A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin

RNA SILENCING SYSTEMS AND THEIR RELEVANCE TO PLANT DEVELOPMENT

RNA silencing refers to a broad range of phenomena sharing the common feature that large, double-stranded RNAs or stem-loop precursors are processed to ca. 21-26 nucleotide small RNAs, which then guide the cleavage of cognate RNAs, block productive translation of these RNAs, or induce methylation of specific target DNAs. Although the core mechanisms are evolutionarily conserved, epigenetic maintenance of silencing by amplification of small RNAs and the elaboration of mobile, RNA-based silencing signals occur predominantly in plants. Plant RNA silencing systems are organized into a network with shared components and overlapping functions. MicroRNAs, and probably trans-acting small RNAs, help regulate development at the posttranscriptional level. Small interfering RNAs associated with transgene- and virus-induced silencing function primarily in defending against foreign nucleic acids. Another system, which is concerned with RNA-directed methylation of DNA repeats, seems to have roles in epigenetic silencing of certain transposable elements and genes under their control.

Crosstalk between ABA and auxin signaling pathways in roots of Arabidopsis thaliana (L.) Heynh

Studies of abscisic acid (ABA) and auxin have revealed that these pathways impinge on each other. The Daucus carota (L.) Dc3 promoter: uidA (beta-glucuronidase: GUS) chimaeric reporter (ProDc3:GUS) is induced by ABA, osmoticum, and the auxin indole-3-acetic acid (IAA) in vegetative tissues of transgenic Arabidopsis thaliana (L.) Heynh. Here, we describe the root tissue-specific expression of ProDc3:GUS in the ABA-insensitive-2 (abi2-1), auxin-insensitive-1 (aux1), auxin-resistant-4 (axr4), and rooty (rty1) mutants of Arabidopsis in response to ABA, IAA and synthetic auxins naphthalene acetic acid (NAA), and 2, 4-(dichlorophenoxy) acetic acid. Quantitative analysis of ProDc3:GUS expression showed that the abi2-1 mutant had reduced GUS activity in response to ABA, IAA, or 2, 4-D: , but not to NAA. Similarly, chromogenic staining of ProDc3:GUS activity showed that the aux1 and axr4 mutants gave predictable hypomorphic ProDc3:GUS expression phenotypes in roots treated with IAA or 2, 4-D: , but not the diffusible auxin NAA. Likewise the rty mutant, which accumulates auxin, showed elevated ProDc3:GUS expression in the absence or presence of hormones relative to wild type. Interestingly, the aux1 and axr4 mutants showed a hypomorphic effect on ABA-inducible ProDc3:GUS expression, demonstrating that ABA and IAA signaling pathways interact in roots. Possible mechanisms of crosstalk between ABA and auxin signaling are discussed.

Identification of further Craterostigma plantagineum cdt mutants affected in abscisic acid mediated desiccation tolerance

The resurrection plant (Craterostigma plantagineum) is desiccation tolerant. However, callus derived from this plant, when propagated in vitro, requires exogenously applied abscisic acid (ABA) in order to survive desiccation. Treatment of callus tissue with ABA induces most of the genes that are induced by dehydration in the whole plant. This property has been exploited for the isolation of mutants that show dominant phenotypes resulting from the ectopic expression of endogenous genes induced by the insertion of a foreign promoter. Here we describe new T-DNA tagged Craterostigma desiccation-tolerant (cdt) mutants with different molecular and physiological characteristics, suggesting that different pathways of desiccation tolerance are affected. One of the mutants, cdt-2, constitutively expresses known osmoprotective Lea genes in callus and leaf tissue. Further analysis of this mutant revealed that the tagged locus is similar to a previously characterised gene, CDT-1, which codes for a signalling molecule that confers desiccation tolerance. The nature of the T-DNA insertion provides insight into the mechanism by which the CDT-1/2 gene family functions in ABA signal transduction.

Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis

The plant root cap mediates the direction of root tip growth and protects internal cells. Root cap cells are continuously produced from distal stem cells, and the phytohormone auxin provides position information for root distal organization. Here, we identify the Arabidopsis thaliana auxin response factors ARF10 and ARF16, targeted by microRNA160 (miR160), as the controller of root cap cell formation. The Pro(35S):MIR160 plants, in which the expression of ARF10 and ARF16 is repressed, and the arf10-2 arf16-2 double mutants display the same root tip defect, with uncontrolled cell division and blocked cell differentiation in the root distal region and show a tumor-like root apex and loss of gravity-sensing. ARF10 and ARF16 play a role in restricting stem cell niche and promoting columella cell differentiation; although functionally redundant, the two ARFs are indispensable for root cap development, and the auxin signal cannot bypass them to initiate columella cell production. In root, auxin and miR160 regulate the expression of ARF10 and ARF16 genes independently, generating a pattern consistent with root cap development. We further demonstrate that miR160-uncoupled production of ARF16 exerts pleiotropic effects on plant phenotypes, and miR160 plays an essential role in regulating Arabidopsis development and growth.

Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses

The phytohormone abscisic acid (ABA) modulates the expression of many genes important to plant growth and development and to stress adaptation. In this study, we found that an APETALA2/EREBP-type transcription factor, AtERF7, plays an important role in ABA responses. AtERF7 interacts with the protein kinase PKS3, which has been shown to be a global regulator of ABA responses. AtERF7 binds to the GCC box and acts as a repressor of gene transcription. AtERF7 interacts with the Arabidopsis thaliana homolog of a human global corepressor of transcription, AtSin3, which in turn may interact with HDA19, a histone deacetylase. The transcriptional repression activity of AtERF7 is enhanced by HDA19 and AtSin3. Arabidopsis plants overexpressing AtERF7 show reduced sensitivity of guard cells to ABA and increased transpirational water loss. By contrast, AtERF7 and AtSin3 RNA interference lines show increased sensitivity to ABA during germination. Together, our results suggest that AtERF7 plays an important role in ABA responses and may be part of a transcriptional repressor complex and be regulated by PKS3.

The double-stranded RNA-binding motif, a versatile macromolecular docking platform

The double-stranded RNA-binding motif (dsRBM) is an alphabetabetabetaalpha fold with a well-characterized function to bind structured RNA molecules. This motif is widely distributed in eukaryotic proteins, as well as in proteins from bacteria and viruses. dsRBM-containing proteins are involved in processes ranging from RNA editing to protein phosphorylation in translational control and contain a variable number of dsRBM domains. The structural work of the past five years has identified a common mode of RNA target recognition by dsRBMs and dissected this recognition into two functionally separated interaction modes. The first involves the recognition of specific moieties of the RNA A-form helix by two protein loops, while the second is based on the interaction between structural elements flanking the RNA duplex with the first helix of the dsRBM. The latter interaction can be tuned by other protein elements. Recent work has made clear that dsRBMs can also recognize non-RNA targets (proteins and DNA), and act in combination with other dsRBMs and non-dsRBM motifs to play a regulatory role in catalytic processes. The elucidation of functional networks coordinated by dsRBM folds will require information on the precise functional relationship between different dsRBMs and a clarification of the principles underlying dsRBM-protein recognition.

