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

RNA regulation in plant abiotic stress responses

RNA regulatory processes such as transcription, degradation and stabilization control are the major mechanisms that determine the levels of mRNAs in plants. Transcriptional and post-transcriptional regulations of RNAs are drastically altered during plant stress responses. As a result of these molecular processes, plants are capable of adjusting to changing environmental conditions. Understanding the role of these mechanisms in plant stress responses is important and necessary for the engineering of stress-tolerant plants. Recent studies in the area of RNA regulation have increased our understanding of how plants respond to environmental stresses. This review highlights recent progress in RNA regulatory processes that are involved in plant stress responses, such as small RNAs, alternative splicing, RNA granules and RNA-binding proteins. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

Roles for farnesol and ABA in Arabidopsis flower development

The Arabidopsis FOLK (At5g58560) gene encodes farnesol kinase, which phosphorylates farnesol to farnesyl phosphate. Loss-of-function mutations in the FOLK gene are associated with enhanced sensitivity to abscisic acid (ABA), suggesting that FOLK negatively regulates ABA signaling. Moreover, folk flowers develop supernumerary carpels under water stress, providing evidence for a molecular link between farnesol metabolism, abiotic stress signaling and flower development. Here, we show that farnesol increases ABA sensitivity and that ABA affects flower development in Arabidopsis.

Transcriptional analysis of soybean root response to Fusarium virguliforme, the causal agent of sudden death syndrome

Sudden death syndrome (SDS) of soybean can be caused by any of four distinct Fusarium species, with F. virguliforme and F. tucumaniae being the main casual agents in North and South America, respectively. Although the fungal tissue is largely confined to the roots, the fungus releases a toxin that is translocated to leaf tissues, in which it causes interveinal chlorosis and necrosis leading to scorching symptoms and possible defoliation. In this study, we report on an Affymetrix analysis measuring transcript abundances in resistant (PI 567.374) and susceptible (Essex) roots upon infection by F. virguliforme, 5 and 7 days postinoculation. Many of the genes with increased expression were common between resistant and susceptible plants (including genes related to programmed cell death, the phenylpropanoid pathway, defense, signal transduction, and transcription factors), but some genotype-specific expression was noted. Changes in small (sm)RNA levels between inoculated and mock-treated samples were also studied and implicate a role for these molecules in this interaction. In total, 2,467 genes were significantly changing in the experiment, with 1,694 changing in response to the pathogen; 93 smRNA and 42 microRNA that have putative soybean gene targets were identified from infected tissue. Comparing genotypes, 247 genes were uniquely modulating in the resistant host, whereas 378 genes were uniquely modulating in the susceptible host. Comparing locations of differentially expressed genes to known resistant quantitative trait loci as well as identifying smRNA that increased while their putative targets decreased (or vice versa) allowed for the narrowing of candidate SDS defense-associated genes.

Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis

The majority of plants are able to form the arbuscular mycorrhizal (AM) symbiosis in association with AM fungi. During symbiosis development, plant cells undergo a complex reprogramming resulting in profound morphological and physiological changes. MicroRNAs (miRNAs) are important components of the regulatory network of plant cells. To unravel the impact of miRNAs and miRNA-mediated mRNA cleavage on root cell reprogramming during AM symbiosis, we carried out high-throughput (Illumina) sequencing of small RNAs and degradome tags of Medicago truncatula roots. This led to the annotation of 243 novel miRNAs. An increased accumulation of several novel and conserved miRNAs in mycorrhizal roots suggest a role of these miRNAs during AM symbiosis. The degradome analysis led to the identification of 185 root transcripts as mature miRNA and also miRNA*-mediated mRNA cleavage targets. Several of the identified miRNA targets are known to be involved in root symbioses. In summary, the increased accumulation of specific miRNAs and the miRNA-mediated cleavage of symbiosis-relevant genes indicate that miRNAs are an important part of the regulatory network leading to symbiosis development.

The Arabidopsis mitochondria-localized pentatricopeptide repeat protein PGN functions in defense against necrotrophic fungi and abiotic stress tolerance

Pentatricopeptide repeat (PPR) proteins (PPRPs) are encoded by a large gene family in Arabidopsis (Arabidopsis thaliana), and their functions are largely unknown. The few studied PPRPs are implicated in different developmental processes through their function in RNA metabolism and posttranscriptional regulation in plant organelles. Here, we studied the functions of Arabidopsis PENTATRICOPEPTIDE REPEAT PROTEIN FOR GERMINATION ON NaCl (PGN) in plant defense and abiotic stress responses. Inactivation of PGN results in susceptibility to necrotrophic fungal pathogens as well as hypersensitivity to abscisic acid (ABA), glucose, and salinity. Interestingly, ectopic expression of PGN results in the same phenotypes as the pgn null allele, indicating that a tight regulation of the PGN transcript is required for normal function. Loss of PGN function dramatically enhanced reactive oxygen species accumulation in seedlings in response to salt stress. Inhibition of ABA synthesis and signaling partially alleviates the glucose sensitivity of pgn, suggesting that the mutant accumulates high endogenous ABA. Accordingly, induction of NCED3, encoding the rate-limiting enzyme in stress-induced ABA biosynthesis, is significantly higher in pgn, and the mutant has higher basal ABA levels, which may underlie its phenotypes. The pgn mutant has altered expression of other ABA-related genes as well as mitochondria-associated transcripts, most notably elevated levels of ABI4 and ALTERNATIVE OXIDASE1a, which are known for their roles in retrograde signaling induced by changes in or inhibition of mitochondrial function. These data, coupled with its mitochondrial localization, suggest that PGN functions in regulation of reactive oxygen species homeostasis in mitochondria during abiotic and biotic stress responses, likely through involvement in retrograde signaling.

