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BBA - Gene Regulatory Mechanisms (v.1819, #2)

Editorial Board (pp. i).

Plant gene regulation in response to abiotic stress by Lars Hennig (pp. 85-85).

AP2/ERF family transcription factors in plant abiotic stress responses by Junya Mizoi; Kazuo Shinozaki; Kazuko Yamaguchi-Shinozaki (pp. 86-96).

In terrestrial environments, temperature and water conditions are highly variable, and extreme temperatures and water conditions affect the survival, growth and reproduction of plants. To protect cells and sustain growth under such conditions of abiotic stress, plants respond to unfavourable changes in their environments in developmental, physiological and biochemical ways. These responses require expression of stress-responsive genes, which are regulated by a network of transcription factors. The AP2/ERF family is a large family of plant-specific transcription factors that share a well-conserved DNA-binding domain. This transcription factor family includes DRE-binding proteins (DREBs), which activate the expression of abiotic stress-responsive genes via specific binding to the dehydration-responsive element/C-repeat (DRE/CRT) cis-acting element in their promoters. In this review, we discuss the functions of the AP2/ERF-type transcription factors in plant abiotic stress responses, with special emphasis on the regulations and functions of two major types of DREBs, DREB1/CBF and DREB2. In addition, we summarise the involvement of other AP2/ERF-type transcription factors in abiotic stress responses, which has recently become clear. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► DREB1s/CBFs function in cold-stress responses and are mainly regulated at the transcriptional level. ► DREB2s function in both drought- and heat-stress responses and are regulated at multiple levels. ► Unique functions of other AP2/ERF family transcription factors in stress responses have been discovered.

Keywords: Abbreviations; AP2/ERF; APETALA 2/ERE binding factor; ABA; abscisic acid; ABRE; ABA-responsive element; bHLH; basic helix-loop-helix; CAMTA; calmodulin-binding transcription activator; CBF; C-repeat binding factor; CE; coupling element; DREB; DRE-binding protein; DRE/CRT; dehydration-responsive element/C-repeat; EAR motif; ERF-associated amphiphilic repression motif; EE; evening element; ERE; ethylene-responsive element; EST; expressed sequence tag; LEA; late embryogenesis abundant; HSE; heat shock element; HSF; heat shock transcription factor; GA; gibberellin; ICEr; induction of CBF expression region; QTL; quantitative trait locusAbiotic stress; DRE/CRT; AP2/ERF family transcription factor; DREB1/CBF; DREB2

NAC transcription factors in plant abiotic stress responses by Kazuo Nakashima; Hironori Takasaki; Junya Mizoi; Kazuo Shinozaki; Kazuko Yamaguchi-Shinozaki (pp. 97-103).

Abiotic stresses such as drought and high salinity adversely affect the growth and productivity of plants, including crops. The development of stress-tolerant crops will be greatly advantageous for modern agriculture in areas that are prone to such stresses. In recent years, several advances have been made towards identifying potential stress related genes which are capable of increasing the tolerance of plants to abiotic stress. NAC proteins are plant-specific transcription factors and more than 100 NAC genes have been identified in Arabidopsis and rice to date. Phylogenetic analyses indicate that the six major groups were already established at least in an ancient moss lineage. NAC transcription factors have a variety of important functions not only in plant development but also in abiotic stress responses. Stress-inducible NAC genes have been shown to be involved in abiotic stress tolerance. Transgenic Arabidopsis and rice plants overexpressing stress-responsive NAC (SNAC) genes have exhibited improved drought tolerance. These studies indicate that SNAC factors have important roles for the control of abiotic stress tolerance and that their overexpression can improve stress tolerance via biotechnological approaches. Although these transcription factors can bind to the same core NAC recognition sequence, recent studies have demonstrated that the effects of NAC factors for growth are different. Moreover, the NAC proteins are capable of functioning as homo- or hetero-dimer forms. Thus, SNAC factors can be useful for improving stress tolerance in transgenic plants, although the mechanism for mediating the stress tolerance of these homologous factors is complex in plants. Recent studies also suggest that crosstalk may exist between stress responses and plant growth. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► Abiotic stresses adversely affect the growth and productivity of plants. ► NAC proteins are plant-specific transcription factors. ► Stress-inducible NAC genes have been shown to be involved in abiotic stress response. ► We review the progress on characterization of plant stress-inducible NAC proteins.

Keywords: Abbreviations; ABA; abscisic acid; ABRE; ABA-responsive element; AREB; ABRE-binding protein; DRE; dehydration-responsive element; DREB; DRE-binding protein; LEA; late embryogenesis abundant; MeJA; methyl jasmonic acid; NAC; NAM, ATAF, and CUC transcription factor; NACRS; NAC recognition sequence; SNAC; stress-responsive NAC; TF; transcription factor; TM; transmembraneAbiotic stress; NAC transcription factor; Arabidopsis; Rice; Stress tolerance

The plant heat stress transcription factor (Hsf) family: Structure, function and evolution by Klaus-Dieter Scharf; Thomas Berberich; Ingo Ebersberger; Lutz Nover (pp. 104-119).

