Genome reprogramming and small interfering RNA in the Arabidopsis germline

The movement of mobile small RNA signals between cells has garnered much interest over the last few years, and has recently been extended to germ cells during gamete development. Focusing on plants, we review mobile RNA signals that arise following reprogramming in the germline, and their effect on transposable element silencing on the one hand and on meiotic and apomictic germ cell fate on the other. A potential role for reprogramming and small RNA in hybrid formation and speciation is proposed.     

Plant small RNAs as morphogens

RNA interference (RNAi) in plants has long been known to produce a non-cell autonomous signal capable of silencing target genes over great cellular distances. However, only recently have RNAi-derived small RNAs been formally shown to comprise that mobile signal. Interestingly, some of these mobile small RNAs play critical roles in plant development, forming gradients that regulate the activity of their targets in a dosage-dependent manner. These properties resemble features of morphogens in animals, leading us to postulate that such cell-fate-defining small RNAs employ similar principles for the generation, stabilization and interpretation of their expression gradients. Here we review our understanding of small RNA mobility in plants, evaluate their potential as morphogen-like signals, and consider how the graded accumulation patterns that underlie their patterning/biological activity could be created and maintained.     

植物中 RNA 分子系统运输的研究进展

RNA 分子主要以单链的形式存在于生物体内,既担负着贮存及转移遗传信息的作用,又能作为核酶直接在细胞内发挥代谢功能 . 在植物中 RNA 也可作为活跃的信号分子调控基因表达和发育 . 介绍了包括病毒 RNA 、 RNA 沉默信号、特异内源 RNA 等 RNA 分子,在植物体内的系统运输及其在植物基因表达调控中所起作用的研究进展 .     

Trans-kingdom Cross-Talk: Small RNAs on the Move

This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.     

Plant Mobile Small RNAs

In plants, RNA silencing is a fundamental regulator of gene expression, heterochromatin formation, suppression of transposable elements, and defense against viruses. The sequence specificity of these processes relies on small noncoding RNA (sRNA) molecules. Although the spreading of RNA silencing across the plant has been recognized for nearly two decades, only recently have sRNAs been formally demonstrated as the mobile silencing signals. Here, we discuss the various types of mobile sRNA molecules, their short- and long-range movement, and their function in recipient cells.RNA silencing is a regulatory mechanism that controls the expression of endogenous genes and exogenous molecular parasites such as viruses, transgenes, and transposable elements. One of the most fascinating aspects of RNA silencing found in plants and invertebrates is its mobile nature—in other words, its ability to spread from the cell where it has been initiated to neighboring cells. This phenomenon relies on the movement of small noncoding RNA molecules (sRNA, 21–24 nucleotides [nt] in length) that provide the sequence specificity of the silencing effects. In plants, there are two major classes of sRNAs: short interfering RNAs (siRNAs) and micro RNAs (miRNAs). These sRNAs are generated by diverse and sometimes interacting biochemical pathways, which may influence their mobility. Movement of plant sRNAs falls into two main categories: cell-to-cell (short-range) and systemic (long-range) movement (Melnyk et al. 2011).     

Intercellular and systemic movement of RNA silencing signals

In most eukaryotes, double-stranded RNA is processed into small RNAs that are potent regulators of gene expression. This gene silencing process is known as RNA silencing or RNA interference (RNAi) and, in plants and nematodes, it is associated with the production of a mobile signal that can travel from cell-to-cell and over long distances. The sequence-specific nature of systemic RNA silencing indicates that a nucleic acid is a component of the signalling complex. Recent work has shed light on the mobile RNA species, the genes involved in the production and transport of the signal. This review discusses the advances in systemic RNAi and presents the current challenges and questions in this rapidly evolving field.     

植物化学通讯研究进展

 生物的信息传递是生命科学中引人入胜的研究领域之一,生物种间种内和个体内都存在着物理和化学等各种信息交流方式。植物种间种内是否通过物理信号进行通讯交流还是一个未知数,但邻近的同种或异种植物通过化学物质为媒介的通讯关系确是客观存在的。最近,愈来愈多的研究证明：许多陆生植物种可以合成并释放特定的次生物质,这些次生物质可以通过空气和土壤两种载体进行信息传递,尤其是在植物受到侵袭和寄生条件下。茉莉酮酸甲酯、水杨酸甲酯和乙烯等挥发性次生物质被确证为以空气为媒介进行植物种间和种内通讯的化学信号分子。植物根分泌的黄酮和氢醌等分子也可以经土壤媒介传递信息。由于在自然条件下植物根系分泌物的收集和活性信号分子的俘获及鉴定技术还未能突破,这增加了以土壤为媒介的植物种间和种内化学通讯关系研究的难度。但不论如何,植物的化学通讯是植物种间和种内交流的主要方式,植物间的化学通讯关系的研究还处于突破的前夜,这方面的任一研究成果都会引起世界性的关注。因此,破译植物种间和种内化学通讯密码具有重要的学术价值。     

Exploration of small RNAs

For several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and modifications. Detailed analyses revealed several pathways associated with the function of small RNAs. Although these pathways show evolutional conservation, there are substantial differences. Advanced technologies to profile RNAs have accelerated the field further resulting in the discovery of an increasing number of novel species, suggesting that we are only just beginning to appreciate the complexity of small RNAs and their functions. Here, we review recent progress in novel small RNA exploration, including discovered small RNA species, their pathways, and devised technologies.     

Distribution of root mRNA species in other vegetative organs of pea (Pisum sativum L.)

Summary A cDNA library was prepared from, poly(A)⁺ RNA from roots of pea (Pisum sativum L.). Twenty five clones were selected by use of random numbers and used as probes on Northern blots to analyse the distribution of their corresponding mRNA species in other vegetative pea organs: leaf, stem and developing cotyledon. Fifteen cDNA inserts hybridised to single mRNA species, five hybridised to two mRNA species and one hybridised to five homologous mRNAs. Four cDNA clones (16% of those selected) gave no hybridization signals, indicating that the steady state levels of mRNAs were below the detection limit (i.e.less than 2.5 x 10^-5% of poly(A)⁺ RNA). Most of the root mRNAs were represented in all four pea organs as sequences of low and medium abundance. All but two cDNAs encoded mRNA species enhanced in root. However, cDNA clones appeared not to encode mRNA species expressed in a strictly organ-specific manner, as no mRNA unique to root was found. Thus, if organ-unique mRNA species are present, they are only present at a very low level of abundance in the poly(A)⁺RNA population.     

Long‐distance movement of phosphate starvation‐responsive microRNAs in Arabidopsis

• Plant microRNAs are small RNAs that are important for genetic regulation of processes such as plant development or environmental responses. Specific microRNAs accumulate in the phloem during phosphate starvation, and may act as long‐distance signalling molecules.
• We performed quantitative PCR on Arabidopsis hypocotyl micrograft tissues of wild‐type and hen1‐6 mutants to assess the mobility of several phosphate starvation‐responsive microRNA species.
• In addition to the previously confirmed mobile species miR399d, the corresponding microRNA* (miR399d*) was identified for the first time as mobile between shoots and roots. Translocation by phosphate‐responsive microRNAs miR827 and miR2111a between shoots and roots during phosphate starvation was evident, while their respective microRNA*s were not mobile.
• The results suggest that long‐distance mobility of microRNA species is selective and can occur without the corresponding duplex strand. Movement of miR399d* and root‐localised accumulation of miR2111a* opens the potential for persisting microRNA*s to be mobile and functional in novel pathways during phosphate starvation responses.