Lipids are vital cellular constituents in plant, and lipid peroxidation metabolites are critical defence substances in plants. In this study, mass spectrometry along with projections to latent structures discriminant analysis (PLS-DA) was used to detect lipid metabolism changes in Arabidopsis thaliana in response to oligochitosan (an effective resistance elicitor for the control of plant diseases). The PLS-DA showed that lipid metabolites of Arabidopsis thaliana were influenced by oligochitosan treatment. The total content of oxylipin containing monogalactosyldiacylglycerols, oxylipin-containing digalactosyldiacylglycerols, and oxylipin-containing phosphatidylglycerols increased firstly (after 1 h), and then decreased with the increase of oligochitosan treatment duration. In contrast, the total content of monogalactosyldiacylglycerols, phosphatidylcholines, phosphatidyl-ethanolamine, and phosphatidylglycerols decreased firstly, and then increased with the increase of oligochitosan treatment duration. The amounts of free fatty acids (C16:2, C16:3, C18:2, and C18:3) were lower after treatment with oligochitosan for 1, 3, and 6 h than in the control, while the production of volatile organic compounds such as 2-hexenal (except for 3 h) and nonanal was higher than in the control. In conclusion, lipid metabolites of Arabidopsis thaliana were influenced by oligochitosan treatment, and the synthesized lipids and oxylipin-containing lipids were remodelled and free fatty acids was metabolized to volatile organic compounds.

Potassium (K) plays an important role in plant development and in plant responses to various environmental stresses; however, its involvement in the mitigation of heavy metal stress by altering the binding capacity of the cell wall in Arabidopsis thaliana remains elusive. Here, we examined the effect of K (0–12 mM) in the regulation of cadmium (Cd) resistance in Arabidopsis thaliana. Toxic levels of Cd (50 μM) cause chlorosis in young leaves; however, the application of 3 mM K significantly alleviated this symptom in Arabidopsis thaliana, while other K concentrations did not rescue this phenotype. Moreover, 3 mM K significantly increased cell wall polysaccharide (hemicellulose) content and Cd adsorption in the root cell walls, suggesting that the modification of the cell wall composition is responsible for the Cd retention in the root under 3 mM K application. The 3 mM K treatment significantly reduced the expression of genes related to Cd uptake when plants were exposed to Cd, implying a decrease in Cd entering the cells. Furthermore, endogenous Nitric oxide (NO) was demonstrated to be involved in 3 mM K ameliorated-Cd toxicity as nia1nia2 and noa1 mutants, which are defective in NO biosynthesis, this positive effect of 3 mM K on Cd toxicity was abolished. Taken together, our results indicated that the 3 mM K alleviated deleterious effects of Cd by modifying the cell wall Cd binding capacity, particularly through the regulation of the NO accumulation in Arabidopsis thaliana.

CmFT homologous gene in muskmelon was obtained by homologous cloning, introducing CmFT gene by Agrobacterium-mediated transformation. The results of subcellular localization showed that CmFT protein was expressed in cytoplasm and nucleus. qRT-PCR results showed that the expression levels of AtLFY, AtFT, AtCO, AtFLC, AtSOC1 and AtAP1 were upregulated in the 35S::MeFT Arabidopsis line. The CmFT gene was introduced into wild-type Arabidopsis by Agrobacterium-mediated transformation, and the growth status of T2 transgenic Arabidopsis thaliana and wild-type A. thaliana was observed. The results showed that wild-type Arabidopsis began to bolt on the 25th day after sowing, we can initially confirm that the FT gene of melon can promote the early flowering of melon in the growth and development of melon.

An ethyl acetate extract of Arabidopsis thaliana plants was tested for the presence of endogenous suppressor(s) (ES), and the active fraction, which partitioned into water phase contained a molecule(s) < 3000 Da based on a rough estimate using sized membrane filters. Foliar application of the ES enabled typically nonpathogenic fungi (non-adapted pathogens) to cause disease symptoms on A. thaliana. Consistently, the ES fraction severely suppressed the oxidative burst and the expression of defense-related genes such as FRK1, NHO1, WRKY22, WRKY29, PEN2, and PEN3 in plants challenged with non-adapted fungus Colletotrichum gloeosporioides or the fungal elicitor chitin.

