Differential stress responses of early salt-stress responding genes in common wheat

Four early salt-stress responding genes (WESR1-4) in common wheat (Triticum aestivum L.) were analyzed for their temporal accumulation of mRNA during salt stress, osmotic stress and abscisic acid (ABA) treatment. All genes showed transient stimulation by 0.15 M NaCl treatment. WESR1 and WESR2 were induced by both osmotic stress and exogenous ABA treatment. WESR3 responded to exogenous ABA, but not to osmotic stress. WESR4 did not show significant response to either osmotic stress or exogenous ABA treatment. These results suggest that wheat has at least two salt stress signal transduction pathways, an ABA-dependent and ABA-independent pathway.     

Unraveling salt stress signaling in plants

Salt stress is a major environmental factor limiting plant growth and productivity. A better understanding of the mechanisms mediating salt resistance will help researchers design ways to improve crop performance under adverse environmental conditions. Salt stress can lead to ionic stress, osmotic stress and secondary stresses, particularly oxidative stress, in plants. Therefore,to adapt to salt stress, plants rely on signals and pathways that re-establish cellular ionic, osmotic, and reactive oxygen species(ROS) homeostasis. Over the past two decades, genetic and biochemical analyses have revealed several core stress signaling pathways that participate in salt resistance. The Salt Overly Sensitive signaling pathway plays a key role in maintaining ionic homeostasis,via extruding sodium ions into the apoplast. Mitogenactivated protein kinase cascades mediate ionic, osmotic,and ROS homeostasis. SnR K2(sucrose nonfermenting1-related protein kinase 2) proteins are involved in maintaining osmotic homeostasis. In this review, we discuss recent progress in identifying the components and pathways involved in the plant's response to salt stress and their regulatory mechanisms. We also review progress in identifying sensors involved in salt-induced stress signaling in plants.     

Arabidopsis EIN2 modulates stress response through abscisic acid response pathway

The nuclear protein ETHYLENE INSENSITIVE2 (EIN2) is a central component of the ethylene signal transduction pathway in plants, and plays an important role in mediating cross-links between several hormone response pathways, including abscisic acid (ABA). ABA mediates stress responses in plants, but there is no report on the role of EIN2 on plant response to salt and osmotic stresses. Here, we show that EIN2 gene regulates plant response to osmotic and salt stress through an ABA-dependent pathway in Arabidopsis. The expression of the EIN2 gene is down-regulated by salt and osmotic stress. An Arabidopsis EIN2 null mutant was supersensitive to both salt and osmotic stress conditions. Disruption of EIN2 specifically altered the expression pattern of stress marker gene RD29B in response to the stresses, but not the stress- or ABA-responsive genes RD29A and RD22, suggesting EIN2 modulates plant stress responses through the RD29B branch of the ABA response. Furthermore, disruption of EIN2 caused substantial increase in ABA. Lastly, our data showed that mutations of other key genes in ethylene pathway also had altered sensitivity to abiotic stresses, indicating that the intact ethylene may involve in the stress response. Taken together, the results identified EIN2 as a cross-link node in ethylene, ABA and stress signaling pathways, and EIN2 is necessary to induce developmental arrest during seed germination, and seedling establishment, as well as subsequent vegetative growth, thereby allowing the survival and growth of plants under the adverse environmental conditions. Youning Wang and Chuang Liu contributed equally to this work.     

Reorganization of interphase microtubules in root cells of <Emphasis Type="Italic">Medicago sativa</Emphasis> L. during acclimation to osmotic and salt stress

We examined the organization of microtubule system of interphase cells in roots of Medicago sativa L. during acclimation to salt and osmotic stress at different concentrations of NaCl, Na₂SO₄, and mannitol. We identified morphological changes of tubulin cytoskeleton in different root tissues during the acclimation to salt and osmotic stress: (1) decreased density of the cortical microtubule network, (2) random orientation of cortical microtubule bundles, (4) thickening of the bundles, (3) nonuniform density of the bundles, (4) fragmentation of the bundles, and (5) formation of microtubule converging centers. Network thinning and thickening of the bundles were observed both under osmotic and salt stress. Random orientation of cortical microtubules was visualized under osmotic stress but not during salt stress. Fragmentation of microtubule bundles took place under salt stress with a high concentration of mannitol. Formation of microtubule converging centers was common under prolonged action of sodium sulfate, less evident under sodium chloride, and not found after mannitol treatment. Our data show that, in alfalfa root cells, cortical microtubules rearrange not only in response to different ions, but also to osmotic pressure. Thus, the signaling pathways and molecular mechanisms inducing reorganization of the microtubule system may be triggered by sodium cations, as well as by sulfate and chloride anions at concentrations that do not cause irreversible cell damage.     

Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach

The adaptation to osmotic stress is crucial for growth and survival of Bacillus subtilis in its natural ecosystem. Dual channel imaging and warping of 2-D protein gels were used to visualize global changes in the protein synthesis pattern of cells in response to osmotic stress (6% NaCl). Many vegetative enzymes were repressed in response to salt stress and derepressed after resumption of growth. The enzymes catalyzing the metabolic steps from glucose to 2-oxoglutarate, however, were almost constantly synthesized during salt stress despite the growth arrest. This indicates an enhanced need for the proline precursor glutamate. The synthesis of enzymes involved in sulfate assimilation and in the formation of Fe-S clusters was also induced, suggesting an enhanced need for the formation or repair of Fe-S clusters in response to salt stress. One of the most obvious changes in the protein synthesis profile can be followed by the very strong induction of the SigB regulon. Furthermore, members of the SigW regulon and of the PerR regulon, indicating oxidative stress after salt challenge, were also induced. This proteomic approach provides an overview of cell adaptation to an osmotic upshift in B. subtilis visualizing the most dramatic changes in the protein synthesis pattern.     

Phenotypic characterization of <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis> under osmotic stress conditions using elementary mode analysis

Corynebacterium glutamicum, a soil bacterium, is used to produce amino acids such as lysine and glutamate. C. glutamicum is often exposed to osmolality changes in its medium, and the bacterium has therefore evolved several adaptive response mechanisms to overcome them. In this study we quantify the metabolic response of C. glutamicum under osmotic stress using elementary mode analysis (EMA). Further, we obtain the optimal phenotypic space for the synthesis of lysine and formation of biomass. The analysis demonstrated that with increasing osmotic stress, the flux towards trehalose formation and energy-generating pathways increased, while the flux of anabolic reactions diminished. Nodal analysis indicated that glucose-6-phosphate, phosphoenol pyruvate, and pyruvate nodes were capable of adapting to osmotic stress, whereas the oxaloacetic acid node was relatively unresponsive. Fewer elementary modes were active under stress indicating the rigid behavior of the metabolism in response to high osmolality. Optimal phenotypic space analysis revealed that under normal conditions the organism optimized growth during the initial log phase and lysine and trehalose formation during the stationary phase. However, under osmotic stress, the analysis demonstrated that the organism operates under suboptimal conditions for growth, and lysine and trehalose formation.     

短期盐胁迫下盐穗木的转录组分析

盐穗木（Halostachys caspica）是荒漠盐碱地广泛分布的盐生植物,具有极强的耐盐性。为揭示盐胁迫下盐穗木基因组层面的基因表达变化特性,通过对300和500mmol·L^-1 NaCl胁迫3h的盐穗木同化枝进行了转录组测序。有效序列组装共得到153298条平均长度为643bp的unigenes,进行GO和KEGG功能聚类,分别获得47个GO功能小类和118个KEGG通路。差异表达基因分析显示,短期低盐（300mmol·L^-1）响应基因有4432个,高盐（500mmol·L^-1）响应基因有2580个,两个胁迫的共差异基因有1245个,主要富集在细胞过程、代谢过程和响应刺激等类别中。从短期盐胁迫下盐穗木转录组筛选出渗透调节和活性氧清除的相关基因,大多为上调基因。说明盐穗木能够通过促进渗透调节和增强活性氧清除提高短期的盐胁迫适应能力。     

Genome-wide RNAi screen and in vivo protein aggregation reporters identify degradation of damaged proteins as an essential hypertonic stress response

