Histidine kinase Hik33 is an important participant in cold-signal transduction in cyanobacteria

Acclimation of living organisms to cold stress begins with the perception and transduction of the cold signal. However, traditional methods failed to identify the sensors and transducers of cold stress. Therefore, we combined systematic mutagenesis of potential sensors and transducers with DNA microarray analysis in an attempt to identify these components in the cyanobacterium Synechocystis sp. PCC 6803. We identified histidine kinase Hik33 as a potential cold sensor and found that Hik33 participates in the regulation of the expression of more than 60% of the cold-inducible genes. Further study revealed that Hik33 is also involved in the perception of hyperosmotic stress and salt stress and transduction of the signals. Complexity of responses to cold and other environmental stresses is discussed.     

Exploitation of genomic sequences in a systematic analysis to access how cyanobacteria sense environmental stress

The perception and subsequent transduction of environmental signals are primary events in the acclimation of living organisms to changes in their environment. Many of the molecular sensors and transducers of environmental stress cannot be identified by traditional and conventional methods. Therefore, the genomic information has been exploited in a systematic approach to this problem, performing systematic mutagenesis of potential sensors and transducers, namely, histidine kinases and response regulators, respectively, in combination with DNA microarray analysis, to examine the genome-wide expression of genes in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Using targeted mutagenesis, 44 out of the 47 histidine kinases and 42 out of the 45 response regulators of this organism have successfully been inactivated. The resultant mutant libraries were screened by genome-wide DNA microarray analysis and by slot-blot hybridization analysis under various stress and non-stress conditions. Histidine kinases have been identified that perceive and transduce signals of low-temperature, hyperosmotic, and salt stress, as well as manganese deficiency.     

DNA microarray technology in toxicogenomics of aquatic models: methods and applications

Toxicogenomics represents the merging of toxicology with genomics and bioinformatics to investigate biological functions of genome in response to environmental contaminants. Aquatic species have traditionally been used as models in toxicology to characterize the actions of environmental stresses. Recent completion of the DNA sequencing for several fish species has spurred the development of DNA microarrays allowing investigators access to toxicogenomic approaches. However, since microarray technology is thus far limited to only a few aquatic species and derivation of biological meaning from microarray data is highly dependent on statistical arguments, the full potential of microarray in aquatic species research has yet to be realized. Herein we review some of the issues related to construction, probe design, statistical and bioinformatical data analyses, and current applications of DNA microarrays. As a model a recently developed medaka (Oryzias latipes) oligonucleotide microarray was described to highlight some of the issues related to array technology and its application in aquatic species exposed to hypoxia. Although there are known non-biological variations present in microarray data, it remains unquestionable that array technology will have a great impact on aquatic toxicology. Microarray applications in aquatic toxicogenomics will range from the discovery of diagnostic biomarkers, to establishment of stress-specific signatures and molecular pathways hallmarking the adaptation to new environmental conditions.     

从水分胁迫的识别到ABA积累的细胞信号转导

由于植物在生长和发育过程中不可避免地要遭受各种环境胁迫的影响,植物只有通过对环境胁迫的快速感知和主动反应才得以生存和发展.植物这种对环境胁迫的快速感知和主动反应体现在环境胁迫下植物可以通过一系列基因的表达调控来实现各种抗逆的生理生化反应.虽然得以鉴定的水分胁迫应答基因越来越多,但其中只有极少的基因在抗逆中的基本功能已得到初步认识.从细胞对水分胁迫原初信号的感知到基因表达调控包括了一系列复杂的细胞逆境信息传递过程.脱落酸(abscisic acid, ABA)作为重要的细胞逆境信号物质介导了一系列基因表达,因此从细胞对水分胁迫原初信号的感知到编码ABA生物合成关键酶基因的表达是一条最为关键的细胞逆境信息传递途径.逆境应答基因功能的鉴定以及对整个细胞信号传递过程中详尽的分子机制的了解无疑是今后最有趣的也是最为重要的研究课题.     

