Plant genomes are the source of large numbers of small RNAs, generated via a variety of genetically separable pathways. Several of these pathways converge in the production of phased, secondary, small interfering RNAs (phasiRNAs), originally designated as trans-acting small interfering RNAs or tasiRNAs. PhasiRNA biogenesis requires the involvement of microRNAs as well as the cellular machinery for the production of siRNAs. PhasiRNAs in Arabidopsis thaliana have been well described for their ability to function in trans to suppress target transcript levels. Plant genomic data from an expanding set of species have demonstrated that Arabidopsis is relatively sparing in its use of phasiRNAs, while other genomes contain hundreds or even thousands of phasiRNA-generating loci. In the dicots, targets of those phasiRNAs include several large or conserved families of genes, such as those encoding disease resistance proteins or transcription factors. Suppression of nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes by small RNAs is particularly unusual because of a high level of redundancy. In this review, we discuss plant phasiRNAs and the possible mechanistic significance of phasiRNA-based regulation of the NB-LRRs.

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

The microRNA miR393 has been shown to play a role in plant development and in the stress response by targeting mRNAs that code for the auxin receptors in Arabidopsis. In this study, we verified that two rice auxin receptor gene homologs (OsTIR1 and OsAFB2) could be targeted by OsmiR393 (Os for Oryza sativa). Two new phenotypes (increased tillers and early flowering) and two previously observed phenotypes (reduced tolerance to salt and drought and hyposensitivity to auxin) were observed in the OsmiR393-overexpressing rice plants. The OsmiR393-overexpressing rice demonstrated hyposensitivity to synthetic auxin-analog treatments. These data indicated that the phenotypes of OsmiR393-overexpressing rice may be caused through hyposensitivity to the auxin signal by reduced expression of two auxin receptor genes (OsTIR1 and OsAFB2). The expression of an auxin transporter (OsAUX1) and a tillering inhibitor (OsTB1) were downregulated by overexpression of OsmiR393, which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1, which affected the transportation of auxin, then to OsTB1, which finally controlled tillering. The positive phenotypes (increased tillers and early flowering) and negative phenotypes (reduced tolerance to salt and hyposensitivity to auxin) of OsmiR393-overexpressing rice present a dilemma for molecular breeding.

/pdf/ostir1-and-osafb2-downregulation-via-osmir393-overexpression-3gas66t5xy.pdf

OsTIR1 and OsAFB2 Downregulation via OsmiR393 Overexpression Leads to More Tillers, Early Flowering and Less Tolerance to Salt and Drought in Rice

Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bidirectional movement of viruses, proteins and mRNAs between host and parasite, but the functional effects of these movements are not known. Here we show that Cuscuta campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana. Many of these miRNAs are 22 nucleotides in length. Plant miRNAs of this length are uncommon, and are associated with amplification of target silencing through secondary short interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by 22-nucleotide C. campestris miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation. Hosts with mutations in two of the loci that encode target mRNAs supported significantly higher growth of C. campestris. The same miRNAs that are expressed and active when C. campestris parasitizes A. thaliana are also expressed and active when it infects Nicotiana benthamiana. Homologues of target mRNAs from many other plant species also contain the predicted target sites for the induced C. campestris miRNAs. These data show that C. campestris miRNAs act as trans-species regulators of host-gene expression, and suggest that they may act as virulence factors during parasitism.

/pdf/micrornas-from-the-parasitic-plant-cuscuta-campestris-target-zbp5do7q27.pdf

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs.

Phytohormones are signal molecules produced within the plant that control its growth and development through the regulation of gene expression. Interaction between different phytohormone pathways is essential in coordinating tissue outgrowth in response to environmental changes, such as the adaptation of root development to water deficit or the initiation of seed germination during imbibition. Recently, microRNAs (miRNAs) have emerged as key regulators of phytohormone response pathways in planta by affecting their metabolism, distribution, and perception. Here we review current knowledge on the miRNA-mediated regulations involved in phytohormone crosstalk. We focus on the miRNAs exhibiting regulatory links with more than one phytohormone pathway and discuss their possible implication in coordinating multiple phytohormone responses during specific developmental processes.

miRNAs in the crosstalk between phytohormone signalling pathways

Plant Immunity: From Signaling to Epigenetic Control of Defense.

The phytohormone auxin is a key regulator of plant growth and development that exerts its functions through F-box receptors. Arabidopsis (Arabidopsis thaliana) has four partially redundant of these receptors that comprise the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX1 auxin receptor (TAAR) clade. Recent studies have shown that the microRNA miR393 regulates the expression of different sets of TAAR genes following pathogen infection or nitrate treatment. Here we report that miR393 helps regulate auxin-related development of leaves. We found that AtMIR393B is the predominant source for miR393 in all aerial organs and that miR393 down-regulates all four TAAR genes by guiding the cleavage of their mRNAs. A mutant unable to produce miR393 shows developmental abnormalities of leaves and cotyledons reminiscent of enhanced auxin perception by TAARs. Interestingly, miR393 initiates the biogenesis of secondary siRNAs from the transcripts of at least two of the four TAAR genes. Our results indicate that these siRNAs, which we call siTAARs, help regulate the expression of TAAR genes as well as several unrelated genes by guiding the cleavage of their mRNAs. Thus, miR393 and possibly siTAARs regulate auxin perception and certain auxin-related aspects of leaf development.

http://www.plantphysiol.org/content/plantphysiol/early/2011/08/09/pp.111.180083.full.pdf

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

Epigenetic states and even certain environmental responses in nematodes, mammals and seed plants can be inherited over successive generations. These transgenerational effects challenge traditional views of heredity and could have evolutionary consequences. RNAi in plants is an epigenetic form of RNA degradation that is normally reset early in development. In contrast, competence, i.e., the susceptibility of a transgene for RNAi, is believed to be genetically determined and faithfully transmitted over many generations. Unexpectedly, we found that the same yellow fluorescent protein (YFP) transgene in a monogenic, homozygous line of Arabidopsis exhibited two epigenetic states of RNAi: type I, which is initiated in rosette leaves and is stable in later developmental stages, and, type II, which is initiated after floral induction and is unstable. The incidence of type I plants descended from type I parents decreased over three successive generations of self-fertilized plants. By the third generation, a substantial fraction of plants from type I parents exhibited either the type II phenotype or remained high-YFP expressing throughout sporophytic development, indicating that silencing had been completely lost. Similarly, plants descended from type II parents showed a progressive shift from the type II phenotype and a complete loss of silencing. These results show that the silencing types (or states) of parental plants have significant influence on both silencing determination and silencing types (or states) of their offspring, however, this influence fades through several generations of self; as regardless of the types of the parental lines, competence for RNA silencing tends to loss after generations. Thus, we propose that RNA silencing in plants can be the target of transgenerational effects. While the underlying mechanisms are still unknown, our findings in the Arabidopsis RNA silencing system complement the current understanding of heritable RNAi in C. elegans, that this phenomenon is likely a common mechanism in Eukaryote systems.

/pdf/epigenetic-transgenerational-effects-on-rnai-in-arabidopsis-bn5665lj4n.pdf

Epigenetic transgenerational effects on RNAi in Arabidopsis

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miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

Epigenetic transgenerational effects on RNAi in Arabidopsis