Distinct Proteome Remodeling of Industrial Saccharomyces cerevisiae in Response to Prolonged Thermal Stress or Transient Heat Shock

Abstract

To gain a deep understanding of yeast-cell response to heat stress, multiple laboratory strains have been intensively studied via genome-wide expression analysis for the mechanistic dissection of classical heat-shock response (HSR). However, robust industrial strains of Saccharomyces cerevisiae have hardly been explored in global analysis for elucidation of the mechanism of thermotolerant response (TR) during fermentation. Herein, we employed data-independent acquisition and sequential window acquisition of all theoretical mass spectra based proteomic workflows to characterize proteome remodeling of an industrial strain, ScY01, responding to prolonged thermal stress or transient heat shock. By comparing the proteomic signatures of ScY01 in TR versus HSR as well as the HSR of the industrial strain versus a laboratory strain, our study revealed disparate response mechanisms of ScY01 during thermotolerant growth or under heat shock. In addition, through proteomics data-mining for decoding transcription factor interaction networks followed by validation experiments, we uncovered the functions of two novel transcription factors, Mig1 and Srb2, in enhancing the thermotolerance of the industrial strain. This study has demonstrated that accurate and high-throughput quantitative proteomics not only provides new insights into the molecular basis for complex microbial phenotypes but also pinpoints upstream regulators that can be targeted for improving the desired traits of industrial microorganisms.

Metabolic engineering of Yarrowia lipolytica for thermoresistance and enhanced erythritol productivity

“…Therefore, increasing the thermotolerance of strain HCY115 ( Δku70Δura3Δmdh2Δeyd1 ) for several degrees is of interest to develop an efficient erythritol production process. Several strategies have been used for that purpose in yeast, such as overexpression of heat shock proteins (HSP) or transcription factors [ 31 – 34 ]. In Saccharomyces cerevisiae , overexpression of gene RSP5 encoding ubiquitin ligase allowed the cell to grow up to 41 °C [ 35 ].…”

QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast

“…Elevated thermotolerance is a highly valuable trait of industrial yeasts that can substantially reduce the production costs. Previous studies have identified several causative genes and gained some insights into the underlying mechanism of this complex trait via various efficient approaches, especially QTL methodology [5, 10, 12]. A major challenge of QTL analysis is to efficiently identify minor QTLs linked to the inferior parent strain.…”

“…Previous study indicated that industrial yeast has evolved complex but subtle mechanisms to protect the organism from high-temperature lesion by activating and regulating of specific thermal tolerance-related genes to synthesize specific compounds [7]. To identify novel genes and elucidate the intricate mechanism of thermotolerance, many methods were developed [8–12]. Although these approaches have disclosed a number of causative genes and revealed some compounds, e.g.…”

Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions

“…In past years, some attempts have been made to elucidate the thermal response of S. cerevisiae [3][4][5][6][7][8][9][10][11] . Much of the current knowledge has been derived from studies on the effects of abrupt temperature shocks rather than prolonged thermal stress.…”

“…Although proteomic analysis techniques are not as straightforward as those used in transcriptomics, they offer the advantage of studying proteins, which represent the actual functional molecules in the cell 16 . To our knowledge, there are only two proteomic studies that examine the tolerance mechanisms of yeast grown at high temperature 4,5 , and one at low temperature 17 . However, only the study performed by García-Ríos et al (2016) was conducted under adapted stress conditions such as chemostats 17 .…”