从水分胁迫的识别到ABA积累的细胞信号转导

由于植物在生长和发育过程中不可避免地要遭受各种环境胁迫的影响 ,植物只有通过对环境胁迫的快速感知和主动反应才得以生存和发展。植物这种对环境胁迫的快速感知和主动反应体现在环境胁迫下植物可以通过一系列基因的表达调控来实现各种抗逆的生理生化反应。虽然得以鉴定的水分胁迫应答基因越来越多 ,但其中只有极少的基因在抗逆中的基本功能已得到初步认识。从细胞对水分胁迫原初信号的感知到基因表达调控包括了一系列复杂的细胞逆境信息传递过程。脱落酸 (abscisicacid ,ABA)作为重要的细胞逆境信号物质介导了一系列基因表达 ,因此从细胞对水分胁迫原初信号的感知到编码ABA生物合成关键酶基因的表达是一条最为关键的细胞逆境信息传递途径。逆境应答基因功能的鉴定以及对整个细胞信号传递过程中详尽的分子机制的了解无疑是今后最有趣的也是最为重要的研究课题。     

Signal transduction during cold, salt, and drought stresses in plants

Abiotic stresses, especially cold, salinity and drought, are the primary causes of crop loss worldwide. Plant adaptation to environmental stresses is dependent upon the activation of cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Plants have stress-specific adaptive responses as well as responses which protect the plants from more than one environmental stress. There are multiple stress perception and signaling pathways, some of which are specific, but others may cross-talk at various steps. In this review article, we first expound the general stress signal transduction pathways, and then highlight various aspects of biotic stresses signal transduction networks. On the genetic analysis, many cold induced pathways are activated to protect plants from deleterious effects of cold stress, but till date, most studied pathway is ICE-CBF-COR signaling pathway. The Salt-Overly-Sensitive (SOS) pathway, identified through isolation and study of the sos1, sos2, and sos3 mutants, is essential for maintaining favorable ion ratios in the cytoplasm and for tolerance of salt stress. Both ABA-dependent and -independent signaling pathways appear to be involved in osmotic stress tolerance. ROS play a dual role in the response of plants to abiotic stresses functioning as toxic by-products of stress metabolism, as well as important signal transduction molecules and the ROS signaling networks can control growth, development, and stress response. Finally, we talk about the common regulatory system and cross-talk among biotic stresses, with particular emphasis on the MAPK cascades and the cross-talk between ABA signaling and biotic signaling.     

eIF2alpha phosphorylation, stress perception, and the shutdown of global protein synthesis in cultured CHO cells

The perception of environmental stress in animal cells engineered to produce heterologous protein leads to the induction of stress signaling pathways and ultimately apoptosis and cell death. Protein synthesis is regulated in response to various environmental stresses by phosphorylation of the alpha subunit of the eukaryotic initiation factor 2 (eIF2). In this study we have utilized a model system of Chinese hamster ovary cells engineered to secrete recombinant TIMP-1 protein to investigate the relationship between the cellular rate of protein synthesis, eIF2alpha phosphorylation, cellular stress perception, and the rate of cell specific recombinant protein synthesis. The rate of total protein synthesis was maximal after 48 hours of culture, remaining relatively high until 96 hours of culture, after which a decline was observed. Towards the end of culture a marked increase in labeled secreted protein was observed. Total eIF2alpha expression levels were high during the exponential growth phase and decreased slightly towards the end of culture. On the other hand, the relative expression of phosphorylated eIF2alpha showed a bi-phasic response with a small increase in phosphorylated eIF2alpha observed at 48 hours of culture, and a significant increase at 120 hours post-inoculation. The large increase in phosphorylated eIF2alpha coincided with the observed increase in labeled secreted protein and the decline in total cellular protein synthesis. A marked increase in ubiquitination was also observed at 120 hours post-inoculation that coincided with reduced rates of cellular protein synthesis and mRNA translation attenuation. We suggest that eIF2alpha phosphorylation is an indicator of cellular stress perception, which could be exploited in recombinant protein manufacturing to commence feeding and engineering strategies.     

