5 research outputs found
TALENs-Assisted Multiplex Editing for Accelerated Genome Evolution To Improve Yeast Phenotypes
Genome
editing is an important tool for building novel genotypes
with a desired phenotype. However, the fundamental challenge is to
rapidly generate desired alterations on a genome-wide scale. Here,
we report TALENs (transcription activator-like effector nucleases)-assisted
multiplex editing (TAME), based on the interaction of designed TALENs
with the DNA sequences between the critical TATA and GC boxes, for
generating multiple targeted genomic modifications. Through iterative
cycles of TAME to induce abundant semirational <i>indels</i> coupled with efficient screening using a reporter, the targeted
fluorescent trait can be continuously and rapidly improved by accumulating
multiplex beneficial genetic modifications in the evolving yeast genome.
To further evaluate its efficiency, we also demonstrate the application
of TAME for significantly improving ethanol tolerance of yeast in
a short amount of time. Therefore, TAME is a broadly generalizable
platform for accelerated genome evolution to rapidly improve yeast
phenotypes
Additional file 1. of Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae
Supplementary figures
Additional file 1: of Genome shuffling of the nonconventional yeast Pichia anomala for improved sugar alcohol production
Fig. S1. The colorimetric assay of sugar alcohols. a The flow chart of the colorimetric method for sugar alcohol screening. b The correlation of the two sugar alcohol-detection methods by linear regression. H and C represent the HPLC and colorimetric methods, respectively. Fig. S2. Comparison of the DNA content among the parent and shuffled strains, as determined by flow cytometry. The DNA content is shown for a haploid control strain S. cerevisiae BY4741, haploid parent strain P. anomala HP, diploid strain P. anomala TIB-x229 and shuffled strains GS2-1, GS2-2 and GS2-3
Distinct Proteome Remodeling of Industrial <i>Saccharomyces cerevisiae</i> in Response to Prolonged Thermal Stress or Transient Heat Shock
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 <i>Saccharomyces
cerevisiae</i> 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
Distinct Proteome Remodeling of Industrial <i>Saccharomyces cerevisiae</i> in Response to Prolonged Thermal Stress or Transient Heat Shock
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 <i>Saccharomyces
cerevisiae</i> 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