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Ribonucleases and Their Regulatory Role in Gene Expression

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Ribonucleases are essential for the proper biogenesis and turnover of RNAs, and therefore have a major impact on the proper control and fidelity of gene expression. The budding yeast Saccharomyces cerevisiae contain various ribonucleases, each with their own specific substrates, specificities and role in RNA metabolism. Due to the complex nature of these ribonucleases, many questions regarding their regulatory role and relative contribution to various cellular pathways remain to be discovered. In this dissertation, we present our findings on two ribonucleases, the exoribonuclease Rrp6p and the RNase III Rnt1p. First, we show a unique regulatory role of Rrp6p for the proper expression of cell wall proteins during heat stress. This process requires the cooperation of the cell wall integrity (CWI) pathway, as demonstrated through the synthetic lethal interaction observed between Rrp6p and CWI factors under heat stress. Strikingly, Rrp6p participates in this pathway independent of its exonuclease activity or association with the nuclear exosome. These results suggest a unique function of Rrp6p and how it contributes to cellular fitness during stress. In chapter 3, we explore the nuclear RNase III Rnt1p and the regulation of its activity under various stresses. Previously, we have shown that Rnt1p display a drastic increase in cleavage activity towards a select few of its target substrates during high salt stress. However, the mechanism governing this hyperactivation of Rnt1p remains unclear. Here, we show that the salt stress induced hyperactivation of Rnt1p on the substrate RNA of BDF2 is recapitulated when the processing and export of mRNAs are hindered. This suggests that the activity of Rnt1p can be regulated through the nuclear retention of its RNA substrates. Furthermore, we show that the identity of the Rnt1p recognition stem loop on its target RNAs may affect its cleavage efficiency in vivo and in vitro. Altogether, this work reveals significant insights on the regulatory role of ribonucleases and how they may contribute to overall cell health.

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