Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in Maintaining Cell Wall Stability in Yeast.

Ana Novačić,Nikša Bekavac,Igor Stuparević,Nada Šupljika,Bojan Žunar,Erik F Y Hom

doi:10.1128/spectrum.00295-21

Abstract

ABSTRACTYeast cell wall stability is important for cell division and survival under stress conditions. The expression of cell-wall-related proteins is regulated by several pathways involving RNA-binding proteins and RNases. The multiprotein RNA exosome complex provides the 3′→5′ exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. In this work, we show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele. This gene encodes the RNA-binding protein Ssd1, which is involved in the posttranscriptional regulation of cell-wall-related genes. Expression of the functional SSD1-V allele from its native genomic locus or from a centromeric plasmid suppresses the growth defects and aberrant morphology of RNA exosome mutant cells at high temperatures or upon treatment with cell wall stressors. Moreover, combined inactivation of the RNA exosome catalytic subunit Rrp6 and Ssd1 results in a synthetically sick phenotype of cell wall instability, as these proteins may function in parallel pathways (i.e., via different mRNA targets) to maintain cell wall stability.IMPORTANCE Stressful conditions such as high temperatures can compromise cellular integrity and cause bursting. In microorganisms surrounded by a cell wall, such as yeast, the cell wall is the primary shield that protects cells from environmental stress. Therefore, remodeling its structure requires inputs from multiple signaling pathways and regulators. In this work, we identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd1 as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. This work highlights the contribution of RNA-binding proteins in the regulation of yeast cell wall structure, providing new insights into yeast physiology.

Highlights

Yeast cell wall stability is important for cell division and survival under stress conditions
The absence of the RNA exosome catalytic subunit Rrp6 leads to cell wall instability, which manifests as cell lysis and inviability under conditions of high temperature or other forms of cell wall stress [19]
The Ssd1 family is closely related to the Dis3L2 39!59 exonucleases, which belong to the same RNase II/RNB family as the catalytic subunit of the RNA exosome Dis3 [22]

Summary

Introduction

Yeast cell wall stability is important for cell division and survival under stress conditions. The multiprotein RNA exosome complex provides the 39!59 exoribonuclease activity that is critical for maintaining the stability and integrity of the yeast cell wall under stress conditions such as high temperatures. We show that the temperature sensitivity of RNA exosome mutants is most pronounced in the W303 genetic background due to the nonfunctional ssd1-d allele This gene encodes the RNA-binding protein Ssd, which is involved in the posttranscriptional regulation of cell-wall-related genes. We identify the interplay of the RNA exosome complex and the RNA-binding protein Ssd as an important factor in the yeast cell wall stress response. These proteins operate in independent pathways to support yeast cell wall stability. The SSD1 gene is hypomorphic in a commonly used laboratory strain, W303, which accounts for a number of phenotypic differences between W303 and other strain backgrounds [9,10,11,12,13]

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Results

Conclusion