The ATP-dependent DEAD-box RNA Helicase Dbp2 regulates the glucose/nitrogen stress response in baker’s yeast by modulating reversible nuclear retention and decay of SKS1 mRNA

Description

In baker's yeast Saccharomyces cerevisiae, a small subset of total cellular mRNAs called special mRNAs are exported slowly and are retained preferentially in the nucleus. However, the mechanism of their slow export as well as the physiological significance of their nuclear retention remained elusive. In this work, we investigate the mechanistic aspect of the preferential nuclear retention of "Special" mRNAs in Saccharomyces cerevisiae, using SKS1 mRNA as a model special mRNA encoding a glucose-sensing serine/threonine kinase. Nuclear retention of the SKS1 mRNA triggered by a 202 nt “export-retarding” nuclear zip code (NZ) element promotes its rapid degradation in the nucleus by the nuclear exosome/CTEXT. We demonstrate that Dbp2p, an ATP-dependent DEAD-box RNA helicase binds to SKS1 and other special mRNAs and thereby inhibits their export by antagonizing with the binding of the export factors Mex67p/Yra1p. Consistent with this observation, a significant portion of these special mRNAs were found to localize into the cytoplasm in a yeast strain carrying a deletion in the DBP2 gene with the concomitant enhancement of its steady-state level and stability. This observation supports the view that Dbp2p promotes the nuclear retention of special mRNAs to trigger their subsequent nuclear degradation. Further analysis revealed that Dbp2p-dependent nuclear retention of SKS1 mRNA is reversible, which plays a crucial role in the adaptability and viability of the yeast cells in low concentrations of glucose/nitrogen in the growth medium. At high nutrient levels when the function of Sks1p is not necessary, SKS1 mRNA is retained in the nucleus and degraded. In contrast, during low glucose/nitrogen levels when Sks1p is vital to respond to such situations, the nuclear retention of SKS1 mRNA is relieved to permit its increased nuclear export and translation leading to a huge burst of cytoplasmic Sks1p.

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The detailed methodology followed in this investigation is mentioned in accompanying paper which is submitted for peer review. The methodology should be rigorously followed to reproduce the data.

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