Genome-wide expression analysis of ahk mutants compared to Col-0 wild-type
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ABSTRACT: The experiment was designed to enable comparison between Columbia and ahk2/ahk3, ahk3/ahk4 double and ahk2/ahk3/ahk4 triple mutants Arabidopsis seedlings
Project description:The Columbia (Col-0) ecotype of Arabidopsis thaliana was used as wild type. lbd16, lbd18 single and lbd16 lbd18 double mutants were used as mutants.
Project description:Pro35SLBD16:GR or Pro35SLBD18:GR transgenic seedlings that overexpress LBD16 or LBD18 fused to glucocorticoidsteroid hormone binding domain(GR) under CaMV35S promoter were grown for 12 days under long-day conditions (16h light/ 8h dark).
Project description:DCA (3,5-Dichloroanthranilic acid) is a newly identified synthetic defense elicitor. To perform a comparative analysis of defense responses triggered by DCA and the structurally related defense inducer INA (2,6-Dichloroisonicotinic acid) Affymetrix chip experiments were performed with Arabidopsis thaliana seedlings treated with one of these two compounds. Experiment Overall Design: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study. Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment. Final DMSO concentrations never exceeded 0.002%. Mock treatments were application of 0.002% DMSO in water. For harvesting the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturerâ??s instructions. RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturerâ??s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility. Three independent biological replicates were performed for each treatment.
Project description:Early establishment of the apical-basal axis is prerequesite for correct embryonic development in Arabidopsis. The hypophysis is derived from the basal cell of the early embryo and is indispensible for root development; it gives rise to the root quiescent center and the central columella. Arabidopsis pvip1 pvip2 mutants show defects in embryonic root development and give rise to rootless seedlings. We used microarrays to study the gene regulation of rootless mutant embryos in comparison with wild type. Experiment Overall Design: Arabidopsis pvip1 pvip2 mutant and Col-0 wild type seedlings (10 days after germination) were compared using Affymetrix ATH1 arrays. Roots of wild type seedlings were removed and the vestigial hypocotyl of mutants was cut to control for wounding effects.
Project description:We exposed plants to methyl viologen (MV), a redox cycling herbicide in the light, and perform biochemical and Affymetrix ATH1 GeneChip experiments under conditions in which photosynthesis was active and the antioxidant response well conserved. Samples of total RNA were obtained from a pool of 25 Arabidopsis specimens from two independent biological replicates from the aerial parts of 2h MV-treated and non-treated control seedlings.
Project description:Arabidopsis Lon1 serves dual roles as a mitochondrial protease and chaperone. Loss of Lon1 function reduced autophagy flux at transcriptional, protein and cellular levels. Meanwhile, changes occurred in the levels of cellular subunit proteins, especially a significant upregulation of mitochondrial proteins overall in lon1 mutants. Lon1 is a key enzyme in maintaining mitochondrial protein homeostasis. In lon1 mutants, other mitochondrial proteases including mitochondrial autophagy receptor proteins showed significant increases in abundance. Mitophagy is an important mechanism for cellular quality control. lon1-2atg5-1 double mutant were constructed to investigate how they cooperatively regulate mitochondrial protein homeostasis. Transcriptome sequencing results revealed that Lon1 inactivation led to widespread unfolded protein responses (UPRs) pathway activation in lon1-2atg5-1, consistent with lon1-2, while loss function of ATG5 inactivation did not affect mitochondrial homeostasis. The double mutant also exhibited independent plant phenotypes from single parents, yet more severe seed number and embryo development issues, suggesting an additive effect of lon1-2 and atg5-1. Protein Storage Vacuole (PSV) and oil body phenotypes also showed more severe developmental damage in the double mutants. Brassinosteroid (BR) acts as a key plant hormone controlling seed and embryo development. GO and KEGG analysis of genes simultaneously downregulated in lon1-2, atg5-1, and lon1-2atg5-1 revealed significant downregulation of genes involved in BR biosynthesis and its homeostasis, indicating that this may be one of the key factors leading to abnormal seed and embryo development in the mutants. In general, the loss function of Lon1 reduces autophagy flux and induces UPRs to regulate protein homeostasis. Meanwhile, the simultaneous absence of Lon1 and autophagy significantly down-regulates the expression of genes related to BR biosynthesis and homeostasis, thereby leading to pronounced blockage in the development of double mutant seeds and embryos.
Project description:RNA prepared from specialized replum cells within siliques provided targets for profiling the Arabidopsis genome during replum cell development.