Ten years after the first overview of a complete plant Hsf family was presented for Arabidopsis thaliana by Nover et al. [1], we compiled data for 252 Hsfs from nine plant species (five eudicots and four monocots) with complete or almost complete genome sequences. The new data set provides interesting insights into phylogenetic relationships within the Hsf family in plants and allows the refinement of their classification into distinct groups. Numerous publications over the last decade document the diversification and functional interaction of Hsfs as well as their integration into the complex stress signaling and response networks of plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► Current knowledge of multiplicity, structure and function of the plant Hsf family. ► Structure and phylogenetic relationship compiled for 250 Hsfs from 9 species. ► Diversification and specific Hsf interactions are major aspects of Hsf function. ► Hsf activity, localization and stability are specifically regulated by chaperones. ► Hsfs linked to signaling and response networks of abiotic stress and development.

Keywords: Heat stress; Abiotic stress response; Transcriptional regulation; Chaperone activity; Protein homeostasis; Stress tolerance

The role of WRKY transcription factors in plant abiotic stresses by Ligang Chen; Yu Song; Shujia Li; Liping Zhang; Changsong Zou; Diqiu Yu (pp. 120-128).

The WRKY gene family has been suggested to play important roles in the regulation of transcriptional reprogramming associated with plant stress responses. Modification of the expression patterns of WRKY genes and/or changes in their activity contribute to the elaboration of various signaling pathways and regulatory networks. Furthermore, a single WRKY gene often responds to several stress factors, and then their proteins may participate in the regulation of several seemingly disparate processes as negative or positive regulators. WRKY proteins also function via protein–protein interaction and autoregulation or cross-regulation is extensively recorded among WRKY genes, which help us understand the complex mechanisms of signaling and transcriptional reprogramming controlled by WRKY proteins. Here, we review recent progress made in starting to reveal the role of WRKY transcription factors in plant abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► WRKY gene super-family, one of the largest transcription factor gene families, has been suggested to play important roles in the regulation of transcriptional reprogramming associated with plant stress responses. ► Modification of the expression patterns of WRKY genes and/or changes in their activity contributes to the elaboration of various signaling pathways and regulatory networks. ► A single WRKY gene often responds to several stress factors, and then their proteins may participate in the regulation of several seemingly disparate processes as negative or positive regulators. ► WRKY proteins function via protein–protein interaction and auto-regulation or cross-regulation exists extensively in the WRKY family.

Keywords: WRKY transcription factor; Transcriptional reprogramming; Abiotic stress

Chromatin modifications and remodeling in plant abiotic stress responses by Ming Luo; Xuncheng Liu; Prashant Singh; Yuhai Cui; Laurent Zimmerli; Keqiang Wu (pp. 129-136).

Sensing environmental changes and initiating a gene expression response are important for plants as sessile autotrophs. The ability of epigenetic status to alter rapidly and reversibly could be a key component to the flexibility of plant responses to the environment. The involvement of epigenetic mechanisms in the response to environmental cues and to different types of abiotic stresses has been documented. Different environmental stresses lead to altered methylation status of DNA as well as modifications of nucleosomal histones. Understanding how epigenetic mechanisms are involved in plant response to environmental stress is highly desirable, not just for a better understanding of molecular mechanisms of plant stress response but also for possible application in the genetic manipulation of plants. In this review, we highlight our current understanding of the epigenetic mechanisms of chromatin modifications and remodeling, with emphasis on the roles of specific modification enzymes and remodeling factors in plant abiotic stress responses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► Environmental stresses lead to altered methylation status of DNA as well as modifications of nucleosomal histones. ► Epigenetic mechanisms may have a decisive function in regulating plant responses to abiotic stresses. ► The involvement of chromatin modification and remodeling proteins in plant abiotic stress response is discussed.

Keywords: Epigenetics; Chromatin remodeling; Histone modification; Abiotic stress; Arabidopsis

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants by Basel Khraiwesh; Jian-Kang Zhu; Jianhua Zhu (pp. 137-148).

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.► Small RNAs are important regulators of gene expression in plants and animals. ► Plant small RNAs play a role in biotic and abiotic stress responses. ► The expression of many miRNAs is responsive to various stresses. ► Stress-responsive small RNAs are crucial components in gene regulatory networks.

Keywords: miRNA; siRNA; Biotic; Abiotic; Stress responses; Plant

RNA regulation in plant abiotic stress responses by Kentaro Nakaminami; Akihiro Matsui; Kazuo Shinozaki; Motoaki Seki (pp. 149-153).

