Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rice plants under the Md2 (pF2.5) condition in shoot basal region

ABSTRACT: In this series of experiments, we wanted to study the transcriptional responses of plants to different levels of water limitation. For mild drought stress, we controlled water potential (a scientific concept for dryness of soil) by using an automated watering system. This system adds water to soil based on the pF values reported by a pF sensor in soil. pF is a classical and widely used index of water potential that was first defined by Schofield (1935). For severe stress conditions, we withheld watering or even dried plants on a lab bench. Here, the transcriptional profiles were compared between well-watered and Md2-treated rice seedling shoot basal region.
Md2 (Mild drought level 2): We designated Md2 as a term that means the level of drought severity corresponding to pF2.5, which is equal to a soil matric potential of -31.0 kPa. pF2.5: The value of pF shows the soil matric potential of -31.0 kPa. pF is an index that is equivalent to the effort required for plant root systems to extract water stored in soil.

ORGANISM(S): Oryza sativa

SUBMITTER: Junya Mizoi

PROVIDER: E-MTAB-4139 | 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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Transcription profiling of rice plants under the Md2 (pF2.5) condition in shoot basal region

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