Epigenetic memory and priming in plants.

In nature, plants are regularly exposed to biotic and abiotic stress conditions. These conditions create potential risks for survival. Plants have evolved in order to compete with these stress conditions through physiological adjustments that are based on epigenetic background. Thus, the ecological signals create different levels of stress memory. Recent studies have shown that this stress-induced environmental memory is mediated by epigenetic mechanisms that have fundamental roles in the aspect of controlling gene expression via DNA methylation, histone modifications and, small RNAs and these modifications could be transmitted to the next generations. Thus, they provide alternative mechanisms to constitute stress memories in plants. In this review, we summarized the epigenetic memory mechanisms related with biotic and abiotic stress conditions, and relationship between priming and epigenetic memory in plants by believing that it can be useful for analyzing memory mechanisms and see what is missing out in order to develop plants more resistant and productive under diverse environmental cues.

Molecular cloning and biotic elicitation response of phenylalanine ammonia-lyase gene of Astragalus chrysochlorus.

Phenylalanine ammonia lyase (PAL) is the first enzyme of the phenylpropanoid pathway, and it is necessary to upregulate flavonoid biosynthesis in most of the plant species. In this study, we have cloned PAL gene from endemic Astragalus chrysochlorus which is a producer of phenolic nicotiflorin (kaempferol-3-O-rutinoside). The cDNA encoding PAL was cloned from A. chrysochlorus using RT-PCR (reverse transcription-polymerase chain reaction) with conserved primer pairs. Amino acid sequence alignments showed that AcPAL (2160 bp, Accession number: KM189182) has more than 95% amino acid identity with their homologues in other Astragalus species. The coding sequence for the protein of AcPAL is 720 amino acids with a calculated molecular weight of 78.53 kDa. Full length AcPAL was cloned and expressed in Escherichia coli. qPCR (quantitative real-time PCR) analysis of the expression of PAL gene of A. chrysochlorus suggested that maximum transcript level was observed in 3 h yeast extract elicited suspension cells. Our findings suggest that AcPAL plays role in early response for yeast extract treatment. The isolation of AcPAL gene could be result in further studies for overproduction of secondary metabolite, nicotiflorin.

The AtMYB12 activation domain maps to a short C-terminal region of the transcription factor.

The Arabidopsis thaliana R2R3-MYB transcription factor MYB12 is a light-inducible, flavonol-specific activator of flavonoid biosynthesis. The transactivation activity of the AtMYB12 protein was analyzed using a C-terminal deletion series in a transient A. thaliana protoplast assay with the goal of mapping the activation domain (AD). Although the deletion of the last 46 C-terminal amino acids did not affect the activation capacity, the deletion of the last 98 amino acids almost totally abolished transactivation of two different target promoters. A domain swap experiment using the yeast GAL4 DNA-binding domain revealed that the region from positions 282 to 328 of AtMYB12 was sufficient for transactivation. In contrast to the R2R3-MYB ADs known thus far, that of AtMYB12 is not located at the rearmost C-terminal end of the protein. The AtMYB12 AD is conserved in other experimentally proven R2R3-MYB flavonol regulators from different species.

Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure.

Altered expression of tumor suppressor genes and oncogenes, which is regulated in part at the level of DNA methylation, is an important event involved in non-genotoxic carcinogenesis. This may serve as a marker for early detection of non-genotoxic carcinogens. Therefore, we evaluated the effects of non-genotoxic hepatocarcinogens, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), hexachlorobenzene (HCB), methapyrilene (MPY) and male rat kidney carcinogens, d-limonene, p-dichlorobenzene (DCB), chloroform and ochratoxin A (OTA) on global and CpG island promoter methylation in their respective target tissues in rats. No significant dose-related effects on global DNA hypomethylation were observed in tissues of rats compared to vehicle controls using LC-MS/MS in response to short-term non-genotoxic carcinogen exposure. Initial experiments investigating gene-specific methylation using methylation-specific PCR and bisulfite sequencing, revealed partial methylation of p16 in the liver of rats treated with HCB and TCDD. However, no treatment related effects on the methylation status of Cx32, e-cadherin, VHL, c-myc, Igfbp2, and p15 were observed. We therefore applied genome-wide DNA methylation analysis using methylated DNA immunoprecipitation combined with microarrays to identify alterations in gene-specific methylation. Under the conditions of our study, some genes were differentially methylated in response to MPY and TCDD, whereas d-limonene, DCB and chloroform did not induce any methylation changes. 90-day OTA treatment revealed enrichment of several categories of genes important in protein kinase activity and mTOR cell signaling process which are related to OTA nephrocarcinogenicity.

