Dataset for suppressors of amyloid-β toxicity and their functions in recombinant protein production in yeast

Xin Chen; Xiaowei Li; Boyang Ji; Yanyan Wang; Olena P Ishchuk; Egor Vorontsov; Dina Petranovic; Verena Siewers; Martin K M Engqvist

doi:10.1016/j.dib.2022.108322

Dataset for suppressors of amyloid-β toxicity and their functions in recombinant protein production in yeast

Data Brief. 2022 May 27:42:108322. doi: 10.1016/j.dib.2022.108322. eCollection 2022 Jun.

Authors

Xin Chen^{1

2}, Xiaowei Li¹, Boyang Ji^{1

3}, Yanyan Wang¹, Olena P Ishchuk¹, Egor Vorontsov⁴, Dina Petranovic^{1

2}, Verena Siewers^{1

2}, Martin K M Engqvist¹

Affiliations

¹ Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
² Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
³ BioInnovation Institute, Ole Måløes Vej 3, Copenhagen DK-2200, Denmark.
⁴ Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, SE-413 90, Gothenburg, Sweden.

Abstract

The production of recombinant proteins at high levels often induces stress-related phenotypes by protein misfolding or aggregation. These are similar to those of the yeast Alzheimer's disease (AD) model in which amyloid-β peptides (Aβ42) were accumulated [1], [2]. We have previously identified suppressors of Aβ42 cytotoxicity via the genome-wide synthetic genetic array (SGA) [3] and here we use them as metabolic engineering targets to evaluate their potentiality on recombinant protein production in yeast Saccharomyces cerevisiae. In order to investigate the mechanisms linking the genetic modifications to the improved recombinant protein production, we perform systems biology approaches (transcriptomics and proteomics) on the resulting strain and intermediate strains. The RNAseq data are preprocessed by the nf-core/RNAseq pipeline and analyzed using the Platform for Integrative Analysis of Omics (PIANO) package [4]. The quantitative proteome is analyzed on an Orbitrap Fusion Lumos mass spectrometer interfaced with an Easy-nLC1200 liquid chromatography (LC) system. LC-MS data files are processed by Proteome Discoverer version 2.4 with Mascot 2.5.1 as a database search engine. The original data presented in this work can be found in the research paper titled "Suppressors of Amyloid-β Toxicity Improve Recombinant Protein Production in yeast by Reducing Oxidative Stress and Tuning Cellular Metabolism", by Chen et al. [5].

Keywords: Amyloid-β; Gene engineering; Proteome; Transcriptome; Yeast Saccharomyces cerevisiae.