Transcriptome analysis of Arthrobacter in the phyllosphere
ABSTRACT: Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
Project description:au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition. Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate. Keywords: gene knock-out, time course 6 dye-swap - CATMA arrays
Project description:The genus Collimonas consists of soil bacteria that are well known for their antifungal activity and for mycophagy, i.e. the ability to grow at the expense of living fungi. The aim of the current study was to gain a better understanding of the mechanisms of antagonism of Collimonas bacteria towards fungi, the involvement of the mycophagous phenotype, and the role of the fungus as a responsive partner in the interaction. In order to reach this aim, the bacterium Collimonas fungivorans and the fungus Aspergillus niger were confronted in vitro. Bacterial and fungal RNA were isolated at two time points during the interaction and analyzed by microarray analysis. Objective: Investigate the expression profile of a bacterium when it was challenged by the presence of an antagonist fungus (control was the expression profile of the bacterium when it was alone). In parallel investigate the expression profile of the antagonist fungus when it was challenged by the presence of the bacterium (control was the expression profile of the fungus when it was alone).(Additional file available in additional.zip)
Project description:au07-03_myb77 - wt/myb77 - Transcriptome analysis of Myb77 knock out mutant line or of Myb77fragment overxpressing transgenic line. - Plants were grown in vitro on 1/2 MS medium, 3% sucrose, 0.8% agar for 21 days under balance day cycle (12 hours daylight at 22°C; 12 hours dark at 20°C) in climate chamber. The whole plants were collected for RNAs extraction. Keywords: gene knock in (transgenic),gene knock out 4 dye-swap - CATMA arrays
Project description:Temperate bacteriophages (prophages) have recently been demonstrated in Campylobacter jejuni. However, what they do there is largely unknown. In the series of studies that are the subject of these submissions we have investigated the relative expression levels of proteins in C. jejuni isolates that differ in the presence or absence of the CJIE1 prophage. At the time of the initial investigations whole genome sequence data were not available for the isolates used, though DNA microarray data indicated that the isolates were very closely related. The overall project was carried out through four separate experiments. Previous work in the scientific literature indicated that growth on medium lacking blood but containing sodium deoxycholate induced the expression of at least some proteins associated with virulence and provided data thought to be of relevance to the virulence of the bacterium. The second set of experiments (experiment 2) therefore compared protein expression in 4-plex iTRAQ experiments using two isolates. Isolate 00-2425 carried the CJIE1 prophage while the second isolate, 00-2426, did not. Three replicate experiments were done. Each isolate was grown on Mueller Hinton agar base and Mueller Hinton agar containing 0.1% sodium deoxycholate.
Project description:rs09-09_della-dark - della-regulation in darkness versus light - Identification of DELLA-dependent downstream targets in darkness - Aim was to determine downstream target of DELLA proteins involved in skotomorphogenesis. Wt, ga1-3, ga1-3_rga_gai_rgl1_rgl2_rgl3 global seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4°C. Plates were placed in growth cabinet at 22°C for 5 days in darkness or in continous light. Keywords: gene knock out 9 dye-swap - CATMA arrays
Project description:rs10-04_mad - comparison of transcriptomes in mad mutants - What gene sets are differentially expressed in mad mutants? - Seeds of GFP171.1 (parental line), mad1, mad2, mad3, mad6 and dcl1-12 were sterilized and germinated on Murashige/Skoog medium with 0.9% agar. Plates were stratified at 4C in the dark for 4 days. The plates were then transferred to a growth cabinet at 21C under a 16h light/8h darkness light regime, and the seedlings were harvested 18 days after transfer to the growth cabinet. 10 dye-swap - genotype comparaison
Project description:rs06-07_della - della-regulation of salt stress responses - Identification of DELLA-dependent dowtream targets in response to salt stress - Aim was to determine downstream target of DELLA proteins involved in salt stress tolerance. Wt, ga1-3, penta seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4degreeC. Plates were placed in growth cabinet for 9 days. Seedlings were transferred to 24 well-plates, with 2 seedlings per well (0.5 ml MS liquid per well). Plates were placed in the same condition for 3 days. Finally, NaCl were added (final concentration 200 mM), except for the control. The salt treatment was applied for 30 min and 1h. Treatment was stopped by freezing in liquid nitrogen. Keywords: dose response,gene knock out,time course 12 dye-swap - CATMA arrays
Project description:au10-14_fer - response of ein3eil1 mutants to fe deficiency - Response of ein3eil1 mutants to Fe deficiency - Wild type seedlings and ethylene insensitive ein3eil1 seedlings were germinated and grown in the presence of 50 µM Fe or absence of Fe (0 µM) on Hoagland medium agar plates until the age of 6 days. Under these growth conditions symptoms of Fe deficiency develop in the 0 Fe plants. Ethylene is known to promote Fe acquisition responses. Whole seedlings were harvested for transcriptome analysis, in a total of three biological replicates. 12 dye-swap - gene knock out,treated vs untreated comparison
Project description:Temperate bacteriophages (prophages) have recently been demonstrated in Campylobacter jejuni. However, what they do there is largely unknown. In the series of studies that are the subject of these submissions we have investigated the relative expression levels of proteins in C. jejuni isolates that differ in the presence or absence of the CJIE1 prophage. At the time of the initial investigations whole genome sequence data were not available for the isolates used, though DNA microarray data indicated that the isolates were very closely related. The overall project was carried out through four separate experiments. In experiment 1, relative levels of protein expression of three isolates carryint the CJIE1 prophage were compared with one lacking the prophage after growth on Mueller-Hinton agar containing blood. Previous work in the scientific literature indicated that growth on medium lacking blood but containing sodium deoxycholate induced the expression of at least some proteins associated with virulence and provided data thought to be of relevance to the virulence of the bacterium. Therefore experiment 2 was done (previous submission) to evaluate in a single 4-plex iTRAQ experiment the effect of sodium deoxycholate on protein expression and whether the presence of the CJIE1 prophage had any effect. The third set of experiments (experiment 3) was done to consolidate the previous observations into a single experiment for a single strain. In three replicate experiments C. jejuni isolate 00-2425 was grown on Mueller Hinton (MH) agar base, MH agar + 10% blood, MH agar containing 0.1% sodium deoxycholate and, to further investigate the nature and extent of the bile response, MH agar containing 2.5% Oxgall.