Transcriptomic analysis reveals responses to Cycloastragenol in Arabidopsis thaliana.

Cycloastragenol (CAG), a molecule isolated from 'Astragalus membranaceus', stimulates the telomerase activity and cell proliferation significantly. It has been proven that CAG has the ability to prevent some diseases in humans. In this study, we aimed to figure out the CAG effects on the different signaling mechanisms in plants and to broadly analyze the genome-wide transcriptional responses in order to demonstrate CAG as a new key molecule that can potentially help plants to overcome different environmental stresses. RNA-seq strategy was employed to assess the transcriptional profiles in A. thaliana calli. Our work primarily focused on an overall study on the transcriptomic responses of A. thaliana to CAG. A total of 22593 unigenes have been detected, among which 1045 unigenes associated with 213 GO terms were differentially expressed and were assigned to 118 KEGG pathways. The up-regulated genes are principally involved in cellular and metabolic processes in addition to the response to a stimulus. The data analysis revealed genes associated with defense signaling pathways such as cytochrome P450s transporter, antioxidant system genes, and stress-responsive protein families were significantly upregulated. The obtained results can potentially help in better understanding biotic and/or abiotic tolerance mechanisms in response to CAG.

Detection of Potato ring rot Pathogen Clavibacter michiganensis subsp. sepedonicus by Loop-mediated isothermal amplification (LAMP) assay.

Clavibacter michiganensis subsp. sepedonicus (CMS) is an important bacterial plant pathogen causing potato ring rot disease. Rapid diagnosis of CMS is crucial because of the economic losses caused by serious harvest losses. Although there are serological tests used in the rapid diagnosis of CMS, they are not widely used because of their low sensitivity. The DNA-based PCR methods, which are highly sensitive, do not have the possibility of on-site diagnosis, especially since they require serious laboratory infrastructure. In recent years, scientists have been working on alternative amplification methods to develop DNA-based point of care (POC) diagnostic methods. Accordingly, the loop-mediated isothermal amplification (LAMP) method, which was developed in the early 2000s, provides an important convenience for DNA-based tests to use in the field. Due to the unique design of primers, more amplification products could be create in a shorter time than conventional amplification methods without needing a temperature cycle, and it can be applied with the aid of a simple heater without requiring a laboratory environment. In this study, efficient LAMP method for the detection of CMS has optimized. For device-independent detection of LAMP products, colorimetric method and LFD has used.

Genetic, Morphological, and Biochemical Diversity of Argan Tree (Argania spinosa L.) (Sapotaceae) in Tunisia.

Argan trees are normally endemic to Morocco and Algeria, but hundreds of argan trees exist in Tunisia, some introduced from Morocco and some from unknown origins. The aim of the present study was to evaluate the genetic, morphological, and biochemical diversity of the argan trees in Tunisia. In this study, we used morphometric data collected from vegetative tissue, as well as pomological characteristics related to fruits, stones, and kernels. Genetic variation in 60 trees of Tunisian Argania spinosa L. was estimated using inter-simple sequence repeats (ISSRs). Mutation screening and genotyping by high-resolution melting (HRM) was performed to detect delta-6-desaturase (D6D) variants in the tested individuals, and finally fatty acid analysis of argan leaves with gas chromatography (GC) was performed. The plant materials used in this study originated from four different sites in Tunisia. Analysis of morphological characteristics showed large variability both within and between the studied collections. The analysis of ISSR polymorphisms gave information about the diversity within and between populations. HRM analysis showed that all 60 argan individuals were grouped into 10 different categories. The results of the gas chromatography analysis showed that the presence of omega-3 fatty acids EPA and DHA was noticeable in some argan leaves.

De Novo Transcriptome Assembly and Comparative Analysis Elucidate Complicated Mechanism Regulating Astragalus chrysochlorus Response to Selenium Stimuli.

Astragalus species are medicinal plants that are used in the world for years. Some Astragalus species are known for selenium accumulation and tolerance and one of them is Astragalus chrysochlorus, a secondary selenium accumulator. In this study, we employed Illumina deep sequencing technology for the first time to de novo assemble A. chrysochlorus transcriptome and identify the differentially expressed genes after selenate treatment. Totally, 59,656 unigenes were annotated with different databases and 53,960 unigenes were detected in NR database. Transcriptome in A. chrysochlorus is closer to Glycine max than other plant species with 43,1 percentage of similarity. Annotated unigenes were also used for gene ontology enrichment and pathway enrichment analysis. The most significant genes and pathways were ABC transporters, plant pathogen interaction, biosynthesis of secondary metabolites and carbohydrate metabolism. Our results will help to enlighten the selenium accumulation and tolerance mechanisms, respectively in plants.