Role of SSD1 in Phenotypic Variation of Saccharomyces cerevisiae Strains Lacking DEG1-Dependent Pseudouridylation.

Bahar Khonsari,Roland Klassen,Raffael Schaffrath

doi:10.3390/ijms22168753

Bahar Khonsari, Roland Klassen + Show 1 more

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https://doi.org/10.3390/ijms22168753

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Abstract

Yeast phenotypes associated with the lack of wobble uridine (U34) modifications in tRNA were shown to be modulated by an allelic variation of SSD1, a gene encoding an mRNA-binding protein. We demonstrate that phenotypes caused by the loss of Deg1-dependent tRNA pseudouridylation are similarly affected by SSD1 allelic status. Temperature sensitivity and protein aggregation are elevated in deg1 mutants and further increased in the presence of the ssd1-d allele, which encodes a truncated form of Ssd1. In addition, chronological lifespan is reduced in a deg1 ssd1-d mutant, and the negative genetic interactions of the U34 modifier genes ELP3 and URM1 with DEG1 are aggravated by ssd1-d. A loss of function mutation in SSD1, ELP3, and DEG1 induces pleiotropic and overlapping phenotypes, including sensitivity against target of rapamycin (TOR) inhibitor drug and cell wall stress by calcofluor white. Additivity in ssd1 deg1 double mutant phenotypes suggests independent roles of Ssd1 and tRNA modifications in TOR signaling and cell wall integrity. However, other tRNA modification defects cause growth and drug sensitivity phenotypes, which are not further intensified in tandem with ssd1-d. Thus, we observed a modification-specific rather than general effect of SSD1 status on phenotypic variation in tRNA modification mutants. Our results highlight how the cellular consequences of tRNA modification loss can be influenced by protein targeting specific mRNAs.

Highlights

Post-transcriptional RNA modifications are abundant in tRNA, where they may support stability, integrity, and translational efficiency [1,2,3]
An tRNA modification that is important for the normal growth of yeast cells is pseudouridylation at positions 38 and 39 (Ψ38/39), which is introduced by pseudouridine synthase Deg1. tRNAGlnUUG overexpression suppresses the general growth defects of deg1 mutants, revealing a functional dependency of this tRNA on Deg1-dependent Ψ38/39 [7,8]
To analyze whether the SSD1 allelic variants influence phenotypes induced by lack of pseudouridine synthase Deg1 in the yeast S. cerevisiae, we generated deg1 mutants in both SSD1-v (BY4741) and ssd1-d (W303-1B) strain backgrounds

Summary

Introduction

Post-transcriptional RNA modifications are abundant in tRNA, where they may support stability, integrity, and translational efficiency [1,2,3]. Different modifications are introduced at different positions of specific tRNAs. Some modifications are installed in a sequential order, and several modification genes show strong genetic interactions because independent modifications may contribute to the same tRNA functional aspect [4,5]. Some specific modification genes are linked to growth phenotypes in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe [6]. An tRNA modification that is important for the normal growth of yeast cells is pseudouridylation at positions 38 and 39 (Ψ38/39), which is introduced by pseudouridine synthase Deg. There are several additional Ψ synthases responsible for pseudouridylation at other tRNA positions, and defects in some of these enzymes (including the Deg orthologue Pus3) are linked to neurodegenerative diseases such as intellectual disability in humans [13,14]. The absence of Deg influences neutral lipid content, amino acid levels, and sensitivity against rapamycin (an inhibitor of the TORC1 (target of rapamycin) kinase complex [15,16,17,18]), which might contribute to the general growth defect

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