Modulation of floral development by a gibberellin-regulated microRNA

Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species

Recent studies demonstrated that pattern formation in plants involves regulation of transcription factor families by microRNAs (miRNAs). To explore the potency, autonomy, target range, and functional conservation of miRNA genes, a systematic comparison between plants ectopically expressing pre-miRNAs and plants with corresponding multiple mutant combinations of target genes was performed. We show that regulated expression of several Arabidopsis thaliana pre-miRNA genes induced a range of phenotypic alterations, the most extreme ones being a phenocopy of combined loss of their predicted target genes. This result indicates quantitative regulation by miRNA as a potential source for diversity in developmental outcomes. Remarkably, custom-made, synthetic miRNAs vectored by endogenous pre-miRNA backbones also produced phenocopies of multiple mutant combinations of genes that are not naturally regulated by miRNA. Arabidopsis-based endogenous and synthetic pre-miRNAs were also processed effectively in tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum). Synthetic miR-ARF targeting Auxin Response Factors 2, 3, and 4 induced dramatic transformations of abaxial tissues into adaxial ones in all three species, which could not cross graft joints. Likewise, organ-specific expression of miR165b that coregulates the PHABULOSA-like adaxial identity genes induced localized abaxial transformations. Thus, miRNAs provide a flexible, quantitative, and autonomous platform that can be employed for regulated expression of multiple related genes in diverse species.

Conservation and divergence of plant microRNA genes

MicroRNA (miRNA) is one class of newly identified, small, non-coding RNAs that play versatile and important roles in post-transcriptional gene regulation. All miRNAs have similar secondary hairpin structures; many of these are evolutionarily conserved. This suggests a powerful approach to predict the existence of new miRNA orthologs or homologs in other species. We developed a comprehensive strategy to identify new miRNA homologs by mining the repository of available ESTs. A total of 481 miRNAs, belonging to 37 miRNA families in 71 different plant species, were identified from more than 6 million EST sequences in plants. The potential targets of the EST-predicted miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the real existence of these miRNAs in the given plant species. Some plant miRNAs were physically clustered together, suggesting that these miRNAs have similar gene expression patterns and are transcribed together as a polycistron, as observed among animal miRNAs. The uracil nucleotide is dominant in the first position of 5' mature miRNAs. Our results indicate that many miRNA families are evolutionarily conserved across all major lineages of plants, including mosses, gymnosperms, monocots and eudicots. Additionally, the number of miRNAs discovered was directly related to the number of available ESTs and not to evolutionary relatedness to Arabidopsis thaliana, indicating that miRNAs are conserved and little phylogenetic signal exists in the presence or absence of these miRNAs. Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years.

How floral meristems are built

The formation of flowers involves the activity of a genetic network that acts in meristems to specify floral identity. The main output of this network is the initiation of a developmental patterning program for the generation of floral organs. The first characteristic of meristem identity genes is their capacity to integrate the environmental and endogenous cues that regulate the onset of flowering. This mechanism synchronizes temporal and spatial information, ensuring that flowers arise in the correct location at the appropriate time. The second characteristic of this network is the mutual regulatory interactions established between meristem identity genes. These interactions provide flexibility and robustness against environmental noise and prevent reversion once the decision to flower has been made. Finally, the third feature is the overlap between the meristem identity and other developmental programs that operate simultaneously to regulate different aspects of the construction of flowers.

Evolution of Arabidopsis microRNA families through duplication events

Recently there has been a great interest in the identification of microRNAs and their targets as well as understanding the spatial and temporal regulation of microRNA genes. To understand how microRNA genes evolve, we looked at several rapidly evolving families in Arabidopsis thaliana, and found that they arose from a process of genome-wide duplication, tandem duplication, and segmental duplication followed by dispersal and diversification, similar to the processes that drive the evolution of protein gene families. Using multiple expression data sets to examine the transcription patterns of different members of the microRNA families, we find the sequence diversification of duplicated microRNA genes to be accompanied by a change in spatial and temporal expression patterns, suggesting that duplicated copies acquire new functionality as they evolve.