The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation

The phytohormone abscisic acid (ABA) mediates many complex aspects of plant development including seed maturation, dormancy, and germination as well as root growth. The B3-domain transcription factor abscisic acid-insensitive 3 (ABI3) is a central regulator in ABA signaling, but little is known of how this factor is regulated. Here, we show that ABI3 is an unstable protein and that an ABI3-interacting protein (AIP2), which contains a RING motif, can polyubiquitinate ABI3 in vitro. The AIP2 E3 ligase activity is abolished by mutations (C230S; C231S) in the RING motif and the AIP2 (C/S) mutant functions in a dominant-negative manner. AIP2 has a stronger binding affinity for the B2 + B3 domain of ABI3 than the A1 + B1 domain, but only ubiquitinates the latter. In double-transgenic plants, induced AIP2 expression leads to a decrease in ABI3 protein levels. In contrast, ABI3 levels are elevated upon induced expression of the AIP2 RING mutant, which interferes with the endogenous AIP2 E3 activity. An aip2-1-null mutant shows higher ABI3 protein levels compared with wild type after seed stratification, and is hypersensitive to ABA, mimicking the ABI3-overexpression phenotype, whereas AIP2-overexpression plants contain lower levels of ABI3 protein than wild type and are more resistant to ABA, phenocopying abi3. Our results indicate that AIP2 negatively regulates ABA signaling by targeting ABI3 for post-translational destruction.

Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation

Poaceae species present a conserved distichous phyllotaxy (leaf position along the stem) and share common properties with respect to leaf initiation. The goal of this work was to determine if these common traits imply common genes. Therefore, homologues of the maize TERMINAL EAR1 gene in Poaceae were studied. This gene encodes an RNA-binding motif (RRM) protein, that is suggested to regulate leaf initiation. Using degenerate primers, one unique tel (terminal ear1-like) gene from seven Poaceae members, covering almost all the phylogenetic tree of the family, was identified by PCR. These genes present a very high degree of similarity, a much conserved exon-intron structure, and the three RRMs and TEL characteristic motifs. The evolution of tel sequences in Poaceae strongly correlates with the known phylogenetic tree of this family. RT-PCR gene expression analyses show conserved tel expression in the shoot apex in all species, suggesting functional orthology between these genes. In addition, in situ hybridization experiments with specific antisense probes show tel transcript accumulation in all differentiating cells of the leaf, from the recruitment of leaf founder cells to leaf margins cells. Tel expression is not restricted to initiating leaves as it is also found in pro-vascular tissues, root meristems, and immature inflorescences. Therefore, these results suggest that TEL is not only associated with leaf initiation but more generally with cell differentiation in Poaceae.

Photomorphogenesis of leaves: shade-avoidance and differentiation of sun and shade leaves

Leaf shape is an important factor in optimal plant growth, because leaves are the main photosynthetic organs. Plants exhibit plasticity in leaf shape and structure, allowing them to optimize photosynthetic efficiency. In Arabidopsis thaliana(L.) Heynh., several types of leaves develop differentially, according to light intensity and quality. When shaded, the expansion of leaf lamina is inhibited, while the petiole elongation is enhanced. This phenomenon is part of the so-called shade-avoidance syndrome. Under low light, A. thaliana develops shade leaves with only one layer of palisade tissue, whereas under high light, it develops sun leaves that have nearly two complete layers of palisade tissue. Although the molecular mechanisms of these photomorphogenic phenomena in leaves are not well understood, recent studies of A. thaliana have provided some insight. For example, some cytochrome P450s may be involved in the specific control of the petiole length during photomorphogenesis. On the other hand, switching between sun and shade leaves is regulated by long-distance signaling from mature leaves in Chenopodium album. Here we provide an overview of the mechanisms of photomorphogenesis in leaves based on recent findings.

HYL1 gene maintains venation and polarity of leaves

For genetic analysis of the mechanism of leaf curvature, we chose hyl1 mutant of Arabidopsis as a model for dissection of leaf venation pattern and adaxial/abaxial polarity. In leaves of hyl1 mutants that were hyponastic and curved upward, the complexity of the secondary veins was reduced, and the discontinuity of veins increased. In the lateral areas of the leaves where transverse curvature arises, dorsoventral polarity was lost due to the unclear spongy cells, and the epidermal cells became smaller on the adaxial surface than those of the abaxial surface, whereas the number of epidermal cells on the two surfaces were almost the same. In this case, less complexity of venation, decreased cell growth on the adaxial surface was attributed to leaf curvature. To depict the role of HYL1 in leaf venation and polarity, we constructed pHYL1:: GUS to drive the uidA (beta-glucuronidase) gene, and observed that the GUS signal appeared primarily in the petioles and mid-veins of rosette leaves, and were restricted to vascular tissues, demonstrating that HYL1 promoter directs the process of leaf venation by the uneven expression of the HYL1 gene in leaves. In situ hybridization indicates that HYL1 gene is preferentially expressed in leaf blades as well as vasculature. In curved leaves of hyl1 mutants, the expression level of adaxial identity gene REV was increased and the expression position restricted mainly in vasculature and on both sides of growing leaves near the margins while expression of the miR165 gene was remarkably reduced, suggesting that HYL1 maintain venation and polarity of growing leaves by altering the level of microRNA that direct the cleavage of REV transcripts.

The role of ARGONAUTE1 (AGO1) in meristem formation and identity

The ARGONAUTE gene family is involved in the regulation of gene expression via the RNAi Silencing Complex (RISC). microRNA (miRNA) are 20-22bp RNAs that direct RISC to target genes. Several miRNA have been characterized in plants. Their roles include control of flowering time, floral organ identity, cell division patterns, and leaf polarity. ARGONAUTE1 (AGO1) is required for stem cell function and organ polarity, as is the closely related protein PINHEAD/ZWILLE (PNH/ZLL). Through phenotypic and double mutant analysis, we show that AGO1 regulates stem cell function via SHOOT MERISTEMLESS (STM). CUPSHAPED COTYLEDONS1 and 2 (CUC1 and CUC2) positively regulate STM and are targets of miRNA. The effect of AGO1 on leaf polarity is dependent, in part, on its role in meristem function revealed by interactions with ASYMMETRIC LEAVES1(AS1). AGO1 is required for full expression of LEAFY (LFY), APETALA1 (AP1) and AGAMOUS (AG). Flowering time is unaffected but floral meristem identity is partially restored in a curlyleaf (clf) background and this is not due to clf's affects on AG expression. CLF is over expressed in ago1, showing that the RNAi pathway regulates polycomb-type epigenetic modifiers.

