Small RNAs as big players in plant abiotic stress responses and nutrient deprivation

Profiling of cold-stress-responsive miRNAs in rice by microarrays

MicroRNAs (miRNAs) are small single-stranded RNAs with a length of about 21 nt; these non-coding RNAs regulate developmental and stress responses in plants by cleaving mRNAs. Cold stress is one of the most severe abiotic stresses and adversely affects rice yields by restraining sowing time, causing tissue damage, and stunting growth. Although many miRNAs have been identified in rice, little is known about the role of miRNAs in the response to cold stress. In this study, we identified 18 cold-responsive rice miRNAs using microarrays. Most were down-regulated. Members of the miR-167 and miR-319 families showed similar profiles. Intriguingly, members of miR-171 family showed diverse expression patterns. Three miRNAs derived from transposable element sequence were clustered within an intron and proved to be co-transcribed with the host gene only under cold stress. The existence of hormone-responsive elements in the upstream regions of the cold-responsive miRNAs indicates the importance of hormones in this defense system mediated by miRNAs. Two miRNA target pairs validated by 5' RACE showed opposite expression profiles under cold stress. Finally, the predicted stress-related targets of these miRNAs provided further evidence supporting our results. These findings confirm the role of miRNAs as ubiquitous regulators in rice.

osa-MIR393: a salinity- and alkaline stress-related microRNA gene

Salinity and alkalinity are the two main environmental factors that limit rice production. Better understanding of the mechanisms responsible for salinity and alkaline stress tolerance would allow researchers to modify rice to increase its resistance to salinity and alkaline stress. MicroRNAs (miRNAs) are ~21-nucleotide RNAs that are ubiquitous regulators of gene expression in eukaryotic organisms. Some miRNAs acts as an important endogenous regulator in plant responses to abiotic stressors. miR393 is a conservative miRNA family that occurs in a variety of different plants. The two members of the miR393 family found in rice are named osa-MIR393 and osa-MIR393b. We found that the osa-MIR393 expression level changed under salinity and alkaline stress, whereas that of osa-MIR393b did not. Target genes of osa-MIR393 were predicted, and some of these putative targets are abiotic related genes. Furthermore, we generated transgenic rice and Arabidopsis thaliana that over-expressed osa-MIR393, and the phenotype analysis showed that these transgenic plants were more sensitive to salt and alkali treatment compared to wild-type plants. These results illustrate that over-expression of osa-MIR393 can negatively regulate rice salt-alkali stress tolerance.

Research on plant abiotic stress responses in the post-genome era: past, present and future

Understanding abiotic stress responses in plants is an important and challenging topic in plant research. Physiological and molecular biological analyses have allowed us to draw a picture of abiotic stress responses in various plants, and determination of the Arabidopsis genome sequence has had a great impact on this research field. The availability of the complete genome sequence has facilitated access to essential information for all genes, e.g. gene products and their function, transcript levels, putative cis-regulatory elements, and alternative splicing patterns. These data have been obtained from comprehensive transcriptome analyses and studies using full-length cDNA collections and T-DNA- or transposon-tagged mutant lines, which were also enhanced by genome sequence information. Moreover, studies on novel regulatory mechanisms involving use of small RNA molecules, chromatin modulation and genomic DNA modification have enabled us to recognize that plants have evolved complicated and sophisticated systems in response to complex abiotic stresses. Integrated data obtained with various 'omics' approaches have provided a more comprehensive picture of abiotic stress responses. In addition, research on stress responses in various plant species other than Arabidopsis has increased our knowledge regarding the mechanisms of plant stress tolerance in nature. Based on this progress, improvements in crop stress tolerance have been attempted by means of gene transfer and marker-assisted breeding. In this review, we summarize recent progress in abiotic stress studies, especially in the post-genomic era, and offer new perspectives on research directions for the next decade.

Mechanisms of microRNA-mediated auxin signaling inferred from the rice mutant osaxr

Auxin, known as the central hormone, plays essential roles in plant growth and development. In auxin signaling pathways, the tiny RNA molecules, i.e., microRNAs (miRNAs), show their strong potential in modulating the auxin signal transduction. Recently, we isolated a novel auxin resistant rice mutant osaxr (Oryza sativa auxin resistant) that exhibited plethoric root defects. Microarray experiments were carried out to investigate the expression patterns of both the miRNAs and the protein-coding genes in osaxr. A number of miRNAs showed reduced auxin sensitivity in osaxr compared with the wild type (WT), which may contribute to the auxin-resistant phenotype of the mutant. Auxin response elements (AuxREs) were demonstrated to be more frequently present in the promoters of auxin-related miRNAs. In our previous report, a comparative analysis of miRNA and protein-coding gene expression datasets uncovered a number of reciprocally expressed miRNA-target pairs. A feedback circuit between miRNA and auxin response factor (ARF) was then proposed. Here, we will discuss in-depth some points raised in the previous report, in particular, the organ-specific expression patterns of miR164, the feedback regulatory model between miR167 and certain ARFs, and the potential signal interactions between auxin and nutrition or stress that are mediated by miRNAs in rice roots.

