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Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [CRISPR screen]

ABSTRACT: Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [CRISPR screen]

PROVIDER: PRJNA1091351 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28431324_1.fastq.gz	Fastqsanger.gz
	SRR28431324_2.fastq.gz	Fastqsanger.gz
	SRR28431325_1.fastq.gz	Fastqsanger.gz
	SRR28431325_2.fastq.gz	Fastqsanger.gz
	SRR28431326_1.fastq.gz	Fastqsanger.gz

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Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [CRISPR screen]

Project description:Lignocellulosic biomass is an abundant renewable resource with tremendous potential to alleviate climate crisis. Yarrowia lipolytica is an attractive biochemical production host, while the presence of inhibitors furfural and acetic acid in lignocellulosic hydrolysate restricts the efficient utilization of this resource. Given a deficient understanding of the inherent interactions between these inhibitors and cellular metabolism, sufficiently mining relevant genes is necessary. Herein, 14 novel gene targets were discovered using CRISPR interference library in Y. lipolytica, achieving tolerance to 0.35% (v/v) acetic acid (the highest concentration reported in Y. lipolytica), 4.8 mM furfural, or a combination of 2.4 mM furfural and 0.15% (v/v) acetic acid. The tolerance mechanism might involve improvements of signal transduction, PP pathway, and TCA cycle. Transcriptional repression of effective gene targets still enabled tolerance when xylose was a carbon source. This work forms a robust foundation for significantly improving microbial tolerance to inhibitors in lignocellulosic hydrolysate and profoundly revealing underlying mechanism.

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Project description:Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library [RNA-seq]

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Molecular mechanism of Engineered Zymomonas mobilis response to furfural and acetic acid stress

Project description:This study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using genomics, transcriptomics and label free quantitative proteome. By Sanger sequencing technology we re-verified of previously identified 19 mutations in ZM532, but we found a total of 23 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS; 4) and intergenic region (19) in ZM532. Six SNPs were however novel in this study. We also identified a total of 1865 and 14 novel differentially expressed genes (DEGs) in ZM532 and wild-type ZM4. Further we identified 1,532 proteins by label free proteome. These proteins and genes are involved in amino acid biosynthesis, macromolecules repair, glycolysis, flagella assembly, ABC transporter, fermentation, and ATP synthesis pathways and stress response. The exclusively found genes and proteins in ZM532 confirmed and help to unravel the acetic acid and furfural tolerance mechanism between ZM532 and wild-type ZM4. May be these proteins and genes play key roles in ZM532 regulation with strong expressions under acids stress conditions. Furthermore, we knocked-out and overexpressed two differentially expressed genes (DEGs), ZMO_RS02740 up-regulated and ZMO_RS06525 down-regulated to investigate their roles in acetic acid and furfural tolerance. Our knockout and complementary experiments revealed that up-regulated expression gene ZMO RS02740 and the down-regulated expression gene ZMO-RS06525 play important roles in dealing with Furfural and acetic acid stress. ZM532 can be used to substitute ZM4 as a biocatalyst for bioethanol under acetic acid and furfural condition, with a shorter fermentation time and higher productivity.

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Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome clustered regularly interspaced short palindromic repeats interference library

Project description:In this study, a whole-genome CRISPRi library was developed in Y. lipolytica and applied for enforcing the tolerance to furfural and acetic acid. Several novel gene targets were discovered through NGS before and after screening. And to analyze the tolerance mechanism caused by transcriptional repression of the most prominent gene targets, the transcriptome and proteomics were performed.

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Investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural by using RNA-seq

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