to the toxic ammonium analog methylammonium and a decrease in the ammonium influx of up to 70% relative to wild-type plants. These results suggest an additive contribution of AMT1;1 and AMT1;3 to the overall ammonium uptake capacity in Arabidopsis roots under nitrogen-deficiency conditions.

The transcription factor FUSCA3 controls developmental timing in Arabidopsis through the hormones gibberellin and abscisic acid

Although plants continually produce different organs throughout their life cycle, little is known about the factors that regulate the timing of a given developmental program. Here we report that the restricted expression of FUS3 to the epidermis is sufficient to control foliar organ identity in Arabidopsis by regulating the synthesis of two hormones, abscisic acid and gibberellin. These hormones in turn regulate the rates of cell cycling during organ formation to determine whether an embryonic or adult leaf will emerge. We also show that FUS3 expression is influenced by the patterning hormone, auxin, and therefore acts as a nexus of hormone action during embryogenesis. The identification of lipophillic hormones downstream of a heterochronic regulator in Arabidopsis has parallels to mechanisms of developmental timing in animals and suggests a common logic for temporal control of developmental programs between these two kingdoms.

Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us

Genetic screens have been extremely useful in identifying genes involved in hormone signal transduction. However, although these screens were originally designed to identify specific components involved in early hormone signalling, mutations in these genes often confer changes in sensitivity to more than one hormone at the whole-plant level. Moreover, a variety of hormone response genes has been identified through screens that were originally designed to uncover regulators of sugar metabolism. Together, these facts indicate that the linear representation of the hormone signalling pathways controlling a specific aspect of plant growth and development is not sufficient, and that hormones interact with each other and with a variety of developmental and metabolic signals. Following the advent of arabidopsis molecular genetics we are beginning to understand some of the mechanisms by which a hormone is transduced into a cellular response. In this Botanical Briefing we review a subset of genes in arabidopsis that influence hormonal cross-talk, with emphasis on the gibberellin, abscisic acid and ethylene pathways. In some cases it appears that modulation of hormone sensitivity can cause changes in the synthesis of an unrelated hormone, while in other cases a hormone response gene defines a node of interaction between two response pathways. It also appears that a variety of hormones may converge to regulate the turnover of important regulators involved in growth and development. Examples are cited of the recent use of suppressor and enhancer analysis to identify new nodes of interaction between these pathways.

Voltage-dependence of virus-encoded miniature K+ channel Kcv

Kcv is a K+-selective channel encoded by the Paramecium bursaria Chlorella virus 1 (PBVC-1). Expression of this protein, so far the smallest known functional K+ channel, in Xenopus oocytes reveals an instantaneous and a time-dependent component during voltage-clamp steps. These two components have an identical sensitivity to the inhibitor amantadine, implying that they reflect distinct kinetic features of the same channel. About 70% of the channels are always open; at hyperpolarizing voltages the time-dependent channels (30%) open in a voltage-dependent manner reaching half-maximal activation at about ?70 mV. At both extreme positive and negative voltages the open-channel conductance decreases in a voltage-dependent manner. To examine the mechanism underlying the voltage-dependence of Kcv we neutralized the two charged amino acids in the lipophilic N-terminus. However, this double mutation had no effect on the voltage-dependence of the channel, ruling against the possibility that these charged amino acids represent a membrane-embedded voltage sensor. We have considered whether a block by external divalent cations is involved in the voltage-dependence of the channel. The Kcv current was increased about 4-fold on reduction of external Ca2+ concentration by a factor of ten. This pronounced increase in current was observed on lowering Ca2+ but not Mg2+ and was voltage-independent. These data indicate a Ca2+-selective, but voltage-independent mechanism for regulation of channel conductance.

Genetic interactions between ABA, ethylene and sugar signaling pathways

The identification of genes through mutant screens is beginning to reveal the structure of a number of signaling pathways in plants. In the past year, genes that determine the plant's response to the hormones ethylene and abscisic acid have also been shown to be involved in sugar sensing in early seedlings. These results suggest that hormone signaling and carbon homeostasis are tightly coupled but that the architecture of these interactions is complex. Part of this complexity may be because some genetic screens on exogenous compounds produce signaling linkages that are not necessarily pertinent under normal growth conditions. Because many of the genes identified in these screens are cloned, the relevance of these interactions can now be unraveled at the molecular level.

The molecular physiology of ammonium uptake and retrieval

Plants are able to take up ammonium from the soil, or through symbiotic interactions with microorganisms, via the root system. Using functional complementation of yeast mutants, it has been possible to identify a new class of membrane proteins, the ammonium transporter/methylammonium permease (AMT/MEP) family, that mediate secondary active ammonium uptake in eukaryotic and prokaryotic organisms. In plants, the AMT gene family can be subdivided according to their amino-acid sequences into three subfamilies: a large subfamily of AMT1 genes and two additional subfamilies each with single members (LeAMT1;3 from tomato and AtAMT2;1 from Arabidopsis thaliana). These transporters vary especially in their kinetic properties and regulatory mechanism. High-affinity transporters are induced in nitrogen-starved roots, whereas other transporters may be considered as the 'work horses' that are active when conditions are conducive to ammonium assimilation. The expression of several AMTs in root hairs further supports a role in nutrient acquisition. These studies provide basic information that will be needed for the dissection of nitrogen uptake by plants at the molecular level and for determining the role of individual AMTs in nutrient uptake and potentially in nutrient efficiency.