Application of functional genomics and proteomics to plant cryopreservation

Plant cryobiology has primarily emerged from the classical fields of cryobiology and plant stress physiology. Cryopreservation tools are now available to geneticists for germplasm preservation and the field itself is advancing significantly through the use of molecular techniques. Long-term preservation of vegetatively propagated tissues can minimize the risks of long-term maintenance under tissue culture or field conditions. Cells can be successfully cryopreserved when the adverse affects of ice crystal formation are mitigated by the removal of water or procedures to limit ice formation and crystal growth. The addition of cryoprotectant solutions to hydrated cells may improve the survival of microdissected shoot tips or embryonic axes. Recent discoveries in the genetic pathways leading to cold acclimation and freezing tolerance suggest the involvement of key cold-regulated genes in the acquisition of cold tolerance in plant tissues. Model systems of banana and Arabidopsis have revealed the involvement of genes and proteins in the glycolytic and other metabolic pathways, particularly processes involved in dehydration tolerance, osmoprotection, and membrane transport. Furthermore, successful recovery appears to be dependent upon the presence of antioxidant protection from reactive oxygen species. Characterization of specific genes and proteins will lead to significant advances in plant cryobiology research.

Regulation of phosphate starvation responses in plants: signaling players and cross-talks

Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.

Energy signaling in the regulation of gene expression during stress

Maintenance of homeostasis is pivotal to all forms of life. In the case of plants, homeostasis is constantly threatened by the inability to escape environmental fluctuations, and therefore sensitive mechanisms must have evolved to allow rapid perception of environmental cues and concomitant modification of growth and developmental patterns for adaptation and survival. Re-establishment of homeostasis in response to environmental perturbations requires reprogramming of metabolism and gene expression to shunt energy sources from growth-related biosynthetic processes to defense, acclimation, and, ultimately, adaptation. Failure to mount an initial 'emergency' response may result in nutrient deprivation and irreversible senescence and cell death. Early signaling events largely determine the capacity of plants to orchestrate a successful adaptive response. Early events, on the other hand, are likely to be shared by different conditions through the generation of similar signals and before more specific responses are elaborated. Recent studies lend credence to this hypothesis, underpinning the importance of a shared energy signal in the transcriptional response to various types of stress. Energy deficiency is associated with most environmental perturbations due to their direct or indirect deleterious impact on photosynthesis and/or respiration. Several systems are known to have evolved for monitoring the available resources and triggering metabolic, growth, and developmental decisions accordingly. In doing so, energy-sensing systems regulate gene expression at multiple levels to allow flexibility in the diversity and the kinetics of the stress response.

Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses

Most of the physiological processes are controlled by the small RNAs in several organisms including plants. A huge database exists on one type of small RNA, i.e., microRNAs (miRs) identified from diverse species. However, the processes of data-mining of miRs in most of the species are still incomplete. Rice feeds the hungry trillions and hence understanding its developmental processes as well as its stress biology, which might be largely controlled by the small RNA pathways, is certainly a worthwhile task. Here, we report the cloning and identification of approximately 40 new putative miRs from local basmati rice variety in accordance to the annotation suggested by Meyers et al. (Plant Cell 20:3186-3190, 2008). About 23 sequences were derived from rice exposed to salt stress while 18 were derived from rice infected with tungro virus. A few of these putative miRs were common to both. Our data showed that at least two of these miRs were up-regulated in response to both abiotic and biotic stresses. The miR target predictions indicate that most of the putative miRs target specific metabolic processes. The up-regulation of similar miRs in response to two entirely different types of stresses suggests a converging functional role of miRs in managing various stresses. Our findings suggest that more rice miRs need to be identified and a thorough understanding of the function of such miRs will help unravel the mysteries of rice stress biology.

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana

One of the most striking examples of plant developmental plasticity to changing environmental conditions is the modulation of root system architecture (RSA) in response to nitrate supply. Despite the fundamental and applied significance of understanding this process, the molecular mechanisms behind nitrate-regulated changes in developmental programs are still largely unknown. Small RNAs (sRNAs) have emerged as master regulators of gene expression in plants and other organisms. To evaluate the role of sRNAs in the nitrate response, we sequenced sRNAs from control and nitrate-treated Arabidopsis seedlings using the 454 sequencing technology. miR393 was induced by nitrate in these experiments. miR393 targets transcripts that code for a basic helix-loop-helix (bHLH) transcription factor and for the auxin receptors TIR1, AFB1, AFB2, and AFB3. However, only AFB3 was regulated by nitrate in roots under our experimental conditions. Analysis of the expression of this miR393/AFB3 module, revealed an incoherent feed-forward mechanism that is induced by nitrate and repressed by N metabolites generated by nitrate reduction and assimilation. To understand the functional role of this N-regulatory module for plant development, we analyzed the RSA response to nitrate in AFB3 insertional mutant plants and in miR393 overexpressors. RSA analysis in these plants revealed that both primary and lateral root growth responses to nitrate were altered. Interestingly, regulation of RSA by nitrate was specifically mediated by AFB3, indicating that miR393/AFB3 is a unique N-responsive module that controls root system architecture in response to external and internal N availability in Arabidopsis.

Isolation and functional characterization of DgZFP: a gene encoding a Cys2/His2-type zinc finger protein in chrysanthemum

A Cys2/His2-type zinc finger protein gene, DgZFP, was isolated from chrysanthemum by rapid amplification of cDNA ends (RACE) approach. The DgZFP encodes a protein of 211 amino acids residues with a calculated molecular mass of 22.9 kDa and theoretical isoelectric point is 8.59. DgZFP contains two Cys2/His2-type zinc finger motifs, one nuclear localization domain, one Leu-rich domain, and one ethylene-responsive element-binding factor (ERF)-associated amphiphilic repression (EAR) domain. The transcript of DgZFP was enriched in flowers than in roots, stems, and leaves of the adult chrysanthemum plants. The gene expression was strongly induced by NaCl, drought and cold treatment, and weakly by ABA treatment in the seedlings. Subcellular localization revealed that DgZFP was localized preferentially distributed to nucleus. Overexpression of DgZFP improved salt tolerance and resulted in growth suppression in transgenic tobacco. We argued that DgZFP is a new member of the Cys2/His2-type zinc finger protein genes, and it maybe function as a regulator in response to salt stress in plants.

