Project description:Lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17) are two bacterial compounds that have been shown to positively influence plant growth of both legumes and non-legumes. Arabidopsis thaliana responded positively to treatment with the bacterial signal compounds LCO and Th17 in the presence of salt stress (up to 250 mM NaCl). Shotgun proteomics of unstressed and 250 mM NaCl stressed A. thaliana rosettes (7 days post stress) in combination with the LCO and Th17 revealed many known, putative, hypothetical and unknown proteins. Overall, carbon and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with these signals. PEP carboxylase, Rubisco-oxygenase large subunit, pyruvate kinase, and proteins of photosystem I and II were some of the noteworthy proteins enhanced by the signals, along with other stress related proteins. These findings suggest that the proteome of A. thaliana rosettes is altered by the bacterial signals tested, and more so under salt stress, thereby imparting a positive effect on plant growth under high salt stress. The roles of the identified proteins are discussed here in relation to salt stress adaptation, which, when translated to field grown crops can be a crucial component and of significant importance in agriculture and global food production.
Project description:Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papillionoid legumes. In contrast to symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we analyzed RNA-seq data of free-living P. phymatum growing under nitrogen replete and limited conditions, the latter partially mimicking the situation in nitrogen deprived soils. Among the genes up-regulated under nitrogen limitation, we found genes involved in exopolysaccharide production and motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly up-regulated during symbiosis, we identified an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities suggesting an important role of the cytochrome for respiration inside the nodule. Analysis of mutant strains for RNA polymerase transcription factor rpoN (σ54) and its activator NifA indicated that – similar to the situation in α-rhizobia – P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris. Overall design: Unraveling the molecular basis of the nitrogen-fixing symbiosis between P. vulgaris and P. phymatum.
Project description:Congenital myasthenic syndromes (CMS) are a group of rare, inherited disorders characterised by compromised function of the neuromuscular junction (NMJ), manifesting with fatigable muscle weakness. Mutations in MYO9A were previously identified as causative for CMS but the precise pathomechanism remained to be characterised. Based on the role of MYO9A as a negative regulator of RhoA and an actin-based molecular motor, loss of MYO9A was hypothesised to affect the neuronal cytoskeleton, thus leading to impaired vesicular protein transport within the neuron. MYO9A-depleted NSC-34 cells (mouse motor neuron-derived cells) were used to assess the effect on the cytoskeleton revealing altered expression of a number of cytoskeletal proteins important for neuronal cell structure and intracellular transport. Based on these findings, the effect on vesicular protein transport was determined using a vesicular recycling assay revealing impaired recycling of neuronal relevant growth factor receptor. In addition, an unbiased approach utilising proteomic profiling of control and MYO9A-depleted NSC-34 cells was utilised to identify key players of the pathophysiology. Proteomic data support a role for defective vesicular transport and identified affected proteins which are also involved in the manifestation of other neuromuscular disorders. Prompted by the clear indication of perturbed protein transportation, further proteomics-based secretomic analysis of NSC-34 cells have been performed to identify whether secretion is similarly affected. Indeed, this led to the identification of a potential therapeutic target, agrin. Zebrafish lacking MYO9A orthologues (myo9aa/ab) were treated with "Agrin Biologic", an agrin compound, and amelioration of defects in neurite extension and in movement of the zebrafish was observed. Our combined data not only allow new insights into the pathophysiology of CMS and show that loss of MYO9A affects the neuronal cytoskeleton, leading to impaired transport and vesicular recycling of proteins, but on a more general note also represent a successful biomedical approach: from the identification of the underlying pathomechanism to the definition of a therapeutic intervention concept.
Project description:time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops Overall design: 6 samples of Medicago truncatula seedlings grown two weeks in hydroponics media 200mM NaCl salt stress material collect at 0, 1, 2, 5, 10, 24 hour after salt stress beginning 2 ug of total RNA was used to synthesize doublestranded cDNA
Project description:In this time course pregnant CD-1 (outbred) dams were exposed to the 2-chloro analogue of 2'-deoxyadenosine (a metabolic toxin) on 8 d.p.c. The test dose of 2.5 mg/kg 2CdA was modeled for a 5% increased risk of microphthalmia in term fetuses. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively blocks p53 protein induction and developmental toxicity induced with 2CdA. Sampling intervals were anchored to the conditional biomarker (p53 protein induction) expressed in 2CdA-treated embryos between 3.0- and 4.5h post-exposure. Since p53 protein induction has been defined as a critical event in 2CdA-induced microphthalmia, these sampling intervals represent times before (3.0h), during (4.5h), and after (6.0h) this critical event. No p53 induction is observed in embryos co-treated with 2CdA and PK11195. All measurements were on RNA from the embryonic headfold. Keywords = time series Keywords = 2-chloro-2'-deoxyadenosine Keywords = PK11195 Keywords = embryo Keywords = p53 protein induction Keywords = microphthalmia Keywords: time-course
Project description:In this time course pregnant CD-1 (outbred) dams were exposed to MeHg as monomethylmercuric chloride intraperitoneally on 9 d.p.c. The test dose of 5.0 mg/kg MeHg was selected as a dose with an estimated 20% increased risk for encephalopathy in term fetuses, with no evidence of maternal toxicosis. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively suppresses developmental toxicity induced with MeHg. The anticipated remediation with 5.0 mg/kg and 4.0 mg/kg PK11195 is <10% malformations. Sampling intervals ranged from 3.0h to 6.0h post-exposure. All measurements were on RNA from the embryonic forebrain (prosencephalon). Keywords = time series Keywords = mercury Keywords = PK11195 Keywords = embryo Keywords = Fetal Minamata Disease Keywords: time-course
Project description:time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops Overall design: 4 samples of Medicago truncatula germinated seedlings grown in Petri dishes for 3 days 180mM NaCl salt stress material collect at 0, 6, 24, 48 hour after salt stress beginning 3 biological replicates 2 ug of total RNA was used to synthesize doublestranded cDNA
| GSE13921 | GEO
Project description:Transcriptome sequencing and marker development for four underutilized legumes