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Changes in translational state from 1 day to 8 day after inoculation in Arabidopsis thaliana T87 cells

ABSTRACT: We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE52468 | GEO | 2013/12/10

SECONDARY ACCESSION(S): PRJNA229061

REPOSITORIES: GEO

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Project description:Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. Comparison of translatome profile changes with corresponding transcriptome profile changes can provide a measure of the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. To provide a direct experimental evaluation of the phenomenon, we decided to study a classical example of transcriptional reprogramming of gene expression: Epidermal Growth Factor (EGF) treatment. This stimulus triggers a well known chain of intracellular transduction events, ultimately resulting in a multifaceted phenotypic spectrum of changes with prevalent induction of cell growth and proliferation. We subjected HeLa cells to serum starvation for 12h and then we added EGF at final concentration of 1 Î¼g/ml, profiling before and after 40 minutes of treatment the transcriptome, the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation, and also the mRNA content of the subpolysomal pool, expected not to be actively translated. Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, EGF starvation release. The comparison between transcriptional and polysomal profiling was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved HeLa cells transcriptome in response to EGF stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA, subpolysomal RNA and total RNA were isolated from HeLa cells serum starved and treated with EGF. Cells lysates were collected before (t = 0 min) and after (t = 40 min) EGF treatment. All experiments were run in triplicates.

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Changes in translational state from 1 day to 8 day after inoculation in Arabidopsis thaliana T87 cells

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