[Advances in mechanism of small RNAs]

The discovery of RNA interference (RNAi) heralded a revolution in RNA biology. Researchers uncovered 'hidden' layers of regulation of gene expression, in which many previously unidentified families of small RNAs (consisting of approximately 20-30 nucleotides) mediate gene silencing in transcriptional and post-transcriptional levels. In eukaryotes, these small RNAs, including siRNAs, miRNAs, piRNAs, scnRNAs, 21U-RNAs, and some others, regulate gene expression, helping to control cellular metabolism, growth, and differentiation, to maintain genome integrity, to regulate stem cell renewal, and to combat viruses and mobile genetic elements. This review summarizes the current advancement in the identification and biosynthesis of small RNAs and their roles in gene regulation.

Comparative transcriptomics for mangrove species: an expanding resource

We present here the Mangrove Transcriptome Database (MTDB), an integrated, web-based platform providing transcript information from all 28 mangrove species for which information is available. Sequences are annotated, and when possible, GO clustered and assigned to KEGG pathways, making MTDB a valuable resource for approaching mangrove or other extremophile biology from the transcriptomic level. As one example outlining the potential of MTDB, we highlight the analysis of mangrove microRNA (miRNA) precursor sequences, miRNA target sites, and their conservation and divergence compared with model plants. MTDB is available at http://mangrove.illinois.edu .

Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development

BACKGROUND

In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs.

RESULTS

We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained approximately 2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively.

CONCLUSIONS

We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.

Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development

BACKGROUND

In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs.

RESULTS

We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained approximately 2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively.

CONCLUSIONS

We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.

Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing

RNA silencing is a highly conserved pathway in the network of interconnected defense responses that are activated during viral infection. As a counter-defense, many plant viruses encode proteins that block silencing, often also interfering with endogenous small RNA pathways. However, the mechanism of action of viral suppressors is not well understood and the role of host factors in the process is just beginning to emerge. Here we report that the ethylene-inducible transcription factor RAV2 is required for suppression of RNA silencing by two unrelated plant viral proteins, potyvirus HC-Pro and carmovirus P38. Using a hairpin transgene silencing system, we find that both viral suppressors require RAV2 to block the activity of primary siRNAs, whereas suppression of transitive silencing is RAV2-independent. RAV2 is also required for many HC-Pro-mediated morphological anomalies in transgenic plants, but not for the associated defects in the microRNA pathway. Whole genome tiling microarray experiments demonstrate that expression of genes known to be required for silencing is unchanged in HC-Pro plants, whereas a striking number of genes involved in other biotic and abiotic stress responses are induced, many in a RAV2-dependent manner. Among the genes that require RAV2 for induction by HC-Pro are FRY1 and CML38, genes implicated as endogenous suppressors of silencing. These findings raise the intriguing possibility that HC-Pro-suppression of silencing is not caused by decreased expression of genes that are required for silencing, but instead, by induction of stress and defense responses, some components of which interfere with antiviral silencing. Furthermore, the observation that two unrelated viral suppressors require the activity of the same factor to block silencing suggests that RAV2 represents a control point that can be readily subverted by viruses to block antiviral silencing.

RNA silencing is an important antiviral defense in plants, and many plant viruses encode proteins that block RNA silencing. However, the mechanism of action of the viral suppressors is complex, and little is known about the role of host plant proteins in the process. Here we report the first example of a host protein that plays a required role in viral suppression of silencing—a transcription factor called RAV2 that is required for suppression of silencing by two different and unrelated viral proteins. Analysis of plant gene expression patterns shows that RAV2 is required for induction of many genes involved in other stress and defense pathways, including genes implicated as plant suppressors of silencing. Overall, the results suggest that RAV2 is an important factor in viral suppression of silencing and that the role of RAV2 is to divert host defenses toward responses that interfere with antiviral silencing.

Abiotic stress-associated miRNAs: detection and functional analysis

MicroRNAs (miRNAs) are small regulatory noncoding RNAs varying in length between 20 and 24 nucleotides. They play a key role during plant development by negatively regulating gene expression at the posttranscriptional level. Moreover, recent studies reported several miRNAs associated with abiotic stress responses. Small RNA cloning and high-throughput deep sequencing methods provide expression profiles of not only known miRNAs, but also novel miRNAs. In this chapter, we describe the methods used to identify and characterize abiotic stress-associated miRNAs and their target genes.

Gene regulation during cold stress acclimation in plants

Cold stress adversely affects plant growth and development and thus limits crop productivity. Diverse plant species tolerate cold stress to a varying degree, which depends on reprogramming gene expression to modify their physiology, metabolism, and growth. Cold signal in plants is transmitted to activate CBF-dependent (C-repeat/drought-responsive element binding factor-dependent) and CBF-independent transcriptional pathway, of which CBF-dependent pathway activates CBF regulon. CBF transcription factor genes are induced by the constitutively expressed ICE1 (inducer of CBF expression 1) by binding to the CBF promoter. ICE1-CBF cold response pathway is conserved in diverse plant species. Transgenic analysis in different plant species revealed that cold tolerance can be significantly enhanced by genetic engineering CBF pathway. Posttranscriptional regulation at pre-mRNA processing and export from nucleus plays a role in cold acclimation. Small noncoding RNAs, namely micro-RNAs (miRNAs) and small interfering RNAs (siRNAs), are emerging as key players of posttranscriptional gene silencing. Cold stress-regulated miRNAs have been identified in Arabidopsis and rice. In this chapter, recent advances on cold stress signaling and tolerance are highlighted.

Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants

MicroRNAs (miRNAs) are approximately 21 nt non-coding RNAs which regulate post-transcriptional gene expression. miRNAs are key regulators of nearly all essential biological processes. Aiming at understanding miRNA's functions in Euphorbiaceae, a large flowering plant family, we performed a genome-scale systematic study of miRNAs in Euphorbiaceae, by combining computational prediction and experimental analysis to overcome the difficulty of lack of genomes for most Euphorbiaceous species. Specifically, we predicted 85 conserved miRNAs in 23 families in the Castor bean (Ricinus communis), and experimentally verified and characterized 58 (68.2%) of the 85 miRNAs in at least one of four Euphorbiaceous species, the Castor bean, the Cassava (Manihot esculenta), the Rubber tree (Hevea brasiliensis) and the Jatropha (Jatropha curcas) during normal seedling development. To elucidate their function in stress response, we verified and profiled 48 (56.5%) of the 85 miRNAs under cold and drought stresses as well as during the processes of stress recovery. The results revealed some species- and condition-specific miRNA expression patterns. Finally, we predicted 258 miRNA:target partners, and identified the cleavage sites of six out of ten miRNA targets by a modified 5' RACE. This study produced the first collection of miRNAs and their targets in Euphorbiaceae. Our results revealed wide conservation of many miRNAs and diverse functions in Euphorbiaceous plants during seedling growth and in response to abiotic stresses.

Sculpting the flower; the role of microRNAs in flower development

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

Array platforms and bioinformatics tools for the analysis of plant transcriptome in response to abiotic stress

Current microarray technologies allow high-density in situ synthesis of oligonucleotides or ex situ spotting of target molecules (cDNA) for conducting genome-wide comparative gene expression profiling studies. The avalanche of available microarray gene expression data from model plant species covering cell-related, tissue-specific, and developmental events, as well as perturbations to a variety of environmental stimuli has triggered many activities regarding the development of adequate bioinformatics tools for the analysis of these complex data sets. In this chapter we summarize the technical issues of different microarray technologies, discuss the availability of bioinformatics tools, and present approaches to extract biologically meaningful knowledge. For case studies of abiotic stress transcriptome analysis we highlight the unprecedented opportunities provided by these high-throughput technologies to understand networks of regulatory and metabolic pathway responses of plant cells to the application of abiotic stress stimuli.

High-throughput approaches for miRNA expression analysis

miRNAs have emerged as key regulators of gene expression in both plants and animals. These small (generally 21-22 nt) RNA molecules, originated from primary "hairpin" transcripts, can induce translational suppression or direct mRNA cleavage. Similar to regular mRNAs, the expression of miRNAs is highly regulated. Their expression pattern could provide critical clues to understanding miRNA functions. However, many previously identified miRNA families have multiple paralogous loci. Within each family, different members are often closely related and sometimes give rise to identical miRNAs. This poses critical challenges in the analysis of individual miRNA genes. This chapter describes several methods that are commonly used for miRNA expression analysis, including high-throughput sequencing, microarrays, and briefly discusses qRT-PCR, northern blotting, and other approaches used for data validation.

An array platform for identification of stress-responsive microRNAs in plants

MicroRNAs (miRNAs) are approximately 22-nucleotide (nt)-long non-coding RNAs that play a key role in plant development and abiotic stresses. We have developed a simple but effective array platform for profiling plant miRNAs from various plant species. The array is composed of 188 non-redundant miRNA probes that can detect both conserved and species-specific miRNAs from most plant species, including Arabidopsis, rice, and poplar. In this chapter, we describe a protocol for developing the miRNA array platform, which can be used to identify stress-responsive miRNAs in diverse plant species. Profiling of miRNAs in tobacco seedlings exposed to different abiotic stress conditions has revealed that a number of miRNAs, miR398, miR399, miR408, miR156, miR164, and miR168, were responsive to stresses. This comprehensive and easy-to-follow protocol will be useful for studying roles of miRNAs in plant stress response.

Genetic engineering for modern agriculture: challenges and perspectives

Abiotic stress conditions such as drought, heat, or salinity cause extensive losses to agricultural production worldwide. Progress in generating transgenic crops with enhanced tolerance to abiotic stresses has nevertheless been slow. The complex field environment with its heterogenic conditions, abiotic stress combinations, and global climatic changes are but a few of the challenges facing modern agriculture. A combination of approaches will likely be needed to significantly improve the abiotic stress tolerance of crops in the field. These will include mechanistic understanding and subsequent utilization of stress response and stress acclimation networks, with careful attention to field growth conditions, extensive testing in the laboratory, greenhouse, and the field; the use of innovative approaches that take into consideration the genetic background and physiology of different crops; the use of enzymes and proteins from other organisms; and the integration of QTL mapping and other genetic and breeding tools.

Dehydration tolerance in plants

Dehydration tolerance in plants is an important but understudied component of the complex phenotype of drought tolerance. Most plants have little capacity to tolerate dehydration; most die at leaf water potentials between -5 and -10 MPa. Some of the non-vascular plants and a small percentage (0.2%) of vascular plants, however, can survive dehydration to -100 MPa and beyond, and it is from studying such plants that we are starting to understand the components of dehydration tolerance in plants. In this chapter we define what dehydration tolerance is and how it can be assessed, important prerequisites to understanding the response of a plant to water loss. The metabolic and mechanical consequences of cellular dehydration in plants prelude a discussion on the role that gene expression responses play in tolerance mechanisms. We finally discuss the key biochemical aspects of tolerance focusing on the roles of carbohydrates, late embryogenesis abundant and heat shock proteins, reactive oxygen scavenging (ROS) pathways, and novel transcription factors. It is clear that we are making significant advances in our understanding of dehydration tolerance and the added stimulus of new model systems will speed our abilities to impact the search for new strategies to improve drought tolerance in major crops.