PLASTOCHRON2 regulates leaf initiation and maturation in rice

In higher plants, leaves initiate in constant spatial and temporal patterns. Although the pattern of leaf initiation is a key element of plant shoot architecture, little is known about how the time interval between initiation events, termed plastochron, is regulated. Here, we present a detailed analysis of plastochron2 (pla2), a rice (Oryza sativa) mutant that exhibits shortened plastochron and precocious maturation of leaves during the vegetative phase and ectopic shoot formation during the reproductive phase. The corresponding PLA2 gene is revealed to be an orthologue of terminal ear1, a maize (Zea mays) gene that encodes a MEI2-like RNA binding protein. PLA2 is expressed predominantly in young leaf primordia. We show that PLA2 normally acts to retard the rate of leaf maturation but does so independently of PLA1, which encodes a member of the P450 family. Based on these analyses, we propose a model in which plastochron is determined by signals from immature leaves that act non-cell-autonomously in the shoot apical meristem to inhibit the initiation of new leaves.

Characterization of an anther- and tapetum-specific gene and its highly specific promoter isolated from tomato

A full-length genomic clone of 2,233 bp long containing an anther- and tapetum-specific gene TomA108 was isolated and characterized from tomato. The gene was present in one copy per haploid genome. The isolated clone contained 5' and 3' untranslated regions of 810 and 170 nucleotides, respectively and a single intron with highly repetitive sequences. The cDNA encoded the protein with an apparent mass of 10.6 kDa and a pI (isoelectric point) of 5.3. It was cysteine-rich and had an N-terminal hydrophobic domain with characteristics of a secretory signal. Amino acid sequence comparisons demonstrated that the protein was closely related to a family of cereal seed storage proteins and protease inhibitors. The fusion of beta-glucuronidase to the TomA108 promoter demonstrated that the promoter was highly active from early-meiosis to free microspores production in tapetum of tobacco. This strong and highly specific promoter can be potentially used to generate male sterility for efficient production of plant hybrids.

microRNAs in seeds: modified detection techniques and potential applications

microRNAs (miRNAs) are small (21–24 nucleotides), single-stranded RNAs that regulate target gene expression at transcriptional and posttranscriptional levels. miRNAs play crucial roles in plant development, maintenance of homeostasis, and responses to environmental signals. miRNAs and their target genes, which can be computationally predicted in plants, are expressed in developing and germinating seeds as in other plant tissues, suggesting that miRNAs may be involved in the regulation of gene expression in seeds. Profiling multiple miRNAs expressed in developing and germinating seeds, characterizing their expression patterns in a spatio-temporal manner, and elucidating their biological functions will provide information essential for understanding the mechanisms of seed development and germination. In this review, an overview of the recent technical advances in seed miRNA research and their potential applications for plant, specifically seed, research are presented.

Integrating hormone signaling and patterning mechanisms in plant development

Plant growth and development are driven by the bustling integration of a vast number of signals, among which plant hormones dominate. Understanding the role of hormones in particular developmental events requires their integration with developmental regulators known to be specific to those events. Using the increasing number of tools that can be utilized to probe hormone biosynthesis, transport and response, several recent studies have taken such an integrative approach, and in so doing have contributed to a clearer picture of precisely how hormones control plant development.

Integration of Plant Responses to Environmentally Activated Phytohormonal Signals

Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.

Integrative plant biology: role of phloem long-distance macromolecular trafficking

Recent studies have revealed the operation of a long-distance communication network operating within the vascular system of higher plants. The evolutionary development of this network reflects the need to communicate environmental inputs, sensed by mature organs, to meristematic regions of the plant. One consequence of such a long-distance signaling system is that newly forming organs can develop properties optimized for the environment into which they will emerge, mature, and function. The phloem translocation stream of the angiosperms contains, in addition to photosynthate and other small molecules, a variety of macromolecules, including mRNA, small RNA, and proteins. This review highlights recent progress in the characterization of phloem-mediated transport of macromolecules as components of an integrated long-distance signaling network. Attention is focused on the role played by these proteins and RNA species in coordination of developmental programs and the plant's response to both environmental cues and pathogen challenge. Finally, the importance of developing phloem transcriptome and proteomic databases is discussed within the context of advances in plant systems biology.

