Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation

Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbia...

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Main Authors:	Barendt, Pamela A., Shah, Najaf A., Barendt, Gregory A., Sarkar, Casim A.
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310771/

id	pubmed-3310771
recordtype	oai_dc
spelling	pubmed-33107712012-03-28 Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation Barendt, Pamela A. Shah, Najaf A. Barendt, Gregory A. Sarkar, Casim A. Research Article Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbiased, high-throughput manner. We applied ribosome display, a powerful in vitro selection method, to enrich only those mRNA sequences which could direct rapid protein translation. In addition to canonical Shine-Dalgarno (SD) motifs, we unexpectedly recovered highly efficient cytosine-rich (C-rich) sequences that exhibit unmistakable complementarity to the 16S rRNA of the small subunit of the ribosome, indicating that broad-specificity base-pairing may be an inherent, general mechanism for efficient translation. Furthermore, given the conservation of ribosomal structure and function across species, the broader relevance of C-rich RBS sequences identified through our in vitro evolution approach is supported by multiple, diverse examples in nature, including C-rich RBSs in several bacteriophage and plants, a poly-C consensus before the start codon in a lower eukaryote, and Kozak-like sequences in vertebrates. Public Library of Science 2012-03-22 /pmc/articles/PMC3310771/ /pubmed/22457640 http://dx.doi.org/10.1371/journal.pgen.1002598 Text en Barendt et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Barendt, Pamela A. Shah, Najaf A. Barendt, Gregory A. Sarkar, Casim A.
spellingShingle	Barendt, Pamela A. Shah, Najaf A. Barendt, Gregory A. Sarkar, Casim A. Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
author_facet	Barendt, Pamela A. Shah, Najaf A. Barendt, Gregory A. Sarkar, Casim A.
author_sort	Barendt, Pamela A.
title	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
title_short	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
title_full	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
title_fullStr	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
title_full_unstemmed	Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
title_sort	broad-specificity mrna–rrna complementarity in efficient protein translation
description	Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbiased, high-throughput manner. We applied ribosome display, a powerful in vitro selection method, to enrich only those mRNA sequences which could direct rapid protein translation. In addition to canonical Shine-Dalgarno (SD) motifs, we unexpectedly recovered highly efficient cytosine-rich (C-rich) sequences that exhibit unmistakable complementarity to the 16S rRNA of the small subunit of the ribosome, indicating that broad-specificity base-pairing may be an inherent, general mechanism for efficient translation. Furthermore, given the conservation of ribosomal structure and function across species, the broader relevance of C-rich RBS sequences identified through our in vitro evolution approach is supported by multiple, diverse examples in nature, including C-rich RBSs in several bacteriophage and plants, a poly-C consensus before the start codon in a lower eukaryote, and Kozak-like sequences in vertebrates.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310771/
_version_	1611516297694150656

Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation

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