Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

• Published in: Proceedings of the National Academy of Sciences - PNAS 2017-07, Vol.114 (28), p.7349-7354
• Main Authors: Sievert, Christian, Nieves, Lizbeth M., Panyon, Larry A., Loeffler, Taylor, Morris, Chandler, Cartwright, Reed A., Wang, Xuan
• Format: Article
• Language: English
• Subjects: Alternative fuels; Amino acids; Binding sites; Biocatalysts; Biological Sciences; Biological Transport; Biomass; Carbon - chemistry; Catabolite Repression; Deoxyribonucleic acid; Directed Molecular Evolution; DNA; DNA, Bacterial - genetics; E coli; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Evolution; Experiments; Fermentation; Genetic Engineering; Genome, Bacterial; Glucose; Glucose - chemistry; Glucose-Xylose; Lactic acid; Lactic Acid - chemistry; Lignin - chemistry; Lignocellulose; Metabolic Engineering; Metabolism; Microorganisms; Monomers; Mutation; Operons; Phenotype; Point mutation; Real-Time Polymerase Chain Reaction; Salts; Sugar; Sugars - chemistry; Transcription; Transcription Factors - genetics; Transcription Factors - metabolism; Xylose; Xylose - chemistry; Xylose - genetics
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1700345114

Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose–xylose mixture (50 g·L−1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.