MicroRNAs and their regulatory roles in animals and plants

microRNAs (miRNAs) are an abundant class of newly identified endogenous non-protein-coding small RNAs. They exist in animals, plants, and viruses, and play an important role in gene silencing. Translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-directed deadenylation of targeted mRNAs are three mechanisms of miRNA-guided gene regulation at the post-transcriptional levels. Many miRNAs are highly conserved in animals and plants, suggesting that they play an essential function in plants and animals. Lots of investigations indicate that miRNAs are involved in multiple biological processes, including stem cell differentiation, organ development, phase change, signaling, disease, cancer, and response to biotic and abiotic environmental stresses. This review provides a general background and current advance on the discovery, history, biogenesis, genomics, mechanisms, and functions of miRNAs.

The small RNA world of plants

RNA has many functions in addition to being a simple messenger between the genome and the proteome. Over two decades, several classes of small noncoding RNAs c. 21 nucleotides (nt) long have been uncovered in eukaryotic genomes, which appear to play a central role in diverse and fundamental processes. In plants, small RNA-based mechanisms are involved in genome stability, gene expression and defense. Many of the discoveries in this new "small RNA world" were made by plant biologists. Here, we discuss the three major classes of small RNAs that are found in the plant kingdom, namely small interfering RNAs, microRNAs, and the recently discovered trans-acting small interfering RNAs. Recent results shed light on the identification, integration and specialization of the different components (Dicer-like, Argonaute, and others) involved in the biogenesis of the different classes of small RNAs in plants. Owing to the development of better experimental and computational methods, an ever increasing number of small noncoding RNAs are uncovered in different plant genomes. In particular the well-studied microRNAs seem to act as key regulators in several different developmental pathways, with a marked preference for transcription factors as targets. In addition, an increasing amount of data suggest that they also play an important role in other mechanisms, such as response to stress or environmental changes.

MicroRNAS and their regulatory roles in plants

MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in plants and animals. In plants, these approximately 21-nucleotide RNAs are processed from stem-loop regions of long primary transcripts by a Dicer-like enzyme and are loaded into silencing complexes, where they generally direct cleavage of complementary mRNAs. Although plant miRNAs have some conserved functions extending beyond development, the importance of miRNA-directed gene regulation during plant development is now particularly clear. Identified in plants less than four years ago, miRNAs are already known to play numerous crucial roles at each major stage of development-typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.

Plant microRNA: a small regulatory molecule with big impact

MicroRNAs (miRNAs) are an abundant new class of non-coding approximately 20-24 nt small RNAs. To date, 872 miRNAs, belonging to 42 families, have been identified in 71 plant species by genetic screening, direct cloning after isolation of small RNAs, computational strategy, and expressed sequence tag (EST) analysis. Many plant miRNAs are evolutionarily conserved from species to species, some from angiosperms to mosses. miRNAs may originate from inverted duplications of target gene sequences in plants. Although miRNA precursors display high variability, their mature sequences display extensive sequence complementarity to their target mRNA sequences. miRNAs play important roles in plant post-transcriptional gene regulation by targeting mRNAs for cleavage or repressing translation. miRNAs are involved in plant development, signal transduction, protein degradation, response to environmental stress and pathogen invasion, and regulate their own biogenesis. miRNAs regulate the expression of many important genes; a majority of these genes are transcriptional factors.

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.