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

BACKGROUND

Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth.

RESULTS

A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa).

CONCLUSIONS

This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.

Identification of potential microRNAs and their targets in Brassica rapa L

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20(th) position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

Abscisic acid signal off the STARting block

The year 2009 marked a real turnaround in our understanding of the mode of abscisic acid (ABA) action. Nearly 25 years had elapsed since the first biochemical detection of ABA-binding proteins in the plasmalemma of Vicia guard cells was reported. This recent--and laudable--achievement is owed largely to the discovery of the soluble ABA receptors whose major interacting proteins happen to be some of the most well-established components of earliest steps in ABA signaling. These soluble receptors, with the double name of PYRABACTIN RESISTANCE (PYR) or REGULATORY COMPONENT OF ABA RECEPTOR (RCAR), are a family of Arabidopsis proteins of about 150-200 amino acids that share a conserved START domain. The ABA signal transduction circuitry under non-stress conditions is muted by the clade A protein phosphatases 2C (PP2C) (notably HAB1, ABI1, and ABI2). During the initial steps of ABA signaling, the binding of the hormone to the receptor induces a conformational change in the latter that allows it to sequester the PP2Cs. This excludes them from the negative regulation of the downstream ABA-activated kinases (OST1/SnRK2.6/SRK2E, SnRK2.2, and SnRK2.3), thus unleashing the pathway by freeing them to phosphorylate downstream targets that now include several b-ZIP transcription factors, ion channels (SLAC1, KAT1), and a NADPH oxidase (AtrbohF). The discovery of this family of soluble receptors and the rich insight already gained from structural studies of their complexes with different isoforms of ABA, PP2C, and the synthetic agonist pyrabactin lay the foundation towards rational design of chemical switches that can bolster drought hardiness in plants.

Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development

The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression.

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

Polyploidy has occurred throughout plant evolution and can result in considerable changes to gene expression when it takes place and over evolutionary time. Little is known about the effects of abiotic stress conditions on duplicate gene expression patterns in polyploid plants. We examined the expression patterns of 60 duplicated genes in leaves, roots and cotyledons of allotetraploid Gossypium hirsutum in response to five abiotic stress treatments (heat, cold, drought, high salt and water submersion) using single-strand conformation polymorphism assays, and 20 genes in a synthetic allotetraploid. Over 70% of the genes showed stress-induced changes in the relative expression levels of the duplicates under one or more stress treatments with frequent variability among treatments. Twelve pairs showed opposite changes in expression levels in response to different abiotic stress treatments. Stress-induced expression changes occurred in the synthetic allopolyploid, but there was little correspondence in patterns between the natural and synthetic polyploids. Our results indicate that abiotic stress conditions can have considerable effects on duplicate gene expression in a polyploid, with the effects varying by gene, stress and organ type. Differential expression in response to environmental stresses may be a factor in the preservation of some duplicated genes in polyploids.

siRNA-mediated chromatin maintenance and its function in Arabidopsis thaliana

Small interfering RNAs (siRNAs) are widespread in various eukaryotes and are involved in maintenance of chromatin modifications, especially those for inert states represented by covalent modifications of cytosine and/or histones. In contrast to mammalian genomes, in which cytosine methylation is restricted mostly to CG dinucleotide sequences, inert chromatin in plants carries cytosine methylation in all sequence contexts, and siRNAs play a major role in directing cytosine methylation through the process of RNA-directed DNA methylation. Recent advances in this field have revealed that siRNA-mediated maintenance of inert chromatin has diverse roles in development as well as in plant responses to the environment. Various proteinaceous factors required for siRNA-mediated chromatin modification have been identified in Arabidopsis thaliana, and much effort has been invested in understanding their function and interaction, resulting in the assignment of many of these factors to specific biochemical activities and engagement with specific steps such as transcription of intergenic RNAs, RNA processing, and cytosine methylation. However, the precise functions of a number of factors remain undesignated, and interactions of distinct pathways for siRNA-mediated chromatin modification are largely unknown. In this review, we summarize the roles of siRNA-mediated chromatin modification in various biological processes of A. thaliana, and present some speculation on the functions and interactions of silencing factors that, while not yet assigned to defined biochemical activities, have been loosely assigned to specific events in siRNA-mediated chromatin modification pathways. Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

HC-Pro silencing suppressor significantly alters the gene expression profile in tobacco leaves and flowers

BACKGROUND

RNA silencing is used in plants as a major defence mechanism against invasive nucleic acids, such as viruses. Accordingly, plant viruses have evolved to produce counter defensive RNA-silencing suppressors (RSSs). These factors interfere in various ways with the RNA silencing machinery in cells, and thereby disturb the microRNA (miRNA) mediated endogene regulation and induce developmental and morphological changes in plants. In this study we have explored these effects using previously characterized transgenic tobacco plants which constitutively express (under CaMV 35S promoter) the helper component-proteinase (HC-Pro) derived from a potyviral genome. The transcript levels of leaves and flowers of these plants were analysed using microarray techniques (Tobacco 4 × 44 k, Agilent).