The damaging effects of hypertonic stress on cellular proteins are poorly defined, and almost nothing is known about the pathways that detect and repair hypertonicity-induced protein damage. To begin addressing these problems, we screened approximately 19,000 Caenorhabditis elegans genes by RNA interference (RNAi) feeding and identified 40 that are essential for survival during acute hypertonic stress. Half (20 of 40) of these genes encode proteins that function to detect, transport, and degrade damaged proteins, including components of the ubiquitin-proteasome system, endosomal sorting complexes, and lysosomes. High-molecular-weight ubiquitin conjugates increase during hypertonic stress, suggesting a global change in the ubiquitinylation state of endogenous proteins. Using a polyglutamine-containing fluorescent reporter, we demonstrate that cell shrinkage induces rapid protein aggregation in vivo and that many of the genes that are essential for survival during hypertonic stress function to prevent accumulation of aggregated proteins. High levels of urea, a strong protein denaturant, do not cause aggregation, suggesting that factors such as macromolecular crowding also contribute to protein aggregate formation during cell shrinkage. Acclimation of C. elegans to mild hypertonicity dramatically increases the osmotic threshold for protein aggregation, demonstrating that protein aggregation-inhibiting pathways are activated by osmotic stress. Our studies demonstrate that hypertonic stress induces protein damage in vivo and that detection and degradation of damaged proteins are essential mechanisms for survival under hypertonic conditions.     

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

Background

Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.

Results

To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.

Conclusions

Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users.     

Autophagy is required for tolerance of drought and salt stress in plants

Autophagy is a protein degradation process in which cells recycle cytoplasmic contents when subjected to environmental stress conditions or during certain stages of development. Upon the induction of autophagy, a double membrane autophagosome forms around cytoplasmic components and delivers them to the vacuole or lysosome for degradation. In plants, autophagy has been shown previously to be induced during abiotic stresses including nutrient starvation and oxidative stress. In this paper, we demonstrate the induction of autophagy in high salt and osmotic stress conditions, concomitant with the upregulation of expression of an Arabidopsis thaliana autophagy-related gene AtATG18a. Autophagy-defective RNAi-AtATG18a plants are more sensitive to salt and drought conditions than wild-type plants, demonstrating a role for autophagy in the response to these stresses. NADPH oxidase inhibitors block autophagy induction upon nutrient starvation and salt stress, but not during osmotic stress, indicating that autophagy can be activated by NADPH oxidase-dependent or -independent pathways. Together our results indicate that diverse environmental stresses can induce autophagy and that autophagy is regulated by distinct signaling pathways in different conditions.     

盐生植物海滨锦葵幼苗盐胁迫下基因差异表达分析

利用cDNA-AFLP技术对海滨锦葵幼苗盐胁迫下叶片和根部的基因差异表达模式进行分析和比较, 并对部分盐胁迫应答的转录衍生片段进行了回收、测序和功能推测, 以从转录水平分析海滨锦葵的耐盐分子机制。结果显示：(1) 盐胁迫下海滨锦葵幼苗叶片和根部的基因差异表达多以量的变化为主, 包括盐胁迫下基因表达上调、下调或随盐处理浓度高低和胁迫时间长短而波动的差异表达模式; 只有少量基因的差异表达表现出质的变化, 如盐胁迫下基因沉默或诱导表达; (2) 仅在盐胁迫处理2 h的海滨锦葵幼苗根部, 基因的差异表达以质的变化为主的类型比例略高于量的变化类型比例; (3) 盐胁迫应答基因在不同组织中上调、下调、诱导或沉默的比例随胁迫处理时段而动态变化, 在刚胁迫时基因表达的差异加剧, 而后随胁迫处理时段的延长而渐趋稳定。结果预示, 从基因表达水平探讨植物的耐盐分子机理, 尽管有一定的规律可循, 但由于不同组织对盐胁迫的应答是动态变化的过程, 海滨锦葵不同组织在盐胁迫不同阶段的基因时、空、序表达特征并没有固定的程式。对部分盐胁迫下上调或诱导表达的转录衍生片段(Trivially distributed file system, TDFs)进行的序列分析和功能推测表明, 苗期海滨锦葵在盐胁迫下应答基因至少涉及3类：(1) 离子平衡重建或减少胁迫损伤相关基因(特别是运转蛋白类); (2) 恢复盐胁迫下植物生长和发育相关基因：如参与能量合成和激素调节途径相关基因等; (3)信号转导相关基因及功能未确定的新基因。文章并对盐胁迫应答基因的差异表达模式与海滨锦葵的耐盐性关系进行了讨论。