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.
Date:
2019-03-20
Copyright:
© 2019, Elsevier Inc. All rights reserved. This manuscript version is made available under the CC BY-NC-ND 4.0 license.
Full text restriction information:
Access to this article is restricted until 12 months after publication by request of the publisher.
Restriction lift date:
2020-03-20
Citation:
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
Abstract:
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.
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