Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution.Synthetic chromosome rearrangement and modification by LoxP-mediated evolution(SCRaMbLE)has been appl...Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution.Synthetic chromosome rearrangement and modification by LoxP-mediated evolution(SCRaMbLE)has been applied to explore large-scale genomic rearrangements,yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym sites.Here,we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes,ranging from 1 to 300 kb.Furthermore,it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of zeaxanthin.Collectively,our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.展开更多
Genomic rearrangements play a significant role in disease,evolution,and tumorigenesis(Mani and Chinnaiyan,2010).While single nucleotide polymorphisms(SNPs)and small insertions/deletions contribute substantially to gen...Genomic rearrangements play a significant role in disease,evolution,and tumorigenesis(Mani and Chinnaiyan,2010).While single nucleotide polymorphisms(SNPs)and small insertions/deletions contribute substantially to genetic variation,discerning the independent impact of structural variations poses a challenge.展开更多
Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene transcription.Omics analyses and reverse engineering enable learning...Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene transcription.Omics analyses and reverse engineering enable learning and subsequent incorporation of novel design strategies for further engineering.Here,we identify the role of the global regulator IhfA for overproduction of free fatty acids(FFAs)using CRISPRi-facilitated reverse engineering and cellular physiological characterization.From the differentially expressed genes in the ihfALstrain,a total of 14 beneficial targets that enhance FFAs production by above 20% are identified,which involve membrane function,oxidative stress,and others.For membrane-related genes,the engineered strains obtain lower cell surface hydrophobicity and increased average length of membrane lipid tails.For oxidative stress-related genes,the engineered strains present decreased reactive oxygen species(ROS)levels.These gene modulations enhance cellular robustness and save cellular resources,contributing to FFAs production.This study provides novel targets and strategies for engineering microbial cell factories with improved FFAs bioproduction.展开更多
基金supported by the National Key Research and Development Program of China(Grant No.2021YFC2100800)the National Natural Science Foundation of China(Grant No.22208241)+1 种基金China Postdoctoral Science Foundation(Grant No.2023M732591)the Key R&D Program of Shandong Province,China(Grant No.2022SFGC0102).
文摘Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution.Synthetic chromosome rearrangement and modification by LoxP-mediated evolution(SCRaMbLE)has been applied to explore large-scale genomic rearrangements,yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym sites.Here,we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes,ranging from 1 to 300 kb.Furthermore,it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of zeaxanthin.Collectively,our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.
文摘Genomic rearrangements play a significant role in disease,evolution,and tumorigenesis(Mani and Chinnaiyan,2010).While single nucleotide polymorphisms(SNPs)and small insertions/deletions contribute substantially to genetic variation,discerning the independent impact of structural variations poses a challenge.
基金supported by the National Key Research and Development Program of China(2021YFC2104400)the National Natural Science Foundation of China(NSFC 22078240)the China Postdoctoral Science Foundation(2022M722359).
文摘Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene transcription.Omics analyses and reverse engineering enable learning and subsequent incorporation of novel design strategies for further engineering.Here,we identify the role of the global regulator IhfA for overproduction of free fatty acids(FFAs)using CRISPRi-facilitated reverse engineering and cellular physiological characterization.From the differentially expressed genes in the ihfALstrain,a total of 14 beneficial targets that enhance FFAs production by above 20% are identified,which involve membrane function,oxidative stress,and others.For membrane-related genes,the engineered strains obtain lower cell surface hydrophobicity and increased average length of membrane lipid tails.For oxidative stress-related genes,the engineered strains present decreased reactive oxygen species(ROS)levels.These gene modulations enhance cellular robustness and save cellular resources,contributing to FFAs production.This study provides novel targets and strategies for engineering microbial cell factories with improved FFAs bioproduction.