RESULTS

Over expression of HC-Pro RSS induced clear phenotypic changes both in growth rate and in leaf and flower morphology of the tobacco plants. The expression of 748 and 332 genes was significantly changed in the leaves and flowers, respectively, in the HC-Pro expressing transgenic plants. Interestingly, these transcriptome alterations in the HC-Pro expressing tobacco plants were similar as those previously detected in plants infected with ssRNA-viruses. Particularly, many defense-related and hormone-responsive genes (e.g. ethylene responsive transcription factor 1, ERF1) were differentially regulated in these plants. Also the expression of several stress-related genes, and genes related to cell wall modifications, protein processing, transcriptional regulation and photosynthesis were strongly altered. Moreover, genes regulating circadian cycle and flowering time were significantly altered, which may have induced a late flowering phenotype in HC-Pro expressing plants. The results also suggest that photosynthetic oxygen evolution, sugar metabolism and energy levels were significantly changed in these transgenic plants. Transcript levels of S-adenosyl-L-methionine (SAM) were also decreased in these plants, apparently leading to decreased transmethylation capacity. The proteome analysis using 2D-PAGE indicated significantly altered proteome profile, which may have been both due to altered transcript levels, decreased translation, and increased proteosomal/protease activity.

CONCLUSION

Expression of the HC-Pro RSS mimics transcriptional changes previously shown to occur in plants infected with intact viruses (e.g. Tobacco etch virus, TEV). The results indicate that the HC-Pro RSS contributes a significant part of virus-plant interactions by changing the levels of multiple cellular RNAs and proteins.

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

BACKGROUND

Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs) are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat.

RESULTS

In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP) 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress.

CONCLUSION

Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.

Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice

Small silencing RNAs (sRNAs) are non-coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem-loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted-repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer-like (DCL)3- and RNA-dependent RNA polymerase (RDR)2-dependent MITE-derived ra-siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single-stranded stem-loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self-pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression.

Auxin and salicylic acid signalings counteract the regulation of adaptive responses to stress

In a previous publication, we performed a phenotypic characterization of Arabidopsis auxin receptor mutants grown under oxidative and salt stresses. In particular, the double mutant for TIR1 and AFB2 receptors, tir1 afb2 displayed increased tolerance against salinity measured as germination rate, root elongation and chlorophyll content. Here, it is reported that salicylic acid (SA)-treated tir1 afb2 mutant shows enhanced transcript level of a pathogenesis related gene, PR1. In addition, SA-mediated repression of auxin signaling was also demonstrated. All these findings allow us to suggest that down-regulation of auxin signaling may be a common mechanism within the plant adaptative response against both biotic and abiotic stresses.

Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana

Nitrogen (N) is an essential macronutrient for plants. In nature, N cycles between different inorganic and organic forms some of which can serve as nutrients for plants. The inorganic N forms nitrate and ammonium are the most important sources of N for plants. However, plants can also uptake and use organic N forms such as amino acids and urea. Besides their nutritional role, nitrate and other forms of N can also act as signals that regulate the expression of hundreds of genes causing modulation of plant metabolism, physiology, growth, and development. Although many genes and processes affected by changes in external or internal N have been identified, the molecular mechanisms involved in N sensing and signaling are still poorly understood. Classic reverse and forward genetics and more recently the advent of genomic and systems approaches have helped to characterize some of the components of the signaling pathways directing Arabidopsis responses to N. Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N.

Detection of novel human MiRNAs responding to X-ray irradiation

Up to now, more than 1048 human miRNAs have been identified. However, the recognition of new human miRNAs is becoming more and more difficult. Based on the hypothesis that the expression of some miRNAs can be induced by ionizing radiation, total RNAs of HeLa cells were isolated 1 h after exposure to 2 Gy of X-rays, and total small RNAs were enriched and sequenced by PAGE and Solexa technology, respectively. As a result, 421 kinds of known miRNAs and 337 kinds of unknown sequences were identified, among which 10 novel miRNAs were characterized by bioinformatic approach and verified by qRT-PCR. Finally, putative targets of these miRNAs were predicted by TargetScan software and compared with known proteins down-regulated by radiation. It was confirmed that some of the targets of these novel miRNAs were radiation-related proteins. These results imply that these 10 novel miRNAs are radiation-related miRNAs. This study reveals a new way to find novel miRNAs.

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks

MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, virulent and avirulent strains of Pst. We identified 15, 27 and 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, Pst DC3000 EV and Pst DC3000 avrRpt2 infections, respectively. In particular, a group of bacteria-regulated miRNAs targets protein-coding genes that are involved in plant hormone biosynthesis and signaling pathways, including those in auxin, abscisic acid, and jasmonic acid pathways. Our results suggest important roles of miRNAs in plant defense signaling by regulating and fine-tuning multiple plant hormone pathways. In addition, we compared the results from sequencing-based profiling of a small set of miRNAs with the results from small RNA Northern blot and that from miRNA quantitative RT-PCR. Our results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with the results from Northern blot or miRNA quantitative RT-PCR. We discussed the procedural differences between these techniques that may cause the inconsistency.

Low and high ψ ways from post-transcriptional RNA regulation to drought tolerance

Plants withstand adverse environmental effects by stress responses governed by a complex multilayer regulatory network. Besides well established transcriptional cascades posttranscriptional modifications give more plasticity to the plant's behavior under unfavorable circumstances. These modifications include various RNA alterations typically interlaced with transcriptional or translational regulation. Recent examples have been described in RNA splicing, processing, translation and degradation, some of which operate through effects of small non-coding RNAs. So far details of physiological output mechanisms affected by RNA regulation have been uncovered in a few cases only, some of those will be detailed in this review. In the well documented example of the nuclear cap binding complex (nCBC) mutants, molecular mechanisms of the regulatory switch and downstream events have been established in detail. New results directly link nCBC function to splicing, RNA processing and abscisic acid (ABA). Potential output mechanisms of this control point have also been implicated, both in fast stress responses and in developmental regulation. This latter aspect provides a new insight into how RNA regulation may contribute to acclimation by facilitating drought tolerant morphology. Recent results pinpoint the importance of cuticular structure in acclimation to drought stress at high water potential (ψ).

Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation

Here we report on the characterization of rice osa-miR827 and its two target genes, OsSPX-MFS1 and OsSPX-MFS2, which encode SPX-MFS proteins predicted to be implicated in phosphate (Pi) sensing or transport. We first show by Northern blot analysis that osa-miR827 is strongly induced by Pi starvation in both shoots and roots. Hybridization of osa-miR827 in situ confirms its strong induction by Pi starvation, with signals concentrated in mesophyll, epidermis and ground tissues of roots. In parallel, we analyzed the responses of the two OsSPX-MFS1 and OsSPX-MFS2 gene targets to Pi starvation. OsSPX-MFS1 mRNA is mainly expressed in shoots under sufficient Pi supply while its expression is reduced on Pi starvation, revealing a direct relationship between induction of osa-miR827 and down-regulation of OsSPX-MFS1. In contrast, OsSPX-MFS2 responds in a diametrically opposed manner to Pi starvation. The accumulation of OsSPX-MFS2 mRNA is dramatically enhanced under Pi starvation, suggesting the involvement of complex regulation of osa-miR827 and its two target genes. We further produced transgenic rice lines overexpressing osa-miR827 and T-DNA knockout mutant lines in which the expression of osa-miR827 is abolished. Compared with wild-type controls, both target mRNAs exhibit similar changes, their expression being reduced and increased in overexpressing and knockout lines, respectively. This suggests that OsSPX-MFS1 and OsSPX-MFS2 are both negatively regulated by osa-miR827 abundance although they respond differently to external Pi conditions. We propose that this is a complex mechanism comprising fine tuning of spatial or temporal regulation of both targets by osa-miR827.

Crucial roles of sucrose and microRNA399 in systemic signaling of P deficiency: a tale of two team players?

MicroRNAs (miRNAs) have been recognized as important regulators in plant response to nutrient deficiencies. Of particular interest is the discovery that miR399 functions systemically in the maintenance of phosphate (Pi) homeostasis in response to external Pi fluctuation. Recent studies have further implicated both miR399 and sugars (mainly sucrose) as potential signal molecules in the shoot-to-root communication of phosphorus (P) status. Given that both miR399 and sucrose are transported via the phloem, their potential interaction (or cross-talk) along the signaling pathway is especially appealing for further exploration. In this mini-review, we highlight recent progress in unraveling crucial roles of both sucrose and miR399 in P-deficiency signaling. In particular, we further discuss recent findings that photosynthetic carbon (C) assimilation and subsequent partitioning, by overriding signaling of low external Pi, act as checkpoints upstream of miR399 for the onset of a systemic P-deficiency status.

The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a robust and widely applied technique used to investigate gene expression. However, for correct analysis and interpretation of results, the choice of a suitable gene to use as an internal control is a crucial factor. These genes, such as housekeeping genes, should have a constant expression level in different tissues and across different conditions. The advances in genome sequencing have provided high-throughput gene expression analysis and have contributed to the identification of new genes, including microRNAs (miRNAs). The miRNAs are fundamental regulatory genes of eukaryotic genomes, acting on several biological functions. In this study, miRNA expression stability was investigated in different soybean tissues and genotypes as well as after abiotic or biotic stress treatments. The present study represents the first investigation into the suitability of miRNAs as housekeeping genes in plants. The transcript stability of 10 miRNAs was compared to those of six previously reported housekeeping genes for the soybean. In this study, we provide evidence that the expression stabilities of miR156b and miR1520d were the highest across the soybean experiments. Furthermore, these miRNAs genes were more stable than the most commonly protein-coding genes used in soybean gene expression studies involving RT-qPCR.

Overexpression of microRNA395c or 395e affects differently the seed germination of Arabidopsis thaliana under stress conditions

The Arabidopsis genome encodes six members of microRNA395 (miR395) family previously determined to regulate the expression of ATP sulfurylase (APS) and the sulfate transporter SULTR2;1. However, the mRNA targets for the individual miR395 family members and the biological consequences produced by target gene regulation of each miR395 remain to be identified. In this study, a transgenic approach was employed to determine the mRNA targets for each miR395 family member as well as the role each member plays in plant growth under abiotic stress conditions. Overexpression of miR395c or miR395e retarded and accelerated, respectively, the seed germination of Arabidopsis under high salt or dehydration stress conditions. Despite a single nucleotide difference between miR395c and miR395e, the cleavage of mRNA targets, APS1, APS3, APS4 and SULTR2;1, was not same in miR395c- and miR395e-overexpressing plants. These results demonstrate that a given miRNA family containing a single nucleotide difference can guide the cleavage of various mRNA targets, thereby acting as a positive or negative regulator of seed germination under stress.

Stress-induced activation of heterochromatic transcription

Constitutive heterochromatin comprising the centromeric and telomeric parts of chromosomes includes DNA marked by high levels of methylation associated with histones modified by repressive marks. These epigenetic modifications silence transcription and ensure stable inheritance of this inert state. Although environmental cues can alter epigenetic marks and lead to modulation of the transcription of genes located in euchromatic parts of the chromosomes, there is no evidence that external stimuli can globally destabilize silencing of constitutive heterochromatin. We have found that heterochromatin-associated silencing in Arabidopsis plants subjected to a particular temperature regime is released in a genome-wide manner. This occurs without alteration of repressive epigenetic modifications and does not involve common epigenetic mechanisms. Such induced release of silencing is mostly transient, and rapid restoration of the silent state occurs without the involvement of factors known to be required for silencing initiation. Thus, our results reveal new regulatory aspects of transcriptional repression in constitutive heterochromatin and open up possibilities to identify the molecular mechanisms involved.