Analysis of small RNA populations using hybridization to DNA tiling arrays

Small RNA (sRNA) populations extracted from Arabidopsis plants submitted or not to biotic stress, were reverse-transcribed into cDNAs, and these were subsequently hybridized after labelling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by Massive Parallel Sequence Signature (MPSS) in the case of untreated plants, but differed substantially after stress treatment. These results demonstrate the utility of hybridization to DNA tiling arrays to detect major changes in small RNA populations.

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

Low-oxygen (hypoxia) stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from hypoxia-treated and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from three families. Hypoxia resulted in changes to the abundance of 46 miRNAs from 19 families, and all three tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the hypoxia-responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to hypoxia, and that a major signal for these responses is likely to be dependent on mitochondrial function.

Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa)

BACKGROUND

Regulation of gene expression by microRNAs (miRNAs) plays a crucial role in many developmental and physiological processes in plants. miRNAs act to repress expression of their target genes via mRNA cleavage or translational repression. Dozens of miRNA families have been identified in rice, 21 of which are conserved between rice and Arabidopsis. miR172 is a conserved miRNA family which has been shown to regulate expression of APETALA2 (AP2)-like transcription factors in Arabidopsis and maize. The rice genome encodes five AP2-like genes predicted to be targets of miR172. To determine whether these rice AP2-like genes are regulated by miR172 and investigate the function of the target genes, we studied the effect of over-expressing two members of the miR172 family on rice plant development.

RESULTS

Analysis of miR172 expression showed that it is most highly expressed in late vegetative stages and developing panicles. Analyses of expression of three miR172 targets showed that SUPERNUMERARY BRACT (SNB) and Os03g60430 have high expression in developing panicles. Expression of miR172 was not inversely correlated with expression of its targets although miR172-mediated cleavage of SNB was detected by 5' rapid amplification of cDNA ends (RACE). Over-expression of miR172b in rice delayed the transition from spikelet meristem to floral meristem, and resulted in floral and seed developmental defects, including changes to the number and identity of floral organs, lower fertility and reduced seed weight. Plants over-expressing miR172b not only phenocopied the T-DNA insertion mutant of SNB but showed additional defects in floret development not seen in the snb mutant. However SNB expression was not reduced in the miR172b over-expression plants.

CONCLUSIONS

The phenotypes resulting from over-expression of miR172b suggests it represses SNB and at least one of the other miR172 targets, most likely Os03g60430, indicating roles for other AP2-like genes in rice floret development. miR172 and the AP2-like genes had overlapping expression patterns in rice and their expression did not show an obvious negative correlation. There was not a uniform decrease in the expression of the AP2-like miR172 target mRNAs in the miR172b over-expression plants. These observations are consistent with miR172 functioning via translational repression or with expression of the AP2-like genes being regulated by a negative feedback loop.

UV-B-responsive microRNAs in Populus tremula

MicroRNAs (miRNAs) play vital roles in down-regulating gene expression at the post-transcriptional level. A set of 24 UV-B stress-responsive miRNAs (13 up-regulated and 11 down-regulated) was identified in Populus tremula plantlet by expression profiling with our in-house miRNA filter array. Six of the UV-B-responsive miRNA and their corresponding target genes were verified for their expressions by RNA blotting and quantitative reverse transcription PCR (qRT-PCR), respectively. The predicted target genes for these miRNAs encode diverse proteins including transcription factors and phytohormone signal-related proteins. Promoter analysis of the UV-B-responsive miRNAs revealed the presence of many light-relevant cis-elements. However, these cis-elements were not necessarily specific to the promoters of UV-responsive miRNAs, indicating that other machinery may be involved in the regulation of UV-responsive miRNAs. Finally, a model was developed to describe the potential regulatory networks mediated by the UV-B-responsive miRNAs in P. tremula. These results provide new insights into the understanding of miRNAs as ubiquitous regulators in plant response to UV-B and other stresses.

Active DNA demethylation mediated by DNA glycosylases

Active DNA demethylation is involved in many vital developmental and physiological processes of plants and animals. Recent genetic and biochemical studies in Arabidopsis have demonstrated that a subfamily of DNA glycosylases function to promote DNA demethylation through a base excision-repair pathway. These specialized bifunctional DNA glycosylases remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, resulting in a gap that is then filled with an unmethylated cytosine nucleotide by as yet unknown DNA polymerase and ligase enzymes. Evidence suggests that active DNA demethylation in mammalian cells is also mediated at least in part by a base excision repair pathway where the AID/Apobec family of deaminases convert 5-methylcytosine to thymine followed by G/T mismatch repair by the DNA glycosylase MBD4 or TDG. This review also discusses other possible mechanisms of active DNA demethylation, how genome DNA methylation status might be sensed to regulate the expression of demethylase genes, and the targeting of demethylases by small RNAs.

A genome-wide characterization of microRNA genes in maize

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

PMRD: plant microRNA database

MicroRNAs (miRNA) are approximately 21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.

Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant

Auxin is one of the central hormones in plants, and auxin response factor (ARF) is a key regulator in the early auxin response. MicroRNAs (miRNAs) play an essential role in auxin signal transduction, but knowledge remains limited about the regulatory network between miRNAs and protein-coding genes (e.g. ARFs) involved in auxin signalling. In this study, we used a novel auxin-resistant rice mutant with plethoric root defects to investigate the miRNA expression patterns using microarray analysis. A number of miRNAs showed reduced auxin sensitivity in the mutant compared with the wild type, consistent with the auxin-resistant phenotype of the mutant. Four miRNAs with significantly altered expression patterns in the mutant were further confirmed by Northern blot, which supported our microarray data. Clustering analysis revealed some novel auxin-sensitive miRNAs in roots. Analysis of miRNA duplication and expression patterns suggested the evolutionary conservation between miRNAs and protein-coding genes. MiRNA promoter analysis suggested the possibility that most plant miRNAs might share the similar transcriptional mechanisms with other non-plant eukaryotic genes transcribed by RNA polymerase II. Auxin response elements were proved to be more frequently present in auxin-related miRNA promoters. Comparative analysis of miRNA and protein-coding gene expression datasets uncovered many reciprocally expressed miRNA-target pairs, which could provide some hints for miRNA downstream analysis. Based on these findings, we also proposed a feedback circuit between miRNA(s) and ARF(s). The results presented here could serve as the basis for further in-depth studies of plant miRNAs involved in auxin signalling.

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

Background

MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs.

Results

High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition.

Conclusion

Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

BACKGROUND

MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs.

RESULTS

High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition.

CONCLUSION

Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana

MicroRNAs (miRNAs) are endogenous small RNAs of ~22 nucleotides (nt) that play a key role in down regulation of gene expression at the post-transcriptional level in plants and animals. Various studies have identified numerous miRNAs that were either up regulated or down regulated upon stress treatment. Here, we sought to understand the temporal regulation of miRNAs in different plant species under abscisic acid (ABA) and salt (NaCl) stress. Our results showed that the regulation of miR398 in response to ABA and salt stress was more dynamic in plants than previously reported. In poplars, miR398 was first induced upon 3-4 h of ABA or salt stress. However, this induction declined after 48 h and finally accumulated again over a prolonged stress (72 h). We referred to this kind of regulation as dynamic regulation. In contrast, such dynamic regulation of miR398 under salt stress was completely absent in Arabidopsis, in which miR398 was steadily and unidirectionally suppressed. Interestingly, ABA treatment caused a deviate dynamic regulation of miR398 in Arabidopsis, showing an opposite response as compared to that in poplars. We referred to the difference in regulation between Arabidopsis and poplars as differential regulation. Furthermore, the expression of the miR398 target, copper superoxide dismutase1 (CSD1), was in reverse correlation with the miR398 level, suggesting a control of this specific target expression predominantly by miR398 under abiotic stress. Together, these data consistently show a correlated regulation between miR398 and its representative target, CSD1, by ABA and salt stresses, and raise the possibility that regulation of miRNAs in plants is twofold: a dynamic regulation within a plant species and a differential regulation between different plant species.

Cloning and characterization of small non-coding RNAs from grape

Small non-coding RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are effectors of regulatory pathways underlying plant development, metabolism, and responses to biotic and abiotic stresses. To address the nature and functions of these regulators in grapevine (Vitis vinifera L.), we have produced a small RNA library from mixed-stage grape berries. Thirteen conserved miRNAs belonging to nine miRNA families, a non-conserved miRNA, and four putative non-conserved miRNAs were isolated, and their expression and targets are described. Experimentally validated targets of non-conserved miRNAs and putative miRNAs included three genes encoding NB-LRR proteins and a gene encoding a heavy metal ion transport/detoxification protein. Of the endogenous and pathogen-derived siRNAs that were also isolated, four endogenous siRNAs mapped to genes encoding RD22-like proteins and two to a gene encoding a cytokinin synthase. The siRNA id65 targeted the cytokinin synthase gene transcript with antisense complementarity, and was specifically expressed in mature berries, in which, by contrast, expression of the cytokinin synthase gene was strongly repressed. 5' RACE revealed that the transcript of this gene was processed in 21 nucleotide increments from the id65 cleavage site, and that further cleavage was mediated by secondary siRNAs in cis. These results indicate that grapevine miRNA- and siRNA-mediated regulatory circuits have evolved to comprise processes associated with defence and fruit ripening, and broaden the range of small RNA-mediated regulation, which was previously associated with auxin, ABA, gibberellins and jasmonate, to encompass cytokinin metabolism.

A novel real-time polymerase chain reaction method for high throughput quantification of small regulatory RNAs

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are important players of both transcriptional and post-transcriptional gene silencing networks. In order to investigate the functions of these small regulatory RNAs, a system with high sensitivity and specificity is desperately needed to quantitatively detect their expression levels in cells and tissues. However, their short length of 19-24 nucleotides and strong similarity between related species render most conventional expression analysis methods ineffective. Here we describe a novel primer for small RNA-specific reverse transcription and a new TaqMan technology-based real-time method for quantification of small RNAs. This method is capable of quantifying miRNA and siRNA in the femtomolar range, which is equivalent to ten copies per cell or fewer. The assay has a high dynamic range and provides linear readout of miRNA concentrations that span seven orders of magnitude and allows us to discriminate small RNAs that differ by as little as one nucleotide. Using the new method, we investigated the expression pattern of gma-miRMON1, a novel miRNA identified from soybean leaves. The results were consistent with our results obtained from Northern blot analysis of gma-miRMON1 and Affymetrix microarray analysis of the gma-miRMON1 precursor, suggesting that the new method can be used in transcription profiling.

MicroPC (microPC): A comprehensive resource for predicting and comparing plant microRNAs

Background

Plant microRNA (miRNA) has an important role in controlling gene regulation in various biological processes such as cell development, signal transduction, and environmental responses. While information on plant miRNAs and their targets is widely available, accessible online plant miRNA resources are limited; most of them are intended for economically important crops or plant model organisms. With abundant sequence data of numerous plants in public databases such as NCBI and PlantGDB, the identification of their miRNAs and targets would benefit researchers as a central resource for the comparative studies of plant miRNAs.