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.     

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.     

Ca2+ signaling in plant responses to abiotic stresses

Adverse variations of abiotic environmental cues that deviate from an optimal range impose stresses to plants. Abiotic stresses severely impede plant physiology and development. Consequently, such stresses dramatically reduce crop yield and negatively impact on ecosystem stability and composition. Physical components of abiotic stresses can be, for example, suboptimal temperature and osmotic perturbations, while representative chemical facets of abiotic stresses can be toxic ions or suboptimal nutrient availability. The sheer complexity of abiotic stresses causes a multitude of diverse components and mechanisms for their sensing and signal transduction. Ca²⁺, as a versatile second messenger, plays multifaceted roles in almost all abiotic stress responses in that, for a certain abiotic stress, Ca²⁺ is not only reciprocally connected with its perception, but also multifunctionally ensures subsequent signal transduction. Here, we will focus on salt/osmotic stress and responses to altered nutrient availability as model cases to detail novel insights into the identity of components that link stress perception to Ca²⁺ signal formation as well as on new insights into mechanisms of Ca²⁺ signal implementation. Finally, we will deduce emerging conceptual consequences of these novel insights and outline arising avenues of future research on the role of Ca²⁺ signaling in abiotic stress responses in plants.     

Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis

During industrial production process using yeast, cells are exposed to the stress due to the accumulation of ethanol, which affects the cell growth activity and productivity of target products, thus, the ethanol stress-tolerant yeast strains are highly desired. To identify the target gene(s) for constructing ethanol stress tolerant yeast strains, we obtained the gene expression profiles of two strains of Saccharomyces cerevisiae, namely, a laboratory strain and a strain used for brewing Japanese rice wine (sake), in the presence of 5% (v/v) ethanol, using DNA microarray. For the selection of target genes for breeding ethanol stress tolerant strains, clustering of DNA microarray data was performed. For further selection, the ethanol sensitivity of the knockout mutants in each of which the gene selected by DNA microarray analysis is deleted, was also investigated. The integration of the DNA microarray data and the ethanol sensitivity data of knockout strains suggests that the enhancement of expression of genes related to tryptophan biosynthesis might confer the ethanol stress tolerance to yeast cells. Indeed, the strains overexpressing tryptophan biosynthesis genes showed a stress tolerance to 5% ethanol. Moreover, the addition of tryptophan to the culture medium and overexpression of tryptophan permease gene conferred ethanol stress tolerance to yeast cells. These results indicate that overexpression of the genes for trypophan biosynthesis increases the ethanol stress tolerance. Tryptophan supplementation to culture and overexpression of the tryptophan permease gene are also effective for the increase in ethanol stress tolerance. Our methodology for the selection of target genes for constructing ethanol stress tolerant strains, based on the data of DNA microarray analysis and phenotypes of knockout mutants, was validated.     

Pseudomonas putida modulates the expression of miRNAs and their target genes in response to drought and salt stresses in chickpea (Cicer arietinum L.)

MicroRNAs are small non-coding regulatory RNA molecules that play an important role in the modulation of gene expression during various environmental stresses. Pseudomonas putida RA, a plant growth promoting rhizobacteria (PGPR) colonizes the root surface of plants improving their growth and development during abiotic stresses modulating the expression of stress-responsive genes; however, the impact of RA on stress responsive-miRNA remains elusive. The present study was an attempt to delineate the role of PGPR in modulating stress responsive-miRNAs in a tolerant desi chickpea genotype exposed to drought and salt stresses. The existence of variable expression patterns of individual miRNAs and their target genes under these stresses at different time points indicate a distinct miRNA-mediated perception and response mechanisms operating under these stresses in the presence or absence of RA in chickpea.