Seidler, J. | Search bioRxiv

bioRxiv2026

Phosphorylation of the mRNP component Yra1 couples heat stress to nuclear mRNA export inhibition

The ability to adapt to changing environmental conditions is essential for cellular survival. A central feature of the eukaryotic stress response is the inhibition of bulk mRNA nuclear export, while stress-induced transcripts are specifically exported. However, the molecular mechanisms that simultaneously inhibit bulk mRNA export while mediating selective export of specific transcripts remain poorly understood. Here, we performed comparative phosphoproteomic analyses of S. cerevisiae under different stress conditions. We identified a heat shock-induced increase in phosphorylation within the N-terminal domain of the mRNA export adaptor Yra1. Preventing this phosphorylation significantly reduces nuclear accumulation of poly(A)+ RNA during heat stress and concomitantly enhances the export of heat-induced transcripts. Mechanistically, Yra1 phosphorylation appears to weaken its interaction with the export receptor Mex67, thereby contributing to nuclear accumulation of bulk poly(A)+ RNA under heat stress. Together, our findings establish Yra1 phosphorylation as a previously unrecognized regulatory mechanism that promotes nuclear mRNA accumulation during heat stress and contributes to selective mRNA export.

Molecular Biology↗

bioRxiv2024

A census of RNA-dependent proteins in yeast

Delineating the constituents and structural composition of RNA-associated protein complexes is essential to mapping the molecular machinery driving RNA metabolism and its impact on cellular function. Here, we present a comprehensive dataset of RNA-dependent proteins and complexes in the phylogenetically distant yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Using R-DeeP--a density gradient-based method that uses quantitative mass spectrometry to profile protein sedimentation in the presence and absence of RNA--we introduce an RNA dependence index (RDI) as a descriptive framework for RNA dependence, enabling the robust comparative analysis of RNA dependence across proteins in both species and relative to existing data from their human counterparts. This identifies a conserved core of RNA-dependent proteins shared across both yeasts, alongside distinct, organism-specific adaptations in complex behaviour. The data further support the analysis of co-sedimentation behaviour of protein complexes with known RNA-directed functions. For instance, we find that the five subunits of the S. cerevisiae THO complex only co-sediment in the absence of RNA, pointing to an underappreciated structural modularity of the well-characterized pentameric complex. The two datasets, available at https://yeast-r-deep.computational.bio, provide a resource for hypothesis-driven research in RNA biology and establish R-DeeP as a broadly applicable tool for comparative analysis of RNA-protein interactions.

molecular biology↗