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Whole genome sequencing analysis of evolved E.coli

ABSTRACT: Whole genome sequencing analysis of evolved E.coli

PROVIDER: PRJEB44483 | ENA |

REPOSITORIES: ENA

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Whole genome sequencing analysis of evolved E.coli

Project description:We created a mutator protein. The mutator, was prepared by fusing a PmCDA1 (Petromyzon marinus Cytidine DeAminase) and E.coli RNA polymerase alpha subunit(EcoRNAP alpha). After 120 cycles, whole genome sequencing was performed on the wild type and evolved sample. After characterization of the mutation capacity of our mutator, we evolved a sucrose utilization strain and we sequenced Suc strain.

2021-05-03 | E-MTAB-10368 | biostudies-arrayexpress

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Total proteome analysis of engineered/adapted E.coli strains with glucose/xylose co-utilization ability

Project description:This project was about developing a bacterial strain that could consume a mixture of glucose and xylose simultaneously with higher ethanol productivity. In this study, an ethanologenic strain (SSK42) was made deficient in Carbon Catabolite Repression (CCR) by deleting the ptsG gene encoding EIIBCGlc component of PTS transport system. This strain (SCD00) was then evolved for several generations on xylose containing minimal media. A strain (SCD78) was finally obtained that, unlike its parent strain could consume glucose and xylose simultaneously. Then we performed proteomics analysis of evolved and un-evolved strain. The strain SSK42 was also considered for proteome analysis as a reference for analysis. The starting strain – SSK42, is the derivative of E.coli B.

2022-10-15 | PXD033577 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of E.coli, Wild Type and ΔrecA Transcriptomes

Project description:Purpose:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived E.coli transcriptome profiling (RNA-seq) of Wild type and ΔrecA with or without antibiotics treatment. Methods:libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument, Sequencing was carried out using a 2x150bp paired-end (PE) configuration, image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. Main data analysis include Quality Control(Cutadapt), Mapping(Bowtie2 (v2.2.6)),Expression analysis(HTSeq (v0.6.1p1)), Differential expression analysis (DESeq2 Bioconductor package). Results:Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the E.coli genome, The treatment of ampicillin affected the transcriptomic profile of either in the wild type or the ΔrecA strain, compared with that of untreated control cells, with changes to the expression of 4373 and 4286 coding sequences, respectively. Analysis of only the genes with a log2 fold change (log2FC) of ≥ ± 2 showed that 161 and 248 genes were differentially expressed in the ampicillin-treated wild type and ΔrecA strains, respectively. Conclusions:Our study represents the detailed analysis of E.coli transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-07-06 | GSE179434 | GEO

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