Results

MicroPC (μPC) is an online plant miRNA resource resulted from large-scale Expressed Sequence Tag (EST) analysis. It consists of 4,006 potential miRNA candidates in 128 families of 125 plant species and 2,995 proteins (4,953 EST sequences) potentially targeted by 78 families of miRNA candidates. In addition, it is incorporated with 1,727 previously reported plant mature miRNA sequences from miRBase. The μPC enables users to compare stored mature or precursor miRNAs and user-supplied sequences among plant species. The search utility allows users to investigate the predicted miRNAs and miRNA targets in detail via various search options such as miRNA family and plant species. To enhance the database usage, the prediction utility provides interactive steps for determining a miRNA or miRNA targets from an input nucleotide sequence and links the prediction results to their homologs in the μPC.

Conclusion

The μPC constitutes the first online resource that enables users to comprehensively compare and predict plant miRNAs and their targets. It imparts a basis for further research on revealing miRNA conservation, function, and evolution across plant species and classification. The μPC is available at http://www.biotec.or.th/isl/micropc.

Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing

Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time polymerase chain reaction platform that allows rapid and sensitive quantification of 177 Arabidopsis primary miR transcripts (pri-miRs). The platform was used to detect phosphorus (P) or nitrogen (N) status-responsive pri-miR species. Several pri-miR169 species as well as pri-miR398a were found to be repressed during N limitation, whereas during P limitation, pri-miR778, pri-miR827, and pri-miR399 species were induced and pri-miR398a was repressed. The corresponding responses of the biologically active, mature miRs were confirmed using specific stem-loop reverse transcription primer quantitative polymerase chain reaction assays and small RNA sequencing. Interestingly, the latter approach also revealed high abundance of some miR star strands. Bioinformatic analysis of small RNA sequences with a modified miRDeep algorithm led to the identification of the novel P limitation-induced miR2111, which is encoded by two loci in the Arabidopsis genome. Furthermore, miR2111, miR169, a miR827-like sequence, and the abundances of several miR star strands were found to be strongly dependent on P or N status in rapeseed (Brassica napus) phloem sap, flagging them as candidate systemic signals. Taken together, these results reveal the existence of complex small RNA-based regulatory networks mediating plant adaptation to mineral nutrient availability.

Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families

MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) have emerged as important regulators of gene expression in higher eukaryotes. Recent studies indicate that genomes in higher plants encode lineage-specific and species-specific miRNAs in addition to the well-conserved miRNAs. Leguminous plants are grown throughout the world for food and forage production. To date the lack of genomic sequence data has prevented systematic examination of small RNAs in leguminous plants. Medicago truncatula, a diploid plant with a near-completely sequenced genome has recently emerged as an important model legume. We sequenced a small RNA library generated from M. truncatula to identify not only conserved miRNAs but also novel small RNAs, if any. Eight novel small RNAs were identified, of which four (miR1507, miR2118, miR2119 and miR2199) are annotated as legume-specific miRNAs because these are conserved in related legumes. Three novel transcripts encoding TIR-NBS-LRR proteins are validated as targets for one of the novel miRNA, miR2118. Small RNA sequence analysis coupled with the small RNA blot analysis, confirmed the expression of around 20 conserved miRNA families in M. truncatula. Fifteen transcripts have been validated as targets for conserved miRNAs. We also characterized Tas3-siRNA biogenesis in M. truncatula and validated three auxin response factor (ARF) transcripts that are targeted by tasiRNAs. These findings indicate that M. truncatula and possibly other related legumes have complex mechanisms of gene regulation involving specific and common small RNAs operating post-transcriptionally.

Molecular mechanisms underlying plant memory in JA-mediated defence responses

Plants must respond to biotic and abiotic challenges to optimize their Darwinian fitness in nature. Many of these challenges occur repeatedly during a plant's lifetime, and their sequence and timing can profoundly influence the fitness outcome of a plant's response. The ability to perceive, store and recall previous stressful events is likely useful for efficient, rapid and cost-effective responses, but we know very little about the mechanisms involved. Using jasmonate-elicited anti-herbivore defence responses as an example, we consider how 'memories' of previous attacks could be created in (1) the biosynthetic processes involved in the generation of the oxylipin bursts elicited by herbivore attacks; (2) the perception of oxylipins and their transduction into cellular events by transcription factors and transcriptional activators; and (3) the role of small RNAs in the formation of long-term stress imprints in plants.

The multilevel and dynamic interplay between plant and pathogen

Phytopathogens invade into plant apoplast and proliferate by assimilating nutrition from plant cells. Plants depend on sophisticated defensive strategies to resist this invasion. Therefore, pathogenic disease and plant disease resistance are two opposite phases. Fascinating molecular mechanisms uncovered that interactions between plant and pathogen are multilevel and dynamic processes. On one side, plant immunity system contains multiple layers mainly including the perception of common pathogen- associated molecular patterns (PAMPs) using distinct cell-surface pattern-recognition receptors (PRRs) to activate intracellular signaling pathways for broad-spectrum immunity, and the recognition of pathogen virulence proteins by the specific intracellular disease resistance (R) proteins for cultivar-specific immunity. On the opposite side, the bacterial pathogens employ virulence factors, such as phytotoxin and type III effectors (T3SEs) to interfere with the host immunity in different levels. Meanwhile, natural selection drives plants and pathogens to evolve new strategies to confront with each other constantly. The present review highlights recent insights about Arabidopsis immunity and mechanisms for Pseudomonas syringae to counteract this immunity to give a full understanding of plant-pathogen interactions.