Identification of microRNAs from rice

MicroRNAs (miRNAs) are important regulators in the development of plants and animals. Several hundred have been identified from animals, and about a dozen have been cloned from plants, mainly Arabidopsis thaliana (L.) Heynh. We have identified nine miRNAs in Oryza sativa L., an important food crop that has been sequenced in recent years. The nine miRNAs include miRNA171 and miRNA167, which were also identified in Arabidopsis. These had the typical properties of miRNAs, including short length, an ability to form a stem-loop structure with a flanking genomic sequence and they could be identified by northern blot analyses. In addition, m-fold program and computational analyses indicted that the potential targets of six of the nine miRNAs are four known gene families and two unknown protein families, which comprise 16 unique genes.

MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision

The elucidation of the architecture of gene regulatory networks that control cell-type specific gene expression programs represents a major challenge in developmental biology. We describe here a cell fate decision between two alternative neuronal fates and the architecture of a gene regulatory network that controls this cell fate decision. The two Caenorhabditis elegans taste receptor neurons "ASE left" (ASEL) and "ASE right" (ASER) share many bilaterally symmetric features, but each cell expresses a distinct set of chemoreceptors that endow the gustatory system with the capacity to sense and discriminate specific environmental inputs. We show that these left/right asymmetric fates develop from a precursor state in which both ASE neurons express equivalent features. This hybrid precursor state is unstable and transitions into the stable ASEL or ASER terminal end state. Although this transition is spatially stereotyped in wild-type animals, mutant analysis reveals that each cell has the potential to transition into either the ASEL or ASER stable end state. The stability and irreversibility of the terminal differentiated state is ensured by the interactions of two microRNAs (miRNAs) and their transcription factor targets in a double-negative feedback loop. Simple feedback loops are found as common motifs in many gene regulatory networks, but the loop described here is unusually complex and involves miRNAs. The interaction of miRNAs in double-negative feedback loops may not only be a means for miRNAs to regulate their own expression but may also represent a general paradigm for how terminal cell fates are selected and stabilized.

MicroRNA biogenesis and function in plants

A microRNA (miRNA) is a 21-24 nucleotide RNA product of a non-protein-coding gene. Plants, like animals, have a large number of miRNA-encoding genes in their genomes. The biogenesis of miRNAs in Arabidopsis is similar to that in animals in that miRNAs are processed from primary precursors by at least two steps mediated by RNAse III-like enzymes and that the miRNAs are incorporated into a protein complex named RISC. However, the biogenesis of plant miRNAs consists of an additional step, i.e., the miRNAs are methylated on the ribose of the last nucleotide by the miRNA methyltransferase HEN1. The high degree of sequence complementarity between plant miRNAs and their target mRNAs has facilitated the bioinformatic prediction of miRNA targets, many of which have been subsequently validated. Plant miRNAs have been predicted or confirmed to regulate a variety of processes, such as development, metabolism, and stress responses. A large category of miRNA targets consists of genes encoding transcription factors that play important roles in patterning the plant form.

Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis

MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.

Expression of Arabidopsis MIRNA genes

MicroRNAs (miRNAs) are approximately 21-nucleotide noncoding RNAs that regulate target transcripts in plants and animals. In addition to miRNAs, plants contain several classes of endogenous small interfering RNAs (siRNAs) involved in target gene regulation and epigenetic silencing. Small RNA libraries were constructed from wild-type Arabidopsis (Arabidopsis thaliana) and mutant plants (rdr2 and dcl3) that were genetically enriched for miRNAs, and a computational procedure was developed to identify candidate miRNAs. Thirty-eight distinct miRNAs corresponding to 22 families were represented in the libraries. Using a 5' rapid amplification of cDNA ends procedure, the transcription start sites for 63 miRNA primary transcripts from 52 MIRNA loci (99 loci tested) were mapped, revealing features consistent with an RNA polymerase II mechanism of transcription. Ten loci (19%) yielded transcripts from multiple start sites. A canonical TATA box motif was identified upstream of the major start site at 45 (86%) of the mapped MIRNA loci. The 5'-mapping data were combined with miRNA cloning and 3'-PCR data to definitively validate expression of at least 73 MIRNA genes. These data provide a molecular basis to explore regulatory mechanisms of miRNA expression in plants.

