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RNA-seq of strains grown under the control of native galactose regulon or synthetic xylose regulon vs constitutive expression of galactose and xylose metabolic genes

ABSTRACT: RNA-seq of strains grown under the control of native galactose regulon or synthetic xylose regulon vs constitutive expression of galactose and xylose metabolic genes

PROVIDER: PRJNA434650 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6749960_1.fastq.gz	Fastqsanger.gz
	SRR6749960_2.fastq.gz	Fastqsanger.gz
	SRR6749961_1.fastq.gz	Fastqsanger.gz
	SRR6749961_2.fastq.gz	Fastqsanger.gz
	SRR6749962_1.fastq.gz	Fastqsanger.gz

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RNA-seq of strains grown under the control of native galactose regulon or synthetic xylose regulon vs constitutive expression of galactose and xylose metabolic genes

Project description:In this study, we first assess the role of the GAL regulon in enabling efficient galactose utilization for cell growth by decoupling its regulatory responses from sugar catabolism. We provide evidence that regulon-controlled galactose assimilation is more efficient than constitutive expression of the catabolic genes in supporting fast growth rates to higher cell densities. Next, we assessed whether a regulon could enable more complete and efficient utilization of a nutrient that is non-native to this yeast – xylose. We first adapt the GAL regulon to respond to xylose through directed evolution of Gal3p, enabling coupling of nutrient stimulus with sensing, computation, and regulatory actuation. Next, by using a rational, model-guided approach, we test two different positive feedback signal transduction loop designs for the regulon and demonstrate their individual merits and weaknesses. We also show that implementation of a GAL-type xylose-responsive regulon can regulate multiple genes across the yeast genome and enable more homogeneous population-wide gene expression. By integrating a minimal set of heterologous catabolic genes into the synthetic regulon we demonstrate high cellular growth rates and high final cell densities on xylose as well as better growth in non-inducing carbon sources. Finally, we compare the genome-wide expression profiles of strains grown with regulon assistance and conventionally engineered strains to identify mechanistic reasons that account for the different phenotypes observed. We posit that this study strongly supports the need to re-evaluate how nutrient assimilation systems are currently implemented and introduces a new and unexplored paradigm of adapting a native regulon for efficient non-native sugar assimilation.

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