Leucine-rich repeat receptor-like kinase1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis

Abscisic acid (ABA) is important in seed maturation, seed dormancy, stomatal closure, and stress response. Many genes that function in ABA signal transduction pathways have been identified. However, most important signaling molecules involved in the perception of the ABA signal or with ABA receptors have not been identified yet. Receptor-like kinase1 (RPK1), a Leu-rich repeat (LRR) receptor kinase in the plasma membrane, is upregulated by ABA in Arabidopsis thaliana. Here, we show the phenotypes of T-DNA insertion mutants and RPK1-antisense plants. Repression of RPK1 expression in Arabidopsis decreased sensitivity to ABA during germination, growth, and stomatal closure; microarray and RNA gel analysis showed that many ABA-inducible genes are downregulated in these plants. Furthermore, overexpression of the RPK1 LRR domain alone or fused with the Brassinosteroid-insensitive1 kinase domain in plants resulted in phenotypes indicating ABA sensitivity. RPK1 is involved in the main ABA signaling pathway and in early ABA perception in Arabidopsis.

The developmental role of microRNA in plants

MicroRNAs (miRNAs) are single-stranded RNA molecules of around 22 nucleotides (nt) in length that are associated with the RNA-induced silencing complex (RISC). They play an important role in plant development, either by targeting mRNA for cleavage or by inhibiting translation. Over the past year, the list of known miRNAs, confirmed targets and developmental effects has expanded, as has the realization that they are conserved during evolution and that small RNAs can play a direct role in cell-cell signaling.

Regulatory Networks of the Phytohormone Abscisic Acid

Structurally similar to retinoic acid (RA), the phytohormone abscisic acid (ABA) controls many developmental and physiological processes via complicated signaling networks that are composed of receptors, secondary messengers, protein kinase/phosphatase cascades, transcription factors, and chromatin-remodeling factors. In addition, ABA signaling is further modulated by mRNA maturation and stability, microRNA (miRNA) levels, nuclear speckling, and protein degradation. This chapter highlights the identified regulators of ABA signaling and reports their homologues in dicotyledonous and monocotyledonous plants.

Hydrotropism: root growth responses to water

The survival of terrestrial plants depends upon the capacity of roots to obtain water and nutrients from the soil. Directed growth of roots in relation to a gradient in moisture is called hydrotropism and begins in the root cap with the sensing of the moisture gradient. Even though the lack of sufficient water is the single-most important factor affecting world agriculture, there are surprisingly few studies on hydrotropism. Recent genetic analysis of hydrotropism in Arabidopsis has provided new insights about the mechanisms that the root cap uses to perceive and respond simultaneously to moisture and gravity signals. This knowledge might enable us to understand how the root cap processes environmental signals that are capable of regulating whole plant growth.

Gravitropic bending and plant hormones

Gravitropism is a complex multistep process that redirects the growth of roots and various above-ground organs in response to changes in the direction of the gravity vector. The anatomy and morphology of these graviresponding organs indicates a certain spatial separation between the sensing region and the responding one, a situation that strongly suggests the requirement of phytohormones as mediators to coordinate the process. The Cholodny-Went hypothesis suggested auxin as the main mediator of gravitropism. So far, ample evidence has been gathered with regard to auxin asymmetrical detection, polar and lateral transport involving influx and efflux carriers, response signaling pathway, and possible modes of action in differential cell elongation, supports its major role in gravitropism at least in roots. However, it is becoming clear that the participation of other hormones, acting in concert with auxin, is necessary as well. Of particular importance is the role of ethylene in shoot gravitropism, possibly associated with the modulation of auxin transport or sensitivity, and the key role implicated for cytokinin as the putative root cap inhibitor that controls early root gravitropism. Therefore, the major advances in the understanding of transport and signaling of auxin, ethylene, and cytokinin may shed light on the possibly tight and complicated interactions between them in gravitropism. Not much convincing evidence has been accumulated regarding the participation of other phytohormones, such as gibberellins, abscisic acid, brassinosteroids, jasmonates, and salicylic acid, in gravitropism. However, the emerging concept of cooperative hormone action opens new possibilities for a better understanding of the complex interactions of all phytohormones and their possible synergistic effects and involvement in the gravitropic bending process.

Nucleocytoplasmic Trafficking in Plant Cells

In a eukaryotic cell, the nuclear envelope (NE) separates genetic information from the environment of biosynthesis and metabolism. Transfer of macromolecules across the NE involves the nuclear pores--large multisubunit protein complexes--and machinery that facilitates rapid, directional, and selective transport. While core elements of the transport process are conserved between kingdoms, different solutions to similar problems have also evolved. Although the structure and composition of the yeast and mammalian nuclear pore have been unraveled recently, the plant nuclear pore remains largely enigmatic. Like any other process, nucleocytoplasmic transport can be regulated. Several examples from plants are discussed that promise insights into the regulation of signaling pathways. While controlling the partitioning of cellular components, the nuclear envelope also presents an obstacle to viruses and transforming agents that need access to the genome, and different mechanisms have evolved to overcome this obstacle. Finally, the recent recognition of the importance of small RNAs for gene regulation emphasizes the need to understand small RNA nuclear export and the levels of its regulation. This review attempts to wed our molecular-mechanistic understanding of nucleocytoplasmic trafficking drawn from all model systems with the intriguing examples of regulated nucleocytoplasmic partitioning in plants.

Abscisic acid and 14-3-3 proteins control K channel activity in barley embryonic root

Germination of seeds proceeds in general in two phases, an initial imbibition phase and a subsequent growth phase. In grasses like barley, the latter phase is evident as the emergence of the embryonic root (radicle). The hormone abscisic acid (ABA) inhibits germination because it prevents the embryo from entering and completing the growth phase. Genetic and physiological studies have identified many steps in the ABA signal transduction cascade, but how it prevents radicle elongation is still not clear. For elongation growth to proceed, uptake of osmotically active substances (mainly K(+)) is essential. Therefore, we have addressed the question of how the activity of K(+) permeable ion channels in the plasma membrane of radicle cells is regulated under conditions of slow (+ABA) and rapid germination (+fusicoccin). We found that ABA arrests radicle growth, inhibits net K(+) uptake and reduces the activity of K(+) (in) channels as measured with the patch-clamp technique. In contrast, fusicoccin (FC), a well-known stimulator of germination, stimulates radicle growth, net K(+) uptake and reduces the activity of K(+) (out) channels. Both types of channels are under the control of 14-3-3 proteins, known as integral components of signal transduction pathways and instrumental in FC action. Intriguingly, 14-3-3 affected both channels in an opposite fashion: whereas K(+) (in) channel activity was fully dependent upon 14-3-3 proteins, K(+) (out) channel activity was reduced by 14-3-3 proteins by 60%. Together with previous data showing that 14-3-3 proteins control the activity of the plasma membrane H(+)-ATPase, this makes 14-3-3 a prime candidate for molecular master regulator of the cellular osmo-pump. Regulation of the osmo-pump activity by ABA and FC is an important mechanism in controlling the growth of the embryonic root during seed germination.

Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana

Proteins that specifically bind double-stranded RNA (dsRNA) are involved in the regulation of cellular signaling events and gene expression, and are characterized by a conserved dsRNA-binding motif (dsRBM). Here we report the biochemical properties of nine such gene products, each containing one or two dsRBMs: four Arabidopsis Dicer-like proteins (DCL1-4), Arabidopsis HYL1 and four of its homologs (DRB2, DRB4, DRB5 and OsDRB1). DCL1, DCL3, HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity, indicating that these proteins are involved in RNA metabolism. The dsRBMs from dsRBM-containing proteins (dsRBPs) also function as a protein-protein interaction domain and homo- and heterodimerization are essential for biological functioning of these proteins. We show that DRB4 interacts specifically with DCL4, and HYL1 most strongly interacts with DCL1. These results indicate that each HYL1/DRB family protein interacts with one specific partner among the four Dicer-like proteins. Localization studies using GFP fusion proteins demonstrate that DCL1, DCL4, HYL1 and DRB4 localize in the nucleus, while DRB2 is present in the cytoplasm. Subcellular localizations of HYL1, DRB4, DCL1 and DCL4 further strengthen the notion that HYL1 and DCL1, and DRB4 and DCL4, exist as complexes. The presented data suggest that each member of the HYL1/DRB protein family may individually modulate Dicer function through heterodimerization with a Dicer-like protein in vivo.

A WRKY Gene from Creosote Bush Encodes an Activator of the Abscisic Acid Signaling Pathway

The creosote bush (Larrea tridentata) is a xerophytic evergreen C3 shrub thriving in vast arid areas of North America. As the first step toward understanding the molecular mechanisms controlling the drought tolerance of this desert plant, we have isolated a dozen genes encoding transcription factors, including LtWRKY21 that encodes a protein of 314 amino acid residues. Transient expression studies with the GFP-LtWRKY21 fusion construct indicate that the LtWRKY21 protein is localized in the nucleus and is able to activate the promoter of an abscisic acid (ABA)-inducible gene, HVA22, in a dosage-dependent manner. The transactivating activity of LtWRKY21 relies on the C-terminal sequence containing the WRKY domain and a N-terminal motif that is essential for the repression activity of some regulators in ethylene signaling. LtWRKY21 interacts synergistically with ABA and transcriptional activators VP1 and ABI5 to control the expression of the HVA22 promoter. Co-expression of VP1, ABI5, and LtWRKY21 leads to a much higher expression of the HVA22 promoter than does the ABA treatment alone. In contrast, the Lt-WRKY21-mediated transactivation is inhibited by two known negative regulators of ABA signaling: 1-butanol, an inhibitor of phospholipase D, and abi1-1, a dominant negative mutant protein phosphatase. Interestingly, abi1-1 does not block the synergistic effect of LtWRKY21, VP1, and ABI5 co-expression, indicating that LtWRKY21, VP1, and ABI5 may form a complex that functions downstream of ABI1 to control ABA-regulated expression of genes.

Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs

Here we describe a set of endogenous short interfering RNAs (siRNAs) in Arabidopsis, some of which direct the cleavage of endogenous mRNAs. These siRNAs correspond to both sense and antisense strands of a noncoding RNA (At2g27400) that apparently is converted to double-stranded RNA and then processed in 21 nt increments. These siRNAs differ from previously described regulatory small RNAs in two respects. First, they require components of the cosuppression pathway (RDR6 and SGS3) and also components of the microRNA (miRNA) pathway (AGO1, DCL1, HEN1, and HYL1) but not components needed for heterochromatic siRNAs (DCL3 and RDR2), another class of endogenous plant siRNAs. Second, these siRNAs repress the expression of genes that have little overall resemblance to the genes from which they originate, a characteristic previously reported only for miRNAs. The identification of this silencing pathway provides yet another dimension to posttranscriptional mRNA regulation in plants.

MicroRNA regulation of gene expression in plants

It has only been a few years since we began to appreciate that microRNAs provide an unanticipated level of gene regulation in both plants and metazoans. The high level of complementarity between plant microRNAs and their target mRNAs has allowed rapid progress towards the elucidation of their varied biological functions. MicroRNAs have been shown to regulate diverse developmental processes, including organ separation, polarity, and identity, and to modulate their own biogenesis and function. Recently, they have also been implicated in some processes outside of plant development.

Isolation and characterization of novel mutants affecting the abscisic acid sensitivity of Arabidopsis germination and seedling growth

To gain more insight into ABA signaling mechanisms, we conducted genetic screens searching for mutants with altered ABA response in germination and post-germination growth. We isolated seven putative ABA-hypersensitive Arabidopsis mutants and named them ABA-hypersensitive germination (ahg). These mutants exhibited diminished germination or growth ability on medium supplemented with ABA. We further studied four of them: ahg1, ahg2, ahg3 and ahg4. Mapping suggested that they were new ABA-hypersensitive loci. Characterization showed that all of them had enhanced sensitivity to salinity and high osmotic stress in germinating seeds, whereas they each had distinct sugar responses. RT-PCR experiments showed that the expression patterns of the ABA-inducible genes RAB18, AtEm1, AtEm6 and ABI5 in germinating seeds were affected by these four ahg mutations, whereas those of ABI3 and ABI4 were not. ahg4 displayed slightly increased mRNA levels of several ABA-inducible genes upon ABA treatment. By contrast, ahg1 had no clear ABA-hypersensitive phenotypes in adult plants despite its strong phenotype in germination. These results suggest that ahg1, ahg2, ahg3 and ahg4 are novel ABA-hypersensitive mutants representing distinct components in the ABA response.

Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed flowering in Arabidopsis

Recessive mutations that suppress the late-flowering phenotype conferred by FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) and which also result in serrated leaf morphology were identified in T-DNA and fast-neutron mutant populations. Molecular analysis showed that the mutations are caused by lesions in the gene encoding the large subunit of the nuclear mRNA cap-binding protein, ABH1 (ABA hypersensitive1). The suppression of late flowering is caused by the inability of FRI to increase FLC mRNA levels in the abh1 mutant background. The serrated leaf morphology of abh1 is similar to the serrate (se) mutant and, like abh1, se is also a suppressor of FRI-mediated late flowering although it is a weaker suppressor than abh1. Unlike se, in abh1 the rate of leaf production and the number of juvenile leaves are not altered. The abh1 lesion affects several developmental processes, perhaps because the processing of certain mRNAs in these pathways is more sensitive to loss of cap-binding activity than the majority of cellular mRNAs.

MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems

We have analysed the role of a microRNA, miR164, in boundary formation during organ initiation from Arabidopsis meristems. The establishment and maintenance of the boundary domain are controlled by three partially redundant genes, CUP-SHAPED COTYLEDON1 (CUC1), CUC2 and CUC3. We show that miR164 overexpression phenocopies the cuc1 cuc2 double mutant by inducing post-transcriptional downregulation of CUC1 and CUC2 but not CUC3 mRNA levels. Disruption of CUC2 regulation by miR164, either by making CUC2 resistant to the miRNA or by reducing miRNA levels leads to similar enlarged boundary domains. We relate this enlargement to the division patterns of the boundary cells. We propose that miR164 constrains the expansion of the boundary domain, by degrading CUC1 and CUC2 mRNAs.

Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis

MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small noncoding RNAs that have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far. In an attempt to identify novel and abiotic stress regulated miRNAs and siRNAs, we constructed a library of small RNAs from Arabidopsis seedlings exposed to dehydration, salinity, or cold stress or to the plant stress hormone abscisic acid. Sequencing of the library and subsequent analysis revealed 26 new miRNAs from 34 loci, forming 15 new families. Two of the new miRNAs from three loci are members of previously reported miR171 and miR319 families. Some of the miRNAs are preferentially expressed in specific tissues, and several are either upregulated or downregulated by abiotic stresses. Ten of the miRNAs are highly conserved in other plant species. Fifty-one potential targets with diverse function were predicted for the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Arabidopsis. These findings suggest that a large number of miRNAs and other small regulatory RNAs are encoded by the Arabidopsis genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.

The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing

MicroRNAs (miRNAs) are 21-24 nucleotides long molecules processed from imperfect double-stranded RNAs (dsRNAs). They regulate gene expression by targeting complementary mRNA for cleavage or interfering with their translation. In Arabidopsis, point mutations in or short truncations of the nuclear DICER-LIKE1 (DCL1) or HEN1 protein reduce miRNA accumulation and increase uncleaved target mRNAs accumulation, resulting in developmental abnormalities. Here, we show that miRNA accumulation also depends on the activity of HYL1, a nuclear dsRNA binding protein. hyl1 mutants exhibit developmental defects overlapping with that of dcl1 and hen1 mutants, suggesting that DCL1, HEN1, and HYL1 act together in the nucleus. We validate additional target mRNAs and show that reduced miRNA accumulation in hyl1 correlates with an increased accumulation of uncleaved target mRNAs, including meristem- and auxin-related genes, providing clues for the developmental abnormalities of hyl1 and for the previous identification of hyl1 as a mutant with altered responses to phytohormones. Lastly, we show that posttranscriptional transgene silencing occurs in hyl1, suggesting that HYL1 has specialized function in the plant miRNA pathway, whereas the HYL1-related RDE-4 and R2D2 proteins associate with DICER in the cytoplasm and act in the RNAi pathway in C. elegans and Drosophila, respectively.

The calcium sensor calcineurin B-like 9 modulates abscisic acid sensitivity and biosynthesis in Arabidopsis

Calcium plays a pivotal role in plant responses to several stimuli, including pathogens, abiotic stresses, and hormones. However, the molecular mechanisms underlying calcium functions are poorly understood. It is hypothesized that calcium serves as second messenger and, in many cases, requires intracellular protein sensors to transduce the signal further downstream in the pathways. The calcineurin B-like proteins (CBLs) represent a unique family of calcium sensors in plant cells. Here, we report our analysis of the CBL9 member of this gene family. Expression of CBL9 was inducible by multiple stress signals and abscisic acid (ABA) in young seedlings. When CBL9 gene function was disrupted in Arabidopsis thaliana plants, the responses to ABA were drastically altered. The mutant plants became hypersensitive to ABA in the early developmental stages, including seed germination and post-germination seedling growth. In addition, seed germination in the mutant also showed increased sensitivity to inhibition by osmotic stress conditions produced by high concentrations of salt and mannitol. Further analyses indicated that increased stress sensitivity in the mutant may be a result of both ABA hypersensitivity and increased accumulation of ABA under the stress conditions. The cbl9 mutant plants showed enhanced expression of genes involved in ABA signaling, such as ABA-INSENSITIVE 4 and 5. This study has identified a calcium sensor as a common element in the ABA signaling and stress-induced ABA biosynthesis pathways.

A mutation in the Cap Binding Protein 20 gene confers drought tolerance to Arabidopsis

In a genetic screen for Arabidopsis mutants displaying pleiotropic alterations in vegetative development and stress responses we have identified a T-DNA insertion mutation in the Cap Binding Protein 20 (CBP20) gene, that encodes the 20kDa subunit of the nuclear mRNA cap binding complex (nCBC). Plants homozygous for the recessive cbp20 mutation show mild developmental abnormalities, such as serrated rosette leaves, delayed development and slightly reduced stature. Loss of the cbp20 function also confers hypersensitivity to abscisic acid during germination, significant reduction of stomatal conductance and greatly enhanced tolerance to drought. Expression of the wild type cDNA by CaMV35S promoter provides full genetic complementation of the pleiotropic cbp20 phenotype. Phenotypic characteristics of the cbp20 mutant are very similar to those of recently described abh1 mutant that is defective in the 80kDa subunit of nCBC. Our data thus confirm that both genes are dedicated to the same function. CBP20 provides a new target for breeding efforts that aim at the improvement of drought tolerance in plants. Our results also show that screening for pleiotropic phenotypes in mutant plant populations may be a fruitful strategy to isolate genes for agronomically important traits.

MicroRNAs: more than a role in plant development?

SUMMARY Eukaryotic small RNA comprises several classes of 21-25 nucleotide non-coding RNA, of which microRNA (miRNA) has gained a great deal of attention because it is directly involved in controlling growth and development in plants. miRNAs are processed by the RNase III-like Dicer, although recent studies have implicated additional gene products in the step-wise maturation of miRNAs from their primary nuclear transcripts. They function as sequence-specific guides to trigger cleavage or translational repression of target mRNAs that have complementary sequences. Natural miRNA targets encode members of large families of transcription factors, which are collectively required for a number of developmental processes. In addition to developmental regulation, some miRNAs might be involved in specific physiological responses to several types of stresses, such as those induced by pathogen infections. Strikingly, the potyviruses, the largest group of plant RNA viruses, are able to interfere with miRNA-guided cleavage of multiple regulatory targets in plants, thus modulating gene expression of the host cell.

Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana

Translational regulation was evaluated for over 2000 genes by measurement of the proportion of individual mRNA species in polysomal (PS) complexes in leaves of non-stressed and moderately dehydration-stressed Arabidopsis. The amount of each mRNA in polysomes ranged from 23 to 97% in non-stressed leaves and was significantly reduced for a large portion of the genes (71%) in response to dehydration. The effect of dehydration on translational status varied extensively between mRNA species. Sixty per cent of the dehydration-inducible mRNAs with twofold or greater increase in abundance maintained PS levels in response to water-deficit stress, while 40% showed impaired ribosome loading (RL). PS association declined significantly for 92% of the mRNAs that displayed a strong decrease in abundance, indicating a relationship between translation and decreased gene transcription and/or mRNA stability. Interestingly, many mRNAs that encode proteins of similar biological function displayed coordinate translational regulation. Thus, the abundance of PS mRNA may provide a more accurate estimate of gene expression than total cellular mRNA because of extensive differential translational regulation.

MicroRNAs: something important between the genes

Non-coding small endogenous RNAs, of 21-24 nucleotides in length, have recently emerged as important regulators of gene expression in both plants and animals. At least three categories of small RNAs exist in plants: short interfering RNAs (siRNAs) deriving from viruses or transgenes and mediating virus resistance or transgene silencing via RNA degradation; siRNAs deriving from transposons or transgene promoters and controlling transposon and transgene silencing probably via chromatin changes; and microRNAs (miRNAs) deriving from intergenic regions of the genome and regulating the expression of endogenous genes either by mRNA cleavage or translational repression. The disruption of miRNA-mediated regulation causes developmental abnormalities in plants, demonstrating that miRNAs play an important role in the regulation of developmental decisions.

Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant

Oligomer-based DNA Affymetrix GeneChips representing about one-third of Arabidopsis (Arabidopsis thaliana) genes were used to profile global gene expression in a single cell type, guard cells, identifying 1309 guard cell-expressed genes. Highly pure preparations of guard cells and mesophyll cells were isolated in the presence of transcription inhibitors that prevented induction of stress-inducible genes during cell isolation procedures. Guard cell expression profiles were compared with those of mesophyll cells, resulting in identification of 64 transcripts expressed preferentially in guard cells. Many large gene families and gene duplications are known to exist in the Arabidopsis genome, giving rise to redundancies that greatly hamper conventional genetic and functional genomic analyses. The presented genomic scale analysis identifies redundant expression of specific isoforms belonging to large gene families at the single cell level, which provides a powerful tool for functional genomic characterization of the many signaling pathways that function in guard cells. Reverse transcription-PCR of 29 genes confirmed the reliability of GeneChip results. Statistical analyses of promoter regions of abscisic acid (ABA)-regulated genes reveal an overrepresented ABA responsive motif, which is the known ABA response element. Interestingly, expression profiling reveals ABA modulation of many known guard cell ABA signaling components at the transcript level. We further identified a highly ABA-induced protein phosphatase 2C transcript, AtP2C-HA, in guard cells. A T-DNA disruption mutation in AtP2C-HA confers ABA-hypersensitive regulation of stomatal closing and seed germination. The presented data provide a basis for cell type-specific genomic scale analyses of gene function.

Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant

Oligomer-based DNA Affymetrix GeneChips representing about one-third of Arabidopsis (Arabidopsis thaliana) genes were used to profile global gene expression in a single cell type, guard cells, identifying 1309 guard cell-expressed genes. Highly pure preparations of guard cells and mesophyll cells were isolated in the presence of transcription inhibitors that prevented induction of stress-inducible genes during cell isolation procedures. Guard cell expression profiles were compared with those of mesophyll cells, resulting in identification of 64 transcripts expressed preferentially in guard cells. Many large gene families and gene duplications are known to exist in the Arabidopsis genome, giving rise to redundancies that greatly hamper conventional genetic and functional genomic analyses. The presented genomic scale analysis identifies redundant expression of specific isoforms belonging to large gene families at the single cell level, which provides a powerful tool for functional genomic characterization of the many signaling pathways that function in guard cells. Reverse transcription-PCR of 29 genes confirmed the reliability of GeneChip results. Statistical analyses of promoter regions of abscisic acid (ABA)-regulated genes reveal an overrepresented ABA responsive motif, which is the known ABA response element. Interestingly, expression profiling reveals ABA modulation of many known guard cell ABA signaling components at the transcript level. We further identified a highly ABA-induced protein phosphatase 2C transcript, AtP2C-HA, in guard cells. A T-DNA disruption mutation in AtP2C-HA confers ABA-hypersensitive regulation of stomatal closing and seed germination. The presented data provide a basis for cell type-specific genomic scale analyses of gene function.

Posttranscriptional control of plant development

Genetic studies have provided increasing evidence that proteins involved in all aspects of RNA metabolism, such as RNA processing, transport, stability, and translation, are required for plant development and for plants' responses to the environment. Such proteins act in floral transition, floral patterning, and signaling by abscisic acid, low temperature and circadian rhythms. Although some of these proteins belong to core RNA metabolic machineries, others may have more specialized cellular functions. Despite the limited knowledge of the underlying molecular mechanisms, posttranscriptional regulation is known to play a key role in the control of plant development.

Gain-of-function and loss-of-function phenotypes of the protein phosphatase 2C HAB1 reveal its role as a negative regulator of abscisic acid signalling

HAB1 was originally cloned on the basis of sequence homology to ABI1 and ABI2, and indeed, a multiple sequence alignment of 32 Arabidopsis protein phosphatases type-2C (PP2Cs) reveals a cluster composed by the four closely related proteins, ABI1, ABI2, HAB1 and At1g17550 (here named HAB2). Characterisation of transgenic plants harbouring a transcriptional fusion ProHAB1: green fluorescent protein (GFP) indicates that HAB1 is broadly expressed within the plant, including key target sites of abscisic acid (ABA) action as guard cells or seeds. The expression of the HAB1 mRNA in vegetative tissues is strongly upregulated in response to exogenous ABA. In this work, we show that constitutive expression of HAB1 in Arabidopsis under a cauliflower mosaic virus (CaMV) 35S promoter led to reduced ABA sensitivity both in seeds and vegetative tissues, compared to wild-type plants. Thus, in the field of ABA signalling, this work represents an example of a stable phenotype in planta after sustained overexpression of a PP2C genes. Additionally, a recessive T-DNA insertion mutant of HAB1 was analysed in this work, whereas previous studies of recessive alleles of PP2C genes were carried out with intragenic revertants of the abi1-1 and abi2-1 mutants that carry missense mutations in conserved regions of the PP2C domain. In the presence of exogenous ABA, hab1-1 mutant shows ABA-hypersensitive inhibition of seed germination; however, its transpiration rate was similar to that of wild-type plants. The ABA-hypersensitive phenotype of hab1-1 seeds together with the reduced ABA sensitivity of 35S:HAB1 plants are consistent with a role of HAB1 as a negative regulator of ABA signalling. Finally, these results provide new genetic evidence on the function of a PP2C in ABA signalling.

