Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed. A two chip study using total RNA recovered from wild-type and motile strains of Sphingomonas. sp A1 grown in 0.5% alginate medium.
Project description:Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the toxic polyaromatic hydrocarbon dibenzofuran (dbf) and its polychlorinated derivatives. Its genome consists of a chromosome and two plasmids, encoding for more than 5300 genes. We studied genome-wide expression of strain RW1 to dbf in three different experimental setups, including both batch cultures and chemostats, comparing in all cases to the transcriptome of cells grown on phenylalanine as carbon source. A short exposure to DBF in chemostat or in batch, provoked the up-regulation of the ECF sigma 24, catalases, peroxiredoxins, chaperones, an aquaporin, several OmpA domain-containing proteins and the down-regulation of genes involved in TCA cycle, oxidative phosphorylation, amino acid metabolism and ribosomal proteins. When growing strain RW1 on DBF, genes known to be involved in DBF degradation were induced 2 to 4 fold. Additionally, two cluster of genes, putatively participating in the gentisate and meta-cleavage branches of the DBF degradation pathway, were induced from 12 to 19 fold.
Project description:The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 inoculated into phenanthrene contaminated soil after 4h and after 10 days of incubation was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium and inoculated at appropriated celld densitites. RNA was extracted both from soil and and from initial inoculum and cDNA was synthesized and labeled with Cy3. Transcriptomic response in soil of three replicates per conditions after both incubation duration were analyzed and compared with the initial inoculum