OBJECTIVES: To uncover key genes and pathways regulated by SCL3, a GRAS transcription factor, in the context of gibberellin (GA) in the roots of the model plant Arabidopsis thaliana. RESULTS: Gene expression profiles of ga1-3 mutant and ga1-3 and scl3 double mutant are considerably similar to each other, revealed by Principal Component Analysis (PCA). More than 400 significantly Differentially Expressed Genes (DEGs) among the Arabidopsis thaliana roots of ga1-3 mutant, ga1-3 and scl3 double mutant and GA loss/SCL3 gain mutant were uncovered by comprehensive bioinformatics analyses. Protein synthesis pathway, including RPL proteins, RPS proteins, etc., and flavonoid biosynthesis pathway, including TT4, F3H, TT5, CHIL, etc. were significantly increased when SCL3 expression was higher than normal by means of pathway enrichment analysis and protein–protein interaction analysis, which is further supported by comparison analyses between wild type samples and SCL3 overexpressed roots. CONCLUSION: Protein synthesis and flavonoid biosynthesis were regulated by SCL3 in the context of GA in Arabidopsis thaliana root system identified by comprehensive bioinformatic analyses.

Epigenetic regulation by DNA methylation and histone marks is crucial to plant development. In Arabidopsis, the otu5 mutant exhibited altered root phenotypes resembling those of phosphate-deficient plants. In low phosphate (Pi) conditions, altered H3K4 and H3K27 trimethylation were associated with the expression of Pi homeostasis-related genes. However, the genetic effect of OTU5 on the epigenomes was left unexplored. We assessed genome-wide DNA methylation, gene expression and histone modifications of roots from both Col-0 and otu5 mutants. We found that OTU5 altered DNA methylation profile with a context-specific effect through targeting local genomic regions. Our analysis showed that in otu5 the abundance of H3K4me3 was clearly associated with the changes of DNA methylation, leading to the transcriptional difference from wildtype. We concluded that OTU5 induced cross-talks among epigenomes that altogether impacted the regulation of approximately 7060 genes. Of which 186 genes associated with root development were likely to be epigenetically regulated.

Abstract Background Introns have been shown to be spliced in a defined order, and this order influences both alternative splicing regulation and splicing fidelity, but previous studies have only considered neighbouring introns. The detailed intron splicing order remains unknown. Results In this work, a method was developed that can calculate the intron splicing orders of all introns in each transcript. A simulation study showed that this method can accurately calculate intron splicing orders. I further applied this method to real S. pombe, fruit fly, Arabidopsis thaliana, and human sequencing datasets and found that intron splicing orders change from gene to gene and that humans contain more not in-order spliced transcripts than S. pombe, fruit fly and Arabidopsis thaliana. In addition, I reconfirmed that the first introns in humans are spliced slower than those in S. pombe, fruit fly, and Arabidopsis thaliana genome-widely. Both the calculated most likely orders and the method developed here are available on the web. Conclusions A novel computational method was developed to calculate the intron splicing orders and applied the method to real sequencing datasets. I obtained intron splicing orders for hundreds or thousands of genes in four organisms. I found humans contain more number of not in-order spliced transcripts.

In recent years, the study of plant three-dimensional nuclear architecture received increasing attention. Enabled by technological advances, our knowledge on nuclear architecture has greatly increased and we can now access large data sets describing its manifold aspects. The principles of nuclear organization in plants do not significantly differ from those in animals. Plant nuclear organization comprises various scales, ranging from gene loops to topologically associating domains to nuclear compartmentalization. However, whether plant three-dimensional chromosomal features also exert similar functions as in animals is less clear. This review discusses recent advances in the fields of three-dimensional chromosome folding and nuclear compartmentalization and describes a novel silencing mechanism, which is closely linked to nuclear architecture.

Arabidopsis thaliana seedlings exhibit longer hypocotyls when they are grown under high ambient temperature, which is defined as thermomorphogenesis. Although it is well established that high temperature triggers auxin biosynthesis to stimulate hypocotyl elongation, the physiological functions of other endogenous phytohormones during thermomorphogenesis are still elusive. Here, we report that exogenous application of abscisic acid (ABA) strongly inhibits hypocotyl elongation under high ambient temperature. Hypocotyl elongations of ABA biosynthesis deficient mutants are more sensitive to high temperature, suggesting that endogenous ABA has a robust inhibition effect. Moreover, blocking ABA perception or signaling impedes the negative effect of ABA. Finally, we show that ABA also suppresses the hypersensitivity to high temperature of an auxin over-accumulation mutant (yuc1D), indicating that activation of auxin signaling is not sufficient to override the repression by ABA. Taken together, we demonstrate that ABA is a negative regulator during plant thermomorphogenesis.