Evolution of MIR168 paralogs in Brassicaceae

Background

In plants, expression of ARGONAUTE1 (AGO1), the catalytic subunit of the RNA-Induced Silencing Complex responsible for post-transcriptional gene silencing, is controlled through a feedback loop involving the miR168 microRNA. This complex auto-regulatory loop, composed of miR168-guided AGO1-catalyzed cleavage of AGO1 mRNA and AGO1-mediated stabilization of miR168, was shown to ensure the maintenance of AGO1 homeostasis that is pivotal for the correct functioning of the miRNA pathway.

Results

We applied different approaches to studying the genomic organization and the structural and functional evolution of MIR168 homologs in Brassicaeae. A whole genome comparison of Arabidopsis and poplar, phylogenetic footprinting and phylogenetic reconstruction were used to date the duplication events originating MIR168 homologs in these genomes. While orthology was lacking between Arabidopsis and poplar MIR168 genes, we successfully isolated orthologs of both loci present in Arabidopsis (MIR168a and MIR168b) from all the Brassicaceae species analyzed, including the basal species Aethionema grandiflora, thus indicating that (1) independent duplication events took place in Arabidopsis and poplar lineages and (2) the origin of MIR168 paralogs predates both the Brassicaceae radiation and the Arabidopsis alpha polyploidization. Different phylogenetic footprints, corresponding to known functionally relevant regions (transcription starting site and double-stranded structures responsible for microRNA biogenesis and function) or for which functions could be proposed, were found to be highly conserved among MIR168 homologs. Comparative predictions of the identified microRNAs also indicate extreme conservation of secondary structure and thermodynamic stability.

Conclusion

We used a comparative phylogenetic footprinting approach to identify the structural and functional constraints that shaped MIR168 evolution in Brassicaceae. Although their duplication happened at least 40 million years ago, we found evidence that both MIR168 paralogs have been maintained throughout the evolution of Brassicaceae, most likely functionally as indicated by the extremely high conservation of functionally relevant regions, predicted secondary structure and thermodynamic profile. Interestingly, the expression patterns observed in Arabidopsis indicate that MIR168b underwent partial subfunctionalization as determined by the experimental characterization of its expression pattern provided in this study. We found further evolutionary evidence that pre-miR168 lower stem (the RNA-duplex structure adjacent to the miR-miR* stem) is significantly longer than animal lower stems and probably plays a relevant role in multi-step miR168 biogenesis.

[Advances in study of plant miRNAs under stressed environmental conditions]

Biotic and abiotic stresses influence plant growth and cause great loss to crop yield. In the long course of evolution, plants have developed intricate biological mechanism to resist stressed conditions. Under various stressed conditions, not only the protein-coding genes, but also the non-protein-coding genes were induced for response. More and more researches showed that the transcripts of these non-protein-coding genes played important role in regulation of gene expression. miRNA is one of the groups in these no-coding regulatory small RNAs. Recent findings showed that in order to resist the biotic and abiotic stresses, expression of microRNA (miRNA) genes will be induced and their transcripts (miRNAs) can regulate gene expression by guiding target mRNA cleavage or translation inhibition. This paper focused on the advances of plant miRNAs research in stressed conditions, especially induced expression of miRNA and target gene regulation and its role on adaptation under stressed conditions. Then, the methods of miRNA researches in stressed environments are discussed.

Molecular mechanisms in response to phosphate starvation in rice

Phosphorus is one of the most important elements that significantly affect plant growth and metabolism. Among the macro-nutrients, phosphorus is the least available to the plants as major phosphorus content of the fertiliser is sorbed by soil particles. An increased knowledge of the regulatory mechanisms controlling plant's phosphorus status is vital for improving phosphorus uptake and P-use efficiency and for reducing excessive input of fertilisers, while maintaining an acceptable yield. Phosphorus use efficiency has been studied using forward and reverse genetic analyses of mutants, quantitative genomic approaches and whole plant physiology but all these studies need to be integrated for a clearer understanding. We provide a critical overview on the molecular mechanisms and the components involved in the plant during phosphorus starvation. Then we summarize the information available on the genes and QTLs involved in phosphorus signalling and also the methods to estimate total phosphate in plant tissue. Also, an effort is made to build a comprehensive picture of phosphorus uptake, homeostasis, assimilation, remobilization, its deposition in the grain and its interaction with other micro- and macro-nutrients as well as phytohormones.

Origin, biogenesis, and activity of plant microRNAs

MicroRNAs (miRNAs) are key posttranscriptional regulators of eukaryotic gene expression. Plants use highly conserved as well as more recently evolved, species-specific miRNAs to control a vast array of biological processes. This Review discusses current advances in our understanding of the origin, biogenesis, and mode of action of plant miRNAs and draws comparisons with their metazoan counterparts.

Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis

MicroRNA398 targets two Cu/Zn superoxide dismutases (CSD1 and CSD2) in higher plants. Previous investigations revealed both decreased miR398 expression during high Cu(2+) or paraquat stress and increased expression under low Cu(2+) or high sucrose in the growth medium. Here, we show that additional abiotic stresses such as ozone and salinity also affect miR398 levels. Ozone fumigation decreased miR398 levels that were gradually restored to normal levels after relieved from the stress. Furthermore, miR398 levels decreased in Arabidopsis leaves infiltrated with avirulent strains of Pseudomonas syringae pv. tomato, Pst DC3000 (avrRpm1 or avrRpt2) but not the virulent strain Pst DC3000. To our knowledge, miR398 is the first miRNA shown to be down-regulated in response to biotic stress (P. syringae). CSD1, but not CSD2, mRNA levels were negatively correlated with miR398 levels during ozone, salinity and biotic stress, suggesting that CSD2 regulation is not strictly under miR398 control during diverse stresses. Overall, this study further establishes a link between oxidative stress and miR398 in Arabidopsis.