A Budding Yeast Model for Human Disease Mutations in theEXOSC2Cap Subunit of the RNA Exosome

Abstract

RNA exosomopathies, a growing family of tissue-specific diseases, are linked to missense mutations in genes encoding the structural subunits of the conserved 10-subunit exoribonuclease complex, the RNA exosome. Such mutations in the cap subunit gene EXOSC2 cause the novel syndrome SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies). In contrast, exosomopathy mutations in the cap subunit gene EXOSC3 cause pontocerebellar hypoplasia type 1b (PCH1b). Though having strikingly different disease pathologies, EXOSC2 and EXOSC3 exosomopathy mutations result in amino acid substitutions in similar, conserved domains of the cap subunits, suggesting that these exosomopathy mutations have distinct consequences for RNA exosome function. We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by introducing the EXOSC2 mutations in the orthologous S. cerevisiae gene RRP4. The resulting rrp4 mutant cells have defects in cell growth and RNA exosome function. We detect significant transcriptomic changes in both coding and non-coding RNAs in the rrp4 variant, rrp4-G226D, which models EXOSC2 p.Gly198Asp. Comparing this rrp4-G226D mutant to the previously studied S. cerevisiae model of EXOSC3 PCH1b mutation, rrp40-W195R, reveals that these mutants have disparate effects on certain RNA targets, providing the first evidence for different mechanistic consequences of these exosomopathy mutations. Congruently, we detect specific negative genetic interactions between RNA exosome cofactor mutants and rrp4-G226D but not rrp40-W195R. These data provide insight into how SHRF mutations could alter the function of the RNA exosome and allow the first direct comparison of exosomopathy mutations that cause distinct pathologies.

Molecular mechanisms underlying cortical (mal)formation: case studies of ESCO2 and EXOSC10

“…Rapamycin inhibits the mTOR pathway, which regulates many processes including autophagy, and thereby augments mRNA turnover (Albig and Decker, 2001;Martinez-Nunez et al, 2017). Additionally, in RNA sequencing analysis of RRP4-G226D yeast cells, expression of several autophagy genes was decreased (Sterrett, 2020). Taken together, defective autophagy seems to play a role in SHRF pathogenesis.…”

“…Indeed, investigation of RRP4-G226D mutant yeast cells modelling the human EXOSC2-G198A variant revealed different RNA targets compared to a yeast model of the human EXOSC3-W238R variant associated with PCH1b (Sterrett, 2020). RRP4-G226D cells display a growth defect, which is worsened by the deletion of Mpp6, a cofactor of the exosome complex (Sterrett, 2020). This effect was not seen in RRP40-W195R cells modelling the human EXOSC3 mutation (Sterrett, 2020).…”

“…Next to cell-type-specific compensation mechanisms, also different substrate specifity conferred by different complex subunits can be a possible explanation of the striking differences in diseases caused by EXOSC2 or EXOSC3 mutations. Indeed, investigation of RRP4-G226D mutant yeast cells modelling the human EXOSC2-G198A variant revealed different RNA targets compared to a yeast model of the human EXOSC3-W238R variant associated with PCH1b (Sterrett, 2020). RRP4-G226D cells display a growth defect, which is worsened by the deletion of Mpp6, a cofactor of the exosome complex (Sterrett, 2020).…”

“…RRP4-G226D cells display a growth defect, which is worsened by the deletion of Mpp6, a cofactor of the exosome complex (Sterrett, 2020). This effect was not seen in RRP40-W195R cells modelling the human EXOSC3 mutation (Sterrett, 2020). Mpp6 stabilizes the interaction between the exosome complex and the RNA helicase MTR4 (Falk et al, 2017).…”

“…Mpp6 stabilizes the interaction between the exosome complex and the RNA helicase MTR4 (Falk et al, 2017). Therefore, the authors suggest that the G226D amino acid substitution could cause a destabilization of the critical interaction of MTR4 and the exosome complex (Sterrett, 2020).…”