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.     

miRNA在植物重金属胁迫应答中的作用

microRNA （miRNA）是一种新型的长度为20~24 nt的非编码RNA,通过对靶基因的表达调节进而参与调控植物体的多种生理代谢活动。重金属是一类重要的环境污染物,严重危害植物的生长发育,甚至导致植物死亡。植物在长期的进化过程中形成了抵御重金属胁迫的多种机制,如miRNA对特定基因转录后水平的调控就在逆境胁迫应答中发挥重要作用。本文综述了植物中参与重金属胁迫应答miRNA的种类及作用机制,为揭示重金属胁迫条件下基因表达调控机制,以及利用基因工程手段改良植物对重金属的耐受性提供了线索和依据。     

CircRNA: a rising star in plant biology

Circular RNAs (circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding miRNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and, particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue- or development-specific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circRNA studies.     

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

Abiotic stress is one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms, particularly in the identification of stress responsive protein-coding genes. In addition to protein coding genes, recently discovered microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have emerged as important players in plant stress responses. Initial clues suggesting that small RNAs are involved in plant stress responses stem from studies showing stress regulation of miRNAs and endogenous siRNAs, as well as from target predictions for some miRNAs. Subsequent studies have demonstrated an important functional role for these small RNAs in abiotic stress responses. This review focuses on recent advances, with emphasis on integration of small RNAs in stress regulatory networks.     

Plant ARGONAUTES

ARGONAUTE (AGO) proteins are integral players in all known small RNA-directed regulatory pathways. Eukaryotes produce numerous types of small RNAs, such as microRNAs (miRNA), small interfering RNAs (siRNA), PIWI-interacting RNAs (piRNAs), scanRNAs and 21U-RNAs, and these RNA species associate with different types of AGO family members, such as AGO, PIWI and group 3 proteins. Small RNA-guided AGO proteins regulate gene expression at various levels, including internal genomic DNA sequence elimination (in ciliates), translational repression (animals), and RNA cleavage (all eukaryotes), which in some cases is followed by DNA methylation and chromatin remodeling. The plant model species Arabidopsis contains ten AGO proteins belonging to three phylogenetic clades. This review covers our current knowledge of plant AGO functions during miRNA- and siRNA-mediated regulation of development and stress responses, siRNA-mediated antiviral immune response, and siRNA-mediated regulation of chromatin structure and transposons.     

Identification and characterization of small RNAs from vernalized<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two major classes of small non-coding RNAs with important roles in the regulation of gene expression, such as mRNA degradation and translational repression, heterochromatin formation, genome defense against transposons and viruses in eukaryotes. MiRNA- and siRNA-directed processes have emerged as a regulatory mechanism for growth and development in both animals and plants. To identify small RNAs that might be involved in vernalization, a process accelerating flowering brought on by a long period of cold, we generated a library of small RNAs from Arabidopsis that had been subject to vernalization. From the analysis of the library, 277 small RNAs were identified. They were distributed throughout all the five chromosomes. While the vast majority of small RNA genes locate on intergenic regions, others locate on repeat-rich regions, centromeric regions, transposon-related genes, and protein-coding genes. Five of them were mapped to convergent overlapping gene pairs. Two-hundred and forty of them were novel endogenous small RNAs that have not been cloned yet from plants grown under normal conditions and other environmental stresses. Seven putative miRNAs were up- or down-regulated by vernalization. In conclusion, many small RNAs were identified from vernalized Arabidopsis and some of these identified small RNAs may play roles in plant responses to vernalization.     

AP2/ERF转录因子调控植物非生物胁迫响应研究进展

低温、干旱、高盐和缺氧等多种不良环境影响植物的生长发育, 植物通过长期进化形成复杂的调节机制来适应这些不利条件。AP2/ERF是植物特有的转录因子, 在各种胁迫响应过程中发挥关键调控作用。近年来, 越来越多的研究表明, 植物激素介导的信号级联通路与逆境胁迫响应关系密切, AP2/ERF转录因子可与激素信号转导协同形成交叉调控网络。许多AP2/ERF转录因子通过响应植物激素脱落酸和乙烯, 激活依赖或不依赖于脱落酸和乙烯的胁迫响应基因的表达。此外, AP2/ERF转录因子参与赤霉素、细胞分裂素和油菜素内酯介导的生长发育和胁迫应答。该文简要综述了AP2/ERF转录因子的结构特征、转录调控、翻译后修饰、结合位点、协同互作蛋白及其参与调控依赖或不依赖激素信号转导途径的非生物胁迫响应研究进展, 为解析不同AP2/ERF转录因子在调控激素和胁迫响应网络中的作用提供理论依据。     

Key players in regulatory RNA realm of bacteria

Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network.     

ABA homeostasis and signaling involving multiple subcellular compartments and multiple receptors

The plant hormone abscisic acid (ABA) plays pivotal roles in many important physiological processes including stomatal closure, seed dormancy, growth and various environmental stresses. In these responses, ABA action is under the control of complex regulatory mechanisms involving homeostasis, perception and signaling. Recent studies provide new insights into these processes, which are of great importance in understanding the mechanisms underlying the evolutionary principle of how plants can survive as a sessile organism under ever-changing environmental conditions. They also form the basis for designing plants that have an enhanced resistance to various stresses in particular abiotic stress.