The molecular physiology of ammonium uptake and retrieval

Plants are able to take up ammonium from the soil, or through symbiotic interactions with microorganisms, via the root system. Using functional complementation of yeast mutants, it has been possible to identify a new class of membrane proteins, the ammonium transporter/methylammonium permease (AMT/MEP) family, that mediate secondary active ammonium uptake in eukaryotic and prokaryotic organisms. In plants, the AMT gene family can be subdivided according to their amino-acid sequences into three subfamilies: a large subfamily of AMT1 genes and two additional subfamilies each with single members (LeAMT1;3 from tomato and AtAMT2;1 from Arabidopsis thaliana). These transporters vary especially in their kinetic properties and regulatory mechanism. High-affinity transporters are induced in nitrogen-starved roots, whereas other transporters may be considered as the 'work horses' that are active when conditions are conducive to ammonium assimilation. The expression of several AMTs in root hairs further supports a role in nutrient acquisition. These studies provide basic information that will be needed for the dissection of nitrogen uptake by plants at the molecular level and for determining the role of individual AMTs in nutrient uptake and potentially in nutrient efficiency.

Mutation in pore domain uncovers cation- and voltage-sensitive recovery from inactivation in KAT1 channel

Effects of threonine substitution by glutamine at position 256 in the pore of the KAT1 channel have been investigated by voltage-clamp, using heterologous gene expression in Xenopus oocytes. The major discrepancy in T256Q from the wild-type channel (wt) was cation specific. While K(+) currents were reduced in a largely scalar fashion, the NH(4)(+) current exhibited slow, voltage-dependent inhibition during hyperpolarization. The same effects could be induced in wt, or intensified in T256Q, by addition of the impermeant cation methylammonium (MA(+)) to the bath. This stresses that both the mutation and MA(+) affect a mechanism already present in the wt. Assuming that current inhibition could be described as entry of the channel into an inactive state, we modeled in both wt and in T256Q the relaxation kinetics of the clamp currents by a C-O-I gating scheme, where C (closed) and I (inactivated) are nonconductive states, and O is an open state allowing K(+) and NH(4)(+) passage. The key reaction is the transition I-O. This cation-sensitive transition step ensures release of the channel from the inactive state and is approximately 30 times smaller in T256Q compared to wt. It can be inhibited by external MA(+) and is stimulated strongly by K(+) and weakly by NH(4)(+). This sensitivity of gating to external cations may prevent K(+) leakage from cation-starved cells.

A potassium channel protein encoded by chlorella virus PBCV-1

The large chlorella virus PBCV-1, which contains double-stranded DNA (dsDNA), encodes a 94-codon open reading frame (ORF) that contains a motif resembling the signature sequence of the pore domain of potassium channel proteins. Phylogenetic analyses of the encoded protein, Kcv, indicate a previously unidentified type of potassium channel. The messenger RNA encoded by the ORF leads to functional expression of a potassium-selective conductance in Xenopus laevis oocytes. The channel blockers amantadine and barium, but not cesium, inhibit this conductance, in addition to virus plaque formation. Thus, PBCV-1 encodes the first known viral protein that functions as a potassium-selective channel and is essential in the virus life cycle.

Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots

Ammonium and nitrate are the prevalent nitrogen sources for growth and development of higher plants. 15N-uptake studies demonstrated that ammonium is preferred up to 20-fold over nitrate by Arabidopsis plants. To study the regulation and complex kinetics of ammonium uptake, we isolated two new ammonium transporter (AMT) genes and showed that they functionally complemented an ammonium uptake-deficient yeast mutant. Uptake studies with 14C-methylammonium and inhibition by ammonium yielded distinct substrate affinities between </=0.5 and 40 microM. Correlation of gene expression with 15NH4+ uptake into plant roots showed that nitrogen supply and time of day differentially regulated the individual carriers. Transcript levels of AtAMT1;1, which possesses an affinity in the nanomolar range, steeply increased with ammonium uptake in roots when nitrogen nutrition became limiting, whereas those of AtAMT1;3 increased slightly, with AtAMT1;2 being more constitutively expressed. All three ammonium transporters showed diurnal variation in expression, but AtAMT1;3 transcript levels peaked with ammonium uptake at the end of the light period, suggesting that AtAMT1;3 provides a link between nitrogen assimilation and carbon provision in roots. Our results show that high-affinity ammonium uptake in roots is regulated in relation to the physiological status of the plant at the transcriptional level and by substrate affinities of individual members of the AMT1 gene family.

Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots

Ammonium and nitrate are the prevalent nitrogen sources for growth and development of higher plants. 15N-uptake studies demonstrated that ammonium is preferred up to 20-fold over nitrate by Arabidopsis plants. To study the regulation and complex kinetics of ammonium uptake, we isolated two new ammonium transporter (AMT) genes and showed that they functionally complemented an ammonium uptake-deficient yeast mutant. Uptake studies with 14C-methylammonium and inhibition by ammonium yielded distinct substrate affinities between </=0.5 and 40 microM. Correlation of gene expression with 15NH4+ uptake into plant roots showed that nitrogen supply and time of day differentially regulated the individual carriers. Transcript levels of AtAMT1;1, which possesses an affinity in the nanomolar range, steeply increased with ammonium uptake in roots when nitrogen nutrition became limiting, whereas those of AtAMT1;3 increased slightly, with AtAMT1;2 being more constitutively expressed. All three ammonium transporters showed diurnal variation in expression, but AtAMT1;3 transcript levels peaked with ammonium uptake at the end of the light period, suggesting that AtAMT1;3 provides a link between nitrogen assimilation and carbon provision in roots. Our results show that high-affinity ammonium uptake in roots is regulated in relation to the physiological status of the plant at the transcriptional level and by substrate affinities of individual members of the AMT1 gene family.