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RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum

ABSTRACT: RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum

PROVIDER: PRJEB27017 | ENA |

REPOSITORIES: ENA

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RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum

Project description:Cells were treated as described in the material and methods section of the manuscript. Briefly, RNA-seq experiments were performed with sorted populations with an size of about 10_E6 Corynebacterium glutamicum cells. As a reference data set RNA-Seq. analysis of unsorted cells were conducted (n=3, induced vs uninduced =2, 2 x 3 = 6 data sets). For the sorting and the counter-silencer based prophage induction, RNAprotect and RNAlater were used and for each agent data sets with two biological relicates were generated (n = 2, RNAprotect + RNAlater = 2, induced vs uninduced = 2, 2 x 2 x 2 = 8 data sets). One data set was generated using 10_E5 cells (n = 1, induced vs uninduced =2, 2 x 1 = 2 data sets) For the subpopulation caused by iron-shift experiments RNAprotect was used (n = 3, positive vs negative, 3 x 2 = 6 data sets). In sum 26 data sets are uploaded. Each consist of two fastq files (due to paired-end sequencing).

2018-09-15 | E-MTAB-6809 | biostudies-arrayexpress

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Project description:To identify genes which are differentially expressed in Corynebacterium glutamicum chassis C1 in comparison to the prophage free strain MB001, we performed DNA microarray analyses of C. glutamicum C1 against MB001. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w v-1) and harvested in the exponential growth phase at an OD600 of 5. Four biological replicates were performed.

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Proteomics of FACS-sorted heterogeneous Corynebacterium glutamicum populations

Project description:The metabolic status of individual cells in microbial cultures can differ being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS. A proteomics workflow optimized for small cell numbers was used to quantitatively compare proteomes of a ?aceE mutant, lacking functional pyruvate dehydrogenase (PD), and the wild type. About 800 proteins could be quantified from 1,000,000 cells. In the ?aceE mutant BCAA production was coordinated with upregulation of the glyoxylate cycle and TCA cycle to counter the lack of acetyl CoA resulting from the deletion of aceE.

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Project description:Metabolically engineered Corynebacterium glutamicum strains were constructed for the enhanced production of L-arginine, and their gene expression profiles were investigated Gene expression profiles of two C. glutamicum strains AR2 and AR6 were examined for the 3043 genes twice.

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Cryo-EM Structure of the bcc-aa3 respiratory chain supercomplex from Corynebacterium glutamicum

Project description:Cryo-EM Structure of the bcc-aa3 respiratory chain supercomplex from Corynebacterium glutamicum

2019-05-29 | MSV000083873 | MassIVE

Cytometry meets next-generation sequencing - RNA-Seq of sorted subpopulations reveals regional replication and iron-triggered prophage induction in Corynebacterium glutamicum.

Project description:Phenotypic diversification is key to microbial adaptation. Currently, advanced technological approaches offer insights into cell-to-cell variation of bacterial populations at a spatiotemporal resolution. However, the underlying molecular causes or consequences often remain obscure. In this study, we developed a workflow combining fluorescence-activated cell sorting and RNA-sequencing, thereby allowing transcriptomic analysis of 106 bacterial cells. As a proof of concept, the workflow was applied to study prophage induction in a subpopulation of Corynebacterium glutamicum. Remarkably, both the phage genes and flanking genomic regions of the CGP3 prophage revealed significantly increased coverage upon prophage induction - a phenomenon that to date has been obscured by bulk approaches. Genome sequencing of prophage-induced populations suggested regional replication at the CGP3 locus in C. glutamicum. Finally, the workflow was applied to unravel iron-triggered prophage induction in early exponential cultures. Here, an up-shift in iron levels resulted in a heterogeneous response of an SOS (PdivS) reporter. RNA-sequencing of the induced subpopulation confirmed induction of the SOS response triggering also activation of the CGP3 prophage. The fraction of CGP3-induced cells was enhanced in a mutant lacking the iron regulator DtxR suffering from enhanced iron uptake. Altogether, these findings demonstrate the potential of the established workflow to gain insights into the phenotypic dynamics of bacterial populations.

| S-EPMC6173762 | biostudies-literature

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