MicroRNA-binding viral protein interferes with Arabidopsis development

MicroRNAs (miRNAs) are small (approximately 21 nt), noncoding RNAs that negatively regulate target mRNAs at the posttranscriptional level that are involved in development. In plants, virus-induced disease symptoms often result in developmental abnormalities resembling perturbation of miRNA-mediated function. Here, we report that expression in transgenic plants of a geminivirus-encoded AC4 protein from African cassava mosaic virus Cameroon Strain (ACMV), a suppressor of posttranscriptional gene silencing, was correlated with decreased accumulation of host miRNAs and increased development abnormalities in Arabidopsis. Down-regulation of miRNA correlated with an up-regulation of target mRNA level. In vitro binding assays revealed the ability of AC4 of ACMV (A-AC4) but not East African cassava mosaic Cameroon virus AC2 to bind single-stranded forms of miRNAs and short interfering RNAs but not double-stranded RNA forms. Normally, a labile intermediate during the miRNA biogenesis/RNA-induced silencing complex assembly, miRNA*, was below the level of detection, indicating that AC4 might interfere at a point downstream of the miRNA duplex unwinding process. The association of AC4 with miRNA was demonstrated by the association of A-AC4-GFP fusion protein, extracted from Arabidopsis protoplasts, with 2'-O-methyloligonucleotide complementary to miR159 (miR159*) and by the presence of miRNA with the A-AC4-GFP fusion protein after immunoprecipitation with antibody against GFP. In both assays, A-AC4 protein and miRNA complexes were copurified. These results provide direct evidence that AC4 is a unique virus-encoded posttranscriptional gene-silencing suppressor protein that binds to and presumably inactivates mature miRNAs and thus blocks the normal miRNA-mediated regulation of target mRNAs, resulting in developmental defects in Arabidopsis.

Specific effects of microRNAs on the plant transcriptome

Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their targets. This is consistent with their primary mode of action being cleavage of target mRNAs, similar to that induced by perfectly complementary small interfering RNAs (siRNAs). However, there are natural targets with up to five mismatches. Furthermore, artificial siRNAs can have substantial effects on so-called off-targets, to which they have only limited complementarity. By analyzing the transcriptome of plants overexpressing different miRNAs, we have deduced a set of empirical parameters for target recognition. Compared to artificial siRNAs, authentic plant miRNAs appear to have much higher specificity, which may reflect their coevolution with the remainder of the transcriptome. We also demonstrate that miR172, previously thought to act primarily by translational repression, can efficiently guide mRNA cleavage, although the effects on steady-state levels of target transcripts are obscured by strong feedback regulation. This finding unifies the view of plant miRNA action.

microRNA172 down-regulates glossy15 to promote vegetative phase change in maize

Shoot development in many higher plant species is characterized by phase change, where meristems and organs transition from one set of identities to another. The transition from a juvenile to adult leaf identity in maize is regulated by the APETALA2-like gene glossy15 (gl15). We demonstrate here that increasing gl15 activity in transgenic maize not only increases the number of leaves expressing juvenile traits, but also delays the onset of reproductive development, indicating that gl15 plays a primary role in the maintenance of the juvenile phase. We also show that the accumulation of a maize microRNA homologous to miR172 increases during shoot development and mediates gl15 mRNA degradation. These data indicate that vegetative phase change in maize is regulated by the opposing actions of gl15 and miR172, with gl15 maintaining the juvenile phase and miR172 promoting the transition to the adult phase by down-regulation of gl15. Our results also suggest that the balance of activities between APETALA2-like genes and miR172 may be a general mechanism for regulating vegetative phase change in higher plants.

