Molecular chaperones shape protein production costs

The production of proteins is fundamentally important for the normal function of cells. This process needs a lot of energy. Therefore, protein production is well coordinated with the needs of the cells to conserve energy. However, under certain conditions, excess protein production may take a substantial fitness cost that is commonly referred to as protein burden. With the objective to improve engineered protein production systems, it is desirable to evaluate how sensitive different species are to protein burden and identify the impact of environmental and genetic factors that could shape the cellular response to protein burden.

Hungarian scientists Zoltán Farkas and colleagues – from Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences – have confirmed that activity of molecular chaperones shapes protein burden that is the fitness costs associated with expression of unneeded proteins. The research article provides a genome-wide genetic interaction screen revealing that chaperones enable tolerance to important changes in genomic expression by decreasing the damaging impact of protein overproduction. The research work is published in eLife

The current study employed a genome-wide approach that is capable to uncover the determinants of protein burden in thousands of different mutant strains of baker’s yeast. By using state-of-the-art synthetic genetic array screens and a robust and precise high-throughput workflow, Zoltán Farkas and colleagues evaluated the fitness of fluorescent protein overproducing baker’s yeast strains in both optimal and stress environments. In addition, the authors also aimed to identify potential changes in the physical interaction landscape of the yeast under protein burden. By having such information, scientists could get some hints to design improved host strains for efficient overproduction of recombinant proteins. As a recombinant protein, the fluorescent yEVenus protein was used in the current study

Their study revealed that accumulation of an unneeded protein in yeast has a relatively mild impact on fitness under stress-free conditions. The fitness costs associated with expressing unneeded proteins was not found to be the result of protein toxicity or impaired metabolic processes. However, the extent of protein burden was substantially different across genetic backgrounds and environmental stresses. The study highlights that protein burden can be increased via the impairment of several cellular systems, as genetic and conditional inactivation of members involved in different steps of the protein production pathway – such as transcription, translation, amino acid metabolism, and protein folding – rendered yeast cells hypersensitive to protein overexpression. Most importantly, as part of the results, the author tested both the impact of high temperature stress on protein burden and the chemical induction of protein misfolding and concluded a crucial role of the Hsp70- associated molecular chaperone network in mitigating protein burden. Moreover, a specific assay also revealed that cellular proteins were more prone to aggregate and became non-functional under protein burden in mutant cells with impaired chaperone network than in the wild-type strain. To provide a mechanistic explanation for protein burden, the authors also performed physical interaction screens. As a result, they found that protein burden could disturb the interactions among the members of the Hsp70-90 chaperone network, specifically by weakening the interactions of a scaffold protein (Sti1p, an important regulator of the chaperone network) and thereby disturbing the activity of the network.

The authors have raised an important implication for future studies in the biotechnology and protein engineering fields. They proposed the possibility that highly expressed proteins may perturb key components of the chaperone network which otherwise would be used to navigate folding of native proteins within the cell. As protein burden can be magnified via high temperature stress, enhanced protein mistranslation and misfolding, they concluded that normal activity of specific molecular chaperones enables tolerance to massive changes in genomic expression by reducing the damaging impact of gratuitous protein overproduction. Collectively, their study provides several lines of evidence that support the substantial importance of molecular chaperones in the mitigation of protein production costs.