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Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome
Meydan, Sezen; Marks, James; Klepacki, Dorota; Sharma, Virag; Baranov, Pavel V.; Firth, Andrew E.; Margus, Tonu; Kefi, Amira; Vázquez-Laslop, Nora; Mankin, Alexander S.
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the “alternative” bacterial proteome. The internal start sites may also play regulatory roles in gene expression.
Keyword(s): Ribosome profiling; Translation initiation; Retapamulin; Alternative initiation; Internal genes
Publication Date:
2019
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: University College Cork
Funder(s): Science Foundation Ireland; Health Research Board
Citation(s): Meydan, S., Marks, J., Klepacki, D., Sharma, V., Baranov, P. V., Firth, A. E., Margus, T., Kefi, A., Vázquez-Laslop, N. and Mankin, A. S. (2019) 'Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome', Molecular Cell, 74(3), pp. 481-493. doi: 10.1016/j.molcel.2019.02.017
Publisher(s): Elsevier Inc.
File Format(s): application/pdf
Related Link(s): http://www.sciencedirect.com/science/article/pii/S1097276519301078
First Indexed: 2019-05-21 06:30:33 Last Updated: 2019-05-21 06:30:33