Small RNAs as big players in plant abiotic stress responses and nutrient deprivation Ramanjulu Sunkar 1 , Viswanathan Chinnusamy 2 , Jianhua Zhu 3 and Jian-Kang Zhu 3 1 Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA 2 Water Technology Centre, Indian Agricultural Research Institute, New Delhi, India 3 Department of Botany and Plant Sciences and Center for Plant Cell Biology, 2150 Batchelor Hall, University of California, Riverside, CA 92521, USA 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 predic- tions 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 integ- ration of small RNAs in stress regulatory networks. Small RNAs are ubiquitous regulators of gene expression Plant development, metabolism and stress responses, as well as a myriad of other functions, depend on the correct regulation of gene expression. This is achieved by multiple mechanisms, with perhaps the most important control being exerted at the level of transcription. However, post-transcriptional events also play a crucial role in regulating gene expression. The stability of mRNAs is regulated by a variety of signals acting on specific sequences within the RNAs. This regulation is often mediated by specific RNA-binding proteins (RBPs) that bind to elements in the untranslated regions (UTRs) of mRNAs and regulate the stability, translation or localization of the mRNA [1–3]. The recent discovery of microRNAs (miRNAs, see Glossary) and small interfering RNAs (siRNAs) revealed another ubiquitous mode of post-transcriptional regulation. These small RNAs are known to silence genes post-transcription- ally by guiding target mRNAs for degradation or by repres- sing translation [4–8]. The role of miRNAs in controlling developmental processes has been at the forefront of plant miRNA research. This is based in part on the fact that many proteins (dcl1, hen1, hyl, se and hst) required for miRNA generation and miRNA target genes ( phb and ago1) were first identified through genetic screens for developmental defects [9–15]. A comprehensive examination of miRNAs in plant development is provided by several excellent recent reviews [5–8,16–18]. In this review, the emerging roles of miRNAs and endogenous siRNAs in plant stress responses are discussed. Overview of the role of miRNAs in plant stress responses Plants are sessile organisms that must endure stressful environments. A large proportion of plant genes are regulated by stresses such as drought, soil salinity and extreme temperatures [19–23]. Of the many gene regulatory mechanisms such as transcriptional, post-transcriptional and post-translational regulation, transcriptional regula- tion is the most widely studied mechanism. The action of specific transcription factors that bind to conserved cis-acting promoter elements is well documented as a cause of changes in gene expression, particularly those induced by abiotic stress [20]. Furthermore, post-transcriptional gene regulation under stress conditions has been documented before, although the underlying mechanism was not known [24–26]. Considering the important roles of small RNAs in guiding post-transcriptional gene silencing, their involve- ment in stress-regulated gene expression seemed likely [27,28]. The discovery that stress can regulate miRNA levels, coupled with the identification of stress-associated genes as miRNA targets provided clues about the role of miRNAs in stress responses. Functional analyses have demonstrated that several plant miRNAs play vital roles in plant resistance to abiotic as well as biotic stresses [29– 34]. Understanding small RNA-guided stress regulatory networks should provide new tools for the genetic improve- ment of plant stress tolerance (Figure 1). Indeed, it has been shown recently that manipulation of miRNA-guided gene regulation can help to engineer plants that will be more stress-resistant [34]. miRNA and oxidative stress Under normal conditions, plants maintain a delicate balance between reactive oxygen species (ROS) production Review TRENDS in Plant Science Vol.12 No.7 Corresponding authors: Sunkar, R. (rsunkar@biochem.okstate.edu); Zhu, J.-K. (jian-kang.zhu@ucr.edu). Available online 18 June 2007. www.sciencedirect.com 1360-1385/$ – see front matter ß 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.tplants.2007.05.001