Work

A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

Year: 2019

Type: article

Abstract: In eukaryotes, ribosome profiling provides insight into the mechanism of protein synthesis at the codon level. In bacteria, however, the method has been more problematic and no consensus has emerged for how to best prepare profiling samples. Here, we identify the sources of these problems and describe new solutions for arresting translation and harvesting cells in order to overcome them. These improvements remove confounding artifacts and improve the resolution to allow analyses of ribosome behavior at the codon level. With a clearer view of the translational landscape in vivo, we observe that filtering cultures leads to translational pauses at serine and glycine codons through the reduction of tRNA aminoacylation levels. This observation illustrates how bacterial ribosome profiling studies can yield insight into the mechanism of protein synthesis at the codon level and how these mechanisms are regulated in response to changes in the physiology of the cell.

Source: eLife

DOI: 10.7554/elife.42591

Authors: Fuad Mohammad, Rachel Green, Allen R Buskirk

Institutions: Johns Hopkins University, Johns Hopkins Medicine, Howard Hughes Medical Institute

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,500

Funders: Howard Hughes Medical Institute, Johns Hopkins University, National Institute of General Medical Sciences