Characterization of gene expression of QM from Caragana jubata, a plant species that grows under extreme cold

Network Pharmacology Integrated with Molecular Docking Elucidates the Mechanism of Wuwei Yuganzi San for the Treatment of Coronary Heart Disease

Introduction: The aim of this study was to investigate the pharmacological mechanism of Wuwei Yuganzi San (WYS) in treating coronary heart disease (CHD) using network pharmacology and molecular docking. Methods: The main active components, related targets, and the target genes related to WYS were investigated by the databases Traditional Chinese Medicine Systems Pharmacology and related articles. Information on the target genes of CHD was acquired through the OMIM database and GeneCards database, and the NCBI Gene Expression Omnibus DataSets (GSE71226) were used to acquire target genes of CHD. A Venn diagram was used to show the common targets of WYS and CHD. The compound-target-disease network was built up by Cytoscape 3.7.2, and the protein–protein interaction (PPI) network was acquired through the STRING database. ClusterProfiler and Pathview packages in RStudio software were used to conduct gene ontology enrichment analysis and KEGG pathway enrichment analysis to reveal the underlying mechanism. Finally, AutoDock Vina software was used to assess the binding affinity of significant ingredients and hub genes. Results: Thirty-four key ingredients of WYS in CHD were screened, which related to 59 targets in CHD. According to the results of enrichment analysis, 59 items in the biological process, 15 items in the molecular function, 10 items in the cellular component, and 52 signaling pathways were associated with efficacy. These processes and pathways were essential for cell survival and were related to several crucial factors of CHD, including a disintegrin and metalloprotease 17 (ADAM17), aldo-keto reductase family 1 member C2 (AKR1C2), albumin (ALB), protein kinase B (AKT1), and alcohol dehydrogenase 1C (ADH1C). Based on the outcomes of the PPI network, we selected ADAM17, AKR1C2, ALB, AKT1, ADH1C, and putative ingredients (sennoside D_qt, quercetin, and procyanidin B-5,3'- O-gallate) to perform molecular docking validation. From the molecular docking outcomes, some vital targets of CHD (including ADAM17, AKR1C2, ALB, AKT1, and ADH1C) could be related to form a stable combination with the putative ingredients of WYS. Conclusions: The network pharmacology and molecular docking study elucidated basically the mechanism of WYS in the treatment of CHD.

Dynamics of biomass and carbon sequestration across a chronosequence of Caragana intermedia plantations on alpine sandy land

Considering the variations in carbon concentrations among different plant components can significantly improve carbon storage estimates. The aim of this study was to estimate the biomass and carbon storage and sequestration in Caragana intermedia Kuang et H. C. Fu plantations for six different ages. The biomass and carbon sequestration in shrub biomass were quantified using a destructive method that involved analysing the carbon concentrations in the leaves, branches, stem bark, stem wood, roots > 5 mm, 2 mm < roots ≤ 5 mm, and roots ≤ 2 mm. The biomass and biomass carbon density of the C. intermedia plantations increased with the age of the stands. The biomass carbon density of the woody components was at its maximum in the 30-year-old plantation (14.27 ± 2.71 t·ha⁻¹), indicating that C. intermedia plantations in alpine sandy land are an important carbon pool. The carbon accumulation rate of the woody components was higher during the early stages of plantation development. The carbon concentrations differed significantly among the components but changed only slightly with the stand age. The weighted mean carbon concentration of the woody components, which was found to be 44%, must be considered when estimating the long-term carbon pools in C. intermedia plantations.

Molecular cloning and functional characterization of a QM protein in large yellow croaker (Larimichthys crocea)

Since it was proposed to be a tumor suppressor in 1991, QM protein has attracted intensive and wide attention in plants, animals and fungi research fields. Up to date, however, the function of QM protein in fish immunity remains unknown. In this investigation, a QM gene (named as LycQM gene) was cloned from large yellow croaker (Larimichthys crocea), and LycQM protein was expressed in Escherichia coli and purified. The LycQM gene was ubiquitously transcribed in multi-tissues, including spleen, muscle, heart, liver, intestine, blood and head kidney. By quantitative real-time RT-PCR analysis, we found the highest and the lowest expression level of LycQM gene in head kidney and in heart, respectively. Time course analysis showed that LycQM expression was obviously up-regulated in blood and head kidney after immunization with polyinosinic polycytidynic acid (poly I:C), formalin-inactive Gram-negative bacterium Vibrio parahaemolyticus and bacterial lipopolysaccharides (LPS). Moreover, as demonstrated by RNAi assays, LycQM protein could regulate the activity of phenoloxidase, a key enzyme in the proPO activation system of immunity. These results suggested that LycQM protein might play an important role in the immune response against microorganisms in large yellow croaker.