In eukaryotic cells, DNA is packaged into chromatin that is present in two different forms named euchromatin and heterochromatin. Gene-rich euchromatin is relaxed and permissive to transcription compared with heterochromatin that essentially contains transcriptionally inert non-coding repeated DNA. The silent state associated with heterochromatin correlates with the presence of distinctive repressive epigenetic modifications. Mutations in genes required for maintenance of these epigenetic marks reactivate heterochromatin transcription, which is otherwise maintained silent in a highly stable manner. In this paper, we defined a specific temperature stress that leads to genome-wide transcriptional activation of sequences located within heterochromatin of Arabidopsis thaliana. Unexpectedly, release of silencing occurs in spite of conservation of the repressive epigenetic marks and independently of common epigenetic regulators. In addition, we provide evidence that stress-induced transcriptional activation is mostly transient, and silencing is rapidly restored upon return to optimal growth conditions. These results are important in that they disclose the dynamics of silencing associated with heterochromatin as well as the existence of a new level of transcriptional control that might play a role in plant acclimation to changing environmental conditions.

Computational identification of microRNAs and their targets from the expressed sequence tags of horsegram (Macrotyloma uniflorum (Lam.) Verdc.)

MicroRNAs (miRNAs) are a class of naturally occurring and small non-coding RNA molecules of about 21-25 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. To predict new miRNAs in plants different computational approaches have been developed. In the present study, an EST based approach has been used to identify novel miRNAs in horsegram. Identification of miRNAs was initiated by mining the EST database available at NCBI. Total of 989 ESTs were obtained for the identification of miRNAs. These ESTs were subjected to CAP3 assembly to remove the redundancy. This resulted in an output of 72 contigs and 606 singletons as non redundant datasets. The miRNAs were then predicted by using miRNA-finder. A total of eight potential miRNAs were predicted and named as hor-miR1 to hor-miR8. None of identified miRNAs showed significant homology with the previously reported in plants and therefore should be considered novel. These miRNAs were inputted to miRU2 program to predict their targets. The target mRNAs for these miRNAs mainly belong to zinc finger, chromosome condensation, protein kinase, abscisic acid-responsive, calcineurin-like phosphoesterase, disease resistance and transcriptional factor family proteins. These targets appeared to be involved in plant growth and development and environmental stress responses.

Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.)

Phosphorus is one of the major factors controlling plant growth and productivity. Although physiological and molecular processes of P deficiency have been intensively investigated, our current understanding of the coordinated regulation of phosphate-responsive genes and signal networks is limited. In the present study, we performed a microarray-based genome-wide transcriptional analysis of miRNAs from soybean (Glycine max L.) under phosphate deficiency. miRNAs extracted from P-deficient and P-sufficient soybean were hybridized to an array containing 853 known plant miRNA sequences. An induction ratio significant at p<0.01 was observed for 57 miRNAs belonging to 27 families. Among these miRNA families, which differentially expressed, 7 and 8 were found to be up-regulated, whereas 17 and 6 were down-regulated in leaves and roots, respectively. Seven representative individual miRNAs were selected for qRT-PCR validation, and most showed an expression pattern similar to that on microarray. We further predicted P-responsive cis-elements from the promoters of miRNAs in response to and non-responding to P deficiency. In total, 125 putative cis-elements were identified for 24 soybean P-deficient responsive miRNAs. Interestingly, those miRNAs (54) not responding to P deficiency were also found to contain the same P-responsive motifs. A comparative analysis revealed that the frequency of the motif occurrence in the promoters of miRNA genes in response to P deficiency was higher than that of miRNA genes not responding to P deficiency. Our study provides initial evidence in soybean that a set of miRNAs with a high frequency of P-responsive cis-elements may coordinately regulate the plant response to P deficiency.

[Advances in plant microRNA and stresses response.]

MicroRNAs (miRNAs) are endogenous 16-29 nt non-coding small RNAs that were are generally found in species and typically encoded by endogenous genes. They play an important regulatory role at post-transcription level by targeting mRNA cleavage and translation repression. More and more plant miRNAs had been predicted and identified along with the development of bioinformatics and experimental techniques. At stress conditions, plant miRNAs also play a role in adaptation by up-regulating or down-regulating the miRNA expression. The biogenesis, action mode with target genes, bio-logical functions of plant miRNAs, as well as the stress-responsive miRNAs, were reviewed and the methodologies of miRNA study were also briefly summarized in this paper.

Identification and characterization of a novel miR159 target not related to MYB in tomato

MicroRNA 159 (miR159) is a highly conserved miRNA with roles in flowering under short days, anther development and seed germination via repression of GAMYB-like genes. In tomato, the function of miR159 (Sl-miR159) is currently unknown and target transcripts have not been experimentally validated. Here, we identified and characterized a new miR159 target gene (SGN-U567133) in Solanum lycopersicum (tomato) that is not related to MYB. SGN-U567133 is predominantly expressed in flowers and encodes a nuclear-localized protein that contains a unique NOZZLE-like domain at its N terminus. In tomato, SGN-U567133 represents a small gene family and orthologs have been identified in other plant species, all containing a conserved miR159 target site in their coding sequence. Accordingly, 5'-RACE cleavage assay supported miRNA-mediated cleavage of SGN-U567133 transcripts in vivo. Moreover, the SGN-U567133 transcript accumulated in P19-HA-expressing tomato leaves in which miRNA-mediated cleavage is inhibited. In addition, transgenic tomato plants expressing a miR159-resistant form of SGN-U567133 accumulated higher levels of the SGN-U567133 transcript and exhibited defects in leaf and flower development. Together, our results suggest that SGN-U567133 represents a novel class of miR159 targets in plants and raise the possibility that its post-transcriptional regulation by Sl-miR159 is essential for normal tomato development.

