Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks

Abstract

The proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding; some with over-lapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. To this effect, we have used S. cerevisiae to understand the route a cell takes as a response when challenged with different proteostasis impairments. Using 14 single deletion strains of genes of Protein Quality Control (PQC) system, we quantify their proteostasis impairment and the transcriptional response. In most cases cellular response was incapable of restoring proteostasis. The response did not activate proteostasis components or pathways that could complement the function of the missing PQC gene. Over-expression of alternate machineries, could restore part of the proteostasis defect in deletion strains. We posit that epistasis guided synthetic biology approaches may be helpful in realizing the true potential of the cellular chaperone machinery.

A comparative study of stress responses elicited by misfolded proteins targeted by bipartite or matrix-targeting signal sequences to yeast mitochondria

“…The transcriptome data was analyzed with a standard Kallisto pipeline as described previously 45 . Briefly, fastq files were trimmed using Trimmomatic and the fastqc files were aligned to the yeast transcriptome using Kallisto Reduction, alkylation and In-gel trypsin digestion was done as described in Shevchenko et al…”