2-Cys peroxiredoxin responds to low temperature and other cues in Caragana jubata, a plant species of cold desert of Himalaya

A 2-Cys peroxiredoxin cDNA (CjPrx) was isolated and characterized from Caragana jubata, a temperate/alpine plant species of high altitude cold desert of Himalaya and Eurasia. The cDNA obtained was 1,064 bp long consisting of an open reading frame of 789 bp encoding 262 amino acids. The calculated molecular mass of the mature protein was 28.88 kDa and pI was 5.84. Deduced amino acid sequence of CjPrx shared a high degree homology with 2-CysPrx proteins from other plants. CjPrx had both the PRX_type 2-Cys domain and thioredoxin-like superfamily domains. CjPrx contained 26.72% α-helices, 6.87% β-turns, 20.61% extended strands and 45.80% random coils, and was a hydrophilic protein. Expression of CjPrx was modulated by low temperature, methyl jasmonate (MJ), salicylic acid and drought stress, but no significant change was observed in response to abscisic acid treatment. Among all the treatments, a strong up-regulation of CjPrx was observed in response to MJ treatment.

Expression profiling of bioactive genes from a medicinal plant Nigella sativa L

Plants respond to stress in part by modulating gene expression either constitutively or in an inducible manner which ultimately leads to the restoration of cellular homeostasis, detoxification of toxins, and recovery of growth. Upon introduction to various elicitors such as pathogen-associated molecular patterns, a massive reprogramming of plant gene expression is initiated. Differential display PCR offers rapid and multiple comparisons of gene expression to various stress durations and intensities. Nigella sativa has acclaimed many medicinal properties in traditional medicine. To explore the underlying molecular mechanisms in response to stress in the plants, Fusarium solani (a fungus) stress was induced at different time intervals ranging from 0 to 48 h. RNA was subjected to complementary DNA (cDNA) synthesis followed by PCR using different sets of anchored primers and arbitrary primers. The expression was visualized after silver staining on urea-PAGE. Out of the 23 upregulated re-amplified cDNA products, ten differential fragments showed significant homologies with domains related to cellular metabolism, signal transduction, and disease resistance. Such genes could be an informative source for developing genetically improved breeds under infectious stress.

Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya

The present work was conducted to understand the basis of adaptation in Caragana jubata in its niche environment at high altitude cold desert of Himalaya. Molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (LT), a major cue operative at high altitude. Importantly, these genes expressed in C. jubata in its natural habitat. Their homologues in Arabidopsis thaliana, Oryza sativa, and Glycine max did not exhibit similar trend of gene expression at LT. Constitutive expression and a quick up-regulation of the above genes suggested the ability of C. jubata to adjust its cellular machinery to maintain growth and development in its niche. This was reflected in LT₅₀ (the temperature at which 50% injury occurred) and LT mediated photosynthetic acclimatory response. Such molecular and physiological plasticity enables C. jubata to thrive in the high altitude cold desert of Himalayas.

Identification and expression analysis of CjLTI, a novel low temperature responsive gene from Caragana jubata

Using rapid amplification of cDNA ends, a full length cDNA (CjLTI) was cloned from apical buds of Caragana jubata, a plant species that grows under extreme cold. The cDNA obtained was 573 bp long consisting of an open reading frame of 351 bp encoding 116 amino acids. Homology analysis did not exhibit significant similarity with any sequence at NCBI database, therefore it was deduced as a novel gene. Secondary structure analysis suggested that the deduced CjLTI contained 25.86% α-helices, 4.31% β-turns, 6.90% extended strands, and 62.93% random coils. The hydropathy profile suggested CjLTI to be a hydrophobic protein having characteristic features of signal peptides at N-terminus. The gene exhibited down-regulation at 5 min of exposure to low temperature (LT, 4 ± 3 °C) followed by a strong up-regulation after 15 min and onwards. Methyl jasmonate (MJ) lead to up-regulation of CjLTI starting at 5 min onwards. The gene exhibited up- and down-regulation of expression pattern in response to abscisic acid (ABA) and salicylic acid (SA). Mild drought stress slightly up-regulated gene expression and at severe drought (up to 115% reduction in leaf water potential) slight down-regulation of gene expression was observed. These results suggested CjLTI to be a LT responsive gene wherein MJ, ABA and SA pathways might be involved in regulating the gene expression.

An RNA isolation system for plant tissues rich in secondary metabolites

Background

Secondary metabolites are reported to interfere with the isolation of RNA particularly with the recipes that use guanidinium-based salt. Such interference was observed in isolation of RNA with medicinal plants rheum (Rheum australe) and arnebia (Arnebia euchroma). A rapid and less cumbersome system for isolation of RNA was essential to facilitate any study related to gene expression.

Findings

An RNA isolation system free of guanidinium salt was developed that successfully isolated RNA from rheum and arnebia. The method took about 45 min and was successfully evaluated on twenty one tissues with varied secondary metabolites. The A_260/280 ratio ranged between 1.8 - 2.0 with distinct 28 S and 18 S rRNA bands visible on a formaldehyde-agarose gel.

Conclusions

The present manuscript describes a rapid protocol for isolation of RNA, which works well with all the tissues examined so far. The remarkable feature was the success in isolation of RNA with those tissues, wherein the most commonly used methods failed. Isolated RNA was amenable to downstream applications such as reverse transcription-polymerase chain reaction (RT-PCR), differential display (DD), suppression subtractive hybridization (SSH) library construction, and northern hybridization.

