A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation

SA Nicolaou, SM Gaida, ET Papoutsakis - Metabolic engineering, 2010 - Elsevier
Metabolites, substrates and substrate impurities may be toxic to cells by damaging biological
molecules, organelles, membranes or disrupting biological processes. Chemical stress is …

Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli

TY Mills, NR Sandoval, RT Gill - Biotechnology for biofuels, 2009 - Springer
The sustainable production of biofuels will require the efficient utilization of lignocellulosic
biomass. A key barrier involves the creation of growth-inhibitory compounds by chemical …

Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production

S Shi, T Chen, Z Zhang, X Chen, X Zhao - Metabolic engineering, 2009 - Elsevier
A comparative transcriptome profiling between a riboflavin-producing Bacillus subtilis strain
RH33 and the wild-type strain B. subtilis 168 was performed, complemented with metabolite …

Genes restoring redox balance in fermentation-deficient E. coli NZN111

A Singh, MD Lynch, RT Gill - Metabolic engineering, 2009 - Elsevier
The objectives of this study were to improve understanding of the biochemical mechanisms
underlying the growth defects resulting from deletion of pflB and ldhA in E. coli (strain …

CRISPR/Cas9 recombineering‐mediated deep mutational scanning of essential genes in Escherichia coli

A Choudhury, JA Fenster, RG Fankhauser… - Molecular Systems …, 2020 - embopress.org
Deep mutational scanning can provide significant insights into the function of essential
genes in bacteria. Here, we developed a high‐throughput method for mutating essential …

Deep scanning lysine metabolism in Escherichia coli

MC Bassalo, AD Garst, A Choudhury… - Molecular Systems …, 2018 - embopress.org
Our limited ability to predict genotype–phenotype relationships has called for strategies that
allow testing of thousands of hypotheses in parallel. Deep scanning mutagenesis has been …

Elucidating acetate tolerance in E. coli using a genome-wide approach

NR Sandoval, TY Mills, M Zhang, RT Gill - Metabolic engineering, 2011 - Elsevier
Engineering organisms for improved performance using lignocellulose feedstocks is an
important step towards a sustainable fuel and chemical industry. Cellulosic feedstocks …

Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli

LBA Woodruff, J Pandhal, SY Ow, A Karimpour-Fard… - Metabolic …, 2013 - Elsevier
The identification of relevant gene targets for engineering a desired trait is a key step in
combinatorial strain engineering. Here, we applied the multi-Scalar Analysis of Library …

Genome-Wide Mapping of Furfural Tolerance Genes in Escherichia coli

TY Glebes, NR Sandoval, PJ Reeder, KD Schilling… - PLoS …, 2014 - journals.plos.org
Advances in genomics have improved the ability to map complex genotype-to-phenotype
relationships, like those required for engineering chemical tolerance. Here, we have applied …

CRISPR perturbation of gene expression alters bacterial fitness under stress and reveals underlying epistatic constraints

PB Otoupal, KE Erickson, A Escalas-Bordoy… - ACS synthetic …, 2017 - ACS Publications
The evolution of antibiotic resistance has engendered an impending global health crisis that
necessitates a greater understanding of how resistance emerges. The impact of nongenetic …