Intergenic sequence between Arabidopsis caseinolytic protease B-cytoplasmic/heat shock protein100 and choline kinase genes functions as a heat-inducible bidirectional promoter

In Arabidopsis (Arabidopsis thaliana), the At1g74310 locus encodes for caseinolytic protease B-cytoplasmic (ClpB-C)/heat shock protein100 protein (AtClpB-C), which is critical for the acquisition of thermotolerance, and At1g74320 encodes for choline kinase (AtCK2) that catalyzes the first reaction in the Kennedy pathway for phosphatidylcholine biosynthesis. Previous work has established that the knockout mutants of these genes display heat-sensitive phenotypes. While analyzing the AtClpB-C promoter and upstream genomic regions in this study, we noted that AtClpB-C and AtCK2 genes are head-to-head oriented on chromosome 1 of the Arabidopsis genome. Expression analysis showed that transcripts of these genes are rapidly induced in response to heat stress treatment. In stably transformed Arabidopsis plants harboring this intergenic sequence between head-to-head oriented green fluorescent protein and beta-glucuronidase reporter genes, both transcripts and proteins of the two reporters were up-regulated upon heat stress. Four heat shock elements were noted in the intergenic region by in silico analysis. In the homozygous transfer DNA insertion mutant Salk_014505, 4,393-bp transfer DNA is inserted at position 2517 upstream of ATG of the AtClpB-C gene. As a result, AtCk2 loses proximity to three of the four heat shock elements in the mutant line. Heat-inducible expression of the AtCK2 transcript was completely lost, whereas the expression of AtClpB-C was not affected in the mutant plants. Our results suggest that the 1,329-bp intergenic fragment functions as a heat-inducible bidirectional promoter and the region governing the heat inducibility is possibly shared between the two genes. We propose a model in which AtClpB-C shares its regulatory region with heat-induced choline kinase, which has a possible role in heat signaling

Fungal endophytes inhabiting mountain-cultivated ginseng (Panax ginseng Meyer) : diversity and biocontrol activity against ginseng pathogens

Fungal endophytes isolated from mountain-cultivated ginseng (MCG, Panax ginseng Meyer) were explored for their diversity and biocontrol activity against ginseng pathogens (Alternaria panax, Botrytis cinerea, Cylindrocarpon destructans, Pythium sp. and Rhizoctonia solani). A total of 1,300 isolates were isolated from three tissues (root, stem and leaf) from MCGs grown in 24 different geographic locations in Korea. In total, 129 different fungal isolates were authenticated by molecular identification based on internal transcribed spacer (ITS) sequences. The fungal endophytes belonged to Ascomycota (81.7%), Basidiomycota (7.08%), Zygomycota (10%) and Unknown (1.15%), with 59 genera. Analysis of diversity indices across sampling sites suggested species abundance as a function of geographical and environmental factors of the locations. Shannon diversity index and richness in the different tissues revealed that root tissues are colonized more than stem and leaf tissues, and also certain fungal endophytes are tissue specific. Assessment of the ethyl acetate extracts from 129 fungal isolates for their biocontrol activity against 5 ginseng pathogens revealed that Trichoderma polysporum produces the antimcriobial metabolite against all the pathogens. This result indicates the promise of its potential usage as a biocontrol agent

Drought-induced susceptibility for Cenangium ferruginosum leads to progression of Cenangium-dieback disease in Pinus koraiensis

Recently, the occurrence of "Cenangium-dieback" has been frequent and devastating. Cenangium-dieback is caused by an endophytic fungus Cenangium ferruginosum in stressed pine trees. Progression of the disease in terms of molecular interaction between host and pathogen is not well studied and there is a need to develop preventive strategies. Thus, we simulated disease conditions and studied the associated transcriptomics, metabolomics, and hormonal changes. Pinus koraiensis seedlings inoculated with C. ferruginosum were analyzed both under drought and well-watered conditions. Transcriptomic analysis suggested decreased expression of defense-related genes in C. ferruginosum-infected seedlings experiencing water-deficit. Further, metabolomic analysis indicated a decrease in the key antimicrobial terpenoids, flavonoids, and phenolic acids. Hormonal analysis revealed a drought-induced accumulation of abscisic acid and a corresponding decline in the defense-associated jasmonic acid levels. Pathogen-associated changes were also studied by treating C. ferruginosum with metabolic extracts from pine seedlings (with and without drought) and polyethylene glycol to simulate the effects of direct drought. From RNA sequencing and metabolomic analysis it was determined that drought did not directly induce pathogenicity of C. ferruginosum. Collectively, we propose that drought weakens pine immunity, which facilitates increased C. ferruginosum growth and results in conversion of the endophyte into the phytopathogen causing dieback

Plants can talk: a new era in plant acoustics

[EN]Plants release chemical signals to interact with their environment when exposed to stress. Khait and colleagues unveiled that plants ‘verbalize’ stress by emitting airborne sounds. These can train machine learning models to identify plant stressors. This unlocks a new path in plant-environment interactions research with multiple possibilities for future applications

Thematic analysis of big data in financial institutions using NLP techniques with a cloud computing perspective : a systematic literature review

This literature review explores the existing work and practices in applying thematic analysis natural language processing techniques to financial data in cloud environments. This work aims to improve two of the five Vs of the big data system. We used the PRISMA approach (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) for the review. We analyzed the research papers published over the last 10 years about the topic in question using a keywordbased search and bibliometric analysis. The systematic literature review was conducted in multiple phases, and filters were applied to exclude papers based on the title and abstract initially, then based on the methodology/conclusion, and, finally, after reading the full text. The remaining papers were then considered and are discussed here. We found that automated data discovery methods can be augmented by applying an NLP-based thematic analysis on the financial data in cloud environments. This can help identify the correct classification/categorization and measure data quality for a sentiment analysis