Rapid and accurate detection of plant miRNAs by liquid northern hybridization

Northern blot analysis is a powerful research tool for discovery, validation and expression of genes, and is currently widely used to detect microRNA (miRNA) accumulation. However, the traditional Northern blot procedure, which is based on a support membrane, is overly elaborate and time-consuming, although it is unsurpassed in accuracy for determining the sizes and amounts of multiple small RNAs sharing high sequence identity. Here we present an alternative method derived from plant miRNAs, liquid Northern hybridization, using fluorescently labeled oligonucleotide probes and characterized by simple and specific miRNA determination and quantitation. The entire detection process is completed within a few hours, and multiple miRNAs can be simultaneously detected in a single experiment.

Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays

MicroRNAs (miRNAs) are short RNA chains (20-24 bp) which are emerging as important regulators of gene expression. miRNAs are encoded by specific genes, and in Arabidopsis, 190 genes have presently been identified. It has been shown that miR399 is essential for the phosphate starvation response, and recent studies have shown transcriptional changes in a number of additional miRNAs in response to a shortage of phosphate. In this study, global profiles of the miRNA in shoots of Arabidopsis plants grown on limited phosphate or full nutrient in combination with sucrose feed were analysed using the miRCURY LNA microRNA Array system. Furthermore, changes in miRNA transcript were compared between a mutant lacking the transcription factor phosphate starvation responses 1 (PHR1) and wild-type plants. The global analysis identified miRNAs belonging to nine families to respond to P deprivation, sucrose or PHR1. Among these, miR399d, miR827, miR866, miR391 and miR163 were most prominently induced upon P starvation, whereas miR169b/c was strongly induced in previously starved plants when provided with sufficient P and more so when combined with an addition of sucrose. This study shows that array analysis is in general agreement with data obtained by other high-throughput technologies. The array data were confirmed by real-time reverse transcriptase-polymerase chain reaction analyses of selected pri-miRNAs. Our data corroborate the implication that several miRNAs are involved in the P-starvation response and further identify miR866 and miR163 as new candidates of miRNAs associated with the regulation of the P-starvation response.

Computational Identification of Novel MicroRNAs and Their Targets in Vigna unguiculata

MicroRNAs (miRNAs) are a class of endogenous, noncoding, short RNAs directly involved in regulating gene expression at the posttranscriptional level. High conservation of miRNAs in plant provides the foundation for identification of new miRNAs in other plant species through homology alignment. Here, previous known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) databases of Vigna unguiculata, and according to a series of filtering criteria, a total of 47 miRNAs belonging to 13 miRNA families were identified, and 30 potential target genes of them were subsequently predicted, most of which seemed to encode transcription factors or enzymes participating in regulation of development, growth, metabolism, and other physiological processes. Overall, our findings lay the foundation for further researches of miRNAs function in Vigna unguiculata.

Identification of quantitative trait loci for ABA responsiveness at the seedling stage associated with ABA-regulated gene expression in common wheat

Responsiveness to abscisic acid (ABA) during vegetative growth plays an important role in regulating adaptive responses to various environmental conditions, including activation of a number of ABA-responsive genes. However, the relationship between gene expression and responsiveness to ABA at the seedling stage has not been well studied in wheat. In the present study, quantitative trait locus (QTL) analysis for ABA responsiveness at the seedling stage was performed using recombinant inbred lines derived from a cross between common wheat cultivars showing different ABA responsiveness. Five QTLs were found to be significant, located on chromosomes 1B, 2A, 3A, 6D and 7B. The QTL with the greatest effect was located on chromosome 6D and explained 11.12% of the variance in ABA responsiveness. The other QTLs each accounted for approximately 5-8% of the phenotypic variation. Expression analyses of three ABA-responsive Cor/Lea genes, Wdhn13, Wrab15 and Wrab17, showed that allelic differences in QTLs on chromosomes 2A, 6D and 7B influenced expression of these genes in seedlings treated with ABA. The 3A QTL appeared to be involved in the regulatory system of Wdhn13 and Wrab15, but not Wrab17. The effects of the 2A and 6D QTLs on gene expression were relatively large. The combination of alleles at the QTLs resulted in an additive or synergistic effect on Cor/Lea expression. These results indicate that the QTLs influencing ABA responsiveness are associated with ABA-regulated gene expression and suggest that the QTL on chromosome 6D with the largest effect acts as a key regulator of ABA responses including seedling growth arrest and gene expression during the vegetative stage.

Expression of ethylene response factor JERF1 in rice improves tolerance to drought

Ethylene response factor (ERF) proteins regulate a variety of stress responses in plant. JERF1, a tomato ERF protein, can be induced by abscisic acid (ABA). Overexpression of JERF1 enhanced the tolerance of transgenic tobacco to high salt concentration, osmotic stress, and low temperature by regulating the expression of stress-responsive genes by binding to DRE/CRT and GCC-box cis-elements. In this research, we further report that overexpression of JERF1 significantly enhanced drought tolerance of transgenic rice. The overexpression activated the expression of stress-responsive genes and increased the synthesis of the osmolyte proline by regulating the expression of OsP5CS, encoding the proline biosynthesis key enzyme deltal-pyrroline-5-carboxylate synthetase. JERF1 also activated the expression of two ABA biosynthesis key enzyme genes, OsABA2 and Os03g0810800, and increased the synthesis of ABA in rice. Analysis of cis-elements of JERF1-targeted genes pointed to the existence of DRE/CRT and/or GCC box in their promoters, indicating that JERF1 could activate the expression of related genes in rice by binding to these cis-elements. Unlike some other ERF proteins, constructive overexpression of JERF1 did not change the growth and development of transgenic rice, which makes JEFR1 a potentially useful source in breeding for greater tolerance to abiotic stress.

MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity

*MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. Information on miRNAs in legumes is as yet scarce. This work investigates miRNAs in an agronomically important legume, common bean (Phaseolus vulgaris). *A hybridization approach employing miRNA macroarrays - printed with oligonucleotides complementary to 68 known miRNAs - was used to detect miRNAs in the leaves, roots and nodules of control and nutrient-stressed (phosphorus, nitrogen, or iron deficiency; acidic pH; and manganese toxicity) common bean plants. *Thirty-three miRNAs were expressed in control plants and another five were only expressed under stress conditions. The miRNA expression ratios (stress:control) were evaluated using principal component and hierarchical cluster analyses. A group of miRNAs responded to nearly all stresses in the three organs analyzed. Other miRNAs showed organ-specific responses. Most of the nodule-responsive miRNAs showed up-regulation. miRNA blot expression analysis confirmed the macroarray results. Novel miRNA target genes were proposed for common bean and the expression of selected targets was evaluated by quantitative reverse transcriptase-polymerase chain reaction. *In addition to the detection of previously reported stress-responsive miRNAs, we discovered novel common bean stress-responsive miRNAs, for manganese toxicity. Our data provide a foundation for evaluating the individual roles of miRNAs in common bean.

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

BACKGROUND

Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of saline-alkaline stress transcriptome is mostly focused on saline (NaCl) stress and only limited information on alkaline (NaHCO3) stress is available.

RESULTS

Using Affymetrix Soybean GeneChip, we conducted transcriptional profiling on Glycine soja roots subjected to 50 mmol/L NaHCO3 treatment. In a total of 7088 probe sets, 3307 were up-regulated and 5720 were down-regulated at various time points. The number of significantly stress regulated genes increased dramatically after 3 h stress treatment and peaked at 6 h. GO enrichment test revealed that most of the differentially expressed genes were involved in signal transduction, energy, transcription, secondary metabolism, transporter, disease and defence response. We also detected 11 microRNAs regulated by NaHCO3 stress.

CONCLUSIONS

This is the first comprehensive wild soybean root transcriptome analysis under alkaline stress. These analyses have identified an inventory of genes with altered expression regulated by alkaline stress. The data extend the current understanding of wild soybean alkali stress response by providing a set of robustly selected, differentially expressed genes for further investigation.

Identification of microRNAs and their targets in switchgrass, a model biofuel plant species

In recent years, several plant species such as switchgrass, Miscanthus and Brachypodium have been recognized as potential model plant species for cellulosic bioenergy production. Of these, switchgrass has attracted much attention in the United States and worldwide because it can grow well on marginal lands and tolerate frequent drought spells. However, little is known about the basic biology of the traits that control these important characteristics in switchgrass. Genome-encoded approximately 21-24nt microRNAs (miRNAs) have emerged as critical regulators of gene expression important for normal growth and development and adaptation to abiotic stress, including nutrient-deprived conditions. To understand miRNA-guided post-transcriptional gene regulatory networks in this plant species, we sought to identify miRNAs in switchgrass. Using computational and experimental approaches, we identified approximately 20 conserved miRNA families. Temporal expression analysis indicated that some miRNAs have distinct tissue-specific expression, although most are ubiquitously expressed. Unlike in Arabidopsis and other plants, miR395 and miR399 were detected in plants grown on optimal levels of sulfate or phosphate in switchgrass, and were only slightly altered when exposed to sulfate or phosphate deficit conditions. Thirty-seven genes were predicted as targets for miRNAs, and 4 target mRNAs (Squamosa promoter binding-like factor, apetala 2-like, NAC domain containing transcription factor and HD-Zip homologs) were validated by 5'-RACE assays. These findings provide a snapshot of the miRNA component and possible targets in switchgrass.

Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum)

MicroRNAs (miRNAs) are a class of non-coding small endogenous RNAs with lengths of approximately 22 nucleotides (nt) that have been shown to regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Although thousands of miRNAs have been identified in many species, miRNAs have not yet been identified in switchgrass (Panicum virgatum), one of the most important bioenergy crops in the United States and around the world. In this study, we identified 121 potential switchgrass miRNAs, belonging to 44 families, using a well-defined comparative genome-based computational approach. We also identified miRNA clusters and antisense miRNAs in switchgrass expressed sequences tags. These identified miRNAs potentially target 839 protein-coding genes, which can act as transcription factors, and take part in multiple biological and metabolic processes including sucrose and fat metabolism, signal transduction, stress response, and plant development. Gene ontology (GO) analysis, based on these targets, showed that 527 biological processes were involved. Twenty-five of these processes were demonstrated to participate in the metabolism of carbon, glucose, starch, fatty acid, and lignin and in xylem formation. According to pathway enrichment analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG), 118 metabolism networks were found. These networks are involved in sucrose metabolism, fat metabolism, carbon fixation, hormone regulation, oxidative stress response, and the processing of other secondary metabolites.

