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Escherichia coli str. K-12 substr. MG1655

ABSTRACT: Clarifying the translational pausing landscape in bacteria by ribosome profiling

PROVIDER: PRJNA295296 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2340141.fastq.gz	Fastqsanger.gz
	SRR2340143.fastq.gz	Fastqsanger.gz
	SRR2340144.fastq.gz	Fastqsanger.gz
	SRR2340146.fastq.gz	Fastqsanger.gz
	SRR2340147.fastq.gz	Fastqsanger.gz

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Escherichia coli str. K-12 substr. MG1655

Project description:High Precision Analysis of Translational Pausing in Bacteria Lacking EFP by Ribosome Profiling

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Clarifying the translational pausing landscape in bacteria by ribosome profiling

Project description:The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling. Ribosome profiling (three replicates) and RNAseq (two replicates) of E. coli MG1655

2016-01-13 | E-GEOD-72899 | biostudies-arrayexpress

RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA.

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RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.

2013-03-26 | E-GEOD-45443 | biostudies-arrayexpress

Escherichia coli str. K-12 substr. MG1655

Project description:Transcription Pausing in E. coli

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Clarifying the translational pausing landscape in bacteria by ribosome profiling

2016-01-13 | GSE72899 | GEO

Escherichia coli str. K-12 substr. MG1655

Project description:Transcription Pausing in E. coli (Part 2)

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Project description:Escherichia coli heat shock translational profiling

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Escherichia coli str. K-12 substr. MG1655

Project description:High resolution view of bacteriophage lambda gene expression by ribosome profiling

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YAMAT-seq of mature tRNA pools in the bacterium Escherichia coli str. K-12 substr. MG1655 and derivatives

Project description:Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.

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