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.► We summarized the recent studies on RNA regulation in plant stress responses. ► Non-coding RNAs regulate the mRNA levels and chromatin modification. ► Alterative splicing events occur in response to the environmental stresses. ► PB and SG play an important role in regulating RNA levels in plant stress responses. ► RNA-binding proteins are a key factor involved in plant stress responses.

Keywords: RNA regulation; Abiotic stress response; Non-coding RNA; Alternative splicing; Post-transcriptional regulation; RNA-binding proteins

Gene regulation in response to DNA damage by Anja Mannuss; Oliver Trapp; Holger Puchta (pp. 154-165).

To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► A number of genes involved in DNA repair are induced after DNA damage. ► Especially genes involved in DSB repair by HR are upregulated. ► Important players are the ATM kinase and the transcription factor SOG1. ► Also the E2F transcription factors seem to be involved.

Keywords: DNA repair; Homologous recombination; NHEJ; ATM; ATR; BER

Prerequisites, performance and profits of transcriptional profiling the abiotic stress response by Joachim Kilian; Florian Peschke; Kenneth W. Berendzen; Klaus Harter; Dierk Wanke (pp. 166-175).

During the last decade, microarrays became a routine tool for the analysis of transcripts in the model plant Arabidopsis thaliana and the crop plant species rice, poplar or barley. The overwhelming amount of data generated by gene expression studies is a valuable resource for every scientist. Here, we summarize the most important findings about the abiotic stress responses in plants. Interestingly, conserved patterns of gene expression responses have been found that are common between different abiotic stresses or that are conserved between different plant species. However, the individual histories of each plant affect the inter-comparability between experiments already before the onset of the actual stress treatment. This review outlines multiple aspects of microarray technology and highlights some of the benefits, limitations and also pitfalls of the technique. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► Common or non-overlapping transcriptional responses during abiotic stresses in plants. ► The plant core environmental stress response contains systemic responses and priming. ► Comparability of expression data and common standards of information (e.g. MIAME). ► Sampling, data processing and systematic errors in designing microarray experiments. ► We discuss evolutionary implications and discuss implications for genetic engineering.

Keywords: AtGenExpress; Abiotic stress; Microarray; Core environmental stress response; Plant-CESR; Experimental comparability

Genetic and epigenetic regulation of stress responses in natural plant populations by Clícia Grativol; Adriana Silva Hemerly; Paulo Cavalcanti Gomes Ferreira (pp. 176-185).

Plants have developed intricate mechanisms involving gene regulatory systems to adjust to stresses. Phenotypic variation in plants under stress is classically attributed to DNA sequence variants. More recently, it was found that epigenetic modifications – DNA methylation-, chromatin- and small RNA-based mechanisms – can contribute separately or together to phenotypes by regulating gene expression in response to the stress effect. These epigenetic modifications constitute an additional layer of complexity to heritable phenotypic variation and the evolutionary potential of natural plant populations because they can affect fitness. Natural populations can show differences in performance when they are exposed to changes in environmental conditions, partly because of their genetic variation but also because of their epigenetic variation. The line between these two components is blurred because little is known about the contribution of genotypes and epigenotypes to stress tolerance in natural populations. Recent insights in this field have just begun to shed light on the behavior of genetic and epigenetic variation in natural plant populations under biotic and abiotic stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► Epigenetic marks have great importance for adaptations to environmental changes. ► Epigenetic and genetic variation may coordinate in the adaptation to stress. ► Epigenetic variation may be a dynamic force for evolutionary changes.

Keywords: Genetic variation; Epigenetic variation; Natural population; Stress; Evolution

Targeting metabolic pathways for genetic engineering abiotic stress-tolerance in crops by Maria Reguera; Zvi Peleg; Eduardo Blumwald (pp. 186-194).

Abiotic stress conditions are the major limitations in modern agriculture. Although many genes associated with plant response(s) to abiotic stresses have been indentified and used to generate stress tolerant plants, the success in producing stress-tolerant crops is limited. New technologies are providing opportunities to generate stress tolerant crops. Biotechnological approaches that emphasize the development of transgenic crops under conditions that mimic the field situation and focus on the plant reproductive stage will significantly improve the opportunities of producing stress tolerant crops. Here, we highlight recent advances and discuss the limitations that hinder the fast integration of transgenic crops into agriculture and suggest possible research directions. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.► A limited success in producing abiotic-stress tolerant cultivars through genetic engineering has been achieved. ► Stresses occurring simultaneously is a common situation for crops that results in a complex system to cope with. ► New technologies provide opportunities to generate transgenic crops able to maintain high yields under stress. ► More emphasis should be given to study abiotic-stress tolerant crops under field conditions focusing on reproductive stage.

Keywords: Abiotic stress; Stress-tolerance; Stress combination; Genetic engineering crops; Yield

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BBA - Gene Regulatory Mechanisms (v.1819, #2)