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

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.

在酿酒酵母（Saccharomyces cerevisiae）中，占总细胞信使RNA（mRNA）一小部分的一类被称为特殊信使RNA（special mRNAs）的分子会以较慢的速率完成核输出，并优先滞留于细胞核内。然而，这类特殊mRNA的慢速输出机制，以及其核滞留的生理学意义，长期以来尚不明确。
本研究以编码葡萄糖感应型丝氨酸/苏氨酸激酶的SKS1 mRNA作为特殊mRNA的模型，对酿酒酵母中特殊mRNA的优先核滞留机制展开了探究。研究发现，一段长202 nt的“输出阻滞型”核邮政编码（nuclear zip code, NZ）元件可触发SKS1 mRNA的核滞留，并通过核外切体/CTEXT复合体促进其在细胞核内的快速降解。
我们证实，Dbp2p作为一种ATP依赖型DEAD-box RNA解旋酶（DEAD-box RNA helicase），可结合SKS1及其他特殊mRNA，通过拮抗输出因子Mex67p/Yra1p的结合，抑制这些mRNA的核输出过程。与此观测结果一致的是，在DBP2基因敲除的酵母菌株中，这类特殊mRNA中有相当一部分会定位于细胞质中，同时其稳态水平与稳定性也同步提升。
该现象支持了“Dbp2p可促进特殊mRNA的核滞留，进而触发其后续的细胞核内降解”这一观点。进一步分析显示，Dbp2p介导的SKS1 mRNA核滞留过程具有可逆性，这对于酵母细胞在生长培养基中低浓度葡萄糖/氮源条件下的适应性与存活能力至关重要。
当营养水平较高、无需Sks1p发挥功能时，SKS1 mRNA会滞留于细胞核内并被降解；与之相反，当葡萄糖/氮源水平较低、Sks1p对细胞应对此类环境至关重要时，SKS1 mRNA的核滞留会被解除，以促进其核输出与翻译过程，最终使细胞质内的Sks1p水平大幅激增。