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

BACKGROUND

MicroRNAs (miRNAs) are a class of small non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. MiRNAs can have large-scale regulatory effects on development and stress response in plants.

RESULTS

To test whether miRNAs play roles in regulating response to powdery mildew infection and heat stress in wheat, by using Solexa high-throughput sequencing we cloned the small RNA from wheat leaves infected by preponderant physiological strain Erysiphe graminis f. sp. tritici (Egt) or by heat stress treatment. A total of 153 miRNAs were identified, which belong to 51 known and 81 novel miRNA families. We found that 24 and 12 miRNAs were responsive to powdery mildew infection and heat stress, respectively. We further predicted that 149 target genes were potentially regulated by the novel wheat miRNA.

CONCLUSIONS

Our results indicated that diverse set of wheat miRNAs were responsive to powdery mildew infection and heat stress and could function in wheat responses to both biotic and abiotic stresses.

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum)

MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression by translational repression or transcript degradation. A large number of miRNAs have been identified from model plant species; however, the character of conserved miRNAs is poorly understood. We studied 42 miRNA families that are conserved within the plant kingdom, using the miRBase database. Some conserved miRNA families were found to be preferentially expressed in dicots relative to monocots, especially miR403, miR472 and miR479. Using an improved homology search-based approach and the conserved miRNAs as the query set, 34 conserved miRNAs and the miR482 family were identified in wheat. Forty-six wheat mRNAs were predicted as their putative target genes. Most conserved wheat miRNAs were found to retain homologous target interactions and have analogous molecular functions. The miR172 displayed a wheat-specific function and was found to have an additional target interaction with succinyl-CoA ligase. We concluded that although miRNAs are conserved, the expression and function of some have drifted during long periods of plant evolution.

Transcriptome-wide identification of microRNA targets in rice

MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice (Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5' ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.

Plant viruses versus RNAi: simple pathogens reveal complex insights on plant antimicrobial defense

RNA interference (RNAi) and related processes serve as a nucleic-acid-mediated surveillance system conserved in almost all eukaryotic organisms. This surveillance system detects various forms of double-stranded RNA (dsRNA) in cells and initiates a cascade of events that degrades dsRNAs into small interfering RNAs (siRNAs) or microRNAs (miRNAs). These small RNAs in turn serve as sequence-specific guides to interfere with the function of other nucleic acids through degradation or translational repression of homologous RNAs, or modification of homologous genome segments. One of the major roles of RNAi in plants and invertebrates is antiviral defense. Conversely, viruses have also evolved to encode suppressors of RNAi (VSRs), which disrupt RNAi at various steps. Research activities focusing on the relationship between plant viruses and RNAi have been essential to our current understanding of RNAi mechanisms.

MicroRNAs with macro-effects on plant stress responses

Being sessile organisms, plants often have to face challenges posed by environmental stresses. To minimize the cellular damage caused by stress, plants have evolved highly complex but well-coordinated adaptive responses operating at the transcriptional, post-transcriptional, translational and post-translational levels. A thorough understanding of regulation at all levels will provide better tools to improve plant's performance under stress. Dramatic changes in the levels of several hundreds or even thousands of mRNAs/proteins were evident under stress as revealed by high-throughput microarray and proteome analyses and such changes were thought to be dependent on transcriptional (induction or suppression of genes) or post-translational regulation (protein stability and degradation). However, recently discovered 21-24 nt small RNAs (microRNAs [miRNAs] and small-interfering RNAs [siRNAs]), which regulate gene expression at the post-transcriptional level, are also modulated during stress and possibly contribute to the stress-induced changes in profiles of mRNAs or proteins. This review highlights our understanding of the role of small RNAs in plant stress responses.

Phloem small RNAs, nutrient stress responses, and systemic mobility

BACKGROUND

Nutrient availabilities and needs have to be tightly coordinated between organs to ensure a balance between uptake and consumption for metabolism, growth, and defense reactions. Since plants often have to grow in environments with sub-optimal nutrient availability, a fine tuning is vital. To achieve this, information has to flow cell-to-cell and over long-distance via xylem and phloem. Recently, specific miRNAs emerged as a new type of regulating molecules during stress and nutrient deficiency responses, and miR399 was suggested to be a phloem-mobile long-distance signal involved in the phosphate starvation response.

RESULTS

We used miRNA microarrays containing all known plant miRNAs and a set of unknown small (s) RNAs earlier cloned from Brassica phloem sap 1, to comprehensively analyze the phloem response to nutrient deficiency by removing sulfate, copper or iron, respectively, from the growth medium. We show that phloem sap contains a specific set of sRNAs that is distinct from leaves and roots, and that the phloem also responds specifically to stress. Upon S and Cu deficiencies phloem sap reacts with an increase of the same miRNAs that were earlier characterized in other tissues, while no clear positive response to -Fe was observed. However, -Fe led to a reduction of Cu- and P-responsive miRNAs. We further demonstrate that under nutrient starvation miR399 and miR395 can be translocated through graft unions from wild type scions to rootstocks of the miRNA processing hen1-1 mutant. In contrast, miR171 was not transported. Translocation of miR395 led to a down-regulation of one of its targets in rootstocks, suggesting that this transport is of functional relevance, and that miR395, in addition to the well characterized miR399, could potentially act as a long-distance information transmitter.

CONCLUSIONS

Phloem sap contains a specific set of sRNAs, of which some specifically accumulate in response to nutrient deprivation. From the observation that miR395 and miR399 are phloem-mobile in grafting experiments we conclude that translocatable miRNAs might be candidates for information-transmitting molecules, but that grafting experiments alone are not sufficient to convincingly assign a signaling function.