Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast

María Micaela Molina-Navarro,Laia Castells-Roca,Gemma Bellí,José García-Martínez,Julia Marín-Navarro,Joaquín Moreno,José E Pérez-Ortín,Enrique Herrero

doi:10.1074/jbc.m800295200

María Micaela Molina-Navarro, Laia Castells-Roca + Show 6 more

Open Access

https://doi.org/10.1074/jbc.m800295200

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Abstract

The oxidative stress response in Saccharomyces cerevisiae has been analyzed by parallel determination of mRNA levels and transcription rates for the entire genome. A mathematical algorithm has been adapted for a dynamic situation such as the response to stress, to calculate theoretical mRNA decay rates from the experimental data. Yeast genes have been grouped into 25 clusters according to mRNA level and transcription rate kinetics, and average mRNA decay rates have been calculated for each cluster. In most of the genes, changes in one or both experimentally determined parameters occur during the stress response. 24% of the genes are transcriptionally induced without an increase in mRNA levels. The lack of parallelism between the evolution of the mRNA amount and transcription rate predicts changes in mRNA stability during stress. Genes for ribosomal proteins and rRNA processing enzymes are abundant among those whose mRNAs are predicted to destabilize. The number of genes whose mRNAs are predicted to stabilize is lower, although some protein folding or proteasomal genes are among the latter. We have confirmed the mathematical predictions for several genes pertaining to different clusters by experimentally determining mRNA decay rates using the regulatable tetO promoter in transcriptional expression conditions not affected by the oxidative stress. This study indicates that the oxidative stress response in yeast cells is not only conditioned by gene transcription but also by the mRNA decay dynamics and that this complex response may be particularly relevant to explain the temporary down-regulation of protein synthesis occurring during stress.

Highlights

Levels to adapt themselves to the new conditions and counteract the possible macromolecular damage caused by the stress situation
To avoid growth arrest, which could mask the direct effects of oxidative stress on general transcription and mRNA stability, we first tested a range of t-BOOH concentrations
Conditions were employed in which growth was not affected after the addition of the oxidant, thereby disthe RA profiles are much more variable, indicating that post- carding transcriptome-level effects caused by growth rate transcriptional mechanisms operate differentially on them. changes

Summary

Introduction

Levels to adapt themselves to the new conditions and counteract the possible macromolecular damage caused by the stress situation. Effect of Oxidative Stress on mRNA Levels and Transcription Rates, Gene Profile Clustering—We have used the GRO experimental procedures [4] to determine the TR and RA during the S. cerevisiae cell response to oxidative stress.

Results

Conclusion