Antiquity of microRNAs and their targets in land plants

MicroRNAs (miRNAs) affect the morphology of flowering plants by the posttranscriptional regulation of genes involved in critical developmental events. Understanding the spatial and temporal dynamics of miRNA activity during development is therefore central for understanding miRNA functions. We describe a microarray suitable for detection of plant miRNAs. Profiling of Arabidopsis thaliana miRNAs during normal development extends previous expression analyses, highlighting differential expression of miRNA families within specific organs and tissue types. Comparison of our miRNA expression data with existing mRNA microarray data provided a global intersection of plant miRNA and mRNA expression profiles and revealed that tissues in which a given miRNA is highly expressed are unlikely to also show high expression of the corresponding targets. Expression profiling was also used in a phylogenetic survey to test the depth of plant miRNA conservation. Of the 23 families of miRNAs tested, expression of 11 was detected in a gymnosperm and eight in a fern, directly demonstrating that many plant miRNAs have remained essentially unchanged since before the emergence of flowering plants. We also describe an empirical strategy for detecting miRNA target genes from unsequenced transcriptomes and show that targets in nonflowering plants as deeply branching as ferns and mosses are homologous to the targets in Arabidopsis. Therefore, several individual miRNA regulatory circuits have ancient origins and have remained intact throughout the evolution and diversification of plants.

microRNA-directed phasing during trans-acting siRNA biogenesis in plants

Plants and animals use small RNAs (microRNAs [miRNAs] and siRNAs) as guides for posttranscriptional and epigenetic regulation. In plants, miRNAs and trans-acting (ta) siRNAs form through distinct biogenesis pathways, although they both interact with target transcripts and guide cleavage. An integrated approach to identify targets of Arabidopsis thaliana miRNAs and ta-siRNAs revealed several new classes of small RNA-regulated genes, including conventional genes such as Argonaute2 and an E2-ubiquitin conjugating enzyme. Surprisingly, five ta-siRNA-generating transcripts were identified as targets of miR173 or miR390. Rather than functioning as negative regulators, miR173- and miR390-guided cleavage was shown to set the 21-nucleotide phase for ta-siRNA precursor processing. These data support a model in which miRNA-guided formation of a 5' or 3' terminus within pre-ta-siRNA transcripts, followed by RDR6-dependent formation of dsRNA and Dicer-like processing, yields phased ta-siRNAs that negatively regulate other genes.

The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis

BACKGROUND

MicroRNAs (miRNAs) are small 20-25 nucleotide non-protein-coding RNAs that negatively regulate expression of genes in many organisms, ranging from plants to humans. The MIR164 family of miRNAs in Arabidopsis consists of three members that share sequence complementarity to transcripts of NAC family transcription factors, including CUP-SHAPED COTYLEDON1 (CUC1) and CUC2. CUC1 and CUC2 are redundantly required for the formation of boundaries between organ primordia. The analysis of transgenic plants that either overexpress miR164a or miR164b or express a miRNA-resistant version of CUC1 or CUC2 has shown that miRNA regulation of CUC1 and CUC2 is necessary for normal flower development. A loss-of-function allele of MIR164b did not result in a mutant phenotype, possibly because of functional redundancy among the three members of the MIR164 family.

RESULTS

In this study, we describe the characterization of the early extra petals1 (eep1) Arabidopsis mutant, whose predominant phenotype is the formation of extra petals in early-arising flowers. We demonstrate that eep1 is a loss-of-function allele of MIR164c, one of three known members of the MIR164 family. Our analyses of miR164c function and eep1 mir164b double mutants reveal that miR164c controls petal number in a nonredundant manner by regulating the transcript accumulation of the transcription factors CUC1 and CUC2.

CONCLUSIONS

The data presented in this study indicate that closely related miRNA family members that are predicted to target the same set of genes can have different functions during development, possibly because of nonoverlapping expression patterns.

MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes

The phytohormone auxin plays critical roles during plant growth, many of which are mediated by the auxin response transcription factor (ARF) family. MicroRNAs (miRNAs), endogenous 21-nucleotide riboregulators, target several mRNAs implicated in auxin responses. miR160 targets ARF10, ARF16, and ARF17, three of the 23 Arabidopsis thaliana ARF genes. Here, we describe roles of miR160-directed ARF17 posttranscriptional regulation. Plants expressing a miRNA-resistant version of ARF17 have increased ARF17 mRNA levels and altered accumulation of auxin-inducible GH3-like mRNAs, YDK1/GH3.2, GH3.3, GH3.5, and DFL1/GH3.6, which encode auxin-conjugating proteins. These expression changes correlate with dramatic developmental defects, including embryo and emerging leaf symmetry anomalies, leaf shape defects, premature inflorescence development, altered phyllotaxy along the stem, reduced petal size, abnormal stamens, sterility, and root growth defects. These defects demonstrate the importance of miR160-directed ARF17 regulation and implicate ARF17 as a regulator of GH3-like early auxin response genes. Many of these defects resemble phenotypes previously observed in plants expressing viral suppressors of RNA silencing and plants with mutations in genes important for miRNA biogenesis or function, providing a molecular rationale for phenotypes previously associated with more general disruptions of miRNA function.

ASRP: the Arabidopsis Small RNA Project Database

Eukaryotes produce functionally diverse classes of small RNAs (20–25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu.

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.

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.

Analysis of flowering pathway integrators in Arabidopsis

Flowering is regulated by an integrated network of several genetic pathways in Arabidopsis. The key genes integrating multiple flowering pathways are FT, SOC1 and LFY. To elucidate the interactions among these integrators, genetic analyses were performed. FT and SOC1 share the common upstream regulators CO, a key component in the long day pathway, and FLC, a flowering repressor integrating autonomous and vernalization pathways. However, the soc1 mutation further delayed the flowering time of long day pathway mutants including ft, demonstrating that SOC1 acts partially independently of FT. Although soc1 did not show an obvious defect in flower meristem determination on its own, it dramatically increased the number of coflorescences in a lfy mutant, which is indicative of a defect in floral initiation. Therefore, double mutant analysis shows that the three integrators have both overlapping and independent functions in the determination of flowering time and floral initiation. The expression analysis showed that FT regulates SOC1 expression, and SOC1 regulates LFY expression, but not vice versa, which is consistent with the fact that FT and LFY have the least overlapping functions among the three integrators. The triple mutation ft soc1 lfy did not block flowering completely under long days, indicating the presence of other integrators. Finally, vernalization accelerated flowering of flc ft soc1 and ft soc1 lfy triple mutants, which shows that the vernalization pathway also has targets other than FLC, FT, SOC1 and LFY. Our genetic analysis reveals the intricate nature of genetic networks for flowering.

A DELLAcate balance: the role of gibberellin in plant morphogenesis

The importance of gibberellin (GA) in vegetative and reproductive development has been known for some time. Recent studies have uncovered new roles of GA in leaf differentiation, photomorphogenesis and pollen-tube growth. Significant contributions to our understanding of GA-regulated morphogenesis include the identification of upstream regulators of GA biosynthesis, the elucidation of the function of GA signaling components, and the isolation of downstream targets. In addition, the mechanisms of interactions between GA and other hormone pathways are beginning to be revealed at the molecular level.

Gibberellin metabolism and signaling

Gibberellins (GAs) are a family of plant hormones controlling many aspects of plant growth and development including stem elongation, germination, and the transition from vegetative growth to flowering. Cloning of the genes encoding GA biosynthetic and inactivating enzymes has led to numerous insights into the developmental regulation of GA hormone accumulation that is subject to both positive and negative feedback regulation. Genetic and biochemical analysis of GA-signaling genes has revealed that posttranslational regulation of DELLA protein accumulation is a key control point in GA response. The highly conserved DELLA proteins are a family of negative regulators of GA signaling that appear subject to GA-stimulated degradation through the ubiquitin-26S proteasome pathway. This review discusses the regulation of GA hormone accumulation and signaling in the context of its role in plant growth and development.

Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.