The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation

The Arabidopsis HYL1 gene encodes a nuclear double-stranded RNA-binding protein. A knockout mutation of the hyl1 gene is recessive and pleiotropic, causing developmental abnormalities, increasing sensitivity to abscisic acid, and reducing sensitivity to auxin and cytokinin. We report that levels of several microRNAs (miRNAs; miR159, -167, and -171) are reduced in homozygous mutant plants, and levels of two of three tested target mRNAs are elevated. Conversely, the miRNA levels are elevated in plants expressing a HYL1 cDNA from a strong promoter, and the corresponding target RNAs are reduced. These changes result from alterations in the stability of the target RNAs. However, double-stranded RNA-induced posttranscriptional gene silencing is unaffected by the hyl1 mutation. One-third to one-half of the cellular HYL1 protein is in a macromolecular complex, and a GFP-HYL1 fusion protein is found predominantly in the nucleus, although it is observed in both nucleus and cytoplasm in some cells. Within nuclei, HYL1 is associated with subnuclear bodies and ring-like structures. These observations provide evidence that the HYL1 protein is part of a nuclear macromolecular complex that is involved in miRNA-mediated gene regulation. Because hyl1 mutants show marked abnormalities in hormone responses, these results further suggest that miRNA-mediated changes in mRNA stability play a vital role in plant hormone signaling.

The 5' UTR negatively regulates quantitative and spatial expression from the ABI3 promoter

The involvement of transcription factors Arabidopsis abscisic acid-insensitive3 (ABI3), maize viviparous1 (VP1) and Phaseolus vulgaris ABI3-like factor (PvALF) in the spatial control of storage protein gene expression is well established. However, little insight exists as to how they are themselves regulated. To address this, a 5.15 kb ABI3 upstream sequence including a 4.6 kb full-length promoter and 519 bp of 5'-untranslated region (UTR) was used to drive either beta-glucuronidase (GUS) or green fluorescent protein (GFP) expression in Arabidopsis. Expression from the full-length (- 4630/ + 519ABI3 ) and various 5'-truncated promoters was detected during embryogenesis in all lines, except those transgenic for promoter elements shorter than 364 bp. Two upstream activating regions, -3600 to -2033 and -2033 to -882, enhanced GUS expression in seeds. The -882 to -364 region was sufficient to confer seed-specific expression of GUS when fused to a - 64/ + 6CaMV 35S minimal promoter. Expression from the ABI3 promoter constructs was seed-specific, except in the presence of exogenous abscisic acid (ABA) (>0.3 microM), when GUS expression was detected in seedling roots. Excision of a 405 bp region containing three upstream open reading frames (uORFs) from the 5'-UTR dramatically increased GUS expression and debilitated constraint of reporter expression in roots. Negative regulation of ABI3 expression by the 5'-UTR may involve a post-transcriptional mechanism analogous to that of tumor suppressor genes which also bear long, uORF-containing, 5'-UTRs, or through interactions with RNA-binding proteins.

Impacts of altered RNA metabolism on abscisic acid signaling

The plant hormone abscisic acid (ABA) regulates many essential processes in growth and development. The recent characterization of ABA-sensitivity mutations in RNA-binding proteins has led to the recognition of a functional link between post-transcriptional mRNA processing and the ABA signal transduction machinery. By influencing transcript abundance, these RNA-binding proteins may modulate ABA signaling through the alteration of mRNA processing events such as splicing, 3' processing, nuclear export, transcript stability and RNA degradation.

Negative regulation of abscisic acid signaling by the Fagus sylvatica FsPP2C1 plays a role in seed dormancy regulation and promotion of seed germination

FsPP2C1 was previously isolated from beech (Fagus sylvatica) seeds as a functional protein phosphatase type-2C (PP2C) with all the conserved features of these enzymes and high homology to ABI1, ABI2, and PP2CA, PP2Cs identified as negative regulators of ABA signaling. The expression of FsPP2C1 was induced upon abscisic acid (ABA) treatment and was also up-regulated during early weeks of stratification. Furthermore, this gene was specifically expressed in ABA-treated seeds and was hardly detectable in vegetative tissues. In this report, to provide genetic evidence on FsPP2C1 function in seed dormancy and germination, we used an overexpression approach in Arabidopsis because transgenic work is not feasible in beech. Constitutive expression of FsPP2C1 under the cauliflower mosaic virus 35S promoter confers ABA insensitivity in Arabidopsis seeds and, consequently, a reduced degree of seed dormancy. Additionally, transgenic 35S:FsPP2C1 plants are able to germinate under unfavorable conditions, as inhibitory concentrations of mannitol, NaCl, or paclobutrazol. In vegetative tissues, Arabidopsis FsPP2C1 transgenic plants show ABA-resistant early root growth and diminished induction of the ABA-response genes RAB18 and KIN2, but no effect on stomatal closure regulation. Seed and vegetative phenotypes of Arabidopsis 35S:FsPP2C1 plants suggest that FsPP2C1 negatively regulates ABA signaling. The ABA inducibility of FsPP2C1 expression, together with the transcript accumulation mainly in seeds, suggest that it could play an important role modulating ABA signaling in beechnuts through a negative feedback loop. Finally, we suggest that negative regulation of ABA signaling by FsPP2C1 is a factor contributing to promote the transition from seed dormancy to germination during early weeks of stratification.

Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling

Maize (Zea mays) Viviparous1 (VP1) and Arabidopsis ABI3 are orthologous transcription factors that regulate key aspects of plant seed development and ABA signaling. To understand VP1-regulated gene expression on a global scale, we have performed oligomicroarray analysis of transgenic Arabidopsis carrying 35S::VP1 in an abi3 null mutant background. We have identified 353 VP1/ABA-regulated genes by GeneChip analysis. Seventy-three percent of the genes were affected by both VP1 and ABA in vegetative tissues, indicating a tight coupling between ABA signaling and VP1 function. A large number of seed-specific genes were ectopically expressed in vegetative tissue of 35S::VP1 plants consistent with evidence that VP1 and ABI3 are key determinants of seed-specific expression. ABI5, a positive regulator of ABA signaling, was activated by VP1, indicating conservation of the feed-forward pathway mediated by ABI3. ABA induction of ABI1 and ABI2, negative regulators of ABA signaling, was strongly inhibited by VP1, revealing a second pathway of feed-forward regulation. These results indicate that VP1 strongly modifies ABA signaling through feed-forward regulation of ABI1/ABI5-related genes. Of the 32 bZIP transcription factors represented on the GeneChip, genes in the ABI5 clade were specifically coregulated by ABA and VP1. Statistical analysis of 5' upstream sequences of the VP1/ABA-regulated genes identified consensus abscisic responsive elements as an enriched element, indicating that many of the genes could be direct targets of the ABI5-related bZIPs. The Sph element is an enriched sequence motif in promoters of genes co-activated by ABA and VP1 but not in promoters of genes activated by ABA alone. This analysis reveals that distinct combinatorial patterns of promoter elements distinguish subclasses of VP1/ABA coregulated genes.

NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis

Reactive oxygen species (ROS) have been proposed to function as second messengers in abscisic acid (ABA) signaling in guard cells. However, the question whether ROS production is indeed required for ABA signal transduction in vivo has not yet been addressed, and the molecular mechanisms mediating ROS production during ABA signaling remain unknown. Here, we report identification of two partially redundant Arabidopsis guard cell-expressed NADPH oxidase catalytic subunit genes, AtrbohD and AtrbohF, in which gene disruption impairs ABA signaling. atrbohD/F double mutations impair ABA-induced stomatal closing, ABA promotion of ROS production, ABA-induced cytosolic Ca(2+) increases and ABA- activation of plasma membrane Ca(2+)-permeable channels in guard cells. Exogenous H(2)O(2) rescues both Ca(2+) channel activation and stomatal closing in atrbohD/F. ABA inhibition of seed germination and root elongation are impaired in atrbohD/F, suggesting more general roles for ROS and NADPH oxidases in ABA signaling. These data provide direct molecular genetic and cell biological evidence that ROS are rate-limiting second messengers in ABA signaling, and that the AtrbohD and AtrbohF NADPH oxidases function in guard cell ABA signal transduction.

The dsRNA binding protein family: critical roles, diverse cellular functions

The dsRNA binding proteins (DRBPs) comprise a growing family of eukaryotic, prokaryotic, and viral-encoded products that share a common evolutionarily conserved motif specifically facilitating interaction with dsRNA. Proteins harboring dsRNA binding domains (DRBDs) have been reported to interact with as little as 11 bp of dsRNA, an event that is independent of nucleotide sequence arrangement. More than 20 DRBPs have been identified and reportedly function in a diverse range of critically important roles in the cell. Examples include the dsRNA-dependent protein kinase PKR that functions in dsRNA signaling and host defense against virus infection and DICER, which is implicated in RNA interference (RNAi) -mediated gene silencing. Other DRBPs such as Staufen, adenosine deaminase acting on RNA (ADAR), and spermatid perinuclear RNA binding protein (SPNR) are known to play essential roles in development, translation, RNA editing, and stability. In many cases, homozygous and even heterozygous disruption of DRBPs in animal models results in embryonic lethality. These results implicate the recognition of dsRNA as an evolutionarily conserved mechanism important in the regulation of gene expression and in host defense and underscore the diversity of essential biological tasks performed by dsRNA-related processes in the cell.

The over-expression of an alfalfa RING-H2 gene induces pleiotropic effects on plant growth and development

The alfalfa MsRH2-1 gene encodes a small protein with a RING-H2 motif and an N-terminal transmembrane domain. The transcript can be found in all tested plant organs, but roots and nodules show the highest levels of RH2-1 mRNA accumulation. Promoter-GUS fusion studies demonstrate that the activity of this gene is closely correlated with development of lateral roots (in alfalfa and Arabidopsis) and symbiotic nodules (in alfalfa). Although antisense-expressing alfalfa plants did not show a significantly different phenotype from the control plants, by contrast, when the level of the MsRH2-1 RNA was raised by introducing the coding part of the gene under the control of the CaMV promoter, both the transgenic alfalfa and Arabidopsis lines exhibited dramatic alterations in plant morphology, including shorter stature, increased apical dominance, leaf hyponasty, and inhibition of leaf venation and lateral root development. Moreover, nodulation of transgenic alfalfa roots was delayed and partially inhibited, and some of the Arabidopsis lines showed abnormal floral development. The nature of pleiotropic developmental phenotypes suggests a hormonal basis. The possible connection between MsRH2-1 function and substrate specific degradation via the ubiquitin pathway involved in auxin signaling is discussed.

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.

Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant

The phytohormone abscisic acid (ABA) plays important regulatory roles in many plant developmental processes including seed dormancy, germination, growth, and stomatal movements. These physiological responses to ABA are in large part brought about by changes in gene expression. To study genome-wide ABA-responsive gene expression we applied massively parallel signature sequencing (MPSS) to samples from Arabidopsis thaliana wildtype (WT) and abi1-1 mutant seedlings. We identified 1354 genes that are either up- or downregulated following ABA treatment of WT seedlings. Among these ABA-responsive genes, many encode signal transduction components. In addition, we identified novel ABA-responsive gene families including those encoding ribosomal proteins and proteins involved in regulated proteolysis. In the ABA-insensitive mutant abi1-1, ABA regulation of about 84.5% and 6.9% of the identified genes was impaired or strongly diminished, respectively; however, 8.6% of the genes remained appropriately regulated. Compared to other methods of gene expression analysis, the high sensitivity and specificity of MPSS allowed us to identify a large number of ABA-responsive genes in WT Arabidopsis thaliana. The database given in our supplementary material (http://jcs.biologists.org/supplemental) provides researchers with the opportunity to rapidly assess whether genes of interest may be regulated by ABA. Regulation of the majority of the genes by ABA was impaired in the ABA-insensitive mutant abi1-1. However, a subset of genes continued to be appropriately regulated by ABA, which suggests the presence of at least two ABA signaling pathways, only one of which is blocked in abi1-1.

Mitogen-activated protein kinase signaling in postgermination arrest of development by abscisic acid

Abscisic acid (ABA) mediates plant responses to environmental stress, particularly to water status. During germination, the embryo emerges from dormancy as the ABA concentration declines. Exposure to exogenous ABA during germination arrests development rapidly, but reversibly, enabling seedlings to withstand early water stress without loss of viability. Postgermination proteolytic degradation of the essential ABI5 transcription factor is interrupted by perception of an increase in ABA concentration, leading to ABI5 accumulation and reactivation of embryonic genes. Making use of the ABA-hypersensitive hyl1 mutant of Arabidopsis, we show that the ABA signal is transmitted to the transcriptional apparatus through mitogen-activated protein kinase signaling.