Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways

The study of abiotic stress response of plants is important because they have to cope with environmental changes to survive. The plant genomes have evolved to meet environmental challenges. Salt, temperature, and drought are the main abiotic stresses. The tolerance and response to stress vary differently in plants. The idea was to analyze the genes showing differential expression under abiotic stresses. There are many pathways connecting the perception of external stimuli to cellular responses. In plants, these pathways play an important role in the transduction of abiotic stresses. In the present study, the gene expression data have been analyzed for their involvement in different steps of signaling pathways. The conserved genes were analyzed for their role in each pathway. The functional annotations of these genes and their response under abiotic stresses in other plant species were also studied. The enzymes of signal pathways, showing similarity with conserved genes, were analyzed for their role in different abiotic stresses. Our findings will help to understand the expression of genes in response to various abiotic stresses. These genes may be used to study the response of different abiotic stresses in other plant species and the molecular basis of stress tolerance.     

Snakin/GASA proteins: Involvement in hormone crosstalk and redox homeostasis

Snakin/GASA proteins are widely distributed among plant species. They are expressed in different plant organs with high tissue and temporal specificity, and their subcellular localization varies among the different members. Interestingly, all of them maintain 12 cysteines of the C-terminus in highly conserved positions of the aminoacid sequences that are essential for their biochemical activity and probably responsible for their protein structure. Despite their common features, their functions are not completely elucidated and little is known about their mode of action. This review focuses on the current knowledge about this intriguing family of peptides and advances comprising gene regulation analyses, expression pattern studies and phenotypic characterization of mutants and transgenic plants. Furthermore, we discuss the roles of Snakin/GASA proteins in several aspects of plant development, plant responses to biotic or abiotic stress and their participation in hormone crosstalk and redox homeostasis.     

Improvement of plant abiotic stress tolerance through modulation of the polyamine pathway

Polyamines(mainly putrescine(Put),spermidine(Spd),and spermine(Spm))have been widely found in a range of physiological processes and in almost all diverse environmental stresses.In various plant species,abiotic stresses modulated the accumulation of polyamines and related gene expression.Studies using loss-of-function mutants and transgenic overexpression plants modulating polyamine metabolic pathways confirmed protective roles of polyamines during plant abiotic stress responses,and indicated the possibility to improve plant tolerance through genetic manipulation of the polyamine pathway.Additionally,putative mechanisms of polyamines involved in plant abiotic stress tolerance were thoroughly discussed and crosstalks among polyamine,abscisic acid,and nitric oxide in plant responses to abiotic stress were emphasized.Special attention was paid to the interaction between polyamine and reactive oxygen species,ion channels,amino acid and carbon metabolism,and other adaptive responses.Further studies are needed to elucidate the polyamine signaling pathway,especially polyamine-regulated downstream targets and the connections between polyamines and other stress responsive molecules.     

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.     

枳LEA基因家族鉴定及其对非生物胁迫的响应

为明确LEA基因在枳非生物胁迫中的作用,研究通过生物信息学方法对枳LEA基因家族进行全基因组的鉴定,并采用qRT-PCR技术分析其在不同非生物胁迫下的表达情况。结果表明:(1)枳基因组中鉴定得到57个LEA基因家族成员,编码蛋白的氨基酸长度在62~945 aa之间,分子质量在6.95~104.98 kD之间。(2)系统进化分析表明,PtrLEA基因可分为8个亚家族,LEA_1~LEA_6、dehydrin和SMP,LEA_2亚族家族成员最多。(3)顺式作用元件分析表明,PtrLEA启动子上存在大量的植物激素、胁迫响应以及生长发育有关的响应元件。(4)转录组数据分析结果显示,LEA基因家族具有组织表达特异性,PtrLEA 15、PtrLEA 17、PtrLEA 23、PtrLEA 51在所有组织中均有高表达,也发现有3个基因在所有组织中不表达。(5)实时荧光定量PCR结果显示:PtrLEA基因在低温、干旱和高盐胁迫处理条件下,与对照相比分别有6、2和6个基因上调表达,推测该基因家族参与多种非生物胁迫应答。     

Chromatin modifications and remodeling in plant abiotic stress responses

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.     

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa

Plant microRNAs have a vital role in various abiotic stress responses by regulating gene expression. Heat stress is one of the most severe abiotic stresses, and affects plant growth and development, even leading to death. To identify heat-responsive miRNAs at the genome-wide level in Populus, Solexa sequencing was employed to sequence two libraries from Populus tomentosa, treated and untreated by heat stress. Sequence analysis identified 134 conserved miRNAs belonging to 30 miRNA families, and 16 novel miRNAs belonging to 14 families. Among these miRNAs, 52 miRNAs from 15 families were responsive to heat stress and most of them were down-regulated. qRT-PCR analysis confirmed that the conserved and novel miRNAs were expressed in P. tomentosa, and revealed similar expression trends to the Solexa sequencing results obtained under heat stress. One hundred and nine targets of the novel miRNAs were predicted. This study opens up a new avenue for understanding the regulatory mechanisms of miRNAs involvement in the heat stress response of trees.     

Improvement of plant abiotic stress tolerance through modulation of the polyamine pathway FA简

Polyamines （mainly putrescine （Put）, spermidine （Spd）, and spermine （Spin）） have been widely found in a range of physiological processes and in almost all diverse environ- mental stresses. In various plant species, abiotic stresses modulated the accumulation of polyamines and related gene expression. Studies using loss-of-function mutants and transgenic overexpression plants modulating polyamine metabolic pathways confirmed protective roles of polyamines during plant abiotic stress responses, and indicated the possibility to improve plant tolerance through genetic manipulation of the polyamine pathway. Additionally, puta- tive mechanisms of polyamines involved in plant abiotic stress tolerance were thoroughly discussed and crosstalks among polyamine, abscisic acid, and nitric oxide in plant responses to abiotic stress were emphasized. Special attention was paid to the interaction between polyamine and reactive oxygen species, ion channels, amino acid and carbon metabolism, and other adaptive responses. Further studies are needed to elucidate the polyamine signaling pathway, especially polyamine-regulated downstream tar- gets and the connections between polyamines and other stress responsive molecules.     

Epigenetic regulation in plant abiotic stress responses

In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress‐responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross‐talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.     

Functions and interaction of plant lipid signalling under abiotic stresses

Lipids are the primary form of energy storage and a major component of plasma membranes, which form the interface between the cell and the extracellular environment. Several lipids — including phosphoinositide, phosphatidic acid, sphingolipids, lysophospholipids, oxylipins, and free fatty acids — also serve as substrates for the generation of signalling molecules. Abiotic stresses, such as drought and temperature stress, are known to affect plant growth. In addition, abiotic stresses can activate certain lipid-dependent signalling pathways that control the expression of stress-responsive genes and contribute to plant stress adaptation. Many studies have focused either on the enzymatic production and metabolism of lipids, or on the mechanisms of abiotic stress response. However, there is little information regarding the roles of plant lipids in plant responses to abiotic stress. In this review, we describe the metabolism of plant lipids and discuss their involvement in plant responses to abiotic stress. As such, this review provides crucial background for further research on the interactions between plant lipids and abiotic stress.