Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon long-term starvation stress

ABSTRACT: This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to long-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 6 months after growth on a rich medium. Survival was monitored by plating, physiological response was examined by flow cytometry and FAME analysis, and this response was related to transcriptomic response as determined by whole-genome microarray analysis. The data showed that decreased gene functions involved in ribosomal proteins biosynthesis, decreased chromosomal replication, increased gene functions involved in stringent regulation of gene expression, increased gene functions involved in genetic exchange and recombination, increased efflux systems, increased degradation of rRNA, and increased M-NM-2-oxidation of fatty acids to access stored nutrients. Genes involved in PAH degradations appears to be with decreased expression. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 starved for 6 month in isotonic solution of 0.01 mM MgS04 was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium to an OD600 of 0.5, washed twice with 0.01 mM MgS04 and resuspended in the same solution to an OD of 0.5. RNA was extracted both from starved cells and from the initial culture (non-starved cells) and cDNA was synthesized and labeled with Cy3. Transcriptomic response of three replicates were analyzed and compared with the initial inoculum

ORGANISM(S): Sphingomonas sp. LH128

SUBMITTER: Tekle Tafese Fida

PROVIDER: E-GEOD-41814 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Spingomonas wittichii strain RW1 can completely oxidize dibenzo-p-dioxins and dibenzofurans, which are persistent contaminants of soils and sediments. For successful application in soil bioremediation systems, strain RW1 must cope with fluctuations in water availability, or water potential. The objectives of this study were to characterize how strain RW1 responses to changes in different components of the total water potential (solute and matric potential) and to then connect these responses to more realistic scenarios of soil desiccation. To accomplish this task, transcriptome profiling was used to investigate the effects of decreasing the solute potential with sodium chloride (solute stress), decreasing the matric potential with high-molecular weight polyethylene glycol (matric stress), or inoculating cells directly into unsaturated sand (sand desiccation stress). Transcriptome profiling revealed a general response to solute, matric, and sand desiccation stress that involved synthesizing trehalose and modifying the composition of exopolysaccarides. Transcriptome profiling also revealed responses that were unique to each stress. Only solute and matric stress triggered the down-regulation of flagella genes. Only solute and sand desiccation stress triggered the up-regulation of two RNA polymerase ECF-type sigma factors along with several membrane proteins, mechanosensitive channels, and solute transporters. Finally, only matric stress triggered the up-regulation of the RNA polymerase sigma-32 factor along with several molecular chaperones. Together, this study revealed a general response to solute, matric and sand desiccation stress but also unique responses to only a subset of these stresses, suggesting that each stress affects strain RW1 in a fundamentally different way. Comparative transcriptome profiling was performed to assess the effects of acute (30 min) solute and matric stress (3 samples for acute solute stress, 3 samples for acute matric stress, 3 controls), the effects of chronic (24 hours) solute and matric stress (3 samples for chronic solute stress, 3 samples for chronic matric stress, 3 controls), and the effects of sand desiccation stress (4 samples for sand desiccation treatment, 3 controls).

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Transcriptomic response of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. LH128 upon long-term starvation stress

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