Molecular mechanisms underlying frost tolerance in perennial grasses adapted to cold climates

We review recent progress in understanding cold and freezing stress responses in forage grass species, notably Lolium and Festuca species. The chromosomal positions of important frost tolerance and winter survival QTLs on Festuca and Lolium chromosomes 4 and 5 are most likely orthologs of QTLs on Triticeae chromosome 5 which correspond to a cluster of CBF-genes and the major vernalization gene. Gene expression and protein accumulation analyses after cold acclimation shed light on general responses to cold stress. These responses involve modulation of transcription levels of genes encoding proteins involved in cell signalling, cellular transport and proteins associated with the cell membrane. Also, abundance levels of proteins directly involved in photosynthesis were found to be different between genotypes of differing frost tolerance levels, stressing the importance of the link between the function of the photosynthetic apparatus under cold stress and frost tolerance levels. The significance of the ability to undergo photosynthetic acclimation and avoid photoinhibition is also evident from numerous studies in forage grasses. Other interesting candidate mechanisms for freezing tolerance in forage grasses are molecular responses to cold stress which have evolved after the divergence of temperate grasses. This includes metabolic machinery for synthesis of fructans and novel ice-binding proteins.

Identification of candidate genes important for frost tolerance in Festuca pratensis Huds. by transcriptional profiling

Studies of differential gene expression between cold acclimated (CA) and non-cold acclimated (NA) plants yield insight into how plants prepare for cold stress at the transcriptional level. Furthermore genes involved in the cold acclimation process are good candidate loci for genetic variation in frost tolerance and winter survival. In this study we combine different approaches to try to decode the genetics of cold acclimation and frost tolerance in meadow fescue (Festuca pratensis Huds). An EST library of cold acclimation responsive genes was established by suppression subtractive hybridization (SSH), and a microarray experiment was used to identify gene expression differences between high and low frost tolerance genotypes in response to cold acclimation. Many genes known to be involved in CA in other species were confirmed to be involved in CA in F. pratensis, however, 18% of the ESTs did not show significant homology to any database proteins. Seven genes were found to be differentially expressed (>2-fold) between high and low frost tolerance genotypes. Two of these genes, FpQM and FpTPT, represent interesting candidate genes for frost tolerance in perennial forage grasses.

Abscisic acid response element binding factor 1 is required for establishment of Arabidopsis seedlings during winter

Abscisic acid (ABA) plays a crucial role in abiotic stress response apart from its influence on growth and development of a plant. Our studies on abscisic acid response element binding factor 1 (ABF1) gene in Arabidopsis demonstrate that it is required for seedling establishment during winter. ABF1 is also involved in regulating seed dormancy and seed germination to some extent. Analysis of transcriptional activity of ABF1 promoter reveals that ABF1 expresses specifically in trichomes of young leaves and constitutively in cotyledons, roots, older leaves and flowers. The expression is induced upon exposure to ABA, cold and heat. The alignment of cDNAs of ABF1 (At1g49720) and At1g49730 (encodes a protein kinase of unknown function), reveals an overlap of 88 bp at their 3' UTR region suggesting that they can potentially form natural cis-antisense mRNAs pair in a tail-to-tail manner. Analysis by Genevestigator microarray stress response viewer further supports the regulatory role of these genes. An inverse proportion is observed in the transcription the two loci in number of stress responses. The abf1 mutants do not show any seedling establishment defects when grown under standard growth conditions. The mutant seedlings exhibit growth defects during winter in the western Himalayan region. Our study also signifies the importance of functional analysis for mutant phenotypes in natural habitats by reverse genetic approaches, in order to identify specific function of particular gene/s whose expression level is altered upon exposure to changes in environmental cues such as temperature and light.

Ectopic expression of a grapevine transcription factor VvWRKY11 contributes to osmotic stress tolerance in Arabidopsis

Plant WRKY transcriptional factors play an important role in response to biotic and abiotic stresses. In this study, a WRKY transcription factor was isolated from grapevine. This transcription factor showed 66% and 58% identity at the DNA and amino acid sequence levels, respectively, with Arabidopsis AtWRKY11 genes, and was therefore designated VvWRKY11. Phylogenetic analysis and structure comparison indicated that VvWRKY11 protein belongs to group IIc. The VvWRKY11 protein was shown to be located in the nucleus based on green fluorescent protein analysis. Yeast one-hybrid analysis further indicated that VvWRKY11 protein binds specifically to the W-box element. The expression profile of VvWRKY11 in response to treatment with phytohormone salicylic acid or pathogen Plasmopara viticola is rapid and transient. Transgenic Arabidopsis seedlings overexpressing VvWRKY11 showed higher tolerance to water stress induced by mannitol than wild-type plants. These results clearly demonstrated that the VvWRKY11 gene is involved in the response to dehydration stress. In addition, the role of VvWRKY11 protein in regulating the expression of two stress response genes, AtRD29A and AtRD29B, is also discussed.