Expression analysis of sound vibration-regulated genes by touch treatment in Arabidopsis

Sound vibration (SV) is considered to be a mechanical stimulus which gives rise to various physiological and molecular changes in plants. Previously, we identified 17 SV-regulated genes (SRGs) which were up-regulated by SV treatments in Arabidopsis. Here, we analyzed the expression pattern of similar genes after an exposure of 500 Hertz at 80 decibels, for various time periods. Simultaneously, we confirmed the SV-mediated expression of these genes under lighted condition as many of them were reported to be dark-induced. For this, we designed an improved SV treatment chamber. Additionally, we checked the electrolyte leakage (EL), photosynthetic performance and expression of mechanosensitive (MS) ion channel genes after 5 days of SV treatment in the illuminated chamber. EL was higher, and the photosynthetic performance index was lower in the SV-treated plants compared to control. Seven out of the 13 MS ion channel genes were differentially expressed after the SV treatment. Simultaneously, we checked the touch mediated expression pattern of 17 SRGs and 13 MS ion channel genes. The distinct expression pattern of 6 SRGs and 1 MS ion channel gene generate an idea that SV as a stimulus is different from touch. Developmental stage-specific expression profiling suggested that the majority of the SRGs were expressed spatiotemporally in different developmental stages of Arabidopsis, especially in imbibed seed, seedlings and leaves

Exposure to sound vibrations lead to transcriptomic, proteomic and hormonal changes in Arabidopsis

Sound vibration (SV) is considered as an external mechanical force that modulates plant growth and development like other mechanical stimuli (e.g., wind, rain, touch and vibration). A number of previous and recent studies reported developmental responses in plants tailored against SV of varied frequencies. This strongly suggests the existence of sophisticated molecular mechanisms for SV perception and signal transduction. Despite this there exists a huge gap in our understanding regarding the SV-mediated molecular alterations, which is a prerequisite to gain insight into SV-mediated plant development. Herein, we investigated the global gene expression changes in Arabidopsis thaliana upon treatment with five different single frequencies of SV at constant amplitude for 1 h. As a next step, we also studied the SV-mediated proteomic changes in Arabidopsis. Data suggested that like other stimuli, SV also activated signature cellular events, for example, scavenging of reactive oxygen species (ROS), alteration of primary metabolism, and hormonal signaling. Phytohormonal analysis indicated that SV-mediated responses were, in part, modulated by specific alterations in phytohormone levels; especially salicylic acid (SA). Notably, several touch regulated genes were also up-regulated by SV treatment suggesting a possible molecular crosstalk among the two mechanical stimuli, sound and touch. Overall, these results provide a molecular basis to SV triggered global transcriptomic, proteomic and hormonal changes in plant

ClpB/Hsp100 proteins and heat stress tolerance in plants

High-temperature stress can disrupt cellular proteostasis, resulting in the accumulation of insoluble protein aggregates. For survival under stressful conditions, it is important for cells to maintain a pool of native soluble proteins by preventing and/or dissociating these aggregates. Chaperones such as GroEL/GroES (Hsp60/Hsp10) and DnaK/DnaJ/GrpE (Hsp70/Hsp40/nucleotide exchange factor) help cells minimize protein aggregation. Protein disaggregation is accomplished by chaperones belonging to the Caseinolytic Protease (Clp) family of proteins. ClpB/Hsp100 proteins are strikingly ubiquitous and are found in bacteria, yeast and multi-cellular plants. The expression of these proteins is regulated by heat stress (HS) and developmental cues. Bacteria and yeast contain one and two forms of ClpB proteins, respectively. Plants possess multiple forms of these proteins that are localized to different cellular compartments (i.e. cytoplasm/nucleus, chloroplast or mitochondria). Overwhelming evidence suggests that ClpB/Hsp100 proteins play decisive roles in cell adaptation to HS. Mutant bacteria and yeast cells lacking active ClpB/Hsp100 proteins are critically sensitive to high-temperature stress. Likewise, Arabidopsis, maize and rice mutants lacking cytoplasmic ClpB proteins are very sensitive to heat. In this study, we present the structural and functional attributes of plant ClpB forms

Voyaging around ClpB/Hsp100 proteins and plant heat tolerance

Temperature is one of the key physical parameters that fine tunes plant growth and development. However, above the optimal range, it can negatively affect the physiology of plants. Supraoptimal temperature brings incongruity in cellular proteostasis resulting in the build-up of insoluble toxic protein aggregates. To prevent protein misfolding and aggregation, cells deploy different strategies including synthesis of heat shock proteins (Hsp) belonging to different families, like small Hsps (sHsps), Hsp40, Hsp60, Hsp70. Once these aggregates are formed, their dissolution and recovery of the functional proteins occurs by the action of Caseinolytic Protease B (ClpB)/Hsp100, which are evolutionarily conserved in bacteria, fungi and plants. ClpB function during heat stress (HS) is important and appears indispensable, as mutant bacteria, yeast as well as plants lacking ClpB protein fail to survive HS. Genetic expression of ClpB proteins is modulated both by high temperature as well as developmental cues. Plant contains three isoforms of ClpB/Hsp100, one each localized to cytoplasm (ClpB-C), chloroplast (ClpB-P) and mitochondria (ClpB-M), against one in bacteria and two in yeast. Among these, ClpB-C protein in particular governs the thermotolerance response in plants. This review introduces plant ClpB proteins, summarizes the knowledge gained hitherto in ClpB biology, critically analyzes the recent findings and brings forth the areas requiring thrust in the upcoming research on ClpBs