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Escherichia coli K-12

ABSTRACT: Time-series transcriptional profiling of MazF-induced E. coli populations

PROVIDER: PRJNA375104 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5264190.fastq.gz	Fastqsanger.gz
	SRR5264191.fastq.gz	Fastqsanger.gz
	SRR5264192.fastq.gz	Fastqsanger.gz
	SRR5264193.fastq.gz	Fastqsanger.gz
	SRR5264194.fastq.gz	Fastqsanger.gz

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Stress-induced MazF-mediated proteins in Escherichia coli

Project description:Escherichia coli (E. coli) mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress the induced MazF generates a Stress induced Translation Machinery (STM), composed of MazF processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here we performed a proteomic analysis of all the E. coli stress-induced proteins that are mediated through chromosomally borne mazF gene . We show that the mRNAs of almost all of them is characterized by the presence of an ACA site up to 100 nucleotides upstream to the AUG initiator. Thereby, under stressful conditions the induced MazF is processing mRNAs that are translated by STM. Furthermore, the presence of the ACA site far enough upstream (up to 100 nucleotides) to the AUG initiator may still permit translation by the canonical translation machinery. Thus, such dual translation mechanisms, enable under stress also to prepare proteins for immediate functions while coming back to normal growth conditions.

2019-02-25 | PXD010101 | Pride

Comparison of Escherichia coli K-12 tynA- with wild type Escherichia coli K-12

Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.

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RNA-seq for identifying toxin MazF and MqsR cleavage sites in toxin expression and subsequent recovery cultures of Escherichia coli (mRNA and ncRNA excluding rRNA)

Project description:Bacterial toxin-antitoxin systems are thought to help bacteria to reduce their metabolism in various stressful conditions. Many toxins of the bacterial toxin-antitoxin systems are ribonucleases. Such toxins have been mostly viewed as degraders of mRNA, however recently it was demonstrated that they are also capable of cleaving non-coding RNA. MazF toxin is also hypothesized to reprogram E. colis translational machinery. Current cDNA libraries are part of a project which aims to identify the major RNA cleavage sites (in mRNA, rRNA and regulatory non-coding RNA) of MazF and MqsR toxins in E. coli. We wanted to elaborate on the roles of MazF and MqsR in E. coli: is MazF really involved in reprogramming the translational machinery or is MazF, along with MqsR, just a robust cleaver of RNA? We extracted total RNA from cultures where the expression of MazF or MqsR was induced for 2h and from cultures that had been recovering from toxin production for 30 minutes; RNA from log phase culture was used as the control. We used strand specific random primed paired end RNA sequencing data to locate the major cleavage sites. To map the cleavage sites, we counted 5’ end stacks of forward reads in each genomic position and compared them with total coverage. MazF and MqsR cleave at specific recognition sequences, ˇACA and GˇC respectively, which allowed us to eliminate the false positives. One of our initial aims was also to look for irregular RNA ligation events following toxin expression, thus we used long, 300 base reads in sequencing.

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Project description:Alkylation damage to DNA occurs when cells encounter alkylating agents in the environment or when active alkylators are generated by nitrosation of amino acids in metabolic pathways. To cope with DNA alkylation damage, cells have evolved genes that encode proteins with alkylation-specific DNA repair activities. It is notable that these repair systems are conserved from bacteria to humans. In Escherichia coli, cells exposed to a low concentration of an alkylating agent, such as N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) or methyl methanesulfonate (MMS), show a remarkable increase in resistance to both the lethal and mutagenic effects of subsequent high-level challenge treatments with the same or other alkylating agents. This increased resistance has been known as “adaptive response” to alkylation damage in DNA. To date, four genes have been identified as components of this response, ada, alkA, alkB and aidB. The ada gene encodes the Ada protein, which has the dual function of a transcriptional regulator for the genes involved in the adaptive response, and a methyltransferase that demethylates two methylated bases (O6meG and O4meT) and methylphosphotriesters produced by methylating agents in the sugar phosphate backbone. The differences between the wild-type and mutant strains were characterized at transcriptome levels. In addition, the global changes in gene expressions in response to alkylating agents (MMS), in E. coli K-12 W3110 and ada mutant strains were also analyzed. The analysis of time- and strain-dependent adaptive responses revealed the regulatory and physiological characteristics of the Ada-dependent adaptive response in E. coli.

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